diff --git a/data/covid/preprints-summary.csv b/data/covid/preprints-summary.csv index fab6c39d..1dddfed2 100644 --- a/data/covid/preprints-summary.csv +++ b/data/covid/preprints-summary.csv @@ -1,47 +1,47 @@ -obstetrics and gynecology,genomics,surgery,oncology,ophthalmology,geriatric medicine,biochemistry,intensive care and critical care medicine,radiology and imaging,biophysics,respiratory medicine,epidemiology,health economics,pediatrics,genetic and genomic medicine,primary care research,pathology,orthopedics,health informatics,allergy and immunology,dermatology,Total,emergency medicine,health policy,infectious diseases,psychiatry and clinical psychology,cardiovascular medicine,neurology,molecular biology,occupational and environmental health,month,evolutionary biology,public and global health,dentistry and oral medicine,scientific communication and education,health systems and quality improvement,hiv aids,microbiology,systems biology,pharmacology and therapeutics,bioinformatics,immunology -,,,,,,,,,,,1,,,,,,,,,,2,,,1,,,,,,Nov-23,,,,,,,,,,, -,,,,,,,,,,1,1,,,,,,,1,,,5,,,1,,,,,,Oct-23,,,,,,,,,,,1 -,,,,,,,,,,,,,,,,,,,,,1,,,1,,,,,,Sep-23,,,,,,,,,,, -,,,,,,,,,,,3,,,,1,,,,,,6,,,,,,,,1,Aug-23,,1,,,,,,,,, -,,,,,,,,,,,3,,,1,,,,,,,7,,,,,,,,,Jul-23,,1,,,2,,,,,, -,,,,,,,,,,,1,,,,,,1,1,,,7,,,2,,,,,1,Jun-23,,,,1,,,,,,, -,,,,,,,,,,1,2,,,,,,,,,,6,,,1,,,,,,May-23,,1,,,,,,,,,1 -,,,,,,,,,,,,,,,,,,,,,3,,,1,,,,,,Apr-23,,2,,,,,,,,, -,,,,,,,,,,,2,,,,,,,,,,9,,,3,1,,,,1,Mar-23,,2,,,,,,,,, -,,,,,,,,,,1,4,,,,,,,,,,8,,,,,,1,,,Feb-23,,2,,,,,,,,, -,,,,,,,,,,,4,,,,,,,,,,5,,,1,,,,,,Jan-23,,,,,,,,,,, -,,,,,,,,,,2,3,,,,,1,,,,,11,,1,3,,,,,,Dec-22,,1,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,4,,,4,,,,,,Nov-22,,,,,,,,,,, -,,,,,,,,,,,1,,,,,,,,,,6,,,2,,1,,,,Oct-22,,2,,,,,,,,, -,,,,,,,,,,1,1,,1,,,,,,,,9,,,2,,,,,2,Sep-22,,1,,,,,1,,,, -,,,,,,,,,,,4,,,,,,,,,,10,,,3,,,,,,Aug-22,,3,,,,,,,,, -,,,,,,,,,,,2,,1,,,,,1,,,7,,,2,,,,,,Jul-22,,,,,,,,,,,1 -,,,,,,,,,,,6,,,1,,,,1,,,18,,,4,5,,,,,Jun-22,,1,,,,,,,,, -,,,,,,,,,,,2,1,,,1,,,,,,14,,,5,2,,,,,May-22,,1,,,1,,1,,,, -,,,,,,,,,,1,5,1,,,,,,,,,15,,,2,,1,,,1,Apr-22,,1,,,2,,1,,,, -,,,,,,,,,,1,8,,,,1,,,,,,17,,,5,1,,,,,Mar-22,1,,,,,,,,,, -,,,,,,,,,,,6,,,,,,,,,,12,,,4,,,1,,,Feb-22,,1,,,,,,,,, -,,,,,,,,,,,5,,,,,,,2,,,14,,,3,,1,,,1,Jan-22,,1,,,,,,,,,1 -,,,,,,,,,,,10,,1,,1,,,,,,24,,,8,,1,1,,,Dec-21,,1,,,,,1,,,, -,1,,,,,,1,,1,,9,,,,1,,,,,,25,,,5,1,,1,,,Nov-21,,3,,,2,,,,,, -,,,,,1,,,,,,4,,1,,,,,,,,11,,,3,2,,,,,Oct-21,,,,,,,,,,, -,,,,,,,1,,,,6,,,,,,,1,,,16,,,4,,1,,,,Sep-21,,2,,,,,,,1,, -,,,,,,,1,,,1,2,,,,,,,1,,,13,,,3,,1,,,1,Aug-21,,3,,,,,,,,, -,,,1,,,,1,,,2,3,,1,1,,,,,,,26,1,,12,,,,,,Jul-21,,4,,,,,,,,, -,,,,,,,1,,,,7,,1,,1,,,1,1,,28,,,7,1,,1,,1,Jun-21,,4,,,1,,,,,,1 -,,,,,,,,,,,11,,,1,,,,1,,1,23,,,7,1,,,,,May-21,,1,,,,,,,,, -,,,,,,,,,,,3,,,,1,,,1,1,,19,,,7,1,,,,2,Apr-21,,1,,,1,,1,,,, -,,1,,,2,1,,1,,,6,,1,,,,,2,,,38,,,17,1,,1,,,Mar-21,,5,,,,,,,,, -,,1,,,,,,,,,9,1,,,,,,1,,,24,,,9,,1,,,,Feb-21,,1,,,1,,,,,, -,,,,,1,,1,,,,4,,,,1,,,,,,22,,1,7,1,,,,,Jan-21,,3,1,,1,,,,,,1 -,2,,,,,,,,,,4,,,,1,,,3,,,23,,,4,2,2,,,,Dec-20,,3,,,1,,1,,,, -,,,,,,,,,,,6,,,,,,,1,,,26,,1,13,,,,,,Nov-20,,4,,,,,,,,1, -,,,1,,1,,1,,,,6,,,,1,,,1,,,28,,1,11,2,,,,,Oct-20,,,,,,,,1,,1,1 -,,,,,,,1,,,,6,,,,1,,,1,,,27,3,,8,2,,,,,Sep-20,,3,,,,1,1,,,, -1,,,,,,,,,,,6,,,1,,,,,,,27,2,,12,,,,1,1,Aug-20,,2,,,1,,,,,, -,1,,,,,,1,,,1,9,,,,,,,,,,26,,,7,1,1,,,,Jul-20,,4,,,,,,,,,1 -,,,1,1,1,,3,,,1,7,,,,,,,1,,,37,,1,10,4,1,,,,Jun-20,,3,,,1,,,,,1,1 -,,,1,,1,,1,,,1,8,1,,,,,,1,,,37,,,10,,2,,,1,May-20,,9,,,,,,,,1, -,1,,,,,,,,,,7,,,2,,,,,,,18,,,6,,,,,,Apr-20,,1,,,1,,,,,, -,,,,,,,,,,,4,,,,,,,,,,8,,,1,,,,,,Mar-20,,3,,,,,,,,, -,,,,,,,,,,,4,,,,,,,,,,7,,,1,,,,,,Feb-20,,2,,,,,,,,, +primary care research,immunology,evolutionary biology,health systems and quality improvement,occupational and environmental health,oncology,psychiatry and clinical psychology,dentistry and oral medicine,month,allergy and immunology,pediatrics,neurology,cardiovascular medicine,pharmacology and therapeutics,obstetrics and gynecology,health economics,epidemiology,infectious diseases,orthopedics,biochemistry,microbiology,intensive care and critical care medicine,public and global health,emergency medicine,surgery,systems biology,Total,genomics,health policy,geriatric medicine,dermatology,molecular biology,genetic and genomic medicine,scientific communication and education,hiv aids,radiology and imaging,pathology,health informatics,respiratory medicine,bioinformatics,biophysics,ophthalmology +,,,,,,,,Nov-23,,,,,,,,1,1,,,,,,,,,2,,,,,,,,,,,,,,, +,1,,,,,,,Oct-23,,,,,,,,1,,,,,,,,,,4,,,,,,,,,,,1,1,,, +,,,,,,,,Sep-23,,,,,,,,,1,,,,,,,,,1,,,,,,,,,,,,,,, +1,,,,1,,,,Aug-23,,,,,,,,3,,,,,,1,,,,6,,,,,,,,,,,,,,, +,,,1,,,,,Jul-23,,,,,,,,2,,,,,,1,,,,5,,,,,,1,,,,,,,,, +,,,,1,,,,Jun-23,,,,,,,,1,2,1,,,,,,,,7,,,,,,,1,,,,1,,,, +,1,,,,,,,May-23,,,,,,,,2,1,,,,,1,,,,6,,,,,,,,,,,,1,,, +,,,,,,,,Apr-23,,,,,,,,,1,,,,,2,,,,3,,,,,,,,,,,,,,, +,,,,1,,1,,Mar-23,,,,,,,,2,3,,,,,2,,,,9,,,,,,,,,,,,,,, +,,,,,,,,Feb-23,,,1,,,,,4,,,,,,2,,,,8,,,,,,,,,,,,1,,, +,,,,,,,,Jan-23,,,,,,,,5,1,,,,,,,,,6,,,,,,,,,,,,,,, +,,,,,,,,Dec-22,,,,,,,,3,4,,,,,1,,,,12,,1,,,,,,,,1,,2,,, +,,,,,,,,Nov-22,,,,,,,,,4,,,,,,,,,4,,,,,,,,,,,,,,, +,,,,,,,,Oct-22,,,,1,,,,1,2,,,,,2,,,,6,,,,,,,,,,,,,,, +,,,,2,,,,Sep-22,,1,,,,,,1,1,,,1,,1,,,,8,,,,,,,,,,,,1,,, +,,,,,,,,Aug-22,,,,,,,,4,3,,,,,3,,,,10,,,,,,,,,,,,,,, +,1,,,,,,,Jul-22,,1,,,,,,2,3,,,,,,,,,8,,,,,,,,,,,1,,,, +,,,,,,5,,Jun-22,,,,,,,,5,4,,,,,1,,,,17,,,,,,1,,,,,1,,,, +1,,,1,,,2,,May-22,,,,,,,1,2,5,,,1,,1,,,,14,,,,,,,,,,,,,,, +,,,2,1,,,,Apr-22,,,,1,,,1,4,3,,,1,,1,,,,15,,,,,,,,,,,,1,,, +1,,1,,,,1,,Mar-22,,,,,,,,8,5,,,,,,,,,17,,,,,,,,,,,,1,,, +,,,,,,,,Feb-22,,,1,,,,,6,3,,,,,1,,,,11,,,,,,,,,,,,,,, +,1,,,1,,,,Jan-22,,,,1,,,,5,3,,,,,1,,,,14,,,,,,,,,,,2,,,, +1,,,,,,,,Dec-21,,1,1,1,,,,10,7,,,1,,1,,,,23,,,,,,,,,,,,,,, +1,,,2,,,1,,Nov-21,,,1,,,,,8,5,,,,1,3,,,,24,1,,,,,,,,,,,,,1, +,,,,,,2,,Oct-21,,1,,,,,,4,3,,,,,,,,,11,,,1,,,,,,,,,,,, +,,,,,,,,Sep-21,,,,1,1,,,6,5,,,,1,2,,,,17,,,,,,,,,,,1,,,, +,,,,1,,,,Aug-21,,,,1,,,,2,3,,,,1,3,,,,13,,,,,,,,,,,1,1,,, +,,,,,1,,,Jul-21,,,,,,,,3,11,,,,1,4,1,,,24,,,,,,1,,,,,,2,,, +1,1,,1,1,,1,,Jun-21,1,1,1,,,,,7,7,,,,1,3,,,,27,,,,,,,,,,,1,,,, +,,,,,,1,,May-21,,,,,,,,11,8,,,,,1,,,,24,,,,1,,1,,,,,1,,,, +1,,,1,2,,1,,Apr-21,1,,,,,,,4,7,,,1,,1,,,,20,,,,,,,,,,,1,,,, +,,,,,,1,,Mar-21,,1,1,,,,,6,17,,1,,,5,,1,,39,,,2,,,1,,,1,,2,,,, +,,,1,,,,,Feb-21,,,,1,,,1,9,8,,,,,,,1,,22,,,,,,,,,,,1,,,, +1,1,,1,,,1,1,Jan-21,,,,,,,,3,8,,,,1,3,,,,22,,1,1,,,,,,,,,,,, +1,,,,,,1,,Dec-20,,,,2,,,,4,3,,,1,,3,,,,20,2,,,,,,,,,,3,,,, +,1,,,,,,,Nov-20,,,,,,,,6,13,,,,,4,,,,27,,1,,,,,,,,,1,,1,, +1,1,,,,1,3,,Oct-20,,,,,,,,6,11,,,,1,,,,1,29,,1,1,,,,,,,,1,,1,, +1,,,,,,2,,Sep-20,,,,,,,,6,8,,,1,1,3,3,,,27,,,,,,,,1,,,1,,,, +,,,1,1,,,,Aug-20,,,,,,1,,6,12,,,,,2,2,,,27,,,,,1,1,,,,,,,,, +,1,,,,,1,,Jul-20,,,,1,,,,10,8,,,,1,4,,,,28,1,,,,,,,,,,,1,,, +,1,,1,,1,4,,Jun-20,,,,1,,,,7,10,,,,3,3,,,,37,,1,1,,,,,,,,1,1,1,,1 +,,,,1,,,,May-20,,,,2,,,1,8,10,,,,1,8,,,,35,,,1,,,,,,,,1,1,1,, +,,,1,,,,,Apr-20,,,,,,,,6,7,,,,,1,,,,18,1,,,,,2,,,,,,,,, +,,,,,,,,Mar-20,,,,,,,,4,1,,,,,3,,,,8,,,,,,,,,,,,,,, +,,,,,,,,Feb-20,,,,,,,,4,1,,,,,2,,,,7,,,,,,,,,,,,,,, diff --git a/data/covid/preprints.csv b/data/covid/preprints.csv index 20a6c260..b189988e 100644 --- a/data/covid/preprints.csv +++ b/data/covid/preprints.csv @@ -1,5 +1,13 @@ site,doi,date,link,title,authors,affiliations,abstract,category,match_type,author_similarity,affiliation_similarity -medRxiv,10.1101/2023.11.09.23298162,2023-11-10,https://medrxiv.org/cgi/content/short/2023.11.09.23298162,One year health outcomes associated with systemic corticosteroids for COVID-19: a longitudinal cohort study,Olivia C Leavy; Richard J Russell; Ewen M Harrison; Nazir I Lone; Steven Kerr; Annemarie B Docherty; Aziz Sheikh; Matthew Richardson; Omer Elneima; Neil J Greening; Victoria Claire Harris; Linzy Houchen-Wolloff; Hamish J C McAuley; Ruth M Saunders; Marco Sereno; Aarti Shikotra; Amisha Singapuri; Raminder Aul; Paul Beirne; Charlotte E Bolton; Jeremy S Brown; Gourab Choudhury; Nawar Diar Bakerly; Nicholas Easom; Carlos Echevarria; Jonathan Fuld; Nick Hart; John R Hurst; Mark Jones; Dhruv Parekh; Paul Pfeffer; Najib M Rahman; Sarah Rowland-Jones; Ajay M Shah; Dan G Wootton; Caroline Jolley; AA Roger Thompson; Trudie Chalder; Melanie J Davies; Anthony De Soyza; John R Geddes; William Greenhalf; Simon Heller; Luke Howard; Joseph Jacob; R Gisli Jenkins; Janet M Lord; Will D-C Man; Gerry P McCann; Stefan Neubauer; Peter JM Openshaw; Joanna Porter; Matthew J Rowland; Janet T Scott; Malcolm G Semple; Sally J Singh; David Thomas; Mark Toshner; Keir Lewis; Liam G Heaney; Andrew Briggs; Bang Zheng; Mathew Thorpe; Jennifer K Quint; James D Chalmers; Ling-Pei Ho; Alex Horsley; Michael Marks; Krisnah Poinasamy; Betty Raman; Louise V Wain; Christopher E Brightling; Rachael A Evans; - PHOSP-COVID Collaborative Group,"Department of Population Health Sciences, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; The Usher Institute, University of Edinburgh, Edinburgh, UK; Roslin Institute, University of Edinburgh, Edinburgh, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; The Usher Institute, University of Edinburgh, Edinburgh, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; Centre for Exercise and Rehabilitation Science, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; St Georges University Hospitals NHS Foundation Trust, London, UK; The Leeds Teaching Hospitals NHS Trust, Leeds, UK; University of Nottingham, Nottingham, UK; UCL Respiratory, Department of Medicine, University College London, Rayne Institute, London, UK; University of Edinburgh, Edinburgh, UK; Manchester Metropolitan University, Manchester, UK; Infection Research Group, Hull University Teaching Hospitals, Hull, UK; The Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK; Department of Respiratory Medicine, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Lane Fox Respiratory Service, Guys and St Thomas NHS Foundation Trust, London, UK; University College London, London, UK; Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK; University of Birmingham, Birmingham, UK; Barts Health NHS Trust, London, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK; University of Sheffield, Sheffield, UK; Kings College London, London, UK; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Kings College London, London, UK; University of Sheffield, Sheffield, UK; Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK; Diabetes Research Centre, University of Leicester, Leicester, UK; Population Health Sciences Institute, Newcastle University, Newcastle Upon Tyne, UK; NIHR Oxford Health Biomedical Research Centre, University of Oxford, Oxford, UK; University of Liverpool, Liverpool, UK; Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK; Imperial College Healthcare NHS Trust, London, UK; Centre for Medical Image Computing, University College London, London, UK; National Heart and Lung Institute, Imperial College London, London, UK; MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK; Royal Brompton and Harefield Clinical Group, Guys and St Thomas NHS Foundation Trust, London, UK; Department of Cardiovascular Sciences, University of Leicester, Leicester, UK; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; National Heart and Lung Institute, Imperial College London, London, UK; UCL Respiratory, Department of Medicine, University College London, Rayne Institute, London, UK; Kadoorie Centre for Critical Care Research, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, U; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; Imperial College London, London, UK; Cambridge NIHR BRC, Cambridge, UK; Hywel Dda University Health Board, Wales, UK; Wellcome-Wolfson Institute for Experimental Medicine, Queens University Belfast, Belfast, UK; London School of Hygiene & Tropical Medicine, London, UK; London School of Hygiene & Tropical Medicine, London, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; NHLI, Imperial College London, London, UK; University of Dundee, Ninewells Hospital and Medical School, Dundee, UK; MRC Human Immunology Unit, University of Oxford, Oxford, UK; Division of Infection, Immunity & Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK; Asthma and Lung UK, London, UK; Radcliffe Department of Medicine, University of Oxford, Oxford, UK; Department of Population Health Sciences, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; ","Background In patients with COVID-19 requiring supplemental oxygen, dexamethasone reduces acute severity and improves survival, but longer-term effects are unknown. We hypothesised that systemic corticosteroid administration during acute COVID-19 would be associated with improved health-related quality of life (HRQoL) one year after discharge. Methods Adults admitted to hospital between February 2020 and March 2021 for COVID-19 and meeting current guideline recommendations for dexamethasone treatment were included using two prospective UK cohort studies. HRQoL, assessed by EQ-5D-5L utility index, pre-hospital and one year after discharge were compared between those receiving corticosteroids or not after propensity weighting for treatment. Secondary outcomes included patient reported recovery, physical and mental health status, and measures of organ impairment. Sensitivity analyses were undertaken to account for survival and selection bias. Findings In 1,888 participants included in the primary analysis, 1,149 received corticosteroids. There was no between-group difference in EQ-5D-5L utility index at one year (mean difference 0.004, 95% CI: -0.026 to 0.034, p = 0.77). A similar reduction in EQ-5D-5L was seen at one year between corticosteroid exposed and non-exposed groups (mean (SD) change -0.12 (0.22) vs -0.11 (0.22), p = 0.32). Overall, there were no differences in secondary outcome measures. After sensitivity analyses modelled using a larger cohort of 109,318 patients admitted to hospital with COVID-19, EQ-5D-5L utility index at one year remained similar between the two groups. Interpretation Systemic corticosteroids for acute COVID-19 have no impact on the large reduction in HRQoL one year after hospital discharge. Treatments to address this are urgently needed.",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2023.11.09.23298162,2023-11-10,https://medrxiv.org/cgi/content/short/2023.11.09.23298162,One year health outcomes associated with systemic corticosteroids for COVID-19: a longitudinal cohort study,Olivia C Leavy; Richard J Russell; Ewen M Harrison; Nazir I Lone; Steven Kerr; Annemarie B Docherty; Aziz Sheikh; Matthew Richardson; Omer Elneima; Neil J Greening; Victoria Claire Harris; Linzy Houchen-Wolloff; Hamish J C McAuley; Ruth M Saunders; Marco Sereno; Aarti Shikotra; Amisha Singapuri; Raminder Aul; Paul Beirne; Charlotte E Bolton; Jeremy S Brown; Gourab Choudhury; Nawar Diar Bakerly; Nicholas Easom; Carlos Echevarria; Jonathan Fuld; Nick Hart; John R Hurst; Mark Jones; Dhruv Parekh; Paul Pfeffer; Najib M Rahman; Sarah Rowland-Jones; Ajay M Shah; Dan G Wootton; Caroline Jolley; AA Roger Thompson; Trudie Chalder; Melanie J Davies; Anthony De Soyza; John R Geddes; William Greenhalf; Simon Heller; Luke Howard; Joseph Jacob; R Gisli Jenkins; Janet M Lord; Will D-C Man; Gerry P McCann; Stefan Neubauer; Peter JM Openshaw; Joanna Porter; Matthew J Rowland; Janet T Scott; Malcolm G Semple; Sally J Singh; David Thomas; Mark Toshner; Keir Lewis; Liam G Heaney; Andrew Briggs; Bang Zheng; Mathew Thorpe; Jennifer K Quint; James D Chalmers; Ling-Pei Ho; Alex Horsley; Michael Marks; Krisnah Poinasamy; Betty Raman; Louise V Wain; Christopher E Brightling; Rachael A Evans; - PHOSP-COVID Collaborative Group,"Department of Population Health Sciences, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; The Usher Institute, University of Edinburgh, Edinburgh, UK; Roslin Institute, University of Edinburgh, Edinburgh, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; The Usher Institute, University of Edinburgh, Edinburgh, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; Centre for Exercise and Rehabilitation Science, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; St Georges University Hospitals NHS Foundation Trust, London, UK; The Leeds Teaching Hospitals NHS Trust, Leeds, UK; University of Nottingham, Nottingham, UK; UCL Respiratory, Department of Medicine, University College London, Rayne Institute, London, UK; University of Edinburgh, Edinburgh, UK; Manchester Metropolitan University, Manchester, UK; Infection Research Group, Hull University Teaching Hospitals, Hull, UK; The Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK; Department of Respiratory Medicine, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Lane Fox Respiratory Service, Guys and St Thomas NHS Foundation Trust, London, UK; University College London, London, UK; Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK; University of Birmingham, Birmingham, UK; Barts Health NHS Trust, London, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK; University of Sheffield, Sheffield, UK; Kings College London, London, UK; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Kings College London, London, UK; University of Sheffield, Sheffield, UK; Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK; Diabetes Research Centre, University of Leicester, Leicester, UK; Population Health Sciences Institute, Newcastle University, Newcastle Upon Tyne, UK; NIHR Oxford Health Biomedical Research Centre, University of Oxford, Oxford, UK; University of Liverpool, Liverpool, UK; Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK; Imperial College Healthcare NHS Trust, London, UK; Centre for Medical Image Computing, University College London, London, UK; National Heart and Lung Institute, Imperial College London, London, UK; MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK; Royal Brompton and Harefield Clinical Group, Guys and St Thomas NHS Foundation Trust, London, UK; Department of Cardiovascular Sciences, University of Leicester, Leicester, UK; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; National Heart and Lung Institute, Imperial College London, London, UK; UCL Respiratory, Department of Medicine, University College London, Rayne Institute, London, UK; Kadoorie Centre for Critical Care Research, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, U; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; Imperial College London, London, UK; Cambridge NIHR BRC, Cambridge, UK; Hywel Dda University Health Board, Wales, UK; Wellcome-Wolfson Institute for Experimental Medicine, Queens University Belfast, Belfast, UK; London School of Hygiene & Tropical Medicine, London, UK; London School of Hygiene & Tropical Medicine, London, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; NHLI, Imperial College London, London, UK; University of Dundee, Ninewells Hospital and Medical School, Dundee, UK; MRC Human Immunology Unit, University of Oxford, Oxford, UK; Division of Infection, Immunity & Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK; Asthma and Lung UK, London, UK; Radcliffe Department of Medicine, University of Oxford, Oxford, UK; Department of Population Health Sciences, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; ","BackgroundIn patients with COVID-19 requiring supplemental oxygen, dexamethasone reduces acute severity and improves survival, but longer-term effects are unknown. We hypothesised that systemic corticosteroid administration during acute COVID-19 would be associated with improved health-related quality of life (HRQoL) one year after discharge. + +MethodsAdults admitted to hospital between February 2020 and March 2021 for COVID-19 and meeting current guideline recommendations for dexamethasone treatment were included using two prospective UK cohort studies. HRQoL, assessed by EQ-5D-5L utility index, pre-hospital and one year after discharge were compared between those receiving corticosteroids or not after propensity weighting for treatment. Secondary outcomes included patient reported recovery, physical and mental health status, and measures of organ impairment. Sensitivity analyses were undertaken to account for survival and selection bias. + +FindingsIn 1,888 participants included in the primary analysis, 1,149 received corticosteroids. There was no between-group difference in EQ-5D-5L utility index at one year (mean difference 0.004, 95% CI: -0.026 to 0.034, p = 0.77). A similar reduction in EQ-5D-5L was seen at one year between corticosteroid exposed and non-exposed groups (mean (SD) change -0.12 (0.22) vs -0.11 (0.22), p = 0.32). Overall, there were no differences in secondary outcome measures. After sensitivity analyses modelled using a larger cohort of 109,318 patients admitted to hospital with COVID-19, EQ-5D-5L utility index at one year remained similar between the two groups. + +InterpretationSystemic corticosteroids for acute COVID-19 have no impact on the large reduction in HRQoL one year after hospital discharge. Treatments to address this are urgently needed. + +Take home messageSystemic corticosteroids given for acute COVID-19 do not affect health-related quality of life or other patient reported outcomes, physical and mental health outcomes, and organ function one year after hospital discharge",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2023.11.06.23298026,2023-11-07,https://medrxiv.org/cgi/content/short/2023.11.06.23298026,"Combining models to generate consensus medium-term projections of hospital admissions, occupancy and deaths relating to COVID-19 in England",Harrison Manley; Thomas Bayley; Gabriel Danelian; Lucy Burton; Thomas Finnie; Andre Charlett; Nick Watkins; Paul Birrell; Daniela De Angelis; Matt J Keeling; Sebastian J Funk; Graham Medley; Lorenzo Pellis; Marc Baguelin; Graeme J Ackland; Johanna Hutchinson; Steven Riley; Jasmina Panovska-Griffiths,"UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; University of Cambridge Cambridge, UK; University of Warwick, Zeeman Institute: SBIDER; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; The University of Manchester; Imperial College London; University of Edinburgh; UK Health Security Agency; UK Health Security Agency; University of Oxford","Mathematical modelling has played an important role in offering informed advice during the COVID-19 pandemic. In England, a cross government and academia collaboration generated Medium-Term Projections (MTPs) of possible epidemic trajectories over the future 4-6 weeks from a collection of epidemiological models.In this paper we outline this collaborative modelling approach and evaluate the accuracy of the combined and individual model projections against the data over the period November 2021-December 2022 when various Omicron subvariants were spreading across England. Using a number of statistical methods, we quantify the predictive performance of the model projections for both the combined and individual MTPs, by evaluating the point and probabilistic accuracy. Our results illustrate that the combined MTPs, produced from an ensemble of heterogeneous epidemiological models, were a closer fit to the data than the individual models during the periods of epidemic growth or decline, with the 90% confidence intervals widest around the epidemic peaks. We also show that the combined MTPs increase the robustness and reduce the biases associated with a single model projection. Learning from our experience of ensemble modelling during the COVID-19 epidemic, our findings highlight the importance of developing cross-institutional multi-model infectious disease hubs for future outbreak control.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2023.10.26.23297598,2023-10-26,https://medrxiv.org/cgi/content/short/2023.10.26.23297598,Assessing the causal effect of air pollution on risk of SARS-CoV-2 infection,Annalan Mathew Dwight Navaratnam; Sarah Beale; Yamina Boukari; Vincent Nguyen; Wing Lam Erica Fong; Isobel Braithwaite; Thomas Edward Byrne; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Parth Patel; Madhumita Shrotri; Alexei Yavlinsky; Andrew Hayward; Haneen Khreis; Robert W Aldridge,University College London; University College London; University College London; University College London; University College London; University College London; University College London; UCL; University College London; University College London; University College London; University College London; University College London; UCL; University of Cambridge; UCL,"IntroductionEmerging evidence suggests association of air pollution exposure with risk of SARS-CoV-2 infection, but many of these findings are limited by study design, lack of individual-level covariate data or are specific to certain subpopulations. We aim to evaluate causal effects of air pollution on risk of infection, whilst overcoming these limitations. @@ -39,7 +47,6 @@ FindingsSwabs taken at 32,937/1,352,979 (2.4%) assessments tested positive for S InterpretationSymptom profiles varied little by aetiology, making distinguishing SARS-CoV-2, influenza and RSV using symptoms challenging. Most symptoms were not explained by these viruses, indicating the importance of other pathogens in syndromic surveillance. Influenza vaccination was associated with lower rates of community influenza test positivity. FundingUK Health Security Agency, Department of Health and Social Care, National Institute for Health Research.",respiratory medicine,fuzzy,100,100 -medRxiv,10.1101/2023.10.06.23296657,2023-10-06,https://medrxiv.org/cgi/content/short/2023.10.06.23296657,The macroeconomic and epidemiological impacts of Covid-19 in Pakistan.,Henning Tarp Jensen; Marcus R. Keogh-Brown; Rosalind M Eggo; Carl A. B. Pearson; Sergio Torres-Rueda; Maryam Huda; Muhammad Khalid; Wahaj Sulfiqar; - CMMID COVID-19 Working Group; Richard D. Smith; Mark Jit; Anna Vassall,"London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; Aga Khan University; Ministry of National Health Services, Regulations & Coordination, Islamabad, Pakistan; Ministry of National Health Services, Regulations & Coordination, Islamabad, Pakistan; -; University of Exeter; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine","""Coronavirus Disease 2019"" (C19) is a respiratory illness caused by ""new Coronavirus"" SARS-CoV-2. The C19 pandemic, which engulfed the world in 2021, also caused a national C19 epidemic in Pakistan, who responded with initial forced lockdowns (15-30 March 2020) and a subsequent switch to a smart lockdown strategy, and, by 31 December 2020, Pakistan had managed to limit confirmed cases and case fatalities to 482,506 (456 per 100,000) and 10,176 (4.8 per 100,000). The early switch to a smart lockdown strategy, and successful follow-up move to central coordination and effective communication and enforcement of Standard Operating Procedures, was motivated by a concern over how broad-based forced lockdowns would affect poor households and day-labour. The current study aims to investigate how the national Pakistan C19 epidemic would have unfolded under an uncontrolled baseline scenario and an alternative set of controlled non-pharmaceutical intervention (NPI) policy lockdown scenarios, including health and macroeconomic outcomes. We employ a dynamically-recursive version of the IFPRI Standard Computable General Equilibrium model framework (Lofgren, Lee Harris and Robinson 2002), and a, by now, well-established epidemiological transmission-dynamic model framework (Davies, Klepac et al 2020) using Pakistan-specific 5-year age-group contact matrices on four types of contact rates, including at home, at work, at school, and at other locations (Prem, Cook & Jit 2017), to characterize an uncontrolled spread of disease. Our simulation results indicate that an uncontrolled C19 epidemic, by itself, would have led to a 0.12% reduction in Pakistani GDP (-721mn USD), and a total of 0.65mn critically ill and 1.52mn severely ill C19 patients during 2020-21, while 405,000 Pakistani citizens would have lost their lives. Since the majority of case fatalities and symptomatic cases, respectively 345,000 and 35.9mn, would have occurred in 2020, the case fatality and confirmed case numbers, observed by 31. December 2020 represents an outcome which is far better than the alternative. Case fatalities by 31. December 2020 could possibly have been somewhat improved either via a more prolonged one-off 10 week forced lockdown (66% reduction) or a 1-month forced lockdown/2-months opening intermittent lockdown strategy (33% reduction), but both sets of strategies would have carried significant GDP costs in the order of 2.2%-6.2% of real GDP.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2023.08.30.23294821,2023-09-01,https://medrxiv.org/cgi/content/short/2023.08.30.23294821,Symptom experience before vs. after confirmed SARS-CoV-2 infection: a population and case control study using prospectively recorded symptom data.,Carole Helene Sudre; Michela Antonelli; Nathan J Cheetham; Erika Molteni; Liane S Canas; Vicky Bowyer; Benjamin Murray; Khaled Rjoob; Marc Modat; Joan Capdevia Pujol; Christina Hu; Jonathan Wolf; Timothy D Spector; Alexander Hammers; Claire J Steves; Sebastien Ourselin; Emma L Duncan,University College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; University College London; King's College London; Zoe Ltd; Zoe Ltd; Zoe Ltd; King's College London; King's College London; King's College London; King's College London; King's College London,"BackgroundSome individuals experience prolonged illness after acute COVID-19. We assessed whether pre-infection symptoms affected post-COVID illness duration. MethodsSurvival analysis was performed in adults (n=23,452) with community-managed SARC-CoV-2 infection prospectively self-logging data through the ZOE COVID Symptom Study app, at least weekly, from 8 weeks before to 12 weeks after COVID-19 onset, conditioned on presence vs. absence of baseline symptoms (4-8 weeks before COVID-19). A case-control study was performed in 1350 individuals with long illness ([≥]8 weeks, 906 [67.1%] with illness [≥]12 weeks), matched 1:1 (for age, sex, body mass index, testing week, prior infection, vaccination, smoking, index of multiple deprivation) with 1350 individuals with short illness (<4 weeks). Baseline symptoms were compared between the two groups; and against post-COVID symptoms. @@ -62,27 +69,6 @@ C_LIO_LIBoth date and reason of test are important confounders to be included wh C_LIO_LIThere was little difference in COVID-19 infection risk by job category after adjusting for test reason; however women were less likely to test positive than men C_LI",occupational and environmental health,fuzzy,100,100 medRxiv,10.1101/2023.08.11.23293977,2023-08-15,https://medrxiv.org/cgi/content/short/2023.08.11.23293977,"Digital Mental Health Service engagement changes during Covid-19 in children and young people across the UK: presenting concerns, service activity, and access by gender, ethnicity, and deprivation",Duleeka Knipe; Santiago de Ossorno Garcia; Louisa Salhi; Lily Mainstone-Cotton; Aaron Sefi; Ann John,University of Bristol School of Social and Community Medicine: University of Bristol Population Health Sciences; Kooth Digital Health; Kooth Digital Health; Kooth Digital Health; Kooth Digital Health; Swansea University,"The adoption of digital health technologies accelerated during Covid-19, with concerns over the equity of access due to digital exclusion. Using data from a text-based online mental health service for children and young people we explore the impact of the pandemic on service access and presenting concerns and whether differences were observed by sociodemographic characteristics in terms of access (gender, ethnicity and deprivation). We used interrupted time-series models to assess whether there was a change in the level and rate of service use during the Covid-19 pandemic (April 2020-April 2021) compared to pre-pandemic trends (June 2019-March 2020). Routinely collected data from 61221 service users were extracted for observation, those represented half of the service population as only those with consent to share their data were used. The majority of users identified as female (74%) and White (80%), with an age range between 13 and 20 years of age. There was evidence of a sudden increase (13%) in service access at the start of the pandemic (RR 1.13 95% CI 1.02, 1.25), followed by a reduced rate (from 25% to 21%) of engagement during the pandemic compared to pre-pandemic trends (RR 0.97 95% CI 0.95,0.98). There was a sudden increase in almost all presenting issues apart from physical complaints. There was evidence of a step increase in the number of contacts for Black/African/Caribbean/Black British (38% increase; 95% CI: 1%-90%) and White ethnic groups (14% increase; 95% CI: 2%-27%)), sudden increase in service use at the start of the pandemic for the most (58% increase; 95% CI: 1%-247%) and least (47% increase; 95% CI: 6%-204%) deprived areas. During the pandemic, contact rates decreased, and referral sources change at the start. Findings on access and service activity align with other studies observing reduced service utilization. The lack of differences in deprivation levels and ethnicity at lockdown suggests exploring equity of access to the anonymous service. The study provides unique insights into changes in digital mental health use during Covid-19 in the UK.",public and global health,fuzzy,100,100 -medRxiv,10.1101/2023.08.07.23293778,2023-08-09,https://medrxiv.org/cgi/content/short/2023.08.07.23293778,"Diabetes following SARS-CoV-2 infection: Incidence, persistence, and implications of COVID-19 vaccination. A cohort study of fifteen million people.",Kurt Taylor; Sophie Eastwood; Venexia Walker; Genevieve Cezard; Rochelle Knight; Marwa Al Arab; Yinghui Wei; Elsie M F Horne; Lucy Teece; Harriet Forbes; Alex Walker; Louis Fisher; Jon Massey; Lisa E M Hopcroft; Tom Palmer; Jose Cuitun Coronado; Samantha Ip; Simon Davy; Iain Dillingham; Caroline Morton; Felix Greaves; John MacLeod; Ben Goldacre; Angela Wood; Nishi Chaturvedi; Jonathan A C Sterne; Rachel Denholm; - CONVALESCENCE Long-COVID study; - Longitudinal Health and Wellbeing and Data and Connectivity UK COVID-19 National Core Studies; - OpenSAFELY collaborative,University of Bristol; University College London; University of Bristol; University of Cambridge; University of Bristol; University of Bristol; University of Plymouth; University of Bristol; University of Leicester; London School of Hygiene & Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Bristol; University of Bristol; University of Cambridge; University of Oxford; University of Oxford; University of Oxford; National Institute for Health and Care Excellence; University of Bristol; University of Oxford; University of Cambridge; University College London; University of Bristol; University of Bristol; -; -; -,"BackgroundType 2 diabetes (T2DM) incidence is increased after diagnosis of COVID-19. The impact of vaccination on this increase, for how long it persists, and the effect of COVID-19 on other types of diabetes remain unclear. - -MethodsWith NHS England approval, we studied diabetes incidence following COVID-19 diagnosis in pre-vaccination (N=15,211,471, January 2020-December 2021), vaccinated (N =11,822,640), and unvaccinated (N=2,851,183) cohorts (June-December 2021), using linked electronic health records. We estimated adjusted hazard ratios (aHRs) comparing diabetes incidence post-COVID-19 diagnosis with incidence before or without diagnosis up to 102 weeks post-diagnosis. Results were stratified by COVID-19 severity (hospitalised/non-hospitalised) and diabetes type. - -FindingsIn the pre-vaccination cohort, aHRS for T2DM incidence after COVID-19 (compared to before or without diagnosis) declined from 3.01 (95% CI: 2.76,3.28) in weeks 1-4 to 1.24 (1.12,1.38) in weeks 53-102. aHRS were higher in unvaccinated than vaccinated people (4.86 (3.69,6.41)) versus 1.42 (1.24,1.62) in weeks 1-4) and for hospitalised COVID-19 (pre-vaccination cohort 21.1 (18.8,23.7) in weeks 1-4 declining to 2.04 (1.65,2.51) in weeks 52-102), than non-hospitalised COVID-19 (1.45 (1.27,1.64) in weeks 1-4, 1.10 (0.98,1.23) in weeks 52-102). T2DM persisted for 4 months after COVID-19 for [~]73% of those diagnosed. Patterns were similar for Type 1 diabetes, though excess incidence did not persist beyond a year post-COVID-19. - -InterpretationElevated T2DM incidence after COVID-19 is greater, and persists longer, in hospitalised than non-hospitalised people. It is markedly less apparent post-vaccination. Testing for T2DM after severe COVID-19 and promotion of vaccination are important tools in addressing this public health problem. - -Research in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed for population-based observational studies published between December 1st 2019 and July 12th 2023 examining associations between SARS-CoV-2 infection or COVID-19 diagnosis (search string: SARS-CoV-2 or COVID* or coronavirus*) and subsequent incident diabetes (search term: diabetes). Of nineteen relevant studies; eight had a composite outcome of diabetes types, six stratified by diabetes type and five pertained to type-1-diabetes (T1DM) only. We did not identify any studies relating to gestational or other types of diabetes. Eleven studies were from the US, three from the UK, two from Germany, one from Canada, one from Denmark and one from South Korea. - -Most studies described cumulative relative risks (for infection versus no infection) one to two years post-SARS-CoV-2 infection of 1.2 to 2.6, though four studies found no associations with T1DM after the post-acute period. All studies lacked the power to compare diabetes relative risk by type, severity, and vaccination status in population subgroups. One study examined relative risks by vaccination status, but this used a composite outcome of diabetes and hyperlipidaemia and was conducted in a predominantly white male population. - -Two studies of T1DM found no evidence of elevated risk beyond 30 days after COVID-19 diagnosis, whilst two reported elevated risks at six months. Two studies of type 2 diabetes (T2DM) examined relative risks by time period post-infection: one study of US insurance claims reported a persistent association six months post-infection, whereas a large UK population-based study reported no associations after 12 weeks. However, the latter study used only primary care data, therefore COVID-19 cases were likely to have been under-ascertained. - -No large studies have investigated the persistence of diabetes diagnosed following COVID-19; key to elucidating the role of stress/steroid-induced hyperglycaemia. - -Added value of this studyThis study, which is the largest to address the question to date, analysed linked primary and secondary care health records with SARS-CoV-2 testing and COVID-19 vaccination data for 15 million people living in England. This enabled us to compare the elevation in diabetes incidence after COVID-19 diagnosis by diabetes type, COVID-19 severity and vaccination status, overall and in population subgroups. Importantly, excess diabetes incidence by time period since infection could also be quantified. Since healthcare in the UK is universal and free-at-the-point-of-delivery, almost the entire population is registered with primary care. Therefore the findings are likely to be generalisable. - -We found that, before availability of COVID-19 vaccination, a COVID-19 diagnosis (vs. no diagnosis) was associated with increased T2DM incidence which remained elevated by approximately 30% beyond one year after diagnosis. Though still present (with around 30% excess incidence at eight weeks), these associations were substantially attenuated in unvaccinated compared with vaccinated people. Excess incidence was greater in people hospitalised with COVID-19 than those who were not hospitalised after diagnosis. T1DM incidence was elevated up to, but not beyond, a year post COVID-19. Around 73% of people diagnosed with incident T2DM after COVID-19 still had evidence of diabetes four months after infection. - -Implications of all the available evidenceThere is a 30-50% elevated T2DM incidence post-COVID-19, but we report the novel finding that there is elevated incidence beyond one-year post-diagnosis. Elevated T1DM incidence did not appear to persist beyond a year, which may explain why previous studies disagree. For the first time in a general-population dataset, we demonstrate that COVID-19 vaccination reduces, but does not entirely ameliorate, excess diabetes incidence after COVID-19. This supports a policy of universal vaccination and suggests that other public health activities, such as enhanced diabetes screening after severe COVID-19, may be warranted, particularly in unvaccinated people.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2023.08.02.23293505,2023-08-06,https://medrxiv.org/cgi/content/short/2023.08.02.23293505,COVID pandemic impact on hypertension management in North-East London: an observational cohort study using electronic health records,Stuart CG Rison; Oliver Redfern; Rohini Mathur; Isabel Dostal; Chris Carvalho; Zahra R Raisi-Estabragh; John P Robson,Queen Mary University of London; University of Oxford; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; William Harvey Research Institute; Queen Mary University of London,"BackgroundThe COVID19 pandemic had a major impact on primary care management of long-term conditions such as hypertension. This observational cohort study of adults with hypertension registered in 193 primary care practices in North-East London between January 2019 and October 2022 investigated the impact of the COVID19 pandemic on the treatment and control of blood pressure including demographic and social inequities. Method and findingsIn 224,329 adults with hypertension, the proportion with a blood pressure (BP) recorded within the preceding 1 year fell from a 91% pre-pandemic peak to 62% at the end of the pandemic lock-down phase and improved to 77% by the end of the study. The proportion with controlled hypertension (<80 years old, BP [≤]140/90mmHg; 80 or more years old: [≤]150/90mmHg) for the same time points was 81%, 50% and 60% respectively. Using blood pressure control (which considered only patients with a valid blood pressure recording) as the indicator attenuated the reduction to 83%, 80% and 78% respectively. @@ -107,6 +93,7 @@ We found two peer-reviewed studies and one briefing by an independent think tank Added value of this studyThis study is the first to quantify changes in fit note rate since the start of the COVID-19 pandemic among people with a reported SARS-CoV-2 infection and how this compares with the general population in the UK. We found that people with evidence of SARS-CoV-2 infection had a higher fit note rate than the general population, even after adjusting for demographics and clinical characteristics. While this increased risk was greatest in 2020 (hazard ratio [HR] = 4.07, 95%CI 4.02-4.12), it continued to a lesser extent even into 2022 (HR = 1.57, 95%CI 1.56-1.58). The fit note rate was greatest in the first 30 days post-diagnosis, suggesting that most sick leave is associated with the acute phase. In subgroup analyses, the groups with the greatest relative increased risk changed over the years. People aged 18-24 years had a larger relative increased risk of fit notes (as measured by HR) in 2022 than 2021, when compared with the general population in each year. Additionally, while in 2020 and 2021 the HR increased along with lessening deprivation, this effect dissipated in 2022. In contrast, people hospitalised with COVID-19 were less likely to be issued a fit note than the pneumonia cohort, suggesting the long-term effects may be similar to comparable severe respiratory infections cases resulting in hospitalisation. Implications of all the available evidenceWhile we have likely underestimated the fit note rate due to overcounting of people in the workforce and misclassification of COVID-19 status, we still identified a substantial increased risk of receiving a fit note in people with COVID-19 compared with the general population over all years, even after adjusting for demographics and a wide range of clinical characteristics. The increased risk persisted into 2022, in an era where most people are vaccinated and the severity of COVID-19 illness is lessened. Given the high infection rates still occurring, these findings provide evidence for a substantial impact of COVID-19 on productivity and further evidence of the long-term impacts of COVID-19.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2023.08.02.23293519,2023-08-04,https://medrxiv.org/cgi/content/short/2023.08.02.23293519,Real-time epidemiological modelling during the COVID-19 emergency in Wales,Michael Gravenor; Mark Dawson; Ed Bennett; Ben Thorpe; Carla White; Alma Rahat; Daniel Archambault; Noemi Picco; Gibin Powathil; Biagio Lucini,Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University,"The sudden outbreak of the COVID-19 pandemic presented governments, policy makers and health services with an unprecedented challenge of taking real-time decisions that could keep the disease under control with non-pharmaceutical interventions, while at the same time limit as much as possible severe consequences of a very strict lockdown. Mathematical modelling has proved to be a crucial element for informing those decisions. Here we report on the rapid development and application of the Swansea Model, a mathematical model of disease spread in real time, to inform policy decisions during the COVID-19 pandemic in Wales.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2023.08.01.23293491,2023-08-02,https://medrxiv.org/cgi/content/short/2023.08.01.23293491,Health inequalities in SARS-CoV-2 infection during the second wave in England: REACT-1 study,Haowei Wang; Kylie E. C. Ainslie; Oliver Eales; Caroline E. Walters; David Haw; Christina Atchinson; Claudio Fronterre; Peter J. Diggle; Deborah Ashby; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Christl A Donnelly; Paul Elliott; Steven Riley,"School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; School of Public Health, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc","ObjectivesThe rapid spread of SARS-CoV-2 infection caused high levels of hospitalisation and deaths in late 2020 and early 2021 during the second wave in England. Severe disease during this period was associated with marked health inequalities across ethnic and sociodemographic subgroups. In this paper, we aimed to investigate how inequalities influence the risk of getting infected across ethnic and sociodemographic subgroups during a key period before widespread vaccination. DesignRepeated cross-sectional community-based study. @@ -159,19 +146,11 @@ HighlightsO_LILong waits for elective care can result in additional healthcare n C_LIO_LIThe large number of long-wait pathways produced as a consequence of COVID-19 disruption allows for a more holistic analysis, covering the full range of elective treatment specialties and wider healthcare impacts across primary, secondary, mental health, and community care, as well as emergency service calls and prescriptions. C_LIO_LIAnalysis of 44,616 elective care pathways reveals evidence of increases in wider healthcare consumption additional to that expected for similar patients not awaiting elective treatment. This suggests a false economy in failing to promptly resolve elective pathways, which should be reflected by healthcare providers in long-term resource allocation decisions. C_LI",health systems and quality improvement,fuzzy,100,100 -medRxiv,10.1101/2023.07.19.23292289,2023-07-23,https://medrxiv.org/cgi/content/short/2023.07.19.23292289,Can computer simulation support strategic service planning? Modelling a large integrated mental health system on recovery from COVID-19,Livia LP Pierotti; Jennifer Cooper; Charlotte James; Rachel Denholm; Kenah Cassels; Emma Gara; Richard Wood,"University of Bristol; University of Bristol; University of Bristol; University of Bristol; Bristol, North Somerset and South Gloucestershire Integrated Care Board, UK National Health Service; Bristol, North Somerset and South Gloucestershire Integrated Care Board, UK National Health Service; Bristol, North Somerset and South Gloucestershire Integrated Care Board, UK National Health Service. HDR UK Southwest.","BackgroundCOVID-19 has had a significant impact on peoples mental health and mental health services. During the first year of the pandemic, existing demand was not fully met while new demand was generated, resulting in large numbers of people requiring support. To support mental health services to recover without being overwhelmed, it was important to know where services will experience increased pressure, and what strategies could be implemented to mitigate this. - -MethodsWe implemented a computer simulation model of patient flow through an integrated mental health service in Southwest England covering General Practice (GP), community-based talking therapies (IAPT), acute hospital care, and specialist care settings. The model was calibrated on data from 1 April 2019 to 1 April 2021. Model parameters included patient demand, service-level length of stay, and probabilities of transitioning to other care settings. We used the model to compare do nothing (baseline) scenarios to what if (mitigation) scenarios, including increasing capacity and reducing length of stay, for two future demand trajectories from 1 April 2021 onwards. - -ResultsThe results from the simulation model suggest that, without mitigation, the impact of COVID-19 will be an increase in pressure on GP and specialist community based services by 50% and 50-100% respectively. Simulating the impact of possible mitigation strategies, results show that increasing capacity in lower-acuity services, such as GP, results in demand being shifted to other parts of the mental health system while decreasing length of stay in higher acuity services is insufficient to mitigate the impact of increased demand. - -ConclusionIn capturing the interrelation of patient flow related dynamics between various mental health care settings, we demonstrate the value of computer simulation for assessing the impact of interventions on system flow.",health systems and quality improvement,fuzzy,100,100 medRxiv,10.1101/2023.07.16.23292705,2023-07-18,https://medrxiv.org/cgi/content/short/2023.07.16.23292705,"Community-onset urinary tract infection in females in the context of COVID-19: a longitudinal population cohort study exploring case presentation, management, and outcomes",Nina J Zhu; Benedict Hayhoe; Raheelah Ahmad; James R Price; Donna Lecky; Monsey McLeod; Elena Ferran; Timothy M Rawson; Emma Carter; Alison H Holmes; Paul Aylin,"National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial ; Department of Primary Care and Public Health, School of Public Health, Imperial College London, London, United Kingdom; Division of Health Services Research and Management, School of Health Sciences, City, University of London, London, United Kingdom; National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial ; Primary Care and Interventions Unit, United Kingdom Health Security Agency (UKHSA), Gloucestershire, United Kingdom; NHS England and NHS Improvement, London, United Kingdom; Barts Health NHS Trust, London, United Kingdom; National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial ; National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial ; National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial ; Primary Care and Interventions Unit, United Kingdom Health Security Agency (UKHSA), Gloucestershire, United Kingdom","BackgroundCOVID-19 affected the epidemiology of other infectious diseases and how they were managed. Urinary tract infection (UTI) is one of the most common infections treated in the community in England. We investigated the impact of the COVID-19 pandemic on UTI primary care consultations and outcomes in female patients. Methods and findingsWe analysed General Practice (GP) consultation and hospital admission records using the Whole Systems Integrated Care (WSIC) data in North West London between 2016 and 2021. We quantified the changes in UTI GP consultation rates using time series analysis before and during the pandemic. We assessed the outcomes of UTI, measured by subsequent bacteraemia and sepsis within 60 days, for consultations delivered face-to-face or remotely, with or without diagnostic tests recommended by the national guidelines, and with or without antibiotic treatment. Between January 2016 and December 2021, we identified 375,859 UTI episodes in 233,450 female patients. Before the COVID-19 pandemic (January 2016 - February 2020), the UTI GP consultation rate stayed level at 522.8 cases per 100,000 population per month, with a seasonal pattern of peaking in October. Since COVID-19, (March 2020 - December 2021), monthly UTI GP consultations declined when COVID-19 cases surged and rose when COVID-19 case fell. During the pandemic, the UTI consultations delivered face-to-face reduced from 72.0% to 29.4%, the UTI consultations with appropriate diagnostic tests, including urine culture and urinalysis, reduced from 17.3% to 10.4%, and the UTI cases treated with antibiotics reduced from 52.0% to 47.8%. The likelihood of antibiotics being prescribed was not affected by whether the consultation was delivered face-to-face or remotely but associated with whether there was a diagnostic test. Regardless of whether the UTI consultation occurred before or during the pandemic, the absence of antibiotic treatment for UTI is associated with a 10-fold increase in the risk of having bacteraemia or sepsis within 60 days, though the patients who consulted GPs for UTI during the pandemic were older and more co-morbid. Across the study period (January 2016 - December 2021), nitrofurantoin remained the first-line antibiotic option for UTI. The percentage of non-prophylactic acute UTI antibiotic prescriptions with durations that exceeded the guideline recommendations was 58.7% before the pandemic, and 49.4% since. This led to 830,522 total excess days of treatment, account for 63.3% of all non-prophylactic acute antibiotics prescribed for UTI. Before the pandemic, excess antibiotic days of UTI drugs had been reducing consistently. However, this decline slowed down during the pandemic. Having a diagnostic test was associated with 0.6 less excess days of antibiotic treatment. ConclusionsThis analysis provides a comprehensive examination of management and outcomes of community-onset UTI in female patients, considering the changes in GP consultations during the COVID-19 pandemic. Our findings highlighted the importance of appropriate urine testing to support UTI diagnosis in symptomatic patients and initiation of antibiotic treatment with appropriate course duration. Continued monitoring is required to assess the overall impact on patients and health systems from the changed landscape of primary care delivery.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2023.07.06.23292295,2023-07-07,https://medrxiv.org/cgi/content/short/2023.07.06.23292295,Spatio-temporal surveillance and early detection of SARS-CoV-2 variants of concern,Massimo Cavallaro; Louise Dyson; Michael J Tildesley; Daniel Todkill; Matt J Keeling,University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick,"The SARS-CoV-2 pandemic has been characterized by the repeated emergence of genetically distinct virus variants of increased transmissibility and immune evasion compared to pre-existing lineages. In many countries, their containment required the intervention of public health authorities and the imposition of control measures. While the primary role of testing is to identify infection, target treatment, and limit spread (through isolation and contact tracing), a secondary benefit is in terms of surveillance and the early detection of new variants. Here we study the spatial invasion and early spread of the Alpha, Delta, and Omicron (BA.1 and BA.2) variants in England from September 2020 to February 2022 using the random neighbourhood covering (RaNCover) method. This is a statistical technique for the detection of aberrations in spatial point processes, which we tailored here to community PCR (polymerase-chain-reaction) test data where the TaqPath kit provides a proxy measure of the switch between variants. Retrospectively, RaNCover detected the earliest signals associated with the four novel variants that led to large infection waves in England. With suitable data our method therefore has the potential to rapidly detect outbreaks of future SARS-CoV-2 variants, thus helping to inform targeted public health interventions.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2023.07.03.23291596,2023-07-05,https://medrxiv.org/cgi/content/short/2023.07.03.23291596,Risk of COVID-19 death in adults who received booster COVID-19 vaccinations: national retrospective cohort study on 14.6 million people in England,Isobel L Ward; Chris Robertson; Utkarsh Agrawal; Lynsey Patterson; Declan T Bradley; Ting Shi; Simon de Lusignan; Richard Hobbs; Aziz Sheikh; Vahe Nafilyan,"Office for National Statistics, Newport, UK; Department of Mathematics and Statistics, Strathclyde University, Glasgow, Scotland and Public Health Scotland, Glasgow, Scotland; Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; Centre for Public Health, Queen's University Belfast, Belfast, UK and Public Health Agency, Belfast, UK; Centre for Public Health, Queen's University Belfast, Belfast, UK and Public Health Agency, Belfast, UK; Usher Institute, University of Edinburgh, Edinburgh, UK; Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; Usher Institute, University of Edinburgh, Edinburgh, UK; Office for National Statistics, Newport, UK","ImportanceThe emergence of the COVID-19 vaccination has been critical in changing the course of the COVID-19 pandemic, with estimates suggesting vaccinations have prevented millions of deaths worldwide. To ensure protection remains high in vulnerable groups booster vaccinations in the UK have been targeted based on age and clinical vulnerabilities. ObjectiveWe sought to identify adults who had received a booster vaccination as part of the autumn 2022 campaign in England yet remained at increased risk of postbooster COVID-19 death and compared to non-COVID-19 risk. @@ -444,6 +423,7 @@ C_LIO_LIData collected include demographics, details on occupation, co-morbiditi C_LIO_LINested within Virus Watch are a serology & PCR cohort study (n=12,877) and a vaccine evaluation study (n=19,555). C_LIO_LIStudy data are deposited in the Office of National Statistics (ONS) Secure Research Service (SRS). Survey data are available under restricted access upon request to ONS SRS. C_LI",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2023.01.29.23285160,2023-01-30,https://medrxiv.org/cgi/content/short/2023.01.29.23285160,High number of SARS-CoV-2 persistent infections uncovered through genetic analysis of samples from a large community-based surveillance study,Mahan Ghafari; Matthew Hall; Tanya Golubchik; Daniel Ayoubkhani; Thomas House; George MacIntyre-Cockett; Helen Fryer; Laura Thomson; Anel Nurtay; David Buck; Angie Green; Amy Trebes; Paolo Piazza; Lorne J Lonie; Ruth Studley; Emma Rourke; Darren Smith; Matthew Bashton; Andrew Nelson; Matthew Crown; Clare McCann; Gregory R Young; Rui Andre Nunes de Santos; Zack Richards; Adnan Tariq; Roberto Cahuantzi; - Wellcome Sanger Institute COVID-19 Surveillance Team; - COVID-19 Infection Survey Group; - The COVID-19 Genomics UK (COG-UK) consortium; Jeff Barrett; Christophe Fraser; David Bonsall; Sarah Walker; Katrina A Lythgoe,University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; University of Manchester; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; Office for National Statistics; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Office for National Statistics; -; -; -; Wellcome Sanger Institute; University of Oxford; University of Oxford; University of Oxford; University of Oxford,"Persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections may act as viral reservoirs that could seed future outbreaks 1-5, give rise to highly divergent lineages 6-8, and contribute to cases with post-acute Coronavirus disease 2019 (COVID-19) sequelae (Long Covid) 9,10. However, the population prevalence of persistent infections, their viral load kinetics, and evolutionary dynamics over the course of infections remain largely unknown. We identified 381 infections lasting at least 30 days, of which 54 lasted at least 60 days. These persistently infected individuals had more than 50% higher odds of self-reporting Long Covid compared to the infected controls, and we estimate that 0.09-0.5% of SARS-CoV-2 infections can become persistent and last for at least 60 days. In nearly 70% of the persistent infections we identified, there were long periods during which there were no consensus changes in virus sequences, consistent with prolonged presence of non-replicating virus. Our findings also suggest reinfections with the same major lineage are rare and that many persistent infections are characterised by relapsing viral load dynamics. Furthermore, we found a strong signal for positive selection during persistent infections, with multiple amino acid substitutions in the Spike and ORF1ab genes emerging independently in different individuals, including mutations that are lineage-defining for SARS-CoV-2 variants, at target sites for several monoclonal antibodies, and commonly found in immunocompromised patients 11-14. This work has significant implications for understanding and characterising SARS-CoV-2 infection, epidemiology, and evolution.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2023.01.24.23284906,2023-01-25,https://medrxiv.org/cgi/content/short/2023.01.24.23284906,The impact of COVID-19 lockdown on a cohort of adults with recurrent major depressive disorder from Catalonia: a decentralized longitudinal study using remote measurement technology,Raffaele Lavalle Sr.; Elena Condominas; Josep Maria Haro; Iago Gine-Vazquez; Raquel Bailon; Estela Laporta; Ester Garcia; Spyridon Kontaxis; Gemma Riquelme; Federica Lombardini; Antonio Preti; Maria Teresa Penarrubia Maria; Marta Coromina; Belen Arranz; Elisabet Vilella; Elena Rubio Abadal; Faith Matcham; Femke Lamers; Matthew Hotopf; Brenda W.J.H Penninx; Peter Annas; Vaibhav Narayan; Sara Katherine Simblett; Sara Siddi,"Dipartimento di neuroscienze, Universita degli studi di Torino, Italia; Parc Sanitari Sant Joan de Deu, Fundacio Sant Joan de Deu, CIBERSAM,Universitat de Barcelona, Barcelona, Spain; Parc Sanitari Sant Joan de Deu, Fundacio Sant Joan de Deu, CIBERSAM,Universitat de Barcelona, Barcelona, Spain; Parc Sanitari Sant Joan de Deu, Fundacio Sant Joan de Deu, CIBERSAM,Universitat de Barcelona, Barcelona, Spain; Aragon Institute of Engineering Research (I3A), University of Zaragoza, Zaragoza, Spain; Centros de investigacion biomedica en red en el area de bioingenieria, biomateriales y nanomedicina (CIBER BBN), Madrid, Spain; Microelectronica y Sistemas Electronicos, Universidad Autonoma de Barcelona, Spain; Centros de Investigacion Biomedica en Red en el Area de Bioingenieria, Biomateriales y Nanomedicina (CIBER BBN), 28029 Madrid, Spain; Parc Sanitari Sant Joan de Deu, Fundacio Sant Joan de Deu, CIBERSAM, Universitat de Barcelona, Barcelona, Spain; Parc Sanitari Sant Joan de Deu, Fundacio Sant Joan de Deu, CIBERSAM,Universitat de Barcelona, Barcelona, Spain; Dipartimento di neuroscienze, Universita degli studi di Torino, Italia; Health Technology Assessment in Primary Care and Mental Health (PRISMA) Research Group, Parc Sanitari Sant Joan de Deu, Institut de Recerca Sant Joan de Deu, St; Parc Sanitari Sant Joan de Deu, Fundacio Sant Joan de Deu, CIBERSAM,Universitat de Barcelona, Barcelona, Spain; Parc Sanitari Sant Joan de Deu, Fundacio Sant Joan de Deu, CIBERSAM,Universitat de Barcelona, Barcelona, Spain; Hospital Universitari Institut Pere Mata, Reus, Spain Institut d'Investigacio Sanitaria Pere Virgili CERCA, Reus, Spain; Universitat Rovira i Virgili, Reus, Spa; Parc Sanitari Sant Joan de Deu, Fundacio Sant Joan de Deu, CIBERSAM,Universitat de Barcelona, Barcelona, Spain; King's College London: London, GB; VU medisch centrum: Amsterdam, Noord-Holland, NL; Kings College London, Institute of Psychiatry, Psychology and Neuroscience, UK; Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Psychiatry, Boelelaan 1117, Amsterdam, The Netherlands; H. Lundbeck A/S, Valby, Denmark; Research and Development Information Technology, Janssen Research & Development, LLC, Titusville, NJ, USA; Kings College London, Institute of Psychiatry, Psychology and Neuroscience, UK; Parc Sanitari Sant Joan de Deu, Fundacio Sant Joan de Deu, CIBERSAM,Universitat de Barcelona, Barcelona, Spain","BackgroundThe present study analyzes the effects of each containment phase of the first COVID-19 wave on depression levels in a cohort of adults with a history of major depressive disorder (MDD). MethodsThis analysis is part of the Remote Assessment of Disease and Relapse-MDD (RADAR-MDD) study. Individuals included had a diagnosis of DSM-5 major depressive disorder (MDD), at least two episodes of major depression (MDE), one of them in the previous two years. Depression was evaluated with the Patient Health Questionnaire-8 (PHQ-8) and anxiety with the Generalized Anxiety Disorder-7 (GAD-7). A total of 121 participants recruited from Catalonia were registered from November 1, 2019, to October 16, 2020. Levels of depression were explored across the phases (pre-lockdown, lockdown, four post-lockdown phases) of the restrictions imposed by the Spanish/Catalan governments. Then, a mixed model was fitted to estimate how depression varied over the phases. @@ -528,6 +508,15 @@ MethodsThis population-based study uses the QResearch(R) database of primary hea We will describe vaccine uptake in pregnant women by trimester and population subgroups defined by demographics and other characteristics. Cox proportional hazards multivariable regression will be used to identify factors associated with vaccine uptake. The effectiveness of COVID-19 vaccines in pregnant women will be assessed using a nested matched case-control design to assess hospitalisation, intensive care admission and death with COVID-19. Cases who had the outcome will be matched with up to 10 controls who did not have the outcome on that date by age, calendar date and trimester of pregnancy using incidence density sampling for the occurrence of each outcome after each vaccine dose compared with unvaccinated individuals. For the safety analysis, we will we use logistic regression analyses to determine unadjusted and adjusted odds ratios for the occurrence of maternal (e.g. miscarriage, ectopic pregnancy and gestational diabetes) and perinatal outcomes (e.g. stillbirth, small for gestational age and congenital anomalies) by vaccination status compared to unvaccinated individuals. For the adverse events of special interest for vaccine safety (e.g. venous thromboembolism, myocarditis and Guillain Barre syndrome), we will use time varying Royston-Palmar regression analyses to determine unadjusted and adjusted hazard ratios for the occurrence of each outcome by vaccination status to unvaccinated individuals. Ethics and disseminationQResearch is a Research Ethics Approved Research Database with ongoing approval from the East Midlands Multi-Centre Research Ethics Committee (Ref: 18/EM/0400). This study was approved by the QResearch Scientific Committee on 9th June 2022. This research protocol has been developed with support from a patient and public involvement panel, who will continue to provide input throughout the duration of the study. Research findings will be submitted to pre-print servers such as MedRxIv, academic publication and disseminated more broadly through media releases and community groups and conference presentations.",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2022.12.16.22283578,2022-12-17,https://medrxiv.org/cgi/content/short/2022.12.16.22283578,"Higher dose corticosteroids in hospitalised COVID-19 patients with hypoxia but not requiring ventilatory support (RECOVERY): a randomised, controlled, open-label, platform trial",Peter W Horby; Jonathan R Emberson; Buddha Basnyat; Mark Campbell; Leon Peto; Guilherme Pessoa-Amorim; Natalie Staplin; Raph L Hamers; John Amuasi; Jeremy Nel; Evelyne Kestelyn; Manisha Rawal; Roshan Kumar Jha; Nguyen Thanh Phong; Uun Samardi; Damodar Paudel; Pham Ngoc Thach; Nasronudin Nasronudin; Emma Stratton; Louise Mew; Rahuldeb Sarkar; J Kenneth Baillie; Maya H Buch; Jeremy N Day; Saul N Faust; Thomas Jaki; Katie Jeffery; Edmund Juszczak; Marian Knight; Wei Shen Lim; Marion Mafham; Alan Montgomery; Andrew Mumford; Kathryn Rowan; Guy Thwaites; Richard Haynes; Martin J Landray,"Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; OUCRU-Nepal, Patan Academy of Health Sciences, Kathmandu, Nepal; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia; Kumasi Center for Collaborative Research in Tropic Medicine, Kumasi, Ghana; Division of Infectious Diseases, Department of Medicine, University of the Witwatersrand, Johannesburg, South Africa; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom; Sukraraj Tropical and Infectious Disease Hospital, Kathmandu, Nepal; Medicine Department, Nepal Armed Police Force Hospital, Chandragiri, Kathmandu, Nepal; Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam; RSUP Dr Hasan Sadikin Hospital, Bandung, West Java, Indonesia; Department of Medicine, Nepal Police Hospital, Maharajgunj, Kathmandu, Nepal; National Hospital for Tropical Diseases, Hanoi, Vietnam; University of Airlangga Teaching Hospital, Surabaya, Indonesia; University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, United Kingdom; Milton Keynes University Hospital, Milton Keynes, United Kingdom; Faculty of Life Sciences and Medicine, King's College, London, United Kingdom; Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom; Centre for Musculoskeletal Research, University of Manchester, Manchester, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom; NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, ; Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom; Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; National Perinatal Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Respiratory Medicine Department, Nottingham University Hospitals NHS Foundation Trust, Nottingham, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom; Intensive Care National Audit and Research Centre, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom","BackgroundLow-dose corticosteroids have been shown to reduce mortality for hypoxic COVID-19 patients requiring oxygen or ventilatory support (non-invasive mechanical ventilation, invasive mechanical ventilation or extra-corporeal membrane oxygenation). We evaluated the use of a higher dose of corticosteroids in this patient group. + +MethodsThis randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]) is assessing multiple possible treatments in patients hospitalised for COVID-19. Eligible and consenting adult patients with clinical evidence of hypoxia (i.e. receiving oxygen or with oxygen saturation <92% on room air) were randomly allocated (1:1) to either usual care with higher dose corticosteroids (dexamethasone 20 mg once daily for 5 days followed by 10 mg once daily for 5 days or until discharge if sooner) or usual standard of care alone (which includes dexamethasone 6 mg once daily for 10 days or until discharge if sooner). The primary outcome was 28-day mortality. On 11 May 2022, the independent Data Monitoring Committee recommended stopping recruitment of patients receiving no oxygen or simple oxygen only to this comparison due to safety concerns. We report the results for these participants only. Recruitment of patients receiving ventilatory support continues. The RECOVERY trial is registered with ISRCTN (50189673) and clinicaltrials.gov (NCT04381936). + +FindingsBetween 25 May 2021 and 12 May 2022, 1272 COVID-19 patients with hypoxia and receiving no oxygen (1%) or simple oxygen only (99%) were randomly allocated to receive usual care plus higher dose corticosteroids versus usual care alone (of whom 87% received low dose corticosteroids during the follow-up period). Of those randomised, 745 (59%) were in Asia, 512 (40%) in the UK and 15 (1%) in Africa. 248 (19%) had diabetes mellitus. Overall, 121 (18%) of 659 patients allocated to higher dose corticosteroids versus 75 (12%) of 613 patients allocated to usual care died within 28 days (rate ratio [RR] 1{middle dot}56; 95% CI 1{middle dot}18-2{middle dot}06; p=0{middle dot}0020). There was also an excess of pneumonia reported to be due to non-COVID infection (10% vs. 6%; absolute difference 3.7%; 95% CI 0.7-6.6) and an increase in hyperglycaemia requiring increased insulin dose (22% vs. 14%; absolute difference 7.4%; 95% CI 3.2-11.5). + +InterpretationIn patients hospitalised for COVID-19 with clinical hypoxia but requiring either no oxygen or simple oxygen only, higher dose corticosteroids significantly increased the risk of death compared to usual care, which included low dose corticosteroids. The RECOVERY trial continues to assess the effects of higher dose corticosteroids in patients hospitalised with COVID-19 who require non-invasive ventilation, invasive mechanical ventilation or extra-corporeal membrane oxygenation. + +FundingUK Research and Innovation (Medical Research Council) and National Institute of Health and Care Research (Grant ref: MC_PC_19056), and Wellcome Trust (Grant Ref: 222406/Z/20/Z).",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2022.12.12.22283200,2022-12-14,https://medrxiv.org/cgi/content/short/2022.12.12.22283200,"COVID-19 Vaccination in Pregnancy: The Impact of Multimorbidity and Smoking Status on Vaccine Hesitancy, a Cohort Study of 25,111 Women in Wales, UK",Mohamed Mhereeg; Hope Jones; Jonathan Kennedy; Mike Seaborne; Michael Parker; Natasha Kennedy; Ashley Akbari; Luisa Zuccolo; Amaya Azcoaga-Lorenzo; Alisha Davies; Krishnarajah Nirantharakumar; Sinead Brophy,"National Centre for Population Health and Wellbeing Research, Swansea University Medical School, Faculty of Medicine, Health and Life Science, Swansea, Wales, U; National Centre for Population Health and Wellbeing Research, Swansea University Medical School, Faculty of Medicine, Health and Life Science, Swansea, Wales, U; National Centre for Population Health and Wellbeing Research, Swansea University Medical School, Faculty of Medicine, Health and Life Science, Swansea, Wales, U; National Centre for Population Health and Wellbeing Research, Swansea University Medical School, Faculty of Medicine, Health and Life Science, Swansea, Wales, U; National Centre for Population Health and Wellbeing Research, Swansea University Medical School, Faculty of Medicine, Health and Life Science, Swansea, Wales, U; National Centre for Population Health and Wellbeing Research, Swansea University Medical School, Faculty of Medicine, Health and Life Science, Swansea, Wales, U; Population Data Science, Swansea University Medical School, Faculty of Medicine, Health and Life Science, Swansea, Wales, UK; Health Data Science Centre, Fondazione Human Technopole, Milan, Italy; School of Medicine, University of St Andrews, Scotland, UK and Hospital Rey Juan Carlos. Instituto de Investigacion Sanitaria Fundacion Jimenez Diaz. Madrid. Sp; Research and Evaluation Division, Public Health Wales, UK.; Institute of Applied Health Research, Birmingham University, Birmingham, UK.; National Centre for Population Health and Wellbeing Research, Swansea University Medical School, Faculty of Medicine, Health and Life Science, Swansea, Wales, U","BackgroundMultimorbidity and pregnancy are two risk factors for more severe outcomes after a SARS-CoV-2 infection, thus vaccination uptake is important for pregnant women living with multimorbidity. This study aimed to examine the impact of multimorbidity, smoking status, and demographics (age, ethnic group, area of deprivation) on vaccine hesitancy among pregnant women in Wales using electronic health records (EHR) linkage. MethodsThis cohort study utilised routinely collected, individual-level, anonymised population-scale linked data within the Secure Anonymised Information Linkage (SAIL) Databank. Pregnant women were identified from 13th April 2021 to 31st December 2021. Survival analysis was utilised to examine and compare the length of time to vaccination uptake in pregnancy by multimorbidity and smoking status, as well as depression, diabetes, asthma, and cardiovascular conditions independently. Variation in uptake by; multimorbidity, smoking status, and demographics was examined jointly and separately for the independent conditions using hazard ratios (HR) from the Cox regression model. A bootstrapping internal validation was conducted to assess the performance of the models. @@ -702,15 +691,6 @@ Existing evidence suggests that COVID-19 vaccines are effective for preventing s However, research directly comparing vaccine effectiveness between pregnant and non-pregnant women of reproductive age at the population level are lacking. What this study addsOur study provides real-world evidence that COVID-19 vaccination reduces the risk of hospital admission by a similar amount for both women infected with SARS-CoV-2 during pregnancy and women who were not pregnant when infected, during the Alpha and Delta dominant periods in England.",public and global health,fuzzy,100,100 -medRxiv,10.1101/2022.09.23.22280285,2022-09-25,https://medrxiv.org/cgi/content/short/2022.09.23.22280285,"Dimethyl fumarate in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial",- RECOVERY Collaborative Group; Peter W Horby; Leon Peto; Natalie Staplin; Mark Campbell; Guilherme Pessoa-Amorim; Marion Mafham; Jonathan R Emberson; Richard Stewart; Benjamin Prudon; Alison Uriel; Christopher A Green; Devesh J Dhasmana; Flora Malein; Jaydip Majumdar; Paul Collini; Jack Shurmer; Bryan Yates; J Kenneth Baillie; Maya H Buch; Jeremy N Day; Saul N Faust; Thomas Jaki; Katie Jeffery; Edmund Juszczak; Marian Knight; Wei Shen Lim; Alan Montgomery; Andrew Mumford; Kathryn Rowan; Guy Thwaites; Richard Haynes; Martin Landray,"; Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, University of Oxford, Oxford, United Kingdom; Milton Keynes University Hospital NHS Foundation Trust; North Tees and Hartlepool NHS Foundation Trust; Manchester University NHS Foundation Trust; University Hospitals Birmingham NHS Foundation Trust; Victoria Hospital Kirkcaldy, NHS Fife; Liverpool University Hospitals NHS Foundation Trust; Mid Cheshire Hospitals NHS Foundation Trust; Sheffield Teaching Hospitals NHS Foundation Trust; Bolton NHS Foundation Trust; Northumbria Healthcare NHS Foundation Trust; Roslin Institute, University of Edinburgh; Centre for Musculoskeletal Research, University of Manchester, Manchester, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam; NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University of Southampton, Southampton, United Kingdom; University of Regensburg, Germany; Oxford University Hospitals NHS Foundation Trust; School of Medicine, University of Nottingham, Nottingham, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom; Intensive Care National Audit & Research Centre, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam; MRC Population Health Research Unit, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom","BackgroundDimethyl fumarate (DMF) is an anti-inflammatory drug that has been proposed as a treatment for patients hospitalised with COVID-19 - -MethodsThis randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), is assessing multiple possible treatments in patients hospitalised for COVID-19. In this initial assessment of DMF, performed at 27 UK hospitals, eligible and consenting adults were randomly allocated (1:1) to either usual standard of care alone or usual standard of care plus DMF 120mg twice daily for 2 days followed by 240mg twice daily for 8 days, or until discharge if sooner. The primary outcome was clinical status on day 5 measured on a seven-point ordinal scale, assessed using a proportional odds model. Secondary outcomes were time to sustained improvement in clinical status, time to discharge, day 5 peripheral blood oxygenation, day 5 C-reactive protein, and improvement in day 10 clinical status. The trial is registered with ISRCTN (50189673) and clinicaltrials.gov (NCT04381936). - -FindingsBetween 2 March 2021 and 18 November 2021, 713 patients were enrolled in the DMF evaluation, of whom 356 were randomly allocated to receive usual care plus DMF, and 357 to usual care alone. 95% of patients were receiving corticosteroids as part of routine care. There was no evidence of a beneficial effect of DMF on clinical status at day 5 (common odds ratio of unfavourable outcome 1.12; 95% CI 0.85-1.46; p=0.42). There was no significant effect of DMF on any secondary outcome. As expected, DMF caused flushing and gastrointestinal symptoms, each in around 6% of patients, but no new adverse effects were identified. - -InterpretationIn adults hospitalised with COVID-19, DMF was not associated with an improvement in clinical outcomes. - -FundingUK Research and Innovation (Medical Research Council) and National Institute of Health Research (Grant ref: MC_PC_19056).",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2022.09.21.22280191,2022-09-21,https://medrxiv.org/cgi/content/short/2022.09.21.22280191,Exploring the relationship between job characteristics and infection: Application of a COVID-19 Job Exposure Matrix to SARS-CoV-2 infection data in the United Kingdom,Sarah Rhodes; Sarah Beale; Jack Wilkinson; Karin Van-Veldhoven; Ioannis Basinas; Will Mueller; Karen Oedehengel; Alex Burdorf; Susan Peters; Zara Stokholm; Vivi Schlunssen; Henrik Kolstad; Anjoeka Pronk; Neil Pearce; Andrew Hayward; Martie van Tongeren,University of Manchester; University College London; University of Manchester; London School of Hygiene and Tropical Medicine; University of Manchester; Institute of Occupational Medicine; Netherlands Organization for Applied Scientific Research; Erasmus Medical Center Rotterdam; Utrecht University; Aarhus University Hospital; Aarhus University; Aarhus University Hospital; Dutch Institution of Applied Science; London School of Hygiene and Tropical Medicine; UCL; University of Manchester,"ObjectivesTo assess whether workplace exposures as estimated via a COVID-19 Job Exposure Matrix (JEM) are associated with SARS-CoV-2. MethodsData on 244,470 participants were available from the ONS Coronavirus Infection Survey (CIS) and 16,801 participants from the Virus Watch Cohort, restricted to workers aged 20 to 64. Analysis used logistic regression models with SARS-CoV-2 as the dependent variable for eight individual JEM domains (number of workers, nature of contacts, contact via surfaces, indoor or outdoor location, ability to social distance, use of face covering, job insecurity, migrant workers) with adjustment for age, sex, ethnicity, Index of Multiple Deprivation (IMD), region, household size, urban vs rural area, and health conditions. Analyses were repeated for three time periods (i) February 2020 (Virus Watch)/April 2020 (CIS) to May 2021), (ii)June 2021 to November 2021, (iii) December 2021 to January 2022. @@ -938,6 +918,13 @@ Methods and analysisThis is a pragmatic, multi-centre, cluster-randomised clinic Ethics and disseminationThe protocol was reviewed by South Central - Berkshire Research Ethics Committee (reference: 21/SC/0416). All participating sites obtained local approvals prior to recruitment. Coverscan has UKCA certification (752965). The first participant was recruited in July 2022 and interim/final results will be disseminated in 2023, in a plan co-developed with public and patient representatives. The results will be presented at national and international conferences, published in peer reviewed medical journals, and shared via media (mainstream and social) and patient support organisations. Trial registration numberISRCTN10665760",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2022.07.14.22277638,2022-07-15,https://medrxiv.org/cgi/content/short/2022.07.14.22277638,Therapeutic potential of IL6R blockade for the treatment of sepsis and sepsis-related death: Findings from a Mendelian randomisation study,Fergus W Hamilton; Matt Thomas; David T Arnold; Tom M Palmer; Ed Moran; Alexander J Mentzer; Nick A Maskell; J Kenneth Baillie; Charlotte Summers; Aroon Dinesh Hingorani; Alasdair P MacGowan; Golam M Khandaker; Ruth E Mitchell; George Davey Smith; Peter Ghazal; Nicholas J Timpson,"University of Bristol; North Bristol NHS Trust; University of Bristol; University of Bristol; North Bristol NHS Trust; University of Oxford; University; Roslin Institute, University of Edinburgh; University of Cambridge; University College London; North Bristol NHS Trust; University of Bristol; University of Bristol; University of Bristol; Cardiff University; University of Bristol","IntroductionSepsis is characterised by dysregulated, life-threatening immune responses, which are thought to be driven by cytokines such as interleukin-6 (IL-6). Genetic variants in IL6R known to downregulate IL-6 signalling are associated with improved COVID-19 outcomes, a finding later confirmed in randomised trials of IL-6 receptor antagonists (IL6RA). We hypothesised that blockade of IL6R could also improve outcomes in sepsis. + +MethodsWe performed a Mendelian randomisation analysis using single nucleotide polymorphisms (SNPs) in and near IL6R to evaluate the likely causal effects of IL6R blockade on sepsis, sepsis severity, other infections, and COVID-19. We weighted SNPs by their effect on CRP and combined results across them in inverse variance weighted meta-analysis, proxying the effect of IL6RA. Our outcomes were measured in UK Biobank, FinnGen, the COVID-19 Host Genetics Initiative (HGI), and the GenOSept and GainS consortium. We performed several sensitivity analyses to test assumptions of our methods, including utilising variants around CRP in a similar analysis. + +ResultsIn the UK Biobank cohort (N=485,825, including 11,643 with sepsis), IL6R blockade was associated with a decreased risk of sepsis (OR=0.80; 95% CI 0.66-0.96, per unit of natural log transformed CRP decrease). The size of this effect increased with severity, with larger effects on 28-day sepsis mortality (OR=0.74; 95% CI 0.38-0.70); critical care admission with sepsis (OR=0.48, 95% CI 0.30-0.78) and critical care death with sepsis (OR=0.37, 95% CI 0.14 - 0.98) Similar associations were seen with severe respiratory infection: OR for pneumonia in critical care 0.69 (95% CI 0.49 - 0.97) and for sepsis survival in critical care (OR=0.22; 95% CI 0.04- 1.31) in the GainS and GenOSept consortium. We also confirm the previously reported protective effect of IL6R blockade on severe COVID-19 (OR=0.69, 95% 0.57 - 0.84) in the COVID-19 HGI, which was of similar magnitude to that seen in sepsis. Sensitivity analyses did not alter our primary results. + +ConclusionsIL6R blockade is causally associated with reduced incidence of sepsis, sepsis related critical care admission, and sepsis related mortality. These effects are comparable in size to the effect seen in severe COVID-19, where IL-6 receptor antagonists were shown to improve survival. This data suggests a randomised trial of IL-6 receptor antagonists in sepsis should be considered.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2022.07.07.22277367,2022-07-10,https://medrxiv.org/cgi/content/short/2022.07.07.22277367,"Non-hospitalised, vaccinated adults with COVID-19 caused by Omicron BA.1 and BA.2 present with changing symptom profiles compared to those with Delta despite similar viral kinetics",Hermaleigh Townsley; Joshua Gahir; Timothy W Russell; Edward J Carr; Matala Dyke; Murad Miah; Bobbi Clayton; Callie Smith; Mauro Miranda; Nicola O'Reilly; Lorin Adams; Harriet V Mears; Christopher Bailey; James RM Black; Ashley S Fowler; Katalin Wilkinson; Matthew Hutchinson; Ruth Harvey; Bobbi Clayton; Gavin Kelly; Rupert Beale; Padmasayee Papineni; Tumena Corrah; Simon Caidan; Jerome Nicod; Steve Gamblin; George Kassiotis; Vincenzo Libri; Bryan Williams; Sonia Gandhi; Adam J Kucharski; Charles Swanton; David LV Bauer; Emma C Wall,"Francis Crick Institute, National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clini; Francis Crick Institute, National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clini; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK; Francis Crick Institute; Francis Crick Institute, National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clini; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute, Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London, UK; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute, Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London, UK; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute, Genotype-to-Phenotype UK National Virology Consortium (G2P-UK); London Northwest University Healthcare NHS Trust, London; London Northwest University Healthcare NHS Trust, London; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute, Department of Infectious Disease, St Mary's Hospital, Imperial College London, London; National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, Lo; National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, Lo; Francis Crick Institute, University College London, Gower Street, London; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK; Francis Crick Institute, University College London, Gower Street, London; Francis Crick Institute, Genotype-to-Phenotype UK National Virology Consortium (G2P-UK); Francis Crick Institute, National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clini","BackgroundSARS-CoV-2 variant Omicron rapidly evolved over 2022, causing three waves of infection due to sub-variants BA.1, BA.2 and BA.4/5. We sought to characterise symptoms and viral loads over the course of COVID-19 infection with these sub-variants in otherwise-healthy, vaccinated, non-hospitalised adults, and compared data to infections with the preceding Delta variant of concern (VOC). MethodsIn a prospective, observational cohort study, healthy vaccinated UK adults who reported a positive PCR or lateral flow test, self-swabbed on alternate days until day 10. We compared symptoms and viral load trajectories between infections caused by VOCs Delta and Omicron (sub-variants BA.1, BA.2 and BA.4/5), and tested for relationships between vaccine dose, symptoms and PCR Ct value as a proxy for viral load. @@ -1034,7 +1021,6 @@ ParticipantsEleven nurses and managers from cardiology, cardiac surgery, oncolog ResultsThree main themes emerged: (i) Implementing NEWS2 challenges and supports; (ii) Value of NEWS2 to alarm, escalate, particularly during the pandemic; and (iii) Digitalisation: EHR integration and automation. The value of NEWS2 was partly positive in escalation, yet there were concerns by nurses who undervalued NEWS2 particularly in cardiac care. Challenges, like clinicians behaviours, lack of resources and training and the perception of NEWS2 value, limit the success of this implementation. Changes in guidelines in the pandemic have led to overlooking NEWS2. EHR integration and automated monitoring are improvement solutions that are not fully employed yet. ConclusionWhether in specialist or general medical settings, the health professionals implementing EWS in healthcare face cultural and systems related challenges to adopting NEWS2 and digital solutions. The validity of NEWS2 in specialised settings and complex conditions is not yet apparent and requires comprehensive validation. EHRs integration and automation are powerful tools to facilitate NEWS2 if its principles are reviewed and rectified, and resources and training are accessible. Further examination of implementation from the cultural and automation domains are needed.",health informatics,fuzzy,100,100 -medRxiv,10.1101/2022.06.13.22276316,2022-06-13,https://medrxiv.org/cgi/content/short/2022.06.13.22276316,Patterns of Reported Infection and Reinfection of SARS-CoV-2 in England,Matt J Keeling,University of Warwick,"One of the key features of any infectious disease is whether infection generates long-lasting immunity or whether repeated reinfection is common. In the former, the long-term dynamics are driven by the birth of susceptible individuals while in the latter the dynamics are governed by the speed of waning immunity. Between these two extremes a range of scenarios is possible. During the early waves of SARS-CoV-2, the underlying paradigm was for long-lasting immunity, but more recent data and in particular the 2022 Omicron waves have shown that reinfection can be relatively common. Here we investigate reported SARS-CoV-2 cases in England, partitioning the data into four main waves, and consider the temporal distribution of first and second reports of infection. We show that a simple low-dimensional statistical model of random (but scaled) reinfection captures much of the observed dynamics, with the value of this scaling, k, providing information of underlying epidemiological patterns. We conclude that there is considerable heterogeneity in risk of reporting reinfection by wave, age-group and location. The high levels of reinfection in the Omicron wave (we estimate that 18% of all Omicron cases had been previously infected, although not necessarily previously reported infection) point to reinfection events dominating future COVID-19 dynamics.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2022.06.12.22276307,2022-06-13,https://medrxiv.org/cgi/content/short/2022.06.12.22276307,"Occupation, Worker Vulnerability, and COVID-19 Vaccination Uptake: Analysis of the Virus Watch prospective cohort study",Sarah Beale; Rachel Burns; Isobel Braithwaite; Thomas Edward Byrne; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Susan J Hoskins; Jana Kovar; Annalan Mathew Dwight Navaratnam; Parth Patel; Alexei Yavlinsky; Martie J Van Tongeren; Robert W Aldridge; Andrew Hayward,University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University of Manchester; University College London; University College London,"BackgroundOccupational disparities in COVID-19 vaccine uptake can impact the effectiveness of vaccination programmes and introduce particular risk for vulnerable workers and those with high workplace exposure. This study aimed to investigate COVID-19 vaccine uptake by occupation, including for vulnerable groups and by occupational exposure status. MethodsWe used data from employed or self-employed adults who provided occupational information as part of the Virus Watch prospective cohort study (n=19,595) and linked this to study-obtained information about vulnerability-relevant characteristics (age, medical conditions, obesity status) and work-related COVID-19 exposure based on the Job Exposure Matrix. Participant vaccination status for the first, second, and third dose of any COVID-19 vaccine was obtained based on linkage to national records and study records. We calculated proportions and Sison-Glaz multinomial 95% confidence intervals for vaccine uptake by occupation overall, by vulnerability-relevant characteristics, and by job exposure. @@ -1188,13 +1174,6 @@ What is already known on this topicSome occupational groups have observed increa What this study addsRelative differences between occupational groups have varied during different stages of the COVID-19 pandemic with risks for healthcare workers diminishing over time and workers in the education sector seeing persistent elevated risks. How this study might affect research, practice or policyIncreased long term mitigation such as ventilation should be considered in sectors with a persistent elevated risk. It is important for workplace policy to be responsive to evolving pandemic risks.",occupational and environmental health,fuzzy,100,100 -medRxiv,10.1101/2022.04.26.22274332,2022-04-27,https://medrxiv.org/cgi/content/short/2022.04.26.22274332,"Community factors and excess mortality in the COVID-19 pandemic in England, Italy and Sweden",Brandon Parkes; Massimo Stafoggia; Daniela Fecht; Bethan Davies; Carl Bonander; Francesca de'Donato; Paola Michelozzi; Frédéric B. Piel; Ulf Strömberg; Marta Blangiardo,Imperial College London; Lazio Regional Health Service; Imperial College London; Imperial College London; University of Gothenburg; Lazio Regional Health Service; Lazio Regional Health Service; Imperial College London; University of Gothenburg; Imperial College London,"BackgroundAnalyses of COVID-19 suggest specific risk factors make communities more or less vulnerable to pandemic related deaths within countries. What is unclear is whether the characteristics affecting vulnerability of small communities within countries produce similar patterns of excess mortality across countries with different demographics and public health responses to the pandemic. Our aim is to quantify community-level variations in excess mortality within England, Italy and Sweden and identify how such spatial variability was driven by community-level characteristics. - -MethodsWe applied a two-stage Bayesian model to quantify inequalities in excess mortality in people aged 40 years and older at the community level in England, Italy and Sweden during the first year of the pandemic (March 2020-February 2021). We used community characteristics measuring deprivation, air pollution, living conditions, population density and movement of people as covariates to quantify their associations with excess mortality. - -ResultsWe found just under half of communities in England (48.1%) and Italy (45.8%) had an excess mortality of over 300 per 100,000 males over the age of 40, while for Sweden that covered 23.1% of communities. We showed that deprivation is a strong predictor of excess mortality across the three countries, and communities with high levels of overcrowding were associated with higher excess mortality in England and Sweden. - -ConclusionThese results highlight some international similarities in factors affecting mortality that will help policy makers target public health measures to increase resilience to the mortality impacts of this and future pandemics.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2022.04.21.22274152,2022-04-27,https://medrxiv.org/cgi/content/short/2022.04.21.22274152,"Health care use attributable to COVID-19: A propensity matched national electronic health records cohort study of 249,390 people in Wales, UK.",Jonathan Kennedy; Michael Parker; Michael Seaborne; Mohamed Mhereeg; Alex J Walker; Venexia Walker; Spiros Denaxas; Natasha Kennedy; Srinivasa Vittal Katikireddi; Sinead Brophy,"Swansea University; Swansea University; Swansea University; Swansea University; Datalab, Nuffield Dept of Primary Care Health Science, Radcliffe Primary Care Building, Oxford, OX2 6GG.; University of Bristol; University College London; Swansea University; University of Glasgow; Swansea University","BackgroundTo determine the extent and nature of changes in infected patients healthcare utilization, we studied healthcare contact in the 1-4 weeks and 5-24 weeks following a COVID-19 diagnosis compared to propensity matched controls. MethodsSurvival analysis was used for time to death and first clinical outcomes including clinical terminology concepts for post-viral illness, fatigue, embolism, respiratory conditions, mental and developmental conditions, fit note, or hospital attendance. Increased instantaneous risk for the occurrence of an outcome for positive individuals was quantified using hazard ratios (HR) from Cox Regression and absolute risk was quantified using relative risk (RR) from life table analysis. @@ -1301,6 +1280,7 @@ Research in contextO_ST_ABSEvidence before the studyC_ST_ABSDespite the risk of Added value of this studyThe Virus Watch study is a prospective community household study across England and Wales. 19,166 participants responded to the monthly questionnaire on glasses and contact lens use, assessing reported frequency, the purpose of use and how likely they were to wear a mask with glasses. Infections were identified in data linked to the Second Generation Surveillance System (Pillar 1 and Pillar 2 testing), weekly surveys seeking self-reports of polymerase chain reaction or lateral flow device results and, in a subset of 11,701, self-collected capillary blood testing for antibodies (nucleocapsid and spike - nucleocapsid antibodies were taken as evidence of prior infection as these are unaffected by vaccination). Our multivariable logistic regression model, controlling for age, sex, household income and occupation, demonstrated 15% lower odds of infection for those who reported always using glasses for general use compared to those who never wear glasses. The protective effect was not observed in those who strongly agreed with the statement, I am less likely to wear a face covering when I have my glasses on because my glasses steam up. Counterfactual analysis of contact lenses did not suggest a protective effect regardless of frequency of use. Implications of all the available evidenceThe findings of this study demonstrate a moderate reduction in risk of SARS-CoV-2 infection in those who always wear glasses compared to never. Unlike other studies, our results are representative of a community setting, adjust for potential confounders and provide a counterfactual analysis with contact lenses. This extends the current evidence to community settings and validates proposed biological mechanisms of eye protection reducing the risk of SARS-CoV-2 transmission.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2022.03.29.22273042,2022-04-04,https://medrxiv.org/cgi/content/short/2022.03.29.22273042,The new normal? Dynamics and scale of the SARS-CoV-2 variant Omicron epidemic in England,Oliver Eales; Leonardo de Oliveira Martins; Andrew Page; Haowei Wang; Barbara Bodinier; David Tang; David Haw; Jakob Jonnerby; Christina Atchison; Deborah Ashby; Wendy Barclay; Graham Taylor; Graham Cooke; Helen Ward; Ara Darzi; Steven Riley; Paul Elliott; Christl A Donnelly; Marc Chadeau-Hyam,"Imperial College London; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Environment and Health, School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Environment and Health, School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Environment and Health, School of Public Health, Imperial College London, UK","The SARS-CoV-2 pandemic has been characterised by the regular emergence of genomic variants which have led to substantial changes in the epidemiology of the virus. With natural and vaccine-induced population immunity at high levels, evolutionary pressure favours variants better able to evade SARS-CoV-2 neutralising antibodies. The Omicron variant was first detected in late November 2021 and exhibited a high degree of immune evasion, leading to increased infection rates in many countries. However, estimates of the magnitude of the Omicron wave have relied mainly on routine testing data, which are prone to several biases. Here we infer the dynamics of the Omicron wave in England using PCR testing and genomic sequencing obtained by the REal-time Assessment of Community Transmission-1 (REACT-1) study, a series of cross-sectional surveys testing random samples of the population of England. We estimate an initial peak in national Omicron prevalence of 6.89% (5.34%, 10.61%) during January 2022, followed by a resurgence in SARS-CoV-2 infections in England during February-March 2022 as the more transmissible Omicron sub-lineage, BA.2 replaced BA.1 and BA.1.1. Assuming the emergence of further distinct genomic variants, intermittent epidemics of similar magnitude as the Omicron wave may become the new normal.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2022.03.24.22272899,2022-03-25,https://medrxiv.org/cgi/content/short/2022.03.24.22272899,Tracking population mental health before and across stages of the COVID-19 pandemic in young adults,Alex Siu Fung Kwong; Kate Northstone; Rebecca M Pearson; Andrew M McIntosh; Nicholas J Timpson,University of Bristol; University of Bristol; University of Bristol; University of Edinburgh; University of Bristol,"The SARS-CoV-2 (COVID-19) pandemic has been associated with worsening mental health. Longitudinal studies have monitored changes in mental health from pre-pandemic levels, identifying critical points for mental health as COVID-19 restrictions evolve. Here we highlight changes in depression and anxiety in the UK from pre-pandemic across four pandemic occasions: April and June 2020, January, and July 2021 - corresponding to changes in COVID-19 restrictions. Data were from >5,000 27-29-year-olds from the Avon Longitudinal Study of Parents and Children (ALSPAC). We found that anxiety almost doubled throughout the pandemic compared to pre-pandemic levels and remained high until July 2021 when COVID-19 restrictions were fully lifted. Depression was lower than pre-pandemic levels in April 2020 but increased as the pandemic evolved until July 2021. Women, those with existing mental/physical health conditions and those with economic hardship were most at risk of sustained poorer mental health across the pandemic. Our results highlight the importance of longitudinal studies for tracking mental health during the COVID-19 pandemic and across virus suppression policy changes.",psychiatry and clinical psychology,fuzzy,100,100 medRxiv,10.1101/2022.03.22.22271707,2022-03-23,https://medrxiv.org/cgi/content/short/2022.03.22.22271707,Vitamin D Supplements for Prevention of Covid-19 or other Acute Respiratory Infections: a Phase 3 Randomized Controlled Trial (CORONAVIT),David Jolliffe; Hayley Holt; Matthew Greenig; Mohammad Talaei; Natalia Perdek; Paul Pfeffer; Giulia Vivaldi; Sheena Maltby; Jane Symons; Nicola Barlow; Alexa Normandale; Rajvinder Garcha; Alex Richter; Sian Faustini; Christopher Orton; David Ford; Ronan Lyons; Gwyneth Davies; Frank Kee; Christopher Griffiths; John Norrie; Aziz Sheikh; Seif Shaheen; Clare Relton; Adrian Martineau,Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Jane Symons Media; City Hospital Birmingham; City Hospital Birmingham; City Hospital Birmingham; University of Birmingham; University of Birmingham; Swansea University; Swansea University; Swansea University; Swansea University; Queen's University Belfast; Queen Mary University of London; University of Edinburgh; University of Edinburgh; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London,"OBJECTIVESTo determine whether population-level implementation of a test-and- treat approach to correction of sub-optimal vitamin D status (25-hydroxyvitamin D [25(OH)D] <75 nmol/L) influences risk of all-cause acute respiratory infection (ARI) or coronavirus disease 2019 (COVID-19). @@ -1371,6 +1351,15 @@ Key pointsO_LIQuestion: What is the prevalence of organ impairment in Long COVID C_LIO_LIFindings: In a prospective study of 536 mainly non-hospitalised individuals, symptom burden decreased, but single organ impairment persisted in 59% at 12 months post-COVID-19. C_LIO_LIMeaning: Organ impairment in Long COVID has implications for symptoms, quality of life and longer-term health, signalling need for prevention and integrated care of Long COVID. C_LI",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2022.03.17.22272414,2022-03-18,https://medrxiv.org/cgi/content/short/2022.03.17.22272414,Modelling the impact of non-pharmaceutical interventions on workplace transmission of SARS-CoV-2 in the home-delivery sector,Carl A Whitfield; Martie Van Tongeren; Yang Han; Hua Wei; Sarah A Daniels; Martyn Regan; David W Denning; Arpana Verma; Lorenzo Pellis; - University of Manchester COVID-19 Modelling Group; Ian Hall,University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchaster; University of Manchester; University of Manchester; ; University of Manchester,"ObjectiveWe aimed to use mathematical models of SARS-COV-2 to assess the potential efficacy of non-pharmaceutical interventions on transmission in the parcel delivery and logistics sector. + +MethodsWe developed a network-based model of workplace contacts based on data and consultations from companies in the parcel delivery and logistics sectors. We used these in stochastic simulations of disease transmission to predict the probability of workplace outbreaks in this settings. Individuals in the model have different viral load trajectories based on SARS-CoV-2 in-host dynamics, which couple to their infectiousness and test positive probability over time, in order to determine the impact of testing and isolation measures. + +ResultsThe baseline model (without any interventions) showed different workplace infection rates for staff in different job roles. Based on our assumptions of contact patterns in the parcel delivery work setting we found that when a delivery driver was the index case, on average they infect only 0.14 other employees, while for warehouse and office workers this went up to 0.65 and 2.24 respectively. In the LIDD setting this was predicted to be 1.40, 0.98, and 1.34 respectively. Nonetheless, the vast majority of simulations resulted in 0 secondary cases among customers (even without contact-free delivery). Our results showed that a combination of social distancing, office staff working from home, and fixed driver pairings (all interventions carried out by the companies we consulted) reduce the risk of workplace outbreaks by 3-4 times. + +ConclusionThis work suggests that, without interventions, significant transmission could have occured in these workplaces, but that these posed minimal risk to customers. We found that identifying and isolating regular close-contacts of infectious individuals (i.e. house-share, carpools, or delivery pairs) is an efficient measure for stopping workplace outbreaks. Regular testing can make these isolation measures even more effective but also increases the number of staff isolating at one time. It is therefore more efficient to use these isolation measures in addition to social distancing and contact reduction interventions, rather than instead of, as these reduce both transmission and the number of people needing to isolate at one time. + +Author summaryDuring the COVID-19 pandemic the home-delivery sector was vital to maintaining peoples access to certain goods, and sustaining levels of economic activity for a variety of businesses. However, this important work necessarily involved contact with a large number of customers as well as colleagues. This means that questions have often been raised about whether enough was being done to keep customers and staff safe. Estimating the potential risk to customers and staff is complex, but here we tackle this problem by building a model of workplace and customer contacts, from which we simulate SARS-CoV-2 transmission. By involving industry representatives in the development of this model, we have simulated interventions that have either been applied or considered, and so the findings of this study are relevant to decisions made in that sector. Furthermore, we can learn generic lessons from this specific case study which apply to many types of shared workplace as well as highlighting implications of the highly stochastic nature of disease transmission in small populations.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2022.03.17.22272535,2022-03-18,https://medrxiv.org/cgi/content/short/2022.03.17.22272535,Comparison of the 2021 COVID-19 'Roadmap' Projections against Public Health Data,Matt J Keeling; Louise J Dyson; Michael Tildesley; Edward M Hill; Sam M Moore,University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick,"Control and mitigation of the COVID-19 pandemic in England has relied on a combination of vaccination and non-pharmaceutical interventions (NPIs). Some of these NPIs are extremely costly (economically and socially), so it was important to relax these promptly without overwhelming already burdened health services. The eventual policy was a Roadmap of four relaxation steps throughout 2021, taking England from lock-down to the cessation of all restrictions on social interaction. In a series of six Roadmap documents generated throughout 2021, models assessed the potential risk of each relaxation step. Here we show that the model projections generated a reliable estimation of medium-term hospital admission trends, with the data points up to September 2021 generally lying within our 95% prediction intervals. The greatest uncertainties in the modelled scenarios came from vaccine efficacy estimates against novel variants, and from assumptions about human behaviour in the face of changing restrictions and risk.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2022.03.15.22272362,2022-03-16,https://medrxiv.org/cgi/content/short/2022.03.15.22272362,Community-level characteristics of COVID-19 vaccine hesitancy in England: A nationwide cross-sectional study,Georges Bucyibaruta; Marta Blangialdo; Garyfallos Konstantinoudis,Imperial College London; Imperial College London; Imperial College London,"One year after the start of the COVID-19 vaccination programme in England, more than 43 million people older than 12 years old had received at least a first dose. Nevertheless, geographical differences persist, and vaccine hesitancy is still a major public health concern; understanding its determinants is crucial to managing the COVID-19 pandemic and preparing for future ones. In this cross-sectional population-based study we used cumulative data on the first dose of vaccine received by 01-01-2022 at Middle Super Output Area level in England. We used Bayesian hierarchical spatial models and investigated if the geographical differences in vaccination uptake can be explained by a range of community-level characteristics covering socio-demographics, political view, COVID-19 health risk awareness and targeting of high risk groups and accessibility. Deprivation is the covariate most strongly associated with vaccine uptake (Odds Ratio 0.55, 95%CI 0.54-0.57; most versus least deprived areas). The most ethnically diverse areas have a 38% (95%CI 36-40%) lower odds of vaccine uptake compared with those least diverse. Areas with the highest proportion of population between 12 and 24 years old had lower odds of vaccination (0.87, 95%CI 0.85-0.89). Finally increase in vaccine accessibility is associated with higher COVID-19 uptake (OR 1.07, 95%CI 1.03-1.12). Our results suggest that one year after the start of the vaccination programme, there is still evidence of inequalities in uptake, affecting particularly minorities and marginalised groups. Strategies including prioritising active outreach across communities and removing practical barriers and factors that make vaccines less accessible are needed to level up the differences.",epidemiology,fuzzy,94,100 medRxiv,10.1101/2022.03.14.22272283,2022-03-14,https://medrxiv.org/cgi/content/short/2022.03.14.22272283,Migrants' primary care utilisation before and during the COVID-19 pandemic in England: An interrupted time series,Claire X Zhang; Yamina Boukari; Neha Pathak; Rohini Mathur; Srinivasa Vittal Katikireddi; Parth Patel; Inês Campos-Matos; Dan Lewer; Vincent Nguyen; Greg Hugenholtz; Rachel Burns; Amy R Mulick; Alasdair Henderson; Robert W Aldridge,UCL; University College London; University College London; London School of Hygiene and Tropical Medicine; University of Glasgow; University College London; Department of Health and Social Care; University College London; University College London; University College London; University College London; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; UCL,"BackgroundHow international migrants access and use primary care in England is poorly understood. We aimed to compare primary care consultation rates between international migrants and non-migrants in England before and during the COVID-19 pandemic (2015- 2020). @@ -1469,27 +1458,6 @@ This is the first study to examine and describe waning of immunity over a one-ye Implications of all the available evidenceTaken together, our findings indicate high short-term immunity against SARS-CoV2 infection and very high immunity against severe clinical outcomes of COVID-19 for LTCF residents and staff following vaccination. However substantial waning in vaccine-derived immunity is seen beyond 3 months, irrespective of vaccine type, suggesting the need for regular boosting to maintain protection in this vulnerable cohort. Although this analysis took place in the pre-Omicron period, these trends of waning immunity over time are likely to be generalisable across variants, carrying important implications for long-term vaccination policy in LTCFs. Ongoing surveillance in this vulnerable cohort remains crucial, in order to describe further changes in vaccine-induced immunity, particularly in the context of new variants.",infectious diseases,fuzzy,100,100 bioRxiv,10.1101/2022.03.08.481609,2022-03-08,https://biorxiv.org/cgi/content/short/2022.03.08.481609,The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK,Verity Hill; Louis du Plessis; Thomas P Alexander Peacock; Dinesh Aggarwal; Alessandro Carabelli; Rachel Colquhoun; Nicholas Ellaby; Eileen Gallagher; Natalie Groves; Ben Jackson; JT McCrone; Anna Price; Theo Sanderson; Emily Scher; Joel Alexander Southgate; Erik Volz; - The COVID-19 genomics UK (COG-UK) consortium; Wendy S Barclay; Jeffrey Barrett; Meera Chand; Thomas R Connor; Ian G. Goodfellow; Ravindra K Gupta; Ewan Harrison; Nicholas Loman; Richard Myers; David L Robertson; Oliver Pybus; Andrew Rambaut,The University of Edinburgh; University of Oxford; University College London (UCL); University of Cambridge; University of Cambridge; University of Edinburgh; UK Health Security Agency; Uk Health Security Agency; UK Health Security Agency; University of Edinburgh; University of Edinburgh; Cardiff University; Sanger Institute; University of Edinburgh; Cardiff University; Imperial College London; -; Imperial College London; Sanger Institute; UK Health Security Agency; Cardiff University; University of Cambridge; University of Cambridge; Sanger Institute; University of Birmingham; UK Health Security Agency; University of Glasgow; University of Oxford; University of Edinburgh,"The first SARS-CoV-2 variant of concern (VOC) to be designated was lineage B.1.1.7, later labelled by the World Health Organisation (WHO) as Alpha. Originating in early Autumn but discovered in December 2020, it spread rapidly and caused large waves of infections worldwide. The Alpha variant is notable for being defined by a long ancestral phylogenetic branch with an increased evolutionary rate, along which only two sequences have been sampled. Alpha genomes comprise a well-supported monophyletic clade within which the evolutionary rate is more typical of SARS-CoV-2. The Alpha epidemic continued to grow despite the continued restrictions on social mixing across the UK, and the imposition of new restrictions, in particular the English national lockdown in November 2020. While these interventions succeeded in reducing the absolute number of cases, the impact of these non-pharmaceutical interventions was predominantly to drive the decline of the SARS-CoV-2 lineages which preceded Alpha. We investigate the only two sampled sequences that fall on the branch ancestral to Alpha. We find that one is likely to be a true intermediate sequence, providing information about the order of mutational events that led to Alpha. We explore alternate hypotheses that can explain how Alpha acquired a large number of mutations yet remained largely unobserved in a region of high genomic surveillance: an under-sampled geographical location, a non-human animal population, or a chronically-infected individual. We conclude that the last hypothesis provides the best explanation of the observed behaviour and dynamics of the variant, although we find that the individual need not be immunocompromised, as persistently-infected immunocompetent hosts also display a higher within-host rate of evolution. Finally, we compare the ancestral branches and mutation profiles of other VOCs to each other, and identify that Delta appears to be an outlier both in terms of the genomic locations of its defining mutations, and its lack of rapid evolutionary rate on the ancestral branch. As new variants, such as Omicron, continue to evolve (potentially through similar mechanisms) it remains important to investigate the origins of other variants to identify ways to potentially disrupt their evolution and emergence.",evolutionary biology,fuzzy,100,100 medRxiv,10.1101/2022.03.06.21267462,2022-03-08,https://medrxiv.org/cgi/content/short/2022.03.06.21267462,Risk of myocarditis and pericarditis following COVID-19 vaccination in England and Wales,Samanatha Ip; Fatemeh Torabi; Spiros Denaxas; Ashley Akbari; Hoda Abbasizanjani; Rochelle Knight; Jennifer Anne Cooper; Rachel Denholm; Spencer Keene; Thomas Bolton; Sam Hollings; Efosa Omigi; Teri-Louise North; Arun Karthikeyan Suseeladevi; Emanuele Di Angelantonio; Kamlesh Khunti; Jonathan A C Sterne; Cathie Sudlow; William Whiteley; Angela Wood; Venexia Walker; - British Heart Foundation Data Science Centre (HDR UK) CVD-COVID-UK/COVID-IMPACT Consortium; - UK Covid-19 Longitudinal Health and Wellbeing National Core Study; - UK Covid-19 Data and Connectivity National Core Study,University of Cambridge; Swansea University; University College London; Swansea University; Swansea University; University of Bristol; University of Bristol; University of Bristol; University of Cambridge; Health Data Research UK; NHS Digital; NHS Digital; University of Bristol; University of Bristol; University of Cambridge; University of Leicester; University of Bristol; Health Data Research UK; University of Edinburgh; University of Cambridge; University of Bristol; ; ; ,"We describe our analyses of data from over 49.7 million people in England, representing near-complete coverage of the relevant population, to assess the risk of myocarditis and pericarditis following BNT162b2 and ChAdOx1 COVID-19 vaccination. A self-controlled case series (SCCS) design has previously reported increased risk of myocarditis after first ChAdOx1, BNT162b2, and mRNA-1273 dose and after second doses of mRNA COVID-19 vaccines in England. Here, we use a cohort design to estimate hazard ratios for hospitalised or fatal myocarditis/pericarditis after first and second doses of BNT162b2 and ChAdOx1 vaccinations. SCCS and cohort designs are subject to different assumptions and biases and therefore provide the opportunity for triangulation of evidence. In contrast to the findings from the SCCS approach previously reported for England, we found evidence for lower incidence of hospitalised or fatal myocarditis/pericarditis after first ChAdOx1 and BNT162b2 vaccination, as well as little evidence to suggest higher incidence of these events after second dose of either vaccination.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2022.03.02.22271762,2022-03-04,https://medrxiv.org/cgi/content/short/2022.03.02.22271762,"Disparities in SARS-CoV-2 case rates by ethnicity, religion, measures of socio-economic position, English proficiency, and self-reported disability: cohort study of 39 million people in England during the Alpha and Delta waves",Tim Larsen; Matthew L Bosworth; Daniel Ayoubkhani; Ryan Schofield; Raghib Ali; Kamlesh Khunti; Ann Sarah Walker; Myer Glickman; Vahe Nafilyan,Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Cambridge; University of Leicester; University of Oxford; Office for National Statistics; Office for National Statistics,"ObjectiveTo examine socio-demographic disparities in SARS-CoV-2 case rates during the second (Alpha) and third (Delta) waves of the COVID-19 pandemic. - -DesignRetrospective, population-based cohort study. - -SettingResident population of England. - -Participants39,006,194 people aged 10 years and over who were enumerated at the 2011 Census, registered with the National Health Service (NHS) and alive on 1 September 2020. - -Main outcome measuresTesting positive for SARS-CoV-2 during the second wave (1 September 2020 to 22 May 2021) or third wave (23 May to 10 December 2021) of the pandemic. We calculated age-standardised case rates by socio-demographic characteristics and used logistic regression models to estimate adjusted odds ratios (ORs). - -ResultsDuring the study period, 5,767,584 individuals tested positive for SARS-CoV-2. In the second wave, the fully-adjusted odds of having a positive test, relative to the White British group, were highest for the Bangladeshi (OR: 1.88, 95% CI 1.86 to 1.90) and Pakistani (1.81, 1.79 to 1.82) ethnic groups. Relative to the Christian group, Muslim and Sikh religious groups had fully-adjusted ORs of 1.58 (1.57 to 1.59) and 1.74 (1.72 to 1.76), respectively. Greater area deprivation, disadvantaged socio-economic position, living in a care home and low English language proficiency were also associated with higher odds of having a positive test. However, the disparities between groups varied over time. Being Christian, White British, non-disabled, and from a more advantaged socio-economic position were all associated with increased odds of testing positive during the third wave. - -ConclusionThere are large socio-demographic disparities on SARS-CoV-2 cases which have varied between different waves of the pandemic. Research is now urgently needed to understand why these disparities exist to inform policy interventions in future waves or pandemics. - -What is already known on this topicPeople with pre-existing health conditions or disability, ethnic minority groups, the elderly, some religious groups, people with low socio-economic status, and those living in deprived areas have been disproportionately affected by the COVID-19 pandemic in terms of risk of infection and adverse outcomes. - -What this study addsUsing linked data on 39 million people in England, we found that during the second wave, COVID-19 case rates were highest among the Bangladeshi and Pakistani ethnic groups, the Muslim religious group, individuals from deprived areas and of low socio-economic position; during the third wave, being Christian, White British, non-disabled, and from a more advantaged socio-economic position were all associated with increased odds of receiving a positive test - -Adjusting for geographical factors, socio-demographic characteristics, and pre-pandemic health status explained some, but not all, of the excess risk - -When stratifying the dataset by broad age groups, the odds of receiving a positive test remained higher among the Bangladeshi and Pakistani ethnic groups aged 65 years and over during the third wave, which may partly explain the continued elevated mortality rates in these groups",epidemiology,fuzzy,100,100 medRxiv,10.1101/2022.03.02.22271623,2022-03-03,https://medrxiv.org/cgi/content/short/2022.03.02.22271623,"Baricitinib in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial and updated meta-analysis",Peter W Horby; Jonathan R Emberson; Marion Mafham; Mark Campbell; Leon Peto; Guilherme Pessoa-Amorim; Enti Spata; Natalie Staplin; Catherine Lowe; David R Chadwick; Christopher Brightling; Richard Stewart; Paul Collini; Abdul Ashish; Christopher A Green; Benjamin Prudon; Tim Felton; Anthony Kerry; J Kenneth Baillie; Maya H Buch; Jeremy N Day; Saul N Faust; Thomas Jaki; Katie Jeffery; Edmund Juszczak; Marian Knight; Wei Shen Lim; Alan Montgomery; Andrew Mumford; Kathryn Rowan; Guy Thwaites; Richard Haynes; Martin J Landray,"Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Liverpool University Hospitals NHS Foundation Trust; Centre for Clinical Infection, James Cook University Hospital, Middlesbrough, United Kingdom; Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, United Kingdom; Milton Keynes University Hospital, Milton Keynes, United Kingdom; Sheffield Teaching Hospitals NHS Foundation Trust and University of Sheffield, Sheffield, United Kingdom; Wrightington, Wigan and Leigh Teaching Hospitals NHS Foundation Trust, Wigan, United Kingdom; University Hospitals Birmingham NHS Foundation Trust; North Tees and Hartlepool NHS Foundation Trust, Hartlepool, United Kingdom; Manchester University NHS Foundation Trust; Great Western Hospitals Foundation Trust, Swindon, United Kingdom; Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom; Centre for Musculoskeletal Research, University of Manchester, Manchester, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom; NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, ; Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom; Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Respiratory Medicine Department, Nottingham University Hospitals NHS Foundation Trust, Nottingham, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom; Intensive Care National Audit and Research Centre, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom","BackgroundWe evaluated the use of baricitinib, a Janus kinase (JAK) 1/2 inhibitor, for the treatment of patients admitted to hospital because of COVID-19. MethodsThis randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), is assessing multiple possible treatments in patients hospitalised for COVID-19. Eligible and consenting patients were randomly allocated (1:1) to either usual standard of care alone (usual care group) or usual care plus baricitinib 4 mg once daily by mouth for 10 days or until discharge if sooner (baricitinib group). The primary outcome was 28-day mortality assessed in the intention-to-treat population. A meta-analysis was conducted that included the results from the RECOVERY trial and all previous randomised controlled trials of baricitinib or other JAK inhibitor in patients hospitalised with COVID-19. The RECOVERY trial is registered with ISRCTN (50189673) and clinicaltrials.gov (NCT04381936). @@ -1552,13 +1520,6 @@ Research in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed, Added value of this studyThis large population-based study, conducted in a population with known pre-vaccination SARS-CoV-2 serostatus, examines a comprehensive range of potential sociodemographic, behavioural, clinical, pharmacological and nutritional determinants of antibody responses to administration of two major SARS-CoV-2 vaccines (i.e., ChAdOx1 or BNT162b2), many of which have not previously been investigated. It is also the first population-based study to characterise antibody responses to booster doses of SARS-CoV-2 vaccines in adults who were seronegative after their primary course of vaccination. Implications of all the available evidenceIncreased risk of seronegativity following two doses of SARS-CoV-2 vaccines was associated with administration of ChAdOx1 vs BNT162b2, shorter interval between first and second vaccine doses, poorer self-assessed general health, immunocompromise and SARS-CoV-2 seronegativity pre-vaccination. Regular intake of vitamin D supplements was associated with reduced risk of post-vaccination seronegativity. Randomised controlled trials are now needed to test for causality. Booster doses of BNT162b2 or mRNA-1273 were highly effective in achieving seroconversion in the majority of people who failed to mount antibody responses following a primary course of vaccination, the few exceptions being a subset of those with primary immunodeficiency or systemic immunosuppressant drugs.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2022.02.10.22270799,2022-02-13,https://medrxiv.org/cgi/content/short/2022.02.10.22270799,Evaluating the effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control teams: the COG-UK hospital-onset COVID-19 infection study,Oliver Stirrup; James Blackstone; Fiona Mapp; Alyson MacNeil; Monica Panca; Alison Holmes; Nicholas Machin; Gee Yen Shin; Tabitha Mahungu; Kordo Saeed; Tranprit Saluja; Yusri Taha; Nikunj Mahida; Cassie Pope; Anu Chawla; Teresa Cutino-Moguel; Asif Tamuri; Rachel Williams; Alistair Darby; David L Robertson; Flavia Flaviani; Eleni Nastouli; Samuel Robson; Darren Smith; Matthew Loose; Kenneth Laing; Irene Monahan; Beatrix Kele; Sam Haldenby; Ryan George; Matthew Bashton; Adam Witney; Matthew Byott; Francesc Coll; Michael Chapman; Sharon Peacock; - COG-UK HOCI Investigators; - COG-UK Consortium; Joseph Hughes; Gaia Nebbia; David G Partridge; Matthew Parker; James Richard Price; Christine Peters; Sunando Roy; Luke B Snell; Thushan I de Silva; Emma Thomson; Paul Flowers; Andrew Copas; Judith Breuer,"Institute for Global Health, UCL, London, UK; Comprehensive Clinical Trials Unit, UCL, London, UK; Institute for Global Health, UCL, London, UK; Comprehensive Clinical Trials Unit, UCL, London, UK; Comprehensive Clinical Trials Unit, UCL, London, UK; Imperial College Healthcare NHS Trust, London, UK; Manchester University NHS Foundation Trust, Manchester, UK; University College London Hospitals NHS Foundation Trust, London, UK; Royal Free NHS Foundation Trust, London, UK; University Hospital Southampton NHS Foundation Trust, Southampton, UK; Sandwell and West Birmingham NHS Trust, UK; Departments of Virology and Infectious Diseases, Newcastle Hospitals NHS Foundation Trust, Newcastle, UK; Nottingham University Hospitals NHS Trust, Nottingham, UK; St George's University Hospitals NHS Foundation Trust, London, UK; Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK; Barts Health NHS Trust, London, UK; Research Computing, UCL, London, UK; Department of Genetics & Genomic Medicine, UCL Great Ormond Street Institute of Child Health, UCL, London, UK; Centre for Genomic Research, University of Liverpool, Liverpool, UK; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK; University College London Hospitals NHS Foundation Trust, London, UK; Centre for Enzyme Innovation, University of Portsmouth, Portsmouth, UK; Department of Applied Sciences, Northumbria University, Newcastle, UK; School of Life Sciences, University of Nottingham, Nottingham, UK; Institute for Infection and Immunity, St George's University of London, London, UK; Institute for Infection and Immunity, St George's University of London, London, UK; Barts Health NHS Trust, London, UK; Centre for Genomic Research, University of Liverpool, Liverpool, UK; Manchester University NHS Foundation Trust, Manchester, UK; The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Northumbria University, Newcastle, UK; Institute for Infection and Immunity, St George's University of London, London, UK; University College London Hospitals NHS Foundation Trust, London, UK; Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; Health Data Research UK Cambridge Hub, Cambridge UK; Department of Medicine, University of Cambridge, Cambridge, UK; ; ; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK; Sheffield Bioinformatics Core, The University of Sheffield, Sheffield, UK; Imperial College Healthcare NHS Trust, London, UK; NHS Greater Glasgow and Clyde, Glasgow, UK; Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, UCL, London, UK; Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK; Department of Infection, Immunity and Cardiovascular Disease, Medical School, The University of Sheffield, Sheffield, UK; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; School of Psychological Sciences and Health, University of Strathclyde, Glasgow, UK; Institute for Global Health, UCL, London, UK; Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, UCL, London, UK","IntroductionViral sequencing of SARS-CoV-2 has been used for outbreak investigation, but there is limited evidence supporting routine use for infection prevention and control (IPC) within hospital settings. - -MethodsWe conducted a prospective non-randomised trial of sequencing at 14 acute UK hospital trusts. Sites each had a 4-week baseline data-collection period, followed by intervention periods comprising 8 weeks of rapid (<48h) and 4 weeks of longer-turnaround (5-10 day) sequencing using a sequence reporting tool (SRT). Data were collected on all hospital onset COVID-19 infections (HOCIs; detected [≥]48h from admission). The impact of the sequencing intervention on IPC knowledge and actions, and on incidence of probable/definite hospital-acquired infections (HAIs) was evaluated. - -ResultsA total of 2170 HOCI cases were recorded from October 2020-April 2021, with sequence reports returned for 650/1320 (49.2%) during intervention phases. We did not detect a statistically significant change in weekly incidence of HAIs in longer-turnaround (IRR 1.60, 95%CI 0.85-3.01; P=0.14) or rapid (0.85, 0.48-1.50; P=0.54) intervention phases compared to baseline phase. However, IPC practice was changed in 7.8% and 7.4% of all HOCI cases in rapid and longer-turnaround phases, respectively, and 17.2% and 11.6% of cases where the report was returned. In a per-protocol sensitivity analysis there was an impact on IPC actions in 20.7% of HOCI cases when the SRT report was returned within 5 days. - -ConclusionWhile we did not demonstrate a direct impact of sequencing on the incidence of nosocomial transmission, our results suggest that sequencing can inform IPC response to HOCIs, particularly when returned within 5 days.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2022.02.07.22270451,2022-02-08,https://medrxiv.org/cgi/content/short/2022.02.07.22270451,Anti-spike antibody trajectories in individuals previously immunised with BNT162b2 or ChAdOx1 following a BNT162b2 booster dose,Alexei Yavlinsky; Sarah Beale; Vincent Nguyen; Madhumita Shrotri; Thomas Edward Byrne; Cyril Geismar; Ellen Fragaszy; Susan J Hoskins; Wing Lam Erica Fong; Annalan Mathew Dwight Navaratnam; Isobel Braithwaite; Parth Patel; Jana Kovar; Andrew C Hayward; Robert W Aldridge,"Institute of Health Informatics, University College London, London, UK; Institute of Epidemiology and Health Care, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, UK; Institute of Health Informatics, University College London, UK; Institute of Health Informatics, University College London, UK; Institute of Health Informatics, University College London, UK; Institute of Epidemiology and Health Care, University College London, London, UK; Institute of Health Informatics, University College London, UK; Institute of Health Informatics, University College London, UK; Institute of Health Informatics, University College London, UK; Institute of Health Informatics, University College London, UK; Institute of Epidemiology and Health Care, University College London, London, UK; Institute of Epidemiology and Health Care, University College London, London, UK; Institute of Health Informatics, University College London, UK","The two most commonly-used SARS-CoV-2 vaccines in the UK, BNT162b2 (Pfizer-BioNTech) and ChAdOx1 nCoV-19 (Oxford-AstraZeneca), employ different immunogenic mechanisms. Compared to BNT162b2, two-dose immunisation with ChAdOx1 induces substantially lower peak anti-spike antibody (anti-S) levels and is associated with a higher risk of breakthrough infections. To provide preliminary indication of how a third booster BNT162b2 dose impacts anti-S levels, we performed a cross-sectional analysis using capillary blood samples from vaccinated adults (aged [≥]18 years) participating in Virus Watch, a prospective community cohort study in England and Wales. Blood samples were analysed using Roche Elecsys Anti-SARS-CoV-2 S immunoassay. We analysed anti-S levels by week since the third dose for vaccines administered on or after September 1, 2021 and stratified the results by second dose vaccine type (ChAdOx1 or BNT162b2), age, sex and clinical vulnerability. Anti-S levels peaked at two weeks post-booster for BNT162b2 (22,185 U/mL; 95%CI: 21,406-22,990) and ChAdOx1 second dose recipients (19,203 U/mL; 95%CI: 18,094-20,377). These were higher than the corresponding peak antibody levels post-second dose for BNT162b2 (12,386 U/mL; 95%CI: 9,801-15,653, week 2) and ChAdOx1 (1,192 U/mL; 95%CI: 818-1735, week 3). No differences emerged by second dose vaccine type, age, sex or clinical vulnerability. Anti-S levels declined post-booster for BNT162b2 (half-life=44 days) and ChAdOx1 second dose recipients (half-life=40 days). These rates of decline were steeper than those post-second dose for BNT162b2 (half-life=54 days) and ChAdOx1 (half-life=80 days). Our findings suggest that peak anti-S levels are higher post-booster than post-second dose, but that levels are projected to be similar after six months for BNT162b2 recipients. Higher peak anti-S levels post-booster may partially explain the increased effectiveness of booster vaccination compared to two-dose vaccination against symptomatic infection with the Omicron variant. Faster waning trajectories post third-dose may have implications for the timing of future booster campaigns or four-dose vaccination regimens for the clinically vulnerable.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2022.02.03.22270365,2022-02-06,https://medrxiv.org/cgi/content/short/2022.02.03.22270365,Post-peak dynamics of a national Omicron SARS-CoV-2 epidemic during January 2022,Paul Elliott; Oliver Eales; Barbara Bodinier; David Tang; Haowei Wang; Jakob Jonnerby; David Haw; Joshua Elliott; Matthew Whitaker; Caroline E. Walters; Christina Atchinson; Peter J. Diggle; Andrew J. Page; Alexander Trotter; Deborah Ashby; Wendy Barclay; Graham Taylor; Helen Ward; Ara Darzi; Graham Cooke; Marc Chadeau-Hyam; Christl A Donnelly,"School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Imperial College Healthcare NHS Trust, UK Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; School of Public Health, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc","BackgroundRapid transmission of the SARS-CoV-2 Omicron variant has led to the highest ever recorded case incidence levels in many countries around the world. @@ -1747,24 +1708,6 @@ ResultsAcross six cohorts, there were a total of 21,283 participants who were el DiscussionWe found evidence of greater effectiveness of receiving BNT162b2 compared to ChAdOx1 vaccines against SARS-CoV-2 infection in England and Wales during a time period when Delta became the most prevalent variant of concern. Our findings demonstrate the importance of booster (third) doses to maintain protection and suggest that these should be prioritised to those who received ChAdOx1 as their primary course.",epidemiology,fuzzy,100,100 bioRxiv,10.1101/2021.12.17.473248,2021-12-21,https://biorxiv.org/cgi/content/short/2021.12.17.473248,"SARS-CoV-2 Omicron spike mediated immune escape, infectivity and cell-cell fusion",Bo Meng; Isabella Ferreira; Adam Abdullahi; Niluka Goonawardane; Akatsuki Saito; Izumi Kimura; Daichi Yamasoba; Steven A Kemp; Guido Papa; Saman Fatihi; Surabhi Rathore; Pehuen Perera Gerba; Terumasa Ikeda; Mako Toyoda; Toong Seng Tan; Jin Kuramochi; Shigeki Mitsunaga; Takamasa Ueno; Oscar Charles; Dami Collier; - CITIID-NIHR BioResource COVID-19 Collaboration; - The Genotype to Phenotype Japan (G2P-Japan) Consortium; - Ecuador-COVID19 Consortium; John Bradley; Jinwook Choi; Kenneth Smith; Elo Madissoon; Kerstin Meyer; Petra Mlcochova; Rainer Doffinger; Sarah A Teichmann; Leo James; Joo Hyeon Lee; Teresa Brevini; Matteo Pizzuto; Myra Hosmillo; Donna Mallery; Samantha Zepeda; Alexandra Walls; Anshu Joshi; John Bowen; John Briggs; Alex Sigal; Laurelle Jackson; Sandile Cele; Anna De Marco; Fotios Sampaziotis; Davide Corti; David Veesler; Nicholas Matheson; Ian Goodfellow; Lipi Thukral; Kei Sato; Ravindra K Gupta,"University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Miyazaki; The University of Tokyo; Kumamoto University; University of Cambridge; LMB Cambridge; CSIR Institute of Genomics and Integrative Biology, Delhi, India; CSIR Institute of Genomics and Integrative Biology, Delhi, India; University of Cambridge; Kumamoto Univ; Kumamoto University, Kumamoto; Kuramochi Clinic Interpark; Kuramochi Clinic Interpark; National Institute of Genetics, Mishima, Shizuoka; Kumamoto University, Kumamoto; University College London; University of Cambridge; -; -; -; University of Cambridge; University of Cambridge; University of Cambridge; Wellcome Sanger Institute; Wellcome Sanger Institute; University of Cambridge; Cambridge University Hospitals NHS Trust; Cambridge University; MRC LMB; University of Cambridge; University of Cambridge; Humabs Biomed SA; University of Cambridge; MRC LMB Cambridge; University of Washington; University of Washington; University of Washington; University of Washington; University of Heidelberg; Africa Health Research Institute, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Humabs Biomed SA; University of Cambridge; Humabs Biomed SA; University of Washington; University of Cambridge; University of Cambridge; CSIR Institute of Genomics and Integrative Biology, Delhi, India; The University of Tokyo; University of Cambridge","The SARS-CoV-2 Omicron BA.1 variant emerged in late 2021 and is characterised by multiple spike mutations across all spike domains. Here we show that Omicron BA.1 has higher affinity for ACE2 compared to Delta, and confers very significant evasion of therapeutic monoclonal and vaccine-elicited polyclonal neutralising antibodies after two doses. mRNA vaccination as a third vaccine dose rescues and broadens neutralisation. Importantly, antiviral drugs remdesevir and molnupiravir retain efficacy against Omicron BA.1. We found that in human nasal epithelial 3D cultures replication was similar for both Omicron and Delta. However, in lower airway organoids, Calu-3 lung cells and gut adenocarcinoma cell lines live Omicron virus demonstrated significantly lower replication in comparison to Delta. We noted that despite presence of mutations predicted to favour spike S1/S2 cleavage, the spike protein is less efficiently cleaved in live Omicron virions compared to Delta virions. We mapped the replication differences between the variants to entry efficiency using spike pseudotyped virus (PV) entry assays. The defect for Omicron PV in specific cell types correlated with higher cellular RNA expression of TMPRSS2, and accordingly knock down of TMPRSS2 impacted Delta entry to a greater extent as compared to Omicron. Furthermore, drug inhibitors targeting specific entry pathways demonstrated that the Omicron spike inefficiently utilises the cellular protease TMPRSS2 that mediates cell entry via plasma membrane fusion. Instead, we demonstrate that Omicron spike has greater dependency on cell entry via the endocytic pathway requiring the activity of endosomal cathepsins to cleave spike. Consistent with suboptimal S1/S2 cleavage and inability to utilise TMPRSS2, syncytium formation by the Omicron spike was dramatically impaired compared to the Delta spike. Overall, Omicron appears to have gained significant evasion from neutralising antibodies whilst maintaining sensitivity to antiviral drugs targeting the polymerase. Omicron has shifted cellular tropism away from TMPRSS2 expressing cells that are enriched in cells found in the lower respiratory and GI tracts, with implications for altered pathogenesis.",microbiology,fuzzy,100,100 -medRxiv,10.1101/2021.12.20.21268098,2021-12-21,https://medrxiv.org/cgi/content/short/2021.12.20.21268098,"Therapies for Long COVID in non-hospitalised individuals - from symptoms, patient-reported outcomes, and immunology to targeted therapies (The TLC Study): Study protocol",Shamil Haroon; Krishnarajah Nirantharakumar; Sarah Hughes; Anuradhaa Subramanian; Olalekan Lee Aiyegbusi; Elin Haf Davies; Puja Myles; Tim Williams; Grace Turner; Joht Singh Chandan; Christel McMullan; Janet Lord; David Wraith; Kirsty McGee; Alastair Denniston; Tom Taverner; Louise Jackson; Elizabeth Sapey; Georgios Gkoutos; Krishna Gokhale; Edward Leggett; Clare Iles; Christopher Frost; Gary McNamara; Amy Bamford; Tom Marshall; Dawit Zemedikun; Gary Price; Steven Marwaha; Nikita Simms-Williams; Kirsty Brown; Anita Walker; Karen Jones; Karen Matthews; Jennifer Camaradou; Michael Saint-Cricq; Sumita Kumar; Yvonne Alder; David Stanton; Lisa Agyen; Megan Baber; Hannah Blaize; Melanie Calvert,University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; Aparito; Medicines and Healthcare Products Regulatory Agency; Medicines and Healthcare Products Regulatory Agency; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University of Birmingham; University of Birmingham; University ofBirmingham; University of Birmingham; Medicines and Healthcare Products Regulatory Agency; Medicines and Healthcare Products Regulatory Agency; Aparito; Aparito; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University of Birmingham; N/A; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; University ofBirmingham,"IntroductionIndividuals with COVID-19 frequently experience symptoms and impaired quality of life beyond 4-12 weeks, commonly referred to as Long COVID. Whether Long COVID is one or several distinct syndromes is unknown. Establishing the evidence base for appropriate therapies is needed. We aim to evaluate the symptom burden and underlying pathophysiology of Long COVID syndromes in non-hospitalised individuals and evaluate potential therapies. - -Methods and analysisA cohort of 4000 non-hospitalised individuals with a past COVID-19 diagnosis and 1000 matched controls will be selected from anonymised primary care records from the Clinical Practice Research Datalink (CPRD) and invited by their general practitioners to participate on a digital platform (Atom5). Individuals will report symptoms, quality of life, work capability, and patient reported outcome measures. Data will be collected monthly for one year. - -Statistical clustering methods will be used to identify distinct Long COVID symptom clusters. Individuals from the four most prevalent clusters and two control groups will be invited to participate in the BioWear sub-study which will further phenotype Long COVID symptom clusters by measurement of immunological parameters and actigraphy. - -We will review existing evidence on interventions for post-viral syndromes and Long COVID to map and prioritise interventions for each newly characterised Long COVID syndrome. Recommendations will be made using the cumulated evidence in an expert consensus workshop. A virtual supportive intervention will be coproduced with patients and health service providers for future evaluation. - -Individuals with lived experience of Long COVID will be involved throughout this programme through a patient and public involvement group. - -Ethics and disseminationEthical approval was obtained from the Solihull Research Ethics Committee, West Midlands (21/WM/0203). The study is registered on the ISRCTN Registry (1567490). Research findings will be presented at international conferences, in peer-reviewed journals, to Long COVID patient support groups and to policymakers. - -Article SummaryO_ST_ABSStrengths and limitations of the studyC_ST_ABSO_LIThe study will generate a nationally representative cohort of individuals with Long COVID recruited from primary care. -C_LIO_LIWe will recruit controls matched on a wide range of demographic and clinical factors to assess differences in symptoms between people with Long COVID and similar individuals without a history of COVID-19. -C_LIO_LIWe will use a newly developed electronic patient reported outcome measure (Symptom Burden Questionnaire) for Long COVID to comprehensively assess a wide range of symptoms highlighted by existing literature, patients, and clinicians. -C_LIO_LIImmunological, proteomic, genetic, and wearable data captured in the study will allow deep phenotyping of Long COVID syndromes to help better target therapies. -C_LIO_LIA limitation is that a significant proportion of non-hospitalised individuals affected by COVID-19 in the first wave of the pandemic will lack confirmatory testing and will be excluded from recruitment to the study. -C_LI",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.12.20.21268113,2021-12-21,https://medrxiv.org/cgi/content/short/2021.12.20.21268113,A nationwide deep learning pipeline to predict stroke and COVID-19 death in atrial fibrillation,Alex Handy; Angela Wood; Cathie Sudlow; Christopher Tomlinson; Frank Kee; Johan H Thygesen; Mohammad Mamouei; Reecha Sofat; Richard Dobson; Hiu Yan (Samantha) Ip; Spiros Denaxas; - CVD-COVID-UK Consortium,"Institute of Health Informatics, University College London, London, UK; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; British Heart Foundation Data Science Centre, Health Data Research UK, London, UK; Institute of Health Informatics, University College London, London, UK; School of Medicine, Dentistry and Biomedical Sciences, Centre for Public Health, Queens University Belfast, UK; Institute of Health Informatics, University College London, London, UK; Deep Medicine, Oxford Martin School, University of Oxford, Oxford, UK; Institute of Health Informatics, University College London, London, UK; Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Institute of Health Informatics, University College London, London, UK; CVD-COVID-UK Consortium","Deep learning (DL) and machine learning (ML) models trained on long-term patient trajectories held as medical codes in electronic health records (EHR) have the potential to improve disease prediction. Anticoagulant prescribing decisions in atrial fibrillation (AF) offer a use case where the benchmark stroke risk prediction tool (CHA2DS2-VASc) could be meaningfully improved by including more information from a patients medical history. In this study, we design and build the first DL and ML pipeline that uses the routinely updated, linked EHR data for 56 million people in England accessed via NHS Digital to predict first ischaemic stroke in people with AF, and as a secondary outcome, COVID-19 death. Our pipeline improves first stroke prediction in AF by 17% compared to CHA2DS2-VASc (0.61 (0.57-0.65) vs 0.52 (0.52-0.52) area under the receiver operating characteristics curves, 95% confidence interval) and provides a generalisable, opensource framework that other researchers and developers can build on.",cardiovascular medicine,fuzzy,100,100 medRxiv,10.1101/2021.12.16.21267934,2021-12-17,https://medrxiv.org/cgi/content/short/2021.12.16.21267934,Predictors of SARS-CoV-2 infection in a multi-ethnic cohort of United Kingdom healthcare workers: a prospective nationwide cohort study (UK-REACH),Christopher A Martin; Daniel Pan; Carl Melbourne; Lucy Teece; Avinash Aujayeb; Rebecca F Baggaley; Luke Bryant; Sue Carr; Bindu Gregary; Amit Gupta; Anna Louise Guyatt; Catherine John; Chris McManus; Joshua Nazareth; Laura B Nellums; Rubina Reza; Sandra Simpson; Martin D Tobin; Katherine Woolf; Stephen Zingwe; Kamlesh Khunti; Keith R Abrams; Laura J Gray; Manish Pareek; - UK-REACH Study Collaborative Group,University of Leicester; University of Leicester; University of Leicester; University of Leicester; Northumbria Specialist Emergency Care Hospital; University of Leicester; University of Leicester; General Medical Council; Royal Preston Hospital; Oxford University Hospitals NHS Foundation Trust; University of Leicester; University of Leicester; University College London; University of Leicester; University of Nottingham; Derbyshire Healthcare NHS Foundation Trust; Nottinghamshire Healthcare NHS Foundation Trust; University of Leicester; University College London; Berkshire Healthcare NHS Foundation Trust; University of Leicester; University of Warwick; University of Leicester; University of Leicester; ,"IntroductionHealthcare workers (HCWs), particularly those from ethnic minority groups, have been shown to be at disproportionately higher risk of infection with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) compared to the general population. However, there is insufficient evidence on how demographic and occupational factors influence infection risk among ethnic minority HCWs. @@ -2081,13 +2024,6 @@ MethodsWe estimated patterns of community prevalence of SARS-CoV-2 infection in ResultsDuring mid- to late-October 2021 (round 15a) weighted prevalence was 1.72% (1.61%, 1.84%) compared to 0.83% (0.76%, 0.89%) in September 2021 (round 14). The overall reproduction number (R) from round 14 to round 15a was 1.12 (1.11, 1.14) with increases in prevalence over this period (September to October) across age groups and regions except Yorkshire and The Humber. However, within round 15a (mid- to late-October) there was evidence of a fall in prevalence with R of 0.76 (0.65, 0.88). The highest weighted prevalence was observed among children aged 5 to 12 years at 5.85% (5.10%, 6.70%) and 13 to 17 years at 5.75% (5.02%, 6.57%). At regional level, there was an almost four-fold increase in weighted prevalence in South West from round 14 at 0.59% (0.43%,0.80%) to round 15a at 2.18% (1.84%, 2.58%), with highest smoothed prevalence at subregional level also found in South West in round 15a. Age, sex, key worker status, and presence of children in the home jointly contributed to the risk of swab-positivity. Among the 126 sequenced positive swabs obtained up until 23 October, all were Delta variant; 13 (10.3%) were identified as the AY.4.2 sub-lineage. DiscussionWe observed the highest overall prevalence of swab-positivity seen in the REACT-1 study in England to date in round 15a (October 2021), with a two-fold rise in swab-positivity from round 14 (September 2021). Despite evidence of a fall in prevalence from mid- to late-October 2021, prevalence remains high, particularly in school-aged children, with evidence also of higher prevalence in households with one or more children. Thus, vaccination of children aged 12 and over remains a high priority (with possible extension to children aged 5-12) to help reduce within-household transmission and disruptions to education, as well as among adults, to lessen the risk of serious disease among those infected.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2021.10.28.21265593,2021-11-02,https://medrxiv.org/cgi/content/short/2021.10.28.21265593,"The UK COVID-19 furlough scheme and associations with smoking, alcohol consumption and vaping: evidence from 8 UK longitudinal population surveys.",Michael J Green PhD; Jane Maddock PhD; Giorgio Di Gessa PhD; Bożena Wielgoszewska PhD; Sam Parsons PhD; Gareth J Griffith PhD; Jazz Croft PhD; Anna J Stevenson PhD; Charlotte F Huggins PhD; Charlotte Booth PhD; Jacques Wels; Richard J Silverwood PhD; Praveetha Patalay PhD; Alun D Hughes PhD; Nishi Chaturvedi MD; Laura D Howe PhD; Emla Fitzsimons PhD; Srinivasa Vittal Katikireddi PhD; George B Ploubidis PhD,"MRC/CSO Social & Public Health Sciences Unit, University of Glasgow; MRC Unit for Lifelong Health and Ageing, University College London; Institute of Epidemiology and Health Care, University College London; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; MRC Integrative Epidemiology Unit, University of Bristol; MRC Integrative Epidemiology Unit, University of Bristol; Centre for Genomic and Experimental Medicine, University of Edinburgh; Centre for Genomic and Experimental Medicine, University of Edinburgh; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; MRC Unit for Lifelong Health and Ageing, University College London; Centre for Longitudinal Studies, UCL Social Research Institute, University College; MRC Unit for Lifelong Health and Ageing, University College London; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; MRC Unit for Lifelong Health and Ageing, University College London; MRC Unit for Lifelong Health and Ageing, University College London; MRC Integrative Epidemiology Unit, University of Bristol; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; MRC/CSO Social & Public Health Sciences Unit, University of Glasgow; Centre for Longitudinal Studies, UCL Social Research Institute, University College London","BackgroundDisruptions to employment status can impact smoking and alcohol consumption. During the COVID-19 pandemic, the UK implemented a furlough scheme to prevent job loss. We examine how furlough was associated with participants smoking, vaping and alcohol consumption behaviours in the early stages of the pandemic. - -MethodsData were from 27,841 participants in eight UK adult longitudinal surveys. Participants self-reported employment status and current smoking, current vaping and drinking alcohol (>4 days/week or 5+ drinks per typical occasion) both before and during the pandemic (April-July 2020). Risk ratios were estimated within each study using modified Poisson regression, adjusting for a range of potential confounders, including pre-pandemic behaviour. Findings were synthesised using random effects meta-analysis. Sub-group analyses were used to identify whether associations differed by gender, age or education. - -ResultsCompared to stable employment, neither furlough, no longer being employed, nor stable unemployment were associated with smoking, vaping or drinking, following adjustment for pre-pandemic characteristics. However, some sex differences in these associations were observed, with stable unemployment associated with smoking for women (ARR=1.35; 95% CI: 1.00-1.82; I2: 47%) but not men (0.84; 95% CI: 0.67-1.05; I2: 0%). No longer being employed was associated with vaping among women (ARR=2.74; 95% CI: 1.59-4.72; I2: 0%) but not men (ARR=1.25; 95% CI: 0.83-1.87; I2: 0%). There was little indication of associations with drinking differing by age, gender or education. - -ConclusionsWe found no clear evidence of furlough or unemployment having adverse impacts on smoking, vaping or drinking behaviours during the early stages of the COVID-19 pandemic in the UK, with differences in risk compared to those who remained employed largely explained by pre-pandemic characteristics.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.11.01.21265660,2021-11-02,https://medrxiv.org/cgi/content/short/2021.11.01.21265660,"Estimating the relationship between mobility, non-pharmaceutical interventions, and COVID-19 transmission in Ghana",Hamish Gibbs; Yang Liu; Sam Abbott; Isaac Baffoe-Nyarko; Dennis O. Laryea; Ernest Akyereko; Patrick Kuma-Aboagye; Ivy Asante; Oriol Mitja; - LSHTM CMMID COVID-19 Working Group; William Ampofo; Franklin Asiedu-Bekoe; Michael Marks; Rosalind M Eggo,London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Ghana Health Service; Ghana Health Service; Ghana Health Service; Ghana Health Service; University of Ghana Noguchi Memorial Institute for Medical Research; Fight Against AIDS Foundation; ; University of Ghana Noguchi Memorial Institute for Medical Research; Ghana Health Service; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine,"BackgroundGovernments around the world have implemented non-pharmaceutical interventions to limit the transmission of COVID-19. While lockdowns and physical distancing have proven effective for reducing COVID-19 transmission, there is still limited understanding of how NPI measures are reflected in indicators of human mobility. Further, there is a lack of understanding about how findings from high-income settings correspond to low and middle-income contexts. MethodsIn this study, we assess the relationship between indicators of human mobility, NPIs, and estimates of Rt, a real-time measure of the intensity of COVID-19 transmission. We construct a multilevel generalised linear mixed model, combining local disease surveillance data from subnational districts of Ghana with the timing of NPIs and indicators of human mobility from Google and Vodafone Ghana. @@ -2212,6 +2148,13 @@ C_LI Section 2: What this study addsO_LIOur study suggests an increased community positive test rate and hospital inpatients had an increased likelihood of a positive SARS-CoV-2 polymerase chain reaction test, whilst one or two doses of vaccination indicated a decreased chance of a positive test. C_LIO_LIOur findings suggest care providers need to stay vigilant despite the vaccination rollout, and extra precautions should be taken when caring for the most vulnerable, especially in a hospital setting. C_LI",geriatric medicine,fuzzy,100,100 +medRxiv,10.1101/2021.09.28.21264260,2021-09-29,https://medrxiv.org/cgi/content/short/2021.09.28.21264260,The impact of SARS-CoV-2 vaccination on Alpha and Delta variant transmission,David W Eyre; Donald Taylor; Mark Purver; David Chapman; Tom Fowler; Koen Pouwels; Ann Sarah Walker; Tim EA Peto,University of Oxford; Department of Health and Social Care; Department of Health and Social Care; Deloitte MCS Ltd; Department of Health and Social Care; University of Oxford; University of Oxford; University of Oxford,"BackgroundPre-Delta, vaccination reduced SARS-CoV-2 transmission from individuals infected despite vaccination, potentially via reducing viral loads. While vaccination still lowers the risk of infection, similar viral loads in vaccinated and unvaccinated individuals infected with Delta question how much vaccination prevents transmission. + +MethodsWe performed a retrospective observational cohort study of adult contacts of SARS-CoV-2-infected adult index cases using English contact testing data. We used multivariable Poisson regression to investigate associations between transmission and index case and contact vaccination, and how these vary with Alpha and Delta variants (classified using S-gene detection/calendar trends) and time since second vaccination. + +Results54,667/146,243(37.4%) PCR-tested contacts of 108,498 index cases were PCR-positive. Two doses of BNT162b2 or ChAdOx1 vaccines in Alpha index cases were independently associated with reduced PCR-positivity in contacts (aRR, adjusted rate ratio vs. unvaccinated=0.32[95%CI 0.21-0.48] and 0.48[0.30-0.78] respectively). The Delta variant attenuated vaccine-associated reductions in transmission: two BNT162b2 doses reduced Delta transmission (aRR=0.50[0.39-0.65]), more than ChAdOx1 (aRR=0.76[0.70-0.82]). Variation in Ct values (indicative of viral load) explained 7-23% of vaccine-associated transmission reductions. Transmission reductions declined over time post-second vaccination, for Delta reaching similar levels to unvaccinated individuals by 12 weeks for ChAdOx1 and attenuating substantially for BNT162b2. Protection in contacts also declined in the 3 months post-second vaccination. + +ConclusionsVaccination reduces transmission of Delta, but by less than the Alpha variant. The impact of vaccination decreased over time. Factors other than PCR Ct values at diagnosis are important in understanding vaccine-associated transmission reductions. Booster vaccinations may help control transmission together with preventing infections.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.09.28.21264240,2021-09-29,https://medrxiv.org/cgi/content/short/2021.09.28.21264240,Predicting hospital-onset COVID-19 infections using dynamic networks of patient contacts: an observational study,Ashlegh C Myall; James Richard Price; Robert L Peach; Mohamed Abbas; Siddharth Mookerjee; Nina Zhu; Isa Ahmad; Damien Keng Yen Ming; Farzan Ramzan; Daniel Teixeira; Christophe Graf; Andrea Y Wiesse; Stephan Harbarth; Alison Holmes; Mauricio Barahona,Imperial College London; Imperial College London; Imperial College London; University Hospital of Geneva; Imperial College London NHS Trust; Imperial College London; Imperial College London; Imperial College London; Imperial College London; University Hospital of Geneva; University Hospital of Geneva; The University of Edinburgh; University Hospital of Geneva; Imperial College London; Imperial College London,"BackgroundReal-time prediction is key to prevention and control of healthcare-associated infections. Contacts between individuals drive infections, yet most prediction frameworks fail to capture the dynamics of contact. We develop a real-time machine learning framework that incorporates dynamic patient contact networks to predict patient-level hospital-onset COVID-19 infections (HOCIs), which we test and validate on international multi-site datasets spanning epidemic and endemic periods. MethodsOur framework extracts dynamic contact networks from routinely collected hospital data and combines them with patient clinical attributes and background contextual hospital data to forecast the infection status of individual patients. We train and test the HOCI prediction framework using 51,157 hospital patients admitted to a UK (London) National Health Service (NHS) Trust from 01 April 2020 to 01 April 2021, spanning UK COVID-19 surges 1 and 2. We then validate the framework by applying it to data from a non-UK (Geneva) hospital site during an epidemic surge (40,057 total inpatients) and to data from the same London Trust from a subsequent period post surge 2, when COVID-19 had become endemic (43,375 total inpatients). @@ -2550,17 +2493,6 @@ Research in contextO_ST_ABSEvidence before this studyC_ST_ABSThere are now multi Added value of this studyThis study, in a uniquely large community-based cohort, uses prospective data capture in a novel effort to identify individuals with COVID-19 in the immediate post-vaccination period. Our results show that early symptoms of SARS-CoV-2 cannot be differentiated from vaccination side-effects robustly. Thus, post-vaccination systemic symptoms should not be ignored, and testing should be considered to prevent COVID-19 dissemination by vaccinated individuals. Implications of all the available evidenceOur study demonstrates the critical importance of testing symptomatic individuals - even if vaccinated - to ensure early detection of SARS-CoV-2 infection, helping to prevent future pandemic waves in the UK and elsewhere.",respiratory medicine,fuzzy,100,100 -medRxiv,10.1101/2021.07.19.21260770,2021-07-22,https://medrxiv.org/cgi/content/short/2021.07.19.21260770,Uptake of infant and pre-school immunisations in Scotland and England during the COVID-19 pandemic: an observational study of routinely collected data,Fiona McQuaid; Rachel Mulholland; Yuma Sangpang Rai; Utkarsh Agrawal; Helen Bedford; Claire Cameron; Cheryl Gibbon; Partho Roy; Aziz Sheikh; Ting Shi; Colin Simpson; Judith Tait; Elise Tessier; Steve Turner; Jaime Villacampa Ortega; Joanne White; Rachael Wood,University of Edinburgh; University of Edinburgh; Public Health England; University of St Andrews; UCL Great Ormond Street Institute of Child Health; Public Health Scotland; Public Health Scotland; Public Health England; University of Edinburgh; University of Edinburgh; Victoria University of Wellington; Public Health Scotland; Public Health England; University of Aberdeen; Public Health Scotland; Public Health England; University of Edinburgh,"BackgroundIn 2020, the COVID-19 pandemic and control measures such as national lockdowns threatened to disrupt routine childhood immunisation programmes. Initial reports from the early weeks of lockdown in the UK and worldwide suggested that uptake could fall putting children at risk from multiple other infectious diseases. In Scotland and England, enhanced surveillance of national data for childhood immunisations was established to inform and rapidly assess the impact of the pandemic on infant and preschool immunisation uptake rates. - -Methods and findingsWe undertook an observational study using routinely collected data for the year prior to the pandemic (2019), and immediately before, during and after the first period of the UK lockdown in 2020. Data were obtained for Scotland from the Public Health Scotland ""COVID19 wider impacts on the health care system"" dashboard (https://scotland.shinyapps.io/phs-covid-wider-impact/) and for England from ImmForm. - -Five vaccinations delivered at different ages were evaluated; three doses of the 6-in-1 DTaP/IPV/Hib/HepB vaccine and two doses of MMR. Uptake in the periods in 2020 compared to that in the baseline year of 2019 using binary logistic regression analysis. For Scotland, we analysed timely uptake of immunisations, defined as uptake within four weeks of the child becoming eligible by age for each immunisation and data were also analysed by geographical region and indices of deprivation. For both Scotland and England, we assessed whether immunisations were up to date at approximately 6 months (all doses 6-in-1) and 16-18 months (first MMR) of age. - -We found that uptake rates within four weeks of eligibility in Scotland for all the five vaccine visits were higher during the 2020 lockdown period than in 2019. The difference ranged from 1.3% for the first dose of the 6-in-1 vaccine (95.3 vs 94%, OR 1.28, CI 1.18-1.39) to 14.3% for the second MMR dose (66.1 vs 51.8 %, OR 1.8, CI 1.74-1.87). Significant increases in uptake were seen across all deprivation levels, though, for MMR, there was evidence of greater improvement for children living in the least deprived areas. - -In England, fewer children who had been due to receive their immunisations during the lockdown period were up to date at 6 months (6-in-1) or 18 months (first dose MMR). The fall in percentage uptake ranged from 0.5% for first 6-in1 (95.8 vs 96.3%, OR 0.89, CI 0.86-0.91) to 2.1% for third 6-in-1 (86.6 vs 88.7%, OR 0.82, CI 0.81-0.83). - -ConclusionsThis study suggests that the national lockdown in Scotland was associated with a positive effect on timely childhood immunisation uptake, however in England a lower percentage of children were up to date at 6 and 18 months. Reason for the improve uptake in Scotland may include active measures taken to promote immunisation at local and national level during this period. Promoting immunisation uptake and addressing potential vaccine hesitancy is particularly important given the ongoing pandemic and COVID-19 vaccination campaigns.",pediatrics,fuzzy,100,100 medRxiv,10.1101/2021.07.21.21260926,2021-07-22,https://medrxiv.org/cgi/content/short/2021.07.21.21260926,"Increasing SARS-CoV-2 antibody prevalence in England at the start of the second wave: REACT-2 Round 4 cross-sectional study in 160,000 adults",Helen Ward; Christina J Atchison; Matt Whitaker; Christl A. Donnelly; Steven Riley; Deborah Ashby; Ara Darzi; Wendy Barclay; Graham Cooke; Paul Elliott,"School of Public Health, Imperial College London; School of Public Health, Imperial College London; School of Public Health, Imperial College London; School of Public Health, Imperial College London; School of Public Health, Imperial College London; School of Public Health, Imperial College London; Institute of Global Health Innovation, Imperial College London; Department of Infectious Disease, Imperial College London; Department of Infectious Disease, Imperial College London; School of Public Health, Imperial College London","BackgroundREACT-2 Study 5 is a population survey of the prevalence of SARS-CoV-2 antibodies in the community in England. MethodsWe contacted a random sample of the population by sending a letter to named individuals aged 18 or over from the NHS GP registrations list. We then sent respondents a lateral flow immunoassay (LFIA) kit for SARS-CoV-2 antibody self-testing and asked them to perform the test at home and complete a questionnaire, including reporting of their test result. Overall, 161,537 adults completed questionnaires and self-administered LFIA tests for IgG against SARS-CoV-2 between 27 October and 10 November 2020. @@ -2575,13 +2507,6 @@ MethodsA retrospective study using routinely collected health data from all adul ResultsDuring the study period, 26,127 patients presented to QEHB hospital. 2301 had a positive SARS-CoV-2 swab. Of these, 1730 (75.2%) did not meet the criteria for the CVW and 571 (24.8%) did. Of the 571, 325 (56.9%) were discharged home within 24 hours and 246 (43.1%) were admitted for 24 hours or longer. Those admitted were older, with increased co-morbidities, 80.9% required hospital-supported acute therapies after the first 24 hours and 10.6% died. Of the 325 discharged, 44 were readmitted (13.5%), 30 (9.2%) with COVID-related symptoms, 5 (1.5%) required ITU and 1 patient (0.3%) died. These results were comparable to published studies with a CVW service. DiscussionIn the current study, discharging patients without a CVW did not confer a greater risk of re-presentation, re-admission, ITU escalation or death. The majority of patients who remained in hospital despite meeting the CVW criteria did so for the provision of treatments or acute assessments. It remains uncertain whether a CVW delivers improvements in hard outcomes, and further research is needed.",respiratory medicine,fuzzy,100,100 -medRxiv,10.1101/2021.07.16.21260628,2021-07-19,https://medrxiv.org/cgi/content/short/2021.07.16.21260628,"Overall and cause-specific hospitalisation and death after COVID-19 hospitalisation in England: cohort study in OpenSAFELY using linked primary care, secondary care and death registration data",Krishnan Bhaskaran; Christopher T Rentsch; George Hickman; William J Hulme; Anna Schultze; Helen J Curtis; Kevin Wing; Charlotte Warren-Gash; Laurie Tomlinson; Christopher Bates; Rohini Mathur; Brian MacKenna; Viyaasan Mahalingasivam; Angel YS Wong; Alex J Walker; Caroline E Morton; Daniel Grint; Amir Mehrkar; Rosalind M Eggo; Peter Inglesby; Ian J Douglas; Helen I McDonald; Jonathan Cockburn; Elizabeth J Williamson; David Evans; John Parry; Frank Hester; Sam Harper; Stephen JW Evans; Sebastian CJ Bacon; Liam Smeeth; Ben Goldacre,London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; TPP; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; TPP; London School of Hygiene and Tropical Medicine; University of Oxford; TPP; TPP; TPP; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford,"BackgroundThere is concern about medium to long-term adverse outcomes following acute COVID-19, but little relevant evidence exists. We aimed to investigate whether risks of hospital admission and death, overall and by specific cause, are raised following discharge from a COVID-19 hospitalisation. - -Methods and FindingsWorking on behalf of NHS-England, we used linked primary care and hospital data in OpenSAFELY to compare risks of hospital admission and death, overall and by specific cause, between people discharged from COVID-19 hospitalisation (February-December 2020), and (i) demographically-matched controls from the 2019 general population; (ii) people discharged from influenza hospitalisation in 2017-19. We used Cox regression adjusted for personal and clinical characteristics. - -24,673 post-discharge COVID-19 patients, 123,362 general population controls, and 16,058 influenza controls were followed for [≤]315 days. Overall risk of hospitalisation or death (30968 events) was higher in the COVID-19 group than general population controls (adjusted-HR 2.23, 2.14-2.31) but similar to the influenza group (adjusted-HR 0.94, 0.91-0.98). All-cause mortality (7439 events) was highest in the COVID-19 group (adjusted-HR 4.97, 4.58-5.40 vs general population controls and 1.73, 1.60-1.87 vs influenza controls). Risks for cause-specific outcomes were higher in COVID-19 survivors than general population controls, and largely comparable between COVID-19 and influenza patients. However, COVID-19 patients were more likely than influenza patients to be readmitted/die due to their initial infection/other lower respiratory tract infection (adjusted-HR 1.37, 1.22-1.54), and to experience mental health or cognitive-related admission/death (adjusted-HR 1.36, 1.01-2.83); in particular, COVID-19 survivors with pre-existing dementia had higher risk of dementia death. One limitation of our study is that reasons for hospitalisation/death may have been misclassified in some cases due to inconsistent use of codes. - -ConclusionsPeople discharged from a COVID-19 hospital admission had markedly higher risks for rehospitalisation and death than the general population, suggesting a substantial extra burden on healthcare. Most risks were similar to those observed after influenza hospitalisations; but COVID-19 patients had higher risks of all-cause mortality, readmissions/death due to the initial infection, and dementia death, highlighting the importance of post-discharge monitoring.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.07.13.21260425,2021-07-18,https://medrxiv.org/cgi/content/short/2021.07.13.21260425,Vaccine Confidence and Hesitancy at the start of COVID-19 vaccine deployment in the UK: An embedded mixed-methods study,Chrissy h Roberts; Hannah Brindle; Nina Trivedy Rogers; Rosalind M Eggo; Luisa Enria; Shelley Lees,"London School of Hygiene & Tropical Medicine (LSHTM); London School of Hygiene & Tropical Medicine; MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, United Kingdom; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London Schoolof Hygiene & Tropical Medicine","IntroductionApproval for the use of COVID-19 vaccines has been granted in a number of countries but there are concerns that vaccine uptake may be low amongst certain groups. MethodsThis study used a mixed methods approach based on online survey and an embedded quantitative/qualitative design to explore perceptions and attitudes that were associated with intention to either accept or refuse offers of vaccination in different demographic groups during the early stages of the UKs mass COVID-19 vaccination programme (December 2020). Analysis used multivariate logistic regression, structural text modelling and anthropological assessments. @@ -2871,26 +2796,6 @@ FindingsBetween 01 November 2020 and 21 March 2021, 7351 patients were randomly InterpretationIn patients hospitalised with COVID-19, aspirin was not associated with reductions in 28-day mortality or in the risk of progressing to invasive mechanical ventilation or death but was associated with a small increase in the rate of being discharged alive within 28 days. FundingUK Research and Innovation (Medical Research Council), National Institute of Health Research (Grant ref: MC_PC_19056), and the Wellcome Trust (Grant Ref: 222406/Z/20/Z) through the COVID-19 Therapeutics Accelerator.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2021.06.03.21258289,2021-06-06,https://medrxiv.org/cgi/content/short/2021.06.03.21258289,Implementation of COVID-19 Preventive Measures in Primary and Secondary Schools Following Reopening of Schools in Autumn 2020; A Cross-Sectional Study of Parents' and Teachers' Experiences in England,Zahin Amin-Chowdhury; Marta Bertran; Meaghan Kall; Georgina Ireland; Felicity Aiano; Annabel Powell; Samuel E Jones; Andrew Brent; Bernadette Brent; Frances Baawuah; Ifeanychukwu Okike; Joanne Beckmann; Joanna Garstang; Shazaad Ahmed; Neisha Sundaram; Chris Bonell; Sinead Langan; James Hargreaves; Shamez N Ladhani,"Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Public Health England; University Hospitals of Derby and Burton NHS foundation Trust; Specialist Children & Young People's Services, East London NHS Foundation Trust; Birmingham Community Healthcare Trust; Public Health England; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Public Health England","ObjectiveThe main objective was to assess implementation of and ease of implementation of control measures in schools as reported by staff and parents. - -DesignCross-sectional study. - -SettingStaff and parents/guardian participants in the 132 primary schools and 20 secondary schools participating in sKIDs and sKIDsPLUS surveillances. - -Main outcome measurePrevalence of control measures implemented in Autumn 2020, parental and staff perception of ease of implementation and acceptability of conducting school surveillance studies. - -ResultsIn total, 56/152 (37%) schools participating in Public Health Englands sKIDs study of COVID in schools accepted the invitation to participate in the survey. By 28 December 2020, 1,953 parent and 986 staff respondents had completed the online questionnaire. While more than half the parents were positive about their children returning to school, roughly a third reported being a little anxious. 90% and 82% of primary and secondary school parents were either completely or partly reassured by the preventive measures implemented in their schools. Among staff, 80% of primary staff and 87% of secondary school staff felt that they were at higher risk of COVID-19 because of their profession; only 52% of primary school staff and 38% of secondary school staff reportedly felt safe. According to the teaching staff, most preventive measures were well-implemented apart from requiring 2-metre distancing between staff. For students, maintaining the 2-metre distance was reported to be particularly difficult. By extension, secondary schools also struggled to maintain small groups at all times or ensuring that the same staff were assigned to each student group (a problem also commonly reported by parents). - -ConclusionsVariable implementation of infection control measures was reported by staff and parents. Whilst the majority were not worried about returning to school, some parents and staff, were concerned about returning to school and the risks posed to children, staff and household members. - -Strengths and limitations of this studyO_ST_ABSStrengthsC_ST_ABSO_LIThis study is one of the few to investigate school staff and parents perceptions of the implementation of control measures implemented following the reopening of schools in England. -C_LIO_LIThe early establishment of COVID-19 surveillance in primary and secondary schools in the summer term 2020 provided a cohort to rapidly evaluate the experiences of parents and school staff during the autumn term before schools were required to close for the subsequent national lockdown. -C_LI - -LimitationsO_LIAs the questionnaire and information provided was available in English only, there is likely to be an under-representation of families for whom English was not their main language. -C_LIO_LISome school responses were only provided by one participant so may not necessarily be representative of the whole school. -C_LIO_LIAlthough the surveillance included schools recruited nationally, a convenience sample was used and as such may not be representative of all primary and secondary schools in England. -C_LI",public and global health,fuzzy,100,100 medRxiv,10.1101/2021.05.28.21257602,2021-06-02,https://medrxiv.org/cgi/content/short/2021.05.28.21257602,Prevalence of persistent symptoms in children during the COVID-19 pandemic: evidence from a household cohort study in England and Wales,Faith Miller; Vincent Nguyen; Annalan MD Navaratnam; Madhumita Shrotri; Jana Kovar; Andrew C Hayward; Ellen Fragaszy; Robert W Aldridge; - Virus Watch Collaborative; Pia Hardelid,UCL; UCL; UCL; UCL; UCL; UCL; UCL; UCL; ; University College London,"Using data from 4678 children participating in VirusWatch, a household cohort study, we estimated the prevalence of persistent symptoms lasting [≥]4 weeks as 1.7%, and 4.6% in children with a history of SARS-CoV-2 infection. Persistent symptom prevalence was higher in girls, teenagers and children with long-term conditions.",pediatrics,fuzzy,100,100 medRxiv,10.1101/2021.05.25.21257730,2021-06-01,https://medrxiv.org/cgi/content/short/2021.05.25.21257730,"Post-COVID assessment in a specialist clinical service: a 12-month, single-centre analysis of symptoms and healthcare needs in 1325 individuals.",Melissa Heightman; Jai Prashar; Toby Hillman; Michael Marks; Rebecca Livingston; Heidi Ridsdale; Kay Roy; Robert Bell; Michael Zandi; Patricia McNamara; Alisha Chauhan; Emma Denneny; Ronan Astin; Helen Purcell; Emily Attree; Lyth Hishmeh; Gordon Prescott; Rebecca Evans; Puja Mehta; Ewen Brennan; Jeremy Brown; Joanna Porter; Sarah Logan; Emma Wall; Hakim-Moulay Dehbi; Stephen Cone; Amitava Banerjee,University College London Hospitals NHS Trust; University College London; University College London NHS Trust; London School of Hygiene & Tropical Medicine; University College London NHS Trust; Central and North West London NHS Foundation Trust; University College London NHS Trust; University College London NHS Trust; University College London; University College London NHS Trust; University College London NHS Trust; University College London NHS Trust; University College London; University College London NHS Trust; UKDoctors#Longcovid; Long COVID SOS; University of Central Lancashire; University College London NHS Trust; University College London; University College London NHS Trust; University College London; University College London; University College London NHS Trust; University College London; University College London; University College London NHS Trust; University College London,"BackgroundComplications following SARS-CoV-2 infection require simultaneous characterisation and management to plan policy and health system responses. We describe the 12-month experience of the first UK dedicated Post-COVID clinical service to include both hospitalised and non-hospitalised patients. @@ -2954,6 +2859,23 @@ InterpretationIn adults hospitalised with COVID-19, colchicine was not associate FundingUK Research and Innovation (Medical Research Council) and National Institute of Health Research (Grant ref: MC_PC_19056). Wellcome Trust (Grant Ref: 222406/Z/20/Z) through the COVID-19 Therapeutics Accelerator.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.05.17.21256818,2021-05-18,https://medrxiv.org/cgi/content/short/2021.05.17.21256818,Local prevalence of transmissible SARS-CoV-2 infection : an integrative causal model for debiasing fine-scale targeted testing data,George Nicholson; Brieuc CL Lehmann; Tullia Padellini; Koen B Pouwels; Radka Jersakova; James Lomax; Ruairidh E King; Ann-Marie Mallon; Peter J Diggle; Sylvia Richardson; Marta Blangiardo; Chris Holmes,University of Oxford; University of Oxford; Imperial College London; University of Oxford; The Alan Turing Institute; The Alan Turing Institute; MRC Harwell Institute; MRC Harwell Institute; Lancaster University; MRC Biostatistics Unit; Imperial College London; University of Oxford,"Targeted surveillance testing schemes for SARS-CoV-2 focus on certain subsets of the population, such as individuals experiencing one or more of a prescribed list of symptoms. These schemes have routinely been used to monitor the spread of SARS-CoV-2 in countries across the world. The number of positive tests in a given region can provide local insights into important epidemiological parameters, such as prevalence and effective reproduction number. Moreover, targeted testing data has been used inform the deployment of localised non-pharmaceutical interventions. However, surveillance schemes typically suffer from ascertainment bias; the individuals who are tested are not necessarily representative of the wider population of interest. Here, we show that data from randomised testing schemes, such as the REACT study in the UK, can be used to debias fine-scale targeted testing data in order to provide accurate localised estimates of the number of infectious individuals. We develop a novel, integrative causal framework that explicitly models the process underlying the selection of individuals for targeted testing. The output from our model can readily be incorporated into longitudinal analyses to provide local estimates of the reproduction number. We apply our model to characterise the size of the infectious population in England between June 2020 and January 2021. Our local estimates of the effective reproduction number are predictive of future changes in positive case numbers. We also capture local increases in both prevalence and effective reproductive number in the South East from November 2020 to December 2020, reflecting the spread of the Kent variant. Our results illustrate the complementary roles of randomised and targeted testing schemes. Preparations for future epidemics should ensure the rapid deployment of both types of schemes to accurately monitor the spread of emerging and ongoing infectious diseases.",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2021.05.15.21257017,2021-05-17,https://medrxiv.org/cgi/content/short/2021.05.15.21257017,Extended interval BNT162b2 vaccination enhances peak antibody generation in older people,Helen M Parry; Rachel Bruton; Christine Stephens; Kevin Brown; Gayatri Amirthalingam; Bassam Hallis; Ashley Otter; Jianmin Zuo; Paul Moss,"University of Birmingham, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham. B15 2TT, UK; Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham. B15 2TT, UK; Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham. B15 2TT, UK; National infection Service, Public Health England, Colindale, London NW9 5EQ, UK; National infection Service, Public Health England, Colindale, London NW9 5EQ, UK; National infection Service, Public Health England, Porton Down, Salisbury, SP4 OJG, UK; National infection Service, Public Health England, Porton Down, Salisbury, SP4 OJG, UK; Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham. B15 2TT, UK; Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham. B15 2TT, UK","ObjectivesTo assess the relative immunogenicity of standard or extended interval BNT162b2 vaccination. + +DesignPopulation based cohort study comparing immune responses 2 weeks after the second vaccine, with appropriate time-matched samples in participants who received standard or extended interval double vaccination. + +SettingPrimary care networks, Birmingham, UK. December 2020 to April 2021. + +Participants172 people aged over 80 years of age. All donors received the BNT162b2 Pfizer/BioNTech vaccination and were vaccinated with either a standard 3 week interval between doses or an extended interval schedule. + +Main outcome measuresPeak quantitative spike-specific antibody and cellular immune responses. + +ResultsIn donors without evidence of previous infection the peak antibody response was 3.5-fold higher in donors who had undergone delayed interval vaccination. Cellular immune responses were 3.6-fold lower. + +ConclusionPeak antibody responses after the second BNT162b2 vaccine are markedly enhanced in older people when this is delayed to 12 weeks although cellular responses are lower. Extended interval vaccination may therefore offer the potential to enhance and extend humoral immunity. Further follow up is now required to assess long term immunity and clinical protection. + +What is already known on this topicThe BNT162b2 vaccine is highly effective against Covid-19 infection and was delivered with a 3-week time interval in registration studies. However, this interval has been extended in many countries in order to extend population coverage with a single vaccine. It is not known how immune responses after the second dose are influenced by delaying the second vaccine. + +What this study addsWe provide the first assessment of immune responses in the first 14 weeks after standard or extended interval BNT162b2 vaccination and show that delaying the second dose acts to strongly boost the peak antibody response in older people. The extended interval vaccination may offer a longer period of clinical protection. This information will be of value in optimizing vaccine regimens and help guide guide vaccination policies.",infectious diseases,fuzzy,100,92 medRxiv,10.1101/2021.05.12.21257123,2021-05-17,https://medrxiv.org/cgi/content/short/2021.05.12.21257123,Occupation and COVID-19 mortality in England: a national linked data study of 14.3 million adults,Vahe Nafilyan; Piotr Pawelek; Daniel Ayoubkhani; Sarah Rhodes; Lucy Pembrey; Melissa Matz; Michel P Coleman; Claudia Allemani; Ben Windsor-Shellard; Martie van Tongeren; Neil Pearce,"Office for National Statistics; Office for National Statistics; Office for National Statistics; School of Health Sciences, University of Manchester; Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine; Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine; Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine; Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine; Office for National Statistics; School of Health Sciences, University of Manchester; London School of Hygiene and Tropical Medicine","ObjectiveTo estimate occupational differences in COVID-19 mortality, and test whether these are confounded by factors, such as regional differences, ethnicity and education or due to non-workplace factors, such as deprivation or pre-pandemic health. DesignRetrospective cohort study @@ -3256,6 +3178,7 @@ MethodA search was undertaken in peer-reviewed databases, pre-print databases, a ResultsThirty-three papers met the inclusion criteria, only three of which were rated as low risk of bias. Public attitudes were generally favourable towards the use of immunity certificates for international travel, but unfavourable towards their use for access to work and other activities. A significant minority was strongly opposed to the use of certificates of immunity for any purpose. The limited evidence suggested that intention to get vaccinated varied with the activity enabled by certification or vaccination (e.g., international travel). Where vaccination is seen as compulsory this could lead to unwillingness to accept a subsequent vaccination. There was some evidence that restricting access to settings and activities to those with antibody test certificates may lead to deliberate exposure to infection in a minority. Behaviours that reduce transmission may decrease upon health certificates based on any of the three indices of Covid-19 status, including physical distancing and handwashing. ConclusionsThe limited evidence suggests that health certification in relation to COVID-19 - outside of the context of international travel - has the potential for harm as well as benefit. Realising the benefits while minimising the harms will require real-time evaluations allowing modifications to maximise the potential contribution of certification to enable safer access to a range of activities.",public and global health,fuzzy,100,100 +medRxiv,10.1101/2021.04.07.21254497,2021-04-09,https://medrxiv.org/cgi/content/short/2021.04.07.21254497,Characterising contact in disease outbreaks via a network model of spatial-temporal proximity,Ashleigh C Myall; Robert L Peach; Yu Wan; Siddharth Mookerjee; Elita Jauneikaite; Frankie Bolt; James Richard Price; Frances Davies; Andrea Yeong Wiesse; Alison Holmes; Mauricio Barahona,Imperial College London; Imperial College London; Imperial College London; Imperial College NHS Trust; Imperial College London; Imperial College London; Imperial College London; Imperial College NHS Trust; University of Edinburgh; Imperial College London; Imperial College London,"Contact tracing is a key tool in epidemiology to identify and control outbreaks of infectious diseases. Existing contact tracing methodologies produce contact maps of individuals based on a binary definition of contact which can be hampered by missing data and indirect contacts. Here, we present a Spatial-temporal Epidemiological Proximity (StEP) model to recover contact maps in disease outbreaks based on movement data. The StEP model accounts for imperfect data by considering probabilistic contacts between individuals based on spatial-temporal proximity of their movement trajectories, creating a robust movement network despite possible missing data and unseen transmission routes. Using real-world data we showcase the potential of StEP for contact tracing with outbreaks of multidrug-resistant bacteria and COVID-19 in a large hospital group in London, UK. In addition to the core structure of contacts that can be recovered using traditional methods of contact tracing, the StEP model reveals missing contacts that connect seemingly separate outbreaks. Comparison with genomic data further confirmed that these recovered contacts indeed improve characterisation of disease transmission and so highlights how the StEP framework can inform effective strategies of infection control and prevention.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.04.01.21254765,2021-04-07,https://medrxiv.org/cgi/content/short/2021.04.01.21254765,"Mental health inequalities in healthcare, economic, and housing disruption during COVID -19: an investigation in 12 longitudinal studies",Giorgio Di Gessa; Jane Maddock; Michael J Green; Ellen J Thompson; Eoin McElroy; Helena L Davies; Jessica Mundy; Anna J Stevenson; Alex S.F Kwong; Gareth J Griffith; Srinivasa Vittal Katikireddi; Claire L Niedzwiedz; George B Ploubidis; Emla Fitzsimons; Morag Henderson; Richard J. Silverwood; Nishi Chaturvedi; Gerome Breen; Claire J Steves; Andrew Steptoe; David J Porteous; Praveetha Patalay,"Institute of Epidemiology and Health Care, University College London; MRC Unit for Lifelong Health and Ageing, University College London; MRC/CSO Social & Public Health Sciences Unit, University of Glasgow; Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, Kings College London; Department of Neuroscience, Psychology and Behaviour, University of Leicester; Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, Kings College London; Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, Kings College London; Centre for Genomic and Experimental Medicine, University of Edinburgh; Division of Psychiatry, University of Edinburgh and MRC Integrative Epidemiology Unit, University of Bristol; MRC Integrative Epidemiology Unit, University of Bristol; MRC/CSO Social & Public Health Sciences Unit, University of Glasgow; Institute of Health & Wellbeing, University of Glasgow; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; MRC Unit for Lifelong Health and Ageing, University College London; Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, Kings College London and Maudsley Biomedical Research Cen; Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, Kings College London; Institute of Epidemiology and Health Care, University College London; Centre for Genomic and Experimental Medicine, University of Edinburgh; Centre for Longitudinal Studies and MRC Unit for Lifelong Health and Ageing, University College London","BackgroundThe COVID-19 pandemic and associated virus suppression measures have disrupted lives and livelihoods and people already experiencing mental ill-health may have been especially vulnerable. AimTo quantify mental health inequalities in disruptions to healthcare, economic activity and housing. @@ -3549,6 +3472,9 @@ ResultsAfter a sharp decline in willingness to vaccinate against COVID-19 betwee ConclusionsWillingness to vaccinate against COVID-19 increased in the US from October 2020 to February 2021. Funding statementN/A",public and global health,fuzzy,100,100 +medRxiv,10.1101/2021.03.04.21252931,2021-03-08,https://medrxiv.org/cgi/content/short/2021.03.04.21252931,A common TMPRSS2 variant protects against severe COVID-19,"Alessia David; Nicholas Parkinson; Thomas P Peacock; Erola Pairo-Castineira; Tarun Khanna; Aurelie Cobat; Albert Tenesa; Vanessa Sancho-Shimizu; - GenOMICC Investigators, ISARIC4C Investigators; Jean-Laurent Casanova; Laurent Abel; Wendy S Barclay; J Kenneth Baillie; Michael J.E. Sternberg","Centre for Integrative System Biology and Bioinformatics, Imperial College London, London; Roslin Institute, University of Edinburgh; Department of Infectious Diseases, Imperial College London; Roslin Institute, University of Edinburgh; Centre for Integrative System Biology and Bioinformatics, Imperial College London; Laboratory of Human Genetics of Infectious Diseases, INSERM; Roslin Institute, University of Edinburgh; Department of Paediatric Infectious Diseases & Virology, Imperial College London; ; St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University; Laboratory of Human Genetics of Infectious Diseases, INSERM; Department of Infectious Diseases, Imperial College London; Roslin Institute, University of Edinburgh; Centre for Integrative System Biology and Bioinformatics, Imperial College London","Infection with SARS-CoV-2 has a wide range of clinical presentations, from asymptomatic to life-threatening. Old age is the strongest factor associated with increased COVID19-related mortality, followed by sex and pre-existing conditions. The importance of genetic and immunological factors on COVID19 outcome is also starting to emerge, as demonstrated by population studies and the discovery of damaging variants in genes controlling type I IFN immunity and of autoantibodies that neutralize type I IFNs. The human protein transmembrane protease serine type 2 (TMPRSS2) plays a key role in SARS-CoV-2 infection, as it is required to activate the virus spike protein, facilitating entry into target cells. We focused on the only common TMPRSS2 non-synonymous variant predicted to be damaging (rs12329760), which has a minor allele frequency of [~]25% in the population. In a large population of SARS-CoV-2 positive patients, we show that this variant is associated with a reduced likelihood of developing severe COVID19 (OR 0.87, 95%CI:0.79-0.97, p=0.01). This association was stronger in homozygous individuals when compared to the general population (OR 0.65, 95%CI:0.50-0.84, p=1.3x10-3). We demonstrate in vitro that this variant, which causes the amino acid substitution valine to methionine, impacts the catalytic activity of TMPRSS2 and is less able to support SARS-CoV-2 spike-mediated entry into cells. + +TMPRSS2 rs12329760 is a common variant associated with a significantly decreased risk of severe COVID19. Further studies are needed to assess the expression of the TMPRSS2 across different age groups. Moreover, our results identify TMPRSS2 as a promising drug target, with a potential role for camostat mesilate, a drug approved for the treatment of chronic pancreatitis and postoperative reflux esophagitis, in the treatment of COVID19. Clinical trials are needed to confirm this.",genetic and genomic medicine,fuzzy,100,100 medRxiv,10.1101/2021.03.04.21252528,2021-03-08,https://medrxiv.org/cgi/content/short/2021.03.04.21252528,Case fatality risk of the SARS-CoV-2 variant of concern B.1.1.7 in England,Daniel J Grint; Kevin Wing; Elizabeth Williamson; Helen I McDonald; Krishnan Bhaskaran; David Evans; Stephen JW Evans; Alex J Walker; George Hickman; Emily Nightingale; Anna Schultze; Christopher T Rentsch; Chris Bates; Jonathan Cockburn; Helen J Curtis; Caroline E Morton; Sebastian Bacon; Simon Davy; Angel YS Wong; Amir Mehrkar; Laurie Tomlinson; Ian J Douglas; Rohini Mathur; Paula Blomquist; Brian MacKenna; Peter Ingelsby; Richard Croker; John Parry; Frank Hester; Sam Harper; Nicolas J DeVito; Will Hulme; John Tazare; Ben Goldacre; Liam Smeeth; Rosalind M Eggo,"Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; Faculty of Public Health and Policy, London School of Hygiene & Tropical Medicine, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, UK; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; COVID-19 Outbreak Surveillance Team, Public Health England, London, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, UK; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, UK; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK",The B.1.1.7 variant of concern (VOC) is increasing in prevalence across Europe. Accurate estimation of disease severity associated with this VOC is critical for pandemic planning. We found increased risk of death for VOC compared with non-VOC cases in England (HR: 1.67 (95% CI: 1.34 - 2.09; P<.0001). Absolute risk of death by 28-days increased with age and comorbidities. VOC has potential to spread faster with higher mortality than the pandemic to date.,infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.03.08.21253112,2021-03-08,https://medrxiv.org/cgi/content/short/2021.03.08.21253112,OpenSAFELY: Risks of COVID-19 hospital admission and death for people with learning disabilities - a cohort study.,Elizabeth Williamson; Helen I McDonald; Krishnan Bhaskaran; Alex J Walker; Sebastian Bacon; Simon Davy; Anna Schultze; Laurie Tomlinson; Chris Bates; Mary Ramsay; Helen J Curtis; Harriet Forbes; Kevin Wing; Caroline Minassian; John Tazare; Caroline E Morton; Emily Nightingale; Amir Mehrkar; Dave Evans; Peter Inglesby; Brian MacKenna; Jonathan Cockburn; Christopher T Rentsch; Rohini Mathur; Angel Wong; Rosalind M Eggo; William J Hulme; Richard Croker; John Parry; Frank Hester; Sam Harper; Ian Douglas; Stephen JW Evans; Liam Smeeth; Ben Goldacre; Hannah Kuper,"London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; NIHR Health Protection Research Unit (HPRU) in Immunisation; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; Public Health England, London; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT","ObjectivesTo assess the association between learning disability and risk of hospitalisation and mortality from COVID-19 in England among adults and children. @@ -3762,21 +3688,6 @@ C_LIO_LIAfter standardising for age, sex and deprivation, people with intellectu C_LIO_LICompared with general population adults, adults with intellectual disabilities had poorer outcomes among non-elderly age-groups particularly those aged 55-65 years, men, and those living in less-deprived neighbourhoods. C_LIO_LINon-pharmaceutical initiatives are important for carers and care-provider organisations, and adults with intellectual disabilities should be prioritised in the national rollouts of COVID-19 vaccination programmes, regardless of age, sex, or neighbourhood deprivation. C_LI",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2021.02.04.21251155,2021-02-08,https://medrxiv.org/cgi/content/short/2021.02.04.21251155,Impact of school closures on the health and well-being of primary school children in Wales UK; a routine data linkage study using the HAPPEN survey (2018-2020).,Michaela James; Emily Marchant; Margaret A Defeyter; Jayne V Woodside; Sinead Brophy,Swansea University; Swansea University; Northumbria University; Queen's University Belfast; Swansea University,"IntroductionIn response to the COVID-19 pandemic, school closures were implemented across the United Kingdom. This study aimed to explore the impact of school closures on childrens health by comparing health and wellbeing outcomes collected during school closures (April - June 2020) with data from the same period in 2019 and 2018. - -MethodsData were collected online via the HAPPEN At Home survey, which captured the typical health behaviours of children aged 8 - 11 years between April - June 2020. These data were compared with data in 2018 and 2019 also collected between April-June, from HAPPEN. Free school meal (FSM) status was used as a proxy for socio-economic deprivation. Analyses were repeated stratifying by FSM. - -ResultsComparing responses between April - June in 2020 (n=1068), 2019 (n=1150) and 2018 (n=475), there were improvements in physical activity levels, sleep time, happiness and general wellbeing for children during school closures compared to previous years. However, children on FSM ate less fruit and vegetables (21% (95%CI (5.7% to 37%)) and had lower self-assessed school competence compared to 2019. Compared to those not on FSM they also spent less time doing physical activity (13.03% (95%CI: 3.3% to 21.7%) and consumed more takeaways (16.3% (95%CI: 2%-30%)) during school closures. - -ConclusionThis study suggests that schools play an important role in reducing inequalities in physical health. The physical health (e.g. physical activity and diet) of children eligible for FSM may be impacted by prolonged school closures. - -What is already known on this subject?In response to the COVID-19 pandemic, by mid-March 2020, 138 countries had implemented national school closures to reduce the number of social contacts between pupils, therefore interrupting the transmission of COVID-19 as part of pandemic plans. UNESCO warned that the global scale and speed of the educational disruption would be unparalleled. There is an ongoing debate with regard to the effectiveness of schools closures on transmission rates, but the fact schools are closed for a long period of time could have detrimental impacts on pupils physical and mental health. - -This study provides evidence of any differences in the health and wellbeing of children prior to and during the COVID-19 enforced lockdown and school closures between March and June 2020. These findings could have a significant impact for the future and support schools to better understand their pupils physical, psychological, emotional and social health. It also contributes to a significant literature gap regarding the impact of school closures on school-aged children. - -What this study adds?Improvements in physical activity levels, sleep time, happiness and general wellbeing were observed in general for children during school closures compared to previous years. However, children on FSM reported eating less fruit and vegetables and had lower self-assessed school competence compared to 2019. Compared to those not on FSM they also spent less time doing physical activity and consumed more takeaways during school closures. These trends are not evident among children not on FSM. All children reported improvements in wellbeing during lockdown especially on the happiness with family measure. - -Overall, findings suggest schools help to reduce inequalities in physical health for socio-economically deprived children. During school closures children from deprived backgrounds are likely to have poorer physical health (e.g. less time spent doing physical activities and poorer diet) and this is not observed in children who are not in receipt of FSM. This research suggests that school closures will result in widening health inequalities and when schools return measures will need to be in place to readdress the widened gap in physical health.",public and global health,fuzzy,100,100 medRxiv,10.1101/2021.02.04.21251087,2021-02-08,https://medrxiv.org/cgi/content/short/2021.02.04.21251087,Staff-Pupil SARS-CoV-2 Infection Pathways in Schools: A Population Level Linked Data Approach,Daniel A Thompson; Hoda Abbasizanjani; Richard Fry; Emily Marchant; Lucy J Griffiths; Ashley Akbari; Joseph Hollinghurst; Laura North; Jane Lyons; Fatemeh Torabi; Gareth Davies; Mike B Gravenor; Ronan A Lyons,Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University,"BackgroundBetter understanding of the role that children and school staff play in the transmission of SARS-CoV-2 is essential to guide policy development on controlling infection whilst minimising disruption to childrens education and wellbeing. MethodsOur national e-cohort (n=500,779) study used anonymised linked data for pupils, staff and associated households linked via educational settings. We estimated the risk of testing positive for SARS-CoV-2 infection for staff and pupils over the period August - December 2020, dependent on measures of recent exposure to known cases linked to their educational settings. @@ -3796,13 +3707,6 @@ C_LIO_LIPupils were found to be at increased risk of testing positive, following C_LI C_TEXTBOX",health informatics,fuzzy,100,100 -medRxiv,10.1101/2021.02.07.21251297,2021-02-08,https://medrxiv.org/cgi/content/short/2021.02.07.21251297,The changing characteristics of COVID-19 presentations: A regional comparison of SARS-CoV-2 hospitalised patients during the first and second wave.,Catherine Atkin; Vicky Kamwa; Vinay Reddy-Kolanu; Dhruv Parekh; Felicity Evison; Peter Nightingale; Suzy Gallier; Simon Ball; Elizabeth Sapey,"Acute Medicine, Birmingham Acute Care Research Group, Institute of Inflammation and Ageing, University of Birmingham; Acute Medicine, Birmingham Acute Care Research Group, Institute of Inflammation and Ageing, University of Birmingham; Acute Medicine, University Hospitals Birmingham NHS Foundation Trust; A. Intensive Care Medicine, University Hospitals Birmingham NHS Foundation Trust, Edgbaston, Birmingham, B15 2GW, UK. B. Birmingham Acute Care Research Grou; Research Analytics Department of Health Informatics, University Hospitals Birmingham NHS Foundation Trust; NIHR Clinical Research Facility Statistician, University Hospitals Birmingham NHS Foundation Trust; PIONEER Technical Director, Lead for Research Analytics Department of Health Informatics, University Hospitals Birmingham NHS Foundation Trust; A. Chief Medical Officer, University Hospitals Birmingham NHS Foundation Trust B. HDR-UK Midlands Site and Better Care Programme, University Hospitals Birmingh; A. Director of PIONEER: Health Data Research UK (HDRUK) Health Data Research Hub for Acute Care B. Birmingham Acute Care Research Group, Institute of Inflammat","BackgroundThis study assesses COVID-19 hospitalised patient demography and outcomes during wave 1 and wave 2, prior to new variants of the virus. - -MethodsAll patients with a positive SARS-CoV-2 swab between 10th March 2020 and 5th July 2020 (wave 1) and 1st September 2020 and 16th November 2020 (wave 2) admitted to University Hospitals Birmingham NHS Foundation Trust were included (n=4856), followed for 28 days. - -ResultsWave 2 patients were younger, more ethnically diverse, had less co-morbidities and disease presentation was milder on presentation. After matching for these factors, mortality was reduced, but without differences in intensive care admissions. - -ConclusionPrior to new SARS-CoV-2 variants, outcomes for hospitalised patients with COVID-19 were improving but with similar intensive care needs.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.02.03.21251054,2021-02-05,https://medrxiv.org/cgi/content/short/2021.02.03.21251054,Age-related heterogeneity in Neutralising antibody responses to SARS-CoV-2 following BNT162b2 vaccination,Dami Collier; Isabella Ferreira; Rawlings Datir; Prasanti Kotagiri; Eleanor Lim; Bo Meng; - The CITIID-NIHR Bioresource COVID-19 Collaboration; Anne Elmer; Nathalie Kingston; Barbara Graves; Barbara Graves; Kenneth GC Smith; John Bradley; Paul Lyons; Lourdes Ceron-Gutierrez; Gabriela Barcenas-Morales; Michelle Linterman; Laura McCoy; Rainer Doffinger; Mark Wills; Ravindra K Gupta,UCL; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; -; Cambridge; NIHR; NIHR; Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; Babraham Institute; UCL; University of Cambridge; University of Cambridge; University of Cambridge,"Two dose mRNA vaccination provides excellent protection against SARS-CoV-2. However, there are few data on vaccine efficacy in elderly individuals above the age of 801. Additionally, new variants of concern (VOC) with reduced sensitivity to neutralising antibodies have raised fears for vulnerable groups. Here we assessed humoral and cellular immune responses following vaccination with mRNA vaccine BNT162b22 in elderly participants prospectively recruited from the community and younger health care workers. Median age was 72 years and 51% were females amongst 140 participants. Neutralising antibody responses after the first vaccine dose diminished with increasing age, with a marked drop in participants over 80 years old. Sera from participants below and above 80 showed significantly lower neutralisation potency against B.1.1.7, B.1.351 and P.1. variants of concern as compared to wild type. Those over 80 were more likely to lack any neutralisation against VOC compared to younger participants following first dose. The adjusted odds ratio for inadequate neutralisation activity against the B.1.1.7, P.1 and B.1.351 variant in the older versus younger age group was 4.3 (95% CI 2.0-9.3, p<0.001), 6.7 (95% CI 1.7-26.3, p=0.008) and 1.7 (95% CI 0.5-5.7, p=0.41). Binding IgG and IgA antibodies were lower in the elderly, as was the frequency of SARS-CoV-2 Spike specific B-memory cells. We observed a trend towards lower somatic hypermutation in participants with suboptimal neutralisation, and elderly participants demonstrated clear reduction in class switched somatic hypermutation, driven by the IgA1/2 isotype. SARS-CoV-2 Spike specific T-cell IFN{gamma} and IL-2 responses fell with increasing age, and both cytokines were secreted primarily by CD4 T cells. We conclude that the elderly are a high risk population that warrant specific measures in order to mitigate against vaccine failure, particularly where variants of concern are circulating.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.02.02.21251043,2021-02-05,https://medrxiv.org/cgi/content/short/2021.02.02.21251043,COVID-19 infection and subsequent thromboembolism: A self-controlled case series analysis of a population cohort,Frederick Ho; Kenneth Man; Mark Toshner; Colin Church; Carlos Celis-Morales; Ian Wong; Colin Berry; Naveed Sattar; Jill Pell,University of Glasgow; UCL; University of Cambridge; NHS Greater Glasgow and Clyde; University of Glasgow; UCL; University of Glasgow; University of Glasgow; University of Glasgow,"ObjectiveAn unexpectedly large number of people infected with Covid-19 had experienced a thrombotic event. This study aims to assess the associations between Covid-19 infection and thromboembolism including myocardial infarction (MI), ischaemic stroke, deep-vein thrombosis (DVT), and pulmonary embolism (PE). @@ -3873,6 +3777,7 @@ We found evidence that all four devices have reduced sensitivity at lower antibo Our estimates of sensitivity and specificity are likely to be higher than would be observed in real use of these devices, as they were based on majority readings of three trained laboratory personnel. Implications of all the available evidenceWhen used in epidemiological studies of antibody prevalence, the estimates of sensitivity and specificity provided in this study can be used to adjust for test errors. Increased precision in error rates will translate to increased precision in seroprevalence estimates. If lateral flow devices were used for individual risk assessment, devices with maximum specificity would be preferable. However, if, for an example, 20% of the tested population had antibodies, we estimate that around 1 in 20 positive results on the most specific device would be incorrect.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2021.01.28.21250606,2021-01-31,https://medrxiv.org/cgi/content/short/2021.01.28.21250606,REACT-1 round 8 final report: high average prevalence with regional heterogeneity of trends in SARS-CoV-2 infection in the community in England during January 2021,Steven Riley; Oliver Eales; Caroline E. Walters; Haowei Wang; Kylie E. C. Ainslie; Christina Atchinson; Claudio Fronterre; Peter J. Diggle; Deborah Ashby; Christl A Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott,"School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear","In early January 2021, England entered its third national lockdown of the COVID-19 pandemic to reduce numbers of deaths and pressure on healthcare services, while rapidly rolling out vaccination to healthcare workers and those most at risk of severe disease and death. REACT-1 is a survey of SARS-CoV-2 prevalence in the community in England, based on repeated cross-sectional samples of the population. Between 6th and 22nd January 2021, out of 167,642 results, 2,282 were positive giving a weighted national prevalence of infection of 1.57% (95% CI, 1.49%, 1.66%). The R number nationally over this period was estimated at 0.98 (0.92, 1.04). Prevalence remained high throughout, but with suggestion of a decline at the end of the study period. The average national trend masked regional heterogeneity, with robustly decreasing prevalence in one region (South West) and increasing prevalence in another (East Midlands). Overall prevalence at regional level was highest in London at 2.83% (2.53%, 3.16%). Although prevalence nationally was highest in the low-risk 18 to 24 year old group at 2.44% (1.96%, 3.03%), it was also high in those over 65 years who are most at risk, at 0.93% (0.82%, 1.05%). Large household size, living in a deprived neighbourhood, and Black and Asian ethnicity were all associated with higher levels of infections compared to smaller households, less deprived neighbourhoods and other ethnicities. Healthcare and care home workers, and other key workers, were more likely to test positive compared to other workers. If sustained lower prevalence is not achieved rapidly in England, pressure on healthcare services and numbers of COVID-19 deaths will remain unacceptably high.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.01.25.21249942,2021-01-30,https://medrxiv.org/cgi/content/short/2021.01.25.21249942,Development and external validation of prognostic models for COVID-19 to support risk stratification in secondary care,Nicola J Adderley; Thomas Taverner; Malcolm Price; Christopher Sainsbury; David Greenwood; Joht Singh Chandan; Yemisi Takwoingi; Rashan Haniffa; Isaac Hosier; Carly Welch; Dhruv Parekh; Suzy Gallier; Krishna M Gokhale; Alastair K Denniston; Elizabeth Sapey; Krishnarajah Nirantharakumar,University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Oxford; University of Birmingham; University of Birmingham; University of Birmingham; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham,"ObjectivesExisting UK prognostic models for patients admitted to hospital with COVID-19 are limited by reliance on comorbidities, which are under-recorded in secondary care, and lack of imaging data among the candidate predictors. Our aims were to develop and externally validate novel prognostic models for adverse outcomes (death, intensive therapy unit (ITU) admission) in UK secondary care; and externally validate the existing 4C score. DesignCandidate predictors included demographic variables, symptoms, physiological measures, imaging, laboratory tests. Final models used logistic regression with stepwise selection. @@ -3893,21 +3798,6 @@ C_LIO_LIIf integrated into hospital electronic medical records systems, the mode C_LIO_LIA limitation of the study was that in the external validation cohort we were unable to examine all of the predictors included in the original full UHB model due to only a reduced set of candidate predictors being available in CovidCollab. Nevertheless, the reduced model performed well and the results suggest it may be applicable in a wide range of datasets where only a reduced set of predictor variables is available. C_LIO_LIFurthermore, it was not possible to carry out stratified analysis by ethnicity as the UHB dataset contained too few patients in most of the strata, and no ethnicity data was available in the CovidCollab dataset. C_LI",public and global health,fuzzy,100,100 -medRxiv,10.1101/2021.01.28.21250680,2021-01-29,https://medrxiv.org/cgi/content/short/2021.01.28.21250680,"The effect of SARS-CoV-2 variant B.1.1.7 on symptomatology, re-infection and transmissibility",Mark S Graham; Carole H Sudre; Anna May; Michela Antonelli; Benjamin Murray; Thomas Varsavsky; Kerstin Klaser; Liane Dos Santos Canas; Erika Molteni; Marc Modat; David Alden Drew; Long Alden Nguyen; Lorenzo Polidori; Somesh Selvachandran; Christina Hu; Joan Capdevila Pujol; - The COVID-19 Genomics UK (COG-UK) consortium; Alexander Hammers; Andrew T Chan; Jonathan Wolf; Timothy Spector; Claire Steves; Sebastien Ourselin,King's College London; MRC Unit for Lifelong Health and Ageing; Zoe Global Limited; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; Massachusetts General Hospital; Massachusetts General Hospital and Harvard Medical School; Zoe Global Limited; Zoe Global Limited; Zoe Global Limited; Zoe Global Limited; ; King's College London; Massachusetts General Hospital; Zoe Global Limited; King's College London; King's College London; King's College London,"BackgroundSARS-CoV-2 variant B.1.1.7 was first identified in December 2020 in England. It is not known if the new variant presents with variation in symptoms or disease course, if previously infected individuals may become reinfected with the new variant, or how the variants increased transmissibility affects measures to reduce its spread. - -MethodsUsing longitudinal symptom reports from 36,920 users of the COVID Symptom Study app testing positive for Covid-19 between 28 September and 27 December 2020, we performed an ecological study to examine the association between the regional proportion of B.1.1.7 and reported symptoms, disease course, rates of reinfection, and transmissibility. - -FindingsWe found no evidence for changes in reported symptoms or disease duration associated with B.1.1.7. We found a likely reinfection rate of 0.7% (95% CI 0.6-0.8), but no evidence that this was higher compared to older strains. We found an increase in R(t) by a factor of 1.35 (95% CI 1.02-1.69). Despite this, we found that R(t) fell below 1 during regional and national lockdowns, even in regions with high proportions of B.1.1.7. - -InterpretationThe lack of change in symptoms indicates existing testing and surveillance infrastructure do not need to change specifically for the new variant, and the reinfection findings suggest that vaccines are likely to remain effective against the new variant. - -FundingZoe Global Limited, Department of Health, Wellcome Trust, EPSRC, NIHR, MRC, Alzheimers Society. - -Research in contextO_ST_ABSEvidence before this studyC_ST_ABSTo identify existing evidence on SARS-CoV-2 variant B.1.1.7 we searched PubMed and Google Scholar for articles between 1 December 2020 and 1 February 2021 using the keywords Covid-19 AND B.1.1.7, finding 281 results. We did not find any studies that investigated B.1.1.7-associated changes in the symptoms experienced, their severity and duration, but found one study showing B.1.1.7 did not change the ratio of symptomatic to asymptomatic infections. We found six articles describing laboratory-based investigations of the responses of B.1.1.7 to vaccine-induced immunity to B.1.1.7, but no work investigating what this means for natural immunity and the likelihood of reinfection outside of the lab. We found five articles demonstrating the increased transmissibility of B.1.1.7. - -Added value of this studyTo our knowledge, this is the first study to explore changes in symptom type and duration, as well as community reinfection rates, associated with B.1.1.7. The work uses self-reported symptom logs from 36,920 users of the COVID Symptom Study app reporting positive test results between 28 September and 27 December 2020. We find that B.1.1.7 is not associated with changes in the symptoms experienced in Covid-19, nor their duration. Building on existing lab studies, our work suggests that natural immunity developed from previous infection provides similar levels of protection to B.1.1.7. We add to the emerging consensus that B.1.1.7 exhibits increased transmissibility. - -Implications of all the available evidenceOur findings suggest that existing criteria for obtaining a Covid-19 test in the community need not change for the rise of B.1.1.7. The fact that immunity developed from infection by wild type variants protects against B.1.1.7 provides an indication that vaccines will remain effective against B.1.1.7. R(t) fell below 1 during the UKs national lockdown, even in regions with high levels of B.1.1.7, but further investigation is required to establish the factors that enabled this, to facilitate countries seeking to control the spread of B.1.1.7.",epidemiology,fuzzy,94,100 medRxiv,10.1101/2021.01.26.21250480,2021-01-28,https://medrxiv.org/cgi/content/short/2021.01.26.21250480,"Individual factors underlie temperature variation in sickness and in health: influence of age, BMI and genetic factors in a multi-cohort study",Rose S. Penfold; Maria Beatrice Zazzara; Marc F. Österdahl; - GSTT CovidCollaborative; Carly Welch; Mary Ni Lochlainn; Maxim Freidin; Ruth C.E. Bowyer; Ellen E.J. Thompson; Michela Antonelli; Yu Xian Rachel Tan; Carole Sudre; Marc Modat; Benjamin Murray; Jonathan Wolf; Sebastien Ourselin; Tonny Veenith; Janet M. Lord; Claire J. Steves,"King's College London, Department of Twin Research & Genetic Epidemiology; Guy's and St Thomas' NHS Foundation Trust; King's College London, Department of Twin Research & Genetic Epidemiology; Catholic University of the Sacred Heart Faculty of Medicine and Surgery, Department ; Guy's and St Thomas' NHS Foundation Trust; ; University of Birmingham, Institute of Inflammation & Ageing; King's College London, Department of Twin Research & Genetic Epidemiology; King's College London, Department of Twin Research & Genetic Epidemiology; King's College London, Department of Twin Research & Genetic Epidemiology; King's College London, Department of Twin Research & Genetic Epidemiology; King's College London, School of Biomedical Engineering & Imaging Sciences London; Royal College of Surgeons in Ireland, Department of Medicine; King's College London, School of Biomedical Engineering & Imaging Sciences London; King's College London, School of Biomedical Engineering & Imaging Sciences; King's College London, School of Biomedical Engineering & Imaging Sciences; Zoe Global Limited London; King's College London, School of Biomedical Engineering & Imaging Sciences; University of Birmingham, Institute of Inflammation and Ageing; University of Birmingham, Institute of Inflammation and Ageing; Department of Twin Research and Genetic Epidemiology, King's College London","IntroductionAgeing affects immune function resulting in aberrant fever response to infection. We assess the effects of biological variables on basal temperature and temperature in COVID-19 infection, proposing an updated temperature threshold for older adults. MethodsParticipants: @@ -4139,13 +4029,6 @@ C_LIO_LIThe effective reproduction number is likely to remain stable or even red C_LIO_LIRelative incidence is likely to become lower in children, but higher in the C_LIO_LIolder (more vulnerable) age groups around the holiday period, which could lead to increased health care burden. C_LI",public and global health,fuzzy,100,100 -medRxiv,10.1101/2020.12.21.20248475,2020-12-22,https://medrxiv.org/cgi/content/short/2020.12.21.20248475,Clinical outcomes and risk factors for COVID-19 among migrant populations in high-income countries: a systematic review,Sally E Hayward; Anna Deal; Cherie Cheng; Alison F Crawshaw; Miriam Orcutt; Tushna F Vandrevala; Marrie Norredam; Manuel Carballo; Yusuf Ciftci; Ana Requena-Mendez; Chris Greenaway; Jessica Carter; Felicity Knights; Anushka Mehrotra; Farah Seedat; Kayvan Bozorgmehr; Apostolos Veizis; Ines Campos-Matos; Fatima Wurie; Teymur Noori; Martin McKee; Bernadette Kumar; Sally Hargreaves,"Institute for Infection and Immunity, St George's University of London; Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine; Institute for Infection and Immunity, St George's University of London; Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine; Institute for Infection and Immunity, St George's University of London; Institute for Infection and Immunity, St George's University of London; Institute for Global Health, University College London; Faculty of Business and Social Sciences, Kingston University; Danish Research Centre for Migration, Ethnicity and Health, University of Copenhagen; International Centre for Migration, Health, and Development; Doctors of the World UK; Department of Medicine-Solna, Karolinska Institutet; and Barcelona Institute for Global Health (ISGlobal-University of Barcelona); Department of Medicine, McGill University; Institute for Infection and Immunity, St George's University of London; Institute for Infection and Immunity, St George's University of London; Institute for Infection and Immunity, St George's University of London; Public Health England; Public Health, Bielefeld University; Section for Health Equity Studies & Migration, Heidelberg University Hospital; Medecins Sans Frontieres Greece; Public Health England; and UCL Collaborative Centre for Inclusion Health; Public Health England; and UCL Research Department of Epidemiology and Public Health; European Centre for Disease Prevention and Control (ECDC); Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine; Norwegian Institute of Public Health; Institute for Infection and Immunity, St George's University of London","BackgroundMigrants, including refugees, asylum seekers, labour migrants, and undocumented migrants, now constitute a considerable proportion of most high-income countries populations, including their skilled and unskilled workforces. Migrants may be at increased risk of COVID-19 due to their health and social circumstances, yet the extent to which they are being affected and their predisposing risk factors are not clearly understood. We did a systematic review to assess clinical outcomes of COVID-19 in migrant populations (cases, hospitalisations, deaths), indirect health and social impacts, and to determine key risk factors. - -MethodsWe did a systematic review following PRISMA guidelines, registered with PROSPERO (CRD42020222135). We searched databases including PubMed, Global Health, Scopus, CINAHL, and pre-print databases (medRxiv) via the WHO Global Research on COVID-19 database to Nov 18, 2020 for peer-reviewed and grey literature pertaining to migrants (defined as foreign born) and COVID-19 in 82 high-income countries. We used our international networks to source national datasets and grey literature. Data were extracted on our primary outcomes (cases, hospitalisations, deaths) and we evaluated secondary outcomes on indirect health and social impacts, and risk factors, using narrative synthesis. - -Results3016 data sources were screened with 158 from 15 countries included in the analysis (35 data sources for primary outcomes: cases [21], hospitalisations [4]; deaths [15]; 123 for secondary outcomes). We found that migrants are at increased risk of infection and are disproportionately represented among COVID-19 cases. Available datasets suggest a similarly disproportionate representation of migrants in reported COVID-19 deaths, as well as increased all-cause mortality in migrants in some countries in 2020. Undocumented migrants, migrant health and care workers, and migrants housed in camps and labour compounds may have been especially affected. In general, migrants have higher levels of many risk factors and vulnerabilities relevant to COVID-19, including increased exposure to SARS-CoV-2 due to high-risk occupations and overcrowded accommodation, and barriers to health care including inadequate information, language barriers, and reduced entitlement to healthcare coverage related to their immigration status. - -ConclusionsMigrants in high-income countries are at high risk of exposure to, and infection with, COVID-19. These data are of immediate relevance to national public health responses to the pandemic and should inform policymaking on strategies for reducing transmission of COVID-19 in this population. Robust data on testing uptake and clinical outcomes in migrants, and barriers and facilitators to COVID-19 vaccination, are urgently needed, alongside strengthening engagement with diverse migrant groups.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.12.18.20248477,2020-12-20,https://medrxiv.org/cgi/content/short/2020.12.18.20248477,Face covering adherence is positively associated with better mental health and wellbeing: a longitudinal analysis of the CovidLife surveys,Drew M Altschul; Chloe Fawns-Ritchie; Alex Kwong; Louise Hartley; Clifford Nangle; Rachel Edwards; Rebecca Dawson; Christie Levein; Archie Campbell; Robin Flaig; Andrew McIntosh; Ian Deary; Riccardo Marioni; Caroline Hayward; Cathie Sudlow; Elaine Douglas; David Bell; David Porteous,The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; University of Stirling; University of Stirling; The University of Edinburgh,"Face masks or coverings are effective at reducing airborne infection rates, yet pandemic mitigation measures, including wearing face coverings, have been suggested to contribute to reductions in quality of life and poorer mental health. Longitudinal analyses of more than 11,000 participants across the UK found no association between lower adherence to face covering guidelines and poorer mental health. The opposite appears to be true. Even after controlling for behavioral, social, and psychological confounds, including measures of pre-pandemic mental health, individuals who wore face coverings ""most of the time"" or ""always"" had better mental health and wellbeing than those who did not. These results suggest that wearing face coverings more often will not negatively impact mental health.",psychiatry and clinical psychology,fuzzy,100,100 medRxiv,10.1101/2020.12.16.20247684,2020-12-18,https://medrxiv.org/cgi/content/short/2020.12.16.20247684,International Comparisons of Harmonized Laboratory Value Trajectories to Predict Severe COVID-19: Leveraging the 4CE Collaborative Across 342 Hospitals and 6 Countries: A Retrospective Cohort Study,Griffin M Weber; Chuan Hong; Nathan P Palmer; Paul Avillach; Shawn N Murphy; Alba Gutiérrez-Sacristán; Zongqi Xia; Arnaud Serret-Larmande; Antoine Neuraz; Gilbert S. Omenn; Shyam Visweswaran; Jeffrey G Klann; Andrew M South; Ne Hooi Will Loh; Mario Cannataro; Brett K Beaulieu-Jones; Riccardo Bellazzi; Giuseppe Agapito; Mario Alessiani; Bruce J Aronow; Douglas S Bell; Antonio Bellasi; Vincent Benoit; Michele Beraghi; Martin Boeker; John Booth; Silvano Bosari; Florence T Bourgeois; Nicholas W Brown; Mauro Bucalo; Luca Chiovato; Lorenzo Chiudinelli; Arianna Dagliati; Batsal Devkota; Scott L DuVall; Robert W Follett; Thomas Ganslandt; Noelia García Barrio; Tobias Gradinger; Romain Griffier; David A Hanauer; John H Holmes; Petar Horki; Kenneth M Huling; Richard W Issitt; Vianney Jouhet; Mark S Keller; Detlef Kraska; Molei Liu; Yuan Luo; Kristine E Lynch; Alberto Malovini; Kenneth D Mandl; Chengsheng Mao; Anupama Maram; Michael E Matheny; Thomas Maulhardt; Maria Mazzitelli; Marianna Milano; Jason H Moore; Jeffrey S Morris; Michele Morris; Danielle L Mowery; Thomas P Naughton; Kee Yuan Ngiam; James B Norman; Lav P Patel; Miguel Pedrera Jimenez; Rachel B Ramoni; Emily R Schriver; Luigia Scudeller; Neil J Sebire; Pablo Serrano Balazote; Anastasia Spiridou; Amelia LM Tan; Byorn W.L. Tan; Valentina Tibollo; Carlo Torti; Enrico M Trecarichi; Michele Vitacca; Alberto Zambelli; Chiara Zucco; - The Consortium for Clinical Characterization of COVID-19 by EHR (4CE); Isaac S Kohane; Tianxi Cai; Gabriel A Brat,"Harvard Medical School; Harvard Medical School; Harvard Medical School; Harvard Medical School; Massachusetts General Hospital; Harvard Medical School; University of Pittsburgh; Hôpital Européen Georges Pompidou, Assistance Publique - Hôpitaux de Paris; Hôpital Necker-Enfants Malade, Assistance Publique Hopitaux de Paris (APHP), University of Paris; University of Michigan; University of Pittsburgh; Massachusetts General Hospital; Brenner Children's Hospital, Wake Forest School of Medicine; National University Health System, Singapore; University Magna Graecia of Catanzaro, Italy; Harvard Medical School; University of Pavia, Italy; University Magna Graecia of Catanzaro, Italy; ASST Pavia, Lombardia Region Health System; Cincinnati Children's Hospital Medical Center, University of Cincinnati; David Geffen School of Medicine at UCLA; ASST Papa Giovanni XXIII, Bergamo; APHP Greater Paris University Hospital; ASST Pavia; Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany; Great Ormond Street Hospital for Children, UK; IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano; Harvard Medical School; Harvard Medical School; BIOMERIS (BIOMedical Research Informatics Solutions); Istituti Clinici Scientifici Maugeri SpA SB IRCCS; ASST Papa Giovanni XXIII, Bergamo; University of Pavia, Italy; The Children's Hospital of Philadelphia; VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System; David Geffen School of Medicine at UCLA; University Medicine Mannheim, Heidelberg University; Hospital Universitario 12 de Octubre, Madrid, Spain; University Medicine Mannheim, Heidelberg University; Bordeaux University Hospital; University of Michigan; University of Pennsylvania Perelman School of Medicine; Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany; Harvard Medical School; Great Ormond Street Hospital for Children, UK; Bordeaux University Hospital; Harvard Medical School; University Hospital Erlangen; Harvard School of Public Health; Northwestern University; VA Informatics and Computing Infrastructure; Istituti Clinici Scientifici Maugeri SpA SB IRCCS, Pavia, Italy.; Boston Children's Hospital; Northwestern University; Harvard Medical School; Tennessee Valley Healthcare System Veterans Affairs Medical Center; Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany; University Magna Graecia of Catanzaro, Italy; University Magna Graecia of Catanzaro, Italy; University of Pennsylvania Perelman School of Medicine; University of Pennysylvania Perelman School of Medicine; University of Pittsburgh; University of Pennsylvania Perelman School of Medicine; Harvard Medical School; National Univerisity Health Systems Singapore; Harvard Medical School; University Of Kansas Medical Center; Hospital Universitario 12 de Octubre, Madrid, Spain; Department of Veterans Affairs; University of Pennsylvania Health System; IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano; Great Ormond Street Hospital for Children NIHR BRC, UK; Hospital Universitario 12 de Octubre, Madrid, Spain; Great Ormond Street Hospital for Children, UK; Harvard Medical School; National University Hospital, Singapore; Istituti Clinici Scientifici Maugeri SpA SB IRCCS, Pavia, Italy.; University Magna Graecia of Catanzaro, Italy; University Magna Graecia of Catanzaro, Italy; ICS S. Maugeri IRCCS Pavia Italy; ASST Papa Giovanni XXIII, Bergamo; University Magna Graecia of Catanzaro, Italy; ; Harvard Medical School; Harvard Medical School; Harvard Medical School","ObjectivesTo perform an international comparison of the trajectory of laboratory values among hospitalized patients with COVID-19 who develop severe disease and identify optimal timing of laboratory value collection to predict severity across hospitals and regions. @@ -4229,7 +4112,6 @@ ResultsRates of cholesterol, blood pressure, HbA1c and INR recording dropped by Following the immediate drop, rates of recorded tests increased on average by 5-9% per week until 27th September 2020. However, the number of recorded measures remained below that expected for the time of year, reaching 51.8% (95% CI 51.8 to 51.9%) for blood pressure, 63.7%, (95% CI 63.7% to 63.8%) for cholesterol measurement and 70.3% (95% CI 70.2% to 70.4%) for HbA1c. Rates of INR recording declined throughout the previous two years, a trend that continued after lockdown. There were no differences in the times series trends based on sex, age, ethnicity or deprivation. ConclusionsCardiovascular disease monitoring in English primary care declined substantially from the time of the first UK lockdown. Despite a consistent recovery in activity, there is still a substantial shortfall in the numbers of recorded measurements to those expected. Strategies are required to ensure cardiovascular disease monitoring is maintained during the COVID-19 pandemic.",primary care research,fuzzy,100,100 -medRxiv,10.1101/2020.12.10.20247155,2020-12-14,https://medrxiv.org/cgi/content/short/2020.12.10.20247155,Self-harm presentations to Emergency Departments and Place of Safety during the first wave of the UK COVID-19 pandemic: South London and Maudsley data on service use from February to June 2020.,Eleanor Nuzum; Evangelia Martin; Gemma Morgan; Rina Dutta; Christoph Mueller; Catherine Polling; Megan Pritchard; Sumithra Velupillai; Robert Stewart,South London and Maudsley NHS Foundation Trust; South London and Maudsley NHS Foundation Trust; South London and Maudsley NHS Foundation Trust; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London,"The lockdown and social distancing policy imposed due to the COVID-19 pandemic has had a substantial impact on both mental health service delivery, and the ways in which people are accessing these services. Previous reports from the South London and Maudsley NHS Trust (SLaM; a large mental health service provider for around 1.2m residents in South London) have highlighted increased use of virtual contacts by mental health teams, with dropping numbers of face-to-face contacts over the first wave of the pandemic. There has been concern that the impact of the COVID-19 pandemic would lead to higher mental health emergencies, particularly instances of self-harm. However, with people advised to stay at home during the first wave lockdown, it is as yet unclear whether this impacted mental health service presentations. Taking advantage of SLaMs Clinical Records Interactive Search (CRIS) data resource with daily updates of information from its electronic mental health records, this paper describes overall presentations to Emergency Department (ED) mental health liaison teams, and those with self-harm. The paper focussed on three periods: i) a pre-lockdown period 1st February to 15th March, ii) a lockdown period 16th March to 10th May and iii) a post-lockdown period 11th May to 28th June. In summary, all attendances to EDs for mental health support decreased during the lockdown period, including those with self-harm. All types of self-harm decreased during lockdown, with self-poisoning remaining the most common. Attendances to EDs for mental health support increased post-lockdown, although were only just approaching pre-lockdown levels by the end of June 2020.",psychiatry and clinical psychology,fuzzy,100,100 medRxiv,10.1101/2020.12.05.20241927,2020-12-11,https://medrxiv.org/cgi/content/short/2020.12.05.20241927,Neutralising antibodies drive Spike mediated SARS-CoV-2 evasion,Steven A Kemp; Dami A Collier; Rawlings Datir; Isabella ATM Ferreira; Salma Gayed; Aminu Jahun; Myra Hosmillo; Chloe Rees-Spear; Petra Mlcochova; Ines Ushiro Lumb; David Roberts; Anita Chandra; Nigel Temperton; - The COVID-19 Genomics UK (COG-UK) Consortium; Katherine Sharrocks; Elizabeth Blane; - The CITIID-NIHR BioResource COVID-19 Collaboration; John A Briggs; Marit van Gils; Ken G Smith; John R Bradley; Chris Smith; Rainer Doffinger; Lourdes Ceron-Gutierrez; Gabriela Barcenas-Morales; David Pollock; Richard Goldstein; Anna Smielewska; Jordan P Skittrall; Theo Gouliouris; Ian G Goodfellow; Effrossyni Gkrania-Klotsas; Chris JR Illingworth; Laura E McCoy; Ravindra K Gupta,"Division of Infection and Immunity, University College London, London, UK; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK.; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK.; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK.; Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK.; Department of Pathology, University of Cambridge, Cambridge; Department of Pathology, University of Cambridge, Cambridge; Division of Infection and Immunity, University College London, London, UK.; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK.; Public Health England, Colindale, London, UK; Public Health England, Colindale, London, UK; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK.; Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, UK; -; Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK.; Department of Medicine, University of Cambridge, Cambridge, UK.; -; Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.; University of Amsterdam; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK.; NIHR Cambridge Clinical Research Facility, Cambridge, UK.; Department of Applied Mathematics and Theoretical Physics, University of Cambridge, UK; Addenbrookes Hospital; Addenbrookes Hospital; Addenbrookes Hospital; University of Colorado School of Medicine; Division of Infection & Immunity, University College London, UK; Department of Virology, Cambridge University NHS Hospitals Foundation Trust; Clinical Microbiology and Public Health Laboratory, Addenbrookes Hospital, Cambridge, UK; Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK.; Department of Pathology, University of Cambridge, Cambridge; Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK.; MRC Biostatistics Unit, University of Cambridge, Cambridge, UK; Division of Infection and Immunity, University College London, London, UK; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK.","SARS-CoV-2 Spike protein is critical for virus infection via engagement of ACE2, and amino acid variation in Spike is increasingly appreciated. Given both vaccines and therapeutics are designed around Wuhan-1 Spike, this raises the theoretical possibility of virus escape, particularly in immunocompromised individuals where prolonged viral replication occurs. Here we report chronic SARS-CoV-2 with reduced sensitivity to neutralising antibodies in an immune suppressed individual treated with convalescent plasma, generating whole genome ultradeep sequences by both short and long read technologies over 23 time points spanning 101 days. Although little change was observed in the overall viral population structure following two courses of remdesivir over the first 57 days, N501Y in Spike was transiently detected at day 55 and V157L in RdRp emerged. However, following convalescent plasma we observed large, dynamic virus population shifts, with the emergence of a dominant viral strain bearing D796H in S2 and{Delta} H69/{Delta}V70 in the S1 N-terminal domain NTD of the Spike protein. As passively transferred serum antibodies diminished, viruses with the escape genotype diminished in frequency, before returning during a final, unsuccessful course of convalescent plasma. In vitro, the Spike escape double mutant bearing{Delta} H69/{Delta}V70 and D796H conferred decreased sensitivity to convalescent plasma, whilst maintaining infectivity similar to wild type. D796H appeared to be the main contributor to decreased susceptibility, but incurred an infectivity defect. The{Delta} H69/{Delta}V70 single mutant had two-fold higher infectivity compared to wild type and appeared to compensate for the reduced infectivity of D796H. Consistent with the observed mutations being outside the RBD, monoclonal antibodies targeting the RBD were not impacted by either or both mutations, but a non RBD binding monoclonal antibody was less potent against{Delta} H69/{Delta}V70 and the double mutant. These data reveal strong selection on SARS-CoV-2 during convalescent plasma therapy associated with emergence of viral variants with reduced susceptibility to neutralising antibodies.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.12.08.20246231,2020-12-11,https://medrxiv.org/cgi/content/short/2020.12.08.20246231,Artificial intelligence-enabled analysis of UK and US public attitudes on Facebook and Twitter towards COVID-19 vaccinations,Amir Hussain; Ahsen Tahir; Zain Hussain; Zakariya Sheikh; Mandar Gogate; Kia Dashtipour; Azhar Ali; Aziz Sheikh,"Edinburgh Napier University, UK; Edinburgh Napier University, UK; Edinburgh Medical School, College of Medicine and Veterinary Medicine, University of Edinburgh, UK; Edinburgh Medical School, College of Medicine and Veterinary Medicine, University of Edinburgh, UK; Edinburgh Napier University, UK; Edinburgh Napier University, UK; NHS Forth Medical Group, UK & Harvard T.H. Chan School of Public Health, USA; Usher Institute, Edinburgh Medical School, University of Edinburgh, UK","BackgroundGlobal efforts towards the development and deployment of a vaccine for SARS-CoV-2 are rapidly advancing. We developed and applied an artificial-intelligence (AI)-based approach to analyse social-media public sentiment in the UK and the US towards COVID-19 vaccinations, to understand public attitude and identify topics of concern. @@ -4264,20 +4146,6 @@ MethodsWorking on behalf of NHS England we conducted a population cohort based s Results20,000 of 164,000 warfarin patients (12.2%) switched to DOACs between March and May 2020, most commonly to edoxaban and apixaban. Factors associated with switching included: older age, recent renal function test, higher number of recent INR tests recorded, atrial fibrillation diagnosis and care home residency. There was a sharp rise in co-prescribing of warfarin and DOACs from typically 50-100 per month to 246 in April 2020, 0.06% of all people receiving a DOAC or warfarin. INR testing fell by 14% to 506.8 patients tested per 1000 warfarin patients each month. We observed a very small increase in elevated INRs (n=470) during April compared with January (n=420). ConclusionsIncreased switching of anticoagulants from warfarin to DOACs was observed at the outset of the COVID-19 pandemic in England following national guidance. There was a small but substantial number of people co-prescribed warfarin and DOACs during this period. Despite a national safety alert on the issue, a widespread rise in elevated INR test results was not found. Primary care has responded rapidly to changes in patient care during the COVID-19 pandemic.",cardiovascular medicine,fuzzy,100,100 -medRxiv,10.1101/2020.11.30.20240010,2020-12-03,https://medrxiv.org/cgi/content/short/2020.11.30.20240010,Is Point-of-Care testing feasible and safe in care homes in England? An exploratory usability and accuracy evaluation of Point-of-Care Polymerase Chain Reaction test for SARS-COV-2,Massimo Micocci; Adam Gordon; Mikyung Kelly Seo; Joy A Allen; Kerrie Davies; Dan Lasserson; Carl Thompson; Karen Spilsbury; Cyd Akrill; Ros Heath; Anita Astle; Claire Sharpe; Rafael Perera; Gail Hayward; Peter Buckle,"NIHR London In Vitro Diagnostics Co-operative, Dept of Surgery and Cancer, Faculty of Medicine, Imperial College London St. Mary's Hospital London; Division of Medical Sciences and Graduate Entry Medicine, University of Nottingham, Nottingham, UK;NIHR Applied Research Collaboration-East Midlands (ARC-EM), N; NIHR London In Vitro Diagnostics Co-operative, Dept of Surgery and Cancer, Faculty of Medicine, Imperial College London St. Mary's Hospital London; NIHR Newcastle In Vitro Diagnostics Co-operative, Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK; Healthcare Associated Infections Research Group, University of Leeds and Leeds Teaching Hospitals NHS Trust, Leeds, UK; Warwick Medical School, University of Warwick, UK; School of Healthcare, University of Leeds, Leeds, UK; School of Healthcare, University of Leeds, Leeds, UK; NIHR Applied Research Collaboration Yorkshire and Humber, UK; Springfield Healthcare, Leeds, UK; Landermeads Nursing Home, Nottingham, UK; Wren Hall Nursing Home, Selston, UK; Ashmere Nottinghamshire Ltd, Notts, UK; Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; NIHR Community Healthcare MedTech and IVD Co-operative,Oxford,UK; NIHR London In Vitro Diagnostics Co-operative, Dept of Surgery and Cancer, Faculty of Medicine, Imperial College London St. Mary's Hospital London","IntroductionReliable rapid testing on COVID-19 is needed in care homes to reduce the risk of outbreaks and enable timely care. Point-of-care testing (POCT) in care homes could provide rapid actionable results. This study aimed to examine the usability and test performance of point of care polymerase chain reaction (PCR) for COVID-19 in care homes. - -MethodsPoint-of-care PCR for detection of SARS-COV2 was evaluated in a purposeful sample of four UK care homes. Test agreement with laboratory real-time PCR and usability and use errors were assessed. - -ResultsPoint of care and laboratory polymerase chain reaction (PCR) tests were performed on 278 participants. The point of care and laboratory tests returned uncertain results or errors for 17 and 5 specimens respectively. Agreement analysis was conducted on 256 specimens. 175 were from staff: 162 asymptomatic; 13 symptomatic. 69 were from residents: 59 asymptomatic; 10 symptomatic. Asymptomatic specimens showed 83.3% (95% CI: 35.9%-99.6%) positive agreement and 98.7% negative agreement (95% CI: 96.2%-99.7%), with overall prevalence and bias-adjusted kappa (PABAK) of 0.965 (95% CI: 0.932 - 0.999). Symptomatic specimens showed 100% (95% CI: 2.5%-100%) positive agreement and 100% negative agreement (95% CI: 85.8%-100%), with overall PABAK of 1. No usability-related hazards emerged from this exploratory study. - -ConclusionApplications of point-of-care PCR testing in care homes can be considered with appropriate preparatory steps and safeguards. Agreement between POCT and laboratory PCR was good. Further diagnostic accuracy evaluations and in-service evaluation studies should be conducted, if the test is to be implemented more widely, to build greater certainty on this initial exploratory analysis. - -Key pointsO_LIPoint of care tests (POCT) in care homes are feasible and could increase testing capacity for the control of COVID-19 infection. -C_LIO_LIThe test of agreement between POCT and laboratory PCR for care home residents and the staff was good. -C_LIO_LIAdoption of POCT in care homes can be considered with appropriate preparatory steps and safeguards in place. -C_LIO_LIRepetitive errors and test malfunctioning can be mitigated with bespoke training for care home staff. -C_LIO_LIIntegrated care pathways should be investigated to test the high variability of the context of use. -C_LI",health systems and quality improvement,fuzzy,90,100 medRxiv,10.1101/2020.12.01.20241729,2020-12-03,https://medrxiv.org/cgi/content/short/2020.12.01.20241729,International estimates of intended uptake and refusal of COVID-19 vaccines: A rapid systematic review and meta-analysis of large nationally representative samples,Eric Robinson; Andrew Jones; India Lesser; Michael Daly,University of Liverpool; University of Liverpool; University of Liverpool; Maynooth University,"BackgroundWidespread uptake of COVID-19 vaccines will be essential to extinguishing the COVID-19 pandemic. Vaccines have been developed in unprecedented time and hesitancy towards vaccination among the general population is unclear. MethodsSystematic review and meta-analysis of studies using large nationally representative samples (n[≥]1000) to examine the percentage of the population intending to vaccinate, unsure, or intending to refuse a COVID-19 vaccine when available. Generic inverse meta-analysis and meta-regression were used to pool estimates and examine time trends. PubMed, Scopus and pre-printer servers were searched from January-November, 2020. Registered on PROSPERO (CRD42020223132). @@ -4375,21 +4243,6 @@ ResultsA total of 563 participants (49 years mean age; 60% women) had available ConclusionsHigh level of knowledge about the COVID-19 pandemic and trust in the Greek authorities was observed, possibly due to the plethora of good quality publicly available information and the timely management of the pandemic at its early stages in Greece. Information campaigns for the COVID-19 pandemic should be encouraged even after the lifting of lockdown measures to increase public awareness.",public and global health,fuzzy,100,100 medRxiv,10.1101/2020.11.11.20229500,2020-11-13,https://medrxiv.org/cgi/content/short/2020.11.11.20229500,Association of social distancing and masking with risk of COVID-19,Sohee Kwon; Amit D. Joshi; Chun-Han Lo; David Alden Drew; Long Nguyen; Chuan-Guo Guo; Wenjie Ma; Raaj S. Mehta; Erica T. Warner; Christina M. Astley; Jordi Merino; Benjamin Murray; Jonathan Wolf; Sebastien Ourselin; Claire Steves; Timothy Spector; Jaime E. Hart; Mingyang Song; Trang VoPham; Andrew T. Chan,Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital and Harvard Medical School; Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Boston Children's Hospital; Massachusetts General Hospital; King's College London; Zoe Global Limited; King's College London; King's College London; King's College London; Harvard T.H. Chan School of Public Health; Massachusetts General Hospital; Fred Hutchinson Cancer Research Center; Massachusetts General Hospital,"Given the continued burden of severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) disease (COVID-19) across the U.S., there is a high unmet need for data to inform decision-making regarding social distancing and universal masking. We examined the association of community-level social distancing measures and individual masking with risk of predicted COVID-19 in a large prospective U.S. cohort study of 198,077 participants. Individuals living in communities with the greatest social distancing had a 31% lower risk of predicted COVID-19 compared with those living in communities with poor social distancing. Self-reported masking was associated with a 63% reduced risk of predicted COVID-19 even among individuals living in a community with poor social distancing. These findings provide support for the efficacy of mask-wearing even in settings of poor social distancing in reducing COVID-19 transmission. In the current environment of relaxed social distancing mandates and practices, universal masking may be particularly important in mitigating risk of infection.",infectious diseases,fuzzy,94,100 -medRxiv,10.1101/2020.11.10.20229278,2020-11-13,https://medrxiv.org/cgi/content/short/2020.11.10.20229278,Changing probability of experiencing food insecurity by socioeconomic and demographic groups during the COVID-19 pandemic in the UK,Jonathan Koltai; Veronica Toffolutti; Martin McKee; David Stuckler,Bocconi University; Bocconi University; The London School of Hygiene & Tropical Medicine; Bocconi University,"BackgroundFood supply concerns have featured prominently in the UK response to the COVID-19 pandemic. We assess changes in food insecurity in the UK population from April to July 2020. - -MethodWe analyze 11,095 respondents from the April through July waves of the Understanding Society COVID-19 longitudinal study survey linked with Wave 9 of the UK Understanding Society study. Food insecurity was defined as having used a food bank in the last 4 weeks; being hungry but not eating in the last week; or not able to eat healthy and nutritious food in the last week. Unadjusted estimates to examine changes in population prevalence and logistic regression were used to assess the association between employment transitions and food insecurity. - -FindingsThe prevalence of reporting at least one form of food insecurity rose from 7{middle dot}1% in April to 20{middle dot}2% by July 2020. Some of the largest increases were among Asian respondents (22{middle dot}91 percentage points), the self-employed (15{middle dot}90 percentage points), and 35-44-year-olds (17{middle dot}08 percentage points). In logistic regression models, those moving from employment to unemployment had higher odds of reporting food insecurity relative to furloughed individuals (OR = 2{middle dot}23; 95% CI: 1{middle dot}20-4{middle dot}131) and to the persistently employed (OR=2{middle dot}38; 95% CI: 1{middle dot}33-4{middle dot}27), adjusting for sociodemographic characteristics. Furloughed individuals did not differ significantly in their probability of experiencing food insecurity compared to the persistently employed (OR=1{middle dot}07; 95% CI: 0{middle dot}83 to 1{middle dot}37). - -InterpretationFood insecurity has increased substantially in the UK. Steps are needed to provide subsidies or food support to vulnerable groups. - -O_TEXTBOXEvidence before this studyWe searched Google Scholar with the terms ""COVID-19"" and ""food insecurity"" and ""UK""; and ""food insecurity"" and ""UK"" and ""coronavirus"", published between January 1st and October 31st, 2020. One cross-sectional report was identified, which found higher levels of food insecurity in early April 2020 relative to 2018. Importantly, the report relied on items used to measure food insecurity that referred to a 12-month time span in 2018 and then a 30-day time span in April 2020, a potential source of bias for examining changes in population prevalence over time. - -Added value of this studyHere we provide the first longitudinal national probability study that tracks temporal changes in population prevalence of food insecurity several months following the initial COVID-19-related lockdown measures in the UK. The prevalence of food insecurity rose for all socioeconomic and demographic and groups from April to July 2020, but did so for some more than others. Some of the largest increases in food insecurity were among Asian respondents, the self-employed, respondents aged 35-44, and those living in Scotland, London, and the North West of England. At the individual level, losing employment was associated with a higher odds of food insecurity compared to those furloughed under the Coronavirus Job Retention Scheme and the persistently employed. Importantly, furloughed individuals did not differ in their probability of food insecurity relative to the persistently employed. - -Implications of all the available evidenceThis study documents an alarming increase in food insecurity in the United Kingdom during the pandemic, with important implications for policy. While Coronavirus the Job Retention Scheme appeared to have conferred some protection, it is clear that not enough has been done to mitigate overall increases food insecurity in the UK. Steps are needed to provide subsidies or food support, especially since during the pandemic emergency food assistance may not be readily accessible. Taken together our results show that, while COVID is first of all a health crisis, it also has potential to become an escalating social and economic crisis if steps are not taken to protect the weak. - -C_TEXTBOX",public and global health,fuzzy,100,100 medRxiv,10.1101/2020.11.11.20220962,2020-11-13,https://medrxiv.org/cgi/content/short/2020.11.11.20220962,Short-term forecasts to inform the response to the COVID-19 epidemic in the UK,Sebastian Funk; Sam Abbott; Benjamin D Atkins; Marc Baguelin; J Kenneth Baillie; Paul J Birrell; Joshua Blake; Nikos I Bosse; Joshua Burton; Jonathan Carruthers; Nicholas G Davies; Daniela de Angelis; Louise Dyson; W. John Edmunds; Rosalind M Eggo; Neil M Ferguson; Katy A M Gaythorpe; Erin Gorsich; Glen Guyver-Fletcher; Joel Hellewell; Edward M Hill; Alexander Holmes; Thomas A House; Chris Jewell; Mark Jit; Thibaut Jombart; Indra Joshi; Matt J Keeling; Edward Kendall; Edward S Knock; Adam J Kucharski; Katrina A Lythgoe; Sophie R Meakin; James D Munday; Peter JM Openshaw; Christopher Overton; Filippo Pagani; Jonathan Pearson; Pablo N Perez-Guzman; Lorenzo Pellis; Francesca Scarabel; Malcolm Gracie Semple; Ming Tang; Michael Tildesley; Edwin van Leeuwen; Lilith Whittles; - CMMID COVID-19 Working Group; - Imperial College COVID-19 Response Team; - ISARIC4C Investigators,"London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; University of Warwick; Imperial College; Roslin Institute, University of Edinburgh; Public Health England; University of Cambridge; London School of Hygiene & Tropical Medicine; University of Manchester; Public Health England; London School of Hygiene and Tropical Medicine; University of Cambridge; University of Warwick; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; Imperial College; Imperial College London; University of Warwick; University of Warwick; London School of Hygiene & Tropical Medicine; University of Warwick; University of Warwick; University of Manchester; Lancaster University; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; NHSX; University of Warwick; NHS England & NHS Improvement; Imperial College; London School of Hygiene & Tropical Medicine; University of Oxford; London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; Imperial College London; Manchester University; Manchester University; NHSX; Imperial College; The University of Manchester; York University; University of Liverpool; NHS England & NHSE Improvement; University of Warwick; Public Health England; Imperial College; ; ; ","BackgroundShort-term forecasts of infectious disease can aid situational awareness and planning for outbreak response. Here, we report on multi-model forecasts of Covid-19 in the UK that were generated at regular intervals starting at the end of March 2020, in order to monitor expected healthcare utilisation and population impacts in real time. MethodsWe evaluated the performance of individual model forecasts generated between 24 March and 14 July 2020, using a variety of metrics including the weighted interval score as well as metrics that assess the calibration, sharpness, bias and absolute error of forecasts separately. We further combined the predictions from individual models into ensemble forecasts using a simple mean as well as a quantile regression average that aimed to maximise performance. We compared model performance to a null model of no change. @@ -4415,6 +4268,7 @@ C_LI How might this impact on clinical practice or future developments?O_LIVariable shielding behaviour amongst patients with IMIDs may be an important confounder when considering differential COVID-19 risk between therapy types, so should be accounted for in analyses where possible. C_LI",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2020.11.06.20227108,2020-11-07,https://medrxiv.org/cgi/content/short/2020.11.06.20227108,Primary school staff reflections on school closures due to COVID-19 and recommendations for the future: a national qualitative survey,Emily Marchant; Charlotte Todd; Michaela James; Tom Crick; Russell Dwyer; Sinead Brophy,Swansea University; Swansea University; Swansea University; Swansea University; St Thomas Community Primary School; Swansea University,"School closures due to the COVID-19 global pandemic are likely to have a range of negative consequences spanning the domains of child development, education and health, in addition to the widening of inequalities and inequities. Research is required to improve understanding of the impact of school closures on the education, health and wellbeing of pupils and school staff, the challenges posed during reopening and importantly to identify how countries can return to in-school education and to inform policy. This qualitative study aimed to reflect on the perspectives and experiences of primary school staff (pupils aged 3-11) in Wales regarding school closures and the initial reopening of schools and to identify recommendations for the future. A total of 208 school staff completed a national online survey through the HAPPEN primary school network, consisting of questions about school closures (March to June 2020), the phased reopening of schools (June to July 2020) and a return to full-time education. Thematic analysis of survey responses highlighted that primary school staff perceive that gaps in learning, health and wellbeing have increased and inequalities have widened during school closures. Findings from this study identified five recommendations; (i) prioritise the health and wellbeing of pupils and staff; (ii) focus on enabling parental engagement and support; (iii) improve digital competence amongst pupils, teachers and parents; (iv) consider opportunities for smaller class sizes and additional staffing; and (v) improve the mechanism of communication between schools and families, and between government and schools.",public and global health,fuzzy,100,100 medRxiv,10.1101/2020.11.05.20223289,2020-11-06,https://medrxiv.org/cgi/content/short/2020.11.05.20223289,Longitudinal proteomic profiling of high-risk patients with COVID-19 reveals markers of severity and predictors of fatal disease,Jack Gisby; Candice L Clarke; Nicholas Medjeral-Thomas; Talat H Malik; Artemis Papadaki; Paige M Mortimer; Norzawani B Buang; Shanice Lewis; Marie Pereira; Frederic Toulza; Ester Fagnano; Marie-Anne Mawhin; Emma E Dutton; Lunnathaya Tapeng; Arianne C Richard; Paul Kirk; Jacques Behmoaras; Eleanor Sandhu; Stephen P McAdoo; Maria F Prendecki; Matthew C Pickering; Marina Botto; Michelle Willicombe; David C Thomas; James E. Peters,Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; University of Cambridge; MRC Biostatistics Unit University of Cambridge; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London,"End-stage kidney disease (ESKD) patients are at high risk of severe COVID-19. We measured 436 circulating proteins in serial blood samples from hospitalised and non-hospitalised ESKD patients with COVID-19 (n=256 samples from 55 patients). Comparison to 51 non-infected patients revealed 221 differentially expressed proteins, with consistent results in a separate subcohort of 46 COVID-19 patients. 203 proteins were associated with clinical severity, including IL6, markers of monocyte recruitment (e.g. CCL2, CCL7), neutrophil activation (e.g. proteinase-3) and epithelial injury (e.g. KRT19). Machine learning identified predictors of severity including IL18BP, CTSD, GDF15, and KRT19. Survival analysis with joint models revealed 69 predictors of death. Longitudinal modelling with linear mixed models uncovered 32 proteins displaying different temporal profiles in severe versus non-severe disease, including integrins and adhesion molecules. These data implicate epithelial damage, innate immune activation, and leucocyte-endothelial interactions in the pathology of severe COVID-19 and provide a resource for identifying drug targets.",infectious diseases,fuzzy,100,100 bioRxiv,10.1101/2020.11.06.369439,2020-11-06,https://biorxiv.org/cgi/content/short/2020.11.06.369439,Allosteric hotspots in the main protease of SARS-CoV-2,Léonie Strömich; Nan Wu; Mauricio Barahona; Sophia N Yaliraki,Imperial College London; Imperial College London; Imperial College London; Imperial College London,"AO_SCPLOWBSTRACTC_SCPLOWInhibiting the main protease of SARS-CoV-2 is of great interest in tackling the COVID-19 pandemic caused by the virus. Most efforts have been centred on inhibiting the binding site of the enzyme. However, considering allosteric sites, distant from the active or orthosteric site, broadens the search space for drug candidates and confers the advantages of allosteric drug targeting. Here, we report the allosteric communication pathways in the main protease dimer by using two novel fully atomistic graph theoretical methods: Bond-to-bond propensity analysis, which has been previously successful in identifying allosteric sites without a priori knowledge in benchmark data sets, and, Markov transient analysis, which has previously aided in finding novel drug targets in catalytic protein families. We further score the highest ranking sites against random sites in similar distances through statistical bootstrapping and identify four statistically significant putative allosteric sites as good candidates for alternative drug targeting.",bioinformatics,fuzzy,100,100 medRxiv,10.1101/2020.11.01.20224014,2020-11-04,https://medrxiv.org/cgi/content/short/2020.11.01.20224014,MODELLING PRESYMPTOMATIC INFECTIOUSNESS IN COVID-19,Russell Cheng; Christopher Dye; John Dagpunar; Brian Williams,University of Southampton; Oxford University; University of Southampton; Stellenbosch University,"This paper considers SEPIR, the extension of an existing parametric SEIR continuous simulation compartment model. Both models can be fitted to real data as they include parameters that can simply be estimated from the data. However SEPIR deploys an additional presymptomatic (also called asymptomatic) infectious stage that is not included in SEIR but which is known to exist in COVID-19. This stage is also parametrised and so can be fitted to data. Both SEPIR and the existing SEIR model assume a homogeneous mixing population, an idealisation that is unrealistic in practice when dynamically varying control strategies are deployed against virus. This means that if either model is to represent more than just a single period in the behaviour of the epidemic, then the parameters of the model will have to be time dependent. This issue is also discussed in this paper.",epidemiology,fuzzy,93,100 @@ -4485,6 +4339,7 @@ Research in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched MEDLINE Added value of this studyThis is the first population-based study to investigate whether the risk of recorded SARS-CoV-2 infection and severe outcomes from COVID-19 differ between adults living in households with and without school-aged children during the UK pandemic. Our findings show that for adults living with children there is no evidence of an increased risk of severe COVID-19 outcomes although there may be a slightly increased risk of recorded SARS-CoV-2 infection for working-age adults living with children aged 12 to 18 years. Working-age adults living with children 0 to 11 years have a lower risk of death from COVID-19 compared to adults living without children, with the effect size being comparable to their lower risk of death from any cause. We observed no consistent changes in risk of recorded SARS-CoV-2 infection and severe outcomes from COVID-19 comparing periods before and after school closure. Implications of all the available evidenceOur results demonstrate no evidence of serious harms from COVID-19 to adults in close contact with children, compared to those living in households without children. This has implications for determining the benefit-harm balance of children attending school in the COVID-19 pandemic.",epidemiology,fuzzy,100,100 +bioRxiv,10.1101/2020.11.01.362319,2020-11-02,https://biorxiv.org/cgi/content/short/2020.11.01.362319,Robust SARS-CoV-2-specific T-cell immunity is maintained at 6 months following primary infection,Jianmin Zuo; Alex Dowell; Hayden Pearce; Kriti Verma; Heather Long; Jusnara Begum; Felicity Aiano; Zahin Amin-Chowdhury; Bassam Hallis; Lorrain Stapley; Ray Borrow; Ezra Linley; Shazaad Ahmad; Ben Parker; Alex Horsley; Gayatri Amirthalingam; Kevin Brown; Mary E Ramsay; Shamez Ladhani; Paul Moss,"Institute of Immunology and Immunotherapy, University of Birmingham; Institute of Immunology and Immunotherapy, University of Birmingham; Institute of Immunology and Immunotherapy, University of Birmingham; Institute of Immunology and Immunotherapy, University of Birmingham; Institute of Immunology and Immunotherapy, University of Birmingham; Institute of Immunology and Immunotherapy, University of Birmingham; Immunisation and Countermeasures Division, National Infection Service, PHE Colindale. 61 Colindale Avenue, London NW9 5EQ.; Immunisation and Countermeasures Division, National Infection Service, PHE Colindale. 61 Colindale Avenue, London NW9 5EQ.; Immunoassay Lab, National Infection Service, Porton Down SP4 0JG; Immunoassay Lab, National Infection Service, Porton Down SP4 0JG; Sero-epidemiology Unit, PHE, Manchester Royal Infirmary, Manchester, M13 9WL; Sero-epidemiology Unit, PHE, Manchester Royal Infirmary, Manchester, M13 9WL; Manchester University NHS Foundation Trust; NIHR Manchester Clinical Research Facility, Manchester Royal Infirmary, Oxford Rd, Manchester, M13 9WL; University of Manchester and NIHR Manchester Clinical Research Facility, Manchester University NHS Foundation Trust, Manchester M23 9LT; Immunisation and Countermeasures Division, National Infection Service, PHE Colindale. 61 Colindale Avenue, London NW9 5EQ.; Immunisation and Countermeasures Division, National Infection Service, PHE Colindale. 61 Colindale Avenue, London NW9 5EQ.; Immunisation and Countermeasures Division, National Infection Service, PHE Colindale. 61 Colindale Avenue, London NW9 5EQ.; Immunisation and Countermeasures Division, National Infection Service, PHE Colindale. 61 Colindale Avenue, London NW9 5EQ.; Institute of Immunology and Immunotherapy, University of Birmingham","The immune response to SARS-CoV-2 is critical in both controlling primary infection and preventing re-infection. However, there is concern that immune responses following natural infection may not be sustained and that this may predispose to recurrent infection. We analysed the magnitude and phenotype of the SARS-CoV-2 cellular immune response in 100 donors at six months following primary infection and related this to the profile of antibody level against spike, nucleoprotein and RBD over the previous six months. T-cell immune responses to SARS-CoV-2 were present by ELISPOT and/or ICS analysis in all donors and are characterised by predominant CD4+ T cell responses with strong IL-2 cytokine expression. Median T-cell responses were 50% higher in donors who had experienced an initial symptomatic infection indicating that the severity of primary infection establishes a setpoint for cellular immunity that lasts for at least 6 months. The T-cell responses to both spike and nucleoprotein/membrane proteins were strongly correlated with the peak antibody level against each protein. The rate of decline in antibody level varied between individuals and higher levels of nucleoprotein-specific T cells were associated with preservation of NP-specific antibody level although no such correlation was observed in relation to spike-specific responses. In conclusion, our data are reassuring that functional SARS-CoV-2-specific T-cell responses are retained at six months following infection although the magnitude of this response is related to the clinical features of primary infection.",immunology,fuzzy,100,100 medRxiv,10.1101/2020.10.29.20222174,2020-10-30,https://medrxiv.org/cgi/content/short/2020.10.29.20222174,COVID-19 collateral: Indirect acute effects of the pandemic on physical and mental health in the UK,Kathryn E Mansfield; Rohini Mathur; John Tazare; Alasdair D Henderson; Amy Mulick; Helena Carreira; Anthony A Matthews; Patrick Bidulka; Alicia Gayle; Harriet Forbes; Sarah Cook; Angel Wong; Helen Strongman; Kevin Wing; Charlotte Warren-Gash; Sharon L Cadogan; Liam Smeeth; Joseph Hayes; Jennifer Quint; Martin McKee; Sinéad Langan,London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; Karolinska Institutet; London School of Hygiene and Tropical Medicine; Imperial College; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University College London; Imperial College; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine,"BackgroundConcerns have been raised that the response to the UK COVID-19 pandemic may have worsened physical and mental health, and reduced use of health services. However, the scale of the problem is unquantified, impeding development of effective mitigations. We asked what has happened to general practice contacts for acute physical and mental health outcomes during the pandemic? MethodsUsing electronic health records from the Clinical Research Practice Datalink (CPRD) Aurum (2017-2020), we calculated weekly primary care contacts for selected acute physical and mental health conditions (including: anxiety, depression, acute alcohol-related events, asthma and chronic obstructive pulmonary disease [COPD] exacerbations, cardiovascular and diabetic emergencies). We used interrupted time series (ITS) analysis to formally quantify changes in conditions after the introduction of population-wide restrictions ( lockdown) compared to the period prior to their introduction in March 2020. @@ -4535,6 +4390,19 @@ Research in contextO_ST_ABSEvidence before this studyC_ST_ABSTo identify instanc Added value of this studyTo our knowledge, we provide the first demonstration of mobile technology to provide national-level disease surveillance. Using over 120 million reports from more than 2.8 million users across England, we estimate incidence, prevalence, and the effective reproduction number. We compare these estimates to those from national community surveys to understand the effectiveness of these digital tools. Furthermore, we demonstrate the large number of users can be used to provide disease surveillance with high geographical granularity, potentially providing a valuable source of information for policymakers seeking to understand the spread of the disease. Implications of all the available evidenceOur findings suggest that mobile technology can be used to provide real-time data on the national and local state of the pandemic, enabling policymakers to make informed decisions in a fast-moving pandemic.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2020.10.26.20219576,2020-10-27,https://medrxiv.org/cgi/content/short/2020.10.26.20219576,Impact of the COVID-19 pandemic on remote mental healthcare and prescribing in psychiatry,Rashmi Patel; Jessica Irving; Aimee Brinn; Matthew Broadbent; Hitesh Shetty; Megan Pritchard; Johnny Downs; Robert Stewart; Robert Harland; Philip McGuire,"King's College London (Institute of Psychiatry, Psychology and Neuroscience), London, UK; King's College London (Institute of Psychiatry, Psychology and Neuroscience), London, UK; King's College London (Institute of Psychiatry, Psychology and Neuroscience), London, UK; South London and Maudsley NHS Foundation Trust, London, UK; South London and Maudsley NHS Foundation Trust, London, UK; South London and Maudsley NHS Foundation Trust, London, UK; King's College London (Institute of Psychiatry, Psychology and Neuroscience), London, UK; King's College London (Institute of Psychiatry, Psychology and Neuroscience), London, UK; South London and Maudsley NHS Foundation Trust, London, UK; King's College London (Institute of Psychiatry, Psychology and Neuroscience), London, UK","ObjectivesThe recent COVID-19 pandemic has disrupted mental healthcare delivery, with many services shifting from in- person to remote patient contact. We investigated the impact of the pandemic on the use of remote consultation and on the prescribing of psychiatric medications. + +Design and settingThe Clinical Record Interactive Search tool (CRIS) was used to examine de-identified electronic health records (EHRs) of people receiving mental healthcare from the South London and Maudsley (SLaM) NHS Foundation Trust. Data from the period before and after the onset of the pandemic were analysed using linear regression, and visualised using locally estimated scatterplot smoothing (LOESS). + +ParticipantsAll patients receiving care from SLaM between 7th January 2019 and 20th September 2020 (around 37,500 patients per week). + +Outcome measuresO_LIThe number of clinical contacts (in-person, remote or non-attended) with mental healthcare professionals per week +C_LIO_LIPrescribing of antipsychotic and mood stabiliser medications per week +C_LI + +ResultsFollowing the onset of the pandemic, the frequency of in-person contacts was significantly reduced compared to that in the previous year ({beta} coefficient: -5829.6 contacts, 95% CI -6919.5 to -4739.6, p<0.001), while the frequency of remote contacts significantly increased ({beta} coefficient: 3338.5 contacts, 95% CI 3074.4 to 3602.7, p<0.001). Rates of remote consultation were lower in older adults than in working age adults, children and adolescents. Despite this change in the type of patient contact, antipsychotic and mood stabiliser prescribing remained at similar levels. + +ConclusionsThe COVID-19 pandemic has been associated with a marked increase in remote consultation, particularly among younger patients. However, there was no evidence that this has led to changes in psychiatric prescribing. Nevertheless, further work is needed to ensure that older patients are able to access mental healthcare remotely.",psychiatry and clinical psychology,fuzzy,100,100 medRxiv,10.1101/2020.10.26.20219550,2020-10-27,https://medrxiv.org/cgi/content/short/2020.10.26.20219550,Human movement can inform the spatial scale of interventions against COVID-19 transmission,Hamish Gibbs; Emily Nightingale; Yang Liu; James Cheshire; Leon Danon; Liam Smeeth; Carl AB Pearson; Chris Grundy; - LSHTM CMMID COVID-19 Working Group; Adam J Kucharski; Rosalind M Eggo,London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University College London; University of Exeter; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; ; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine,"BackgroundIn 2020, the UK enacted an intensive, nationwide lockdown on March 23 to mitigate transmission of COVID-19. As restrictions began to ease, resurgences in transmission were targeted by geographically-limited interventions of various stringencies. Understanding the spatial scale of networks of human interaction, and how these networks change over time, is critical to inform interventions targeted at the most at-risk areas without unnecessarily restricting areas at low risk of resurgence. MethodsWe use detailed human mobility data aggregated from Facebook users to determine how the spatially-explicit network of movements changed before and during the lockdown period, in response to the easing of restrictions, and to the introduction of locally-targeted interventions. We also apply community detection techniques to the weighted, directed network of movements to identify geographically-explicit movement communities and measure the evolution of these community structures through time. @@ -4581,6 +4449,13 @@ Our analysis demonstrated that FebriDx correctly identified 91 out of 100 patien Overall, we have shown that the FebriDx POC test performed well during the UK COVID-19 pandemic when compared with laboratory tests, especially when COVID-19 was indicated. For the future, this means that the FebriDx POC test might be helpful in making a quick clinical decision on whether to isolate a patient with COVID-19-like symptoms arriving in a busy emergency department. However, our results indicate it would not completely replace the need to conduct a laboratory test in certain cases to confirm COVID-19. There are limitations to our findings. For example, we do not know if FebriDx will work in a similar way with patients in different settings such as in the community or care homes. Similarly, we do not know whether other viral and bacterial infections which cause similar COVID-19 symptoms, and are more common in the autumn and winter months, could influence the FebriDx test accuracy. Our findings are also only based on three studies.",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2020.10.15.20208454,2020-10-18,https://medrxiv.org/cgi/content/short/2020.10.15.20208454,Modelling SARS-CoV-2 transmission in a UK university setting,Edward M Hill; Benjamin D Atkins; Matt J Keeling; Michael Tildesley; Louise Dyson,University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick,"Around 40% of school leavers in the UK attend university and individual universities generally host thousands of students each academic year. Bringing together these student communities during the COVID-19 pandemic may require strong interventions to control transmission. Prior modelling analyses of SARS-CoV-2 transmission within universities using compartmental modelling approaches suggest that outbreaks are almost inevitable. + +We constructed a network-based model to capture the interactions of a student population in different settings (housing, social and study). For a single academic term of a representative campus-based university, we ran a susceptible-latent-infectious-recovered type epidemic process, parameterised according to available estimates for SARS-CoV-2. We investigated the impact of: adherence to (or effectiveness of) isolation and test and trace measures; room isolation of symptomatic students; and supplementary mass testing. + +With all adhering to test, trace and isolation measures, we found that 22% (7% - 41%) of the student population could be infected during the autumn term, compared to 69% (56% - 76%) when assuming zero adherence to such measures. Irrespective of the adherence to isolation measures, on average a higher proportion of students resident on-campus became infected compared to students resident off-campus. Room isolation generated minimal benefits. Regular mass testing, together with high adherence to isolation and test and trace measures, could substantially reduce the proportion infected during the term compared to having no testing. + +Our findings suggest SARS-CoV-2 may readily transmit in a university setting if there is limited adherence to nonpharmaceutical interventions and/or there are delays in receiving test results. Following isolation guidance and effective contact tracing curbed transmission and reduced the expected time an adhering student would spend in isolation.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.10.14.20212555,2020-10-16,https://medrxiv.org/cgi/content/short/2020.10.14.20212555,Multi-organ impairment in low-risk individuals with long COVID,Andrea Dennis; Malgorzata Wamil; Sandeep Kapur; Johann Alberts; Andrew Badley; Gustav Anton Decker; Stacey A Rizza; Rajarshi Banerjee; Amitava Banerjee,Perspectum; Great Western Hospitals NHS Foundation Trust; Mayo Clinic Healthcare; Alliance Medical; Mayo Clinic; Mayo Clinic International; Mayo Clinic; Perspectum; University College London,"BackgroundSevere acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) infection has disproportionately affected older individuals and those with underlying medical conditions. Research has focused on short-term outcomes in hospital, and single organ involvement. Consequently, impact of long COVID (persistent symptoms three months post-infection) across multiple organs in low-risk individuals is yet to be assessed. MethodsAn ongoing prospective, longitudinal, two-centre, observational study was performed in individuals symptomatic after recovery from acute SARS-CoV-2 infection. Symptoms and organ function (heart, lungs, kidneys, liver, pancreas, spleen) were assessed by standardised questionnaires (EQ-5D-5L, Dyspnoea-12), blood investigations and quantitative magnetic resonance imaging, defining single and multi-organ impairment by consensus definitions. @@ -4635,23 +4510,6 @@ Added value of this studyIn this matched cohort study of routinely collected ele Implications of all the available evidenceCancer survivorship appears to be an important risk factor for severe influenza outcomes, suggesting that cancer survivors may also be at raised risk of poor COVID-19 outcomes. This should be taken into account in public health policies targeted at protecting clinical risk groups. Influenza vaccination should be encouraged in this group, and may need to be extended to a wider population of medium- to long-term cancer survivors than currently recommended.",oncology,fuzzy,100,100 bioRxiv,10.1101/2020.10.10.331348,2020-10-11,https://biorxiv.org/cgi/content/short/2020.10.10.331348,Single-dose intranasal administration of AdCOVID elicits systemic and mucosal immunity against SARS-CoV-2 in mice,Rodney G. King; Aaron Silva-Sanchez; Jessica N. Peel; Davide Botta; Selene Meza-Perez; Rameeza Allie; Michael D. Schultz; Mingyong Liu; John E. Bradley; Shihong Qiu; Guang Yang; Fen Zhou; Esther Zumaquero; Thomas S. Simpler; Betty Mousseau; John T. Killian Jr.; Brittany Dean; Qiao Shang; Jennifer L. Tipper; Christopher Risley; Kevin S. Harrod; Ray Feng; Young Lee; Bethlehem Shiberu; Vyjayanthi Krishnan; Isabelle Peguillet; Jianfeng Zhang; Todd Green; Troy D. Randall; Bertrand Georges; Frances E Lund; Scot Roberts,"University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; Altimmune Inc.; Altimmune Inc.; Altimmune Inc.; Altimmune Inc.; Altimmune Inc.; Altimmune Inc.; University of Alabama at Birmingham; University of Alabama at Birmingham; Altimmune, Inc.; University of Alabama at Birmingham; Altimmune Inc.","The coronavirus disease 2019 (COVID-19) pandemic has highlighted the urgent need for effective preventive vaccination to reduce burden and spread of severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2) in humans. Intranasal vaccination is an attractive strategy to prevent COVID-19 as the nasal mucosa represents the first-line barrier to SARS-CoV-2 entry before viral spread to the lung. Although SARS-CoV-2 vaccine development is rapidly progressing, the current intramuscular vaccines are designed to elicit systemic immunity without conferring mucosal immunity. Here, we show that AdCOVID, an intranasal adenovirus type 5 (Ad5)-vectored vaccine encoding the receptor binding domain (RBD) of the SARS-CoV-2 spike protein, elicits a strong and focused immune response against RBD through the induction of mucosal IgA, serum neutralizing antibodies and CD4+ and CD8+ T cells with a Th1-like cytokine expression profile. Therefore, AdCOVID, which promotes concomitant systemic and local mucosal immunity, represents a promising COVID-19 vaccine candidate.",immunology,fuzzy,100,92 -medRxiv,10.1101/2020.10.07.20208918,2020-10-09,https://medrxiv.org/cgi/content/short/2020.10.07.20208918,Cardiovascular drugs and COVID-19 clinical outcomes: a living systematic review and meta-analysis,Innocent Gerald Asiimwe; Sudeep Pushpakom; Richard Turner; Ruwanthi Kolamunnage-Dona; Andrea Jorgensen; Munir Pirmohamed,University of Liverpool; University of Liverpool; University of Liverpool; University of Liverpool; University of Liverpool; University of Liverpool,"OBJECTIVETo continually evaluate the rapidly evolving evidence base on the role of cardiovascular drugs in COVID-19 clinical outcomes (susceptibility to infection, hospitalization, hospitalization length, disease severity, and all-cause mortality). - -DESIGNLiving systematic review and meta-analysis. - -DATA SOURCESEligible publications identified from >500 databases indexed through 31st July 2020 and additional studies from reference lists, with planned continual surveillance for at least two years. - -STUDY SELECTIONObservational and interventional studies that report on the association between cardiovascular drugs and COVID-19 clinical outcomes. - -DATA EXTRACTIONSingle-reviewer extraction and quality evaluation (using ROBINS-I), with half the records independently extracted and evaluated by a second reviewer. - -RESULTSOf 23,427 titles screened, 175 studies were included in the quantitative synthesis. The most reported drug classes were angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin receptor blockers (ARBs) with ACEI/ARB exposure being associated with higher odds of testing positive for COVID-19 (pooled unadjusted OR 1.15, 95% CI 1.02 to 1.30). Among patients with COVID-19, unadjusted estimates showed that ACEI/ARB exposure was associated with being hospitalized (OR 2.25, 1.70 to 2.98) and having severe disease (OR 1.50, 1.27 to 1.77) but not with the length of hospitalization (mean difference -0.45, -1.33 to 0.43 days) or all-cause mortality (OR 1.25, CI 0.98 to 1.58). However, after adjustment, ACEI/ARB exposure was not associated with testing positive for COVID-19 (pooled adjusted OR 1.01, 0.93 to 1.10), being hospitalized (OR 1.16, 0.80 to 1.68), having severe disease (1.04, 0.76 to 1.42), or all-cause mortality (0.86, 0.64 to 1.15). Similarly, subgroup analyses involving only hypertensive patients revealed that ACEI/ARB exposure was not associated with being hospitalized (OR 0.84, 0.58 to 1.22), disease severity (OR 0.88, 0.68 to 1.14) or all-cause mortality (OR 0.77, 0.54 to 1.12) while it decreased the length of hospitalization (mean difference -0.71, -1.11 to -0.30 days). After adjusting for relevant covariates, other cardiovascular drug classes were mostly not found to be associated with poor COVID-19 clinical outcomes. However, the validity of these findings is limited by a high level of heterogeneity in terms of effect sizes and a serious risk of bias, mainly due to confounding in the included studies. - -CONCLUSIONOur comprehensive review shows that ACEI/ARB exposure is associated with COVID-19 outcomes such as susceptibility to infection, severity, and hospitalization in unadjusted analyses. However, after adjusting for potential confounding factors, this association is not evident. Patients on cardiovascular drugs should continue taking their medications as currently recommended. Higher quality evidence in the form of randomized controlled trials will be needed to determine any adverse or beneficial effects of cardiovascular drugs. - -PRIMARY FUNDING SOURCENone - -SYSTEMATIC REVIEW REGISTRATIONPROSPERO (CRD42020191283)",infectious diseases,fuzzy,100,100 bioRxiv,10.1101/2020.10.06.328328,2020-10-07,https://biorxiv.org/cgi/content/short/2020.10.06.328328,MAJORA: Continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance,Samuel M Nicholls; Radoslaw Poplawski; Matthew J Bull; Anthony Underwood; Michael Chapman; Khalil Abu-Dahab; Ben Taylor; Ben Jackson; Sara Rey; Roberto Amato; Rich Livett; Sonia Goncalves; Ewan M Harrison; Sharon J Peacock; David M Aanensen; Andrew Rambaut; Thomas R Connor; Nicholas J Loman; - The COVID-19 Genomics UK Consortium (COG-UK),"Institute of Microbiology and Infection, University of Birmingham, Birmingham; Institute of Microbiology and Infection, University of Birmingham, Birmingham; Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff; Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton; Health Data Research UK Cambridge, Wellcome Genome Campus, Hinxton; Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton; Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton; University of Edinburgh; Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff; Wellcome Sanger Institute, Hinxton; Wellcome Sanger Institute, Hinxton; Wellcome Sanger Institute, Hinxton; Wellcome Sanger Institute, Hinxton; University of Cambridge, Department of Medicine, Cambridge; Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton; University of Edinburgh; Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff; Institute of Microbiology and Infection, University of Birmingham, Birmingham; -","Genomic epidemiology has become an increasingly common tool for epidemic response. Recent technological advances have made it possible to sequence genomes rapidly enough to inform outbreak response, and cheaply enough to justify dense sampling of even large epidemics. With increased availability of sequencing it is possible for agile networks of sequencing facilities to collaborate on the sequencing and analysis of epidemic genomic data. In response to the ongoing SARS-CoV-2 pandemic in the United Kingdom, the COVID-19 Genomics UK (COG-UK) consortium was formed with the aim of rapidly sequencing SARS-CoV-2 genomes as part of a national-scale genomic surveillance strategy. The network consists of universities, academic institutes, regional sequencing centres and the four UK Public Health Agencies. @@ -5219,6 +5077,7 @@ MethodsWe examined the disease progression of COVID-19 in 6,914 patients admitte FindingsMeta-analysis of the mortality risk in eight European hospitals estimated odds ratios per one day increase in the admission date to be 0.981 (0.973-0.988, p<0.001) and per increase in ambient temperature of one degree Celsius to be 0.854 (0.773-0.944, p=0.007). Statistically significant decreases of comparable magnitude in median hospital stay, probability of transfer to Intensive Care Unit and need for mechanical ventilation were also observed in most, but not all hospitals. The analysis of individually reported symptoms of 37,187 individuals in the UK also showed the decrease in symptom duration and disease severity with time. InterpretationSeverity of COVID-19 in Europe decreased significantly between March and May and the seasonality of COVID-19 is the most likely explanation. Mucosal barrier and mucociliary clearance can significantly decrease viral load and disease progression, and their inactivation by low relative humidity of indoor air might significantly contribute to severity of the disease.",infectious diseases,fuzzy,94,100 +medRxiv,10.1101/2020.07.12.20151753,2020-07-14,https://medrxiv.org/cgi/content/short/2020.07.12.20151753,"COVID-19 incidence and R decreased on the Isle of Wight after the launch of the Test, Trace, Isolate programme",Michelle Kendall; Luke Milsom; Lucie Abeler-Dorner; Chris Wymant; Luca Ferretti; Mark Briers; Chris Holmes; David Bonsall; Johannes Abeler; Christophe Fraser,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Alan Turing Institute; University of Oxford; Alan Turing Institute; University of Oxford; University of Oxford; University of Oxford,"In May 2020 the UK introduced a Test, Trace, Isolate programme in response to the COVID-19 pandemic. The programme was first rolled out on the Isle of Wight and included Version 1 of the NHS contact tracing app. We used COVID-19 daily case data to infer incidence of new infections and estimate the reproduction number R for each of 150 Upper Tier Local Authorities in England, and at the National level, before and after the launch of the programme on the Isle of Wight. We used Bayesian and Maximum-Likelihood methods to estimate R, and compared the Isle of Wight to other areas using a synthetic control method. We observed significant decreases in incidence and R on the Isle of Wight immediately after the launch. These results are robust across each of our approaches. Our results show that the sub-epidemic on the Isle of Wight was controlled significantly more effectively than the sub-epidemics of most other Upper Tier Local Authorities, changing from having the third highest reproduction number R (of 150) before the intervention to the tenth lowest afterwards. The data is not yet available to establish a causal link. However, the findings highlight the need for further research to determine the causes of this reduction, as these might translate into local and national non-pharmaceutical intervention strategies in the period before a treatment or vaccination becomes available.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.07.10.20150524,2020-07-11,https://medrxiv.org/cgi/content/short/2020.07.10.20150524,Community prevalence of SARS-CoV-2 virus in England during May 2020: REACT study,Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Benjamin Jeffrey; Caroline E. Walters; Christina J Atchison; Peter J. Diggle; Deborah Ashby; Christl A. Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Graham Taylor; Ara Darzi; Paul Elliott,"Dept Inf Dis Epi, Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Lancaster University; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London School of Public Health","BackgroundEngland has experienced one of the highest rates of confirmed COVID-19 mortality in the world. SARS-CoV-2 virus has circulated in hospitals, care homes and the community since January 2020. Our current epidemiological knowledge is largely informed by clinical cases with far less understanding of community transmission. MethodsThe REal-time Assessment of Community Transmission (REACT) study is a nationally representative prevalence survey of SARS-CoV-2 virus swab-positivity in the community in England. We recruited participants regardless of symptom status. @@ -5254,6 +5113,28 @@ ResultsWe estimate that, during March 2020, the median percentage of symptomatic ConclusionsWe found substantial under-ascertainment of symptomatic cases, particularly at the peak of the first wave of the SARS-CoV-2 pandemic, in many countries. Reported case counts will therefore likely underestimate the rate of outbreak growth initially and underestimate the decline in the later stages of an epidemic. Although there was considerable under-reporting in many locations, our estimates were consistent with emerging serological data, suggesting that the proportion of each countrys population infected with SARS-CoV-2 worldwide is generally low. FundingWellcome Trust, Bill & Melinda Gates Foundation, DFID, NIHR, GCRF, ARC.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2020.07.06.20147348,2020-07-07,https://medrxiv.org/cgi/content/short/2020.07.06.20147348,Community prevalence of SARS-CoV-2 in England: Results from the ONS Coronavirus Infection Survey Pilot,Koen B Pouwels; Thomas House; Julie V Robotham; Paul Birrell; Andrew B Gelman; Nikola Bowers; Ian Boreham; Heledd Thomas; James Lewis; Iain Bell; John I Bell; John Newton; Jeremy Farrar; Ian Diamond; Pete Benton; Sarah Walker,University of Oxford; University of Manchester; Public Health England; Public Health England; Columbia University; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; Office for National Statistics; Office for National Statistics; University of Oxford,"ObjectiveTo estimate the percentage of individuals infected with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) over time in the community in England and to quantify risk factors. + +DesignRepeated cross-sectional surveys of population-representative households with longitudinal follow-up if consent given. + +SettingEngland + +Participants34,992 Individuals aged 2 years and over from 16,722 private residential households. Data were collected in a pilot phase of the survey between 26 April and 28 June 2020. + +Main outcome measuresPercentage of individuals in the community testing positive for SARS-CoV-2 RNA using throat and nose swabs. Individuals were asked about any symptoms and potential risk factors. + +ResultsThe percentage of people in private-residential households testing positive for SARS-CoV-2 reduced from 0.32% (95% credible interval (CrI) 0.19% to 0.52%) on 26 April to 0.08% (95% CrI 0.05% to 0.12%) on 28 June, although the prevalence stabilised near the end of the pilot. Factors associated with an increased risk of testing positive included having a job with direct patient contact (relative exposure (RE) 4.06, 95% CrI 2.42 to 6.77)), working outside the home (RE 2.49, 95% CrI 1.39 to 4.45), and having had contact with a hospital (RE 2.20, 95% CrI 1.09 to 4.16 for having been to a hospital individually and RE 1.95, 95% CrI 0.81 to 4.09 for a household member having been to a hospital). In 133 visits where individuals tested positive, 82 (61%, 95% CrI 53% to 69%) reported no symptoms, stably over time. + +ConclusionThe percentage of SARS-CoV-2 positive individuals declined between 26 April and 28 June 2020. Positive tests commonly occurred without symptoms being reported. Working outside your home was an important risk factor, indicating that continued monitoring for SARS-CoV-2 in the community will be essential for early detection of increases in infections following return to work and other relaxations of control measures. + +What is already known on this topic- Unprecedented control measures, such as national lockdowns, have been widely implemented to contain the spread of SARS-CoV-2. +- Previous mass surveillance has been based on data sources such as hospital admission, deaths or self-reported symptoms that do not measure community prevalence of virus directly. +- Decisions regarding the continued need for social distancing measures in the overall population, specific subgroups and geographic areas heavily rely on accurate and up-to-date information about the number of people and risk factors for testing positive. + + +What this study adds- The percentage of individuals from the general community in England testing positive for SARS-CoV-2 clearly declined between 26 April and 28 June 2020 from around one in three 300 to around one in a thousand. +- Risk factors for testing positive included having a job with direct patient contact, having had (indirect) contact with a hospital in the past 2 weeks, and working outside your home. +- Positive tests commonly occurred without symptoms being reported and the percentage of individuals with a positive test that reported no symptoms was stable over time.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.07.03.20145912,2020-07-06,https://medrxiv.org/cgi/content/short/2020.07.03.20145912,Ultraviolet A Radiation and COVID-19 Deaths: A Multi Country Study,Mark Cherrie; Tom Clemens; Claudio Colandrea; Zhiqiang Feng; David Webb; Chris Dibben; Richard B Weller,University of Edinburgh; University of Edinburgh; University of Edinburgh; University of Edinburgh; University of Edinburgh; University of Edinburgh; University of Edinburgh,"ObjectivesTo determine whether UVA exposure might be associated with COVID-19 deaths DesignEcological regression, with replication in two other countries and pooled estimation @@ -5620,19 +5501,6 @@ Key pointsO_ST_ABSQuestionC_ST_ABSWhat is the evidence on the susceptibility and FindingsIn this systematic review and meta-analysis, children and young people under 18-20 years had an 435 lower odds of secondary infection of with SARS-CoV-2 compared to adults 20 years plus, a significant difference. This finding was most marked in children under 12-14 years. Data were insufficient to conclude whether transmission of SARS-CoV-2 by children is lower than by adults. MeaningWe found preliminary evidence that children have a lower susceptibility for SARS-CoV-2 infection compared with adults, although data for adolescents is less clear. The role that children and young people play in transmission of this pandemic remains unclear.",public and global health,fuzzy,100,100 -medRxiv,10.1101/2020.05.21.20108936,2020-05-23,https://medrxiv.org/cgi/content/short/2020.05.21.20108936,Risk Factors for COVID-19 versus non-COVID-19 related in-hospital and community deaths by Local Authority District in Great Britain,Samuel Paul Leighton; Danielle Jane Leighton; James Herron; Rachel Upthegrove; Jonathan Cavanagh; Georgios Gkoutos; Breda Cullen; Pavan K Mallikarjun,University of Glasgow; University of Glasgow; University of Glasgow; University of Birmingham; University of Glasgow; University of Birmingham & Associate Director of Health Data Research UK; University of Glasgow; University of Birmingham,"ObjectivesTo undertake a preliminary hypothesis-generating analysis exploring putative risk factors for coronavirus diseae 2019 (COVID-19) population-adjusted deaths, compared with non-COVID-19 related deaths, at a local authority district (LAD) level in hospital, care homes and at home. - -DesignEcological retrospective cohort study - -SettingLocal authority districts (LADs) in England, Scotland and Wales (Great Britain (GB)). - -ParticipantsAll LAD deaths registered by week 16 of 2020. - -Main Outcome MeasuresDeath registration where COVID-19 is mentioned as a contributing factor per 100,000 people in all settings, and in i) cares homes, ii) hospitals or iii) home only, in comparison to non-COVID-19 related deaths. - -ResultsAcross GB by week 16 of 2020, 20,684 deaths had been registered mentioning COVID-19, equivalent to 25.6 per 100,000 people. Significant risk factors for LAD COVID-19 death in comparison to non-COVID-19 related death were air pollution and proportion of the population who were female. Significant protective factors were higher air temperature and proportion of the population who were ex-smokers. Conversely, for all COVID-19 unrelated deaths in comparison to COVID-19 deaths, higher rates of communal living, higher population rates of chronic kidney disease, chronic obstructive pulmonary disease, cerebrovascular disease deaths under 75 and dementia were predictive of death, whereas, higher rates of flight passengers was protective. Looking at individual setttings, the most notable findings in care homes was Scotland being a significant risk factor for COVID-19 related deaths compared to England. For hospital setting, the proportion of the population who were from black and Asian minority ethnic (BAME) groups significantly predicted COVID-19 related death. - -ConclusionsThis is the first study within GB to assess COVID-19 related deaths in comparison to COVID-19 unrelated deaths across hospital, care homes and home combined. As an ecological study, the results cannot be directly extrapolated to individuals. However, the analysis may be informative for public health policy and protective measures. From our hypothesis-generating analysis, we propose that air pollution is a significant risk factor and high temperature a significant protective factor for COVID-19 related deaths. These factors cannot readily be modelled at an individual level. Scottish local authorities and local authorities with a higher proportion of individuals of BAME origin are potential risk factors for COVID-19 related deaths in care homes and in hospitals, respectively. Altogether, this analysis shows the benefits of access to high quality open data for public information, public health policy and further research.",public and global health,fuzzy,100,100 medRxiv,10.1101/2020.05.22.20109892,2020-05-23,https://medrxiv.org/cgi/content/short/2020.05.22.20109892,"Occupation and risk of COVID-19: prospective cohort study of 120,621 UK Biobank participants",Miriam Mutambudzi; Claire L Niedzwiedz; Ewan B Macdonald; Alastair H Leyland; Frances S Mair; Jana J Anderson; Carlos A Celis-Morales; John Cleland; John Forbes; Jason MR Gill; Claire Hastie; Frederick K Ho; Bhautesh D Jani; Daniel F Mackay; Barbara I Nicholl; Naveed I Sattar; Paul I Welsh; Jill P Pell; Srinivasa Vittal Katikireddi; Evangelia Demou,"University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University Of Glasgow; University of Glasgow, Institute of Health and Wellbeing; University of Glasgow; University of Glasgow","ObjectivesTo investigate severe COVID-19 risk by occupational group. MethodsBaseline UK Biobank data (2006-10) for England were linked to SARS-CoV-2 test results from Public Health England (16 March to 26 July 2020). Included participants were employed or self-employed at baseline, alive and aged less than 65 years in 2020. Poisson regression models adjusted sequentially for baseline demographic, socioeconomic, work-related, health, and lifestyle-related risk factors to assess risk ratios (RRs) for testing positive in hospital or death due to COVID-19 by three occupational classification schemes (including Standard Occupation Classification 2000). @@ -5889,15 +5757,6 @@ medRxiv,10.1101/2020.05.02.20078642,2020-05-06,https://medrxiv.org/cgi/content/s Our key findings are firstly that BAME patients are significantly younger and have different co-morbidity profiles than White individuals. Secondly, there is no significant independent effect of ethnicity on severe outcomes (death or ITU admission) within 14-days of symptom onset, after adjustment for age, sex and comorbidities.",intensive care and critical care medicine,fuzzy,100,100 medRxiv,10.1101/2020.05.02.20086231,2020-05-06,https://medrxiv.org/cgi/content/short/2020.05.02.20086231,Trends in excess cancer and cardiovascular deaths in Scotland during the COVID-19 pandemic 30 December 2019 to 20 April 2020,Jonine Figueroa; Paul Brennan; Evropi Theodoratou; Michael Poon; Karin Purshouse; Farhat Din; Kai Jin; Ines Mesa-Eguiagaray; Malcolm G Dunlop; Peter S Hall; David Cameron; Sarah Wild; Cathie LM Sudlow,University of Edinburgh; University of Edinburgh - Brain Tumour Centre of Excellence; University of Edinburgh - Centre for Clinical Brain Sciences; University of Edinburgh; University of Edinburgh; University of Edinburgh; University of Edinburgh; University of Edinburgh; University of Edinburgh; Institute of Genetics and Molecular Medicine; University of Edinburgh; University of Edinburgh; University of Edinburgh; University of Edinburgh,"Understanding the trends in causes of death for different diseases during the current COVID-19 pandemic is important to determine whether there are excess deaths beyond what is normally expected. Using the most recent report from National Records Scotland (NRS) on 29 April 2020, we examined the percentage difference in crude numbers of deaths in 2020 compared to the average for 2015-2019 by week of death within calendar year. To determine if trends were similar, suggesting underreporting/underdiagnosed COVID-19 related deaths, we also looked at the trends in % differences for cardiovascular disease deaths. From the first 17 weeks of data, we found a peak in excess deaths at week 14 of 2020, about four weeks after the first case in Scotland was detected on 1 March 2020-- but by week 17 these excesses had returned to normal levels, 4 weeks after lockdown in the UK began. Similar observations were seen for cardiovascular disease-related deaths. These observations suggest that the short-term increase in excess cancer and cardiovascular deaths might be associated with undetected/unconfirmed deaths related to COVID-19. Both of these conditions make patients more susceptible to infection and lack of widespread access to testing for COVID-19 are likely to have resulted in under-estimation of COVID-19 mortality. These data further suggest that the cumulative toll of COVID-19 on mortality is likely undercounted. More detailed analysis is needed to determine if these excesses were directly or indirectly related to COVID-19. Disease specific mortality will need constant monitoring for the foreseeable future as changes occur in increasing capacity and access to testing, reporting criteria, changes to health services and different measures are implemented to control the spread of the COVID-19. Multidisciplinary, multi-institutional, national and international collaborations for complementary and population specific data analysis is required to respond and mitigate adverse effects of the COVID-19 pandemic and to inform planning for future pandemics.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2020.04.28.20083170,2020-05-05,https://medrxiv.org/cgi/content/short/2020.04.28.20083170,Quantifying and mitigating the impact of the COVID-19 pandemic on outcomes in colorectal cancer,Amit Sud; Michael Jones; John Broggio; Stephen Scott; Chey Loveday; Bethany Torr; Alice Garrett; David L. Nicol; Shaman Jhanji; Stephen A. Boyce; Matthew Williams; Georgios Lyratzopoulos; Claire Barry; Elio Riboli; Emma Kipps; Ethna McFerran; Mark Lawler; David C. Muller; Muti Abulafi; Richard Houlston; Clare Ann Turnbull,"Institute of Cancer Research; Institute of Cancer Research; Public Health England; RM Partners, West London Cancer Alliance; Institute of Cancer Research; Institute of Cancer Research; Institute of Cancer Research; Royal Marsden NHS Foundation Trust; Royal Marsden NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Imperial College; University College London; RM Partners, West London Cancer Alliance; Imperial College London; Royal Marsden NHS Foundation Trust; Queen's University Belfast; Queen's University Belfast; Imperial College London; Croydon Health Services NHS Trust, on behalf of RMP NICE FIT Steering Group; Institute of Cancer Research; Institute of Cancer Research","BackgroundThe COVID-19 pandemic has caused disruption across cancer pathways for diagnosis and treatment. In England, 32% of colorectal cancer (CRC) is diagnosed via urgent symptomatic referral from primary care, the ""2-week-wait"" (2WW) pathway. Access to routine endoscopy is likely to be a critical bottleneck causing delays in CRC management due to chronic limitation in capacity, acute competition for physician time, and safety concerns. - -MethodsWe used age-specific, stage-specific 10 year CRC survival for England 2007-2017 and 2WW CRC cases volumes. We used per-day hazard ratios of CRC survival generated from observational studies of CRC diagnosis-to-treatment interval to model the effect of different durations of per-patient delay. We utilised data from a large London observational study of faecal immunochemical testing (FIT) in symptomatic patients to model FIT-triage to mitigate delay to colonoscopy. - -FindingsModest delays result in significant reduction in survival from CRC with a 4-month delay resulting across age groups in [≥]20% reduction in survival in Stage 3 disease and in total over a year, 1,419 attributable deaths across the 11,266 CRC patients diagnosed via the 2WW pathway. FIT triage of >10 ug Hb/g would salvage 1,292/1,419 of the attributable deaths and reduce colonoscopy requirements by >80%. Diagnostic colonoscopy offers net survival in all age groups, providing nosocomial COVID-19 infection rates are kept low (<2{middle dot}5%). - -InterpretationTo avoid significant numbers of avoidable deaths from CRC, normal diagnostic and surgical throughput must be maintained. An accrued backlog of cases will present to primary care following release of lockdown, supranormal endoscopy capacity will be required to manage this without undue delays. FIT-triage of symptomatic cases provides a rational approach by which to avoid patient delay and mitigate pressure on capacity in endoscopy. This would also reduce exposure to nosocomial COVID-19 infection, relevant in particular to older patient groups. - -FundingBreast Cancer Now, Cancer Research UK, Bobby Moore Fund for Cancer Research, National Institute for Health Research (NIHR).",oncology,fuzzy,100,100 medRxiv,10.1101/2020.04.29.20084111,2020-05-05,https://medrxiv.org/cgi/content/short/2020.04.29.20084111,Risk of symptomatic Covid-19 among frontline healthcare workers,Long H. Nguyen; David Alden Drew; Amit D. Joshi; Chuan-Guo Guo; Wenjie Ma; Raaj S. Mehta; Daniel R. Sikavi; Chun-Han Lo; Sohee Kwon; Mingyang Song; Lorelei A. Mucci; Meir Stampfer; Walter C. Willett; A. Heather Eliassen; Jaime Hart; Jorge E. Chavarro; Janet Rich-Edwards; Richard Davies; Joan Capdevila; Karla A. Lee; Mary Ni Lochlainn; Thomas Varsavsky; Mark Graham; Carol H. Sudre; M. Jorge Cardoso; Jonathan Wolf; Sebastien Ourselin; Claire Steves; Timothy Spector; Andrew T. Chan,Massachusetts General Hospital and Harvard Medical School; Massachusetts General Hospital; Massachusetts General Hospital and Harvard Medical School; Massachusetts General Hospital and Harvard Medical School; Massachusetts General Hospital and Harvard Medical School; Massachusetts General Hospital and Harvard Medical School; Massachusetts General Hospital and Harvard Medical School; Massachusetts General Hospital and Harvard Medical School; Massachusetts General Hospital and Harvard Medical School; Massachusetts General Hospital and Harvard Medical School; Harvard T.H. Chan School of Public Health; Harvard T.H. Chan School of Public Health; Harvard T.H. Chan School of Public Health; Harvard T.H. Chan School of Public Health; Harvard T.H. Chan School of Public Health; Harvard T.H. Chan School of Public Health; Harvard T.H. Chan School of Public Health; Zoe Global Ltd.; Zoe Global Ltd.; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; Zoe Global Ltd.; King's College London; King's College London; King's College London; Massachusetts General Hospital and Harvard Medical School,"BackgroundData for frontline healthcare workers (HCWs) and risk of SARS-CoV-2 infection are limited and whether personal protective equipment (PPE) mitigates this risk is unknown. We evaluated risk for COVID-19 among frontline HCWs compared to the general community and the influence of PPE. MethodsWe performed a prospective cohort study of the general community, including frontline HCWs, who reported information through the COVID Symptom Study smartphone application beginning on March 24 (United Kingdom, U.K.) and March 29 (United States, U.S.) through April 23, 2020. We used Cox proportional hazards modeling to estimate multivariate-adjusted hazard ratios (aHRs) of a positive COVID-19 test. @@ -5949,6 +5808,19 @@ FindingsAmong 428,225 participants, 340 had confirmed COVID-19. After multivaria InterpretationThese findings suggest that modification of lifestyle may help to reduce the risk of COVID-19 and could be a useful adjunct to other interventions, such as social distancing and shielding of high risk. FundingBritish Heart Foundation, Medical Research Council, Chief Scientist Office.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2020.04.24.20078006,2020-04-29,https://medrxiv.org/cgi/content/short/2020.04.24.20078006,Supplementing the National Early Warning Score (NEWS2) for anticipating early deterioration among patients with COVID-19 infection,Ewan Carr; Rebecca Bendayan; Daniel Bean; Matthew Stammers; Wenjuan Wang; Huayu Zhang; Thomas Searle; Zeljko Kraljevic; Anthony Shek; Hang T T Phan; Walter Muruet; Rishi K Gupta; Anthony J Shinton; Mike Wyatt; Ting Shi; Xin Zhang; Andrew Pickles; Daniel Stahl; Rosita Zakeri; Mahdad Noursadeghi; Kevin O'Gallagher; Matt Rogers; Amos Folarin; Christopher Bourdeaux; Chris McWilliams; Lukasz Roguski; Florina Borca; James Batchelor; Xiaodong Wu; Jiaxing Sun; Ashwin Pinto; Bruce Guthrie; Cormac Breen; Abdel Douiri; Honghan Wu; Vasa Curcin; James T Teo; Ajay Shah; Richard Dobson,"King's College London; King's College London; King's College London; Clinical Informatics Research Unit, University of Southampton; King's College London; University of Edinburgh; King's College London; King's College London; King's College London; Clinical Informatics Research Unit, University of Southampton; King's College London; University College London; UHS Digital, University Hospital Southampton; University Hospitals Bristol NHS Foundation Trust, Bristol, UK; Usher Institute, University of Edinburgh; Department of Pulmonary and Critical Care Medicine, People's Liberation Army Joint Logistic Support Force 920th Hospital, Yunnan, China; King's College London; King's College London; King's College London; UCL Division of Infection and Immunity, University College London Hospitals NHS Trust; King's College London; University Hospitals Bristol NHS Foundation Trust, Bristol, U.K.; King's College London; University Hospitals Bristol NHS Foundation Trust, Bristol, U.K.; Department of Engineering Mathematics, University of Bristol, Bristol, UK; University College London; University of Southampton; Clinical Informatics Research Unit, University of Southampton, Coxford Rd, Southampton SO16 5AF; Department of Pulmonary and Critical Care Medicine, Shanghai East Hospital, Tongji University, Shanghai, China; Department of Pulmonary and Critical Care Medicine, Shanghai East Hospital, Tongji University, Shanghai, China; UHS Digital, University Hospital Southampton; Usher Institute, University of Edinburgh; King's College London; King's College London; University College London; King's College London; Kings College Hospital NHS Foundation Trust; King's College London; Kings College London","BackgroundThe National Early Warning Score (NEWS2) is currently recommended in the United Kingdom for risk stratification of COVID outcomes, but little is known about its ability to detect severe cases. We aimed to evaluate NEWS2 for severe COVID outcome and identify and validate a set of routinely-collected blood and physiological parameters taken at hospital admission to improve the score. + +MethodsTraining cohorts comprised 1276 patients admitted to Kings College Hospital NHS Foundation Trust with COVID-19 disease from 1st March to 30th April 2020. External validation cohorts included 5037 patients from four UK NHS Trusts (Guys and St Thomas Hospitals, University Hospitals Southampton, University Hospitals Bristol and Weston NHS Foundation Trust, University College London Hospitals), and two hospitals in Wuhan, China (Wuhan Sixth Hospital and Taikang Tongji Hospital). The outcome was severe COVID disease (transfer to intensive care unit or death) at 14 days after hospital admission. Age, physiological measures, blood biomarkers, sex, ethnicity and comorbidities (hypertension, diabetes, cardiovascular, respiratory and kidney diseases) measured at hospital admission were considered in the models. + +ResultsA baseline model of NEWS2 + age had poor-to-moderate discrimination for severe COVID infection at 14 days (AUC in training sample = 0.700; 95% CI: 0.680, 0.722; Brier score = 0.192; 95% CI: 0.186, 0.197). A supplemented model adding eight routinely-collected blood and physiological parameters (supplemental oxygen flow rate, urea, age, oxygen saturation, CRP, estimated GFR, neutrophil count, neutrophil/lymphocyte ratio) improved discrimination (AUC = 0.735; 95% CI: 0.715, 0.757) and these improvements were replicated across five UK and non-UK sites. However, there was evidence of miscalibration with the model tending to underestimate risks in most sites. + +ConclusionsNEWS2 score had poor-to-moderate discrimination for medium-term COVID outcome which raises questions about its use as a screening tool at hospital admission. Risk stratification was improved by including readily available blood and physiological parameters measured at hospital admission, but there was evidence of miscalibration in external sites. This highlights the need for a better understanding of the use of early warning scores for COVID. + +KO_SCPLOWEYC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWMESSAGESC_SCPLOWO_LIThe National Early Warning Score (NEWS2), currently recommended for stratification of severe COVID-19 disease in the UK, showed poor-to-moderate discrimination for medium-term outcomes (14-day transfer to ICU or death) among COVID-19 patients. +C_LIO_LIRisk stratification was improved by the addition of routinely-measured blood and physiological parameters routinely at hospital admission (supplemental oxygen, urea, oxygen saturation, CRP, estimated GFR, neutrophil count, neutrophil/lymphocyte ratio) which provided moderate improvements in a risk stratification model for 14-day ICU/death. +C_LIO_LIThis improvement over NEWS2 alone was maintained across multiple hospital trusts but the model tended to be miscalibrated with risks of severe outcomes underestimated in most sites. +C_LIO_LIWe benefited from existing pipelines for informatics at KCH such as CogStack that allowed rapid extraction and processing of electronic health records. This methodological approach provided rapid insights and allowed us to overcome the complications associated with slow data centralisation approaches. +C_LI",infectious diseases,fuzzy,100,100 bioRxiv,10.1101/2020.04.28.066977,2020-04-29,https://biorxiv.org/cgi/content/short/2020.04.28.066977,"Controlling the SARS-CoV-2 outbreak, insights from large scale whole genome sequences generated across the world",Jody Phelan; Wouter Deelder; Daniel Ward; Susana Campino; Martin L Hibberd; Taane G Clark,London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine,"BackgroundSARS-CoV-2 most likely evolved from a bat beta-coronavirus and started infecting humans in December 2019. Since then it has rapidly infected people around the world, with more than 4.5 million confirmed cases by the middle of May 2020. Early genome sequencing of the virus has enabled the development of molecular diagnostics and the commencement of therapy and vaccine development. The analysis of the early sequences showed relatively few evolutionary selection pressures. However, with the rapid worldwide expansion into diverse human populations, significant genetic variations are becoming increasingly likely. The current limitations on social movement between countries also offers the opportunity for these viral variants to become distinct strains with potential implications for diagnostics, therapies and vaccines. MethodsWe used the current sequencing archives (NCBI and GISAID) to investigate 15,487 whole genomes, looking for evidence of strain diversification and selective pressure. @@ -5956,7 +5828,6 @@ MethodsWe used the current sequencing archives (NCBI and GISAID) to investigate ResultsWe used 6,294 SNPs to build a phylogenetic tree of SARS-CoV-2 diversity and noted strong evidence for the existence of two major clades and six sub-clades, unevenly distributed across the world. We also noted that convergent evolution has potentially occurred across several locations in the genome, showing selection pressures, including on the spike glycoprotein where we noted a potentially critical mutation that could affect its binding to the ACE2 receptor. We also report on mutations that could prevent current molecular diagnostics from detecting some of the sub-clades. ConclusionThe worldwide whole genome sequencing effort is revealing the challenge of developing SARS-CoV-2 containment tools suitable for everyone and the need for data to be continually evaluated to ensure accuracy in outbreak estimations.",genomics,fuzzy,100,100 -medRxiv,10.1101/2020.04.23.20076521,2020-04-27,https://medrxiv.org/cgi/content/short/2020.04.23.20076521,"Geo-social gradients in predicted COVID-19 prevalence and severity in Great Britain: results from 2,266,235 users of the COVID-19 Symptoms Tracker app",Ruth Bowyer; Thomas Varsavsky; Carole H Sudre; Benjamin Murray; Maxim Freidin; Darioush Yarand; Sajaysurya Ganesh; Joan Capdevila; Ellen J Thompson; Elco Bakker; M Jorge Cardoso; Richard Davies; Jonathan Wolf; Tim D Spector; Sebastien Ourselin; Claire J Steves; Cristina Menni,King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; Zoe Global Limited; Zoe Global Limited; King's College London; Zoe Global Limited; King's College London; King's College London; Zoe Global Limited; King's College London; King's College London; King's College London; King's College London,"Understanding the geographical distribution of COVID-19 through the general population is key to the provision of adequate healthcare services. Using self-reported data from 2,266,235 unique GB users of the COVID Symptom Tracker app, we find that COVID-19 prevalence and severity became rapidly distributed across the UK within a month of the WHO declaration of the pandemic, with significant evidence of ""urban hot-spots"". We found a geo-social gradient associated with disease severity and prevalence suggesting resources should focus on urban areas and areas of higher deprivation. Our results demonstrate use of self-reported data to inform public health policy and resource allocation.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.04.22.20075663,2020-04-27,https://medrxiv.org/cgi/content/short/2020.04.22.20075663,Ethnic and socioeconomic differences in SARS-CoV2 infection in the UK Biobank cohort study,Claire L Niedzwiedz; Bhautesh D Jani; Evangelia Demou; Frederick K Ho; Carlos Celis-Morales; Barbara I Nicholl; Frances Mair; Paul Welsh; Naveed Sattar; Jill Pell; Srinivasa Vittal Katikireddi,University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University Of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow,"BackgroundUnderstanding of the role of ethnicity and socioeconomic position in the risk of developing SARS-CoV-2 infection is limited. We investigated this in the UK Biobank study. MethodsThe UK Biobank study recruited 40-70 year olds in 2006-2010 from the general population, collecting information about self-defined ethnicity and socioeconomic variables (including area-level socioeconomic deprivation and educational attainment). SARS-CoV-2 test results from Public Health England were linked to baseline UK Biobank data. Poisson regression with robust standard errors was used to assess risk ratios (RRs) between the exposures and dichotomous variables for: being tested, having a positive test and testing positive in hospital. We also investigated whether ethnicity and socioeconomic position were associated with having a positive test amongst those tested. We adjusted for covariates including age, sex, social variables (including healthcare work and household size), behavioural risk factors and baseline health. diff --git a/data/covid/preprints.exact.csv b/data/covid/preprints.exact.csv index c11589f5..c42ee1a3 100644 --- a/data/covid/preprints.exact.csv +++ b/data/covid/preprints.exact.csv @@ -1,5 +1,13 @@ site,doi,date,link,title,authors,affiliations,abstract,category,match_type,author_similarity,affiliation_similarity -medRxiv,10.1101/2023.11.09.23298162,2023-11-10,https://medrxiv.org/cgi/content/short/2023.11.09.23298162,One year health outcomes associated with systemic corticosteroids for COVID-19: a longitudinal cohort study,Olivia C Leavy; Richard J Russell; Ewen M Harrison; Nazir I Lone; Steven Kerr; Annemarie B Docherty; Aziz Sheikh; Matthew Richardson; Omer Elneima; Neil J Greening; Victoria Claire Harris; Linzy Houchen-Wolloff; Hamish J C McAuley; Ruth M Saunders; Marco Sereno; Aarti Shikotra; Amisha Singapuri; Raminder Aul; Paul Beirne; Charlotte E Bolton; Jeremy S Brown; Gourab Choudhury; Nawar Diar Bakerly; Nicholas Easom; Carlos Echevarria; Jonathan Fuld; Nick Hart; John R Hurst; Mark Jones; Dhruv Parekh; Paul Pfeffer; Najib M Rahman; Sarah Rowland-Jones; Ajay M Shah; Dan G Wootton; Caroline Jolley; AA Roger Thompson; Trudie Chalder; Melanie J Davies; Anthony De Soyza; John R Geddes; William Greenhalf; Simon Heller; Luke Howard; Joseph Jacob; R Gisli Jenkins; Janet M Lord; Will D-C Man; Gerry P McCann; Stefan Neubauer; Peter JM Openshaw; Joanna Porter; Matthew J Rowland; Janet T Scott; Malcolm G Semple; Sally J Singh; David Thomas; Mark Toshner; Keir Lewis; Liam G Heaney; Andrew Briggs; Bang Zheng; Mathew Thorpe; Jennifer K Quint; James D Chalmers; Ling-Pei Ho; Alex Horsley; Michael Marks; Krisnah Poinasamy; Betty Raman; Louise V Wain; Christopher E Brightling; Rachael A Evans; - PHOSP-COVID Collaborative Group,"Department of Population Health Sciences, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; The Usher Institute, University of Edinburgh, Edinburgh, UK; Roslin Institute, University of Edinburgh, Edinburgh, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; The Usher Institute, University of Edinburgh, Edinburgh, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; Centre for Exercise and Rehabilitation Science, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; St Georges University Hospitals NHS Foundation Trust, London, UK; The Leeds Teaching Hospitals NHS Trust, Leeds, UK; University of Nottingham, Nottingham, UK; UCL Respiratory, Department of Medicine, University College London, Rayne Institute, London, UK; University of Edinburgh, Edinburgh, UK; Manchester Metropolitan University, Manchester, UK; Infection Research Group, Hull University Teaching Hospitals, Hull, UK; The Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK; Department of Respiratory Medicine, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Lane Fox Respiratory Service, Guys and St Thomas NHS Foundation Trust, London, UK; University College London, London, UK; Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK; University of Birmingham, Birmingham, UK; Barts Health NHS Trust, London, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK; University of Sheffield, Sheffield, UK; Kings College London, London, UK; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Kings College London, London, UK; University of Sheffield, Sheffield, UK; Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK; Diabetes Research Centre, University of Leicester, Leicester, UK; Population Health Sciences Institute, Newcastle University, Newcastle Upon Tyne, UK; NIHR Oxford Health Biomedical Research Centre, University of Oxford, Oxford, UK; University of Liverpool, Liverpool, UK; Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK; Imperial College Healthcare NHS Trust, London, UK; Centre for Medical Image Computing, University College London, London, UK; National Heart and Lung Institute, Imperial College London, London, UK; MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK; Royal Brompton and Harefield Clinical Group, Guys and St Thomas NHS Foundation Trust, London, UK; Department of Cardiovascular Sciences, University of Leicester, Leicester, UK; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; National Heart and Lung Institute, Imperial College London, London, UK; UCL Respiratory, Department of Medicine, University College London, Rayne Institute, London, UK; Kadoorie Centre for Critical Care Research, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, U; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; Imperial College London, London, UK; Cambridge NIHR BRC, Cambridge, UK; Hywel Dda University Health Board, Wales, UK; Wellcome-Wolfson Institute for Experimental Medicine, Queens University Belfast, Belfast, UK; London School of Hygiene & Tropical Medicine, London, UK; London School of Hygiene & Tropical Medicine, London, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; NHLI, Imperial College London, London, UK; University of Dundee, Ninewells Hospital and Medical School, Dundee, UK; MRC Human Immunology Unit, University of Oxford, Oxford, UK; Division of Infection, Immunity & Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK; Asthma and Lung UK, London, UK; Radcliffe Department of Medicine, University of Oxford, Oxford, UK; Department of Population Health Sciences, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; ","Background In patients with COVID-19 requiring supplemental oxygen, dexamethasone reduces acute severity and improves survival, but longer-term effects are unknown. We hypothesised that systemic corticosteroid administration during acute COVID-19 would be associated with improved health-related quality of life (HRQoL) one year after discharge. Methods Adults admitted to hospital between February 2020 and March 2021 for COVID-19 and meeting current guideline recommendations for dexamethasone treatment were included using two prospective UK cohort studies. HRQoL, assessed by EQ-5D-5L utility index, pre-hospital and one year after discharge were compared between those receiving corticosteroids or not after propensity weighting for treatment. Secondary outcomes included patient reported recovery, physical and mental health status, and measures of organ impairment. Sensitivity analyses were undertaken to account for survival and selection bias. Findings In 1,888 participants included in the primary analysis, 1,149 received corticosteroids. There was no between-group difference in EQ-5D-5L utility index at one year (mean difference 0.004, 95% CI: -0.026 to 0.034, p = 0.77). A similar reduction in EQ-5D-5L was seen at one year between corticosteroid exposed and non-exposed groups (mean (SD) change -0.12 (0.22) vs -0.11 (0.22), p = 0.32). Overall, there were no differences in secondary outcome measures. After sensitivity analyses modelled using a larger cohort of 109,318 patients admitted to hospital with COVID-19, EQ-5D-5L utility index at one year remained similar between the two groups. Interpretation Systemic corticosteroids for acute COVID-19 have no impact on the large reduction in HRQoL one year after hospital discharge. Treatments to address this are urgently needed.",infectious diseases,exact,100,100 +medRxiv,10.1101/2023.11.09.23298162,2023-11-10,https://medrxiv.org/cgi/content/short/2023.11.09.23298162,One year health outcomes associated with systemic corticosteroids for COVID-19: a longitudinal cohort study,Olivia C Leavy; Richard J Russell; Ewen M Harrison; Nazir I Lone; Steven Kerr; Annemarie B Docherty; Aziz Sheikh; Matthew Richardson; Omer Elneima; Neil J Greening; Victoria Claire Harris; Linzy Houchen-Wolloff; Hamish J C McAuley; Ruth M Saunders; Marco Sereno; Aarti Shikotra; Amisha Singapuri; Raminder Aul; Paul Beirne; Charlotte E Bolton; Jeremy S Brown; Gourab Choudhury; Nawar Diar Bakerly; Nicholas Easom; Carlos Echevarria; Jonathan Fuld; Nick Hart; John R Hurst; Mark Jones; Dhruv Parekh; Paul Pfeffer; Najib M Rahman; Sarah Rowland-Jones; Ajay M Shah; Dan G Wootton; Caroline Jolley; AA Roger Thompson; Trudie Chalder; Melanie J Davies; Anthony De Soyza; John R Geddes; William Greenhalf; Simon Heller; Luke Howard; Joseph Jacob; R Gisli Jenkins; Janet M Lord; Will D-C Man; Gerry P McCann; Stefan Neubauer; Peter JM Openshaw; Joanna Porter; Matthew J Rowland; Janet T Scott; Malcolm G Semple; Sally J Singh; David Thomas; Mark Toshner; Keir Lewis; Liam G Heaney; Andrew Briggs; Bang Zheng; Mathew Thorpe; Jennifer K Quint; James D Chalmers; Ling-Pei Ho; Alex Horsley; Michael Marks; Krisnah Poinasamy; Betty Raman; Louise V Wain; Christopher E Brightling; Rachael A Evans; - PHOSP-COVID Collaborative Group,"Department of Population Health Sciences, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; The Usher Institute, University of Edinburgh, Edinburgh, UK; Roslin Institute, University of Edinburgh, Edinburgh, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; The Usher Institute, University of Edinburgh, Edinburgh, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; Centre for Exercise and Rehabilitation Science, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; St Georges University Hospitals NHS Foundation Trust, London, UK; The Leeds Teaching Hospitals NHS Trust, Leeds, UK; University of Nottingham, Nottingham, UK; UCL Respiratory, Department of Medicine, University College London, Rayne Institute, London, UK; University of Edinburgh, Edinburgh, UK; Manchester Metropolitan University, Manchester, UK; Infection Research Group, Hull University Teaching Hospitals, Hull, UK; The Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK; Department of Respiratory Medicine, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Lane Fox Respiratory Service, Guys and St Thomas NHS Foundation Trust, London, UK; University College London, London, UK; Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK; University of Birmingham, Birmingham, UK; Barts Health NHS Trust, London, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK; University of Sheffield, Sheffield, UK; Kings College London, London, UK; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Kings College London, London, UK; University of Sheffield, Sheffield, UK; Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK; Diabetes Research Centre, University of Leicester, Leicester, UK; Population Health Sciences Institute, Newcastle University, Newcastle Upon Tyne, UK; NIHR Oxford Health Biomedical Research Centre, University of Oxford, Oxford, UK; University of Liverpool, Liverpool, UK; Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK; Imperial College Healthcare NHS Trust, London, UK; Centre for Medical Image Computing, University College London, London, UK; National Heart and Lung Institute, Imperial College London, London, UK; MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK; Royal Brompton and Harefield Clinical Group, Guys and St Thomas NHS Foundation Trust, London, UK; Department of Cardiovascular Sciences, University of Leicester, Leicester, UK; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; National Heart and Lung Institute, Imperial College London, London, UK; UCL Respiratory, Department of Medicine, University College London, Rayne Institute, London, UK; Kadoorie Centre for Critical Care Research, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, U; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; Imperial College London, London, UK; Cambridge NIHR BRC, Cambridge, UK; Hywel Dda University Health Board, Wales, UK; Wellcome-Wolfson Institute for Experimental Medicine, Queens University Belfast, Belfast, UK; London School of Hygiene & Tropical Medicine, London, UK; London School of Hygiene & Tropical Medicine, London, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; NHLI, Imperial College London, London, UK; University of Dundee, Ninewells Hospital and Medical School, Dundee, UK; MRC Human Immunology Unit, University of Oxford, Oxford, UK; Division of Infection, Immunity & Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK; Asthma and Lung UK, London, UK; Radcliffe Department of Medicine, University of Oxford, Oxford, UK; Department of Population Health Sciences, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; ","BackgroundIn patients with COVID-19 requiring supplemental oxygen, dexamethasone reduces acute severity and improves survival, but longer-term effects are unknown. We hypothesised that systemic corticosteroid administration during acute COVID-19 would be associated with improved health-related quality of life (HRQoL) one year after discharge. + +MethodsAdults admitted to hospital between February 2020 and March 2021 for COVID-19 and meeting current guideline recommendations for dexamethasone treatment were included using two prospective UK cohort studies. HRQoL, assessed by EQ-5D-5L utility index, pre-hospital and one year after discharge were compared between those receiving corticosteroids or not after propensity weighting for treatment. Secondary outcomes included patient reported recovery, physical and mental health status, and measures of organ impairment. Sensitivity analyses were undertaken to account for survival and selection bias. + +FindingsIn 1,888 participants included in the primary analysis, 1,149 received corticosteroids. There was no between-group difference in EQ-5D-5L utility index at one year (mean difference 0.004, 95% CI: -0.026 to 0.034, p = 0.77). A similar reduction in EQ-5D-5L was seen at one year between corticosteroid exposed and non-exposed groups (mean (SD) change -0.12 (0.22) vs -0.11 (0.22), p = 0.32). Overall, there were no differences in secondary outcome measures. After sensitivity analyses modelled using a larger cohort of 109,318 patients admitted to hospital with COVID-19, EQ-5D-5L utility index at one year remained similar between the two groups. + +InterpretationSystemic corticosteroids for acute COVID-19 have no impact on the large reduction in HRQoL one year after hospital discharge. Treatments to address this are urgently needed. + +Take home messageSystemic corticosteroids given for acute COVID-19 do not affect health-related quality of life or other patient reported outcomes, physical and mental health outcomes, and organ function one year after hospital discharge",infectious diseases,exact,100,100 medRxiv,10.1101/2023.10.26.23297598,2023-10-26,https://medrxiv.org/cgi/content/short/2023.10.26.23297598,Assessing the causal effect of air pollution on risk of SARS-CoV-2 infection,Annalan Mathew Dwight Navaratnam; Sarah Beale; Yamina Boukari; Vincent Nguyen; Wing Lam Erica Fong; Isobel Braithwaite; Thomas Edward Byrne; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Parth Patel; Madhumita Shrotri; Alexei Yavlinsky; Andrew Hayward; Haneen Khreis; Robert W Aldridge,University College London; University College London; University College London; University College London; University College London; University College London; University College London; UCL; University College London; University College London; University College London; University College London; University College London; UCL; University of Cambridge; UCL,"IntroductionEmerging evidence suggests association of air pollution exposure with risk of SARS-CoV-2 infection, but many of these findings are limited by study design, lack of individual-level covariate data or are specific to certain subpopulations. We aim to evaluate causal effects of air pollution on risk of infection, whilst overcoming these limitations. MethodsConcentrations for black carbon(BC), particulate matter 10(PM10), particulate matter 2.5(PM2.5), nitrogen dioxide(NO2) and oxides of nitrogen(NOx) from the Department of Environment, Food and Rural Affairs (DEFRA) and Effect of Low-level Air Pollution: A Study in Europe (ELAPSE) were linked to postcodes of 53,683 Virus Watch study participants. The primary outcome was first SARS-CoV-2 infection, between 1st September 2020 and 30th April 2021. Regression analysis used modified Poisson with robust estimates, clustered by household, adjusting for individual (e.g., age, sex, ethnicity) and environmental covariates(e.g., population density, region) to estimate total and direct effects. @@ -31,27 +39,6 @@ C_LIO_LIBoth date and reason of test are important confounders to be included wh C_LIO_LIThere was little difference in COVID-19 infection risk by job category after adjusting for test reason; however women were less likely to test positive than men C_LI",occupational and environmental health,exact,100,100 medRxiv,10.1101/2023.08.11.23293977,2023-08-15,https://medrxiv.org/cgi/content/short/2023.08.11.23293977,"Digital Mental Health Service engagement changes during Covid-19 in children and young people across the UK: presenting concerns, service activity, and access by gender, ethnicity, and deprivation",Duleeka Knipe; Santiago de Ossorno Garcia; Louisa Salhi; Lily Mainstone-Cotton; Aaron Sefi; Ann John,University of Bristol School of Social and Community Medicine: University of Bristol Population Health Sciences; Kooth Digital Health; Kooth Digital Health; Kooth Digital Health; Kooth Digital Health; Swansea University,"The adoption of digital health technologies accelerated during Covid-19, with concerns over the equity of access due to digital exclusion. Using data from a text-based online mental health service for children and young people we explore the impact of the pandemic on service access and presenting concerns and whether differences were observed by sociodemographic characteristics in terms of access (gender, ethnicity and deprivation). We used interrupted time-series models to assess whether there was a change in the level and rate of service use during the Covid-19 pandemic (April 2020-April 2021) compared to pre-pandemic trends (June 2019-March 2020). Routinely collected data from 61221 service users were extracted for observation, those represented half of the service population as only those with consent to share their data were used. The majority of users identified as female (74%) and White (80%), with an age range between 13 and 20 years of age. There was evidence of a sudden increase (13%) in service access at the start of the pandemic (RR 1.13 95% CI 1.02, 1.25), followed by a reduced rate (from 25% to 21%) of engagement during the pandemic compared to pre-pandemic trends (RR 0.97 95% CI 0.95,0.98). There was a sudden increase in almost all presenting issues apart from physical complaints. There was evidence of a step increase in the number of contacts for Black/African/Caribbean/Black British (38% increase; 95% CI: 1%-90%) and White ethnic groups (14% increase; 95% CI: 2%-27%)), sudden increase in service use at the start of the pandemic for the most (58% increase; 95% CI: 1%-247%) and least (47% increase; 95% CI: 6%-204%) deprived areas. During the pandemic, contact rates decreased, and referral sources change at the start. Findings on access and service activity align with other studies observing reduced service utilization. The lack of differences in deprivation levels and ethnicity at lockdown suggests exploring equity of access to the anonymous service. The study provides unique insights into changes in digital mental health use during Covid-19 in the UK.",public and global health,exact,100,100 -medRxiv,10.1101/2023.08.07.23293778,2023-08-09,https://medrxiv.org/cgi/content/short/2023.08.07.23293778,"Diabetes following SARS-CoV-2 infection: Incidence, persistence, and implications of COVID-19 vaccination. A cohort study of fifteen million people.",Kurt Taylor; Sophie Eastwood; Venexia Walker; Genevieve Cezard; Rochelle Knight; Marwa Al Arab; Yinghui Wei; Elsie M F Horne; Lucy Teece; Harriet Forbes; Alex Walker; Louis Fisher; Jon Massey; Lisa E M Hopcroft; Tom Palmer; Jose Cuitun Coronado; Samantha Ip; Simon Davy; Iain Dillingham; Caroline Morton; Felix Greaves; John MacLeod; Ben Goldacre; Angela Wood; Nishi Chaturvedi; Jonathan A C Sterne; Rachel Denholm; - CONVALESCENCE Long-COVID study; - Longitudinal Health and Wellbeing and Data and Connectivity UK COVID-19 National Core Studies; - OpenSAFELY collaborative,University of Bristol; University College London; University of Bristol; University of Cambridge; University of Bristol; University of Bristol; University of Plymouth; University of Bristol; University of Leicester; London School of Hygiene & Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Bristol; University of Bristol; University of Cambridge; University of Oxford; University of Oxford; University of Oxford; National Institute for Health and Care Excellence; University of Bristol; University of Oxford; University of Cambridge; University College London; University of Bristol; University of Bristol; -; -; -,"BackgroundType 2 diabetes (T2DM) incidence is increased after diagnosis of COVID-19. The impact of vaccination on this increase, for how long it persists, and the effect of COVID-19 on other types of diabetes remain unclear. - -MethodsWith NHS England approval, we studied diabetes incidence following COVID-19 diagnosis in pre-vaccination (N=15,211,471, January 2020-December 2021), vaccinated (N =11,822,640), and unvaccinated (N=2,851,183) cohorts (June-December 2021), using linked electronic health records. We estimated adjusted hazard ratios (aHRs) comparing diabetes incidence post-COVID-19 diagnosis with incidence before or without diagnosis up to 102 weeks post-diagnosis. Results were stratified by COVID-19 severity (hospitalised/non-hospitalised) and diabetes type. - -FindingsIn the pre-vaccination cohort, aHRS for T2DM incidence after COVID-19 (compared to before or without diagnosis) declined from 3.01 (95% CI: 2.76,3.28) in weeks 1-4 to 1.24 (1.12,1.38) in weeks 53-102. aHRS were higher in unvaccinated than vaccinated people (4.86 (3.69,6.41)) versus 1.42 (1.24,1.62) in weeks 1-4) and for hospitalised COVID-19 (pre-vaccination cohort 21.1 (18.8,23.7) in weeks 1-4 declining to 2.04 (1.65,2.51) in weeks 52-102), than non-hospitalised COVID-19 (1.45 (1.27,1.64) in weeks 1-4, 1.10 (0.98,1.23) in weeks 52-102). T2DM persisted for 4 months after COVID-19 for [~]73% of those diagnosed. Patterns were similar for Type 1 diabetes, though excess incidence did not persist beyond a year post-COVID-19. - -InterpretationElevated T2DM incidence after COVID-19 is greater, and persists longer, in hospitalised than non-hospitalised people. It is markedly less apparent post-vaccination. Testing for T2DM after severe COVID-19 and promotion of vaccination are important tools in addressing this public health problem. - -Research in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed for population-based observational studies published between December 1st 2019 and July 12th 2023 examining associations between SARS-CoV-2 infection or COVID-19 diagnosis (search string: SARS-CoV-2 or COVID* or coronavirus*) and subsequent incident diabetes (search term: diabetes). Of nineteen relevant studies; eight had a composite outcome of diabetes types, six stratified by diabetes type and five pertained to type-1-diabetes (T1DM) only. We did not identify any studies relating to gestational or other types of diabetes. Eleven studies were from the US, three from the UK, two from Germany, one from Canada, one from Denmark and one from South Korea. - -Most studies described cumulative relative risks (for infection versus no infection) one to two years post-SARS-CoV-2 infection of 1.2 to 2.6, though four studies found no associations with T1DM after the post-acute period. All studies lacked the power to compare diabetes relative risk by type, severity, and vaccination status in population subgroups. One study examined relative risks by vaccination status, but this used a composite outcome of diabetes and hyperlipidaemia and was conducted in a predominantly white male population. - -Two studies of T1DM found no evidence of elevated risk beyond 30 days after COVID-19 diagnosis, whilst two reported elevated risks at six months. Two studies of type 2 diabetes (T2DM) examined relative risks by time period post-infection: one study of US insurance claims reported a persistent association six months post-infection, whereas a large UK population-based study reported no associations after 12 weeks. However, the latter study used only primary care data, therefore COVID-19 cases were likely to have been under-ascertained. - -No large studies have investigated the persistence of diabetes diagnosed following COVID-19; key to elucidating the role of stress/steroid-induced hyperglycaemia. - -Added value of this studyThis study, which is the largest to address the question to date, analysed linked primary and secondary care health records with SARS-CoV-2 testing and COVID-19 vaccination data for 15 million people living in England. This enabled us to compare the elevation in diabetes incidence after COVID-19 diagnosis by diabetes type, COVID-19 severity and vaccination status, overall and in population subgroups. Importantly, excess diabetes incidence by time period since infection could also be quantified. Since healthcare in the UK is universal and free-at-the-point-of-delivery, almost the entire population is registered with primary care. Therefore the findings are likely to be generalisable. - -We found that, before availability of COVID-19 vaccination, a COVID-19 diagnosis (vs. no diagnosis) was associated with increased T2DM incidence which remained elevated by approximately 30% beyond one year after diagnosis. Though still present (with around 30% excess incidence at eight weeks), these associations were substantially attenuated in unvaccinated compared with vaccinated people. Excess incidence was greater in people hospitalised with COVID-19 than those who were not hospitalised after diagnosis. T1DM incidence was elevated up to, but not beyond, a year post COVID-19. Around 73% of people diagnosed with incident T2DM after COVID-19 still had evidence of diabetes four months after infection. - -Implications of all the available evidenceThere is a 30-50% elevated T2DM incidence post-COVID-19, but we report the novel finding that there is elevated incidence beyond one-year post-diagnosis. Elevated T1DM incidence did not appear to persist beyond a year, which may explain why previous studies disagree. For the first time in a general-population dataset, we demonstrate that COVID-19 vaccination reduces, but does not entirely ameliorate, excess diabetes incidence after COVID-19. This supports a policy of universal vaccination and suggests that other public health activities, such as enhanced diabetes screening after severe COVID-19, may be warranted, particularly in unvaccinated people.",epidemiology,exact,100,100 medRxiv,10.1101/2023.07.28.23293269,2023-08-05,https://medrxiv.org/cgi/content/short/2023.07.28.23293269,Fit notes associated with COVID-19 in 24 million patients' primary care records: A cohort study in OpenSAFELY-TPP,Andrea L Schaffer; Robin Y Park; John Tazare; Krishnan Bhaskaran; Brian MacKenna; Spiros Denaxas; Iain Dillingham; - The OpenSAFELY Collaborative; Amir Mehrkar; Christopher Bates; Ben Goldacre; Felix Greaves; John Macleod; Iain Dillingham; - National Core Studies Collaborative; Laurie Tomlinson; Alex J Walker,University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University College London; University of Oxford; -; University of Oxford; TPP; University of Oxford; Imperial College London; NIHR Applied Research Collaboration (ARC) West; University of Oxford; -; London School of Hygiene and Tropical Medicine; University of Oxford,"BackgroundFit notes (""sick notes"") are issued by general practitioners (GPs) when a person cant work for health reasons and is an indication of the public health and economic burden for people recovering from COVID-19. MethodsWith NHS England approval, we used routine clinical data from >24 million patients to compare fit note incidence in people 18-64 years with and without evidence of COVID-19 in 2020, 2021 and 2022. We fit Cox regression models to estimate adjusted hazard ratios, overall and by time post-diagnosis and within demographic subgroups. @@ -67,6 +54,7 @@ We found two peer-reviewed studies and one briefing by an independent think tank Added value of this studyThis study is the first to quantify changes in fit note rate since the start of the COVID-19 pandemic among people with a reported SARS-CoV-2 infection and how this compares with the general population in the UK. We found that people with evidence of SARS-CoV-2 infection had a higher fit note rate than the general population, even after adjusting for demographics and clinical characteristics. While this increased risk was greatest in 2020 (hazard ratio [HR] = 4.07, 95%CI 4.02-4.12), it continued to a lesser extent even into 2022 (HR = 1.57, 95%CI 1.56-1.58). The fit note rate was greatest in the first 30 days post-diagnosis, suggesting that most sick leave is associated with the acute phase. In subgroup analyses, the groups with the greatest relative increased risk changed over the years. People aged 18-24 years had a larger relative increased risk of fit notes (as measured by HR) in 2022 than 2021, when compared with the general population in each year. Additionally, while in 2020 and 2021 the HR increased along with lessening deprivation, this effect dissipated in 2022. In contrast, people hospitalised with COVID-19 were less likely to be issued a fit note than the pneumonia cohort, suggesting the long-term effects may be similar to comparable severe respiratory infections cases resulting in hospitalisation. Implications of all the available evidenceWhile we have likely underestimated the fit note rate due to overcounting of people in the workforce and misclassification of COVID-19 status, we still identified a substantial increased risk of receiving a fit note in people with COVID-19 compared with the general population over all years, even after adjusting for demographics and a wide range of clinical characteristics. The increased risk persisted into 2022, in an era where most people are vaccinated and the severity of COVID-19 illness is lessened. Given the high infection rates still occurring, these findings provide evidence for a substantial impact of COVID-19 on productivity and further evidence of the long-term impacts of COVID-19.",epidemiology,exact,100,100 +medRxiv,10.1101/2023.08.02.23293519,2023-08-04,https://medrxiv.org/cgi/content/short/2023.08.02.23293519,Real-time epidemiological modelling during the COVID-19 emergency in Wales,Michael Gravenor; Mark Dawson; Ed Bennett; Ben Thorpe; Carla White; Alma Rahat; Daniel Archambault; Noemi Picco; Gibin Powathil; Biagio Lucini,Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University,"The sudden outbreak of the COVID-19 pandemic presented governments, policy makers and health services with an unprecedented challenge of taking real-time decisions that could keep the disease under control with non-pharmaceutical interventions, while at the same time limit as much as possible severe consequences of a very strict lockdown. Mathematical modelling has proved to be a crucial element for informing those decisions. Here we report on the rapid development and application of the Swansea Model, a mathematical model of disease spread in real time, to inform policy decisions during the COVID-19 pandemic in Wales.",epidemiology,exact,100,100 medRxiv,10.1101/2023.06.29.23292056,2023-07-01,https://medrxiv.org/cgi/content/short/2023.06.29.23292056,Genome-wide Association Study of Long COVID,Vilma Lammi; Tomoko Nakanishi; Samuel E Jones; Shea J Andrews; Juha Karjalainen; Beatriz Cortes; Heath E O'Brien; Brian E Fulton-Howard; Hele H Haapaniemi; Axel Schmidt; Ruth E Mitchell; Abdou Mousas; Massimo Mangino; Alicia Huerta-Chagoya; Nasa Sinnott-Armstrong; Elizabeth T Cirulli; Marc Vaudel; Alex SF Kwong; Amit K Maiti; Minttu M Marttila; Chiara Batini; Francesca Minnai; Anna R Dearman; CA Robert Warmerdam; Celia B Sequeros; Thomas W Winkler; Daniel M Jordan; Lindsay Guare; Ekaterina Vergasova; Eirini Marouli; Pasquale Striano; Ummu Afeera Zainulabid; Ashutosh Kumar; Hajar Fauzan Ahmad; Ryuya Edahiro; Shuhei Azekawa; - Long COVID Host Genetics Initiative; - FinnGen; - DBDS Genomic Consortium; - GEN-COVID Multicenter Study; Joseph J Grzymski; Makoto Ishii; Yukinori Okada; Noam D Beckmann; Meena Kumari; Ralf Wagner; Iris M Heid; Catherine John; Patrick J Short; Per Magnus; Karina Banasik; Frank Geller; Lude H Franke; Alexander Rakitko; Emma L Duncan; Alessandra Renieri; Konstantinos K Tsilidis; Rafael de Cid; Ahmadreza Niavarani; Teresa Tusie-Luna; Shefali S Verma; George Davey Smith; Nicholas J Timpson; Mark J Daly; Andrea Ganna; Eva C Schulte; J Brent Richards; Kerstin U Ludwig; Michael Hultstrom; Hugo Zeberg; Hanna M Ollila,Institute for Molecular Medicine Finland (FIMM); Department of Human Genetics; Institute for Molecular Medicine Finland (FIMM); University of California San Francisco; Institute for Molecular Medicine Finland (FIMM); Genomes for Life-GCAT lab; Sano Genetics Limited; Genetics and Genomic Sciences; Institute for Molecular Medicine Finland (FIMM); Institute of Human Genetics; Centre for Clinical Brain Sciences; Department of Hygiene and Epidemiology; Department of Twin Research; Departamento de Medicina Genomica y Toxicologia Ambiental; Herbold Computational Biology Program; Helix; Mohn Center for Diabetes Precision Medicine; University of Bristol; Department of Genetics and Genomics; University of Helsinki; Department of Population Health Sciences; Institute for Biomedical Technologies - National Research Council; Institute for Social and Economic Research; Department of Genetics; Novo Nordisk Foundation Center for Protein Research; Department of Genetic Epidemiology; Charles Bronfman Institute for Personalized Medicine; Department of Pathology and Laboratory Medicine; Genotek Ltd.; William Harvey Research Institute; IRCCS G; Department of Internal Medicine; Department of Anatomy; Faculty of Industrial Sciences and Technology; Department of Statistical Genetics; Division of Pulmonary Medicine; ; ; ; ; Center for Genomic Medicine; Division of Pulmonary Medicine; Department of Statistical Genetics; Charles Bronfman Institute for Personalized Medicine; Institute for Social and Economic Research; Institute of Medical Microbiology & Hygiene; Department of Genetic Epidemiology; Department of Population Health Sciences; Sano Genetics Limited; Centre for Fertility and Health; Novo Nordisk Foundation Center for Protein Research; Statens Serum Institute; Department of Genetics; Genotek Ltd.; Department of Twin Research and Genetic Epidemiology; Medical Genetics; Department of Hygiene and Epidemiology; Genomes for Life-GCAT lab; Digestive Oncology Research Center; Instituto de Investigaciones Biomedicas Unam/ Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran; Department of Pathology and Laboratory Medicine; MRC Integrative Epidemiology Unit at the University of Bristol; MRC Integrative Epidemiology Unit at the University of Bristol; Institute for Molecular Medicine Finland (FIMM); Institute for Molecular Medicine Finland (FIMM); Institute of Psychiatric Phenomics & Genomics; Department of Human Genetics; Institute of Human Genetics; Anaesthesiology and Intensive Care Medicine; Department of Evolutionary Genetics; Institute for Molecular Medicine Finland (FIMM),"Infections can lead to persistent or long-term symptoms and diseases such as shingles after varicella zoster, cancers after human papillomavirus, or rheumatic fever after streptococcal infections1, 2. Similarly, infection by SARS-CoV-2 can result in Long COVID, a condition characterized by symptoms of fatigue and pulmonary and cognitive dysfunction3-5. The biological mechanisms that contribute to the development of Long COVID remain to be clarified. We leveraged the COVID-19 Host Genetics Initiative6, 7 to perform a genome-wide association study for Long COVID including up to 6,450 Long COVID cases and 1,093,995 population controls from 24 studies across 16 countries. We identified the first genome-wide significant association for Long COVID at the FOXP4 locus. FOXP4 has been previously associated with COVID-19 severity6, lung function8, and cancers9, suggesting a broader role for lung function in the pathophysiology of Long COVID. While we identify COVID-19 severity as a causal risk factor for Long COVID, the impact of the genetic risk factor located in the FOXP4 locus could not be solely explained by its association to severe COVID-19. Our findings further support the role of pulmonary dysfunction and COVID-19 severity in the development of Long COVID.",genetic and genomic medicine,exact,100,100 medRxiv,10.1101/2023.06.30.23292079,2023-06-30,https://medrxiv.org/cgi/content/short/2023.06.30.23292079,Synthesis and new evidence from the PROTECT UK National Core Study: Determining occupational risks of SARS-CoV-2 infection and COVID-19 mortality,Sarah Rhodes; Sarah Beale; Mark Cherrie; William Mueller; Fiona Holland; Melissa Matz; Ioannis Basinas; Jack D Wilkinson; Matthew Gittins; Bernardine Farrell; Andrew Hayward; Neil Pearce; Martie van Tongeren,University of Manchester; University College London; Institute of Occupational Medicine; Institute of Occupational Medicine; University of Manchester; London School of Hygiene and Tropical Medicine; University of Manchester; University of Manchester; University of Manchester; University of Manchester; UCL; London School of Hygiene and Tropical Medicine; University of Manchester,"IntroductionThe PROTECT National Core Study was funded by the UK Health and Safety Executive (HSE) to investigate routes of transmission for SARS-CoV-2 and variation between settings. @@ -259,6 +247,7 @@ C_LIO_LIData collected include demographics, details on occupation, co-morbiditi C_LIO_LINested within Virus Watch are a serology & PCR cohort study (n=12,877) and a vaccine evaluation study (n=19,555). C_LIO_LIStudy data are deposited in the Office of National Statistics (ONS) Secure Research Service (SRS). Survey data are available under restricted access upon request to ONS SRS. C_LI",epidemiology,exact,100,100 +medRxiv,10.1101/2023.01.29.23285160,2023-01-30,https://medrxiv.org/cgi/content/short/2023.01.29.23285160,High number of SARS-CoV-2 persistent infections uncovered through genetic analysis of samples from a large community-based surveillance study,Mahan Ghafari; Matthew Hall; Tanya Golubchik; Daniel Ayoubkhani; Thomas House; George MacIntyre-Cockett; Helen Fryer; Laura Thomson; Anel Nurtay; David Buck; Angie Green; Amy Trebes; Paolo Piazza; Lorne J Lonie; Ruth Studley; Emma Rourke; Darren Smith; Matthew Bashton; Andrew Nelson; Matthew Crown; Clare McCann; Gregory R Young; Rui Andre Nunes de Santos; Zack Richards; Adnan Tariq; Roberto Cahuantzi; - Wellcome Sanger Institute COVID-19 Surveillance Team; - COVID-19 Infection Survey Group; - The COVID-19 Genomics UK (COG-UK) consortium; Jeff Barrett; Christophe Fraser; David Bonsall; Sarah Walker; Katrina A Lythgoe,University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; University of Manchester; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; Office for National Statistics; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Office for National Statistics; -; -; -; Wellcome Sanger Institute; University of Oxford; University of Oxford; University of Oxford; University of Oxford,"Persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections may act as viral reservoirs that could seed future outbreaks 1-5, give rise to highly divergent lineages 6-8, and contribute to cases with post-acute Coronavirus disease 2019 (COVID-19) sequelae (Long Covid) 9,10. However, the population prevalence of persistent infections, their viral load kinetics, and evolutionary dynamics over the course of infections remain largely unknown. We identified 381 infections lasting at least 30 days, of which 54 lasted at least 60 days. These persistently infected individuals had more than 50% higher odds of self-reporting Long Covid compared to the infected controls, and we estimate that 0.09-0.5% of SARS-CoV-2 infections can become persistent and last for at least 60 days. In nearly 70% of the persistent infections we identified, there were long periods during which there were no consensus changes in virus sequences, consistent with prolonged presence of non-replicating virus. Our findings also suggest reinfections with the same major lineage are rare and that many persistent infections are characterised by relapsing viral load dynamics. Furthermore, we found a strong signal for positive selection during persistent infections, with multiple amino acid substitutions in the Spike and ORF1ab genes emerging independently in different individuals, including mutations that are lineage-defining for SARS-CoV-2 variants, at target sites for several monoclonal antibodies, and commonly found in immunocompromised patients 11-14. This work has significant implications for understanding and characterising SARS-CoV-2 infection, epidemiology, and evolution.",epidemiology,exact,100,100 medRxiv,10.1101/2023.01.24.23284916,2023-01-25,https://medrxiv.org/cgi/content/short/2023.01.24.23284916,"Real-world effectiveness of molnupiravir, nirmatrelvir-ritonavir, and sotrovimab on preventing hospital admission among higher-risk patients with COVID-19 in Wales: a retrospective cohort study",Andrew Evans; Cathy Qi; Lolu Adebayo; Jonathan Underwood; James Coulson; Rowena Bailey; Gareth John; Alison Cooper; Ashley Akbari; Ronan Lyons; Adrian Edwards,"Welsh Government; Swansea University Medical School; Swansea University Medical School; School of Medicine, Cardiff University; School of Medicine, Cardiff University,; Swansea University Medical School; Digital Health and Care Wales; Wales COVID-19 Evidence Centre; Swansea University; Swansea University; Wales COVID-19 Evidence Centre","ObjectiveTo compare the effectiveness of molnupiravir, nirmatrelvir-ritonavir, and sotrovimab with no treatment in preventing hospital admission or death in higher-risk patients infected with SARS-CoV-2 in the community. DesignRetrospective cohort study of non-hospitalised adult patients with COVID-19 using the Secure Anonymised Information Linkage (SAIL) Databank. @@ -406,15 +395,6 @@ Existing evidence suggests that COVID-19 vaccines are effective for preventing s However, research directly comparing vaccine effectiveness between pregnant and non-pregnant women of reproductive age at the population level are lacking. What this study addsOur study provides real-world evidence that COVID-19 vaccination reduces the risk of hospital admission by a similar amount for both women infected with SARS-CoV-2 during pregnancy and women who were not pregnant when infected, during the Alpha and Delta dominant periods in England.",public and global health,exact,100,100 -medRxiv,10.1101/2022.09.23.22280285,2022-09-25,https://medrxiv.org/cgi/content/short/2022.09.23.22280285,"Dimethyl fumarate in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial",- RECOVERY Collaborative Group; Peter W Horby; Leon Peto; Natalie Staplin; Mark Campbell; Guilherme Pessoa-Amorim; Marion Mafham; Jonathan R Emberson; Richard Stewart; Benjamin Prudon; Alison Uriel; Christopher A Green; Devesh J Dhasmana; Flora Malein; Jaydip Majumdar; Paul Collini; Jack Shurmer; Bryan Yates; J Kenneth Baillie; Maya H Buch; Jeremy N Day; Saul N Faust; Thomas Jaki; Katie Jeffery; Edmund Juszczak; Marian Knight; Wei Shen Lim; Alan Montgomery; Andrew Mumford; Kathryn Rowan; Guy Thwaites; Richard Haynes; Martin Landray,"; Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, University of Oxford, Oxford, United Kingdom; Milton Keynes University Hospital NHS Foundation Trust; North Tees and Hartlepool NHS Foundation Trust; Manchester University NHS Foundation Trust; University Hospitals Birmingham NHS Foundation Trust; Victoria Hospital Kirkcaldy, NHS Fife; Liverpool University Hospitals NHS Foundation Trust; Mid Cheshire Hospitals NHS Foundation Trust; Sheffield Teaching Hospitals NHS Foundation Trust; Bolton NHS Foundation Trust; Northumbria Healthcare NHS Foundation Trust; Roslin Institute, University of Edinburgh; Centre for Musculoskeletal Research, University of Manchester, Manchester, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam; NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University of Southampton, Southampton, United Kingdom; University of Regensburg, Germany; Oxford University Hospitals NHS Foundation Trust; School of Medicine, University of Nottingham, Nottingham, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom; Intensive Care National Audit & Research Centre, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam; MRC Population Health Research Unit, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom","BackgroundDimethyl fumarate (DMF) is an anti-inflammatory drug that has been proposed as a treatment for patients hospitalised with COVID-19 - -MethodsThis randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), is assessing multiple possible treatments in patients hospitalised for COVID-19. In this initial assessment of DMF, performed at 27 UK hospitals, eligible and consenting adults were randomly allocated (1:1) to either usual standard of care alone or usual standard of care plus DMF 120mg twice daily for 2 days followed by 240mg twice daily for 8 days, or until discharge if sooner. The primary outcome was clinical status on day 5 measured on a seven-point ordinal scale, assessed using a proportional odds model. Secondary outcomes were time to sustained improvement in clinical status, time to discharge, day 5 peripheral blood oxygenation, day 5 C-reactive protein, and improvement in day 10 clinical status. The trial is registered with ISRCTN (50189673) and clinicaltrials.gov (NCT04381936). - -FindingsBetween 2 March 2021 and 18 November 2021, 713 patients were enrolled in the DMF evaluation, of whom 356 were randomly allocated to receive usual care plus DMF, and 357 to usual care alone. 95% of patients were receiving corticosteroids as part of routine care. There was no evidence of a beneficial effect of DMF on clinical status at day 5 (common odds ratio of unfavourable outcome 1.12; 95% CI 0.85-1.46; p=0.42). There was no significant effect of DMF on any secondary outcome. As expected, DMF caused flushing and gastrointestinal symptoms, each in around 6% of patients, but no new adverse effects were identified. - -InterpretationIn adults hospitalised with COVID-19, DMF was not associated with an improvement in clinical outcomes. - -FundingUK Research and Innovation (Medical Research Council) and National Institute of Health Research (Grant ref: MC_PC_19056).",infectious diseases,exact,100,100 medRxiv,10.1101/2022.09.21.22280191,2022-09-21,https://medrxiv.org/cgi/content/short/2022.09.21.22280191,Exploring the relationship between job characteristics and infection: Application of a COVID-19 Job Exposure Matrix to SARS-CoV-2 infection data in the United Kingdom,Sarah Rhodes; Sarah Beale; Jack Wilkinson; Karin Van-Veldhoven; Ioannis Basinas; Will Mueller; Karen Oedehengel; Alex Burdorf; Susan Peters; Zara Stokholm; Vivi Schlunssen; Henrik Kolstad; Anjoeka Pronk; Neil Pearce; Andrew Hayward; Martie van Tongeren,University of Manchester; University College London; University of Manchester; London School of Hygiene and Tropical Medicine; University of Manchester; Institute of Occupational Medicine; Netherlands Organization for Applied Scientific Research; Erasmus Medical Center Rotterdam; Utrecht University; Aarhus University Hospital; Aarhus University; Aarhus University Hospital; Dutch Institution of Applied Science; London School of Hygiene and Tropical Medicine; UCL; University of Manchester,"ObjectivesTo assess whether workplace exposures as estimated via a COVID-19 Job Exposure Matrix (JEM) are associated with SARS-CoV-2. MethodsData on 244,470 participants were available from the ONS Coronavirus Infection Survey (CIS) and 16,801 participants from the Virus Watch Cohort, restricted to workers aged 20 to 64. Analysis used logistic regression models with SARS-CoV-2 as the dependent variable for eight individual JEM domains (number of workers, nature of contacts, contact via surfaces, indoor or outdoor location, ability to social distance, use of face covering, job insecurity, migrant workers) with adjustment for age, sex, ethnicity, Index of Multiple Deprivation (IMD), region, household size, urban vs rural area, and health conditions. Analyses were repeated for three time periods (i) February 2020 (Virus Watch)/April 2020 (CIS) to May 2021), (ii)June 2021 to November 2021, (iii) December 2021 to January 2022. @@ -683,13 +663,6 @@ What is already known on this topicSome occupational groups have observed increa What this study addsRelative differences between occupational groups have varied during different stages of the COVID-19 pandemic with risks for healthcare workers diminishing over time and workers in the education sector seeing persistent elevated risks. How this study might affect research, practice or policyIncreased long term mitigation such as ventilation should be considered in sectors with a persistent elevated risk. It is important for workplace policy to be responsive to evolving pandemic risks.",occupational and environmental health,exact,100,100 -medRxiv,10.1101/2022.04.26.22274332,2022-04-27,https://medrxiv.org/cgi/content/short/2022.04.26.22274332,"Community factors and excess mortality in the COVID-19 pandemic in England, Italy and Sweden",Brandon Parkes; Massimo Stafoggia; Daniela Fecht; Bethan Davies; Carl Bonander; Francesca de'Donato; Paola Michelozzi; Frédéric B. Piel; Ulf Strömberg; Marta Blangiardo,Imperial College London; Lazio Regional Health Service; Imperial College London; Imperial College London; University of Gothenburg; Lazio Regional Health Service; Lazio Regional Health Service; Imperial College London; University of Gothenburg; Imperial College London,"BackgroundAnalyses of COVID-19 suggest specific risk factors make communities more or less vulnerable to pandemic related deaths within countries. What is unclear is whether the characteristics affecting vulnerability of small communities within countries produce similar patterns of excess mortality across countries with different demographics and public health responses to the pandemic. Our aim is to quantify community-level variations in excess mortality within England, Italy and Sweden and identify how such spatial variability was driven by community-level characteristics. - -MethodsWe applied a two-stage Bayesian model to quantify inequalities in excess mortality in people aged 40 years and older at the community level in England, Italy and Sweden during the first year of the pandemic (March 2020-February 2021). We used community characteristics measuring deprivation, air pollution, living conditions, population density and movement of people as covariates to quantify their associations with excess mortality. - -ResultsWe found just under half of communities in England (48.1%) and Italy (45.8%) had an excess mortality of over 300 per 100,000 males over the age of 40, while for Sweden that covered 23.1% of communities. We showed that deprivation is a strong predictor of excess mortality across the three countries, and communities with high levels of overcrowding were associated with higher excess mortality in England and Sweden. - -ConclusionThese results highlight some international similarities in factors affecting mortality that will help policy makers target public health measures to increase resilience to the mortality impacts of this and future pandemics.",epidemiology,exact,100,100 medRxiv,10.1101/2022.04.21.22274152,2022-04-27,https://medrxiv.org/cgi/content/short/2022.04.21.22274152,"Health care use attributable to COVID-19: A propensity matched national electronic health records cohort study of 249,390 people in Wales, UK.",Jonathan Kennedy; Michael Parker; Michael Seaborne; Mohamed Mhereeg; Alex J Walker; Venexia Walker; Spiros Denaxas; Natasha Kennedy; Srinivasa Vittal Katikireddi; Sinead Brophy,"Swansea University; Swansea University; Swansea University; Swansea University; Datalab, Nuffield Dept of Primary Care Health Science, Radcliffe Primary Care Building, Oxford, OX2 6GG.; University of Bristol; University College London; Swansea University; University of Glasgow; Swansea University","BackgroundTo determine the extent and nature of changes in infected patients healthcare utilization, we studied healthcare contact in the 1-4 weeks and 5-24 weeks following a COVID-19 diagnosis compared to propensity matched controls. MethodsSurvival analysis was used for time to death and first clinical outcomes including clinical terminology concepts for post-viral illness, fatigue, embolism, respiratory conditions, mental and developmental conditions, fit note, or hospital attendance. Increased instantaneous risk for the occurrence of an outcome for positive individuals was quantified using hazard ratios (HR) from Cox Regression and absolute risk was quantified using relative risk (RR) from life table analysis. @@ -716,6 +689,7 @@ Methods534 individuals with Long Covid underwent baseline CMR (T1 and T2 mapping ResultsThe technical success of this multiorgan assessment in non-acute settings was 99.1% at baseline, and 98.3% at follow up, with 99.6% and 98.8% for CMR respectively. Of individuals with Long Covid, 102/534 [19%] had cardiac impairment at baseline; 71/102 had complete paired data at 12 months. Of those, 58% presented with ongoing cardiac impairment at 12 months. High sensitivity cardiac troponin I and B-type natriuretic peptide were not predictive of CMR findings, symptoms, or clinical outcomes. At baseline, low LVEF, high RVEDV and low GLS were associated with cardiac impairment. Low LVEF at baseline was associated with persistent cardiac impairment at 12 months. ConclusionCardiac impairment, other than myocarditis, is present in 1 in 5 individuals with Long Covid at 6 months, persisting in over half of those at 12 months. Cardiac-related blood biomarkers are unable to identify cardiac impairment in Long COVID. Subtypes of disease (based on symptoms, examination, and investigations) and predictive biomarkers are yet to be established. Interventional trials with pre-specified subgroup analyses are required to inform therapeutic options.",cardiovascular medicine,exact,100,100 +medRxiv,10.1101/2022.03.29.22273042,2022-04-04,https://medrxiv.org/cgi/content/short/2022.03.29.22273042,The new normal? Dynamics and scale of the SARS-CoV-2 variant Omicron epidemic in England,Oliver Eales; Leonardo de Oliveira Martins; Andrew Page; Haowei Wang; Barbara Bodinier; David Tang; David Haw; Jakob Jonnerby; Christina Atchison; Deborah Ashby; Wendy Barclay; Graham Taylor; Graham Cooke; Helen Ward; Ara Darzi; Steven Riley; Paul Elliott; Christl A Donnelly; Marc Chadeau-Hyam,"Imperial College London; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Environment and Health, School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Environment and Health, School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Environment and Health, School of Public Health, Imperial College London, UK","The SARS-CoV-2 pandemic has been characterised by the regular emergence of genomic variants which have led to substantial changes in the epidemiology of the virus. With natural and vaccine-induced population immunity at high levels, evolutionary pressure favours variants better able to evade SARS-CoV-2 neutralising antibodies. The Omicron variant was first detected in late November 2021 and exhibited a high degree of immune evasion, leading to increased infection rates in many countries. However, estimates of the magnitude of the Omicron wave have relied mainly on routine testing data, which are prone to several biases. Here we infer the dynamics of the Omicron wave in England using PCR testing and genomic sequencing obtained by the REal-time Assessment of Community Transmission-1 (REACT-1) study, a series of cross-sectional surveys testing random samples of the population of England. We estimate an initial peak in national Omicron prevalence of 6.89% (5.34%, 10.61%) during January 2022, followed by a resurgence in SARS-CoV-2 infections in England during February-March 2022 as the more transmissible Omicron sub-lineage, BA.2 replaced BA.1 and BA.1.1. Assuming the emergence of further distinct genomic variants, intermittent epidemics of similar magnitude as the Omicron wave may become the new normal.",infectious diseases,exact,100,100 medRxiv,10.1101/2022.03.22.22271707,2022-03-23,https://medrxiv.org/cgi/content/short/2022.03.22.22271707,Vitamin D Supplements for Prevention of Covid-19 or other Acute Respiratory Infections: a Phase 3 Randomized Controlled Trial (CORONAVIT),David Jolliffe; Hayley Holt; Matthew Greenig; Mohammad Talaei; Natalia Perdek; Paul Pfeffer; Giulia Vivaldi; Sheena Maltby; Jane Symons; Nicola Barlow; Alexa Normandale; Rajvinder Garcha; Alex Richter; Sian Faustini; Christopher Orton; David Ford; Ronan Lyons; Gwyneth Davies; Frank Kee; Christopher Griffiths; John Norrie; Aziz Sheikh; Seif Shaheen; Clare Relton; Adrian Martineau,Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Jane Symons Media; City Hospital Birmingham; City Hospital Birmingham; City Hospital Birmingham; University of Birmingham; University of Birmingham; Swansea University; Swansea University; Swansea University; Swansea University; Queen's University Belfast; Queen Mary University of London; University of Edinburgh; University of Edinburgh; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London,"OBJECTIVESTo determine whether population-level implementation of a test-and- treat approach to correction of sub-optimal vitamin D status (25-hydroxyvitamin D [25(OH)D] <75 nmol/L) influences risk of all-cause acute respiratory infection (ARI) or coronavirus disease 2019 (COVID-19). DESIGNPhase 3 open-label randomised controlled trial (CORONAVIT) utilising trials-within-cohorts (TwiCs) methodology. @@ -778,6 +752,15 @@ Key pointsO_LIQuestion: What is the prevalence of organ impairment in Long COVID C_LIO_LIFindings: In a prospective study of 536 mainly non-hospitalised individuals, symptom burden decreased, but single organ impairment persisted in 59% at 12 months post-COVID-19. C_LIO_LIMeaning: Organ impairment in Long COVID has implications for symptoms, quality of life and longer-term health, signalling need for prevention and integrated care of Long COVID. C_LI",infectious diseases,exact,100,100 +medRxiv,10.1101/2022.03.17.22272414,2022-03-18,https://medrxiv.org/cgi/content/short/2022.03.17.22272414,Modelling the impact of non-pharmaceutical interventions on workplace transmission of SARS-CoV-2 in the home-delivery sector,Carl A Whitfield; Martie Van Tongeren; Yang Han; Hua Wei; Sarah A Daniels; Martyn Regan; David W Denning; Arpana Verma; Lorenzo Pellis; - University of Manchester COVID-19 Modelling Group; Ian Hall,University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchaster; University of Manchester; University of Manchester; ; University of Manchester,"ObjectiveWe aimed to use mathematical models of SARS-COV-2 to assess the potential efficacy of non-pharmaceutical interventions on transmission in the parcel delivery and logistics sector. + +MethodsWe developed a network-based model of workplace contacts based on data and consultations from companies in the parcel delivery and logistics sectors. We used these in stochastic simulations of disease transmission to predict the probability of workplace outbreaks in this settings. Individuals in the model have different viral load trajectories based on SARS-CoV-2 in-host dynamics, which couple to their infectiousness and test positive probability over time, in order to determine the impact of testing and isolation measures. + +ResultsThe baseline model (without any interventions) showed different workplace infection rates for staff in different job roles. Based on our assumptions of contact patterns in the parcel delivery work setting we found that when a delivery driver was the index case, on average they infect only 0.14 other employees, while for warehouse and office workers this went up to 0.65 and 2.24 respectively. In the LIDD setting this was predicted to be 1.40, 0.98, and 1.34 respectively. Nonetheless, the vast majority of simulations resulted in 0 secondary cases among customers (even without contact-free delivery). Our results showed that a combination of social distancing, office staff working from home, and fixed driver pairings (all interventions carried out by the companies we consulted) reduce the risk of workplace outbreaks by 3-4 times. + +ConclusionThis work suggests that, without interventions, significant transmission could have occured in these workplaces, but that these posed minimal risk to customers. We found that identifying and isolating regular close-contacts of infectious individuals (i.e. house-share, carpools, or delivery pairs) is an efficient measure for stopping workplace outbreaks. Regular testing can make these isolation measures even more effective but also increases the number of staff isolating at one time. It is therefore more efficient to use these isolation measures in addition to social distancing and contact reduction interventions, rather than instead of, as these reduce both transmission and the number of people needing to isolate at one time. + +Author summaryDuring the COVID-19 pandemic the home-delivery sector was vital to maintaining peoples access to certain goods, and sustaining levels of economic activity for a variety of businesses. However, this important work necessarily involved contact with a large number of customers as well as colleagues. This means that questions have often been raised about whether enough was being done to keep customers and staff safe. Estimating the potential risk to customers and staff is complex, but here we tackle this problem by building a model of workplace and customer contacts, from which we simulate SARS-CoV-2 transmission. By involving industry representatives in the development of this model, we have simulated interventions that have either been applied or considered, and so the findings of this study are relevant to decisions made in that sector. Furthermore, we can learn generic lessons from this specific case study which apply to many types of shared workplace as well as highlighting implications of the highly stochastic nature of disease transmission in small populations.",epidemiology,exact,100,100 medRxiv,10.1101/2022.03.09.22272098,2022-03-12,https://medrxiv.org/cgi/content/short/2022.03.09.22272098,"Duration of vaccine effectiveness against SARS-CoV2 infection, hospitalisation, and death in residents and staff of Long-Term Care Facilities (VIVALDI): a prospective cohort study, England, Dec 2020-Dec 2021",Madhumita Shrotri; Maria Krutikov; Hadjer Nacer-Laidi; Borscha Azmi; Tom Palmer; Rebecca Giddings; Chris Fuller; Aidan Irwin-Singer; Verity Baynton; Gokhan Tut; Paul Moss; Andrew Hayward; Andrew Copas; Laura Shallcross,"University College London; University College London; University College London; University College London; University College London; University College London; University College London; UK Government Department of Health & Social Care; UK Government Department of Health & Social Care; University of Birmingham, Medical School; University of Birmingham; UCL; University College London; UCL","BackgroundLong-term care facilities (LTCF) have been prioritised for vaccination, but data on potential waning of vaccine effectiveness (VE) and the impact of booster doses in this vulnerable population remains scarce. MethodsWe included residents and staff from 331 LTCFs enrolled in VIVALDI (ISRCTN 14447421), who underwent routine PCR testing between Dec 8, 2020 - Dec 11, 2021 in a Cox proportional hazards regression, estimating VE against SARS-CoV2 infection, COVID-19-related hospitalisation, and COVID-19-related death after 1-3 vaccine doses, stratifying by previous SARS-CoV2 exposure. @@ -837,13 +820,6 @@ Research in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed, Added value of this studyThis large population-based study, conducted in a population with known pre-vaccination SARS-CoV-2 serostatus, examines a comprehensive range of potential sociodemographic, behavioural, clinical, pharmacological and nutritional determinants of antibody responses to administration of two major SARS-CoV-2 vaccines (i.e., ChAdOx1 or BNT162b2), many of which have not previously been investigated. It is also the first population-based study to characterise antibody responses to booster doses of SARS-CoV-2 vaccines in adults who were seronegative after their primary course of vaccination. Implications of all the available evidenceIncreased risk of seronegativity following two doses of SARS-CoV-2 vaccines was associated with administration of ChAdOx1 vs BNT162b2, shorter interval between first and second vaccine doses, poorer self-assessed general health, immunocompromise and SARS-CoV-2 seronegativity pre-vaccination. Regular intake of vitamin D supplements was associated with reduced risk of post-vaccination seronegativity. Randomised controlled trials are now needed to test for causality. Booster doses of BNT162b2 or mRNA-1273 were highly effective in achieving seroconversion in the majority of people who failed to mount antibody responses following a primary course of vaccination, the few exceptions being a subset of those with primary immunodeficiency or systemic immunosuppressant drugs.",infectious diseases,exact,100,100 -medRxiv,10.1101/2022.02.10.22270799,2022-02-13,https://medrxiv.org/cgi/content/short/2022.02.10.22270799,Evaluating the effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control teams: the COG-UK hospital-onset COVID-19 infection study,Oliver Stirrup; James Blackstone; Fiona Mapp; Alyson MacNeil; Monica Panca; Alison Holmes; Nicholas Machin; Gee Yen Shin; Tabitha Mahungu; Kordo Saeed; Tranprit Saluja; Yusri Taha; Nikunj Mahida; Cassie Pope; Anu Chawla; Teresa Cutino-Moguel; Asif Tamuri; Rachel Williams; Alistair Darby; David L Robertson; Flavia Flaviani; Eleni Nastouli; Samuel Robson; Darren Smith; Matthew Loose; Kenneth Laing; Irene Monahan; Beatrix Kele; Sam Haldenby; Ryan George; Matthew Bashton; Adam Witney; Matthew Byott; Francesc Coll; Michael Chapman; Sharon Peacock; - COG-UK HOCI Investigators; - COG-UK Consortium; Joseph Hughes; Gaia Nebbia; David G Partridge; Matthew Parker; James Richard Price; Christine Peters; Sunando Roy; Luke B Snell; Thushan I de Silva; Emma Thomson; Paul Flowers; Andrew Copas; Judith Breuer,"Institute for Global Health, UCL, London, UK; Comprehensive Clinical Trials Unit, UCL, London, UK; Institute for Global Health, UCL, London, UK; Comprehensive Clinical Trials Unit, UCL, London, UK; Comprehensive Clinical Trials Unit, UCL, London, UK; Imperial College Healthcare NHS Trust, London, UK; Manchester University NHS Foundation Trust, Manchester, UK; University College London Hospitals NHS Foundation Trust, London, UK; Royal Free NHS Foundation Trust, London, UK; University Hospital Southampton NHS Foundation Trust, Southampton, UK; Sandwell and West Birmingham NHS Trust, UK; Departments of Virology and Infectious Diseases, Newcastle Hospitals NHS Foundation Trust, Newcastle, UK; Nottingham University Hospitals NHS Trust, Nottingham, UK; St George's University Hospitals NHS Foundation Trust, London, UK; Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK; Barts Health NHS Trust, London, UK; Research Computing, UCL, London, UK; Department of Genetics & Genomic Medicine, UCL Great Ormond Street Institute of Child Health, UCL, London, UK; Centre for Genomic Research, University of Liverpool, Liverpool, UK; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK; University College London Hospitals NHS Foundation Trust, London, UK; Centre for Enzyme Innovation, University of Portsmouth, Portsmouth, UK; Department of Applied Sciences, Northumbria University, Newcastle, UK; School of Life Sciences, University of Nottingham, Nottingham, UK; Institute for Infection and Immunity, St George's University of London, London, UK; Institute for Infection and Immunity, St George's University of London, London, UK; Barts Health NHS Trust, London, UK; Centre for Genomic Research, University of Liverpool, Liverpool, UK; Manchester University NHS Foundation Trust, Manchester, UK; The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Northumbria University, Newcastle, UK; Institute for Infection and Immunity, St George's University of London, London, UK; University College London Hospitals NHS Foundation Trust, London, UK; Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; Health Data Research UK Cambridge Hub, Cambridge UK; Department of Medicine, University of Cambridge, Cambridge, UK; ; ; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK; Sheffield Bioinformatics Core, The University of Sheffield, Sheffield, UK; Imperial College Healthcare NHS Trust, London, UK; NHS Greater Glasgow and Clyde, Glasgow, UK; Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, UCL, London, UK; Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK; Department of Infection, Immunity and Cardiovascular Disease, Medical School, The University of Sheffield, Sheffield, UK; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; School of Psychological Sciences and Health, University of Strathclyde, Glasgow, UK; Institute for Global Health, UCL, London, UK; Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, UCL, London, UK","IntroductionViral sequencing of SARS-CoV-2 has been used for outbreak investigation, but there is limited evidence supporting routine use for infection prevention and control (IPC) within hospital settings. - -MethodsWe conducted a prospective non-randomised trial of sequencing at 14 acute UK hospital trusts. Sites each had a 4-week baseline data-collection period, followed by intervention periods comprising 8 weeks of rapid (<48h) and 4 weeks of longer-turnaround (5-10 day) sequencing using a sequence reporting tool (SRT). Data were collected on all hospital onset COVID-19 infections (HOCIs; detected [≥]48h from admission). The impact of the sequencing intervention on IPC knowledge and actions, and on incidence of probable/definite hospital-acquired infections (HAIs) was evaluated. - -ResultsA total of 2170 HOCI cases were recorded from October 2020-April 2021, with sequence reports returned for 650/1320 (49.2%) during intervention phases. We did not detect a statistically significant change in weekly incidence of HAIs in longer-turnaround (IRR 1.60, 95%CI 0.85-3.01; P=0.14) or rapid (0.85, 0.48-1.50; P=0.54) intervention phases compared to baseline phase. However, IPC practice was changed in 7.8% and 7.4% of all HOCI cases in rapid and longer-turnaround phases, respectively, and 17.2% and 11.6% of cases where the report was returned. In a per-protocol sensitivity analysis there was an impact on IPC actions in 20.7% of HOCI cases when the SRT report was returned within 5 days. - -ConclusionWhile we did not demonstrate a direct impact of sequencing on the incidence of nosocomial transmission, our results suggest that sequencing can inform IPC response to HOCIs, particularly when returned within 5 days.",infectious diseases,exact,100,100 medRxiv,10.1101/2022.02.04.22270479,2022-02-06,https://medrxiv.org/cgi/content/short/2022.02.04.22270479,Comparative effectiveness of different primary vaccination courses on mRNA based booster vaccines against SARs-COV-2 infections: A time-varying cohort analysis using trial emulation in the Virus Watch community cohort,Vincent Nguyen; Alexei Yavlinsky; Sarah Beale; Susan J Hoskins; Vasileios J Lampos; Isobel Braithwaite; Thomas Edward Byrne; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Annalan Mathew Dwight Navaratnam; Parth Patel; Madhumita Shrotri; Sophie Weber; Andrew Hayward; Robert W Aldridge,"University College London; University College London; University College London; Univerity College London; University College London; University College London; University College London; University College London, London School of Hygiene &Tropical Medicine; UCL, London School of Hygiene & Tropical Medicine; University College London; University College London; University College London; University College London; Univeristy College London; University College London; University College London; University College London","ImportanceThe Omicron (B.1.1.529) variant has increased SARs-CoV-2 infections in double vaccinated individuals globally, particularly in ChAdOx1 recipients. To tackle rising infections, the UK accelerated booster vaccination programmes used mRNA vaccines irrespective of an individuals primary course vaccine type with booster doses rolled out according to clinical priority. There is limited understanding of the effectiveness of different primary vaccination courses on mRNA based booster vaccines against SARs-COV-2 infections and how time-varying confounders can impact the evaluations comparing different vaccines as primary courses for mRNA boosters. ObjectiveTo evaluate the comparative effectiveness of ChAdOx1 versus BNT162b2 as primary doses against SARs-CoV-2 in booster vaccine recipients whilst accounting for time-varying confounders. @@ -963,24 +939,6 @@ ResultsAcross six cohorts, there were a total of 21,283 participants who were el DiscussionWe found evidence of greater effectiveness of receiving BNT162b2 compared to ChAdOx1 vaccines against SARS-CoV-2 infection in England and Wales during a time period when Delta became the most prevalent variant of concern. Our findings demonstrate the importance of booster (third) doses to maintain protection and suggest that these should be prioritised to those who received ChAdOx1 as their primary course.",epidemiology,exact,100,100 bioRxiv,10.1101/2021.12.17.473248,2021-12-21,https://biorxiv.org/cgi/content/short/2021.12.17.473248,"SARS-CoV-2 Omicron spike mediated immune escape, infectivity and cell-cell fusion",Bo Meng; Isabella Ferreira; Adam Abdullahi; Niluka Goonawardane; Akatsuki Saito; Izumi Kimura; Daichi Yamasoba; Steven A Kemp; Guido Papa; Saman Fatihi; Surabhi Rathore; Pehuen Perera Gerba; Terumasa Ikeda; Mako Toyoda; Toong Seng Tan; Jin Kuramochi; Shigeki Mitsunaga; Takamasa Ueno; Oscar Charles; Dami Collier; - CITIID-NIHR BioResource COVID-19 Collaboration; - The Genotype to Phenotype Japan (G2P-Japan) Consortium; - Ecuador-COVID19 Consortium; John Bradley; Jinwook Choi; Kenneth Smith; Elo Madissoon; Kerstin Meyer; Petra Mlcochova; Rainer Doffinger; Sarah A Teichmann; Leo James; Joo Hyeon Lee; Teresa Brevini; Matteo Pizzuto; Myra Hosmillo; Donna Mallery; Samantha Zepeda; Alexandra Walls; Anshu Joshi; John Bowen; John Briggs; Alex Sigal; Laurelle Jackson; Sandile Cele; Anna De Marco; Fotios Sampaziotis; Davide Corti; David Veesler; Nicholas Matheson; Ian Goodfellow; Lipi Thukral; Kei Sato; Ravindra K Gupta,"University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Miyazaki; The University of Tokyo; Kumamoto University; University of Cambridge; LMB Cambridge; CSIR Institute of Genomics and Integrative Biology, Delhi, India; CSIR Institute of Genomics and Integrative Biology, Delhi, India; University of Cambridge; Kumamoto Univ; Kumamoto University, Kumamoto; Kuramochi Clinic Interpark; Kuramochi Clinic Interpark; National Institute of Genetics, Mishima, Shizuoka; Kumamoto University, Kumamoto; University College London; University of Cambridge; -; -; -; University of Cambridge; University of Cambridge; University of Cambridge; Wellcome Sanger Institute; Wellcome Sanger Institute; University of Cambridge; Cambridge University Hospitals NHS Trust; Cambridge University; MRC LMB; University of Cambridge; University of Cambridge; Humabs Biomed SA; University of Cambridge; MRC LMB Cambridge; University of Washington; University of Washington; University of Washington; University of Washington; University of Heidelberg; Africa Health Research Institute, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Humabs Biomed SA; University of Cambridge; Humabs Biomed SA; University of Washington; University of Cambridge; University of Cambridge; CSIR Institute of Genomics and Integrative Biology, Delhi, India; The University of Tokyo; University of Cambridge","The SARS-CoV-2 Omicron BA.1 variant emerged in late 2021 and is characterised by multiple spike mutations across all spike domains. Here we show that Omicron BA.1 has higher affinity for ACE2 compared to Delta, and confers very significant evasion of therapeutic monoclonal and vaccine-elicited polyclonal neutralising antibodies after two doses. mRNA vaccination as a third vaccine dose rescues and broadens neutralisation. Importantly, antiviral drugs remdesevir and molnupiravir retain efficacy against Omicron BA.1. We found that in human nasal epithelial 3D cultures replication was similar for both Omicron and Delta. However, in lower airway organoids, Calu-3 lung cells and gut adenocarcinoma cell lines live Omicron virus demonstrated significantly lower replication in comparison to Delta. We noted that despite presence of mutations predicted to favour spike S1/S2 cleavage, the spike protein is less efficiently cleaved in live Omicron virions compared to Delta virions. We mapped the replication differences between the variants to entry efficiency using spike pseudotyped virus (PV) entry assays. The defect for Omicron PV in specific cell types correlated with higher cellular RNA expression of TMPRSS2, and accordingly knock down of TMPRSS2 impacted Delta entry to a greater extent as compared to Omicron. Furthermore, drug inhibitors targeting specific entry pathways demonstrated that the Omicron spike inefficiently utilises the cellular protease TMPRSS2 that mediates cell entry via plasma membrane fusion. Instead, we demonstrate that Omicron spike has greater dependency on cell entry via the endocytic pathway requiring the activity of endosomal cathepsins to cleave spike. Consistent with suboptimal S1/S2 cleavage and inability to utilise TMPRSS2, syncytium formation by the Omicron spike was dramatically impaired compared to the Delta spike. Overall, Omicron appears to have gained significant evasion from neutralising antibodies whilst maintaining sensitivity to antiviral drugs targeting the polymerase. Omicron has shifted cellular tropism away from TMPRSS2 expressing cells that are enriched in cells found in the lower respiratory and GI tracts, with implications for altered pathogenesis.",microbiology,exact,100,100 -medRxiv,10.1101/2021.12.20.21268098,2021-12-21,https://medrxiv.org/cgi/content/short/2021.12.20.21268098,"Therapies for Long COVID in non-hospitalised individuals - from symptoms, patient-reported outcomes, and immunology to targeted therapies (The TLC Study): Study protocol",Shamil Haroon; Krishnarajah Nirantharakumar; Sarah Hughes; Anuradhaa Subramanian; Olalekan Lee Aiyegbusi; Elin Haf Davies; Puja Myles; Tim Williams; Grace Turner; Joht Singh Chandan; Christel McMullan; Janet Lord; David Wraith; Kirsty McGee; Alastair Denniston; Tom Taverner; Louise Jackson; Elizabeth Sapey; Georgios Gkoutos; Krishna Gokhale; Edward Leggett; Clare Iles; Christopher Frost; Gary McNamara; Amy Bamford; Tom Marshall; Dawit Zemedikun; Gary Price; Steven Marwaha; Nikita Simms-Williams; Kirsty Brown; Anita Walker; Karen Jones; Karen Matthews; Jennifer Camaradou; Michael Saint-Cricq; Sumita Kumar; Yvonne Alder; David Stanton; Lisa Agyen; Megan Baber; Hannah Blaize; Melanie Calvert,University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; Aparito; Medicines and Healthcare Products Regulatory Agency; Medicines and Healthcare Products Regulatory Agency; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University of Birmingham; University of Birmingham; University ofBirmingham; University of Birmingham; Medicines and Healthcare Products Regulatory Agency; Medicines and Healthcare Products Regulatory Agency; Aparito; Aparito; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University of Birmingham; N/A; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; University ofBirmingham,"IntroductionIndividuals with COVID-19 frequently experience symptoms and impaired quality of life beyond 4-12 weeks, commonly referred to as Long COVID. Whether Long COVID is one or several distinct syndromes is unknown. Establishing the evidence base for appropriate therapies is needed. We aim to evaluate the symptom burden and underlying pathophysiology of Long COVID syndromes in non-hospitalised individuals and evaluate potential therapies. - -Methods and analysisA cohort of 4000 non-hospitalised individuals with a past COVID-19 diagnosis and 1000 matched controls will be selected from anonymised primary care records from the Clinical Practice Research Datalink (CPRD) and invited by their general practitioners to participate on a digital platform (Atom5). Individuals will report symptoms, quality of life, work capability, and patient reported outcome measures. Data will be collected monthly for one year. - -Statistical clustering methods will be used to identify distinct Long COVID symptom clusters. Individuals from the four most prevalent clusters and two control groups will be invited to participate in the BioWear sub-study which will further phenotype Long COVID symptom clusters by measurement of immunological parameters and actigraphy. - -We will review existing evidence on interventions for post-viral syndromes and Long COVID to map and prioritise interventions for each newly characterised Long COVID syndrome. Recommendations will be made using the cumulated evidence in an expert consensus workshop. A virtual supportive intervention will be coproduced with patients and health service providers for future evaluation. - -Individuals with lived experience of Long COVID will be involved throughout this programme through a patient and public involvement group. - -Ethics and disseminationEthical approval was obtained from the Solihull Research Ethics Committee, West Midlands (21/WM/0203). The study is registered on the ISRCTN Registry (1567490). Research findings will be presented at international conferences, in peer-reviewed journals, to Long COVID patient support groups and to policymakers. - -Article SummaryO_ST_ABSStrengths and limitations of the studyC_ST_ABSO_LIThe study will generate a nationally representative cohort of individuals with Long COVID recruited from primary care. -C_LIO_LIWe will recruit controls matched on a wide range of demographic and clinical factors to assess differences in symptoms between people with Long COVID and similar individuals without a history of COVID-19. -C_LIO_LIWe will use a newly developed electronic patient reported outcome measure (Symptom Burden Questionnaire) for Long COVID to comprehensively assess a wide range of symptoms highlighted by existing literature, patients, and clinicians. -C_LIO_LIImmunological, proteomic, genetic, and wearable data captured in the study will allow deep phenotyping of Long COVID syndromes to help better target therapies. -C_LIO_LIA limitation is that a significant proportion of non-hospitalised individuals affected by COVID-19 in the first wave of the pandemic will lack confirmatory testing and will be excluded from recruitment to the study. -C_LI",infectious diseases,exact,100,100 medRxiv,10.1101/2021.12.16.21267904,2021-12-17,https://medrxiv.org/cgi/content/short/2021.12.16.21267904,Deficits in hospital care among clinically vulnerable children aged 0 to 4 years during the COVID-19 pandemic,David Etoori; Katie Harron; Louise Mc Grath-Lone; Maximiliane Verfeurden; Ruth Gilbert; Ruth Blackburn,University College London; University College London; University College London; University College London; University College London; University College London,"ObjectiveTo quantify deficits in hospital care for clinically vulnerable children during the COVID-19 pandemic. DesignBirth cohort in Hospital Episode Statistics (HES). @@ -1205,6 +1163,13 @@ C_LI Section 2: What this study addsO_LIOur study suggests an increased community positive test rate and hospital inpatients had an increased likelihood of a positive SARS-CoV-2 polymerase chain reaction test, whilst one or two doses of vaccination indicated a decreased chance of a positive test. C_LIO_LIOur findings suggest care providers need to stay vigilant despite the vaccination rollout, and extra precautions should be taken when caring for the most vulnerable, especially in a hospital setting. C_LI",geriatric medicine,exact,100,100 +medRxiv,10.1101/2021.09.28.21264260,2021-09-29,https://medrxiv.org/cgi/content/short/2021.09.28.21264260,The impact of SARS-CoV-2 vaccination on Alpha and Delta variant transmission,David W Eyre; Donald Taylor; Mark Purver; David Chapman; Tom Fowler; Koen Pouwels; Ann Sarah Walker; Tim EA Peto,University of Oxford; Department of Health and Social Care; Department of Health and Social Care; Deloitte MCS Ltd; Department of Health and Social Care; University of Oxford; University of Oxford; University of Oxford,"BackgroundPre-Delta, vaccination reduced SARS-CoV-2 transmission from individuals infected despite vaccination, potentially via reducing viral loads. While vaccination still lowers the risk of infection, similar viral loads in vaccinated and unvaccinated individuals infected with Delta question how much vaccination prevents transmission. + +MethodsWe performed a retrospective observational cohort study of adult contacts of SARS-CoV-2-infected adult index cases using English contact testing data. We used multivariable Poisson regression to investigate associations between transmission and index case and contact vaccination, and how these vary with Alpha and Delta variants (classified using S-gene detection/calendar trends) and time since second vaccination. + +Results54,667/146,243(37.4%) PCR-tested contacts of 108,498 index cases were PCR-positive. Two doses of BNT162b2 or ChAdOx1 vaccines in Alpha index cases were independently associated with reduced PCR-positivity in contacts (aRR, adjusted rate ratio vs. unvaccinated=0.32[95%CI 0.21-0.48] and 0.48[0.30-0.78] respectively). The Delta variant attenuated vaccine-associated reductions in transmission: two BNT162b2 doses reduced Delta transmission (aRR=0.50[0.39-0.65]), more than ChAdOx1 (aRR=0.76[0.70-0.82]). Variation in Ct values (indicative of viral load) explained 7-23% of vaccine-associated transmission reductions. Transmission reductions declined over time post-second vaccination, for Delta reaching similar levels to unvaccinated individuals by 12 weeks for ChAdOx1 and attenuating substantially for BNT162b2. Protection in contacts also declined in the 3 months post-second vaccination. + +ConclusionsVaccination reduces transmission of Delta, but by less than the Alpha variant. The impact of vaccination decreased over time. Factors other than PCR Ct values at diagnosis are important in understanding vaccine-associated transmission reductions. Booster vaccinations may help control transmission together with preventing infections.",infectious diseases,exact,100,100 medRxiv,10.1101/2021.09.27.21264166,2021-09-29,https://medrxiv.org/cgi/content/short/2021.09.27.21264166,Prevalence and duration of detectable SARS-CoV-2 nucleocapsid antibody in staff and residents of long-term care facilities over the first year of the pandemic (VIVALDI study): prospective cohort study,Maria Krutikov; Tom Palmer; Gokhan Tut; Christopher Fuller; Borscha Azmi; Rebecca Giddings; Madhumita Shrotri; Nayandeep Kaur; Panagiota Sylla; Tara Lancaster; Aidan Irwin-Singer; Andrew Hayward; Paul Moss; Andrew Copas; Laura Shallcross,"University College London; University College London; University of Birmingham, Medical School; University College London; University College London; University College London; University College London; University of Birmingham; University of Birmingham; University of Birmingham; Department of Health & Social Care; UCL; University of Birmingham; University College London; UCL","BackgroundLong Term Care Facilities (LTCF) have reported high SARS-CoV-2 infection rates and related mortality, but the proportion infected amongst survivors and duration of the antibody response to natural infection is unknown. We determined the prevalence and stability of nucleocapsid antibodies - the standard assay for detection of prior infection - in staff and residents from 201 LTCFs. MethodsProspective cohort study of residents aged >65 years and staff of LTCFs in England (11 June 2020-7 May 2021). Serial blood samples were tested for IgG antibodies against SARS-CoV-2 nucleocapsid protein. Prevalence and cumulative incidence of antibody-positivity were weighted to the LTCF population. Cumulative incidence of sero-reversion was estimated from Kaplan-Meier curves. @@ -1358,17 +1323,6 @@ MethodsA nationally-representative cohort of U.S. adults (N=5,792) in the Unders ResultsVaccination was associated with a 0.09 decline in distress scores (95% CI:-0.15 to -0.04) (0-12 scale), a 5.7% relative decrease compared to mean scores in the wave prior to vaccination. Vaccination was also associated with an 8.44 percentage point reduction in perceived risk of infection (95% CI:-9.15% to -7.73%), a 7.44-point reduction in perceived risk of hospitalization (95% CI:-8.07% to -6.82%), and a 5.03-point reduction in perceived risk of death (95% CI:-5.57% to -4.49%). Adjusting for risk perceptions decreased the vaccination-distress association by two-thirds. Event study models suggest vaccinated and never vaccinated respondents followed similar PHQ-4 trends pre-vaccination, diverging significantly post-vaccination. Analyses were robust to individual and wave fixed effects, time-varying controls, and several alternative modelling strategies. Results were similar across sociodemographic groups. ConclusionReceiving a COVID-19 vaccination was associated with declines in distress and perceived risks of infection, hospitalization, and death. Vaccination campaigns could promote these additional benefits of being vaccinated.",public and global health,exact,100,100 -medRxiv,10.1101/2021.07.19.21260770,2021-07-22,https://medrxiv.org/cgi/content/short/2021.07.19.21260770,Uptake of infant and pre-school immunisations in Scotland and England during the COVID-19 pandemic: an observational study of routinely collected data,Fiona McQuaid; Rachel Mulholland; Yuma Sangpang Rai; Utkarsh Agrawal; Helen Bedford; Claire Cameron; Cheryl Gibbon; Partho Roy; Aziz Sheikh; Ting Shi; Colin Simpson; Judith Tait; Elise Tessier; Steve Turner; Jaime Villacampa Ortega; Joanne White; Rachael Wood,University of Edinburgh; University of Edinburgh; Public Health England; University of St Andrews; UCL Great Ormond Street Institute of Child Health; Public Health Scotland; Public Health Scotland; Public Health England; University of Edinburgh; University of Edinburgh; Victoria University of Wellington; Public Health Scotland; Public Health England; University of Aberdeen; Public Health Scotland; Public Health England; University of Edinburgh,"BackgroundIn 2020, the COVID-19 pandemic and control measures such as national lockdowns threatened to disrupt routine childhood immunisation programmes. Initial reports from the early weeks of lockdown in the UK and worldwide suggested that uptake could fall putting children at risk from multiple other infectious diseases. In Scotland and England, enhanced surveillance of national data for childhood immunisations was established to inform and rapidly assess the impact of the pandemic on infant and preschool immunisation uptake rates. - -Methods and findingsWe undertook an observational study using routinely collected data for the year prior to the pandemic (2019), and immediately before, during and after the first period of the UK lockdown in 2020. Data were obtained for Scotland from the Public Health Scotland ""COVID19 wider impacts on the health care system"" dashboard (https://scotland.shinyapps.io/phs-covid-wider-impact/) and for England from ImmForm. - -Five vaccinations delivered at different ages were evaluated; three doses of the 6-in-1 DTaP/IPV/Hib/HepB vaccine and two doses of MMR. Uptake in the periods in 2020 compared to that in the baseline year of 2019 using binary logistic regression analysis. For Scotland, we analysed timely uptake of immunisations, defined as uptake within four weeks of the child becoming eligible by age for each immunisation and data were also analysed by geographical region and indices of deprivation. For both Scotland and England, we assessed whether immunisations were up to date at approximately 6 months (all doses 6-in-1) and 16-18 months (first MMR) of age. - -We found that uptake rates within four weeks of eligibility in Scotland for all the five vaccine visits were higher during the 2020 lockdown period than in 2019. The difference ranged from 1.3% for the first dose of the 6-in-1 vaccine (95.3 vs 94%, OR 1.28, CI 1.18-1.39) to 14.3% for the second MMR dose (66.1 vs 51.8 %, OR 1.8, CI 1.74-1.87). Significant increases in uptake were seen across all deprivation levels, though, for MMR, there was evidence of greater improvement for children living in the least deprived areas. - -In England, fewer children who had been due to receive their immunisations during the lockdown period were up to date at 6 months (6-in-1) or 18 months (first dose MMR). The fall in percentage uptake ranged from 0.5% for first 6-in1 (95.8 vs 96.3%, OR 0.89, CI 0.86-0.91) to 2.1% for third 6-in-1 (86.6 vs 88.7%, OR 0.82, CI 0.81-0.83). - -ConclusionsThis study suggests that the national lockdown in Scotland was associated with a positive effect on timely childhood immunisation uptake, however in England a lower percentage of children were up to date at 6 and 18 months. Reason for the improve uptake in Scotland may include active measures taken to promote immunisation at local and national level during this period. Promoting immunisation uptake and addressing potential vaccine hesitancy is particularly important given the ongoing pandemic and COVID-19 vaccination campaigns.",pediatrics,exact,100,100 medRxiv,10.1101/2021.07.16.21260651,2021-07-20,https://medrxiv.org/cgi/content/short/2021.07.16.21260651,Evaluating discharges and readmissions using a COVID Virtual Ward model: a retrospective data study assessing patient outcomes and the likely staffing commitment,Suzy Gallier; Catherine Atkin; Vinay Reddy-Kolanu; Dhruv Parekh; Xiaoxu Zou; felicity Evison; Simon Ball; Elizabeth Sapey,University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University Hospitals Birmingham NHS Foundation Trust; University Hospitals Birmingham NHS Foundation Trust; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham,"BackgroundCOVID-19 has placed a catastrophic burden on acute hospitals. In an attempt to reduce admissions and enable safe early discharge, a COVID virtual ward (CVW) care pathway has been supported by NHS England. This includes discharging people who meet objective criteria based on acuity scores and oxygen saturations, with pulse oximeters and daily phone calls for up to 14 days. Observational studies have reported the safety of this system, but without describing the outcomes from usual care. MethodsA retrospective study using routinely collected health data from all adults with a confirmed positive severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) swab result between 1st June 2020 and 31st Jan 2021 who attended the Emergency Department or Acute Medical Unit at QEHB, which does not have a CVW service. Criteria for CVW were applied using data from the first 24 hours of presentation to hospital and subsequent health outcomes were included for 28 days, including re-presentation, re-admission, ITU escalation and death. Results were compared to reported studies based in secondary care. @@ -1376,13 +1330,6 @@ MethodsA retrospective study using routinely collected health data from all adul ResultsDuring the study period, 26,127 patients presented to QEHB hospital. 2301 had a positive SARS-CoV-2 swab. Of these, 1730 (75.2%) did not meet the criteria for the CVW and 571 (24.8%) did. Of the 571, 325 (56.9%) were discharged home within 24 hours and 246 (43.1%) were admitted for 24 hours or longer. Those admitted were older, with increased co-morbidities, 80.9% required hospital-supported acute therapies after the first 24 hours and 10.6% died. Of the 325 discharged, 44 were readmitted (13.5%), 30 (9.2%) with COVID-related symptoms, 5 (1.5%) required ITU and 1 patient (0.3%) died. These results were comparable to published studies with a CVW service. DiscussionIn the current study, discharging patients without a CVW did not confer a greater risk of re-presentation, re-admission, ITU escalation or death. The majority of patients who remained in hospital despite meeting the CVW criteria did so for the provision of treatments or acute assessments. It remains uncertain whether a CVW delivers improvements in hard outcomes, and further research is needed.",respiratory medicine,exact,100,100 -medRxiv,10.1101/2021.07.16.21260628,2021-07-19,https://medrxiv.org/cgi/content/short/2021.07.16.21260628,"Overall and cause-specific hospitalisation and death after COVID-19 hospitalisation in England: cohort study in OpenSAFELY using linked primary care, secondary care and death registration data",Krishnan Bhaskaran; Christopher T Rentsch; George Hickman; William J Hulme; Anna Schultze; Helen J Curtis; Kevin Wing; Charlotte Warren-Gash; Laurie Tomlinson; Christopher Bates; Rohini Mathur; Brian MacKenna; Viyaasan Mahalingasivam; Angel YS Wong; Alex J Walker; Caroline E Morton; Daniel Grint; Amir Mehrkar; Rosalind M Eggo; Peter Inglesby; Ian J Douglas; Helen I McDonald; Jonathan Cockburn; Elizabeth J Williamson; David Evans; John Parry; Frank Hester; Sam Harper; Stephen JW Evans; Sebastian CJ Bacon; Liam Smeeth; Ben Goldacre,London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; TPP; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; TPP; London School of Hygiene and Tropical Medicine; University of Oxford; TPP; TPP; TPP; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford,"BackgroundThere is concern about medium to long-term adverse outcomes following acute COVID-19, but little relevant evidence exists. We aimed to investigate whether risks of hospital admission and death, overall and by specific cause, are raised following discharge from a COVID-19 hospitalisation. - -Methods and FindingsWorking on behalf of NHS-England, we used linked primary care and hospital data in OpenSAFELY to compare risks of hospital admission and death, overall and by specific cause, between people discharged from COVID-19 hospitalisation (February-December 2020), and (i) demographically-matched controls from the 2019 general population; (ii) people discharged from influenza hospitalisation in 2017-19. We used Cox regression adjusted for personal and clinical characteristics. - -24,673 post-discharge COVID-19 patients, 123,362 general population controls, and 16,058 influenza controls were followed for [≤]315 days. Overall risk of hospitalisation or death (30968 events) was higher in the COVID-19 group than general population controls (adjusted-HR 2.23, 2.14-2.31) but similar to the influenza group (adjusted-HR 0.94, 0.91-0.98). All-cause mortality (7439 events) was highest in the COVID-19 group (adjusted-HR 4.97, 4.58-5.40 vs general population controls and 1.73, 1.60-1.87 vs influenza controls). Risks for cause-specific outcomes were higher in COVID-19 survivors than general population controls, and largely comparable between COVID-19 and influenza patients. However, COVID-19 patients were more likely than influenza patients to be readmitted/die due to their initial infection/other lower respiratory tract infection (adjusted-HR 1.37, 1.22-1.54), and to experience mental health or cognitive-related admission/death (adjusted-HR 1.36, 1.01-2.83); in particular, COVID-19 survivors with pre-existing dementia had higher risk of dementia death. One limitation of our study is that reasons for hospitalisation/death may have been misclassified in some cases due to inconsistent use of codes. - -ConclusionsPeople discharged from a COVID-19 hospital admission had markedly higher risks for rehospitalisation and death than the general population, suggesting a substantial extra burden on healthcare. Most risks were similar to those observed after influenza hospitalisations; but COVID-19 patients had higher risks of all-cause mortality, readmissions/death due to the initial infection, and dementia death, highlighting the importance of post-discharge monitoring.",infectious diseases,exact,100,100 medRxiv,10.1101/2021.07.14.21260497,2021-07-18,https://medrxiv.org/cgi/content/short/2021.07.14.21260497,"Vaccine uptake and SARS-CoV-2 antibody prevalence among 207,337 adults during May 2021 in England: REACT-2 study",Helen Ward; Matthew Whitaker; Sonja N Tang; Christina J Atchison; Ara Darzi; Christl A. Donnelly; Peter Diggle; Deborah Ashby; Steven Riley; Wendy S Barclay; Paul Elliott; Graham S Cooke,"Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Lancaster University; Imperial College London; Dept Inf Dis Epi, Imperial College; Imperial College London; Imperial College London School of Public Health; Imperial College","BackgroundThe programme to vaccinate adults in England has been rapidly implemented since it began in December 2020. The community prevalence of SARS-CoV-2 anti-spike protein antibodies provides an estimate of total cumulative response to natural infection and vaccination. We describe the distribution of SARS-CoV-2 IgG antibodies in adults in England in May 2021 at a time when approximately 7 in 10 adults had received at least one dose of vaccine. MethodsSixth round of REACT-2 (REal-time Assessment of Community Transmission-2), a cross-sectional random community survey of adults in England, from 12 to 25 May 2021; 207,337 participants completed questionnaires and self-administered a lateral flow immunoassay test producing a positive or negative result. @@ -1456,26 +1403,6 @@ C_LIO_LIThe diagnostic interview component of the study will allow us to establi C_LIO_LIThe qualitative interviews will give deeper insight into the support programmes that HCWs find most helpful, and provide ideas for Trusts to improve their offer to staff. C_LIO_LIThe three components of the study give breadth and depth lacking in much of the mental health and wellbeing research currently available, but there is a risk of over-burdening already stretched HCWs. C_LI",psychiatry and clinical psychology,exact,100,100 -medRxiv,10.1101/2021.06.03.21258289,2021-06-06,https://medrxiv.org/cgi/content/short/2021.06.03.21258289,Implementation of COVID-19 Preventive Measures in Primary and Secondary Schools Following Reopening of Schools in Autumn 2020; A Cross-Sectional Study of Parents' and Teachers' Experiences in England,Zahin Amin-Chowdhury; Marta Bertran; Meaghan Kall; Georgina Ireland; Felicity Aiano; Annabel Powell; Samuel E Jones; Andrew Brent; Bernadette Brent; Frances Baawuah; Ifeanychukwu Okike; Joanne Beckmann; Joanna Garstang; Shazaad Ahmed; Neisha Sundaram; Chris Bonell; Sinead Langan; James Hargreaves; Shamez N Ladhani,"Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Public Health England; University Hospitals of Derby and Burton NHS foundation Trust; Specialist Children & Young People's Services, East London NHS Foundation Trust; Birmingham Community Healthcare Trust; Public Health England; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Public Health England","ObjectiveThe main objective was to assess implementation of and ease of implementation of control measures in schools as reported by staff and parents. - -DesignCross-sectional study. - -SettingStaff and parents/guardian participants in the 132 primary schools and 20 secondary schools participating in sKIDs and sKIDsPLUS surveillances. - -Main outcome measurePrevalence of control measures implemented in Autumn 2020, parental and staff perception of ease of implementation and acceptability of conducting school surveillance studies. - -ResultsIn total, 56/152 (37%) schools participating in Public Health Englands sKIDs study of COVID in schools accepted the invitation to participate in the survey. By 28 December 2020, 1,953 parent and 986 staff respondents had completed the online questionnaire. While more than half the parents were positive about their children returning to school, roughly a third reported being a little anxious. 90% and 82% of primary and secondary school parents were either completely or partly reassured by the preventive measures implemented in their schools. Among staff, 80% of primary staff and 87% of secondary school staff felt that they were at higher risk of COVID-19 because of their profession; only 52% of primary school staff and 38% of secondary school staff reportedly felt safe. According to the teaching staff, most preventive measures were well-implemented apart from requiring 2-metre distancing between staff. For students, maintaining the 2-metre distance was reported to be particularly difficult. By extension, secondary schools also struggled to maintain small groups at all times or ensuring that the same staff were assigned to each student group (a problem also commonly reported by parents). - -ConclusionsVariable implementation of infection control measures was reported by staff and parents. Whilst the majority were not worried about returning to school, some parents and staff, were concerned about returning to school and the risks posed to children, staff and household members. - -Strengths and limitations of this studyO_ST_ABSStrengthsC_ST_ABSO_LIThis study is one of the few to investigate school staff and parents perceptions of the implementation of control measures implemented following the reopening of schools in England. -C_LIO_LIThe early establishment of COVID-19 surveillance in primary and secondary schools in the summer term 2020 provided a cohort to rapidly evaluate the experiences of parents and school staff during the autumn term before schools were required to close for the subsequent national lockdown. -C_LI - -LimitationsO_LIAs the questionnaire and information provided was available in English only, there is likely to be an under-representation of families for whom English was not their main language. -C_LIO_LISome school responses were only provided by one participant so may not necessarily be representative of the whole school. -C_LIO_LIAlthough the surveillance included schools recruited nationally, a convenience sample was used and as such may not be representative of all primary and secondary schools in England. -C_LI",public and global health,exact,100,100 medRxiv,10.1101/2021.05.28.21257602,2021-06-02,https://medrxiv.org/cgi/content/short/2021.05.28.21257602,Prevalence of persistent symptoms in children during the COVID-19 pandemic: evidence from a household cohort study in England and Wales,Faith Miller; Vincent Nguyen; Annalan MD Navaratnam; Madhumita Shrotri; Jana Kovar; Andrew C Hayward; Ellen Fragaszy; Robert W Aldridge; - Virus Watch Collaborative; Pia Hardelid,UCL; UCL; UCL; UCL; UCL; UCL; UCL; UCL; ; University College London,"Using data from 4678 children participating in VirusWatch, a household cohort study, we estimated the prevalence of persistent symptoms lasting [≥]4 weeks as 1.7%, and 4.6% in children with a history of SARS-CoV-2 infection. Persistent symptom prevalence was higher in girls, teenagers and children with long-term conditions.",pediatrics,exact,100,100 medRxiv,10.1101/2021.05.25.21257730,2021-06-01,https://medrxiv.org/cgi/content/short/2021.05.25.21257730,"Post-COVID assessment in a specialist clinical service: a 12-month, single-centre analysis of symptoms and healthcare needs in 1325 individuals.",Melissa Heightman; Jai Prashar; Toby Hillman; Michael Marks; Rebecca Livingston; Heidi Ridsdale; Kay Roy; Robert Bell; Michael Zandi; Patricia McNamara; Alisha Chauhan; Emma Denneny; Ronan Astin; Helen Purcell; Emily Attree; Lyth Hishmeh; Gordon Prescott; Rebecca Evans; Puja Mehta; Ewen Brennan; Jeremy Brown; Joanna Porter; Sarah Logan; Emma Wall; Hakim-Moulay Dehbi; Stephen Cone; Amitava Banerjee,University College London Hospitals NHS Trust; University College London; University College London NHS Trust; London School of Hygiene & Tropical Medicine; University College London NHS Trust; Central and North West London NHS Foundation Trust; University College London NHS Trust; University College London NHS Trust; University College London; University College London NHS Trust; University College London NHS Trust; University College London NHS Trust; University College London; University College London NHS Trust; UKDoctors#Longcovid; Long COVID SOS; University of Central Lancashire; University College London NHS Trust; University College London; University College London NHS Trust; University College London; University College London; University College London NHS Trust; University College London; University College London; University College London NHS Trust; University College London,"BackgroundComplications following SARS-CoV-2 infection require simultaneous characterisation and management to plan policy and health system responses. We describe the 12-month experience of the first UK dedicated Post-COVID clinical service to include both hospitalised and non-hospitalised patients. @@ -1739,6 +1666,9 @@ MethodsWe tested the hypothesis that hospital discharge events increased the int FindingsIn regression analysis, after adjusting for care home size, we found no significant association between hospital discharge and subsequent increases in care home case numbers (odds ratio: 0.99, 95% CI 0.82, 1.90). Risk factors for increased cases included care home size, care home resident density, and provision of nursing care. Using our outbreak model, we found a significant effect of hospital discharge on the subsequent intensity of cases. However, the effect was small, and considerably less than the effect of care home size, suggesting the highest risk of introduction came from interaction with the community. We estimated approximately 1.8% of hospital discharged patients may have been infected. InterpretationThere is growing evidence in the UK that the risk of transfer of COVID-19 from the high-risk hospital setting to the high-risk care home setting during the early stages of the pandemic was relatively small. Although access to testing was limited to initial symptomatic cases in each care home at this time, our results suggest that reduced numbers of discharges, selection of patients, and action taken within care homes following transfer all may have contributed to mitigation. The precise key transmission routes from the community remain to be quantified.",health informatics,exact,100,100 +medRxiv,10.1101/2021.03.04.21252931,2021-03-08,https://medrxiv.org/cgi/content/short/2021.03.04.21252931,A common TMPRSS2 variant protects against severe COVID-19,"Alessia David; Nicholas Parkinson; Thomas P Peacock; Erola Pairo-Castineira; Tarun Khanna; Aurelie Cobat; Albert Tenesa; Vanessa Sancho-Shimizu; - GenOMICC Investigators, ISARIC4C Investigators; Jean-Laurent Casanova; Laurent Abel; Wendy S Barclay; J Kenneth Baillie; Michael J.E. Sternberg","Centre for Integrative System Biology and Bioinformatics, Imperial College London, London; Roslin Institute, University of Edinburgh; Department of Infectious Diseases, Imperial College London; Roslin Institute, University of Edinburgh; Centre for Integrative System Biology and Bioinformatics, Imperial College London; Laboratory of Human Genetics of Infectious Diseases, INSERM; Roslin Institute, University of Edinburgh; Department of Paediatric Infectious Diseases & Virology, Imperial College London; ; St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University; Laboratory of Human Genetics of Infectious Diseases, INSERM; Department of Infectious Diseases, Imperial College London; Roslin Institute, University of Edinburgh; Centre for Integrative System Biology and Bioinformatics, Imperial College London","Infection with SARS-CoV-2 has a wide range of clinical presentations, from asymptomatic to life-threatening. Old age is the strongest factor associated with increased COVID19-related mortality, followed by sex and pre-existing conditions. The importance of genetic and immunological factors on COVID19 outcome is also starting to emerge, as demonstrated by population studies and the discovery of damaging variants in genes controlling type I IFN immunity and of autoantibodies that neutralize type I IFNs. The human protein transmembrane protease serine type 2 (TMPRSS2) plays a key role in SARS-CoV-2 infection, as it is required to activate the virus spike protein, facilitating entry into target cells. We focused on the only common TMPRSS2 non-synonymous variant predicted to be damaging (rs12329760), which has a minor allele frequency of [~]25% in the population. In a large population of SARS-CoV-2 positive patients, we show that this variant is associated with a reduced likelihood of developing severe COVID19 (OR 0.87, 95%CI:0.79-0.97, p=0.01). This association was stronger in homozygous individuals when compared to the general population (OR 0.65, 95%CI:0.50-0.84, p=1.3x10-3). We demonstrate in vitro that this variant, which causes the amino acid substitution valine to methionine, impacts the catalytic activity of TMPRSS2 and is less able to support SARS-CoV-2 spike-mediated entry into cells. + +TMPRSS2 rs12329760 is a common variant associated with a significantly decreased risk of severe COVID19. Further studies are needed to assess the expression of the TMPRSS2 across different age groups. Moreover, our results identify TMPRSS2 as a promising drug target, with a potential role for camostat mesilate, a drug approved for the treatment of chronic pancreatitis and postoperative reflux esophagitis, in the treatment of COVID19. Clinical trials are needed to confirm this.",genetic and genomic medicine,exact,100,100 medRxiv,10.1101/2021.03.02.21252444,2021-03-03,https://medrxiv.org/cgi/content/short/2021.03.02.21252444,An overview of the National COVID-19 Chest Imaging Database: data quality and cohort analysis,Dominic Cushnan; Oscar Bennett; Rosalind Berka; Ottavia Bertolli; Ashwin Chopra; Samie Dorgham; Alberto Favaro; Tara Ganepola; Mark Halling-Brown; Gergely Imreh; Joseph Jacob; Emily Jefferson; François Lemarchand; Daniel Schofield; Jeremy C Wyatt; - NCCID Collaborative,"AI Lab, NHSX, London, UK; Faculty, London, UK; Faculty, London, UK; Faculty, London, UK; Faculty, London, UK; Faculty, London, UK; Faculty, London, UK; Faculty, London, UK; Scientific Computing, Royal Surrey NHS Foundation Trust, Guildford, UK; Faculty, London, UK; Centre for Medical Image Computing, University College London, London, UK; Health Informatics Centre (HIC), School of Medicine, University of Dundee, UK; AI Lab, NHSX, London, UK; AI Lab, NHSX, London, UK; University of Southampton, Southampton, UK; ","The National COVID-19 Chest Imaging Database (NCCID) is a centralised database containing chest X-rays, chest Computed Tomography (CT) scans and cardiac Magnetic Resonance Images (MRI) from patients across the UK, jointly established by NHSX, the British Society of Thoracic Imaging (BSTI), Royal Surrey NHS Foundation Trust (RSNFT) and Faculty. The objective of the initiative is to support a better understanding of the coronavirus SARS-CoV-2 disease (COVID-19) and development of machine learning (ML) technologies that will improve care for patients hospitalised with a severe COVID-19 infection. The NCCID is now accumulating data from 20 NHS Trusts and Health Boards across England and Wales, with a total contribution of approximately 25,000 imaging studies in the training set (at time of writing) and is actively being used as a research tool by several organisations. This paper introduces the training dataset, including a snapshot analysis performed by NHSX covering: the completeness of clinical data, the availability of image data for the various use-cases (diagnosis, prognosis and longitudinal risk) and potential model confounders within the imaging data. The aim is to inform both existing and potential data users of the NCCIDs suitability for developing diagnostic/prognostic models. In addition, a cohort analysis was performed to measure the representativeness of the NCCID to the wider COVID-19 affected population. Three major aspects were included: geographic, demographic and temporal coverage, revealing good alignment in some categories, e.g., sex and identifying areas for improvements to data collection methods, particularly with respect to geographic coverage. All analyses and discussions are focused on the implications for building ML tools that will generalise well to the clinical use cases.",radiology and imaging,exact,100,100 medRxiv,10.1101/2021.02.27.21252593,2021-03-01,https://medrxiv.org/cgi/content/short/2021.02.27.21252593,Surgical activity in England and Wales during the COVID-19 pandemic: a nationwide observational cohort study,Thomas D Dobbs; John A G Gibson; Alexander J Fowler; Tom E Abbott; Tasnin Shahid; Fatemeh Torabi; Rowena Griffiths; Ronan A Lyons; Rupert M Pearse; Iain S Whitaker,"Swansea University Medical School; Swansea University Medical School; Queen Mary, University of London; Queen Mary University of London; Queen Mary University of London; Swansea University; Swansea University; Swansea University; Queen Mary University of London; Swansea University Medical School","ObjectivesTo report the volume of surgical activity and the number of cancelled surgical procedures during the COVID-19 pandemic. @@ -1805,21 +1735,6 @@ MethodsWorking on behalf of NHS England, we used data from the OpenSAFELY platfo ResultsFor all outcomes except death there was a lower count of events in April 2020 compared to April 2019. For most outcomes the minimum count of events was in April 2020, where the decrease compared to April 2019 in events ranged from 5.9% (PE) to 40.0% (heart failure). Despite hospitalised COVID-19 patients making up just 0.14% of the population in April 2020, these patients accounted for an extremely high proportion of cardiometabolic and respiratory events in that month (range of proportions 10.3% (DVT) to 33.5% (AKI)). InterpretationWe observed a substantial drop in the incidence of cardiometabolic and pulmonary events in the non-COVID-19 general population, but high occurrence of COVID-19 among patients with these events. Shortcomings in routine NHS secondary care data, especially around the timing and order of events, make causal interpretations challenging. We caution that the intermediate findings reported here should be used to inform the design and interpretation of any studies using a general population comparator to evaluate the relationship between COVID-19 and other clinical events.",epidemiology,exact,100,100 -medRxiv,10.1101/2021.02.04.21251155,2021-02-08,https://medrxiv.org/cgi/content/short/2021.02.04.21251155,Impact of school closures on the health and well-being of primary school children in Wales UK; a routine data linkage study using the HAPPEN survey (2018-2020).,Michaela James; Emily Marchant; Margaret A Defeyter; Jayne V Woodside; Sinead Brophy,Swansea University; Swansea University; Northumbria University; Queen's University Belfast; Swansea University,"IntroductionIn response to the COVID-19 pandemic, school closures were implemented across the United Kingdom. This study aimed to explore the impact of school closures on childrens health by comparing health and wellbeing outcomes collected during school closures (April - June 2020) with data from the same period in 2019 and 2018. - -MethodsData were collected online via the HAPPEN At Home survey, which captured the typical health behaviours of children aged 8 - 11 years between April - June 2020. These data were compared with data in 2018 and 2019 also collected between April-June, from HAPPEN. Free school meal (FSM) status was used as a proxy for socio-economic deprivation. Analyses were repeated stratifying by FSM. - -ResultsComparing responses between April - June in 2020 (n=1068), 2019 (n=1150) and 2018 (n=475), there were improvements in physical activity levels, sleep time, happiness and general wellbeing for children during school closures compared to previous years. However, children on FSM ate less fruit and vegetables (21% (95%CI (5.7% to 37%)) and had lower self-assessed school competence compared to 2019. Compared to those not on FSM they also spent less time doing physical activity (13.03% (95%CI: 3.3% to 21.7%) and consumed more takeaways (16.3% (95%CI: 2%-30%)) during school closures. - -ConclusionThis study suggests that schools play an important role in reducing inequalities in physical health. The physical health (e.g. physical activity and diet) of children eligible for FSM may be impacted by prolonged school closures. - -What is already known on this subject?In response to the COVID-19 pandemic, by mid-March 2020, 138 countries had implemented national school closures to reduce the number of social contacts between pupils, therefore interrupting the transmission of COVID-19 as part of pandemic plans. UNESCO warned that the global scale and speed of the educational disruption would be unparalleled. There is an ongoing debate with regard to the effectiveness of schools closures on transmission rates, but the fact schools are closed for a long period of time could have detrimental impacts on pupils physical and mental health. - -This study provides evidence of any differences in the health and wellbeing of children prior to and during the COVID-19 enforced lockdown and school closures between March and June 2020. These findings could have a significant impact for the future and support schools to better understand their pupils physical, psychological, emotional and social health. It also contributes to a significant literature gap regarding the impact of school closures on school-aged children. - -What this study adds?Improvements in physical activity levels, sleep time, happiness and general wellbeing were observed in general for children during school closures compared to previous years. However, children on FSM reported eating less fruit and vegetables and had lower self-assessed school competence compared to 2019. Compared to those not on FSM they also spent less time doing physical activity and consumed more takeaways during school closures. These trends are not evident among children not on FSM. All children reported improvements in wellbeing during lockdown especially on the happiness with family measure. - -Overall, findings suggest schools help to reduce inequalities in physical health for socio-economically deprived children. During school closures children from deprived backgrounds are likely to have poorer physical health (e.g. less time spent doing physical activities and poorer diet) and this is not observed in children who are not in receipt of FSM. This research suggests that school closures will result in widening health inequalities and when schools return measures will need to be in place to readdress the widened gap in physical health.",public and global health,exact,100,100 medRxiv,10.1101/2021.02.04.21251087,2021-02-08,https://medrxiv.org/cgi/content/short/2021.02.04.21251087,Staff-Pupil SARS-CoV-2 Infection Pathways in Schools: A Population Level Linked Data Approach,Daniel A Thompson; Hoda Abbasizanjani; Richard Fry; Emily Marchant; Lucy J Griffiths; Ashley Akbari; Joseph Hollinghurst; Laura North; Jane Lyons; Fatemeh Torabi; Gareth Davies; Mike B Gravenor; Ronan A Lyons,Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University,"BackgroundBetter understanding of the role that children and school staff play in the transmission of SARS-CoV-2 is essential to guide policy development on controlling infection whilst minimising disruption to childrens education and wellbeing. MethodsOur national e-cohort (n=500,779) study used anonymised linked data for pupils, staff and associated households linked via educational settings. We estimated the risk of testing positive for SARS-CoV-2 infection for staff and pupils over the period August - December 2020, dependent on measures of recent exposure to known cases linked to their educational settings. @@ -2026,7 +1941,6 @@ ConclusionsWe successfully delivered an open source software framework to descri medRxiv,10.1101/2020.12.30.20248603,2021-01-01,https://medrxiv.org/cgi/content/short/2020.12.30.20248603,SARS-CoV-2 positivity in asymptomatic-screened dental patients,David I Conway; Shauna Culshaw; Maura Edwards; Claire Clark; Chris Watling; Chris Robertson; Raymond Braid; Emma O'Keefe; Niall McGoldrick; Jacky Burns; Stacey Provan; Harper VanSteenhouse; Jodie Hay; Rory Gunson; - Dental COVID-19 Surveillance Survey Group,University of Glasgow and Public Health Scotland; University of Glasgow; NHS Ayrshire and Arran; Public Health Scotland; Public Health Scotland; Strathclyde University and Public Health Scotland; Public Health Scotland; NHS Fife; NHS Fife; NHS Fife; NHS Greater Glasgow & Clyde; BioClavis Ltd; University of Glasgow; NHS Greater Glasgow & Clyde; ,"Enhanced community surveillance is a key pillar of the public health response to COVID-19. Asymptomatic carriage of SARS-CoV-2 is a potentially significant source of transmission, yet remains relatively poorly understood. Disruption of dental services continues with significantly reduced capacity. Ongoing precautions include pre- and/or at appointment COVID-19 symptom screening and use of enhanced personal protective equipment (PPE). This study aimed to investigate SARS-CoV-2 infection in dental patients to inform community surveillance and improve understanding of risks in the dental setting. Thirty-one dental care centres across Scotland invited asymptomatic screened patients over 5-years-old to participate. Following verbal consent and completion of sociodemographic and symptom history questionnaire, trained dental teams took a combined oropharyngeal and nasal swab sample using standardised VTM-containing testkits. Samples were processed by the Lighthouse Lab and patients informed of their results by SMS/e-mail with appropriate self-isolation guidance in the event of a positive test. Over a 13-week period (from 3August to 31October2020) n=4,032 patients, largely representative of the population, were tested. Of these n=22 (0.5%; 95%CI 0.5%, 0.8%) tested positive for SARS-CoV-2. The positivity rate increased over the period, commensurate with uptick in community prevalence identified across all national testing monitoring data streams. All positive cases were successfully followed up by the national contact tracing program. To the best of our knowledge this is the first report of a COVID-19 testing survey in asymptomatic-screened patients presenting in a dental setting. The positivity rate in this patient group reflects the underlying prevalence in community at the time. These data are a salient reminder, particularly when community infection levels are rising, of the importance of appropriate ongoing Infection Prevention Control and PPE vigilance, which is relevant as healthcare team fatigue increases as the pandemic continues. Dental settings are a valuable location for public health surveillance.",dentistry and oral medicine,exact,100,100 bioRxiv,10.1101/2020.12.23.424229,2020-12-25,https://biorxiv.org/cgi/content/short/2020.12.23.424229,Patterns of within-host genetic diversity in SARS-CoV-2,Gerry Tonkin-Hill; Inigo Martincorena; Roberto Amato; Andrew R J Lawson; Moritz Gerstung; Ian Johnston; David K Jackson; Naomi R Park; Stefanie V Lensing; Michael A Quail; Sónia Gonçalves; Cristina Ariani; Michael Spencer Chapman; William L Hamilton; Luke W Meredith; Grant Hall; Aminu S Jahun; Yasmin Chaudhry; Myra Hosmillo; Malte L Pinckert; Iliana Georgana; Anna Yakovleva; Laura G Caller; Sarah L Caddy; Theresa Feltwell; Fahad A Khokhar; Charlotte J Houldcroft; Martin D Curran; Surendra Parmar; - The COVID-19 Genomics UK (COG-UK) Consortium; Alex Alderton; Rachel Nelson; Ewan Harrison; John Sillitoe; Stephen D Bentley; Jeffrey C Barrett; M. Estee Torok; Ian G Goodfellow; Cordelia Langford; Dominic Kwiatkowski; - Wellcome Sanger Institute COVID-19 Surveillance Team,"Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; European Bioinformatics Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Department of Medicine, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge and The Francis Crick Institute; Department of Medicine, University of Cambridge; Department of Pathology, University of Cambridge; Department of Medicine, University of Cambridge and Cambridge Institute of Therapeutic Immunology and Infectious Disease; Department of Medicine, University of Cambridge; Public Health England; Public Health England; COG-UK; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute and European Bioinformatics Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Department of Medicine, University of Cambridge; Department of Pathology, University of Cambridge; Wellcome Sanger Institute; Wellcome Sanger Institute and Oxford University; ","Monitoring the spread of SARS-CoV-2 and reconstructing transmission chains has become a major public health focus for many governments around the world. The modest mutation rate and rapid transmission of SARS-CoV-2 prevents the reconstruction of transmission chains from consensus genome sequences, but within-host genetic diversity could theoretically help identify close contacts. Here we describe the patterns of within-host diversity in 1,181 SARS-CoV-2 samples sequenced to high depth in duplicate. 95% of samples show within-host mutations at detectable allele frequencies. Analyses of the mutational spectra revealed strong strand asymmetries suggestive of damage or RNA editing of the plus strand, rather than replication errors, dominating the accumulation of mutations during the SARS-CoV-2 pandemic. Within and between host diversity show strong purifying selection, particularly against nonsense mutations. Recurrent within-host mutations, many of which coincide with known phylogenetic homoplasies, display a spectrum and patterns of purifying selection more suggestive of mutational hotspots than recombination or convergent evolution. While allele frequencies suggest that most samples result from infection by a single lineage, we identify multiple putative examples of co-infection. Integrating these results into an epidemiological inference framework, we find that while sharing of within-host variants between samples could help the reconstruction of transmission chains, mutational hotspots and rare cases of superinfection can confound these analyses.",genomics,exact,100,100 medRxiv,10.1101/2020.12.18.20248477,2020-12-20,https://medrxiv.org/cgi/content/short/2020.12.18.20248477,Face covering adherence is positively associated with better mental health and wellbeing: a longitudinal analysis of the CovidLife surveys,Drew M Altschul; Chloe Fawns-Ritchie; Alex Kwong; Louise Hartley; Clifford Nangle; Rachel Edwards; Rebecca Dawson; Christie Levein; Archie Campbell; Robin Flaig; Andrew McIntosh; Ian Deary; Riccardo Marioni; Caroline Hayward; Cathie Sudlow; Elaine Douglas; David Bell; David Porteous,The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; University of Stirling; University of Stirling; The University of Edinburgh,"Face masks or coverings are effective at reducing airborne infection rates, yet pandemic mitigation measures, including wearing face coverings, have been suggested to contribute to reductions in quality of life and poorer mental health. Longitudinal analyses of more than 11,000 participants across the UK found no association between lower adherence to face covering guidelines and poorer mental health. The opposite appears to be true. Even after controlling for behavioral, social, and psychological confounds, including measures of pre-pandemic mental health, individuals who wore face coverings ""most of the time"" or ""always"" had better mental health and wellbeing than those who did not. These results suggest that wearing face coverings more often will not negatively impact mental health.",psychiatry and clinical psychology,exact,100,100 -medRxiv,10.1101/2020.12.10.20247155,2020-12-14,https://medrxiv.org/cgi/content/short/2020.12.10.20247155,Self-harm presentations to Emergency Departments and Place of Safety during the first wave of the UK COVID-19 pandemic: South London and Maudsley data on service use from February to June 2020.,Eleanor Nuzum; Evangelia Martin; Gemma Morgan; Rina Dutta; Christoph Mueller; Catherine Polling; Megan Pritchard; Sumithra Velupillai; Robert Stewart,South London and Maudsley NHS Foundation Trust; South London and Maudsley NHS Foundation Trust; South London and Maudsley NHS Foundation Trust; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London,"The lockdown and social distancing policy imposed due to the COVID-19 pandemic has had a substantial impact on both mental health service delivery, and the ways in which people are accessing these services. Previous reports from the South London and Maudsley NHS Trust (SLaM; a large mental health service provider for around 1.2m residents in South London) have highlighted increased use of virtual contacts by mental health teams, with dropping numbers of face-to-face contacts over the first wave of the pandemic. There has been concern that the impact of the COVID-19 pandemic would lead to higher mental health emergencies, particularly instances of self-harm. However, with people advised to stay at home during the first wave lockdown, it is as yet unclear whether this impacted mental health service presentations. Taking advantage of SLaMs Clinical Records Interactive Search (CRIS) data resource with daily updates of information from its electronic mental health records, this paper describes overall presentations to Emergency Department (ED) mental health liaison teams, and those with self-harm. The paper focussed on three periods: i) a pre-lockdown period 1st February to 15th March, ii) a lockdown period 16th March to 10th May and iii) a post-lockdown period 11th May to 28th June. In summary, all attendances to EDs for mental health support decreased during the lockdown period, including those with self-harm. All types of self-harm decreased during lockdown, with self-poisoning remaining the most common. Attendances to EDs for mental health support increased post-lockdown, although were only just approaching pre-lockdown levels by the end of June 2020.",psychiatry and clinical psychology,exact,100,100 medRxiv,10.1101/2020.12.07.20245183,2020-12-07,https://medrxiv.org/cgi/content/short/2020.12.07.20245183,"Indicators of COVID-19 status in a cohort study of university staff and post-graduate research students, including results from home antibody testing",Katrina A S Davis; Ewan Carr; Daniel Leightley; Valentina Vitiello; Gabriella Bergin Cartwright; Grace Lavelle; Alice Wickersham; Michael H Malim; Carolin Oetzmann; Catherine Polling; Sharon A.M. Stevelink; Reza Razavi; Matthew Hotopf; - KCL-CHECK research team,"KCL Institute of Psychiatry, Psychology and Neuroscience; KCL Institute of Psychiatry Psychology and Neuroscience; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; ","Background Definitive diagnosis of COVID-19 requires resources frequently restricted to the severely ill. Cohort studies must rely on surrogate indicators to define cases of COVID-19 in the community. We describe the prevalence and overlap of potential indicators including self-reported symptoms, suspicion, and routine test results, plus home antibody testing. Methods An occupational cohort of 2807 staff and postgraduate students at a large London university. Repeated surveys covering March to June 2020. Antibody test results from 'lateral flow' IgG/IgM cassettes in June 2020. Results 1882 participants had valid antibody test results, and 124 (7%) were positive. Core symptoms of COVID-19 were common (770 participants positive, 41%), although fewer met criteria on a symptom algorithm (n=297, 16%). Suspicion of COVID-19 (n=509, 27%) was much higher than positive external tests (n=39, 2%). Positive antibody tests were rare in people who had no suspicion (n=4, 1%) or no core symptoms (n=10, 2%). In those who reported external antibody tests, 15% were positive on the study antibody test, compared with 24% on earlier external antibody tests. Discussion Our results demonstrate the agreement between different COVID indicators. Antibody testing using lateral flow devices at home can detect asymptomatic cases and provide greater certainty to self-report; but due to weak and waning antibody responses to mild infection, may under-ascertain. Multiple indicators used in combination can provide a more complete story than one used alone. Cohort studies need to consider how they deal with different, sometimes conflicting, indicators of COVID-19 illness to understand its long-term outcomes.",epidemiology,exact,100,100 medRxiv,10.1101/2020.12.03.20243535,2020-12-04,https://medrxiv.org/cgi/content/short/2020.12.03.20243535,OpenSAFELY: impact of national guidance on switching from warfarin to direct oral anticoagulants (DOACs) in early phase of COVID-19 pandemic in England,Helen J Curtis; Brian MacKenna; Alex J Walker; Richard Croker; Amir Mehrkar; Caroline E Morton; Seb Bacon; George Hickman; Peter Inglesby; Chris Bates; David Evans; Tom Ward; Jonathan Cockburn; Simon Davy; Krishnan Bhaskaran; Anna Schultze; Christopher T Rentsch; Elizabeth Williamson; William Hulme; Helen I McDonald; Laurie Tomlinson; Rohini Mathur; Henry Drysdale; Rosalind M Eggo; Kevin Wing; Angel Wong; Harriet Forbes; John Parry; Frank Hester; Sam Harper; Stephen JW Evans; Ian J Douglas; Liam Smeeth; Ben Goldacre,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; University of Oxford; TPP; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; TPP; TPP; TPP; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford,"BackgroundEarly in the COVID-19 pandemic the NHS recommended that appropriate patients anticoagulated with warfarin should be switched to direct acting oral anticoagulants (DOACs), requiring less frequent blood testing. Subsequently, a national safety alert was issued regarding patients being inappropriately co-prescribed two anticoagulants following a medication change, and associated monitoring. @@ -2061,6 +1975,7 @@ C_LIO_LIImplications for COVID-19 vaccine efficacy trials and wider public healt C_LI",health informatics,exact,100,100 medRxiv,10.1101/2020.11.19.20234120,2020-11-23,https://medrxiv.org/cgi/content/short/2020.11.19.20234120,Actionable druggable genome-wide Mendelian randomization identifies repurposingopportunities for COVID-19,Liam Gaziano; Claudia Giambartolomei; Alexandre C Pereira; Anna Gaulton; Daniel C Posner; Sonja A Swanson; Yuk Lam Ho; Sudha K Iyengar; Nicole M Kosik; Marijana Vujkovic; David R Gagnon; A Patricia Bento; Pedro Beltrao; Inigo Barrio Hernandez; Lars Ronnblom; Niklas Hagberg; Christian Lundtoft; Claudia Langenberg; Maik Pietzner; Dennis Valentine; Elias Allara; Praveen Surendran; Stephen Burgess; Jing Hua Zhao; James E Peters; Bram P Prins; John Danesh; Poornima Devineni; Yunling Shi; Kristine E Lynch; Scott L DuVall; Helene Garcon; Lauren Thomann; Jin J Zhou; Bryan R Gorman; Jennifer E Huffman; Christopher J O'Donnell; Philip S Tsao; Jean C Beckham; Saiju Pyarajan; Sumitra Muralidhar; Grant D Huang; Rachel Ramoni; Adriana M Hung; Kyong-Mi Chang; Yan V Sun; Jacob Joseph; Andrew R Leach; Todd L Edwards; Kelly Cho; J Michael Gaziano; Adam S Butterworth; Juan P Casas,"VA Boston Healthcare System, University of Cambridge; Instituto Italiano di Tecnologia, University of California Los Angeles; University of Sao Paulo, Harvard University; European Molecular Biology Laboratory, European Bioinformatics Institute; VA Boston Healthcare System; Erasmus Medical Center; VA Boston Healthcare System; Case Western Reserve University and Louis Stoke Cleveland VAMC; VA Boston Healthcare System; The Corporal Michael J. Crescenz VA Medical Center, the University of Pennsylvania Perelman School of Medicine; Boston University, VA Boston Healthcare System; European Molecular Biology Laboratory, European Bioinformatics Institute; European Molecular Biology Laboratory, European Bioinformatics Institute; European Molecular Biology Laboratory, European Bioinformatics Institute; Uppsala University; Uppsala University; Uppsala University; Charite University Medicine Berlin, Universityof Cambridge; Universityof Cambridge; University College London; University of Cambridge; Wellcome Genome Campus and University of Cambridge; University of Cambridge; University of Cambridge; Imperial College London; Wellcome Genome Campus and University of Cambridge; University of Cambridge; VA Boston Healthcare System; VA Boston Healthcare System; VA Salt Lake City Health Care System, University of Utah; VA Salt Lake City Health Care System, University of Utah; VA Boston Healthcare System; VA Boston Healthcare System; University of Arizona, Phoenix VA Health Care System; VA Boston Healthcare System; VA Boston Healthcare System; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; VA Palo Alto Health Care System, Stanford University School of Medicine; Durham VA Medical Center, Duke University School of Medicine; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; Department of Veterans Affairs; Department of Veterans Affairs; Department of Veterans Affairs; Department of Veterans Affairs, Vanderbilt University; The Corporal Michael J. Crescenz VA Medical Center, University of Pennsylvania; Atlanta VA Health Care System, Emory University Rollins School of Public Health; VA Boston Healthcare System and Brigham & Women's Hospital; European Molecular Biology Laboratory, European Bioinformatics Institute; Department of Veterans Affairs Tennessee Valley Healthcare System, Vanderbilt Genetics Institute Vanderbilt University Medical Center; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; University of Cambridge, Wellcome Genome Campus and University of Cambridge; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School","Drug repurposing provides a rapid approach to meet the urgent need for therapeutics to address COVID-19. To identify therapeutic targets relevant to COVID-19, we conducted Mendelian randomization (MR) analyses, deriving genetic instruments based on transcriptomic and proteomic data for 1,263 actionable proteins that are targeted by approved drugs or in clinical phase of drug development. Using summary statistics from the Host Genetics Initiative and the Million Veteran Program, we studied 7,554 patients hospitalized with COVID-19 and >1 million controls. We found significant Mendelian randomization results for three proteins (ACE2: P=1.6x10-6, IFNAR2: P=9.8x10-11, and IL-10RB: P=1.9x10-14) using cis-eQTL genetic instruments that also had strong evidence for colocalization with COVID-19 hospitalization. To disentangle the shared eQTL signal for IL10RB and IFNAR2, we conducted phenome-wide association scans and pathway enrichment analysis, which suggested that IFNAR2 is more likely to play a role in COVID-19 hospitalization. Our findings prioritize trials of drugs targeting IFNAR2 and ACE2 for early management of COVID-19.",epidemiology,exact,100,100 medRxiv,10.1101/2020.11.19.20234849,2020-11-22,https://medrxiv.org/cgi/content/short/2020.11.19.20234849,Community factors and excess mortality in first wave of the COVID-19 pandemic.,Bethan Davies; Brandon L Parkes; James Bennett; Daniela Fecht; Marta Blangiardo; Majid Ezzati; Paul Elliott,Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London,"Risk factors for increased risk of death from Coronavirus Disease 19 (COVID-19) have been identified1,2 but less is known on characteristics that make communities resilient or vulnerable to the mortality impacts of the pandemic. We applied a two-stage Bayesian spatial model to quantify inequalities in excess mortality at the community level during the first wave of the pandemic in England. We used geocoded data on all deaths in people aged 40 years and older during March-May 2020 compared with 2015-2019 in 6,791 local communities. Here we show that communities with an increased risk of excess mortality had a high density of care homes, and/or high proportion of residents on income support, living in overcrowded homes and/or high percent of people with a non-White ethnicity (including Black, Asian and other minority ethnic groups). Conversely, after accounting for other community characteristics, we found no association between population density or air pollution and excess mortality. Overall, the social and environmental variables accounted for around 15% of the variation in mortality at community level. Effective and timely public health and healthcare measures that target the communities at greatest risk are urgently needed if England and other industrialised countries are to avoid further widening of inequalities in mortality patterns during the second wave.",epidemiology,exact,100,100 +medRxiv,10.1101/2020.11.06.20227108,2020-11-07,https://medrxiv.org/cgi/content/short/2020.11.06.20227108,Primary school staff reflections on school closures due to COVID-19 and recommendations for the future: a national qualitative survey,Emily Marchant; Charlotte Todd; Michaela James; Tom Crick; Russell Dwyer; Sinead Brophy,Swansea University; Swansea University; Swansea University; Swansea University; St Thomas Community Primary School; Swansea University,"School closures due to the COVID-19 global pandemic are likely to have a range of negative consequences spanning the domains of child development, education and health, in addition to the widening of inequalities and inequities. Research is required to improve understanding of the impact of school closures on the education, health and wellbeing of pupils and school staff, the challenges posed during reopening and importantly to identify how countries can return to in-school education and to inform policy. This qualitative study aimed to reflect on the perspectives and experiences of primary school staff (pupils aged 3-11) in Wales regarding school closures and the initial reopening of schools and to identify recommendations for the future. A total of 208 school staff completed a national online survey through the HAPPEN primary school network, consisting of questions about school closures (March to June 2020), the phased reopening of schools (June to July 2020) and a return to full-time education. Thematic analysis of survey responses highlighted that primary school staff perceive that gaps in learning, health and wellbeing have increased and inequalities have widened during school closures. Findings from this study identified five recommendations; (i) prioritise the health and wellbeing of pupils and staff; (ii) focus on enabling parental engagement and support; (iii) improve digital competence amongst pupils, teachers and parents; (iv) consider opportunities for smaller class sizes and additional staffing; and (v) improve the mechanism of communication between schools and families, and between government and schools.",public and global health,exact,100,100 medRxiv,10.1101/2020.11.03.20220699,2020-11-04,https://medrxiv.org/cgi/content/short/2020.11.03.20220699,A prospective study of risk factors associated with seroprevalence of SARS-CoV-2 antibodies in healthcare workers at a large UK teaching hospital,Daniel J Cooper; Sara Lear; Laura Watson; Ashley Shaw; Mark Ferris; Rainer Doffinger; Rachel Bousfield; Katherine Sharrocks; Michael Weekes; Ben Warne; Dominic Sparkes; Nick K Jones; Lucy Rivett; Matthew Routledge; Afzal Chaudhry; Katherine Dempsey; Montgomery Matson; Adil Lakha; George Gathercole; Olivia O'Connor; Emily Wilson; Orthi Shahzad; Kieran Toms; Rachel Thompson; Ian Halsall; David Halsall; Sally Houghton; Sofia Papadia; Nathalie Kingston; Kathleen Stirrups; Barbara Graves; Neil Walker; Hannah Stark; - The CITIID-NIHR BioResource COVID-19 Collaboration; Daniela De Angelis; Shaun Seaman; John Bradley; M Estée Török; Ian G. Goodfellow; Stephen Baker,"Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; NIHR Cambridge Clinical Research Facility; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; NIHR Cambridge Clinical Research Facility.; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; NIHR BioResource, NIHR Cambridge Biomedical Research Centre; NIHR BioResource, NIHR Cambridge Biomedical Research Centre; NIHR BioResource, NIHR Cambridge Biomedical Research Centre; NIHR BioResource, NIHR Cambridge Biomedical Research Centre; NIHR BioResource, NIHR Cambridge Biomedical Research Centre; NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust; ; MRC Biostatistics Unit, University of Cambridge; MRC Biostatistics Unit, University of Cambridge; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Department of pathology, Division of virology, University of Cambridge; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK","BackgroundThe COVID-19 pandemic continues to grow at an unprecedented rate. Healthcare workers (HCWs) are at higher risk of SARS-CoV-2 infection than the general population but risk factors for HCW infection are not well described. MethodsWe conducted a prospective sero-epidemiological study of HCWs at a UK teaching hospital using a SARS-CoV-2 immunoassay. Risk factors for seropositivity were analysed using multivariate logistic regression. @@ -2545,6 +2460,7 @@ Results2,075/9,339 residents developed COVID-19 symptoms (22.2% [95% confidence ConclusionsFindings suggest many deaths occurred in people who were infected with COVID-19, but not tested. Higher occupancy and lower staffing levels were independently associated with risks of infection. Protecting staff and residents from infection requires regular testing for COVID-19 and fundamental changes to staffing and care home occupancy.",infectious diseases,exact,100,100 medRxiv,10.1101/2020.07.13.20152710,2020-07-14,https://medrxiv.org/cgi/content/short/2020.07.13.20152710,Excess mortality in mental health service users during the COVID-19 pandemic described by ethnic group: South London and Maudsley data,Robert Stewart; Matthew Broadbent; Jayati Das-Munshi,King's College London; South London and Maudsley NHS Foundation Trust; King's College London,"The COVID-19 pandemic in the UK was accompanied by excess all-cause mortality at a national level, only part of which was accounted for by known infections. Excess mortality has previously been described in people who had received care from the South London and Maudsley NHS Foundation Trust (SLaM), a large mental health service provider for 1.2m residents in south London. SLaMs Clinical Record Interactive Search (CRIS) data resource receives 24-hourly updates from its full electronic health record, including regularly sourced national mortality on all past and present SLaM service users. SLaMs urban catchment has high levels of deprivation and is ethnically diverse, so the objective of the descriptive analyses reported in this manuscript was to compare mortality in SLaM service users from 16th March to 15th May 2020 to that for the same period in 2019 within specific ethnic groups: i) White British, ii) Other White, iii) Black African/Caribbean, iv) South Asian, v) Other, and vi) missing/not stated. For Black African/Caribbean patients (the largest minority ethnic group) this ratio was 3.33, compared to 2.47 for White British patients. Considering premature mortality (restricting to deaths below age 70), these ratios were 2.74 and 1.96 respectively. Ratios were also high for those from Other ethnic groups (2.63 for all mortality, 3.07 for premature mortality).",psychiatry and clinical psychology,exact,100,100 +medRxiv,10.1101/2020.07.12.20151753,2020-07-14,https://medrxiv.org/cgi/content/short/2020.07.12.20151753,"COVID-19 incidence and R decreased on the Isle of Wight after the launch of the Test, Trace, Isolate programme",Michelle Kendall; Luke Milsom; Lucie Abeler-Dorner; Chris Wymant; Luca Ferretti; Mark Briers; Chris Holmes; David Bonsall; Johannes Abeler; Christophe Fraser,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Alan Turing Institute; University of Oxford; Alan Turing Institute; University of Oxford; University of Oxford; University of Oxford,"In May 2020 the UK introduced a Test, Trace, Isolate programme in response to the COVID-19 pandemic. The programme was first rolled out on the Isle of Wight and included Version 1 of the NHS contact tracing app. We used COVID-19 daily case data to infer incidence of new infections and estimate the reproduction number R for each of 150 Upper Tier Local Authorities in England, and at the National level, before and after the launch of the programme on the Isle of Wight. We used Bayesian and Maximum-Likelihood methods to estimate R, and compared the Isle of Wight to other areas using a synthetic control method. We observed significant decreases in incidence and R on the Isle of Wight immediately after the launch. These results are robust across each of our approaches. Our results show that the sub-epidemic on the Isle of Wight was controlled significantly more effectively than the sub-epidemics of most other Upper Tier Local Authorities, changing from having the third highest reproduction number R (of 150) before the intervention to the tenth lowest afterwards. The data is not yet available to establish a causal link. However, the findings highlight the need for further research to determine the causes of this reduction, as these might translate into local and national non-pharmaceutical intervention strategies in the period before a treatment or vaccination becomes available.",epidemiology,exact,100,100 medRxiv,10.1101/2020.07.10.20150524,2020-07-11,https://medrxiv.org/cgi/content/short/2020.07.10.20150524,Community prevalence of SARS-CoV-2 virus in England during May 2020: REACT study,Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Benjamin Jeffrey; Caroline E. Walters; Christina J Atchison; Peter J. Diggle; Deborah Ashby; Christl A. Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Graham Taylor; Ara Darzi; Paul Elliott,"Dept Inf Dis Epi, Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Lancaster University; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London School of Public Health","BackgroundEngland has experienced one of the highest rates of confirmed COVID-19 mortality in the world. SARS-CoV-2 virus has circulated in hospitals, care homes and the community since January 2020. Our current epidemiological knowledge is largely informed by clinical cases with far less understanding of community transmission. MethodsThe REal-time Assessment of Community Transmission (REACT) study is a nationally representative prevalence survey of SARS-CoV-2 virus swab-positivity in the community in England. We recruited participants regardless of symptom status. @@ -2570,6 +2486,28 @@ ResultsThe 872 cases comprised 48.1% Black, 33.7% White, 12.6% Mixed/Other and 5 ConclusionsBlack and Mixed ethnicity are independently associated with greater admission risk with COVID-19 and may be risk factors for development of severe disease. Comorbidities and socioeconomic factors only partly account for this and additional ethnicity-related factors may play a large role. The impact of COVID-19 may be different in Asians. Funding sourcesBritish Heart Foundation (CH/1999001/11735 and RE/18/2/34213 to AMS); the National Institute for Health Research Biomedical Research Centre (NIHR BRC) at Guys & St Thomas NHS Foundation Trust and Kings College London (IS-BRC-1215-20006); and the NIHR BRC at South London and Maudsley NHS Foundation Trust and Kings College London (IS-BRC-1215-20018).",public and global health,exact,100,100 +medRxiv,10.1101/2020.07.06.20147348,2020-07-07,https://medrxiv.org/cgi/content/short/2020.07.06.20147348,Community prevalence of SARS-CoV-2 in England: Results from the ONS Coronavirus Infection Survey Pilot,Koen B Pouwels; Thomas House; Julie V Robotham; Paul Birrell; Andrew B Gelman; Nikola Bowers; Ian Boreham; Heledd Thomas; James Lewis; Iain Bell; John I Bell; John Newton; Jeremy Farrar; Ian Diamond; Pete Benton; Sarah Walker,University of Oxford; University of Manchester; Public Health England; Public Health England; Columbia University; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; Office for National Statistics; Office for National Statistics; University of Oxford,"ObjectiveTo estimate the percentage of individuals infected with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) over time in the community in England and to quantify risk factors. + +DesignRepeated cross-sectional surveys of population-representative households with longitudinal follow-up if consent given. + +SettingEngland + +Participants34,992 Individuals aged 2 years and over from 16,722 private residential households. Data were collected in a pilot phase of the survey between 26 April and 28 June 2020. + +Main outcome measuresPercentage of individuals in the community testing positive for SARS-CoV-2 RNA using throat and nose swabs. Individuals were asked about any symptoms and potential risk factors. + +ResultsThe percentage of people in private-residential households testing positive for SARS-CoV-2 reduced from 0.32% (95% credible interval (CrI) 0.19% to 0.52%) on 26 April to 0.08% (95% CrI 0.05% to 0.12%) on 28 June, although the prevalence stabilised near the end of the pilot. Factors associated with an increased risk of testing positive included having a job with direct patient contact (relative exposure (RE) 4.06, 95% CrI 2.42 to 6.77)), working outside the home (RE 2.49, 95% CrI 1.39 to 4.45), and having had contact with a hospital (RE 2.20, 95% CrI 1.09 to 4.16 for having been to a hospital individually and RE 1.95, 95% CrI 0.81 to 4.09 for a household member having been to a hospital). In 133 visits where individuals tested positive, 82 (61%, 95% CrI 53% to 69%) reported no symptoms, stably over time. + +ConclusionThe percentage of SARS-CoV-2 positive individuals declined between 26 April and 28 June 2020. Positive tests commonly occurred without symptoms being reported. Working outside your home was an important risk factor, indicating that continued monitoring for SARS-CoV-2 in the community will be essential for early detection of increases in infections following return to work and other relaxations of control measures. + +What is already known on this topic- Unprecedented control measures, such as national lockdowns, have been widely implemented to contain the spread of SARS-CoV-2. +- Previous mass surveillance has been based on data sources such as hospital admission, deaths or self-reported symptoms that do not measure community prevalence of virus directly. +- Decisions regarding the continued need for social distancing measures in the overall population, specific subgroups and geographic areas heavily rely on accurate and up-to-date information about the number of people and risk factors for testing positive. + + +What this study adds- The percentage of individuals from the general community in England testing positive for SARS-CoV-2 clearly declined between 26 April and 28 June 2020 from around one in three 300 to around one in a thousand. +- Risk factors for testing positive included having a job with direct patient contact, having had (indirect) contact with a hospital in the past 2 weeks, and working outside your home. +- Positive tests commonly occurred without symptoms being reported and the percentage of individuals with a positive test that reported no symptoms was stable over time.",infectious diseases,exact,100,100 medRxiv,10.1101/2020.07.03.20145839,2020-07-04,https://medrxiv.org/cgi/content/short/2020.07.03.20145839,"The Impact of COVID-19 on Adjusted Mortality Risk in Care Homes for Older Adults in Wales, United Kingdom: A retrospective population-based cohort study for mortality in 2016-2020",Joe Hollinghurst; Jane Lyons; Richard Fry; Ashley Akbari; Mike Gravenor; Alan Watkins; Fiona Verity; Ronan A Lyons,Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University,"BackgroundMortality in care homes has had a prominent focus during the COVID-19 outbreak. Multiple and interconnected challenges face the care home sector in the prevention and management of outbreaks of COVID-19, including adequate supply of personal protective equipment, staff shortages, and insufficient or lack of timely COVID-19 testing. Care homes are particularly vulnerable to infectious diseases. AimTo analyse the mortality of older care home residents in Wales during COVID-19 lockdown and compare this across the population of Wales and the previous 4-years. @@ -2809,15 +2747,19 @@ ConclusionsWe have quantified a range of clinical risk factors for death from CO medRxiv,10.1101/2020.05.02.20078642,2020-05-06,https://medrxiv.org/cgi/content/short/2020.05.02.20078642,Impact of ethnicity on outcome of severe COVID-19 infection. Data from an ethnically diverse UK tertiary centre,James T Teo; Daniel Bean; Rebecca Bendayan; Richard Dobson; Ajay Shah,Kings College Hospital NHS Foundation Trust; King's College London; King's College London; Kings College London; King's College London,"During the current COVID-19 pandemic, it has been suggested that BAME background patients may be disproportionately affected compared to White but few detailed data are available. We took advantage of near real-time hospital data access and analysis pipelines to look at the impact of ethnicity in 1200 consecutive patients admitted between 1st March 2020 and 12th May 2020 to Kings College Hospital NHS Trust in London (UK). Our key findings are firstly that BAME patients are significantly younger and have different co-morbidity profiles than White individuals. Secondly, there is no significant independent effect of ethnicity on severe outcomes (death or ITU admission) within 14-days of symptom onset, after adjustment for age, sex and comorbidities.",intensive care and critical care medicine,exact,100,100 -medRxiv,10.1101/2020.04.28.20083170,2020-05-05,https://medrxiv.org/cgi/content/short/2020.04.28.20083170,Quantifying and mitigating the impact of the COVID-19 pandemic on outcomes in colorectal cancer,Amit Sud; Michael Jones; John Broggio; Stephen Scott; Chey Loveday; Bethany Torr; Alice Garrett; David L. Nicol; Shaman Jhanji; Stephen A. Boyce; Matthew Williams; Georgios Lyratzopoulos; Claire Barry; Elio Riboli; Emma Kipps; Ethna McFerran; Mark Lawler; David C. Muller; Muti Abulafi; Richard Houlston; Clare Ann Turnbull,"Institute of Cancer Research; Institute of Cancer Research; Public Health England; RM Partners, West London Cancer Alliance; Institute of Cancer Research; Institute of Cancer Research; Institute of Cancer Research; Royal Marsden NHS Foundation Trust; Royal Marsden NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Imperial College; University College London; RM Partners, West London Cancer Alliance; Imperial College London; Royal Marsden NHS Foundation Trust; Queen's University Belfast; Queen's University Belfast; Imperial College London; Croydon Health Services NHS Trust, on behalf of RMP NICE FIT Steering Group; Institute of Cancer Research; Institute of Cancer Research","BackgroundThe COVID-19 pandemic has caused disruption across cancer pathways for diagnosis and treatment. In England, 32% of colorectal cancer (CRC) is diagnosed via urgent symptomatic referral from primary care, the ""2-week-wait"" (2WW) pathway. Access to routine endoscopy is likely to be a critical bottleneck causing delays in CRC management due to chronic limitation in capacity, acute competition for physician time, and safety concerns. +medRxiv,10.1101/2020.04.24.20078006,2020-04-29,https://medrxiv.org/cgi/content/short/2020.04.24.20078006,Supplementing the National Early Warning Score (NEWS2) for anticipating early deterioration among patients with COVID-19 infection,Ewan Carr; Rebecca Bendayan; Daniel Bean; Matthew Stammers; Wenjuan Wang; Huayu Zhang; Thomas Searle; Zeljko Kraljevic; Anthony Shek; Hang T T Phan; Walter Muruet; Rishi K Gupta; Anthony J Shinton; Mike Wyatt; Ting Shi; Xin Zhang; Andrew Pickles; Daniel Stahl; Rosita Zakeri; Mahdad Noursadeghi; Kevin O'Gallagher; Matt Rogers; Amos Folarin; Christopher Bourdeaux; Chris McWilliams; Lukasz Roguski; Florina Borca; James Batchelor; Xiaodong Wu; Jiaxing Sun; Ashwin Pinto; Bruce Guthrie; Cormac Breen; Abdel Douiri; Honghan Wu; Vasa Curcin; James T Teo; Ajay Shah; Richard Dobson,"King's College London; King's College London; King's College London; Clinical Informatics Research Unit, University of Southampton; King's College London; University of Edinburgh; King's College London; King's College London; King's College London; Clinical Informatics Research Unit, University of Southampton; King's College London; University College London; UHS Digital, University Hospital Southampton; University Hospitals Bristol NHS Foundation Trust, Bristol, UK; Usher Institute, University of Edinburgh; Department of Pulmonary and Critical Care Medicine, People's Liberation Army Joint Logistic Support Force 920th Hospital, Yunnan, China; King's College London; King's College London; King's College London; UCL Division of Infection and Immunity, University College London Hospitals NHS Trust; King's College London; University Hospitals Bristol NHS Foundation Trust, Bristol, U.K.; King's College London; University Hospitals Bristol NHS Foundation Trust, Bristol, U.K.; Department of Engineering Mathematics, University of Bristol, Bristol, UK; University College London; University of Southampton; Clinical Informatics Research Unit, University of Southampton, Coxford Rd, Southampton SO16 5AF; Department of Pulmonary and Critical Care Medicine, Shanghai East Hospital, Tongji University, Shanghai, China; Department of Pulmonary and Critical Care Medicine, Shanghai East Hospital, Tongji University, Shanghai, China; UHS Digital, University Hospital Southampton; Usher Institute, University of Edinburgh; King's College London; King's College London; University College London; King's College London; Kings College Hospital NHS Foundation Trust; King's College London; Kings College London","BackgroundThe National Early Warning Score (NEWS2) is currently recommended in the United Kingdom for risk stratification of COVID outcomes, but little is known about its ability to detect severe cases. We aimed to evaluate NEWS2 for severe COVID outcome and identify and validate a set of routinely-collected blood and physiological parameters taken at hospital admission to improve the score. -MethodsWe used age-specific, stage-specific 10 year CRC survival for England 2007-2017 and 2WW CRC cases volumes. We used per-day hazard ratios of CRC survival generated from observational studies of CRC diagnosis-to-treatment interval to model the effect of different durations of per-patient delay. We utilised data from a large London observational study of faecal immunochemical testing (FIT) in symptomatic patients to model FIT-triage to mitigate delay to colonoscopy. +MethodsTraining cohorts comprised 1276 patients admitted to Kings College Hospital NHS Foundation Trust with COVID-19 disease from 1st March to 30th April 2020. External validation cohorts included 5037 patients from four UK NHS Trusts (Guys and St Thomas Hospitals, University Hospitals Southampton, University Hospitals Bristol and Weston NHS Foundation Trust, University College London Hospitals), and two hospitals in Wuhan, China (Wuhan Sixth Hospital and Taikang Tongji Hospital). The outcome was severe COVID disease (transfer to intensive care unit or death) at 14 days after hospital admission. Age, physiological measures, blood biomarkers, sex, ethnicity and comorbidities (hypertension, diabetes, cardiovascular, respiratory and kidney diseases) measured at hospital admission were considered in the models. -FindingsModest delays result in significant reduction in survival from CRC with a 4-month delay resulting across age groups in [≥]20% reduction in survival in Stage 3 disease and in total over a year, 1,419 attributable deaths across the 11,266 CRC patients diagnosed via the 2WW pathway. FIT triage of >10 ug Hb/g would salvage 1,292/1,419 of the attributable deaths and reduce colonoscopy requirements by >80%. Diagnostic colonoscopy offers net survival in all age groups, providing nosocomial COVID-19 infection rates are kept low (<2{middle dot}5%). +ResultsA baseline model of NEWS2 + age had poor-to-moderate discrimination for severe COVID infection at 14 days (AUC in training sample = 0.700; 95% CI: 0.680, 0.722; Brier score = 0.192; 95% CI: 0.186, 0.197). A supplemented model adding eight routinely-collected blood and physiological parameters (supplemental oxygen flow rate, urea, age, oxygen saturation, CRP, estimated GFR, neutrophil count, neutrophil/lymphocyte ratio) improved discrimination (AUC = 0.735; 95% CI: 0.715, 0.757) and these improvements were replicated across five UK and non-UK sites. However, there was evidence of miscalibration with the model tending to underestimate risks in most sites. -InterpretationTo avoid significant numbers of avoidable deaths from CRC, normal diagnostic and surgical throughput must be maintained. An accrued backlog of cases will present to primary care following release of lockdown, supranormal endoscopy capacity will be required to manage this without undue delays. FIT-triage of symptomatic cases provides a rational approach by which to avoid patient delay and mitigate pressure on capacity in endoscopy. This would also reduce exposure to nosocomial COVID-19 infection, relevant in particular to older patient groups. +ConclusionsNEWS2 score had poor-to-moderate discrimination for medium-term COVID outcome which raises questions about its use as a screening tool at hospital admission. Risk stratification was improved by including readily available blood and physiological parameters measured at hospital admission, but there was evidence of miscalibration in external sites. This highlights the need for a better understanding of the use of early warning scores for COVID. -FundingBreast Cancer Now, Cancer Research UK, Bobby Moore Fund for Cancer Research, National Institute for Health Research (NIHR).",oncology,exact,100,100 +KO_SCPLOWEYC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWMESSAGESC_SCPLOWO_LIThe National Early Warning Score (NEWS2), currently recommended for stratification of severe COVID-19 disease in the UK, showed poor-to-moderate discrimination for medium-term outcomes (14-day transfer to ICU or death) among COVID-19 patients. +C_LIO_LIRisk stratification was improved by the addition of routinely-measured blood and physiological parameters routinely at hospital admission (supplemental oxygen, urea, oxygen saturation, CRP, estimated GFR, neutrophil count, neutrophil/lymphocyte ratio) which provided moderate improvements in a risk stratification model for 14-day ICU/death. +C_LIO_LIThis improvement over NEWS2 alone was maintained across multiple hospital trusts but the model tended to be miscalibrated with risks of severe outcomes underestimated in most sites. +C_LIO_LIWe benefited from existing pipelines for informatics at KCH such as CogStack that allowed rapid extraction and processing of electronic health records. This methodological approach provided rapid insights and allowed us to overcome the complications associated with slow data centralisation approaches. +C_LI",infectious diseases,exact,100,100 bioRxiv,10.1101/2020.04.28.066977,2020-04-29,https://biorxiv.org/cgi/content/short/2020.04.28.066977,"Controlling the SARS-CoV-2 outbreak, insights from large scale whole genome sequences generated across the world",Jody Phelan; Wouter Deelder; Daniel Ward; Susana Campino; Martin L Hibberd; Taane G Clark,London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine,"BackgroundSARS-CoV-2 most likely evolved from a bat beta-coronavirus and started infecting humans in December 2019. Since then it has rapidly infected people around the world, with more than 4.5 million confirmed cases by the middle of May 2020. Early genome sequencing of the virus has enabled the development of molecular diagnostics and the commencement of therapy and vaccine development. The analysis of the early sequences showed relatively few evolutionary selection pressures. However, with the rapid worldwide expansion into diverse human populations, significant genetic variations are becoming increasingly likely. The current limitations on social movement between countries also offers the opportunity for these viral variants to become distinct strains with potential implications for diagnostics, therapies and vaccines. MethodsWe used the current sequencing archives (NCBI and GISAID) to investigate 15,487 whole genomes, looking for evidence of strain diversification and selective pressure. diff --git a/data/covid/preprints.exact.json b/data/covid/preprints.exact.json index f6b4eb74..27d820ac 100644 --- a/data/covid/preprints.exact.json +++ b/data/covid/preprints.exact.json @@ -7,7 +7,7 @@ "title": "One year health outcomes associated with systemic corticosteroids for COVID-19: a longitudinal cohort study", "authors": "Olivia C Leavy; Richard J Russell; Ewen M Harrison; Nazir I Lone; Steven Kerr; Annemarie B Docherty; Aziz Sheikh; Matthew Richardson; Omer Elneima; Neil J Greening; Victoria Claire Harris; Linzy Houchen-Wolloff; Hamish J C McAuley; Ruth M Saunders; Marco Sereno; Aarti Shikotra; Amisha Singapuri; Raminder Aul; Paul Beirne; Charlotte E Bolton; Jeremy S Brown; Gourab Choudhury; Nawar Diar Bakerly; Nicholas Easom; Carlos Echevarria; Jonathan Fuld; Nick Hart; John R Hurst; Mark Jones; Dhruv Parekh; Paul Pfeffer; Najib M Rahman; Sarah Rowland-Jones; Ajay M Shah; Dan G Wootton; Caroline Jolley; AA Roger Thompson; Trudie Chalder; Melanie J Davies; Anthony De Soyza; John R Geddes; William Greenhalf; Simon Heller; Luke Howard; Joseph Jacob; R Gisli Jenkins; Janet M Lord; Will D-C Man; Gerry P McCann; Stefan Neubauer; Peter JM Openshaw; Joanna Porter; Matthew J Rowland; Janet T Scott; Malcolm G Semple; Sally J Singh; David Thomas; Mark Toshner; Keir Lewis; Liam G Heaney; Andrew Briggs; Bang Zheng; Mathew Thorpe; Jennifer K Quint; James D Chalmers; Ling-Pei Ho; Alex Horsley; Michael Marks; Krisnah Poinasamy; Betty Raman; Louise V Wain; Christopher E Brightling; Rachael A Evans; - PHOSP-COVID Collaborative Group", "affiliations": "Department of Population Health Sciences, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; The Usher Institute, University of Edinburgh, Edinburgh, UK; Roslin Institute, University of Edinburgh, Edinburgh, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; The Usher Institute, University of Edinburgh, Edinburgh, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; Centre for Exercise and Rehabilitation Science, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; St Georges University Hospitals NHS Foundation Trust, London, UK; The Leeds Teaching Hospitals NHS Trust, Leeds, UK; University of Nottingham, Nottingham, UK; UCL Respiratory, Department of Medicine, University College London, Rayne Institute, London, UK; University of Edinburgh, Edinburgh, UK; Manchester Metropolitan University, Manchester, UK; Infection Research Group, Hull University Teaching Hospitals, Hull, UK; The Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK; Department of Respiratory Medicine, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Lane Fox Respiratory Service, Guys and St Thomas NHS Foundation Trust, London, UK; University College London, London, UK; Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK; University of Birmingham, Birmingham, UK; Barts Health NHS Trust, London, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK; University of Sheffield, Sheffield, UK; Kings College London, London, UK; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Kings College London, London, UK; University of Sheffield, Sheffield, UK; Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK; Diabetes Research Centre, University of Leicester, Leicester, UK; Population Health Sciences Institute, Newcastle University, Newcastle Upon Tyne, UK; NIHR Oxford Health Biomedical Research Centre, University of Oxford, Oxford, UK; University of Liverpool, Liverpool, UK; Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK; Imperial College Healthcare NHS Trust, London, UK; Centre for Medical Image Computing, University College London, London, UK; National Heart and Lung Institute, Imperial College London, London, UK; MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK; Royal Brompton and Harefield Clinical Group, Guys and St Thomas NHS Foundation Trust, London, UK; Department of Cardiovascular Sciences, University of Leicester, Leicester, UK; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; National Heart and Lung Institute, Imperial College London, London, UK; UCL Respiratory, Department of Medicine, University College London, Rayne Institute, London, UK; Kadoorie Centre for Critical Care Research, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, U; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; Imperial College London, London, UK; Cambridge NIHR BRC, Cambridge, UK; Hywel Dda University Health Board, Wales, UK; Wellcome-Wolfson Institute for Experimental Medicine, Queens University Belfast, Belfast, UK; London School of Hygiene & Tropical Medicine, London, UK; London School of Hygiene & Tropical Medicine, London, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; NHLI, Imperial College London, London, UK; University of Dundee, Ninewells Hospital and Medical School, Dundee, UK; MRC Human Immunology Unit, University of Oxford, Oxford, UK; Division of Infection, Immunity & Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK; Asthma and Lung UK, London, UK; Radcliffe Department of Medicine, University of Oxford, Oxford, UK; Department of Population Health Sciences, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; ", - "abstract": "Background In patients with COVID-19 requiring supplemental oxygen, dexamethasone reduces acute severity and improves survival, but longer-term effects are unknown. We hypothesised that systemic corticosteroid administration during acute COVID-19 would be associated with improved health-related quality of life (HRQoL) one year after discharge. Methods Adults admitted to hospital between February 2020 and March 2021 for COVID-19 and meeting current guideline recommendations for dexamethasone treatment were included using two prospective UK cohort studies. HRQoL, assessed by EQ-5D-5L utility index, pre-hospital and one year after discharge were compared between those receiving corticosteroids or not after propensity weighting for treatment. Secondary outcomes included patient reported recovery, physical and mental health status, and measures of organ impairment. Sensitivity analyses were undertaken to account for survival and selection bias. Findings In 1,888 participants included in the primary analysis, 1,149 received corticosteroids. There was no between-group difference in EQ-5D-5L utility index at one year (mean difference 0.004, 95% CI: -0.026 to 0.034, p = 0.77). A similar reduction in EQ-5D-5L was seen at one year between corticosteroid exposed and non-exposed groups (mean (SD) change -0.12 (0.22) vs -0.11 (0.22), p = 0.32). Overall, there were no differences in secondary outcome measures. After sensitivity analyses modelled using a larger cohort of 109,318 patients admitted to hospital with COVID-19, EQ-5D-5L utility index at one year remained similar between the two groups. Interpretation Systemic corticosteroids for acute COVID-19 have no impact on the large reduction in HRQoL one year after hospital discharge. Treatments to address this are urgently needed.", + "abstract": "BackgroundIn patients with COVID-19 requiring supplemental oxygen, dexamethasone reduces acute severity and improves survival, but longer-term effects are unknown. We hypothesised that systemic corticosteroid administration during acute COVID-19 would be associated with improved health-related quality of life (HRQoL) one year after discharge.\n\nMethodsAdults admitted to hospital between February 2020 and March 2021 for COVID-19 and meeting current guideline recommendations for dexamethasone treatment were included using two prospective UK cohort studies. HRQoL, assessed by EQ-5D-5L utility index, pre-hospital and one year after discharge were compared between those receiving corticosteroids or not after propensity weighting for treatment. Secondary outcomes included patient reported recovery, physical and mental health status, and measures of organ impairment. Sensitivity analyses were undertaken to account for survival and selection bias.\n\nFindingsIn 1,888 participants included in the primary analysis, 1,149 received corticosteroids. There was no between-group difference in EQ-5D-5L utility index at one year (mean difference 0.004, 95% CI: -0.026 to 0.034, p = 0.77). A similar reduction in EQ-5D-5L was seen at one year between corticosteroid exposed and non-exposed groups (mean (SD) change -0.12 (0.22) vs -0.11 (0.22), p = 0.32). Overall, there were no differences in secondary outcome measures. After sensitivity analyses modelled using a larger cohort of 109,318 patients admitted to hospital with COVID-19, EQ-5D-5L utility index at one year remained similar between the two groups.\n\nInterpretationSystemic corticosteroids for acute COVID-19 have no impact on the large reduction in HRQoL one year after hospital discharge. Treatments to address this are urgently needed.\n\nTake home messageSystemic corticosteroids given for acute COVID-19 do not affect health-related quality of life or other patient reported outcomes, physical and mental health outcomes, and organ function one year after hospital discharge", "category": "infectious diseases", "match_type": "exact", "author_similarity": 100, @@ -69,20 +69,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2023.08.07.23293778", - "date": "2023-08-09", - "link": "https://medrxiv.org/cgi/content/short/2023.08.07.23293778", - "title": "Diabetes following SARS-CoV-2 infection: Incidence, persistence, and implications of COVID-19 vaccination. A cohort study of fifteen million people.", - "authors": "Kurt Taylor; Sophie Eastwood; Venexia Walker; Genevieve Cezard; Rochelle Knight; Marwa Al Arab; Yinghui Wei; Elsie M F Horne; Lucy Teece; Harriet Forbes; Alex Walker; Louis Fisher; Jon Massey; Lisa E M Hopcroft; Tom Palmer; Jose Cuitun Coronado; Samantha Ip; Simon Davy; Iain Dillingham; Caroline Morton; Felix Greaves; John MacLeod; Ben Goldacre; Angela Wood; Nishi Chaturvedi; Jonathan A C Sterne; Rachel Denholm; - CONVALESCENCE Long-COVID study; - Longitudinal Health and Wellbeing and Data and Connectivity UK COVID-19 National Core Studies; - OpenSAFELY collaborative", - "affiliations": "University of Bristol; University College London; University of Bristol; University of Cambridge; University of Bristol; University of Bristol; University of Plymouth; University of Bristol; University of Leicester; London School of Hygiene & Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Bristol; University of Bristol; University of Cambridge; University of Oxford; University of Oxford; University of Oxford; National Institute for Health and Care Excellence; University of Bristol; University of Oxford; University of Cambridge; University College London; University of Bristol; University of Bristol; -; -; -", - "abstract": "BackgroundType 2 diabetes (T2DM) incidence is increased after diagnosis of COVID-19. The impact of vaccination on this increase, for how long it persists, and the effect of COVID-19 on other types of diabetes remain unclear.\n\nMethodsWith NHS England approval, we studied diabetes incidence following COVID-19 diagnosis in pre-vaccination (N=15,211,471, January 2020-December 2021), vaccinated (N =11,822,640), and unvaccinated (N=2,851,183) cohorts (June-December 2021), using linked electronic health records. We estimated adjusted hazard ratios (aHRs) comparing diabetes incidence post-COVID-19 diagnosis with incidence before or without diagnosis up to 102 weeks post-diagnosis. Results were stratified by COVID-19 severity (hospitalised/non-hospitalised) and diabetes type.\n\nFindingsIn the pre-vaccination cohort, aHRS for T2DM incidence after COVID-19 (compared to before or without diagnosis) declined from 3.01 (95% CI: 2.76,3.28) in weeks 1-4 to 1.24 (1.12,1.38) in weeks 53-102. aHRS were higher in unvaccinated than vaccinated people (4.86 (3.69,6.41)) versus 1.42 (1.24,1.62) in weeks 1-4) and for hospitalised COVID-19 (pre-vaccination cohort 21.1 (18.8,23.7) in weeks 1-4 declining to 2.04 (1.65,2.51) in weeks 52-102), than non-hospitalised COVID-19 (1.45 (1.27,1.64) in weeks 1-4, 1.10 (0.98,1.23) in weeks 52-102). T2DM persisted for 4 months after COVID-19 for [~]73% of those diagnosed. Patterns were similar for Type 1 diabetes, though excess incidence did not persist beyond a year post-COVID-19.\n\nInterpretationElevated T2DM incidence after COVID-19 is greater, and persists longer, in hospitalised than non-hospitalised people. It is markedly less apparent post-vaccination. Testing for T2DM after severe COVID-19 and promotion of vaccination are important tools in addressing this public health problem.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed for population-based observational studies published between December 1st 2019 and July 12th 2023 examining associations between SARS-CoV-2 infection or COVID-19 diagnosis (search string: SARS-CoV-2 or COVID* or coronavirus*) and subsequent incident diabetes (search term: diabetes). Of nineteen relevant studies; eight had a composite outcome of diabetes types, six stratified by diabetes type and five pertained to type-1-diabetes (T1DM) only. We did not identify any studies relating to gestational or other types of diabetes. Eleven studies were from the US, three from the UK, two from Germany, one from Canada, one from Denmark and one from South Korea.\n\nMost studies described cumulative relative risks (for infection versus no infection) one to two years post-SARS-CoV-2 infection of 1.2 to 2.6, though four studies found no associations with T1DM after the post-acute period. All studies lacked the power to compare diabetes relative risk by type, severity, and vaccination status in population subgroups. One study examined relative risks by vaccination status, but this used a composite outcome of diabetes and hyperlipidaemia and was conducted in a predominantly white male population.\n\nTwo studies of T1DM found no evidence of elevated risk beyond 30 days after COVID-19 diagnosis, whilst two reported elevated risks at six months. Two studies of type 2 diabetes (T2DM) examined relative risks by time period post-infection: one study of US insurance claims reported a persistent association six months post-infection, whereas a large UK population-based study reported no associations after 12 weeks. However, the latter study used only primary care data, therefore COVID-19 cases were likely to have been under-ascertained.\n\nNo large studies have investigated the persistence of diabetes diagnosed following COVID-19; key to elucidating the role of stress/steroid-induced hyperglycaemia.\n\nAdded value of this studyThis study, which is the largest to address the question to date, analysed linked primary and secondary care health records with SARS-CoV-2 testing and COVID-19 vaccination data for 15 million people living in England. This enabled us to compare the elevation in diabetes incidence after COVID-19 diagnosis by diabetes type, COVID-19 severity and vaccination status, overall and in population subgroups. Importantly, excess diabetes incidence by time period since infection could also be quantified. Since healthcare in the UK is universal and free-at-the-point-of-delivery, almost the entire population is registered with primary care. Therefore the findings are likely to be generalisable.\n\nWe found that, before availability of COVID-19 vaccination, a COVID-19 diagnosis (vs. no diagnosis) was associated with increased T2DM incidence which remained elevated by approximately 30% beyond one year after diagnosis. Though still present (with around 30% excess incidence at eight weeks), these associations were substantially attenuated in unvaccinated compared with vaccinated people. Excess incidence was greater in people hospitalised with COVID-19 than those who were not hospitalised after diagnosis. T1DM incidence was elevated up to, but not beyond, a year post COVID-19. Around 73% of people diagnosed with incident T2DM after COVID-19 still had evidence of diabetes four months after infection.\n\nImplications of all the available evidenceThere is a 30-50% elevated T2DM incidence post-COVID-19, but we report the novel finding that there is elevated incidence beyond one-year post-diagnosis. Elevated T1DM incidence did not appear to persist beyond a year, which may explain why previous studies disagree. For the first time in a general-population dataset, we demonstrate that COVID-19 vaccination reduces, but does not entirely ameliorate, excess diabetes incidence after COVID-19. This supports a policy of universal vaccination and suggests that other public health activities, such as enhanced diabetes screening after severe COVID-19, may be warranted, particularly in unvaccinated people.", - "category": "epidemiology", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2023.07.28.23293269", @@ -97,6 +83,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2023.08.02.23293519", + "date": "2023-08-04", + "link": "https://medrxiv.org/cgi/content/short/2023.08.02.23293519", + "title": "Real-time epidemiological modelling during the COVID-19 emergency in Wales", + "authors": "Michael Gravenor; Mark Dawson; Ed Bennett; Ben Thorpe; Carla White; Alma Rahat; Daniel Archambault; Noemi Picco; Gibin Powathil; Biagio Lucini", + "affiliations": "Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University", + "abstract": "The sudden outbreak of the COVID-19 pandemic presented governments, policy makers and health services with an unprecedented challenge of taking real-time decisions that could keep the disease under control with non-pharmaceutical interventions, while at the same time limit as much as possible severe consequences of a very strict lockdown. Mathematical modelling has proved to be a crucial element for informing those decisions. Here we report on the rapid development and application of the Swansea Model, a mathematical model of disease spread in real time, to inform policy decisions during the COVID-19 pandemic in Wales.", + "category": "epidemiology", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2023.06.29.23292056", @@ -433,6 +433,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2023.01.29.23285160", + "date": "2023-01-30", + "link": "https://medrxiv.org/cgi/content/short/2023.01.29.23285160", + "title": "High number of SARS-CoV-2 persistent infections uncovered through genetic analysis of samples from a large community-based surveillance study", + "authors": "Mahan Ghafari; Matthew Hall; Tanya Golubchik; Daniel Ayoubkhani; Thomas House; George MacIntyre-Cockett; Helen Fryer; Laura Thomson; Anel Nurtay; David Buck; Angie Green; Amy Trebes; Paolo Piazza; Lorne J Lonie; Ruth Studley; Emma Rourke; Darren Smith; Matthew Bashton; Andrew Nelson; Matthew Crown; Clare McCann; Gregory R Young; Rui Andre Nunes de Santos; Zack Richards; Adnan Tariq; Roberto Cahuantzi; - Wellcome Sanger Institute COVID-19 Surveillance Team; - COVID-19 Infection Survey Group; - The COVID-19 Genomics UK (COG-UK) consortium; Jeff Barrett; Christophe Fraser; David Bonsall; Sarah Walker; Katrina A Lythgoe", + "affiliations": "University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; University of Manchester; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; Office for National Statistics; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Office for National Statistics; -; -; -; Wellcome Sanger Institute; University of Oxford; University of Oxford; University of Oxford; University of Oxford", + "abstract": "Persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections may act as viral reservoirs that could seed future outbreaks 1-5, give rise to highly divergent lineages 6-8, and contribute to cases with post-acute Coronavirus disease 2019 (COVID-19) sequelae (Long Covid) 9,10. However, the population prevalence of persistent infections, their viral load kinetics, and evolutionary dynamics over the course of infections remain largely unknown. We identified 381 infections lasting at least 30 days, of which 54 lasted at least 60 days. These persistently infected individuals had more than 50% higher odds of self-reporting Long Covid compared to the infected controls, and we estimate that 0.09-0.5% of SARS-CoV-2 infections can become persistent and last for at least 60 days. In nearly 70% of the persistent infections we identified, there were long periods during which there were no consensus changes in virus sequences, consistent with prolonged presence of non-replicating virus. Our findings also suggest reinfections with the same major lineage are rare and that many persistent infections are characterised by relapsing viral load dynamics. Furthermore, we found a strong signal for positive selection during persistent infections, with multiple amino acid substitutions in the Spike and ORF1ab genes emerging independently in different individuals, including mutations that are lineage-defining for SARS-CoV-2 variants, at target sites for several monoclonal antibodies, and commonly found in immunocompromised patients 11-14. This work has significant implications for understanding and characterising SARS-CoV-2 infection, epidemiology, and evolution.", + "category": "epidemiology", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2023.01.24.23284916", @@ -615,20 +629,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.09.23.22280285", - "date": "2022-09-25", - "link": "https://medrxiv.org/cgi/content/short/2022.09.23.22280285", - "title": "Dimethyl fumarate in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial", - "authors": "- RECOVERY Collaborative Group; Peter W Horby; Leon Peto; Natalie Staplin; Mark Campbell; Guilherme Pessoa-Amorim; Marion Mafham; Jonathan R Emberson; Richard Stewart; Benjamin Prudon; Alison Uriel; Christopher A Green; Devesh J Dhasmana; Flora Malein; Jaydip Majumdar; Paul Collini; Jack Shurmer; Bryan Yates; J Kenneth Baillie; Maya H Buch; Jeremy N Day; Saul N Faust; Thomas Jaki; Katie Jeffery; Edmund Juszczak; Marian Knight; Wei Shen Lim; Alan Montgomery; Andrew Mumford; Kathryn Rowan; Guy Thwaites; Richard Haynes; Martin Landray", - "affiliations": "; Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, University of Oxford, Oxford, United Kingdom; Milton Keynes University Hospital NHS Foundation Trust; North Tees and Hartlepool NHS Foundation Trust; Manchester University NHS Foundation Trust; University Hospitals Birmingham NHS Foundation Trust; Victoria Hospital Kirkcaldy, NHS Fife; Liverpool University Hospitals NHS Foundation Trust; Mid Cheshire Hospitals NHS Foundation Trust; Sheffield Teaching Hospitals NHS Foundation Trust; Bolton NHS Foundation Trust; Northumbria Healthcare NHS Foundation Trust; Roslin Institute, University of Edinburgh; Centre for Musculoskeletal Research, University of Manchester, Manchester, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam; NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University of Southampton, Southampton, United Kingdom; University of Regensburg, Germany; Oxford University Hospitals NHS Foundation Trust; School of Medicine, University of Nottingham, Nottingham, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom; Intensive Care National Audit & Research Centre, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam; MRC Population Health Research Unit, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom", - "abstract": "BackgroundDimethyl fumarate (DMF) is an anti-inflammatory drug that has been proposed as a treatment for patients hospitalised with COVID-19\n\nMethodsThis randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), is assessing multiple possible treatments in patients hospitalised for COVID-19. In this initial assessment of DMF, performed at 27 UK hospitals, eligible and consenting adults were randomly allocated (1:1) to either usual standard of care alone or usual standard of care plus DMF 120mg twice daily for 2 days followed by 240mg twice daily for 8 days, or until discharge if sooner. The primary outcome was clinical status on day 5 measured on a seven-point ordinal scale, assessed using a proportional odds model. Secondary outcomes were time to sustained improvement in clinical status, time to discharge, day 5 peripheral blood oxygenation, day 5 C-reactive protein, and improvement in day 10 clinical status. The trial is registered with ISRCTN (50189673) and clinicaltrials.gov (NCT04381936).\n\nFindingsBetween 2 March 2021 and 18 November 2021, 713 patients were enrolled in the DMF evaluation, of whom 356 were randomly allocated to receive usual care plus DMF, and 357 to usual care alone. 95% of patients were receiving corticosteroids as part of routine care. There was no evidence of a beneficial effect of DMF on clinical status at day 5 (common odds ratio of unfavourable outcome 1.12; 95% CI 0.85-1.46; p=0.42). There was no significant effect of DMF on any secondary outcome. As expected, DMF caused flushing and gastrointestinal symptoms, each in around 6% of patients, but no new adverse effects were identified.\n\nInterpretationIn adults hospitalised with COVID-19, DMF was not associated with an improvement in clinical outcomes.\n\nFundingUK Research and Innovation (Medical Research Council) and National Institute of Health Research (Grant ref: MC_PC_19056).", - "category": "infectious diseases", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.09.21.22280191", @@ -1021,20 +1021,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.04.26.22274332", - "date": "2022-04-27", - "link": "https://medrxiv.org/cgi/content/short/2022.04.26.22274332", - "title": "Community factors and excess mortality in the COVID-19 pandemic in England, Italy and Sweden", - "authors": "Brandon Parkes; Massimo Stafoggia; Daniela Fecht; Bethan Davies; Carl Bonander; Francesca de'Donato; Paola Michelozzi; Fr\u00e9d\u00e9ric B. Piel; Ulf Str\u00f6mberg; Marta Blangiardo", - "affiliations": "Imperial College London; Lazio Regional Health Service; Imperial College London; Imperial College London; University of Gothenburg; Lazio Regional Health Service; Lazio Regional Health Service; Imperial College London; University of Gothenburg; Imperial College London", - "abstract": "BackgroundAnalyses of COVID-19 suggest specific risk factors make communities more or less vulnerable to pandemic related deaths within countries. What is unclear is whether the characteristics affecting vulnerability of small communities within countries produce similar patterns of excess mortality across countries with different demographics and public health responses to the pandemic. Our aim is to quantify community-level variations in excess mortality within England, Italy and Sweden and identify how such spatial variability was driven by community-level characteristics.\n\nMethodsWe applied a two-stage Bayesian model to quantify inequalities in excess mortality in people aged 40 years and older at the community level in England, Italy and Sweden during the first year of the pandemic (March 2020-February 2021). We used community characteristics measuring deprivation, air pollution, living conditions, population density and movement of people as covariates to quantify their associations with excess mortality.\n\nResultsWe found just under half of communities in England (48.1%) and Italy (45.8%) had an excess mortality of over 300 per 100,000 males over the age of 40, while for Sweden that covered 23.1% of communities. We showed that deprivation is a strong predictor of excess mortality across the three countries, and communities with high levels of overcrowding were associated with higher excess mortality in England and Sweden.\n\nConclusionThese results highlight some international similarities in factors affecting mortality that will help policy makers target public health measures to increase resilience to the mortality impacts of this and future pandemics.", - "category": "epidemiology", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.04.21.22274152", @@ -1091,6 +1077,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2022.03.29.22273042", + "date": "2022-04-04", + "link": "https://medrxiv.org/cgi/content/short/2022.03.29.22273042", + "title": "The new normal? Dynamics and scale of the SARS-CoV-2 variant Omicron epidemic in England", + "authors": "Oliver Eales; Leonardo de Oliveira Martins; Andrew Page; Haowei Wang; Barbara Bodinier; David Tang; David Haw; Jakob Jonnerby; Christina Atchison; Deborah Ashby; Wendy Barclay; Graham Taylor; Graham Cooke; Helen Ward; Ara Darzi; Steven Riley; Paul Elliott; Christl A Donnelly; Marc Chadeau-Hyam", + "affiliations": "Imperial College London; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Environment and Health, School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Environment and Health, School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Environment and Health, School of Public Health, Imperial College London, UK", + "abstract": "The SARS-CoV-2 pandemic has been characterised by the regular emergence of genomic variants which have led to substantial changes in the epidemiology of the virus. With natural and vaccine-induced population immunity at high levels, evolutionary pressure favours variants better able to evade SARS-CoV-2 neutralising antibodies. The Omicron variant was first detected in late November 2021 and exhibited a high degree of immune evasion, leading to increased infection rates in many countries. However, estimates of the magnitude of the Omicron wave have relied mainly on routine testing data, which are prone to several biases. Here we infer the dynamics of the Omicron wave in England using PCR testing and genomic sequencing obtained by the REal-time Assessment of Community Transmission-1 (REACT-1) study, a series of cross-sectional surveys testing random samples of the population of England. We estimate an initial peak in national Omicron prevalence of 6.89% (5.34%, 10.61%) during January 2022, followed by a resurgence in SARS-CoV-2 infections in England during February-March 2022 as the more transmissible Omicron sub-lineage, BA.2 replaced BA.1 and BA.1.1. Assuming the emergence of further distinct genomic variants, intermittent epidemics of similar magnitude as the Omicron wave may become the new normal.", + "category": "infectious diseases", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2022.03.22.22271707", @@ -1133,6 +1133,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2022.03.17.22272414", + "date": "2022-03-18", + "link": "https://medrxiv.org/cgi/content/short/2022.03.17.22272414", + "title": "Modelling the impact of non-pharmaceutical interventions on workplace transmission of SARS-CoV-2 in the home-delivery sector", + "authors": "Carl A Whitfield; Martie Van Tongeren; Yang Han; Hua Wei; Sarah A Daniels; Martyn Regan; David W Denning; Arpana Verma; Lorenzo Pellis; - University of Manchester COVID-19 Modelling Group; Ian Hall", + "affiliations": "University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchaster; University of Manchester; University of Manchester; ; University of Manchester", + "abstract": "ObjectiveWe aimed to use mathematical models of SARS-COV-2 to assess the potential efficacy of non-pharmaceutical interventions on transmission in the parcel delivery and logistics sector.\n\nMethodsWe developed a network-based model of workplace contacts based on data and consultations from companies in the parcel delivery and logistics sectors. We used these in stochastic simulations of disease transmission to predict the probability of workplace outbreaks in this settings. Individuals in the model have different viral load trajectories based on SARS-CoV-2 in-host dynamics, which couple to their infectiousness and test positive probability over time, in order to determine the impact of testing and isolation measures.\n\nResultsThe baseline model (without any interventions) showed different workplace infection rates for staff in different job roles. Based on our assumptions of contact patterns in the parcel delivery work setting we found that when a delivery driver was the index case, on average they infect only 0.14 other employees, while for warehouse and office workers this went up to 0.65 and 2.24 respectively. In the LIDD setting this was predicted to be 1.40, 0.98, and 1.34 respectively. Nonetheless, the vast majority of simulations resulted in 0 secondary cases among customers (even without contact-free delivery). Our results showed that a combination of social distancing, office staff working from home, and fixed driver pairings (all interventions carried out by the companies we consulted) reduce the risk of workplace outbreaks by 3-4 times.\n\nConclusionThis work suggests that, without interventions, significant transmission could have occured in these workplaces, but that these posed minimal risk to customers. We found that identifying and isolating regular close-contacts of infectious individuals (i.e. house-share, carpools, or delivery pairs) is an efficient measure for stopping workplace outbreaks. Regular testing can make these isolation measures even more effective but also increases the number of staff isolating at one time. It is therefore more efficient to use these isolation measures in addition to social distancing and contact reduction interventions, rather than instead of, as these reduce both transmission and the number of people needing to isolate at one time.\n\nAuthor summaryDuring the COVID-19 pandemic the home-delivery sector was vital to maintaining peoples access to certain goods, and sustaining levels of economic activity for a variety of businesses. However, this important work necessarily involved contact with a large number of customers as well as colleagues. This means that questions have often been raised about whether enough was being done to keep customers and staff safe. Estimating the potential risk to customers and staff is complex, but here we tackle this problem by building a model of workplace and customer contacts, from which we simulate SARS-CoV-2 transmission. By involving industry representatives in the development of this model, we have simulated interventions that have either been applied or considered, and so the findings of this study are relevant to decisions made in that sector. Furthermore, we can learn generic lessons from this specific case study which apply to many types of shared workplace as well as highlighting implications of the highly stochastic nature of disease transmission in small populations.", + "category": "epidemiology", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2022.03.09.22272098", @@ -1203,20 +1217,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.02.10.22270799", - "date": "2022-02-13", - "link": "https://medrxiv.org/cgi/content/short/2022.02.10.22270799", - "title": "Evaluating the effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control teams: the COG-UK hospital-onset COVID-19 infection study", - "authors": "Oliver Stirrup; James Blackstone; Fiona Mapp; Alyson MacNeil; Monica Panca; Alison Holmes; Nicholas Machin; Gee Yen Shin; Tabitha Mahungu; Kordo Saeed; Tranprit Saluja; Yusri Taha; Nikunj Mahida; Cassie Pope; Anu Chawla; Teresa Cutino-Moguel; Asif Tamuri; Rachel Williams; Alistair Darby; David L Robertson; Flavia Flaviani; Eleni Nastouli; Samuel Robson; Darren Smith; Matthew Loose; Kenneth Laing; Irene Monahan; Beatrix Kele; Sam Haldenby; Ryan George; Matthew Bashton; Adam Witney; Matthew Byott; Francesc Coll; Michael Chapman; Sharon Peacock; - COG-UK HOCI Investigators; - COG-UK Consortium; Joseph Hughes; Gaia Nebbia; David G Partridge; Matthew Parker; James Richard Price; Christine Peters; Sunando Roy; Luke B Snell; Thushan I de Silva; Emma Thomson; Paul Flowers; Andrew Copas; Judith Breuer", - "affiliations": "Institute for Global Health, UCL, London, UK; Comprehensive Clinical Trials Unit, UCL, London, UK; Institute for Global Health, UCL, London, UK; Comprehensive Clinical Trials Unit, UCL, London, UK; Comprehensive Clinical Trials Unit, UCL, London, UK; Imperial College Healthcare NHS Trust, London, UK; Manchester University NHS Foundation Trust, Manchester, UK; University College London Hospitals NHS Foundation Trust, London, UK; Royal Free NHS Foundation Trust, London, UK; University Hospital Southampton NHS Foundation Trust, Southampton, UK; Sandwell and West Birmingham NHS Trust, UK; Departments of Virology and Infectious Diseases, Newcastle Hospitals NHS Foundation Trust, Newcastle, UK; Nottingham University Hospitals NHS Trust, Nottingham, UK; St George's University Hospitals NHS Foundation Trust, London, UK; Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK; Barts Health NHS Trust, London, UK; Research Computing, UCL, London, UK; Department of Genetics & Genomic Medicine, UCL Great Ormond Street Institute of Child Health, UCL, London, UK; Centre for Genomic Research, University of Liverpool, Liverpool, UK; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK; University College London Hospitals NHS Foundation Trust, London, UK; Centre for Enzyme Innovation, University of Portsmouth, Portsmouth, UK; Department of Applied Sciences, Northumbria University, Newcastle, UK; School of Life Sciences, University of Nottingham, Nottingham, UK; Institute for Infection and Immunity, St George's University of London, London, UK; Institute for Infection and Immunity, St George's University of London, London, UK; Barts Health NHS Trust, London, UK; Centre for Genomic Research, University of Liverpool, Liverpool, UK; Manchester University NHS Foundation Trust, Manchester, UK; The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Northumbria University, Newcastle, UK; Institute for Infection and Immunity, St George's University of London, London, UK; University College London Hospitals NHS Foundation Trust, London, UK; Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; Health Data Research UK Cambridge Hub, Cambridge UK; Department of Medicine, University of Cambridge, Cambridge, UK; ; ; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK; Sheffield Bioinformatics Core, The University of Sheffield, Sheffield, UK; Imperial College Healthcare NHS Trust, London, UK; NHS Greater Glasgow and Clyde, Glasgow, UK; Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, UCL, London, UK; Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK; Department of Infection, Immunity and Cardiovascular Disease, Medical School, The University of Sheffield, Sheffield, UK; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; School of Psychological Sciences and Health, University of Strathclyde, Glasgow, UK; Institute for Global Health, UCL, London, UK; Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, UCL, London, UK", - "abstract": "IntroductionViral sequencing of SARS-CoV-2 has been used for outbreak investigation, but there is limited evidence supporting routine use for infection prevention and control (IPC) within hospital settings.\n\nMethodsWe conducted a prospective non-randomised trial of sequencing at 14 acute UK hospital trusts. Sites each had a 4-week baseline data-collection period, followed by intervention periods comprising 8 weeks of rapid (<48h) and 4 weeks of longer-turnaround (5-10 day) sequencing using a sequence reporting tool (SRT). Data were collected on all hospital onset COVID-19 infections (HOCIs; detected [≥]48h from admission). The impact of the sequencing intervention on IPC knowledge and actions, and on incidence of probable/definite hospital-acquired infections (HAIs) was evaluated.\n\nResultsA total of 2170 HOCI cases were recorded from October 2020-April 2021, with sequence reports returned for 650/1320 (49.2%) during intervention phases. We did not detect a statistically significant change in weekly incidence of HAIs in longer-turnaround (IRR 1.60, 95%CI 0.85-3.01; P=0.14) or rapid (0.85, 0.48-1.50; P=0.54) intervention phases compared to baseline phase. However, IPC practice was changed in 7.8% and 7.4% of all HOCI cases in rapid and longer-turnaround phases, respectively, and 17.2% and 11.6% of cases where the report was returned. In a per-protocol sensitivity analysis there was an impact on IPC actions in 20.7% of HOCI cases when the SRT report was returned within 5 days.\n\nConclusionWhile we did not demonstrate a direct impact of sequencing on the incidence of nosocomial transmission, our results suggest that sequencing can inform IPC response to HOCIs, particularly when returned within 5 days.", - "category": "infectious diseases", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.02.04.22270479", @@ -1413,20 +1413,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.12.20.21268098", - "date": "2021-12-21", - "link": "https://medrxiv.org/cgi/content/short/2021.12.20.21268098", - "title": "Therapies for Long COVID in non-hospitalised individuals - from symptoms, patient-reported outcomes, and immunology to targeted therapies (The TLC Study): Study protocol", - "authors": "Shamil Haroon; Krishnarajah Nirantharakumar; Sarah Hughes; Anuradhaa Subramanian; Olalekan Lee Aiyegbusi; Elin Haf Davies; Puja Myles; Tim Williams; Grace Turner; Joht Singh Chandan; Christel McMullan; Janet Lord; David Wraith; Kirsty McGee; Alastair Denniston; Tom Taverner; Louise Jackson; Elizabeth Sapey; Georgios Gkoutos; Krishna Gokhale; Edward Leggett; Clare Iles; Christopher Frost; Gary McNamara; Amy Bamford; Tom Marshall; Dawit Zemedikun; Gary Price; Steven Marwaha; Nikita Simms-Williams; Kirsty Brown; Anita Walker; Karen Jones; Karen Matthews; Jennifer Camaradou; Michael Saint-Cricq; Sumita Kumar; Yvonne Alder; David Stanton; Lisa Agyen; Megan Baber; Hannah Blaize; Melanie Calvert", - "affiliations": "University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; Aparito; Medicines and Healthcare Products Regulatory Agency; Medicines and Healthcare Products Regulatory Agency; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University of Birmingham; University of Birmingham; University ofBirmingham; University of Birmingham; Medicines and Healthcare Products Regulatory Agency; Medicines and Healthcare Products Regulatory Agency; Aparito; Aparito; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University of Birmingham; N/A; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; University ofBirmingham", - "abstract": "IntroductionIndividuals with COVID-19 frequently experience symptoms and impaired quality of life beyond 4-12 weeks, commonly referred to as Long COVID. Whether Long COVID is one or several distinct syndromes is unknown. Establishing the evidence base for appropriate therapies is needed. We aim to evaluate the symptom burden and underlying pathophysiology of Long COVID syndromes in non-hospitalised individuals and evaluate potential therapies.\n\nMethods and analysisA cohort of 4000 non-hospitalised individuals with a past COVID-19 diagnosis and 1000 matched controls will be selected from anonymised primary care records from the Clinical Practice Research Datalink (CPRD) and invited by their general practitioners to participate on a digital platform (Atom5). Individuals will report symptoms, quality of life, work capability, and patient reported outcome measures. Data will be collected monthly for one year.\n\nStatistical clustering methods will be used to identify distinct Long COVID symptom clusters. Individuals from the four most prevalent clusters and two control groups will be invited to participate in the BioWear sub-study which will further phenotype Long COVID symptom clusters by measurement of immunological parameters and actigraphy.\n\nWe will review existing evidence on interventions for post-viral syndromes and Long COVID to map and prioritise interventions for each newly characterised Long COVID syndrome. Recommendations will be made using the cumulated evidence in an expert consensus workshop. A virtual supportive intervention will be coproduced with patients and health service providers for future evaluation.\n\nIndividuals with lived experience of Long COVID will be involved throughout this programme through a patient and public involvement group.\n\nEthics and disseminationEthical approval was obtained from the Solihull Research Ethics Committee, West Midlands (21/WM/0203). The study is registered on the ISRCTN Registry (1567490). Research findings will be presented at international conferences, in peer-reviewed journals, to Long COVID patient support groups and to policymakers.\n\nArticle SummaryO_ST_ABSStrengths and limitations of the studyC_ST_ABSO_LIThe study will generate a nationally representative cohort of individuals with Long COVID recruited from primary care.\nC_LIO_LIWe will recruit controls matched on a wide range of demographic and clinical factors to assess differences in symptoms between people with Long COVID and similar individuals without a history of COVID-19.\nC_LIO_LIWe will use a newly developed electronic patient reported outcome measure (Symptom Burden Questionnaire) for Long COVID to comprehensively assess a wide range of symptoms highlighted by existing literature, patients, and clinicians.\nC_LIO_LIImmunological, proteomic, genetic, and wearable data captured in the study will allow deep phenotyping of Long COVID syndromes to help better target therapies.\nC_LIO_LIA limitation is that a significant proportion of non-hospitalised individuals affected by COVID-19 in the first wave of the pandemic will lack confirmatory testing and will be excluded from recruitment to the study.\nC_LI", - "category": "infectious diseases", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.12.16.21267904", @@ -1791,6 +1777,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.09.28.21264260", + "date": "2021-09-29", + "link": "https://medrxiv.org/cgi/content/short/2021.09.28.21264260", + "title": "The impact of SARS-CoV-2 vaccination on Alpha and Delta variant transmission", + "authors": "David W Eyre; Donald Taylor; Mark Purver; David Chapman; Tom Fowler; Koen Pouwels; Ann Sarah Walker; Tim EA Peto", + "affiliations": "University of Oxford; Department of Health and Social Care; Department of Health and Social Care; Deloitte MCS Ltd; Department of Health and Social Care; University of Oxford; University of Oxford; University of Oxford", + "abstract": "BackgroundPre-Delta, vaccination reduced SARS-CoV-2 transmission from individuals infected despite vaccination, potentially via reducing viral loads. While vaccination still lowers the risk of infection, similar viral loads in vaccinated and unvaccinated individuals infected with Delta question how much vaccination prevents transmission.\n\nMethodsWe performed a retrospective observational cohort study of adult contacts of SARS-CoV-2-infected adult index cases using English contact testing data. We used multivariable Poisson regression to investigate associations between transmission and index case and contact vaccination, and how these vary with Alpha and Delta variants (classified using S-gene detection/calendar trends) and time since second vaccination.\n\nResults54,667/146,243(37.4%) PCR-tested contacts of 108,498 index cases were PCR-positive. Two doses of BNT162b2 or ChAdOx1 vaccines in Alpha index cases were independently associated with reduced PCR-positivity in contacts (aRR, adjusted rate ratio vs. unvaccinated=0.32[95%CI 0.21-0.48] and 0.48[0.30-0.78] respectively). The Delta variant attenuated vaccine-associated reductions in transmission: two BNT162b2 doses reduced Delta transmission (aRR=0.50[0.39-0.65]), more than ChAdOx1 (aRR=0.76[0.70-0.82]). Variation in Ct values (indicative of viral load) explained 7-23% of vaccine-associated transmission reductions. Transmission reductions declined over time post-second vaccination, for Delta reaching similar levels to unvaccinated individuals by 12 weeks for ChAdOx1 and attenuating substantially for BNT162b2. Protection in contacts also declined in the 3 months post-second vaccination.\n\nConclusionsVaccination reduces transmission of Delta, but by less than the Alpha variant. The impact of vaccination decreased over time. Factors other than PCR Ct values at diagnosis are important in understanding vaccine-associated transmission reductions. Booster vaccinations may help control transmission together with preventing infections.", + "category": "infectious diseases", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.09.27.21264166", @@ -2057,20 +2057,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.07.19.21260770", - "date": "2021-07-22", - "link": "https://medrxiv.org/cgi/content/short/2021.07.19.21260770", - "title": "Uptake of infant and pre-school immunisations in Scotland and England during the COVID-19 pandemic: an observational study of routinely collected data", - "authors": "Fiona McQuaid; Rachel Mulholland; Yuma Sangpang Rai; Utkarsh Agrawal; Helen Bedford; Claire Cameron; Cheryl Gibbon; Partho Roy; Aziz Sheikh; Ting Shi; Colin Simpson; Judith Tait; Elise Tessier; Steve Turner; Jaime Villacampa Ortega; Joanne White; Rachael Wood", - "affiliations": "University of Edinburgh; University of Edinburgh; Public Health England; University of St Andrews; UCL Great Ormond Street Institute of Child Health; Public Health Scotland; Public Health Scotland; Public Health England; University of Edinburgh; University of Edinburgh; Victoria University of Wellington; Public Health Scotland; Public Health England; University of Aberdeen; Public Health Scotland; Public Health England; University of Edinburgh", - "abstract": "BackgroundIn 2020, the COVID-19 pandemic and control measures such as national lockdowns threatened to disrupt routine childhood immunisation programmes. Initial reports from the early weeks of lockdown in the UK and worldwide suggested that uptake could fall putting children at risk from multiple other infectious diseases. In Scotland and England, enhanced surveillance of national data for childhood immunisations was established to inform and rapidly assess the impact of the pandemic on infant and preschool immunisation uptake rates.\n\nMethods and findingsWe undertook an observational study using routinely collected data for the year prior to the pandemic (2019), and immediately before, during and after the first period of the UK lockdown in 2020. Data were obtained for Scotland from the Public Health Scotland \"COVID19 wider impacts on the health care system\" dashboard (https://scotland.shinyapps.io/phs-covid-wider-impact/) and for England from ImmForm.\n\nFive vaccinations delivered at different ages were evaluated; three doses of the 6-in-1 DTaP/IPV/Hib/HepB vaccine and two doses of MMR. Uptake in the periods in 2020 compared to that in the baseline year of 2019 using binary logistic regression analysis. For Scotland, we analysed timely uptake of immunisations, defined as uptake within four weeks of the child becoming eligible by age for each immunisation and data were also analysed by geographical region and indices of deprivation. For both Scotland and England, we assessed whether immunisations were up to date at approximately 6 months (all doses 6-in-1) and 16-18 months (first MMR) of age.\n\nWe found that uptake rates within four weeks of eligibility in Scotland for all the five vaccine visits were higher during the 2020 lockdown period than in 2019. The difference ranged from 1.3% for the first dose of the 6-in-1 vaccine (95.3 vs 94%, OR 1.28, CI 1.18-1.39) to 14.3% for the second MMR dose (66.1 vs 51.8 %, OR 1.8, CI 1.74-1.87). Significant increases in uptake were seen across all deprivation levels, though, for MMR, there was evidence of greater improvement for children living in the least deprived areas.\n\nIn England, fewer children who had been due to receive their immunisations during the lockdown period were up to date at 6 months (6-in-1) or 18 months (first dose MMR). The fall in percentage uptake ranged from 0.5% for first 6-in1 (95.8 vs 96.3%, OR 0.89, CI 0.86-0.91) to 2.1% for third 6-in-1 (86.6 vs 88.7%, OR 0.82, CI 0.81-0.83).\n\nConclusionsThis study suggests that the national lockdown in Scotland was associated with a positive effect on timely childhood immunisation uptake, however in England a lower percentage of children were up to date at 6 and 18 months. Reason for the improve uptake in Scotland may include active measures taken to promote immunisation at local and national level during this period. Promoting immunisation uptake and addressing potential vaccine hesitancy is particularly important given the ongoing pandemic and COVID-19 vaccination campaigns.", - "category": "pediatrics", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.07.16.21260651", @@ -2085,20 +2071,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.07.16.21260628", - "date": "2021-07-19", - "link": "https://medrxiv.org/cgi/content/short/2021.07.16.21260628", - "title": "Overall and cause-specific hospitalisation and death after COVID-19 hospitalisation in England: cohort study in OpenSAFELY using linked primary care, secondary care and death registration data", - "authors": "Krishnan Bhaskaran; Christopher T Rentsch; George Hickman; William J Hulme; Anna Schultze; Helen J Curtis; Kevin Wing; Charlotte Warren-Gash; Laurie Tomlinson; Christopher Bates; Rohini Mathur; Brian MacKenna; Viyaasan Mahalingasivam; Angel YS Wong; Alex J Walker; Caroline E Morton; Daniel Grint; Amir Mehrkar; Rosalind M Eggo; Peter Inglesby; Ian J Douglas; Helen I McDonald; Jonathan Cockburn; Elizabeth J Williamson; David Evans; John Parry; Frank Hester; Sam Harper; Stephen JW Evans; Sebastian CJ Bacon; Liam Smeeth; Ben Goldacre", - "affiliations": "London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; TPP; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; TPP; London School of Hygiene and Tropical Medicine; University of Oxford; TPP; TPP; TPP; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford", - "abstract": "BackgroundThere is concern about medium to long-term adverse outcomes following acute COVID-19, but little relevant evidence exists. We aimed to investigate whether risks of hospital admission and death, overall and by specific cause, are raised following discharge from a COVID-19 hospitalisation.\n\nMethods and FindingsWorking on behalf of NHS-England, we used linked primary care and hospital data in OpenSAFELY to compare risks of hospital admission and death, overall and by specific cause, between people discharged from COVID-19 hospitalisation (February-December 2020), and (i) demographically-matched controls from the 2019 general population; (ii) people discharged from influenza hospitalisation in 2017-19. We used Cox regression adjusted for personal and clinical characteristics.\n\n24,673 post-discharge COVID-19 patients, 123,362 general population controls, and 16,058 influenza controls were followed for [≤]315 days. Overall risk of hospitalisation or death (30968 events) was higher in the COVID-19 group than general population controls (adjusted-HR 2.23, 2.14-2.31) but similar to the influenza group (adjusted-HR 0.94, 0.91-0.98). All-cause mortality (7439 events) was highest in the COVID-19 group (adjusted-HR 4.97, 4.58-5.40 vs general population controls and 1.73, 1.60-1.87 vs influenza controls). Risks for cause-specific outcomes were higher in COVID-19 survivors than general population controls, and largely comparable between COVID-19 and influenza patients. However, COVID-19 patients were more likely than influenza patients to be readmitted/die due to their initial infection/other lower respiratory tract infection (adjusted-HR 1.37, 1.22-1.54), and to experience mental health or cognitive-related admission/death (adjusted-HR 1.36, 1.01-2.83); in particular, COVID-19 survivors with pre-existing dementia had higher risk of dementia death. One limitation of our study is that reasons for hospitalisation/death may have been misclassified in some cases due to inconsistent use of codes.\n\nConclusionsPeople discharged from a COVID-19 hospital admission had markedly higher risks for rehospitalisation and death than the general population, suggesting a substantial extra burden on healthcare. Most risks were similar to those observed after influenza hospitalisations; but COVID-19 patients had higher risks of all-cause mortality, readmissions/death due to the initial infection, and dementia death, highlighting the importance of post-discharge monitoring.", - "category": "infectious diseases", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.07.14.21260497", @@ -2239,20 +2211,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.06.03.21258289", - "date": "2021-06-06", - "link": "https://medrxiv.org/cgi/content/short/2021.06.03.21258289", - "title": "Implementation of COVID-19 Preventive Measures in Primary and Secondary Schools Following Reopening of Schools in Autumn 2020; A Cross-Sectional Study of Parents' and Teachers' Experiences in England", - "authors": "Zahin Amin-Chowdhury; Marta Bertran; Meaghan Kall; Georgina Ireland; Felicity Aiano; Annabel Powell; Samuel E Jones; Andrew Brent; Bernadette Brent; Frances Baawuah; Ifeanychukwu Okike; Joanne Beckmann; Joanna Garstang; Shazaad Ahmed; Neisha Sundaram; Chris Bonell; Sinead Langan; James Hargreaves; Shamez N Ladhani", - "affiliations": "Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Public Health England; University Hospitals of Derby and Burton NHS foundation Trust; Specialist Children & Young People's Services, East London NHS Foundation Trust; Birmingham Community Healthcare Trust; Public Health England; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Public Health England", - "abstract": "ObjectiveThe main objective was to assess implementation of and ease of implementation of control measures in schools as reported by staff and parents.\n\nDesignCross-sectional study.\n\nSettingStaff and parents/guardian participants in the 132 primary schools and 20 secondary schools participating in sKIDs and sKIDsPLUS surveillances.\n\nMain outcome measurePrevalence of control measures implemented in Autumn 2020, parental and staff perception of ease of implementation and acceptability of conducting school surveillance studies.\n\nResultsIn total, 56/152 (37%) schools participating in Public Health Englands sKIDs study of COVID in schools accepted the invitation to participate in the survey. By 28 December 2020, 1,953 parent and 986 staff respondents had completed the online questionnaire. While more than half the parents were positive about their children returning to school, roughly a third reported being a little anxious. 90% and 82% of primary and secondary school parents were either completely or partly reassured by the preventive measures implemented in their schools. Among staff, 80% of primary staff and 87% of secondary school staff felt that they were at higher risk of COVID-19 because of their profession; only 52% of primary school staff and 38% of secondary school staff reportedly felt safe. According to the teaching staff, most preventive measures were well-implemented apart from requiring 2-metre distancing between staff. For students, maintaining the 2-metre distance was reported to be particularly difficult. By extension, secondary schools also struggled to maintain small groups at all times or ensuring that the same staff were assigned to each student group (a problem also commonly reported by parents).\n\nConclusionsVariable implementation of infection control measures was reported by staff and parents. Whilst the majority were not worried about returning to school, some parents and staff, were concerned about returning to school and the risks posed to children, staff and household members.\n\nStrengths and limitations of this studyO_ST_ABSStrengthsC_ST_ABSO_LIThis study is one of the few to investigate school staff and parents perceptions of the implementation of control measures implemented following the reopening of schools in England.\nC_LIO_LIThe early establishment of COVID-19 surveillance in primary and secondary schools in the summer term 2020 provided a cohort to rapidly evaluate the experiences of parents and school staff during the autumn term before schools were required to close for the subsequent national lockdown.\nC_LI\n\nLimitationsO_LIAs the questionnaire and information provided was available in English only, there is likely to be an under-representation of families for whom English was not their main language.\nC_LIO_LISome school responses were only provided by one participant so may not necessarily be representative of the whole school.\nC_LIO_LIAlthough the surveillance included schools recruited nationally, a convenience sample was used and as such may not be representative of all primary and secondary schools in England.\nC_LI", - "category": "public and global health", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.05.28.21257602", @@ -2701,6 +2659,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.03.04.21252931", + "date": "2021-03-08", + "link": "https://medrxiv.org/cgi/content/short/2021.03.04.21252931", + "title": "A common TMPRSS2 variant protects against severe COVID-19", + "authors": "Alessia David; Nicholas Parkinson; Thomas P Peacock; Erola Pairo-Castineira; Tarun Khanna; Aurelie Cobat; Albert Tenesa; Vanessa Sancho-Shimizu; - GenOMICC Investigators, ISARIC4C Investigators; Jean-Laurent Casanova; Laurent Abel; Wendy S Barclay; J Kenneth Baillie; Michael J.E. Sternberg", + "affiliations": "Centre for Integrative System Biology and Bioinformatics, Imperial College London, London; Roslin Institute, University of Edinburgh; Department of Infectious Diseases, Imperial College London; Roslin Institute, University of Edinburgh; Centre for Integrative System Biology and Bioinformatics, Imperial College London; Laboratory of Human Genetics of Infectious Diseases, INSERM; Roslin Institute, University of Edinburgh; Department of Paediatric Infectious Diseases & Virology, Imperial College London; ; St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University; Laboratory of Human Genetics of Infectious Diseases, INSERM; Department of Infectious Diseases, Imperial College London; Roslin Institute, University of Edinburgh; Centre for Integrative System Biology and Bioinformatics, Imperial College London", + "abstract": "Infection with SARS-CoV-2 has a wide range of clinical presentations, from asymptomatic to life-threatening. Old age is the strongest factor associated with increased COVID19-related mortality, followed by sex and pre-existing conditions. The importance of genetic and immunological factors on COVID19 outcome is also starting to emerge, as demonstrated by population studies and the discovery of damaging variants in genes controlling type I IFN immunity and of autoantibodies that neutralize type I IFNs. The human protein transmembrane protease serine type 2 (TMPRSS2) plays a key role in SARS-CoV-2 infection, as it is required to activate the virus spike protein, facilitating entry into target cells. We focused on the only common TMPRSS2 non-synonymous variant predicted to be damaging (rs12329760), which has a minor allele frequency of [~]25% in the population. In a large population of SARS-CoV-2 positive patients, we show that this variant is associated with a reduced likelihood of developing severe COVID19 (OR 0.87, 95%CI:0.79-0.97, p=0.01). This association was stronger in homozygous individuals when compared to the general population (OR 0.65, 95%CI:0.50-0.84, p=1.3x10-3). We demonstrate in vitro that this variant, which causes the amino acid substitution valine to methionine, impacts the catalytic activity of TMPRSS2 and is less able to support SARS-CoV-2 spike-mediated entry into cells.\n\nTMPRSS2 rs12329760 is a common variant associated with a significantly decreased risk of severe COVID19. Further studies are needed to assess the expression of the TMPRSS2 across different age groups. Moreover, our results identify TMPRSS2 as a promising drug target, with a potential role for camostat mesilate, a drug approved for the treatment of chronic pancreatitis and postoperative reflux esophagitis, in the treatment of COVID19. Clinical trials are needed to confirm this.", + "category": "genetic and genomic medicine", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.03.02.21252444", @@ -2785,20 +2757,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.02.04.21251155", - "date": "2021-02-08", - "link": "https://medrxiv.org/cgi/content/short/2021.02.04.21251155", - "title": "Impact of school closures on the health and well-being of primary school children in Wales UK; a routine data linkage study using the HAPPEN survey (2018-2020).", - "authors": "Michaela James; Emily Marchant; Margaret A Defeyter; Jayne V Woodside; Sinead Brophy", - "affiliations": "Swansea University; Swansea University; Northumbria University; Queen's University Belfast; Swansea University", - "abstract": "IntroductionIn response to the COVID-19 pandemic, school closures were implemented across the United Kingdom. This study aimed to explore the impact of school closures on childrens health by comparing health and wellbeing outcomes collected during school closures (April - June 2020) with data from the same period in 2019 and 2018.\n\nMethodsData were collected online via the HAPPEN At Home survey, which captured the typical health behaviours of children aged 8 - 11 years between April - June 2020. These data were compared with data in 2018 and 2019 also collected between April-June, from HAPPEN. Free school meal (FSM) status was used as a proxy for socio-economic deprivation. Analyses were repeated stratifying by FSM.\n\nResultsComparing responses between April - June in 2020 (n=1068), 2019 (n=1150) and 2018 (n=475), there were improvements in physical activity levels, sleep time, happiness and general wellbeing for children during school closures compared to previous years. However, children on FSM ate less fruit and vegetables (21% (95%CI (5.7% to 37%)) and had lower self-assessed school competence compared to 2019. Compared to those not on FSM they also spent less time doing physical activity (13.03% (95%CI: 3.3% to 21.7%) and consumed more takeaways (16.3% (95%CI: 2%-30%)) during school closures.\n\nConclusionThis study suggests that schools play an important role in reducing inequalities in physical health. The physical health (e.g. physical activity and diet) of children eligible for FSM may be impacted by prolonged school closures.\n\nWhat is already known on this subject?In response to the COVID-19 pandemic, by mid-March 2020, 138 countries had implemented national school closures to reduce the number of social contacts between pupils, therefore interrupting the transmission of COVID-19 as part of pandemic plans. UNESCO warned that the global scale and speed of the educational disruption would be unparalleled. There is an ongoing debate with regard to the effectiveness of schools closures on transmission rates, but the fact schools are closed for a long period of time could have detrimental impacts on pupils physical and mental health.\n\nThis study provides evidence of any differences in the health and wellbeing of children prior to and during the COVID-19 enforced lockdown and school closures between March and June 2020. These findings could have a significant impact for the future and support schools to better understand their pupils physical, psychological, emotional and social health. It also contributes to a significant literature gap regarding the impact of school closures on school-aged children.\n\nWhat this study adds?Improvements in physical activity levels, sleep time, happiness and general wellbeing were observed in general for children during school closures compared to previous years. However, children on FSM reported eating less fruit and vegetables and had lower self-assessed school competence compared to 2019. Compared to those not on FSM they also spent less time doing physical activity and consumed more takeaways during school closures. These trends are not evident among children not on FSM. All children reported improvements in wellbeing during lockdown especially on the happiness with family measure.\n\nOverall, findings suggest schools help to reduce inequalities in physical health for socio-economically deprived children. During school closures children from deprived backgrounds are likely to have poorer physical health (e.g. less time spent doing physical activities and poorer diet) and this is not observed in children who are not in receipt of FSM. This research suggests that school closures will result in widening health inequalities and when schools return measures will need to be in place to readdress the widened gap in physical health.", - "category": "public and global health", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.02.04.21251087", @@ -3079,20 +3037,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.12.10.20247155", - "date": "2020-12-14", - "link": "https://medrxiv.org/cgi/content/short/2020.12.10.20247155", - "title": "Self-harm presentations to Emergency Departments and Place of Safety during the first wave of the UK COVID-19 pandemic: South London and Maudsley data on service use from February to June 2020.", - "authors": "Eleanor Nuzum; Evangelia Martin; Gemma Morgan; Rina Dutta; Christoph Mueller; Catherine Polling; Megan Pritchard; Sumithra Velupillai; Robert Stewart", - "affiliations": "South London and Maudsley NHS Foundation Trust; South London and Maudsley NHS Foundation Trust; South London and Maudsley NHS Foundation Trust; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London", - "abstract": "The lockdown and social distancing policy imposed due to the COVID-19 pandemic has had a substantial impact on both mental health service delivery, and the ways in which people are accessing these services. Previous reports from the South London and Maudsley NHS Trust (SLaM; a large mental health service provider for around 1.2m residents in South London) have highlighted increased use of virtual contacts by mental health teams, with dropping numbers of face-to-face contacts over the first wave of the pandemic. There has been concern that the impact of the COVID-19 pandemic would lead to higher mental health emergencies, particularly instances of self-harm. However, with people advised to stay at home during the first wave lockdown, it is as yet unclear whether this impacted mental health service presentations. Taking advantage of SLaMs Clinical Records Interactive Search (CRIS) data resource with daily updates of information from its electronic mental health records, this paper describes overall presentations to Emergency Department (ED) mental health liaison teams, and those with self-harm. The paper focussed on three periods: i) a pre-lockdown period 1st February to 15th March, ii) a lockdown period 16th March to 10th May and iii) a post-lockdown period 11th May to 28th June. In summary, all attendances to EDs for mental health support decreased during the lockdown period, including those with self-harm. All types of self-harm decreased during lockdown, with self-poisoning remaining the most common. Attendances to EDs for mental health support increased post-lockdown, although were only just approaching pre-lockdown levels by the end of June 2020.", - "category": "psychiatry and clinical psychology", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.12.07.20245183", @@ -3177,6 +3121,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.11.06.20227108", + "date": "2020-11-07", + "link": "https://medrxiv.org/cgi/content/short/2020.11.06.20227108", + "title": "Primary school staff reflections on school closures due to COVID-19 and recommendations for the future: a national qualitative survey", + "authors": "Emily Marchant; Charlotte Todd; Michaela James; Tom Crick; Russell Dwyer; Sinead Brophy", + "affiliations": "Swansea University; Swansea University; Swansea University; Swansea University; St Thomas Community Primary School; Swansea University", + "abstract": "School closures due to the COVID-19 global pandemic are likely to have a range of negative consequences spanning the domains of child development, education and health, in addition to the widening of inequalities and inequities. Research is required to improve understanding of the impact of school closures on the education, health and wellbeing of pupils and school staff, the challenges posed during reopening and importantly to identify how countries can return to in-school education and to inform policy. This qualitative study aimed to reflect on the perspectives and experiences of primary school staff (pupils aged 3-11) in Wales regarding school closures and the initial reopening of schools and to identify recommendations for the future. A total of 208 school staff completed a national online survey through the HAPPEN primary school network, consisting of questions about school closures (March to June 2020), the phased reopening of schools (June to July 2020) and a return to full-time education. Thematic analysis of survey responses highlighted that primary school staff perceive that gaps in learning, health and wellbeing have increased and inequalities have widened during school closures. Findings from this study identified five recommendations; (i) prioritise the health and wellbeing of pupils and staff; (ii) focus on enabling parental engagement and support; (iii) improve digital competence amongst pupils, teachers and parents; (iv) consider opportunities for smaller class sizes and additional staffing; and (v) improve the mechanism of communication between schools and families, and between government and schools.", + "category": "public and global health", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.11.03.20220699", @@ -3989,6 +3947,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.07.12.20151753", + "date": "2020-07-14", + "link": "https://medrxiv.org/cgi/content/short/2020.07.12.20151753", + "title": "COVID-19 incidence and R decreased on the Isle of Wight after the launch of the Test, Trace, Isolate programme", + "authors": "Michelle Kendall; Luke Milsom; Lucie Abeler-Dorner; Chris Wymant; Luca Ferretti; Mark Briers; Chris Holmes; David Bonsall; Johannes Abeler; Christophe Fraser", + "affiliations": "University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Alan Turing Institute; University of Oxford; Alan Turing Institute; University of Oxford; University of Oxford; University of Oxford", + "abstract": "In May 2020 the UK introduced a Test, Trace, Isolate programme in response to the COVID-19 pandemic. The programme was first rolled out on the Isle of Wight and included Version 1 of the NHS contact tracing app. We used COVID-19 daily case data to infer incidence of new infections and estimate the reproduction number R for each of 150 Upper Tier Local Authorities in England, and at the National level, before and after the launch of the programme on the Isle of Wight. We used Bayesian and Maximum-Likelihood methods to estimate R, and compared the Isle of Wight to other areas using a synthetic control method. We observed significant decreases in incidence and R on the Isle of Wight immediately after the launch. These results are robust across each of our approaches. Our results show that the sub-epidemic on the Isle of Wight was controlled significantly more effectively than the sub-epidemics of most other Upper Tier Local Authorities, changing from having the third highest reproduction number R (of 150) before the intervention to the tenth lowest afterwards. The data is not yet available to establish a causal link. However, the findings highlight the need for further research to determine the causes of this reduction, as these might translate into local and national non-pharmaceutical intervention strategies in the period before a treatment or vaccination becomes available.", + "category": "epidemiology", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.07.10.20150524", @@ -4031,6 +4003,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.07.06.20147348", + "date": "2020-07-07", + "link": "https://medrxiv.org/cgi/content/short/2020.07.06.20147348", + "title": "Community prevalence of SARS-CoV-2 in England: Results from the ONS Coronavirus Infection Survey Pilot", + "authors": "Koen B Pouwels; Thomas House; Julie V Robotham; Paul Birrell; Andrew B Gelman; Nikola Bowers; Ian Boreham; Heledd Thomas; James Lewis; Iain Bell; John I Bell; John Newton; Jeremy Farrar; Ian Diamond; Pete Benton; Sarah Walker", + "affiliations": "University of Oxford; University of Manchester; Public Health England; Public Health England; Columbia University; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; Office for National Statistics; Office for National Statistics; University of Oxford", + "abstract": "ObjectiveTo estimate the percentage of individuals infected with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) over time in the community in England and to quantify risk factors.\n\nDesignRepeated cross-sectional surveys of population-representative households with longitudinal follow-up if consent given.\n\nSettingEngland\n\nParticipants34,992 Individuals aged 2 years and over from 16,722 private residential households. Data were collected in a pilot phase of the survey between 26 April and 28 June 2020.\n\nMain outcome measuresPercentage of individuals in the community testing positive for SARS-CoV-2 RNA using throat and nose swabs. Individuals were asked about any symptoms and potential risk factors.\n\nResultsThe percentage of people in private-residential households testing positive for SARS-CoV-2 reduced from 0.32% (95% credible interval (CrI) 0.19% to 0.52%) on 26 April to 0.08% (95% CrI 0.05% to 0.12%) on 28 June, although the prevalence stabilised near the end of the pilot. Factors associated with an increased risk of testing positive included having a job with direct patient contact (relative exposure (RE) 4.06, 95% CrI 2.42 to 6.77)), working outside the home (RE 2.49, 95% CrI 1.39 to 4.45), and having had contact with a hospital (RE 2.20, 95% CrI 1.09 to 4.16 for having been to a hospital individually and RE 1.95, 95% CrI 0.81 to 4.09 for a household member having been to a hospital). In 133 visits where individuals tested positive, 82 (61%, 95% CrI 53% to 69%) reported no symptoms, stably over time.\n\nConclusionThe percentage of SARS-CoV-2 positive individuals declined between 26 April and 28 June 2020. Positive tests commonly occurred without symptoms being reported. Working outside your home was an important risk factor, indicating that continued monitoring for SARS-CoV-2 in the community will be essential for early detection of increases in infections following return to work and other relaxations of control measures.\n\nWhat is already known on this topic- Unprecedented control measures, such as national lockdowns, have been widely implemented to contain the spread of SARS-CoV-2.\n- Previous mass surveillance has been based on data sources such as hospital admission, deaths or self-reported symptoms that do not measure community prevalence of virus directly.\n- Decisions regarding the continued need for social distancing measures in the overall population, specific subgroups and geographic areas heavily rely on accurate and up-to-date information about the number of people and risk factors for testing positive.\n\n\nWhat this study adds- The percentage of individuals from the general community in England testing positive for SARS-CoV-2 clearly declined between 26 April and 28 June 2020 from around one in three 300 to around one in a thousand.\n- Risk factors for testing positive included having a job with direct patient contact, having had (indirect) contact with a hospital in the past 2 weeks, and working outside your home.\n- Positive tests commonly occurred without symptoms being reported and the percentage of individuals with a positive test that reported no symptoms was stable over time.", + "category": "infectious diseases", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.07.03.20145839", @@ -4425,14 +4411,14 @@ }, { "site": "medRxiv", - "doi": "10.1101/2020.04.28.20083170", - "date": "2020-05-05", - "link": "https://medrxiv.org/cgi/content/short/2020.04.28.20083170", - "title": "Quantifying and mitigating the impact of the COVID-19 pandemic on outcomes in colorectal cancer", - "authors": "Amit Sud; Michael Jones; John Broggio; Stephen Scott; Chey Loveday; Bethany Torr; Alice Garrett; David L. Nicol; Shaman Jhanji; Stephen A. Boyce; Matthew Williams; Georgios Lyratzopoulos; Claire Barry; Elio Riboli; Emma Kipps; Ethna McFerran; Mark Lawler; David C. Muller; Muti Abulafi; Richard Houlston; Clare Ann Turnbull", - "affiliations": "Institute of Cancer Research; Institute of Cancer Research; Public Health England; RM Partners, West London Cancer Alliance; Institute of Cancer Research; Institute of Cancer Research; Institute of Cancer Research; Royal Marsden NHS Foundation Trust; Royal Marsden NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Imperial College; University College London; RM Partners, West London Cancer Alliance; Imperial College London; Royal Marsden NHS Foundation Trust; Queen's University Belfast; Queen's University Belfast; Imperial College London; Croydon Health Services NHS Trust, on behalf of RMP NICE FIT Steering Group; Institute of Cancer Research; Institute of Cancer Research", - "abstract": "BackgroundThe COVID-19 pandemic has caused disruption across cancer pathways for diagnosis and treatment. In England, 32% of colorectal cancer (CRC) is diagnosed via urgent symptomatic referral from primary care, the \"2-week-wait\" (2WW) pathway. Access to routine endoscopy is likely to be a critical bottleneck causing delays in CRC management due to chronic limitation in capacity, acute competition for physician time, and safety concerns.\n\nMethodsWe used age-specific, stage-specific 10 year CRC survival for England 2007-2017 and 2WW CRC cases volumes. We used per-day hazard ratios of CRC survival generated from observational studies of CRC diagnosis-to-treatment interval to model the effect of different durations of per-patient delay. We utilised data from a large London observational study of faecal immunochemical testing (FIT) in symptomatic patients to model FIT-triage to mitigate delay to colonoscopy.\n\nFindingsModest delays result in significant reduction in survival from CRC with a 4-month delay resulting across age groups in [≥]20% reduction in survival in Stage 3 disease and in total over a year, 1,419 attributable deaths across the 11,266 CRC patients diagnosed via the 2WW pathway. FIT triage of >10 ug Hb/g would salvage 1,292/1,419 of the attributable deaths and reduce colonoscopy requirements by >80%. Diagnostic colonoscopy offers net survival in all age groups, providing nosocomial COVID-19 infection rates are kept low (<2{middle dot}5%).\n\nInterpretationTo avoid significant numbers of avoidable deaths from CRC, normal diagnostic and surgical throughput must be maintained. An accrued backlog of cases will present to primary care following release of lockdown, supranormal endoscopy capacity will be required to manage this without undue delays. FIT-triage of symptomatic cases provides a rational approach by which to avoid patient delay and mitigate pressure on capacity in endoscopy. This would also reduce exposure to nosocomial COVID-19 infection, relevant in particular to older patient groups.\n\nFundingBreast Cancer Now, Cancer Research UK, Bobby Moore Fund for Cancer Research, National Institute for Health Research (NIHR).", - "category": "oncology", + "doi": "10.1101/2020.04.24.20078006", + "date": "2020-04-29", + "link": "https://medrxiv.org/cgi/content/short/2020.04.24.20078006", + "title": "Supplementing the National Early Warning Score (NEWS2) for anticipating early deterioration among patients with COVID-19 infection", + "authors": "Ewan Carr; Rebecca Bendayan; Daniel Bean; Matthew Stammers; Wenjuan Wang; Huayu Zhang; Thomas Searle; Zeljko Kraljevic; Anthony Shek; Hang T T Phan; Walter Muruet; Rishi K Gupta; Anthony J Shinton; Mike Wyatt; Ting Shi; Xin Zhang; Andrew Pickles; Daniel Stahl; Rosita Zakeri; Mahdad Noursadeghi; Kevin O'Gallagher; Matt Rogers; Amos Folarin; Christopher Bourdeaux; Chris McWilliams; Lukasz Roguski; Florina Borca; James Batchelor; Xiaodong Wu; Jiaxing Sun; Ashwin Pinto; Bruce Guthrie; Cormac Breen; Abdel Douiri; Honghan Wu; Vasa Curcin; James T Teo; Ajay Shah; Richard Dobson", + "affiliations": "King's College London; King's College London; King's College London; Clinical Informatics Research Unit, University of Southampton; King's College London; University of Edinburgh; King's College London; King's College London; King's College London; Clinical Informatics Research Unit, University of Southampton; King's College London; University College London; UHS Digital, University Hospital Southampton; University Hospitals Bristol NHS Foundation Trust, Bristol, UK; Usher Institute, University of Edinburgh; Department of Pulmonary and Critical Care Medicine, People's Liberation Army Joint Logistic Support Force 920th Hospital, Yunnan, China; King's College London; King's College London; King's College London; UCL Division of Infection and Immunity, University College London Hospitals NHS Trust; King's College London; University Hospitals Bristol NHS Foundation Trust, Bristol, U.K.; King's College London; University Hospitals Bristol NHS Foundation Trust, Bristol, U.K.; Department of Engineering Mathematics, University of Bristol, Bristol, UK; University College London; University of Southampton; Clinical Informatics Research Unit, University of Southampton, Coxford Rd, Southampton SO16 5AF; Department of Pulmonary and Critical Care Medicine, Shanghai East Hospital, Tongji University, Shanghai, China; Department of Pulmonary and Critical Care Medicine, Shanghai East Hospital, Tongji University, Shanghai, China; UHS Digital, University Hospital Southampton; Usher Institute, University of Edinburgh; King's College London; King's College London; University College London; King's College London; Kings College Hospital NHS Foundation Trust; King's College London; Kings College London", + "abstract": "BackgroundThe National Early Warning Score (NEWS2) is currently recommended in the United Kingdom for risk stratification of COVID outcomes, but little is known about its ability to detect severe cases. We aimed to evaluate NEWS2 for severe COVID outcome and identify and validate a set of routinely-collected blood and physiological parameters taken at hospital admission to improve the score.\n\nMethodsTraining cohorts comprised 1276 patients admitted to Kings College Hospital NHS Foundation Trust with COVID-19 disease from 1st March to 30th April 2020. External validation cohorts included 5037 patients from four UK NHS Trusts (Guys and St Thomas Hospitals, University Hospitals Southampton, University Hospitals Bristol and Weston NHS Foundation Trust, University College London Hospitals), and two hospitals in Wuhan, China (Wuhan Sixth Hospital and Taikang Tongji Hospital). The outcome was severe COVID disease (transfer to intensive care unit or death) at 14 days after hospital admission. Age, physiological measures, blood biomarkers, sex, ethnicity and comorbidities (hypertension, diabetes, cardiovascular, respiratory and kidney diseases) measured at hospital admission were considered in the models.\n\nResultsA baseline model of NEWS2 + age had poor-to-moderate discrimination for severe COVID infection at 14 days (AUC in training sample = 0.700; 95% CI: 0.680, 0.722; Brier score = 0.192; 95% CI: 0.186, 0.197). A supplemented model adding eight routinely-collected blood and physiological parameters (supplemental oxygen flow rate, urea, age, oxygen saturation, CRP, estimated GFR, neutrophil count, neutrophil/lymphocyte ratio) improved discrimination (AUC = 0.735; 95% CI: 0.715, 0.757) and these improvements were replicated across five UK and non-UK sites. However, there was evidence of miscalibration with the model tending to underestimate risks in most sites.\n\nConclusionsNEWS2 score had poor-to-moderate discrimination for medium-term COVID outcome which raises questions about its use as a screening tool at hospital admission. Risk stratification was improved by including readily available blood and physiological parameters measured at hospital admission, but there was evidence of miscalibration in external sites. This highlights the need for a better understanding of the use of early warning scores for COVID.\n\nKO_SCPLOWEYC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWMESSAGESC_SCPLOWO_LIThe National Early Warning Score (NEWS2), currently recommended for stratification of severe COVID-19 disease in the UK, showed poor-to-moderate discrimination for medium-term outcomes (14-day transfer to ICU or death) among COVID-19 patients.\nC_LIO_LIRisk stratification was improved by the addition of routinely-measured blood and physiological parameters routinely at hospital admission (supplemental oxygen, urea, oxygen saturation, CRP, estimated GFR, neutrophil count, neutrophil/lymphocyte ratio) which provided moderate improvements in a risk stratification model for 14-day ICU/death.\nC_LIO_LIThis improvement over NEWS2 alone was maintained across multiple hospital trusts but the model tended to be miscalibrated with risks of severe outcomes underestimated in most sites.\nC_LIO_LIWe benefited from existing pipelines for informatics at KCH such as CogStack that allowed rapid extraction and processing of electronic health records. This methodological approach provided rapid insights and allowed us to overcome the complications associated with slow data centralisation approaches.\nC_LI", + "category": "infectious diseases", "match_type": "exact", "author_similarity": 100, "affiliation_similarity": 100 diff --git a/data/covid/preprints.json b/data/covid/preprints.json index 7759a9be..8ba4399d 100644 --- a/data/covid/preprints.json +++ b/data/covid/preprints.json @@ -7,7 +7,7 @@ "title": "One year health outcomes associated with systemic corticosteroids for COVID-19: a longitudinal cohort study", "authors": "Olivia C Leavy; Richard J Russell; Ewen M Harrison; Nazir I Lone; Steven Kerr; Annemarie B Docherty; Aziz Sheikh; Matthew Richardson; Omer Elneima; Neil J Greening; Victoria Claire Harris; Linzy Houchen-Wolloff; Hamish J C McAuley; Ruth M Saunders; Marco Sereno; Aarti Shikotra; Amisha Singapuri; Raminder Aul; Paul Beirne; Charlotte E Bolton; Jeremy S Brown; Gourab Choudhury; Nawar Diar Bakerly; Nicholas Easom; Carlos Echevarria; Jonathan Fuld; Nick Hart; John R Hurst; Mark Jones; Dhruv Parekh; Paul Pfeffer; Najib M Rahman; Sarah Rowland-Jones; Ajay M Shah; Dan G Wootton; Caroline Jolley; AA Roger Thompson; Trudie Chalder; Melanie J Davies; Anthony De Soyza; John R Geddes; William Greenhalf; Simon Heller; Luke Howard; Joseph Jacob; R Gisli Jenkins; Janet M Lord; Will D-C Man; Gerry P McCann; Stefan Neubauer; Peter JM Openshaw; Joanna Porter; Matthew J Rowland; Janet T Scott; Malcolm G Semple; Sally J Singh; David Thomas; Mark Toshner; Keir Lewis; Liam G Heaney; Andrew Briggs; Bang Zheng; Mathew Thorpe; Jennifer K Quint; James D Chalmers; Ling-Pei Ho; Alex Horsley; Michael Marks; Krisnah Poinasamy; Betty Raman; Louise V Wain; Christopher E Brightling; Rachael A Evans; - PHOSP-COVID Collaborative Group", "affiliations": "Department of Population Health Sciences, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; The Usher Institute, University of Edinburgh, Edinburgh, UK; Roslin Institute, University of Edinburgh, Edinburgh, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; The Usher Institute, University of Edinburgh, Edinburgh, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; Centre for Exercise and Rehabilitation Science, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; St Georges University Hospitals NHS Foundation Trust, London, UK; The Leeds Teaching Hospitals NHS Trust, Leeds, UK; University of Nottingham, Nottingham, UK; UCL Respiratory, Department of Medicine, University College London, Rayne Institute, London, UK; University of Edinburgh, Edinburgh, UK; Manchester Metropolitan University, Manchester, UK; Infection Research Group, Hull University Teaching Hospitals, Hull, UK; The Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK; Department of Respiratory Medicine, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Lane Fox Respiratory Service, Guys and St Thomas NHS Foundation Trust, London, UK; University College London, London, UK; Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK; University of Birmingham, Birmingham, UK; Barts Health NHS Trust, London, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK; University of Sheffield, Sheffield, UK; Kings College London, London, UK; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Kings College London, London, UK; University of Sheffield, Sheffield, UK; Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK; Diabetes Research Centre, University of Leicester, Leicester, UK; Population Health Sciences Institute, Newcastle University, Newcastle Upon Tyne, UK; NIHR Oxford Health Biomedical Research Centre, University of Oxford, Oxford, UK; University of Liverpool, Liverpool, UK; Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK; Imperial College Healthcare NHS Trust, London, UK; Centre for Medical Image Computing, University College London, London, UK; National Heart and Lung Institute, Imperial College London, London, UK; MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK; Royal Brompton and Harefield Clinical Group, Guys and St Thomas NHS Foundation Trust, London, UK; Department of Cardiovascular Sciences, University of Leicester, Leicester, UK; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; National Heart and Lung Institute, Imperial College London, London, UK; UCL Respiratory, Department of Medicine, University College London, Rayne Institute, London, UK; Kadoorie Centre for Critical Care Research, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, U; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; Imperial College London, London, UK; Cambridge NIHR BRC, Cambridge, UK; Hywel Dda University Health Board, Wales, UK; Wellcome-Wolfson Institute for Experimental Medicine, Queens University Belfast, Belfast, UK; London School of Hygiene & Tropical Medicine, London, UK; London School of Hygiene & Tropical Medicine, London, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; NHLI, Imperial College London, London, UK; University of Dundee, Ninewells Hospital and Medical School, Dundee, UK; MRC Human Immunology Unit, University of Oxford, Oxford, UK; Division of Infection, Immunity & Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK; Asthma and Lung UK, London, UK; Radcliffe Department of Medicine, University of Oxford, Oxford, UK; Department of Population Health Sciences, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; ", - "abstract": "Background In patients with COVID-19 requiring supplemental oxygen, dexamethasone reduces acute severity and improves survival, but longer-term effects are unknown. We hypothesised that systemic corticosteroid administration during acute COVID-19 would be associated with improved health-related quality of life (HRQoL) one year after discharge. Methods Adults admitted to hospital between February 2020 and March 2021 for COVID-19 and meeting current guideline recommendations for dexamethasone treatment were included using two prospective UK cohort studies. HRQoL, assessed by EQ-5D-5L utility index, pre-hospital and one year after discharge were compared between those receiving corticosteroids or not after propensity weighting for treatment. Secondary outcomes included patient reported recovery, physical and mental health status, and measures of organ impairment. Sensitivity analyses were undertaken to account for survival and selection bias. Findings In 1,888 participants included in the primary analysis, 1,149 received corticosteroids. There was no between-group difference in EQ-5D-5L utility index at one year (mean difference 0.004, 95% CI: -0.026 to 0.034, p = 0.77). A similar reduction in EQ-5D-5L was seen at one year between corticosteroid exposed and non-exposed groups (mean (SD) change -0.12 (0.22) vs -0.11 (0.22), p = 0.32). Overall, there were no differences in secondary outcome measures. After sensitivity analyses modelled using a larger cohort of 109,318 patients admitted to hospital with COVID-19, EQ-5D-5L utility index at one year remained similar between the two groups. Interpretation Systemic corticosteroids for acute COVID-19 have no impact on the large reduction in HRQoL one year after hospital discharge. Treatments to address this are urgently needed.", + "abstract": "BackgroundIn patients with COVID-19 requiring supplemental oxygen, dexamethasone reduces acute severity and improves survival, but longer-term effects are unknown. We hypothesised that systemic corticosteroid administration during acute COVID-19 would be associated with improved health-related quality of life (HRQoL) one year after discharge.\n\nMethodsAdults admitted to hospital between February 2020 and March 2021 for COVID-19 and meeting current guideline recommendations for dexamethasone treatment were included using two prospective UK cohort studies. HRQoL, assessed by EQ-5D-5L utility index, pre-hospital and one year after discharge were compared between those receiving corticosteroids or not after propensity weighting for treatment. Secondary outcomes included patient reported recovery, physical and mental health status, and measures of organ impairment. Sensitivity analyses were undertaken to account for survival and selection bias.\n\nFindingsIn 1,888 participants included in the primary analysis, 1,149 received corticosteroids. There was no between-group difference in EQ-5D-5L utility index at one year (mean difference 0.004, 95% CI: -0.026 to 0.034, p = 0.77). A similar reduction in EQ-5D-5L was seen at one year between corticosteroid exposed and non-exposed groups (mean (SD) change -0.12 (0.22) vs -0.11 (0.22), p = 0.32). Overall, there were no differences in secondary outcome measures. After sensitivity analyses modelled using a larger cohort of 109,318 patients admitted to hospital with COVID-19, EQ-5D-5L utility index at one year remained similar between the two groups.\n\nInterpretationSystemic corticosteroids for acute COVID-19 have no impact on the large reduction in HRQoL one year after hospital discharge. Treatments to address this are urgently needed.\n\nTake home messageSystemic corticosteroids given for acute COVID-19 do not affect health-related quality of life or other patient reported outcomes, physical and mental health outcomes, and organ function one year after hospital discharge", "category": "infectious diseases", "match_type": "fuzzy", "author_similarity": 100, @@ -83,20 +83,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2023.10.06.23296657", - "date": "2023-10-06", - "link": "https://medrxiv.org/cgi/content/short/2023.10.06.23296657", - "title": "The macroeconomic and epidemiological impacts of Covid-19 in Pakistan.", - "authors": "Henning Tarp Jensen; Marcus R. Keogh-Brown; Rosalind M Eggo; Carl A. B. Pearson; Sergio Torres-Rueda; Maryam Huda; Muhammad Khalid; Wahaj Sulfiqar; - CMMID COVID-19 Working Group; Richard D. Smith; Mark Jit; Anna Vassall", - "affiliations": "London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; Aga Khan University; Ministry of National Health Services, Regulations & Coordination, Islamabad, Pakistan; Ministry of National Health Services, Regulations & Coordination, Islamabad, Pakistan; -; University of Exeter; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine", - "abstract": "\"Coronavirus Disease 2019\" (C19) is a respiratory illness caused by \"new Coronavirus\" SARS-CoV-2. The C19 pandemic, which engulfed the world in 2021, also caused a national C19 epidemic in Pakistan, who responded with initial forced lockdowns (15-30 March 2020) and a subsequent switch to a smart lockdown strategy, and, by 31 December 2020, Pakistan had managed to limit confirmed cases and case fatalities to 482,506 (456 per 100,000) and 10,176 (4.8 per 100,000). The early switch to a smart lockdown strategy, and successful follow-up move to central coordination and effective communication and enforcement of Standard Operating Procedures, was motivated by a concern over how broad-based forced lockdowns would affect poor households and day-labour. The current study aims to investigate how the national Pakistan C19 epidemic would have unfolded under an uncontrolled baseline scenario and an alternative set of controlled non-pharmaceutical intervention (NPI) policy lockdown scenarios, including health and macroeconomic outcomes. We employ a dynamically-recursive version of the IFPRI Standard Computable General Equilibrium model framework (Lofgren, Lee Harris and Robinson 2002), and a, by now, well-established epidemiological transmission-dynamic model framework (Davies, Klepac et al 2020) using Pakistan-specific 5-year age-group contact matrices on four types of contact rates, including at home, at work, at school, and at other locations (Prem, Cook & Jit 2017), to characterize an uncontrolled spread of disease. Our simulation results indicate that an uncontrolled C19 epidemic, by itself, would have led to a 0.12% reduction in Pakistani GDP (-721mn USD), and a total of 0.65mn critically ill and 1.52mn severely ill C19 patients during 2020-21, while 405,000 Pakistani citizens would have lost their lives. Since the majority of case fatalities and symptomatic cases, respectively 345,000 and 35.9mn, would have occurred in 2020, the case fatality and confirmed case numbers, observed by 31. December 2020 represents an outcome which is far better than the alternative. Case fatalities by 31. December 2020 could possibly have been somewhat improved either via a more prolonged one-off 10 week forced lockdown (66% reduction) or a 1-month forced lockdown/2-months opening intermittent lockdown strategy (33% reduction), but both sets of strategies would have carried significant GDP costs in the order of 2.2%-6.2% of real GDP.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2023.08.30.23294821", @@ -139,20 +125,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2023.08.07.23293778", - "date": "2023-08-09", - "link": "https://medrxiv.org/cgi/content/short/2023.08.07.23293778", - "title": "Diabetes following SARS-CoV-2 infection: Incidence, persistence, and implications of COVID-19 vaccination. A cohort study of fifteen million people.", - "authors": "Kurt Taylor; Sophie Eastwood; Venexia Walker; Genevieve Cezard; Rochelle Knight; Marwa Al Arab; Yinghui Wei; Elsie M F Horne; Lucy Teece; Harriet Forbes; Alex Walker; Louis Fisher; Jon Massey; Lisa E M Hopcroft; Tom Palmer; Jose Cuitun Coronado; Samantha Ip; Simon Davy; Iain Dillingham; Caroline Morton; Felix Greaves; John MacLeod; Ben Goldacre; Angela Wood; Nishi Chaturvedi; Jonathan A C Sterne; Rachel Denholm; - CONVALESCENCE Long-COVID study; - Longitudinal Health and Wellbeing and Data and Connectivity UK COVID-19 National Core Studies; - OpenSAFELY collaborative", - "affiliations": "University of Bristol; University College London; University of Bristol; University of Cambridge; University of Bristol; University of Bristol; University of Plymouth; University of Bristol; University of Leicester; London School of Hygiene & Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Bristol; University of Bristol; University of Cambridge; University of Oxford; University of Oxford; University of Oxford; National Institute for Health and Care Excellence; University of Bristol; University of Oxford; University of Cambridge; University College London; University of Bristol; University of Bristol; -; -; -", - "abstract": "BackgroundType 2 diabetes (T2DM) incidence is increased after diagnosis of COVID-19. The impact of vaccination on this increase, for how long it persists, and the effect of COVID-19 on other types of diabetes remain unclear.\n\nMethodsWith NHS England approval, we studied diabetes incidence following COVID-19 diagnosis in pre-vaccination (N=15,211,471, January 2020-December 2021), vaccinated (N =11,822,640), and unvaccinated (N=2,851,183) cohorts (June-December 2021), using linked electronic health records. We estimated adjusted hazard ratios (aHRs) comparing diabetes incidence post-COVID-19 diagnosis with incidence before or without diagnosis up to 102 weeks post-diagnosis. Results were stratified by COVID-19 severity (hospitalised/non-hospitalised) and diabetes type.\n\nFindingsIn the pre-vaccination cohort, aHRS for T2DM incidence after COVID-19 (compared to before or without diagnosis) declined from 3.01 (95% CI: 2.76,3.28) in weeks 1-4 to 1.24 (1.12,1.38) in weeks 53-102. aHRS were higher in unvaccinated than vaccinated people (4.86 (3.69,6.41)) versus 1.42 (1.24,1.62) in weeks 1-4) and for hospitalised COVID-19 (pre-vaccination cohort 21.1 (18.8,23.7) in weeks 1-4 declining to 2.04 (1.65,2.51) in weeks 52-102), than non-hospitalised COVID-19 (1.45 (1.27,1.64) in weeks 1-4, 1.10 (0.98,1.23) in weeks 52-102). T2DM persisted for 4 months after COVID-19 for [~]73% of those diagnosed. Patterns were similar for Type 1 diabetes, though excess incidence did not persist beyond a year post-COVID-19.\n\nInterpretationElevated T2DM incidence after COVID-19 is greater, and persists longer, in hospitalised than non-hospitalised people. It is markedly less apparent post-vaccination. Testing for T2DM after severe COVID-19 and promotion of vaccination are important tools in addressing this public health problem.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed for population-based observational studies published between December 1st 2019 and July 12th 2023 examining associations between SARS-CoV-2 infection or COVID-19 diagnosis (search string: SARS-CoV-2 or COVID* or coronavirus*) and subsequent incident diabetes (search term: diabetes). Of nineteen relevant studies; eight had a composite outcome of diabetes types, six stratified by diabetes type and five pertained to type-1-diabetes (T1DM) only. We did not identify any studies relating to gestational or other types of diabetes. Eleven studies were from the US, three from the UK, two from Germany, one from Canada, one from Denmark and one from South Korea.\n\nMost studies described cumulative relative risks (for infection versus no infection) one to two years post-SARS-CoV-2 infection of 1.2 to 2.6, though four studies found no associations with T1DM after the post-acute period. All studies lacked the power to compare diabetes relative risk by type, severity, and vaccination status in population subgroups. One study examined relative risks by vaccination status, but this used a composite outcome of diabetes and hyperlipidaemia and was conducted in a predominantly white male population.\n\nTwo studies of T1DM found no evidence of elevated risk beyond 30 days after COVID-19 diagnosis, whilst two reported elevated risks at six months. Two studies of type 2 diabetes (T2DM) examined relative risks by time period post-infection: one study of US insurance claims reported a persistent association six months post-infection, whereas a large UK population-based study reported no associations after 12 weeks. However, the latter study used only primary care data, therefore COVID-19 cases were likely to have been under-ascertained.\n\nNo large studies have investigated the persistence of diabetes diagnosed following COVID-19; key to elucidating the role of stress/steroid-induced hyperglycaemia.\n\nAdded value of this studyThis study, which is the largest to address the question to date, analysed linked primary and secondary care health records with SARS-CoV-2 testing and COVID-19 vaccination data for 15 million people living in England. This enabled us to compare the elevation in diabetes incidence after COVID-19 diagnosis by diabetes type, COVID-19 severity and vaccination status, overall and in population subgroups. Importantly, excess diabetes incidence by time period since infection could also be quantified. Since healthcare in the UK is universal and free-at-the-point-of-delivery, almost the entire population is registered with primary care. Therefore the findings are likely to be generalisable.\n\nWe found that, before availability of COVID-19 vaccination, a COVID-19 diagnosis (vs. no diagnosis) was associated with increased T2DM incidence which remained elevated by approximately 30% beyond one year after diagnosis. Though still present (with around 30% excess incidence at eight weeks), these associations were substantially attenuated in unvaccinated compared with vaccinated people. Excess incidence was greater in people hospitalised with COVID-19 than those who were not hospitalised after diagnosis. T1DM incidence was elevated up to, but not beyond, a year post COVID-19. Around 73% of people diagnosed with incident T2DM after COVID-19 still had evidence of diabetes four months after infection.\n\nImplications of all the available evidenceThere is a 30-50% elevated T2DM incidence post-COVID-19, but we report the novel finding that there is elevated incidence beyond one-year post-diagnosis. Elevated T1DM incidence did not appear to persist beyond a year, which may explain why previous studies disagree. For the first time in a general-population dataset, we demonstrate that COVID-19 vaccination reduces, but does not entirely ameliorate, excess diabetes incidence after COVID-19. This supports a policy of universal vaccination and suggests that other public health activities, such as enhanced diabetes screening after severe COVID-19, may be warranted, particularly in unvaccinated people.", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2023.08.02.23293505", @@ -181,6 +153,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2023.08.02.23293519", + "date": "2023-08-04", + "link": "https://medrxiv.org/cgi/content/short/2023.08.02.23293519", + "title": "Real-time epidemiological modelling during the COVID-19 emergency in Wales", + "authors": "Michael Gravenor; Mark Dawson; Ed Bennett; Ben Thorpe; Carla White; Alma Rahat; Daniel Archambault; Noemi Picco; Gibin Powathil; Biagio Lucini", + "affiliations": "Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University", + "abstract": "The sudden outbreak of the COVID-19 pandemic presented governments, policy makers and health services with an unprecedented challenge of taking real-time decisions that could keep the disease under control with non-pharmaceutical interventions, while at the same time limit as much as possible severe consequences of a very strict lockdown. Mathematical modelling has proved to be a crucial element for informing those decisions. Here we report on the rapid development and application of the Swansea Model, a mathematical model of disease spread in real time, to inform policy decisions during the COVID-19 pandemic in Wales.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2023.08.01.23293491", @@ -223,20 +209,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2023.07.19.23292289", - "date": "2023-07-23", - "link": "https://medrxiv.org/cgi/content/short/2023.07.19.23292289", - "title": "Can computer simulation support strategic service planning? Modelling a large integrated mental health system on recovery from COVID-19", - "authors": "Livia LP Pierotti; Jennifer Cooper; Charlotte James; Rachel Denholm; Kenah Cassels; Emma Gara; Richard Wood", - "affiliations": "University of Bristol; University of Bristol; University of Bristol; University of Bristol; Bristol, North Somerset and South Gloucestershire Integrated Care Board, UK National Health Service; Bristol, North Somerset and South Gloucestershire Integrated Care Board, UK National Health Service; Bristol, North Somerset and South Gloucestershire Integrated Care Board, UK National Health Service. HDR UK Southwest.", - "abstract": "BackgroundCOVID-19 has had a significant impact on peoples mental health and mental health services. During the first year of the pandemic, existing demand was not fully met while new demand was generated, resulting in large numbers of people requiring support. To support mental health services to recover without being overwhelmed, it was important to know where services will experience increased pressure, and what strategies could be implemented to mitigate this.\n\nMethodsWe implemented a computer simulation model of patient flow through an integrated mental health service in Southwest England covering General Practice (GP), community-based talking therapies (IAPT), acute hospital care, and specialist care settings. The model was calibrated on data from 1 April 2019 to 1 April 2021. Model parameters included patient demand, service-level length of stay, and probabilities of transitioning to other care settings. We used the model to compare do nothing (baseline) scenarios to what if (mitigation) scenarios, including increasing capacity and reducing length of stay, for two future demand trajectories from 1 April 2021 onwards.\n\nResultsThe results from the simulation model suggest that, without mitigation, the impact of COVID-19 will be an increase in pressure on GP and specialist community based services by 50% and 50-100% respectively. Simulating the impact of possible mitigation strategies, results show that increasing capacity in lower-acuity services, such as GP, results in demand being shifted to other parts of the mental health system while decreasing length of stay in higher acuity services is insufficient to mitigate the impact of increased demand.\n\nConclusionIn capturing the interrelation of patient flow related dynamics between various mental health care settings, we demonstrate the value of computer simulation for assessing the impact of interventions on system flow.", - "category": "health systems and quality improvement", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2023.07.16.23292705", @@ -251,20 +223,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2023.07.06.23292295", - "date": "2023-07-07", - "link": "https://medrxiv.org/cgi/content/short/2023.07.06.23292295", - "title": "Spatio-temporal surveillance and early detection of SARS-CoV-2 variants of concern", - "authors": "Massimo Cavallaro; Louise Dyson; Michael J Tildesley; Daniel Todkill; Matt J Keeling", - "affiliations": "University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick", - "abstract": "The SARS-CoV-2 pandemic has been characterized by the repeated emergence of genetically distinct virus variants of increased transmissibility and immune evasion compared to pre-existing lineages. In many countries, their containment required the intervention of public health authorities and the imposition of control measures. While the primary role of testing is to identify infection, target treatment, and limit spread (through isolation and contact tracing), a secondary benefit is in terms of surveillance and the early detection of new variants. Here we study the spatial invasion and early spread of the Alpha, Delta, and Omicron (BA.1 and BA.2) variants in England from September 2020 to February 2022 using the random neighbourhood covering (RaNCover) method. This is a statistical technique for the detection of aberrations in spatial point processes, which we tailored here to community PCR (polymerase-chain-reaction) test data where the TaqPath kit provides a proxy measure of the switch between variants. Retrospectively, RaNCover detected the earliest signals associated with the four novel variants that led to large infection waves in England. With suitable data our method therefore has the potential to rapidly detect outbreaks of future SARS-CoV-2 variants, thus helping to inform targeted public health interventions.", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2023.07.03.23291596", @@ -755,6 +713,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2023.01.29.23285160", + "date": "2023-01-30", + "link": "https://medrxiv.org/cgi/content/short/2023.01.29.23285160", + "title": "High number of SARS-CoV-2 persistent infections uncovered through genetic analysis of samples from a large community-based surveillance study", + "authors": "Mahan Ghafari; Matthew Hall; Tanya Golubchik; Daniel Ayoubkhani; Thomas House; George MacIntyre-Cockett; Helen Fryer; Laura Thomson; Anel Nurtay; David Buck; Angie Green; Amy Trebes; Paolo Piazza; Lorne J Lonie; Ruth Studley; Emma Rourke; Darren Smith; Matthew Bashton; Andrew Nelson; Matthew Crown; Clare McCann; Gregory R Young; Rui Andre Nunes de Santos; Zack Richards; Adnan Tariq; Roberto Cahuantzi; - Wellcome Sanger Institute COVID-19 Surveillance Team; - COVID-19 Infection Survey Group; - The COVID-19 Genomics UK (COG-UK) consortium; Jeff Barrett; Christophe Fraser; David Bonsall; Sarah Walker; Katrina A Lythgoe", + "affiliations": "University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; University of Manchester; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; Office for National Statistics; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Office for National Statistics; -; -; -; Wellcome Sanger Institute; University of Oxford; University of Oxford; University of Oxford; University of Oxford", + "abstract": "Persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections may act as viral reservoirs that could seed future outbreaks 1-5, give rise to highly divergent lineages 6-8, and contribute to cases with post-acute Coronavirus disease 2019 (COVID-19) sequelae (Long Covid) 9,10. However, the population prevalence of persistent infections, their viral load kinetics, and evolutionary dynamics over the course of infections remain largely unknown. We identified 381 infections lasting at least 30 days, of which 54 lasted at least 60 days. These persistently infected individuals had more than 50% higher odds of self-reporting Long Covid compared to the infected controls, and we estimate that 0.09-0.5% of SARS-CoV-2 infections can become persistent and last for at least 60 days. In nearly 70% of the persistent infections we identified, there were long periods during which there were no consensus changes in virus sequences, consistent with prolonged presence of non-replicating virus. Our findings also suggest reinfections with the same major lineage are rare and that many persistent infections are characterised by relapsing viral load dynamics. Furthermore, we found a strong signal for positive selection during persistent infections, with multiple amino acid substitutions in the Spike and ORF1ab genes emerging independently in different individuals, including mutations that are lineage-defining for SARS-CoV-2 variants, at target sites for several monoclonal antibodies, and commonly found in immunocompromised patients 11-14. This work has significant implications for understanding and characterising SARS-CoV-2 infection, epidemiology, and evolution.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2023.01.24.23284906", @@ -867,6 +839,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2022.12.16.22283578", + "date": "2022-12-17", + "link": "https://medrxiv.org/cgi/content/short/2022.12.16.22283578", + "title": "Higher dose corticosteroids in hospitalised COVID-19 patients with hypoxia but not requiring ventilatory support (RECOVERY): a randomised, controlled, open-label, platform trial", + "authors": "Peter W Horby; Jonathan R Emberson; Buddha Basnyat; Mark Campbell; Leon Peto; Guilherme Pessoa-Amorim; Natalie Staplin; Raph L Hamers; John Amuasi; Jeremy Nel; Evelyne Kestelyn; Manisha Rawal; Roshan Kumar Jha; Nguyen Thanh Phong; Uun Samardi; Damodar Paudel; Pham Ngoc Thach; Nasronudin Nasronudin; Emma Stratton; Louise Mew; Rahuldeb Sarkar; J Kenneth Baillie; Maya H Buch; Jeremy N Day; Saul N Faust; Thomas Jaki; Katie Jeffery; Edmund Juszczak; Marian Knight; Wei Shen Lim; Marion Mafham; Alan Montgomery; Andrew Mumford; Kathryn Rowan; Guy Thwaites; Richard Haynes; Martin J Landray", + "affiliations": "Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; OUCRU-Nepal, Patan Academy of Health Sciences, Kathmandu, Nepal; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia; Kumasi Center for Collaborative Research in Tropic Medicine, Kumasi, Ghana; Division of Infectious Diseases, Department of Medicine, University of the Witwatersrand, Johannesburg, South Africa; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom; Sukraraj Tropical and Infectious Disease Hospital, Kathmandu, Nepal; Medicine Department, Nepal Armed Police Force Hospital, Chandragiri, Kathmandu, Nepal; Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam; RSUP Dr Hasan Sadikin Hospital, Bandung, West Java, Indonesia; Department of Medicine, Nepal Police Hospital, Maharajgunj, Kathmandu, Nepal; National Hospital for Tropical Diseases, Hanoi, Vietnam; University of Airlangga Teaching Hospital, Surabaya, Indonesia; University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, United Kingdom; Milton Keynes University Hospital, Milton Keynes, United Kingdom; Faculty of Life Sciences and Medicine, King's College, London, United Kingdom; Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom; Centre for Musculoskeletal Research, University of Manchester, Manchester, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom; NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, ; Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom; Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; National Perinatal Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Respiratory Medicine Department, Nottingham University Hospitals NHS Foundation Trust, Nottingham, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom; Intensive Care National Audit and Research Centre, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom", + "abstract": "BackgroundLow-dose corticosteroids have been shown to reduce mortality for hypoxic COVID-19 patients requiring oxygen or ventilatory support (non-invasive mechanical ventilation, invasive mechanical ventilation or extra-corporeal membrane oxygenation). We evaluated the use of a higher dose of corticosteroids in this patient group.\n\nMethodsThis randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]) is assessing multiple possible treatments in patients hospitalised for COVID-19. Eligible and consenting adult patients with clinical evidence of hypoxia (i.e. receiving oxygen or with oxygen saturation <92% on room air) were randomly allocated (1:1) to either usual care with higher dose corticosteroids (dexamethasone 20 mg once daily for 5 days followed by 10 mg once daily for 5 days or until discharge if sooner) or usual standard of care alone (which includes dexamethasone 6 mg once daily for 10 days or until discharge if sooner). The primary outcome was 28-day mortality. On 11 May 2022, the independent Data Monitoring Committee recommended stopping recruitment of patients receiving no oxygen or simple oxygen only to this comparison due to safety concerns. We report the results for these participants only. Recruitment of patients receiving ventilatory support continues. The RECOVERY trial is registered with ISRCTN (50189673) and clinicaltrials.gov (NCT04381936).\n\nFindingsBetween 25 May 2021 and 12 May 2022, 1272 COVID-19 patients with hypoxia and receiving no oxygen (1%) or simple oxygen only (99%) were randomly allocated to receive usual care plus higher dose corticosteroids versus usual care alone (of whom 87% received low dose corticosteroids during the follow-up period). Of those randomised, 745 (59%) were in Asia, 512 (40%) in the UK and 15 (1%) in Africa. 248 (19%) had diabetes mellitus. Overall, 121 (18%) of 659 patients allocated to higher dose corticosteroids versus 75 (12%) of 613 patients allocated to usual care died within 28 days (rate ratio [RR] 1{middle dot}56; 95% CI 1{middle dot}18-2{middle dot}06; p=0{middle dot}0020). There was also an excess of pneumonia reported to be due to non-COVID infection (10% vs. 6%; absolute difference 3.7%; 95% CI 0.7-6.6) and an increase in hyperglycaemia requiring increased insulin dose (22% vs. 14%; absolute difference 7.4%; 95% CI 3.2-11.5).\n\nInterpretationIn patients hospitalised for COVID-19 with clinical hypoxia but requiring either no oxygen or simple oxygen only, higher dose corticosteroids significantly increased the risk of death compared to usual care, which included low dose corticosteroids. The RECOVERY trial continues to assess the effects of higher dose corticosteroids in patients hospitalised with COVID-19 who require non-invasive ventilation, invasive mechanical ventilation or extra-corporeal membrane oxygenation.\n\nFundingUK Research and Innovation (Medical Research Council) and National Institute of Health and Care Research (Grant ref: MC_PC_19056), and Wellcome Trust (Grant Ref: 222406/Z/20/Z).", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2022.12.12.22283200", @@ -1147,20 +1133,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.09.23.22280285", - "date": "2022-09-25", - "link": "https://medrxiv.org/cgi/content/short/2022.09.23.22280285", - "title": "Dimethyl fumarate in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial", - "authors": "- RECOVERY Collaborative Group; Peter W Horby; Leon Peto; Natalie Staplin; Mark Campbell; Guilherme Pessoa-Amorim; Marion Mafham; Jonathan R Emberson; Richard Stewart; Benjamin Prudon; Alison Uriel; Christopher A Green; Devesh J Dhasmana; Flora Malein; Jaydip Majumdar; Paul Collini; Jack Shurmer; Bryan Yates; J Kenneth Baillie; Maya H Buch; Jeremy N Day; Saul N Faust; Thomas Jaki; Katie Jeffery; Edmund Juszczak; Marian Knight; Wei Shen Lim; Alan Montgomery; Andrew Mumford; Kathryn Rowan; Guy Thwaites; Richard Haynes; Martin Landray", - "affiliations": "; Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, University of Oxford, Oxford, United Kingdom; Milton Keynes University Hospital NHS Foundation Trust; North Tees and Hartlepool NHS Foundation Trust; Manchester University NHS Foundation Trust; University Hospitals Birmingham NHS Foundation Trust; Victoria Hospital Kirkcaldy, NHS Fife; Liverpool University Hospitals NHS Foundation Trust; Mid Cheshire Hospitals NHS Foundation Trust; Sheffield Teaching Hospitals NHS Foundation Trust; Bolton NHS Foundation Trust; Northumbria Healthcare NHS Foundation Trust; Roslin Institute, University of Edinburgh; Centre for Musculoskeletal Research, University of Manchester, Manchester, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam; NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University of Southampton, Southampton, United Kingdom; University of Regensburg, Germany; Oxford University Hospitals NHS Foundation Trust; School of Medicine, University of Nottingham, Nottingham, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom; Intensive Care National Audit & Research Centre, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam; MRC Population Health Research Unit, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom", - "abstract": "BackgroundDimethyl fumarate (DMF) is an anti-inflammatory drug that has been proposed as a treatment for patients hospitalised with COVID-19\n\nMethodsThis randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), is assessing multiple possible treatments in patients hospitalised for COVID-19. In this initial assessment of DMF, performed at 27 UK hospitals, eligible and consenting adults were randomly allocated (1:1) to either usual standard of care alone or usual standard of care plus DMF 120mg twice daily for 2 days followed by 240mg twice daily for 8 days, or until discharge if sooner. The primary outcome was clinical status on day 5 measured on a seven-point ordinal scale, assessed using a proportional odds model. Secondary outcomes were time to sustained improvement in clinical status, time to discharge, day 5 peripheral blood oxygenation, day 5 C-reactive protein, and improvement in day 10 clinical status. The trial is registered with ISRCTN (50189673) and clinicaltrials.gov (NCT04381936).\n\nFindingsBetween 2 March 2021 and 18 November 2021, 713 patients were enrolled in the DMF evaluation, of whom 356 were randomly allocated to receive usual care plus DMF, and 357 to usual care alone. 95% of patients were receiving corticosteroids as part of routine care. There was no evidence of a beneficial effect of DMF on clinical status at day 5 (common odds ratio of unfavourable outcome 1.12; 95% CI 0.85-1.46; p=0.42). There was no significant effect of DMF on any secondary outcome. As expected, DMF caused flushing and gastrointestinal symptoms, each in around 6% of patients, but no new adverse effects were identified.\n\nInterpretationIn adults hospitalised with COVID-19, DMF was not associated with an improvement in clinical outcomes.\n\nFundingUK Research and Innovation (Medical Research Council) and National Institute of Health Research (Grant ref: MC_PC_19056).", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.09.21.22280191", @@ -1469,6 +1441,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2022.07.14.22277638", + "date": "2022-07-15", + "link": "https://medrxiv.org/cgi/content/short/2022.07.14.22277638", + "title": "Therapeutic potential of IL6R blockade for the treatment of sepsis and sepsis-related death: Findings from a Mendelian randomisation study", + "authors": "Fergus W Hamilton; Matt Thomas; David T Arnold; Tom M Palmer; Ed Moran; Alexander J Mentzer; Nick A Maskell; J Kenneth Baillie; Charlotte Summers; Aroon Dinesh Hingorani; Alasdair P MacGowan; Golam M Khandaker; Ruth E Mitchell; George Davey Smith; Peter Ghazal; Nicholas J Timpson", + "affiliations": "University of Bristol; North Bristol NHS Trust; University of Bristol; University of Bristol; North Bristol NHS Trust; University of Oxford; University; Roslin Institute, University of Edinburgh; University of Cambridge; University College London; North Bristol NHS Trust; University of Bristol; University of Bristol; University of Bristol; Cardiff University; University of Bristol", + "abstract": "IntroductionSepsis is characterised by dysregulated, life-threatening immune responses, which are thought to be driven by cytokines such as interleukin-6 (IL-6). Genetic variants in IL6R known to downregulate IL-6 signalling are associated with improved COVID-19 outcomes, a finding later confirmed in randomised trials of IL-6 receptor antagonists (IL6RA). We hypothesised that blockade of IL6R could also improve outcomes in sepsis.\n\nMethodsWe performed a Mendelian randomisation analysis using single nucleotide polymorphisms (SNPs) in and near IL6R to evaluate the likely causal effects of IL6R blockade on sepsis, sepsis severity, other infections, and COVID-19. We weighted SNPs by their effect on CRP and combined results across them in inverse variance weighted meta-analysis, proxying the effect of IL6RA. Our outcomes were measured in UK Biobank, FinnGen, the COVID-19 Host Genetics Initiative (HGI), and the GenOSept and GainS consortium. We performed several sensitivity analyses to test assumptions of our methods, including utilising variants around CRP in a similar analysis.\n\nResultsIn the UK Biobank cohort (N=485,825, including 11,643 with sepsis), IL6R blockade was associated with a decreased risk of sepsis (OR=0.80; 95% CI 0.66-0.96, per unit of natural log transformed CRP decrease). The size of this effect increased with severity, with larger effects on 28-day sepsis mortality (OR=0.74; 95% CI 0.38-0.70); critical care admission with sepsis (OR=0.48, 95% CI 0.30-0.78) and critical care death with sepsis (OR=0.37, 95% CI 0.14 - 0.98) Similar associations were seen with severe respiratory infection: OR for pneumonia in critical care 0.69 (95% CI 0.49 - 0.97) and for sepsis survival in critical care (OR=0.22; 95% CI 0.04- 1.31) in the GainS and GenOSept consortium. We also confirm the previously reported protective effect of IL6R blockade on severe COVID-19 (OR=0.69, 95% 0.57 - 0.84) in the COVID-19 HGI, which was of similar magnitude to that seen in sepsis. Sensitivity analyses did not alter our primary results.\n\nConclusionsIL6R blockade is causally associated with reduced incidence of sepsis, sepsis related critical care admission, and sepsis related mortality. These effects are comparable in size to the effect seen in severe COVID-19, where IL-6 receptor antagonists were shown to improve survival. This data suggests a randomised trial of IL-6 receptor antagonists in sepsis should be considered.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2022.07.07.22277367", @@ -1651,20 +1637,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.06.13.22276316", - "date": "2022-06-13", - "link": "https://medrxiv.org/cgi/content/short/2022.06.13.22276316", - "title": "Patterns of Reported Infection and Reinfection of SARS-CoV-2 in England", - "authors": "Matt J Keeling", - "affiliations": "University of Warwick", - "abstract": "One of the key features of any infectious disease is whether infection generates long-lasting immunity or whether repeated reinfection is common. In the former, the long-term dynamics are driven by the birth of susceptible individuals while in the latter the dynamics are governed by the speed of waning immunity. Between these two extremes a range of scenarios is possible. During the early waves of SARS-CoV-2, the underlying paradigm was for long-lasting immunity, but more recent data and in particular the 2022 Omicron waves have shown that reinfection can be relatively common. Here we investigate reported SARS-CoV-2 cases in England, partitioning the data into four main waves, and consider the temporal distribution of first and second reports of infection. We show that a simple low-dimensional statistical model of random (but scaled) reinfection captures much of the observed dynamics, with the value of this scaling, k, providing information of underlying epidemiological patterns. We conclude that there is considerable heterogeneity in risk of reporting reinfection by wave, age-group and location. The high levels of reinfection in the Omicron wave (we estimate that 18% of all Omicron cases had been previously infected, although not necessarily previously reported infection) point to reinfection events dominating future COVID-19 dynamics.", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.06.12.22276307", @@ -1945,20 +1917,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.04.26.22274332", - "date": "2022-04-27", - "link": "https://medrxiv.org/cgi/content/short/2022.04.26.22274332", - "title": "Community factors and excess mortality in the COVID-19 pandemic in England, Italy and Sweden", - "authors": "Brandon Parkes; Massimo Stafoggia; Daniela Fecht; Bethan Davies; Carl Bonander; Francesca de'Donato; Paola Michelozzi; Fr\u00e9d\u00e9ric B. Piel; Ulf Str\u00f6mberg; Marta Blangiardo", - "affiliations": "Imperial College London; Lazio Regional Health Service; Imperial College London; Imperial College London; University of Gothenburg; Lazio Regional Health Service; Lazio Regional Health Service; Imperial College London; University of Gothenburg; Imperial College London", - "abstract": "BackgroundAnalyses of COVID-19 suggest specific risk factors make communities more or less vulnerable to pandemic related deaths within countries. What is unclear is whether the characteristics affecting vulnerability of small communities within countries produce similar patterns of excess mortality across countries with different demographics and public health responses to the pandemic. Our aim is to quantify community-level variations in excess mortality within England, Italy and Sweden and identify how such spatial variability was driven by community-level characteristics.\n\nMethodsWe applied a two-stage Bayesian model to quantify inequalities in excess mortality in people aged 40 years and older at the community level in England, Italy and Sweden during the first year of the pandemic (March 2020-February 2021). We used community characteristics measuring deprivation, air pollution, living conditions, population density and movement of people as covariates to quantify their associations with excess mortality.\n\nResultsWe found just under half of communities in England (48.1%) and Italy (45.8%) had an excess mortality of over 300 per 100,000 males over the age of 40, while for Sweden that covered 23.1% of communities. We showed that deprivation is a strong predictor of excess mortality across the three countries, and communities with high levels of overcrowding were associated with higher excess mortality in England and Sweden.\n\nConclusionThese results highlight some international similarities in factors affecting mortality that will help policy makers target public health measures to increase resilience to the mortality impacts of this and future pandemics.", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.04.21.22274152", @@ -2141,6 +2099,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2022.03.29.22273042", + "date": "2022-04-04", + "link": "https://medrxiv.org/cgi/content/short/2022.03.29.22273042", + "title": "The new normal? Dynamics and scale of the SARS-CoV-2 variant Omicron epidemic in England", + "authors": "Oliver Eales; Leonardo de Oliveira Martins; Andrew Page; Haowei Wang; Barbara Bodinier; David Tang; David Haw; Jakob Jonnerby; Christina Atchison; Deborah Ashby; Wendy Barclay; Graham Taylor; Graham Cooke; Helen Ward; Ara Darzi; Steven Riley; Paul Elliott; Christl A Donnelly; Marc Chadeau-Hyam", + "affiliations": "Imperial College London; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Environment and Health, School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Environment and Health, School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Environment and Health, School of Public Health, Imperial College London, UK", + "abstract": "The SARS-CoV-2 pandemic has been characterised by the regular emergence of genomic variants which have led to substantial changes in the epidemiology of the virus. With natural and vaccine-induced population immunity at high levels, evolutionary pressure favours variants better able to evade SARS-CoV-2 neutralising antibodies. The Omicron variant was first detected in late November 2021 and exhibited a high degree of immune evasion, leading to increased infection rates in many countries. However, estimates of the magnitude of the Omicron wave have relied mainly on routine testing data, which are prone to several biases. Here we infer the dynamics of the Omicron wave in England using PCR testing and genomic sequencing obtained by the REal-time Assessment of Community Transmission-1 (REACT-1) study, a series of cross-sectional surveys testing random samples of the population of England. We estimate an initial peak in national Omicron prevalence of 6.89% (5.34%, 10.61%) during January 2022, followed by a resurgence in SARS-CoV-2 infections in England during February-March 2022 as the more transmissible Omicron sub-lineage, BA.2 replaced BA.1 and BA.1.1. Assuming the emergence of further distinct genomic variants, intermittent epidemics of similar magnitude as the Omicron wave may become the new normal.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2022.03.24.22272899", @@ -2211,6 +2183,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2022.03.17.22272414", + "date": "2022-03-18", + "link": "https://medrxiv.org/cgi/content/short/2022.03.17.22272414", + "title": "Modelling the impact of non-pharmaceutical interventions on workplace transmission of SARS-CoV-2 in the home-delivery sector", + "authors": "Carl A Whitfield; Martie Van Tongeren; Yang Han; Hua Wei; Sarah A Daniels; Martyn Regan; David W Denning; Arpana Verma; Lorenzo Pellis; - University of Manchester COVID-19 Modelling Group; Ian Hall", + "affiliations": "University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchaster; University of Manchester; University of Manchester; ; University of Manchester", + "abstract": "ObjectiveWe aimed to use mathematical models of SARS-COV-2 to assess the potential efficacy of non-pharmaceutical interventions on transmission in the parcel delivery and logistics sector.\n\nMethodsWe developed a network-based model of workplace contacts based on data and consultations from companies in the parcel delivery and logistics sectors. We used these in stochastic simulations of disease transmission to predict the probability of workplace outbreaks in this settings. Individuals in the model have different viral load trajectories based on SARS-CoV-2 in-host dynamics, which couple to their infectiousness and test positive probability over time, in order to determine the impact of testing and isolation measures.\n\nResultsThe baseline model (without any interventions) showed different workplace infection rates for staff in different job roles. Based on our assumptions of contact patterns in the parcel delivery work setting we found that when a delivery driver was the index case, on average they infect only 0.14 other employees, while for warehouse and office workers this went up to 0.65 and 2.24 respectively. In the LIDD setting this was predicted to be 1.40, 0.98, and 1.34 respectively. Nonetheless, the vast majority of simulations resulted in 0 secondary cases among customers (even without contact-free delivery). Our results showed that a combination of social distancing, office staff working from home, and fixed driver pairings (all interventions carried out by the companies we consulted) reduce the risk of workplace outbreaks by 3-4 times.\n\nConclusionThis work suggests that, without interventions, significant transmission could have occured in these workplaces, but that these posed minimal risk to customers. We found that identifying and isolating regular close-contacts of infectious individuals (i.e. house-share, carpools, or delivery pairs) is an efficient measure for stopping workplace outbreaks. Regular testing can make these isolation measures even more effective but also increases the number of staff isolating at one time. It is therefore more efficient to use these isolation measures in addition to social distancing and contact reduction interventions, rather than instead of, as these reduce both transmission and the number of people needing to isolate at one time.\n\nAuthor summaryDuring the COVID-19 pandemic the home-delivery sector was vital to maintaining peoples access to certain goods, and sustaining levels of economic activity for a variety of businesses. However, this important work necessarily involved contact with a large number of customers as well as colleagues. This means that questions have often been raised about whether enough was being done to keep customers and staff safe. Estimating the potential risk to customers and staff is complex, but here we tackle this problem by building a model of workplace and customer contacts, from which we simulate SARS-CoV-2 transmission. By involving industry representatives in the development of this model, we have simulated interventions that have either been applied or considered, and so the findings of this study are relevant to decisions made in that sector. Furthermore, we can learn generic lessons from this specific case study which apply to many types of shared workplace as well as highlighting implications of the highly stochastic nature of disease transmission in small populations.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2022.03.17.22272535", @@ -2351,20 +2337,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.03.02.22271762", - "date": "2022-03-04", - "link": "https://medrxiv.org/cgi/content/short/2022.03.02.22271762", - "title": "Disparities in SARS-CoV-2 case rates by ethnicity, religion, measures of socio-economic position, English proficiency, and self-reported disability: cohort study of 39 million people in England during the Alpha and Delta waves", - "authors": "Tim Larsen; Matthew L Bosworth; Daniel Ayoubkhani; Ryan Schofield; Raghib Ali; Kamlesh Khunti; Ann Sarah Walker; Myer Glickman; Vahe Nafilyan", - "affiliations": "Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Cambridge; University of Leicester; University of Oxford; Office for National Statistics; Office for National Statistics", - "abstract": "ObjectiveTo examine socio-demographic disparities in SARS-CoV-2 case rates during the second (Alpha) and third (Delta) waves of the COVID-19 pandemic.\n\nDesignRetrospective, population-based cohort study.\n\nSettingResident population of England.\n\nParticipants39,006,194 people aged 10 years and over who were enumerated at the 2011 Census, registered with the National Health Service (NHS) and alive on 1 September 2020.\n\nMain outcome measuresTesting positive for SARS-CoV-2 during the second wave (1 September 2020 to 22 May 2021) or third wave (23 May to 10 December 2021) of the pandemic. We calculated age-standardised case rates by socio-demographic characteristics and used logistic regression models to estimate adjusted odds ratios (ORs).\n\nResultsDuring the study period, 5,767,584 individuals tested positive for SARS-CoV-2. In the second wave, the fully-adjusted odds of having a positive test, relative to the White British group, were highest for the Bangladeshi (OR: 1.88, 95% CI 1.86 to 1.90) and Pakistani (1.81, 1.79 to 1.82) ethnic groups. Relative to the Christian group, Muslim and Sikh religious groups had fully-adjusted ORs of 1.58 (1.57 to 1.59) and 1.74 (1.72 to 1.76), respectively. Greater area deprivation, disadvantaged socio-economic position, living in a care home and low English language proficiency were also associated with higher odds of having a positive test. However, the disparities between groups varied over time. Being Christian, White British, non-disabled, and from a more advantaged socio-economic position were all associated with increased odds of testing positive during the third wave.\n\nConclusionThere are large socio-demographic disparities on SARS-CoV-2 cases which have varied between different waves of the pandemic. Research is now urgently needed to understand why these disparities exist to inform policy interventions in future waves or pandemics.\n\nWhat is already known on this topicPeople with pre-existing health conditions or disability, ethnic minority groups, the elderly, some religious groups, people with low socio-economic status, and those living in deprived areas have been disproportionately affected by the COVID-19 pandemic in terms of risk of infection and adverse outcomes.\n\nWhat this study addsUsing linked data on 39 million people in England, we found that during the second wave, COVID-19 case rates were highest among the Bangladeshi and Pakistani ethnic groups, the Muslim religious group, individuals from deprived areas and of low socio-economic position; during the third wave, being Christian, White British, non-disabled, and from a more advantaged socio-economic position were all associated with increased odds of receiving a positive test\n\nAdjusting for geographical factors, socio-demographic characteristics, and pre-pandemic health status explained some, but not all, of the excess risk\n\nWhen stratifying the dataset by broad age groups, the odds of receiving a positive test remained higher among the Bangladeshi and Pakistani ethnic groups aged 65 years and over during the third wave, which may partly explain the continued elevated mortality rates in these groups", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.03.02.22271623", @@ -2449,20 +2421,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.02.10.22270799", - "date": "2022-02-13", - "link": "https://medrxiv.org/cgi/content/short/2022.02.10.22270799", - "title": "Evaluating the effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control teams: the COG-UK hospital-onset COVID-19 infection study", - "authors": "Oliver Stirrup; James Blackstone; Fiona Mapp; Alyson MacNeil; Monica Panca; Alison Holmes; Nicholas Machin; Gee Yen Shin; Tabitha Mahungu; Kordo Saeed; Tranprit Saluja; Yusri Taha; Nikunj Mahida; Cassie Pope; Anu Chawla; Teresa Cutino-Moguel; Asif Tamuri; Rachel Williams; Alistair Darby; David L Robertson; Flavia Flaviani; Eleni Nastouli; Samuel Robson; Darren Smith; Matthew Loose; Kenneth Laing; Irene Monahan; Beatrix Kele; Sam Haldenby; Ryan George; Matthew Bashton; Adam Witney; Matthew Byott; Francesc Coll; Michael Chapman; Sharon Peacock; - COG-UK HOCI Investigators; - COG-UK Consortium; Joseph Hughes; Gaia Nebbia; David G Partridge; Matthew Parker; James Richard Price; Christine Peters; Sunando Roy; Luke B Snell; Thushan I de Silva; Emma Thomson; Paul Flowers; Andrew Copas; Judith Breuer", - "affiliations": "Institute for Global Health, UCL, London, UK; Comprehensive Clinical Trials Unit, UCL, London, UK; Institute for Global Health, UCL, London, UK; Comprehensive Clinical Trials Unit, UCL, London, UK; Comprehensive Clinical Trials Unit, UCL, London, UK; Imperial College Healthcare NHS Trust, London, UK; Manchester University NHS Foundation Trust, Manchester, UK; University College London Hospitals NHS Foundation Trust, London, UK; Royal Free NHS Foundation Trust, London, UK; University Hospital Southampton NHS Foundation Trust, Southampton, UK; Sandwell and West Birmingham NHS Trust, UK; Departments of Virology and Infectious Diseases, Newcastle Hospitals NHS Foundation Trust, Newcastle, UK; Nottingham University Hospitals NHS Trust, Nottingham, UK; St George's University Hospitals NHS Foundation Trust, London, UK; Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK; Barts Health NHS Trust, London, UK; Research Computing, UCL, London, UK; Department of Genetics & Genomic Medicine, UCL Great Ormond Street Institute of Child Health, UCL, London, UK; Centre for Genomic Research, University of Liverpool, Liverpool, UK; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK; University College London Hospitals NHS Foundation Trust, London, UK; Centre for Enzyme Innovation, University of Portsmouth, Portsmouth, UK; Department of Applied Sciences, Northumbria University, Newcastle, UK; School of Life Sciences, University of Nottingham, Nottingham, UK; Institute for Infection and Immunity, St George's University of London, London, UK; Institute for Infection and Immunity, St George's University of London, London, UK; Barts Health NHS Trust, London, UK; Centre for Genomic Research, University of Liverpool, Liverpool, UK; Manchester University NHS Foundation Trust, Manchester, UK; The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Northumbria University, Newcastle, UK; Institute for Infection and Immunity, St George's University of London, London, UK; University College London Hospitals NHS Foundation Trust, London, UK; Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; Health Data Research UK Cambridge Hub, Cambridge UK; Department of Medicine, University of Cambridge, Cambridge, UK; ; ; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK; Sheffield Bioinformatics Core, The University of Sheffield, Sheffield, UK; Imperial College Healthcare NHS Trust, London, UK; NHS Greater Glasgow and Clyde, Glasgow, UK; Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, UCL, London, UK; Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK; Department of Infection, Immunity and Cardiovascular Disease, Medical School, The University of Sheffield, Sheffield, UK; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; School of Psychological Sciences and Health, University of Strathclyde, Glasgow, UK; Institute for Global Health, UCL, London, UK; Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, UCL, London, UK", - "abstract": "IntroductionViral sequencing of SARS-CoV-2 has been used for outbreak investigation, but there is limited evidence supporting routine use for infection prevention and control (IPC) within hospital settings.\n\nMethodsWe conducted a prospective non-randomised trial of sequencing at 14 acute UK hospital trusts. Sites each had a 4-week baseline data-collection period, followed by intervention periods comprising 8 weeks of rapid (<48h) and 4 weeks of longer-turnaround (5-10 day) sequencing using a sequence reporting tool (SRT). Data were collected on all hospital onset COVID-19 infections (HOCIs; detected [≥]48h from admission). The impact of the sequencing intervention on IPC knowledge and actions, and on incidence of probable/definite hospital-acquired infections (HAIs) was evaluated.\n\nResultsA total of 2170 HOCI cases were recorded from October 2020-April 2021, with sequence reports returned for 650/1320 (49.2%) during intervention phases. We did not detect a statistically significant change in weekly incidence of HAIs in longer-turnaround (IRR 1.60, 95%CI 0.85-3.01; P=0.14) or rapid (0.85, 0.48-1.50; P=0.54) intervention phases compared to baseline phase. However, IPC practice was changed in 7.8% and 7.4% of all HOCI cases in rapid and longer-turnaround phases, respectively, and 17.2% and 11.6% of cases where the report was returned. In a per-protocol sensitivity analysis there was an impact on IPC actions in 20.7% of HOCI cases when the SRT report was returned within 5 days.\n\nConclusionWhile we did not demonstrate a direct impact of sequencing on the incidence of nosocomial transmission, our results suggest that sequencing can inform IPC response to HOCIs, particularly when returned within 5 days.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.02.07.22270451", @@ -2841,20 +2799,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.12.20.21268098", - "date": "2021-12-21", - "link": "https://medrxiv.org/cgi/content/short/2021.12.20.21268098", - "title": "Therapies for Long COVID in non-hospitalised individuals - from symptoms, patient-reported outcomes, and immunology to targeted therapies (The TLC Study): Study protocol", - "authors": "Shamil Haroon; Krishnarajah Nirantharakumar; Sarah Hughes; Anuradhaa Subramanian; Olalekan Lee Aiyegbusi; Elin Haf Davies; Puja Myles; Tim Williams; Grace Turner; Joht Singh Chandan; Christel McMullan; Janet Lord; David Wraith; Kirsty McGee; Alastair Denniston; Tom Taverner; Louise Jackson; Elizabeth Sapey; Georgios Gkoutos; Krishna Gokhale; Edward Leggett; Clare Iles; Christopher Frost; Gary McNamara; Amy Bamford; Tom Marshall; Dawit Zemedikun; Gary Price; Steven Marwaha; Nikita Simms-Williams; Kirsty Brown; Anita Walker; Karen Jones; Karen Matthews; Jennifer Camaradou; Michael Saint-Cricq; Sumita Kumar; Yvonne Alder; David Stanton; Lisa Agyen; Megan Baber; Hannah Blaize; Melanie Calvert", - "affiliations": "University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; Aparito; Medicines and Healthcare Products Regulatory Agency; Medicines and Healthcare Products Regulatory Agency; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University of Birmingham; University of Birmingham; University ofBirmingham; University of Birmingham; Medicines and Healthcare Products Regulatory Agency; Medicines and Healthcare Products Regulatory Agency; Aparito; Aparito; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University of Birmingham; N/A; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; University ofBirmingham", - "abstract": "IntroductionIndividuals with COVID-19 frequently experience symptoms and impaired quality of life beyond 4-12 weeks, commonly referred to as Long COVID. Whether Long COVID is one or several distinct syndromes is unknown. Establishing the evidence base for appropriate therapies is needed. We aim to evaluate the symptom burden and underlying pathophysiology of Long COVID syndromes in non-hospitalised individuals and evaluate potential therapies.\n\nMethods and analysisA cohort of 4000 non-hospitalised individuals with a past COVID-19 diagnosis and 1000 matched controls will be selected from anonymised primary care records from the Clinical Practice Research Datalink (CPRD) and invited by their general practitioners to participate on a digital platform (Atom5). Individuals will report symptoms, quality of life, work capability, and patient reported outcome measures. Data will be collected monthly for one year.\n\nStatistical clustering methods will be used to identify distinct Long COVID symptom clusters. Individuals from the four most prevalent clusters and two control groups will be invited to participate in the BioWear sub-study which will further phenotype Long COVID symptom clusters by measurement of immunological parameters and actigraphy.\n\nWe will review existing evidence on interventions for post-viral syndromes and Long COVID to map and prioritise interventions for each newly characterised Long COVID syndrome. Recommendations will be made using the cumulated evidence in an expert consensus workshop. A virtual supportive intervention will be coproduced with patients and health service providers for future evaluation.\n\nIndividuals with lived experience of Long COVID will be involved throughout this programme through a patient and public involvement group.\n\nEthics and disseminationEthical approval was obtained from the Solihull Research Ethics Committee, West Midlands (21/WM/0203). The study is registered on the ISRCTN Registry (1567490). Research findings will be presented at international conferences, in peer-reviewed journals, to Long COVID patient support groups and to policymakers.\n\nArticle SummaryO_ST_ABSStrengths and limitations of the studyC_ST_ABSO_LIThe study will generate a nationally representative cohort of individuals with Long COVID recruited from primary care.\nC_LIO_LIWe will recruit controls matched on a wide range of demographic and clinical factors to assess differences in symptoms between people with Long COVID and similar individuals without a history of COVID-19.\nC_LIO_LIWe will use a newly developed electronic patient reported outcome measure (Symptom Burden Questionnaire) for Long COVID to comprehensively assess a wide range of symptoms highlighted by existing literature, patients, and clinicians.\nC_LIO_LIImmunological, proteomic, genetic, and wearable data captured in the study will allow deep phenotyping of Long COVID syndromes to help better target therapies.\nC_LIO_LIA limitation is that a significant proportion of non-hospitalised individuals affected by COVID-19 in the first wave of the pandemic will lack confirmatory testing and will be excluded from recruitment to the study.\nC_LI", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.12.20.21268113", @@ -3401,20 +3345,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.10.28.21265593", - "date": "2021-11-02", - "link": "https://medrxiv.org/cgi/content/short/2021.10.28.21265593", - "title": "The UK COVID-19 furlough scheme and associations with smoking, alcohol consumption and vaping: evidence from 8 UK longitudinal population surveys.", - "authors": "Michael J Green PhD; Jane Maddock PhD; Giorgio Di Gessa PhD; Bo\u017cena Wielgoszewska PhD; Sam Parsons PhD; Gareth J Griffith PhD; Jazz Croft PhD; Anna J Stevenson PhD; Charlotte F Huggins PhD; Charlotte Booth PhD; Jacques Wels; Richard J Silverwood PhD; Praveetha Patalay PhD; Alun D Hughes PhD; Nishi Chaturvedi MD; Laura D Howe PhD; Emla Fitzsimons PhD; Srinivasa Vittal Katikireddi PhD; George B Ploubidis PhD", - "affiliations": "MRC/CSO Social & Public Health Sciences Unit, University of Glasgow; MRC Unit for Lifelong Health and Ageing, University College London; Institute of Epidemiology and Health Care, University College London; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; MRC Integrative Epidemiology Unit, University of Bristol; MRC Integrative Epidemiology Unit, University of Bristol; Centre for Genomic and Experimental Medicine, University of Edinburgh; Centre for Genomic and Experimental Medicine, University of Edinburgh; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; MRC Unit for Lifelong Health and Ageing, University College London; Centre for Longitudinal Studies, UCL Social Research Institute, University College; MRC Unit for Lifelong Health and Ageing, University College London; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; MRC Unit for Lifelong Health and Ageing, University College London; MRC Unit for Lifelong Health and Ageing, University College London; MRC Integrative Epidemiology Unit, University of Bristol; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; MRC/CSO Social & Public Health Sciences Unit, University of Glasgow; Centre for Longitudinal Studies, UCL Social Research Institute, University College London", - "abstract": "BackgroundDisruptions to employment status can impact smoking and alcohol consumption. During the COVID-19 pandemic, the UK implemented a furlough scheme to prevent job loss. We examine how furlough was associated with participants smoking, vaping and alcohol consumption behaviours in the early stages of the pandemic.\n\nMethodsData were from 27,841 participants in eight UK adult longitudinal surveys. Participants self-reported employment status and current smoking, current vaping and drinking alcohol (>4 days/week or 5+ drinks per typical occasion) both before and during the pandemic (April-July 2020). Risk ratios were estimated within each study using modified Poisson regression, adjusting for a range of potential confounders, including pre-pandemic behaviour. Findings were synthesised using random effects meta-analysis. Sub-group analyses were used to identify whether associations differed by gender, age or education.\n\nResultsCompared to stable employment, neither furlough, no longer being employed, nor stable unemployment were associated with smoking, vaping or drinking, following adjustment for pre-pandemic characteristics. However, some sex differences in these associations were observed, with stable unemployment associated with smoking for women (ARR=1.35; 95% CI: 1.00-1.82; I2: 47%) but not men (0.84; 95% CI: 0.67-1.05; I2: 0%). No longer being employed was associated with vaping among women (ARR=2.74; 95% CI: 1.59-4.72; I2: 0%) but not men (ARR=1.25; 95% CI: 0.83-1.87; I2: 0%). There was little indication of associations with drinking differing by age, gender or education.\n\nConclusionsWe found no clear evidence of furlough or unemployment having adverse impacts on smoking, vaping or drinking behaviours during the early stages of the COVID-19 pandemic in the UK, with differences in risk compared to those who remained employed largely explained by pre-pandemic characteristics.", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.11.01.21265660", @@ -3583,6 +3513,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.09.28.21264260", + "date": "2021-09-29", + "link": "https://medrxiv.org/cgi/content/short/2021.09.28.21264260", + "title": "The impact of SARS-CoV-2 vaccination on Alpha and Delta variant transmission", + "authors": "David W Eyre; Donald Taylor; Mark Purver; David Chapman; Tom Fowler; Koen Pouwels; Ann Sarah Walker; Tim EA Peto", + "affiliations": "University of Oxford; Department of Health and Social Care; Department of Health and Social Care; Deloitte MCS Ltd; Department of Health and Social Care; University of Oxford; University of Oxford; University of Oxford", + "abstract": "BackgroundPre-Delta, vaccination reduced SARS-CoV-2 transmission from individuals infected despite vaccination, potentially via reducing viral loads. While vaccination still lowers the risk of infection, similar viral loads in vaccinated and unvaccinated individuals infected with Delta question how much vaccination prevents transmission.\n\nMethodsWe performed a retrospective observational cohort study of adult contacts of SARS-CoV-2-infected adult index cases using English contact testing data. We used multivariable Poisson regression to investigate associations between transmission and index case and contact vaccination, and how these vary with Alpha and Delta variants (classified using S-gene detection/calendar trends) and time since second vaccination.\n\nResults54,667/146,243(37.4%) PCR-tested contacts of 108,498 index cases were PCR-positive. Two doses of BNT162b2 or ChAdOx1 vaccines in Alpha index cases were independently associated with reduced PCR-positivity in contacts (aRR, adjusted rate ratio vs. unvaccinated=0.32[95%CI 0.21-0.48] and 0.48[0.30-0.78] respectively). The Delta variant attenuated vaccine-associated reductions in transmission: two BNT162b2 doses reduced Delta transmission (aRR=0.50[0.39-0.65]), more than ChAdOx1 (aRR=0.76[0.70-0.82]). Variation in Ct values (indicative of viral load) explained 7-23% of vaccine-associated transmission reductions. Transmission reductions declined over time post-second vaccination, for Delta reaching similar levels to unvaccinated individuals by 12 weeks for ChAdOx1 and attenuating substantially for BNT162b2. Protection in contacts also declined in the 3 months post-second vaccination.\n\nConclusionsVaccination reduces transmission of Delta, but by less than the Alpha variant. The impact of vaccination decreased over time. Factors other than PCR Ct values at diagnosis are important in understanding vaccine-associated transmission reductions. Booster vaccinations may help control transmission together with preventing infections.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.09.28.21264240", @@ -4101,20 +4045,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.07.19.21260770", - "date": "2021-07-22", - "link": "https://medrxiv.org/cgi/content/short/2021.07.19.21260770", - "title": "Uptake of infant and pre-school immunisations in Scotland and England during the COVID-19 pandemic: an observational study of routinely collected data", - "authors": "Fiona McQuaid; Rachel Mulholland; Yuma Sangpang Rai; Utkarsh Agrawal; Helen Bedford; Claire Cameron; Cheryl Gibbon; Partho Roy; Aziz Sheikh; Ting Shi; Colin Simpson; Judith Tait; Elise Tessier; Steve Turner; Jaime Villacampa Ortega; Joanne White; Rachael Wood", - "affiliations": "University of Edinburgh; University of Edinburgh; Public Health England; University of St Andrews; UCL Great Ormond Street Institute of Child Health; Public Health Scotland; Public Health Scotland; Public Health England; University of Edinburgh; University of Edinburgh; Victoria University of Wellington; Public Health Scotland; Public Health England; University of Aberdeen; Public Health Scotland; Public Health England; University of Edinburgh", - "abstract": "BackgroundIn 2020, the COVID-19 pandemic and control measures such as national lockdowns threatened to disrupt routine childhood immunisation programmes. Initial reports from the early weeks of lockdown in the UK and worldwide suggested that uptake could fall putting children at risk from multiple other infectious diseases. In Scotland and England, enhanced surveillance of national data for childhood immunisations was established to inform and rapidly assess the impact of the pandemic on infant and preschool immunisation uptake rates.\n\nMethods and findingsWe undertook an observational study using routinely collected data for the year prior to the pandemic (2019), and immediately before, during and after the first period of the UK lockdown in 2020. Data were obtained for Scotland from the Public Health Scotland \"COVID19 wider impacts on the health care system\" dashboard (https://scotland.shinyapps.io/phs-covid-wider-impact/) and for England from ImmForm.\n\nFive vaccinations delivered at different ages were evaluated; three doses of the 6-in-1 DTaP/IPV/Hib/HepB vaccine and two doses of MMR. Uptake in the periods in 2020 compared to that in the baseline year of 2019 using binary logistic regression analysis. For Scotland, we analysed timely uptake of immunisations, defined as uptake within four weeks of the child becoming eligible by age for each immunisation and data were also analysed by geographical region and indices of deprivation. For both Scotland and England, we assessed whether immunisations were up to date at approximately 6 months (all doses 6-in-1) and 16-18 months (first MMR) of age.\n\nWe found that uptake rates within four weeks of eligibility in Scotland for all the five vaccine visits were higher during the 2020 lockdown period than in 2019. The difference ranged from 1.3% for the first dose of the 6-in-1 vaccine (95.3 vs 94%, OR 1.28, CI 1.18-1.39) to 14.3% for the second MMR dose (66.1 vs 51.8 %, OR 1.8, CI 1.74-1.87). Significant increases in uptake were seen across all deprivation levels, though, for MMR, there was evidence of greater improvement for children living in the least deprived areas.\n\nIn England, fewer children who had been due to receive their immunisations during the lockdown period were up to date at 6 months (6-in-1) or 18 months (first dose MMR). The fall in percentage uptake ranged from 0.5% for first 6-in1 (95.8 vs 96.3%, OR 0.89, CI 0.86-0.91) to 2.1% for third 6-in-1 (86.6 vs 88.7%, OR 0.82, CI 0.81-0.83).\n\nConclusionsThis study suggests that the national lockdown in Scotland was associated with a positive effect on timely childhood immunisation uptake, however in England a lower percentage of children were up to date at 6 and 18 months. Reason for the improve uptake in Scotland may include active measures taken to promote immunisation at local and national level during this period. Promoting immunisation uptake and addressing potential vaccine hesitancy is particularly important given the ongoing pandemic and COVID-19 vaccination campaigns.", - "category": "pediatrics", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.07.21.21260926", @@ -4143,20 +4073,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.07.16.21260628", - "date": "2021-07-19", - "link": "https://medrxiv.org/cgi/content/short/2021.07.16.21260628", - "title": "Overall and cause-specific hospitalisation and death after COVID-19 hospitalisation in England: cohort study in OpenSAFELY using linked primary care, secondary care and death registration data", - "authors": "Krishnan Bhaskaran; Christopher T Rentsch; George Hickman; William J Hulme; Anna Schultze; Helen J Curtis; Kevin Wing; Charlotte Warren-Gash; Laurie Tomlinson; Christopher Bates; Rohini Mathur; Brian MacKenna; Viyaasan Mahalingasivam; Angel YS Wong; Alex J Walker; Caroline E Morton; Daniel Grint; Amir Mehrkar; Rosalind M Eggo; Peter Inglesby; Ian J Douglas; Helen I McDonald; Jonathan Cockburn; Elizabeth J Williamson; David Evans; John Parry; Frank Hester; Sam Harper; Stephen JW Evans; Sebastian CJ Bacon; Liam Smeeth; Ben Goldacre", - "affiliations": "London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; TPP; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; TPP; London School of Hygiene and Tropical Medicine; University of Oxford; TPP; TPP; TPP; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford", - "abstract": "BackgroundThere is concern about medium to long-term adverse outcomes following acute COVID-19, but little relevant evidence exists. We aimed to investigate whether risks of hospital admission and death, overall and by specific cause, are raised following discharge from a COVID-19 hospitalisation.\n\nMethods and FindingsWorking on behalf of NHS-England, we used linked primary care and hospital data in OpenSAFELY to compare risks of hospital admission and death, overall and by specific cause, between people discharged from COVID-19 hospitalisation (February-December 2020), and (i) demographically-matched controls from the 2019 general population; (ii) people discharged from influenza hospitalisation in 2017-19. We used Cox regression adjusted for personal and clinical characteristics.\n\n24,673 post-discharge COVID-19 patients, 123,362 general population controls, and 16,058 influenza controls were followed for [≤]315 days. Overall risk of hospitalisation or death (30968 events) was higher in the COVID-19 group than general population controls (adjusted-HR 2.23, 2.14-2.31) but similar to the influenza group (adjusted-HR 0.94, 0.91-0.98). All-cause mortality (7439 events) was highest in the COVID-19 group (adjusted-HR 4.97, 4.58-5.40 vs general population controls and 1.73, 1.60-1.87 vs influenza controls). Risks for cause-specific outcomes were higher in COVID-19 survivors than general population controls, and largely comparable between COVID-19 and influenza patients. However, COVID-19 patients were more likely than influenza patients to be readmitted/die due to their initial infection/other lower respiratory tract infection (adjusted-HR 1.37, 1.22-1.54), and to experience mental health or cognitive-related admission/death (adjusted-HR 1.36, 1.01-2.83); in particular, COVID-19 survivors with pre-existing dementia had higher risk of dementia death. One limitation of our study is that reasons for hospitalisation/death may have been misclassified in some cases due to inconsistent use of codes.\n\nConclusionsPeople discharged from a COVID-19 hospital admission had markedly higher risks for rehospitalisation and death than the general population, suggesting a substantial extra burden on healthcare. Most risks were similar to those observed after influenza hospitalisations; but COVID-19 patients had higher risks of all-cause mortality, readmissions/death due to the initial infection, and dementia death, highlighting the importance of post-discharge monitoring.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.07.13.21260425", @@ -4703,20 +4619,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.06.03.21258289", - "date": "2021-06-06", - "link": "https://medrxiv.org/cgi/content/short/2021.06.03.21258289", - "title": "Implementation of COVID-19 Preventive Measures in Primary and Secondary Schools Following Reopening of Schools in Autumn 2020; A Cross-Sectional Study of Parents' and Teachers' Experiences in England", - "authors": "Zahin Amin-Chowdhury; Marta Bertran; Meaghan Kall; Georgina Ireland; Felicity Aiano; Annabel Powell; Samuel E Jones; Andrew Brent; Bernadette Brent; Frances Baawuah; Ifeanychukwu Okike; Joanne Beckmann; Joanna Garstang; Shazaad Ahmed; Neisha Sundaram; Chris Bonell; Sinead Langan; James Hargreaves; Shamez N Ladhani", - "affiliations": "Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Public Health England; University Hospitals of Derby and Burton NHS foundation Trust; Specialist Children & Young People's Services, East London NHS Foundation Trust; Birmingham Community Healthcare Trust; Public Health England; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Public Health England", - "abstract": "ObjectiveThe main objective was to assess implementation of and ease of implementation of control measures in schools as reported by staff and parents.\n\nDesignCross-sectional study.\n\nSettingStaff and parents/guardian participants in the 132 primary schools and 20 secondary schools participating in sKIDs and sKIDsPLUS surveillances.\n\nMain outcome measurePrevalence of control measures implemented in Autumn 2020, parental and staff perception of ease of implementation and acceptability of conducting school surveillance studies.\n\nResultsIn total, 56/152 (37%) schools participating in Public Health Englands sKIDs study of COVID in schools accepted the invitation to participate in the survey. By 28 December 2020, 1,953 parent and 986 staff respondents had completed the online questionnaire. While more than half the parents were positive about their children returning to school, roughly a third reported being a little anxious. 90% and 82% of primary and secondary school parents were either completely or partly reassured by the preventive measures implemented in their schools. Among staff, 80% of primary staff and 87% of secondary school staff felt that they were at higher risk of COVID-19 because of their profession; only 52% of primary school staff and 38% of secondary school staff reportedly felt safe. According to the teaching staff, most preventive measures were well-implemented apart from requiring 2-metre distancing between staff. For students, maintaining the 2-metre distance was reported to be particularly difficult. By extension, secondary schools also struggled to maintain small groups at all times or ensuring that the same staff were assigned to each student group (a problem also commonly reported by parents).\n\nConclusionsVariable implementation of infection control measures was reported by staff and parents. Whilst the majority were not worried about returning to school, some parents and staff, were concerned about returning to school and the risks posed to children, staff and household members.\n\nStrengths and limitations of this studyO_ST_ABSStrengthsC_ST_ABSO_LIThis study is one of the few to investigate school staff and parents perceptions of the implementation of control measures implemented following the reopening of schools in England.\nC_LIO_LIThe early establishment of COVID-19 surveillance in primary and secondary schools in the summer term 2020 provided a cohort to rapidly evaluate the experiences of parents and school staff during the autumn term before schools were required to close for the subsequent national lockdown.\nC_LI\n\nLimitationsO_LIAs the questionnaire and information provided was available in English only, there is likely to be an under-representation of families for whom English was not their main language.\nC_LIO_LISome school responses were only provided by one participant so may not necessarily be representative of the whole school.\nC_LIO_LIAlthough the surveillance included schools recruited nationally, a convenience sample was used and as such may not be representative of all primary and secondary schools in England.\nC_LI", - "category": "public and global health", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.05.28.21257602", @@ -4871,6 +4773,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.05.15.21257017", + "date": "2021-05-17", + "link": "https://medrxiv.org/cgi/content/short/2021.05.15.21257017", + "title": "Extended interval BNT162b2 vaccination enhances peak antibody generation in older people", + "authors": "Helen M Parry; Rachel Bruton; Christine Stephens; Kevin Brown; Gayatri Amirthalingam; Bassam Hallis; Ashley Otter; Jianmin Zuo; Paul Moss", + "affiliations": "University of Birmingham, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham. B15 2TT, UK; Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham. B15 2TT, UK; Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham. B15 2TT, UK; National infection Service, Public Health England, Colindale, London NW9 5EQ, UK; National infection Service, Public Health England, Colindale, London NW9 5EQ, UK; National infection Service, Public Health England, Porton Down, Salisbury, SP4 OJG, UK; National infection Service, Public Health England, Porton Down, Salisbury, SP4 OJG, UK; Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham. B15 2TT, UK; Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham. B15 2TT, UK", + "abstract": "ObjectivesTo assess the relative immunogenicity of standard or extended interval BNT162b2 vaccination.\n\nDesignPopulation based cohort study comparing immune responses 2 weeks after the second vaccine, with appropriate time-matched samples in participants who received standard or extended interval double vaccination.\n\nSettingPrimary care networks, Birmingham, UK. December 2020 to April 2021.\n\nParticipants172 people aged over 80 years of age. All donors received the BNT162b2 Pfizer/BioNTech vaccination and were vaccinated with either a standard 3 week interval between doses or an extended interval schedule.\n\nMain outcome measuresPeak quantitative spike-specific antibody and cellular immune responses.\n\nResultsIn donors without evidence of previous infection the peak antibody response was 3.5-fold higher in donors who had undergone delayed interval vaccination. Cellular immune responses were 3.6-fold lower.\n\nConclusionPeak antibody responses after the second BNT162b2 vaccine are markedly enhanced in older people when this is delayed to 12 weeks although cellular responses are lower. Extended interval vaccination may therefore offer the potential to enhance and extend humoral immunity. Further follow up is now required to assess long term immunity and clinical protection.\n\nWhat is already known on this topicThe BNT162b2 vaccine is highly effective against Covid-19 infection and was delivered with a 3-week time interval in registration studies. However, this interval has been extended in many countries in order to extend population coverage with a single vaccine. It is not known how immune responses after the second dose are influenced by delaying the second vaccine.\n\nWhat this study addsWe provide the first assessment of immune responses in the first 14 weeks after standard or extended interval BNT162b2 vaccination and show that delaying the second dose acts to strongly boost the peak antibody response in older people. The extended interval vaccination may offer a longer period of clinical protection. This information will be of value in optimizing vaccine regimens and help guide guide vaccination policies.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 92 + }, { "site": "medRxiv", "doi": "10.1101/2021.05.12.21257123", @@ -5291,6 +5207,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.04.07.21254497", + "date": "2021-04-09", + "link": "https://medrxiv.org/cgi/content/short/2021.04.07.21254497", + "title": "Characterising contact in disease outbreaks via a network model of spatial-temporal proximity", + "authors": "Ashleigh C Myall; Robert L Peach; Yu Wan; Siddharth Mookerjee; Elita Jauneikaite; Frankie Bolt; James Richard Price; Frances Davies; Andrea Yeong Wiesse; Alison Holmes; Mauricio Barahona", + "affiliations": "Imperial College London; Imperial College London; Imperial College London; Imperial College NHS Trust; Imperial College London; Imperial College London; Imperial College London; Imperial College NHS Trust; University of Edinburgh; Imperial College London; Imperial College London", + "abstract": "Contact tracing is a key tool in epidemiology to identify and control outbreaks of infectious diseases. Existing contact tracing methodologies produce contact maps of individuals based on a binary definition of contact which can be hampered by missing data and indirect contacts. Here, we present a Spatial-temporal Epidemiological Proximity (StEP) model to recover contact maps in disease outbreaks based on movement data. The StEP model accounts for imperfect data by considering probabilistic contacts between individuals based on spatial-temporal proximity of their movement trajectories, creating a robust movement network despite possible missing data and unseen transmission routes. Using real-world data we showcase the potential of StEP for contact tracing with outbreaks of multidrug-resistant bacteria and COVID-19 in a large hospital group in London, UK. In addition to the core structure of contacts that can be recovered using traditional methods of contact tracing, the StEP model reveals missing contacts that connect seemingly separate outbreaks. Comparison with genomic data further confirmed that these recovered contacts indeed improve characterisation of disease transmission and so highlights how the StEP framework can inform effective strategies of infection control and prevention.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.04.01.21254765", @@ -5753,6 +5683,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.03.04.21252931", + "date": "2021-03-08", + "link": "https://medrxiv.org/cgi/content/short/2021.03.04.21252931", + "title": "A common TMPRSS2 variant protects against severe COVID-19", + "authors": "Alessia David; Nicholas Parkinson; Thomas P Peacock; Erola Pairo-Castineira; Tarun Khanna; Aurelie Cobat; Albert Tenesa; Vanessa Sancho-Shimizu; - GenOMICC Investigators, ISARIC4C Investigators; Jean-Laurent Casanova; Laurent Abel; Wendy S Barclay; J Kenneth Baillie; Michael J.E. Sternberg", + "affiliations": "Centre for Integrative System Biology and Bioinformatics, Imperial College London, London; Roslin Institute, University of Edinburgh; Department of Infectious Diseases, Imperial College London; Roslin Institute, University of Edinburgh; Centre for Integrative System Biology and Bioinformatics, Imperial College London; Laboratory of Human Genetics of Infectious Diseases, INSERM; Roslin Institute, University of Edinburgh; Department of Paediatric Infectious Diseases & Virology, Imperial College London; ; St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University; Laboratory of Human Genetics of Infectious Diseases, INSERM; Department of Infectious Diseases, Imperial College London; Roslin Institute, University of Edinburgh; Centre for Integrative System Biology and Bioinformatics, Imperial College London", + "abstract": "Infection with SARS-CoV-2 has a wide range of clinical presentations, from asymptomatic to life-threatening. Old age is the strongest factor associated with increased COVID19-related mortality, followed by sex and pre-existing conditions. The importance of genetic and immunological factors on COVID19 outcome is also starting to emerge, as demonstrated by population studies and the discovery of damaging variants in genes controlling type I IFN immunity and of autoantibodies that neutralize type I IFNs. The human protein transmembrane protease serine type 2 (TMPRSS2) plays a key role in SARS-CoV-2 infection, as it is required to activate the virus spike protein, facilitating entry into target cells. We focused on the only common TMPRSS2 non-synonymous variant predicted to be damaging (rs12329760), which has a minor allele frequency of [~]25% in the population. In a large population of SARS-CoV-2 positive patients, we show that this variant is associated with a reduced likelihood of developing severe COVID19 (OR 0.87, 95%CI:0.79-0.97, p=0.01). This association was stronger in homozygous individuals when compared to the general population (OR 0.65, 95%CI:0.50-0.84, p=1.3x10-3). We demonstrate in vitro that this variant, which causes the amino acid substitution valine to methionine, impacts the catalytic activity of TMPRSS2 and is less able to support SARS-CoV-2 spike-mediated entry into cells.\n\nTMPRSS2 rs12329760 is a common variant associated with a significantly decreased risk of severe COVID19. Further studies are needed to assess the expression of the TMPRSS2 across different age groups. Moreover, our results identify TMPRSS2 as a promising drug target, with a potential role for camostat mesilate, a drug approved for the treatment of chronic pancreatitis and postoperative reflux esophagitis, in the treatment of COVID19. Clinical trials are needed to confirm this.", + "category": "genetic and genomic medicine", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.03.04.21252528", @@ -6061,20 +6005,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.02.04.21251155", - "date": "2021-02-08", - "link": "https://medrxiv.org/cgi/content/short/2021.02.04.21251155", - "title": "Impact of school closures on the health and well-being of primary school children in Wales UK; a routine data linkage study using the HAPPEN survey (2018-2020).", - "authors": "Michaela James; Emily Marchant; Margaret A Defeyter; Jayne V Woodside; Sinead Brophy", - "affiliations": "Swansea University; Swansea University; Northumbria University; Queen's University Belfast; Swansea University", - "abstract": "IntroductionIn response to the COVID-19 pandemic, school closures were implemented across the United Kingdom. This study aimed to explore the impact of school closures on childrens health by comparing health and wellbeing outcomes collected during school closures (April - June 2020) with data from the same period in 2019 and 2018.\n\nMethodsData were collected online via the HAPPEN At Home survey, which captured the typical health behaviours of children aged 8 - 11 years between April - June 2020. These data were compared with data in 2018 and 2019 also collected between April-June, from HAPPEN. Free school meal (FSM) status was used as a proxy for socio-economic deprivation. Analyses were repeated stratifying by FSM.\n\nResultsComparing responses between April - June in 2020 (n=1068), 2019 (n=1150) and 2018 (n=475), there were improvements in physical activity levels, sleep time, happiness and general wellbeing for children during school closures compared to previous years. However, children on FSM ate less fruit and vegetables (21% (95%CI (5.7% to 37%)) and had lower self-assessed school competence compared to 2019. Compared to those not on FSM they also spent less time doing physical activity (13.03% (95%CI: 3.3% to 21.7%) and consumed more takeaways (16.3% (95%CI: 2%-30%)) during school closures.\n\nConclusionThis study suggests that schools play an important role in reducing inequalities in physical health. The physical health (e.g. physical activity and diet) of children eligible for FSM may be impacted by prolonged school closures.\n\nWhat is already known on this subject?In response to the COVID-19 pandemic, by mid-March 2020, 138 countries had implemented national school closures to reduce the number of social contacts between pupils, therefore interrupting the transmission of COVID-19 as part of pandemic plans. UNESCO warned that the global scale and speed of the educational disruption would be unparalleled. There is an ongoing debate with regard to the effectiveness of schools closures on transmission rates, but the fact schools are closed for a long period of time could have detrimental impacts on pupils physical and mental health.\n\nThis study provides evidence of any differences in the health and wellbeing of children prior to and during the COVID-19 enforced lockdown and school closures between March and June 2020. These findings could have a significant impact for the future and support schools to better understand their pupils physical, psychological, emotional and social health. It also contributes to a significant literature gap regarding the impact of school closures on school-aged children.\n\nWhat this study adds?Improvements in physical activity levels, sleep time, happiness and general wellbeing were observed in general for children during school closures compared to previous years. However, children on FSM reported eating less fruit and vegetables and had lower self-assessed school competence compared to 2019. Compared to those not on FSM they also spent less time doing physical activity and consumed more takeaways during school closures. These trends are not evident among children not on FSM. All children reported improvements in wellbeing during lockdown especially on the happiness with family measure.\n\nOverall, findings suggest schools help to reduce inequalities in physical health for socio-economically deprived children. During school closures children from deprived backgrounds are likely to have poorer physical health (e.g. less time spent doing physical activities and poorer diet) and this is not observed in children who are not in receipt of FSM. This research suggests that school closures will result in widening health inequalities and when schools return measures will need to be in place to readdress the widened gap in physical health.", - "category": "public and global health", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.02.04.21251087", @@ -6089,20 +6019,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.02.07.21251297", - "date": "2021-02-08", - "link": "https://medrxiv.org/cgi/content/short/2021.02.07.21251297", - "title": "The changing characteristics of COVID-19 presentations: A regional comparison of SARS-CoV-2 hospitalised patients during the first and second wave.", - "authors": "Catherine Atkin; Vicky Kamwa; Vinay Reddy-Kolanu; Dhruv Parekh; Felicity Evison; Peter Nightingale; Suzy Gallier; Simon Ball; Elizabeth Sapey", - "affiliations": "Acute Medicine, Birmingham Acute Care Research Group, Institute of Inflammation and Ageing, University of Birmingham; Acute Medicine, Birmingham Acute Care Research Group, Institute of Inflammation and Ageing, University of Birmingham; Acute Medicine, University Hospitals Birmingham NHS Foundation Trust; A. Intensive Care Medicine, University Hospitals Birmingham NHS Foundation Trust, Edgbaston, Birmingham, B15 2GW, UK. B. Birmingham Acute Care Research Grou; Research Analytics Department of Health Informatics, University Hospitals Birmingham NHS Foundation Trust; NIHR Clinical Research Facility Statistician, University Hospitals Birmingham NHS Foundation Trust; PIONEER Technical Director, Lead for Research Analytics Department of Health Informatics, University Hospitals Birmingham NHS Foundation Trust; A. Chief Medical Officer, University Hospitals Birmingham NHS Foundation Trust B. HDR-UK Midlands Site and Better Care Programme, University Hospitals Birmingh; A. Director of PIONEER: Health Data Research UK (HDRUK) Health Data Research Hub for Acute Care B. Birmingham Acute Care Research Group, Institute of Inflammat", - "abstract": "BackgroundThis study assesses COVID-19 hospitalised patient demography and outcomes during wave 1 and wave 2, prior to new variants of the virus.\n\nMethodsAll patients with a positive SARS-CoV-2 swab between 10th March 2020 and 5th July 2020 (wave 1) and 1st September 2020 and 16th November 2020 (wave 2) admitted to University Hospitals Birmingham NHS Foundation Trust were included (n=4856), followed for 28 days.\n\nResultsWave 2 patients were younger, more ethnically diverse, had less co-morbidities and disease presentation was milder on presentation. After matching for these factors, mortality was reduced, but without differences in intensive care admissions.\n\nConclusionPrior to new SARS-CoV-2 variants, outcomes for hospitalised patients with COVID-19 were improving but with similar intensive care needs.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.02.03.21251054", @@ -6201,6 +6117,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.01.28.21250606", + "date": "2021-01-31", + "link": "https://medrxiv.org/cgi/content/short/2021.01.28.21250606", + "title": "REACT-1 round 8 final report: high average prevalence with regional heterogeneity of trends in SARS-CoV-2 infection in the community in England during January 2021", + "authors": "Steven Riley; Oliver Eales; Caroline E. Walters; Haowei Wang; Kylie E. C. Ainslie; Christina Atchinson; Claudio Fronterre; Peter J. Diggle; Deborah Ashby; Christl A Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott", + "affiliations": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear", + "abstract": "In early January 2021, England entered its third national lockdown of the COVID-19 pandemic to reduce numbers of deaths and pressure on healthcare services, while rapidly rolling out vaccination to healthcare workers and those most at risk of severe disease and death. REACT-1 is a survey of SARS-CoV-2 prevalence in the community in England, based on repeated cross-sectional samples of the population. Between 6th and 22nd January 2021, out of 167,642 results, 2,282 were positive giving a weighted national prevalence of infection of 1.57% (95% CI, 1.49%, 1.66%). The R number nationally over this period was estimated at 0.98 (0.92, 1.04). Prevalence remained high throughout, but with suggestion of a decline at the end of the study period. The average national trend masked regional heterogeneity, with robustly decreasing prevalence in one region (South West) and increasing prevalence in another (East Midlands). Overall prevalence at regional level was highest in London at 2.83% (2.53%, 3.16%). Although prevalence nationally was highest in the low-risk 18 to 24 year old group at 2.44% (1.96%, 3.03%), it was also high in those over 65 years who are most at risk, at 0.93% (0.82%, 1.05%). Large household size, living in a deprived neighbourhood, and Black and Asian ethnicity were all associated with higher levels of infections compared to smaller households, less deprived neighbourhoods and other ethnicities. Healthcare and care home workers, and other key workers, were more likely to test positive compared to other workers. If sustained lower prevalence is not achieved rapidly in England, pressure on healthcare services and numbers of COVID-19 deaths will remain unacceptably high.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.01.25.21249942", @@ -6215,20 +6145,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.01.28.21250680", - "date": "2021-01-29", - "link": "https://medrxiv.org/cgi/content/short/2021.01.28.21250680", - "title": "The effect of SARS-CoV-2 variant B.1.1.7 on symptomatology, re-infection and transmissibility", - "authors": "Mark S Graham; Carole H Sudre; Anna May; Michela Antonelli; Benjamin Murray; Thomas Varsavsky; Kerstin Klaser; Liane Dos Santos Canas; Erika Molteni; Marc Modat; David Alden Drew; Long Alden Nguyen; Lorenzo Polidori; Somesh Selvachandran; Christina Hu; Joan Capdevila Pujol; - The COVID-19 Genomics UK (COG-UK) consortium; Alexander Hammers; Andrew T Chan; Jonathan Wolf; Timothy Spector; Claire Steves; Sebastien Ourselin", - "affiliations": "King's College London; MRC Unit for Lifelong Health and Ageing; Zoe Global Limited; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; Massachusetts General Hospital; Massachusetts General Hospital and Harvard Medical School; Zoe Global Limited; Zoe Global Limited; Zoe Global Limited; Zoe Global Limited; ; King's College London; Massachusetts General Hospital; Zoe Global Limited; King's College London; King's College London; King's College London", - "abstract": "BackgroundSARS-CoV-2 variant B.1.1.7 was first identified in December 2020 in England. It is not known if the new variant presents with variation in symptoms or disease course, if previously infected individuals may become reinfected with the new variant, or how the variants increased transmissibility affects measures to reduce its spread.\n\nMethodsUsing longitudinal symptom reports from 36,920 users of the COVID Symptom Study app testing positive for Covid-19 between 28 September and 27 December 2020, we performed an ecological study to examine the association between the regional proportion of B.1.1.7 and reported symptoms, disease course, rates of reinfection, and transmissibility.\n\nFindingsWe found no evidence for changes in reported symptoms or disease duration associated with B.1.1.7. We found a likely reinfection rate of 0.7% (95% CI 0.6-0.8), but no evidence that this was higher compared to older strains. We found an increase in R(t) by a factor of 1.35 (95% CI 1.02-1.69). Despite this, we found that R(t) fell below 1 during regional and national lockdowns, even in regions with high proportions of B.1.1.7.\n\nInterpretationThe lack of change in symptoms indicates existing testing and surveillance infrastructure do not need to change specifically for the new variant, and the reinfection findings suggest that vaccines are likely to remain effective against the new variant.\n\nFundingZoe Global Limited, Department of Health, Wellcome Trust, EPSRC, NIHR, MRC, Alzheimers Society.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSTo identify existing evidence on SARS-CoV-2 variant B.1.1.7 we searched PubMed and Google Scholar for articles between 1 December 2020 and 1 February 2021 using the keywords Covid-19 AND B.1.1.7, finding 281 results. We did not find any studies that investigated B.1.1.7-associated changes in the symptoms experienced, their severity and duration, but found one study showing B.1.1.7 did not change the ratio of symptomatic to asymptomatic infections. We found six articles describing laboratory-based investigations of the responses of B.1.1.7 to vaccine-induced immunity to B.1.1.7, but no work investigating what this means for natural immunity and the likelihood of reinfection outside of the lab. We found five articles demonstrating the increased transmissibility of B.1.1.7.\n\nAdded value of this studyTo our knowledge, this is the first study to explore changes in symptom type and duration, as well as community reinfection rates, associated with B.1.1.7. The work uses self-reported symptom logs from 36,920 users of the COVID Symptom Study app reporting positive test results between 28 September and 27 December 2020. We find that B.1.1.7 is not associated with changes in the symptoms experienced in Covid-19, nor their duration. Building on existing lab studies, our work suggests that natural immunity developed from previous infection provides similar levels of protection to B.1.1.7. We add to the emerging consensus that B.1.1.7 exhibits increased transmissibility.\n\nImplications of all the available evidenceOur findings suggest that existing criteria for obtaining a Covid-19 test in the community need not change for the rise of B.1.1.7. The fact that immunity developed from infection by wild type variants protects against B.1.1.7 provides an indication that vaccines will remain effective against B.1.1.7. R(t) fell below 1 during the UKs national lockdown, even in regions with high levels of B.1.1.7, but further investigation is required to establish the factors that enabled this, to facilitate countries seeking to control the spread of B.1.1.7.", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 94, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.01.26.21250480", @@ -6551,20 +6467,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.12.21.20248475", - "date": "2020-12-22", - "link": "https://medrxiv.org/cgi/content/short/2020.12.21.20248475", - "title": "Clinical outcomes and risk factors for COVID-19 among migrant populations in high-income countries: a systematic review", - "authors": "Sally E Hayward; Anna Deal; Cherie Cheng; Alison F Crawshaw; Miriam Orcutt; Tushna F Vandrevala; Marrie Norredam; Manuel Carballo; Yusuf Ciftci; Ana Requena-Mendez; Chris Greenaway; Jessica Carter; Felicity Knights; Anushka Mehrotra; Farah Seedat; Kayvan Bozorgmehr; Apostolos Veizis; Ines Campos-Matos; Fatima Wurie; Teymur Noori; Martin McKee; Bernadette Kumar; Sally Hargreaves", - "affiliations": "Institute for Infection and Immunity, St George's University of London; Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine; Institute for Infection and Immunity, St George's University of London; Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine; Institute for Infection and Immunity, St George's University of London; Institute for Infection and Immunity, St George's University of London; Institute for Global Health, University College London; Faculty of Business and Social Sciences, Kingston University; Danish Research Centre for Migration, Ethnicity and Health, University of Copenhagen; International Centre for Migration, Health, and Development; Doctors of the World UK; Department of Medicine-Solna, Karolinska Institutet; and Barcelona Institute for Global Health (ISGlobal-University of Barcelona); Department of Medicine, McGill University; Institute for Infection and Immunity, St George's University of London; Institute for Infection and Immunity, St George's University of London; Institute for Infection and Immunity, St George's University of London; Public Health England; Public Health, Bielefeld University; Section for Health Equity Studies & Migration, Heidelberg University Hospital; Medecins Sans Frontieres Greece; Public Health England; and UCL Collaborative Centre for Inclusion Health; Public Health England; and UCL Research Department of Epidemiology and Public Health; European Centre for Disease Prevention and Control (ECDC); Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine; Norwegian Institute of Public Health; Institute for Infection and Immunity, St George's University of London", - "abstract": "BackgroundMigrants, including refugees, asylum seekers, labour migrants, and undocumented migrants, now constitute a considerable proportion of most high-income countries populations, including their skilled and unskilled workforces. Migrants may be at increased risk of COVID-19 due to their health and social circumstances, yet the extent to which they are being affected and their predisposing risk factors are not clearly understood. We did a systematic review to assess clinical outcomes of COVID-19 in migrant populations (cases, hospitalisations, deaths), indirect health and social impacts, and to determine key risk factors.\n\nMethodsWe did a systematic review following PRISMA guidelines, registered with PROSPERO (CRD42020222135). We searched databases including PubMed, Global Health, Scopus, CINAHL, and pre-print databases (medRxiv) via the WHO Global Research on COVID-19 database to Nov 18, 2020 for peer-reviewed and grey literature pertaining to migrants (defined as foreign born) and COVID-19 in 82 high-income countries. We used our international networks to source national datasets and grey literature. Data were extracted on our primary outcomes (cases, hospitalisations, deaths) and we evaluated secondary outcomes on indirect health and social impacts, and risk factors, using narrative synthesis.\n\nResults3016 data sources were screened with 158 from 15 countries included in the analysis (35 data sources for primary outcomes: cases [21], hospitalisations [4]; deaths [15]; 123 for secondary outcomes). We found that migrants are at increased risk of infection and are disproportionately represented among COVID-19 cases. Available datasets suggest a similarly disproportionate representation of migrants in reported COVID-19 deaths, as well as increased all-cause mortality in migrants in some countries in 2020. Undocumented migrants, migrant health and care workers, and migrants housed in camps and labour compounds may have been especially affected. In general, migrants have higher levels of many risk factors and vulnerabilities relevant to COVID-19, including increased exposure to SARS-CoV-2 due to high-risk occupations and overcrowded accommodation, and barriers to health care including inadequate information, language barriers, and reduced entitlement to healthcare coverage related to their immigration status.\n\nConclusionsMigrants in high-income countries are at high risk of exposure to, and infection with, COVID-19. These data are of immediate relevance to national public health responses to the pandemic and should inform policymaking on strategies for reducing transmission of COVID-19 in this population. Robust data on testing uptake and clinical outcomes in migrants, and barriers and facilitators to COVID-19 vaccination, are urgently needed, alongside strengthening engagement with diverse migrant groups.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.12.18.20248477", @@ -6677,20 +6579,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.12.10.20247155", - "date": "2020-12-14", - "link": "https://medrxiv.org/cgi/content/short/2020.12.10.20247155", - "title": "Self-harm presentations to Emergency Departments and Place of Safety during the first wave of the UK COVID-19 pandemic: South London and Maudsley data on service use from February to June 2020.", - "authors": "Eleanor Nuzum; Evangelia Martin; Gemma Morgan; Rina Dutta; Christoph Mueller; Catherine Polling; Megan Pritchard; Sumithra Velupillai; Robert Stewart", - "affiliations": "South London and Maudsley NHS Foundation Trust; South London and Maudsley NHS Foundation Trust; South London and Maudsley NHS Foundation Trust; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London", - "abstract": "The lockdown and social distancing policy imposed due to the COVID-19 pandemic has had a substantial impact on both mental health service delivery, and the ways in which people are accessing these services. Previous reports from the South London and Maudsley NHS Trust (SLaM; a large mental health service provider for around 1.2m residents in South London) have highlighted increased use of virtual contacts by mental health teams, with dropping numbers of face-to-face contacts over the first wave of the pandemic. There has been concern that the impact of the COVID-19 pandemic would lead to higher mental health emergencies, particularly instances of self-harm. However, with people advised to stay at home during the first wave lockdown, it is as yet unclear whether this impacted mental health service presentations. Taking advantage of SLaMs Clinical Records Interactive Search (CRIS) data resource with daily updates of information from its electronic mental health records, this paper describes overall presentations to Emergency Department (ED) mental health liaison teams, and those with self-harm. The paper focussed on three periods: i) a pre-lockdown period 1st February to 15th March, ii) a lockdown period 16th March to 10th May and iii) a post-lockdown period 11th May to 28th June. In summary, all attendances to EDs for mental health support decreased during the lockdown period, including those with self-harm. All types of self-harm decreased during lockdown, with self-poisoning remaining the most common. Attendances to EDs for mental health support increased post-lockdown, although were only just approaching pre-lockdown levels by the end of June 2020.", - "category": "psychiatry and clinical psychology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.12.05.20241927", @@ -6775,20 +6663,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.11.30.20240010", - "date": "2020-12-03", - "link": "https://medrxiv.org/cgi/content/short/2020.11.30.20240010", - "title": "Is Point-of-Care testing feasible and safe in care homes in England? An exploratory usability and accuracy evaluation of Point-of-Care Polymerase Chain Reaction test for SARS-COV-2", - "authors": "Massimo Micocci; Adam Gordon; Mikyung Kelly Seo; Joy A Allen; Kerrie Davies; Dan Lasserson; Carl Thompson; Karen Spilsbury; Cyd Akrill; Ros Heath; Anita Astle; Claire Sharpe; Rafael Perera; Gail Hayward; Peter Buckle", - "affiliations": "NIHR London In Vitro Diagnostics Co-operative, Dept of Surgery and Cancer, Faculty of Medicine, Imperial College London St. Mary's Hospital London; Division of Medical Sciences and Graduate Entry Medicine, University of Nottingham, Nottingham, UK;NIHR Applied Research Collaboration-East Midlands (ARC-EM), N; NIHR London In Vitro Diagnostics Co-operative, Dept of Surgery and Cancer, Faculty of Medicine, Imperial College London St. Mary's Hospital London; NIHR Newcastle In Vitro Diagnostics Co-operative, Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK; Healthcare Associated Infections Research Group, University of Leeds and Leeds Teaching Hospitals NHS Trust, Leeds, UK; Warwick Medical School, University of Warwick, UK; School of Healthcare, University of Leeds, Leeds, UK; School of Healthcare, University of Leeds, Leeds, UK; NIHR Applied Research Collaboration Yorkshire and Humber, UK; Springfield Healthcare, Leeds, UK; Landermeads Nursing Home, Nottingham, UK; Wren Hall Nursing Home, Selston, UK; Ashmere Nottinghamshire Ltd, Notts, UK; Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; NIHR Community Healthcare MedTech and IVD Co-operative,Oxford,UK; NIHR London In Vitro Diagnostics Co-operative, Dept of Surgery and Cancer, Faculty of Medicine, Imperial College London St. Mary's Hospital London", - "abstract": "IntroductionReliable rapid testing on COVID-19 is needed in care homes to reduce the risk of outbreaks and enable timely care. Point-of-care testing (POCT) in care homes could provide rapid actionable results. This study aimed to examine the usability and test performance of point of care polymerase chain reaction (PCR) for COVID-19 in care homes.\n\nMethodsPoint-of-care PCR for detection of SARS-COV2 was evaluated in a purposeful sample of four UK care homes. Test agreement with laboratory real-time PCR and usability and use errors were assessed.\n\nResultsPoint of care and laboratory polymerase chain reaction (PCR) tests were performed on 278 participants. The point of care and laboratory tests returned uncertain results or errors for 17 and 5 specimens respectively. Agreement analysis was conducted on 256 specimens. 175 were from staff: 162 asymptomatic; 13 symptomatic. 69 were from residents: 59 asymptomatic; 10 symptomatic. Asymptomatic specimens showed 83.3% (95% CI: 35.9%-99.6%) positive agreement and 98.7% negative agreement (95% CI: 96.2%-99.7%), with overall prevalence and bias-adjusted kappa (PABAK) of 0.965 (95% CI: 0.932 - 0.999). Symptomatic specimens showed 100% (95% CI: 2.5%-100%) positive agreement and 100% negative agreement (95% CI: 85.8%-100%), with overall PABAK of 1. No usability-related hazards emerged from this exploratory study.\n\nConclusionApplications of point-of-care PCR testing in care homes can be considered with appropriate preparatory steps and safeguards. Agreement between POCT and laboratory PCR was good. Further diagnostic accuracy evaluations and in-service evaluation studies should be conducted, if the test is to be implemented more widely, to build greater certainty on this initial exploratory analysis.\n\nKey pointsO_LIPoint of care tests (POCT) in care homes are feasible and could increase testing capacity for the control of COVID-19 infection.\nC_LIO_LIThe test of agreement between POCT and laboratory PCR for care home residents and the staff was good.\nC_LIO_LIAdoption of POCT in care homes can be considered with appropriate preparatory steps and safeguards in place.\nC_LIO_LIRepetitive errors and test malfunctioning can be mitigated with bespoke training for care home staff.\nC_LIO_LIIntegrated care pathways should be investigated to test the high variability of the context of use.\nC_LI", - "category": "health systems and quality improvement", - "match_type": "fuzzy", - "author_similarity": 90, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.12.01.20241729", @@ -6999,20 +6873,6 @@ "author_similarity": 94, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.11.10.20229278", - "date": "2020-11-13", - "link": "https://medrxiv.org/cgi/content/short/2020.11.10.20229278", - "title": "Changing probability of experiencing food insecurity by socioeconomic and demographic groups during the COVID-19 pandemic in the UK", - "authors": "Jonathan Koltai; Veronica Toffolutti; Martin McKee; David Stuckler", - "affiliations": "Bocconi University; Bocconi University; The London School of Hygiene & Tropical Medicine; Bocconi University", - "abstract": "BackgroundFood supply concerns have featured prominently in the UK response to the COVID-19 pandemic. We assess changes in food insecurity in the UK population from April to July 2020.\n\nMethodWe analyze 11,095 respondents from the April through July waves of the Understanding Society COVID-19 longitudinal study survey linked with Wave 9 of the UK Understanding Society study. Food insecurity was defined as having used a food bank in the last 4 weeks; being hungry but not eating in the last week; or not able to eat healthy and nutritious food in the last week. Unadjusted estimates to examine changes in population prevalence and logistic regression were used to assess the association between employment transitions and food insecurity.\n\nFindingsThe prevalence of reporting at least one form of food insecurity rose from 7{middle dot}1% in April to 20{middle dot}2% by July 2020. Some of the largest increases were among Asian respondents (22{middle dot}91 percentage points), the self-employed (15{middle dot}90 percentage points), and 35-44-year-olds (17{middle dot}08 percentage points). In logistic regression models, those moving from employment to unemployment had higher odds of reporting food insecurity relative to furloughed individuals (OR = 2{middle dot}23; 95% CI: 1{middle dot}20-4{middle dot}131) and to the persistently employed (OR=2{middle dot}38; 95% CI: 1{middle dot}33-4{middle dot}27), adjusting for sociodemographic characteristics. Furloughed individuals did not differ significantly in their probability of experiencing food insecurity compared to the persistently employed (OR=1{middle dot}07; 95% CI: 0{middle dot}83 to 1{middle dot}37).\n\nInterpretationFood insecurity has increased substantially in the UK. Steps are needed to provide subsidies or food support to vulnerable groups.\n\nO_TEXTBOXEvidence before this studyWe searched Google Scholar with the terms \"COVID-19\" and \"food insecurity\" and \"UK\"; and \"food insecurity\" and \"UK\" and \"coronavirus\", published between January 1st and October 31st, 2020. One cross-sectional report was identified, which found higher levels of food insecurity in early April 2020 relative to 2018. Importantly, the report relied on items used to measure food insecurity that referred to a 12-month time span in 2018 and then a 30-day time span in April 2020, a potential source of bias for examining changes in population prevalence over time.\n\nAdded value of this studyHere we provide the first longitudinal national probability study that tracks temporal changes in population prevalence of food insecurity several months following the initial COVID-19-related lockdown measures in the UK. The prevalence of food insecurity rose for all socioeconomic and demographic and groups from April to July 2020, but did so for some more than others. Some of the largest increases in food insecurity were among Asian respondents, the self-employed, respondents aged 35-44, and those living in Scotland, London, and the North West of England. At the individual level, losing employment was associated with a higher odds of food insecurity compared to those furloughed under the Coronavirus Job Retention Scheme and the persistently employed. Importantly, furloughed individuals did not differ in their probability of food insecurity relative to the persistently employed.\n\nImplications of all the available evidenceThis study documents an alarming increase in food insecurity in the United Kingdom during the pandemic, with important implications for policy. While Coronavirus the Job Retention Scheme appeared to have conferred some protection, it is clear that not enough has been done to mitigate overall increases food insecurity in the UK. Steps are needed to provide subsidies or food support, especially since during the pandemic emergency food assistance may not be readily accessible. Taken together our results show that, while COVID is first of all a health crisis, it also has potential to become an escalating social and economic crisis if steps are not taken to protect the weak.\n\nC_TEXTBOX", - "category": "public and global health", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.11.11.20220962", @@ -7055,6 +6915,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.11.06.20227108", + "date": "2020-11-07", + "link": "https://medrxiv.org/cgi/content/short/2020.11.06.20227108", + "title": "Primary school staff reflections on school closures due to COVID-19 and recommendations for the future: a national qualitative survey", + "authors": "Emily Marchant; Charlotte Todd; Michaela James; Tom Crick; Russell Dwyer; Sinead Brophy", + "affiliations": "Swansea University; Swansea University; Swansea University; Swansea University; St Thomas Community Primary School; Swansea University", + "abstract": "School closures due to the COVID-19 global pandemic are likely to have a range of negative consequences spanning the domains of child development, education and health, in addition to the widening of inequalities and inequities. Research is required to improve understanding of the impact of school closures on the education, health and wellbeing of pupils and school staff, the challenges posed during reopening and importantly to identify how countries can return to in-school education and to inform policy. This qualitative study aimed to reflect on the perspectives and experiences of primary school staff (pupils aged 3-11) in Wales regarding school closures and the initial reopening of schools and to identify recommendations for the future. A total of 208 school staff completed a national online survey through the HAPPEN primary school network, consisting of questions about school closures (March to June 2020), the phased reopening of schools (June to July 2020) and a return to full-time education. Thematic analysis of survey responses highlighted that primary school staff perceive that gaps in learning, health and wellbeing have increased and inequalities have widened during school closures. Findings from this study identified five recommendations; (i) prioritise the health and wellbeing of pupils and staff; (ii) focus on enabling parental engagement and support; (iii) improve digital competence amongst pupils, teachers and parents; (iv) consider opportunities for smaller class sizes and additional staffing; and (v) improve the mechanism of communication between schools and families, and between government and schools.", + "category": "public and global health", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.11.05.20223289", @@ -7195,6 +7069,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "bioRxiv", + "doi": "10.1101/2020.11.01.362319", + "date": "2020-11-02", + "link": "https://biorxiv.org/cgi/content/short/2020.11.01.362319", + "title": "Robust SARS-CoV-2-specific T-cell immunity is maintained at 6 months following primary infection", + "authors": "Jianmin Zuo; Alex Dowell; Hayden Pearce; Kriti Verma; Heather Long; Jusnara Begum; Felicity Aiano; Zahin Amin-Chowdhury; Bassam Hallis; Lorrain Stapley; Ray Borrow; Ezra Linley; Shazaad Ahmad; Ben Parker; Alex Horsley; Gayatri Amirthalingam; Kevin Brown; Mary E Ramsay; Shamez Ladhani; Paul Moss", + "affiliations": "Institute of Immunology and Immunotherapy, University of Birmingham; Institute of Immunology and Immunotherapy, University of Birmingham; Institute of Immunology and Immunotherapy, University of Birmingham; Institute of Immunology and Immunotherapy, University of Birmingham; Institute of Immunology and Immunotherapy, University of Birmingham; Institute of Immunology and Immunotherapy, University of Birmingham; Immunisation and Countermeasures Division, National Infection Service, PHE Colindale. 61 Colindale Avenue, London NW9 5EQ.; Immunisation and Countermeasures Division, National Infection Service, PHE Colindale. 61 Colindale Avenue, London NW9 5EQ.; Immunoassay Lab, National Infection Service, Porton Down SP4 0JG; Immunoassay Lab, National Infection Service, Porton Down SP4 0JG; Sero-epidemiology Unit, PHE, Manchester Royal Infirmary, Manchester, M13 9WL; Sero-epidemiology Unit, PHE, Manchester Royal Infirmary, Manchester, M13 9WL; Manchester University NHS Foundation Trust; NIHR Manchester Clinical Research Facility, Manchester Royal Infirmary, Oxford Rd, Manchester, M13 9WL; University of Manchester and NIHR Manchester Clinical Research Facility, Manchester University NHS Foundation Trust, Manchester M23 9LT; Immunisation and Countermeasures Division, National Infection Service, PHE Colindale. 61 Colindale Avenue, London NW9 5EQ.; Immunisation and Countermeasures Division, National Infection Service, PHE Colindale. 61 Colindale Avenue, London NW9 5EQ.; Immunisation and Countermeasures Division, National Infection Service, PHE Colindale. 61 Colindale Avenue, London NW9 5EQ.; Immunisation and Countermeasures Division, National Infection Service, PHE Colindale. 61 Colindale Avenue, London NW9 5EQ.; Institute of Immunology and Immunotherapy, University of Birmingham", + "abstract": "The immune response to SARS-CoV-2 is critical in both controlling primary infection and preventing re-infection. However, there is concern that immune responses following natural infection may not be sustained and that this may predispose to recurrent infection. We analysed the magnitude and phenotype of the SARS-CoV-2 cellular immune response in 100 donors at six months following primary infection and related this to the profile of antibody level against spike, nucleoprotein and RBD over the previous six months. T-cell immune responses to SARS-CoV-2 were present by ELISPOT and/or ICS analysis in all donors and are characterised by predominant CD4+ T cell responses with strong IL-2 cytokine expression. Median T-cell responses were 50% higher in donors who had experienced an initial symptomatic infection indicating that the severity of primary infection establishes a setpoint for cellular immunity that lasts for at least 6 months. The T-cell responses to both spike and nucleoprotein/membrane proteins were strongly correlated with the peak antibody level against each protein. The rate of decline in antibody level varied between individuals and higher levels of nucleoprotein-specific T cells were associated with preservation of NP-specific antibody level although no such correlation was observed in relation to spike-specific responses. In conclusion, our data are reassuring that functional SARS-CoV-2-specific T-cell responses are retained at six months following infection although the magnitude of this response is related to the clinical features of primary infection.", + "category": "immunology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.10.29.20222174", @@ -7279,6 +7167,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.10.26.20219576", + "date": "2020-10-27", + "link": "https://medrxiv.org/cgi/content/short/2020.10.26.20219576", + "title": "Impact of the COVID-19 pandemic on remote mental healthcare and prescribing in psychiatry", + "authors": "Rashmi Patel; Jessica Irving; Aimee Brinn; Matthew Broadbent; Hitesh Shetty; Megan Pritchard; Johnny Downs; Robert Stewart; Robert Harland; Philip McGuire", + "affiliations": "King's College London (Institute of Psychiatry, Psychology and Neuroscience), London, UK; King's College London (Institute of Psychiatry, Psychology and Neuroscience), London, UK; King's College London (Institute of Psychiatry, Psychology and Neuroscience), London, UK; South London and Maudsley NHS Foundation Trust, London, UK; South London and Maudsley NHS Foundation Trust, London, UK; South London and Maudsley NHS Foundation Trust, London, UK; King's College London (Institute of Psychiatry, Psychology and Neuroscience), London, UK; King's College London (Institute of Psychiatry, Psychology and Neuroscience), London, UK; South London and Maudsley NHS Foundation Trust, London, UK; King's College London (Institute of Psychiatry, Psychology and Neuroscience), London, UK", + "abstract": "ObjectivesThe recent COVID-19 pandemic has disrupted mental healthcare delivery, with many services shifting from in- person to remote patient contact. We investigated the impact of the pandemic on the use of remote consultation and on the prescribing of psychiatric medications.\n\nDesign and settingThe Clinical Record Interactive Search tool (CRIS) was used to examine de-identified electronic health records (EHRs) of people receiving mental healthcare from the South London and Maudsley (SLaM) NHS Foundation Trust. Data from the period before and after the onset of the pandemic were analysed using linear regression, and visualised using locally estimated scatterplot smoothing (LOESS).\n\nParticipantsAll patients receiving care from SLaM between 7th January 2019 and 20th September 2020 (around 37,500 patients per week).\n\nOutcome measuresO_LIThe number of clinical contacts (in-person, remote or non-attended) with mental healthcare professionals per week\nC_LIO_LIPrescribing of antipsychotic and mood stabiliser medications per week\nC_LI\n\nResultsFollowing the onset of the pandemic, the frequency of in-person contacts was significantly reduced compared to that in the previous year ({beta} coefficient: -5829.6 contacts, 95% CI -6919.5 to -4739.6, p<0.001), while the frequency of remote contacts significantly increased ({beta} coefficient: 3338.5 contacts, 95% CI 3074.4 to 3602.7, p<0.001). Rates of remote consultation were lower in older adults than in working age adults, children and adolescents. Despite this change in the type of patient contact, antipsychotic and mood stabiliser prescribing remained at similar levels.\n\nConclusionsThe COVID-19 pandemic has been associated with a marked increase in remote consultation, particularly among younger patients. However, there was no evidence that this has led to changes in psychiatric prescribing. Nevertheless, further work is needed to ensure that older patients are able to access mental healthcare remotely.", + "category": "psychiatry and clinical psychology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.10.26.20219550", @@ -7363,6 +7265,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.10.15.20208454", + "date": "2020-10-18", + "link": "https://medrxiv.org/cgi/content/short/2020.10.15.20208454", + "title": "Modelling SARS-CoV-2 transmission in a UK university setting", + "authors": "Edward M Hill; Benjamin D Atkins; Matt J Keeling; Michael Tildesley; Louise Dyson", + "affiliations": "University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick", + "abstract": "Around 40% of school leavers in the UK attend university and individual universities generally host thousands of students each academic year. Bringing together these student communities during the COVID-19 pandemic may require strong interventions to control transmission. Prior modelling analyses of SARS-CoV-2 transmission within universities using compartmental modelling approaches suggest that outbreaks are almost inevitable.\n\nWe constructed a network-based model to capture the interactions of a student population in different settings (housing, social and study). For a single academic term of a representative campus-based university, we ran a susceptible-latent-infectious-recovered type epidemic process, parameterised according to available estimates for SARS-CoV-2. We investigated the impact of: adherence to (or effectiveness of) isolation and test and trace measures; room isolation of symptomatic students; and supplementary mass testing.\n\nWith all adhering to test, trace and isolation measures, we found that 22% (7% - 41%) of the student population could be infected during the autumn term, compared to 69% (56% - 76%) when assuming zero adherence to such measures. Irrespective of the adherence to isolation measures, on average a higher proportion of students resident on-campus became infected compared to students resident off-campus. Room isolation generated minimal benefits. Regular mass testing, together with high adherence to isolation and test and trace measures, could substantially reduce the proportion infected during the term compared to having no testing.\n\nOur findings suggest SARS-CoV-2 may readily transmit in a university setting if there is limited adherence to nonpharmaceutical interventions and/or there are delays in receiving test results. Following isolation guidance and effective contact tracing curbed transmission and reduced the expected time an adhering student would spend in isolation.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.10.14.20212555", @@ -7503,20 +7419,6 @@ "author_similarity": 100, "affiliation_similarity": 92 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.10.07.20208918", - "date": "2020-10-09", - "link": "https://medrxiv.org/cgi/content/short/2020.10.07.20208918", - "title": "Cardiovascular drugs and COVID-19 clinical outcomes: a living systematic review and meta-analysis", - "authors": "Innocent Gerald Asiimwe; Sudeep Pushpakom; Richard Turner; Ruwanthi Kolamunnage-Dona; Andrea Jorgensen; Munir Pirmohamed", - "affiliations": "University of Liverpool; University of Liverpool; University of Liverpool; University of Liverpool; University of Liverpool; University of Liverpool", - "abstract": "OBJECTIVETo continually evaluate the rapidly evolving evidence base on the role of cardiovascular drugs in COVID-19 clinical outcomes (susceptibility to infection, hospitalization, hospitalization length, disease severity, and all-cause mortality).\n\nDESIGNLiving systematic review and meta-analysis.\n\nDATA SOURCESEligible publications identified from >500 databases indexed through 31st July 2020 and additional studies from reference lists, with planned continual surveillance for at least two years.\n\nSTUDY SELECTIONObservational and interventional studies that report on the association between cardiovascular drugs and COVID-19 clinical outcomes.\n\nDATA EXTRACTIONSingle-reviewer extraction and quality evaluation (using ROBINS-I), with half the records independently extracted and evaluated by a second reviewer.\n\nRESULTSOf 23,427 titles screened, 175 studies were included in the quantitative synthesis. The most reported drug classes were angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin receptor blockers (ARBs) with ACEI/ARB exposure being associated with higher odds of testing positive for COVID-19 (pooled unadjusted OR 1.15, 95% CI 1.02 to 1.30). Among patients with COVID-19, unadjusted estimates showed that ACEI/ARB exposure was associated with being hospitalized (OR 2.25, 1.70 to 2.98) and having severe disease (OR 1.50, 1.27 to 1.77) but not with the length of hospitalization (mean difference -0.45, -1.33 to 0.43 days) or all-cause mortality (OR 1.25, CI 0.98 to 1.58). However, after adjustment, ACEI/ARB exposure was not associated with testing positive for COVID-19 (pooled adjusted OR 1.01, 0.93 to 1.10), being hospitalized (OR 1.16, 0.80 to 1.68), having severe disease (1.04, 0.76 to 1.42), or all-cause mortality (0.86, 0.64 to 1.15). Similarly, subgroup analyses involving only hypertensive patients revealed that ACEI/ARB exposure was not associated with being hospitalized (OR 0.84, 0.58 to 1.22), disease severity (OR 0.88, 0.68 to 1.14) or all-cause mortality (OR 0.77, 0.54 to 1.12) while it decreased the length of hospitalization (mean difference -0.71, -1.11 to -0.30 days). After adjusting for relevant covariates, other cardiovascular drug classes were mostly not found to be associated with poor COVID-19 clinical outcomes. However, the validity of these findings is limited by a high level of heterogeneity in terms of effect sizes and a serious risk of bias, mainly due to confounding in the included studies.\n\nCONCLUSIONOur comprehensive review shows that ACEI/ARB exposure is associated with COVID-19 outcomes such as susceptibility to infection, severity, and hospitalization in unadjusted analyses. However, after adjusting for potential confounding factors, this association is not evident. Patients on cardiovascular drugs should continue taking their medications as currently recommended. Higher quality evidence in the form of randomized controlled trials will be needed to determine any adverse or beneficial effects of cardiovascular drugs.\n\nPRIMARY FUNDING SOURCENone\n\nSYSTEMATIC REVIEW REGISTRATIONPROSPERO (CRD42020191283)", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "bioRxiv", "doi": "10.1101/2020.10.06.328328", @@ -8595,6 +8497,20 @@ "author_similarity": 94, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.07.12.20151753", + "date": "2020-07-14", + "link": "https://medrxiv.org/cgi/content/short/2020.07.12.20151753", + "title": "COVID-19 incidence and R decreased on the Isle of Wight after the launch of the Test, Trace, Isolate programme", + "authors": "Michelle Kendall; Luke Milsom; Lucie Abeler-Dorner; Chris Wymant; Luca Ferretti; Mark Briers; Chris Holmes; David Bonsall; Johannes Abeler; Christophe Fraser", + "affiliations": "University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Alan Turing Institute; University of Oxford; Alan Turing Institute; University of Oxford; University of Oxford; University of Oxford", + "abstract": "In May 2020 the UK introduced a Test, Trace, Isolate programme in response to the COVID-19 pandemic. The programme was first rolled out on the Isle of Wight and included Version 1 of the NHS contact tracing app. We used COVID-19 daily case data to infer incidence of new infections and estimate the reproduction number R for each of 150 Upper Tier Local Authorities in England, and at the National level, before and after the launch of the programme on the Isle of Wight. We used Bayesian and Maximum-Likelihood methods to estimate R, and compared the Isle of Wight to other areas using a synthetic control method. We observed significant decreases in incidence and R on the Isle of Wight immediately after the launch. These results are robust across each of our approaches. Our results show that the sub-epidemic on the Isle of Wight was controlled significantly more effectively than the sub-epidemics of most other Upper Tier Local Authorities, changing from having the third highest reproduction number R (of 150) before the intervention to the tenth lowest afterwards. The data is not yet available to establish a causal link. However, the findings highlight the need for further research to determine the causes of this reduction, as these might translate into local and national non-pharmaceutical intervention strategies in the period before a treatment or vaccination becomes available.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.07.10.20150524", @@ -8665,6 +8581,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.07.06.20147348", + "date": "2020-07-07", + "link": "https://medrxiv.org/cgi/content/short/2020.07.06.20147348", + "title": "Community prevalence of SARS-CoV-2 in England: Results from the ONS Coronavirus Infection Survey Pilot", + "authors": "Koen B Pouwels; Thomas House; Julie V Robotham; Paul Birrell; Andrew B Gelman; Nikola Bowers; Ian Boreham; Heledd Thomas; James Lewis; Iain Bell; John I Bell; John Newton; Jeremy Farrar; Ian Diamond; Pete Benton; Sarah Walker", + "affiliations": "University of Oxford; University of Manchester; Public Health England; Public Health England; Columbia University; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; Office for National Statistics; Office for National Statistics; University of Oxford", + "abstract": "ObjectiveTo estimate the percentage of individuals infected with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) over time in the community in England and to quantify risk factors.\n\nDesignRepeated cross-sectional surveys of population-representative households with longitudinal follow-up if consent given.\n\nSettingEngland\n\nParticipants34,992 Individuals aged 2 years and over from 16,722 private residential households. Data were collected in a pilot phase of the survey between 26 April and 28 June 2020.\n\nMain outcome measuresPercentage of individuals in the community testing positive for SARS-CoV-2 RNA using throat and nose swabs. Individuals were asked about any symptoms and potential risk factors.\n\nResultsThe percentage of people in private-residential households testing positive for SARS-CoV-2 reduced from 0.32% (95% credible interval (CrI) 0.19% to 0.52%) on 26 April to 0.08% (95% CrI 0.05% to 0.12%) on 28 June, although the prevalence stabilised near the end of the pilot. Factors associated with an increased risk of testing positive included having a job with direct patient contact (relative exposure (RE) 4.06, 95% CrI 2.42 to 6.77)), working outside the home (RE 2.49, 95% CrI 1.39 to 4.45), and having had contact with a hospital (RE 2.20, 95% CrI 1.09 to 4.16 for having been to a hospital individually and RE 1.95, 95% CrI 0.81 to 4.09 for a household member having been to a hospital). In 133 visits where individuals tested positive, 82 (61%, 95% CrI 53% to 69%) reported no symptoms, stably over time.\n\nConclusionThe percentage of SARS-CoV-2 positive individuals declined between 26 April and 28 June 2020. Positive tests commonly occurred without symptoms being reported. Working outside your home was an important risk factor, indicating that continued monitoring for SARS-CoV-2 in the community will be essential for early detection of increases in infections following return to work and other relaxations of control measures.\n\nWhat is already known on this topic- Unprecedented control measures, such as national lockdowns, have been widely implemented to contain the spread of SARS-CoV-2.\n- Previous mass surveillance has been based on data sources such as hospital admission, deaths or self-reported symptoms that do not measure community prevalence of virus directly.\n- Decisions regarding the continued need for social distancing measures in the overall population, specific subgroups and geographic areas heavily rely on accurate and up-to-date information about the number of people and risk factors for testing positive.\n\n\nWhat this study adds- The percentage of individuals from the general community in England testing positive for SARS-CoV-2 clearly declined between 26 April and 28 June 2020 from around one in three 300 to around one in a thousand.\n- Risk factors for testing positive included having a job with direct patient contact, having had (indirect) contact with a hospital in the past 2 weeks, and working outside your home.\n- Positive tests commonly occurred without symptoms being reported and the percentage of individuals with a positive test that reported no symptoms was stable over time.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.07.03.20145912", @@ -9309,20 +9239,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.05.21.20108936", - "date": "2020-05-23", - "link": "https://medrxiv.org/cgi/content/short/2020.05.21.20108936", - "title": "Risk Factors for COVID-19 versus non-COVID-19 related in-hospital and community deaths by Local Authority District in Great Britain", - "authors": "Samuel Paul Leighton; Danielle Jane Leighton; James Herron; Rachel Upthegrove; Jonathan Cavanagh; Georgios Gkoutos; Breda Cullen; Pavan K Mallikarjun", - "affiliations": "University of Glasgow; University of Glasgow; University of Glasgow; University of Birmingham; University of Glasgow; University of Birmingham & Associate Director of Health Data Research UK; University of Glasgow; University of Birmingham", - "abstract": "ObjectivesTo undertake a preliminary hypothesis-generating analysis exploring putative risk factors for coronavirus diseae 2019 (COVID-19) population-adjusted deaths, compared with non-COVID-19 related deaths, at a local authority district (LAD) level in hospital, care homes and at home.\n\nDesignEcological retrospective cohort study\n\nSettingLocal authority districts (LADs) in England, Scotland and Wales (Great Britain (GB)).\n\nParticipantsAll LAD deaths registered by week 16 of 2020.\n\nMain Outcome MeasuresDeath registration where COVID-19 is mentioned as a contributing factor per 100,000 people in all settings, and in i) cares homes, ii) hospitals or iii) home only, in comparison to non-COVID-19 related deaths.\n\nResultsAcross GB by week 16 of 2020, 20,684 deaths had been registered mentioning COVID-19, equivalent to 25.6 per 100,000 people. Significant risk factors for LAD COVID-19 death in comparison to non-COVID-19 related death were air pollution and proportion of the population who were female. Significant protective factors were higher air temperature and proportion of the population who were ex-smokers. Conversely, for all COVID-19 unrelated deaths in comparison to COVID-19 deaths, higher rates of communal living, higher population rates of chronic kidney disease, chronic obstructive pulmonary disease, cerebrovascular disease deaths under 75 and dementia were predictive of death, whereas, higher rates of flight passengers was protective. Looking at individual setttings, the most notable findings in care homes was Scotland being a significant risk factor for COVID-19 related deaths compared to England. For hospital setting, the proportion of the population who were from black and Asian minority ethnic (BAME) groups significantly predicted COVID-19 related death.\n\nConclusionsThis is the first study within GB to assess COVID-19 related deaths in comparison to COVID-19 unrelated deaths across hospital, care homes and home combined. As an ecological study, the results cannot be directly extrapolated to individuals. However, the analysis may be informative for public health policy and protective measures. From our hypothesis-generating analysis, we propose that air pollution is a significant risk factor and high temperature a significant protective factor for COVID-19 related deaths. These factors cannot readily be modelled at an individual level. Scottish local authorities and local authorities with a higher proportion of individuals of BAME origin are potential risk factors for COVID-19 related deaths in care homes and in hospitals, respectively. Altogether, this analysis shows the benefits of access to high quality open data for public information, public health policy and further research.", - "category": "public and global health", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.05.22.20109892", @@ -9659,20 +9575,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.04.28.20083170", - "date": "2020-05-05", - "link": "https://medrxiv.org/cgi/content/short/2020.04.28.20083170", - "title": "Quantifying and mitigating the impact of the COVID-19 pandemic on outcomes in colorectal cancer", - "authors": "Amit Sud; Michael Jones; John Broggio; Stephen Scott; Chey Loveday; Bethany Torr; Alice Garrett; David L. Nicol; Shaman Jhanji; Stephen A. Boyce; Matthew Williams; Georgios Lyratzopoulos; Claire Barry; Elio Riboli; Emma Kipps; Ethna McFerran; Mark Lawler; David C. Muller; Muti Abulafi; Richard Houlston; Clare Ann Turnbull", - "affiliations": "Institute of Cancer Research; Institute of Cancer Research; Public Health England; RM Partners, West London Cancer Alliance; Institute of Cancer Research; Institute of Cancer Research; Institute of Cancer Research; Royal Marsden NHS Foundation Trust; Royal Marsden NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Imperial College; University College London; RM Partners, West London Cancer Alliance; Imperial College London; Royal Marsden NHS Foundation Trust; Queen's University Belfast; Queen's University Belfast; Imperial College London; Croydon Health Services NHS Trust, on behalf of RMP NICE FIT Steering Group; Institute of Cancer Research; Institute of Cancer Research", - "abstract": "BackgroundThe COVID-19 pandemic has caused disruption across cancer pathways for diagnosis and treatment. In England, 32% of colorectal cancer (CRC) is diagnosed via urgent symptomatic referral from primary care, the \"2-week-wait\" (2WW) pathway. Access to routine endoscopy is likely to be a critical bottleneck causing delays in CRC management due to chronic limitation in capacity, acute competition for physician time, and safety concerns.\n\nMethodsWe used age-specific, stage-specific 10 year CRC survival for England 2007-2017 and 2WW CRC cases volumes. We used per-day hazard ratios of CRC survival generated from observational studies of CRC diagnosis-to-treatment interval to model the effect of different durations of per-patient delay. We utilised data from a large London observational study of faecal immunochemical testing (FIT) in symptomatic patients to model FIT-triage to mitigate delay to colonoscopy.\n\nFindingsModest delays result in significant reduction in survival from CRC with a 4-month delay resulting across age groups in [≥]20% reduction in survival in Stage 3 disease and in total over a year, 1,419 attributable deaths across the 11,266 CRC patients diagnosed via the 2WW pathway. FIT triage of >10 ug Hb/g would salvage 1,292/1,419 of the attributable deaths and reduce colonoscopy requirements by >80%. Diagnostic colonoscopy offers net survival in all age groups, providing nosocomial COVID-19 infection rates are kept low (<2{middle dot}5%).\n\nInterpretationTo avoid significant numbers of avoidable deaths from CRC, normal diagnostic and surgical throughput must be maintained. An accrued backlog of cases will present to primary care following release of lockdown, supranormal endoscopy capacity will be required to manage this without undue delays. FIT-triage of symptomatic cases provides a rational approach by which to avoid patient delay and mitigate pressure on capacity in endoscopy. This would also reduce exposure to nosocomial COVID-19 infection, relevant in particular to older patient groups.\n\nFundingBreast Cancer Now, Cancer Research UK, Bobby Moore Fund for Cancer Research, National Institute for Health Research (NIHR).", - "category": "oncology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.04.29.20084111", @@ -9743,6 +9645,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.04.24.20078006", + "date": "2020-04-29", + "link": "https://medrxiv.org/cgi/content/short/2020.04.24.20078006", + "title": "Supplementing the National Early Warning Score (NEWS2) for anticipating early deterioration among patients with COVID-19 infection", + "authors": "Ewan Carr; Rebecca Bendayan; Daniel Bean; Matthew Stammers; Wenjuan Wang; Huayu Zhang; Thomas Searle; Zeljko Kraljevic; Anthony Shek; Hang T T Phan; Walter Muruet; Rishi K Gupta; Anthony J Shinton; Mike Wyatt; Ting Shi; Xin Zhang; Andrew Pickles; Daniel Stahl; Rosita Zakeri; Mahdad Noursadeghi; Kevin O'Gallagher; Matt Rogers; Amos Folarin; Christopher Bourdeaux; Chris McWilliams; Lukasz Roguski; Florina Borca; James Batchelor; Xiaodong Wu; Jiaxing Sun; Ashwin Pinto; Bruce Guthrie; Cormac Breen; Abdel Douiri; Honghan Wu; Vasa Curcin; James T Teo; Ajay Shah; Richard Dobson", + "affiliations": "King's College London; King's College London; King's College London; Clinical Informatics Research Unit, University of Southampton; King's College London; University of Edinburgh; King's College London; King's College London; King's College London; Clinical Informatics Research Unit, University of Southampton; King's College London; University College London; UHS Digital, University Hospital Southampton; University Hospitals Bristol NHS Foundation Trust, Bristol, UK; Usher Institute, University of Edinburgh; Department of Pulmonary and Critical Care Medicine, People's Liberation Army Joint Logistic Support Force 920th Hospital, Yunnan, China; King's College London; King's College London; King's College London; UCL Division of Infection and Immunity, University College London Hospitals NHS Trust; King's College London; University Hospitals Bristol NHS Foundation Trust, Bristol, U.K.; King's College London; University Hospitals Bristol NHS Foundation Trust, Bristol, U.K.; Department of Engineering Mathematics, University of Bristol, Bristol, UK; University College London; University of Southampton; Clinical Informatics Research Unit, University of Southampton, Coxford Rd, Southampton SO16 5AF; Department of Pulmonary and Critical Care Medicine, Shanghai East Hospital, Tongji University, Shanghai, China; Department of Pulmonary and Critical Care Medicine, Shanghai East Hospital, Tongji University, Shanghai, China; UHS Digital, University Hospital Southampton; Usher Institute, University of Edinburgh; King's College London; King's College London; University College London; King's College London; Kings College Hospital NHS Foundation Trust; King's College London; Kings College London", + "abstract": "BackgroundThe National Early Warning Score (NEWS2) is currently recommended in the United Kingdom for risk stratification of COVID outcomes, but little is known about its ability to detect severe cases. We aimed to evaluate NEWS2 for severe COVID outcome and identify and validate a set of routinely-collected blood and physiological parameters taken at hospital admission to improve the score.\n\nMethodsTraining cohorts comprised 1276 patients admitted to Kings College Hospital NHS Foundation Trust with COVID-19 disease from 1st March to 30th April 2020. External validation cohorts included 5037 patients from four UK NHS Trusts (Guys and St Thomas Hospitals, University Hospitals Southampton, University Hospitals Bristol and Weston NHS Foundation Trust, University College London Hospitals), and two hospitals in Wuhan, China (Wuhan Sixth Hospital and Taikang Tongji Hospital). The outcome was severe COVID disease (transfer to intensive care unit or death) at 14 days after hospital admission. Age, physiological measures, blood biomarkers, sex, ethnicity and comorbidities (hypertension, diabetes, cardiovascular, respiratory and kidney diseases) measured at hospital admission were considered in the models.\n\nResultsA baseline model of NEWS2 + age had poor-to-moderate discrimination for severe COVID infection at 14 days (AUC in training sample = 0.700; 95% CI: 0.680, 0.722; Brier score = 0.192; 95% CI: 0.186, 0.197). A supplemented model adding eight routinely-collected blood and physiological parameters (supplemental oxygen flow rate, urea, age, oxygen saturation, CRP, estimated GFR, neutrophil count, neutrophil/lymphocyte ratio) improved discrimination (AUC = 0.735; 95% CI: 0.715, 0.757) and these improvements were replicated across five UK and non-UK sites. However, there was evidence of miscalibration with the model tending to underestimate risks in most sites.\n\nConclusionsNEWS2 score had poor-to-moderate discrimination for medium-term COVID outcome which raises questions about its use as a screening tool at hospital admission. Risk stratification was improved by including readily available blood and physiological parameters measured at hospital admission, but there was evidence of miscalibration in external sites. This highlights the need for a better understanding of the use of early warning scores for COVID.\n\nKO_SCPLOWEYC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWMESSAGESC_SCPLOWO_LIThe National Early Warning Score (NEWS2), currently recommended for stratification of severe COVID-19 disease in the UK, showed poor-to-moderate discrimination for medium-term outcomes (14-day transfer to ICU or death) among COVID-19 patients.\nC_LIO_LIRisk stratification was improved by the addition of routinely-measured blood and physiological parameters routinely at hospital admission (supplemental oxygen, urea, oxygen saturation, CRP, estimated GFR, neutrophil count, neutrophil/lymphocyte ratio) which provided moderate improvements in a risk stratification model for 14-day ICU/death.\nC_LIO_LIThis improvement over NEWS2 alone was maintained across multiple hospital trusts but the model tended to be miscalibrated with risks of severe outcomes underestimated in most sites.\nC_LIO_LIWe benefited from existing pipelines for informatics at KCH such as CogStack that allowed rapid extraction and processing of electronic health records. This methodological approach provided rapid insights and allowed us to overcome the complications associated with slow data centralisation approaches.\nC_LI", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "bioRxiv", "doi": "10.1101/2020.04.28.066977", @@ -9757,20 +9673,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.04.23.20076521", - "date": "2020-04-27", - "link": "https://medrxiv.org/cgi/content/short/2020.04.23.20076521", - "title": "Geo-social gradients in predicted COVID-19 prevalence and severity in Great Britain: results from 2,266,235 users of the COVID-19 Symptoms Tracker app", - "authors": "Ruth Bowyer; Thomas Varsavsky; Carole H Sudre; Benjamin Murray; Maxim Freidin; Darioush Yarand; Sajaysurya Ganesh; Joan Capdevila; Ellen J Thompson; Elco Bakker; M Jorge Cardoso; Richard Davies; Jonathan Wolf; Tim D Spector; Sebastien Ourselin; Claire J Steves; Cristina Menni", - "affiliations": "King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; Zoe Global Limited; Zoe Global Limited; King's College London; Zoe Global Limited; King's College London; King's College London; Zoe Global Limited; King's College London; King's College London; King's College London; King's College London", - "abstract": "Understanding the geographical distribution of COVID-19 through the general population is key to the provision of adequate healthcare services. Using self-reported data from 2,266,235 unique GB users of the COVID Symptom Tracker app, we find that COVID-19 prevalence and severity became rapidly distributed across the UK within a month of the WHO declaration of the pandemic, with significant evidence of \"urban hot-spots\". We found a geo-social gradient associated with disease severity and prevalence suggesting resources should focus on urban areas and areas of higher deprivation. Our results demonstrate use of self-reported data to inform public health policy and resource allocation.", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.04.22.20075663", diff --git a/data/covid/raw-preprints.json b/data/covid/raw-preprints.json index bfdaac21..11c5064e 100644 --- a/data/covid/raw-preprints.json +++ b/data/covid/raw-preprints.json @@ -1,11 +1,493 @@ [ + { + "rel_doi": "10.1101/2023.11.13.23298480", + "rel_title": "Integrating stimulus-organism-response model and theory of planned behavior to explore athletes intention to receive the COVID-19 vaccine booster - A moderated mediation model", + "rel_date": "2023-11-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.13.23298480", + "rel_abs": "This study aims to investigate the factors influencing athletes' intention to receive the COVID-19 vaccine booster in Mainland China by integrating the stimulus-organization-response (SOR) model and theory of planned behavior (TPB) as the theoretical framework. Purposive sampling was used to select respondents from the National Games of the People's Republic of China. Hard-copy questionnaires were utilized to collect data, resulting in 981 valid responses. Descriptive analysis and partial least squares structural equation modeling were used to analyze the data. The findings reveal that athletes' subjective norm and knowledge significantly influence attitude, commitment, and perceived behavioral control. Attitude, commitment, and perceived behavioral control are verified as full mediators between subjective norm, knowledge, and intention to receive the COVID-19 vaccine booster. Knowledge to commitment is the most powerful path to predict athletes' intention to receive the COVID-19 vaccine booster. Motivation moderates the relationships between knowledge, attitude, commitment, and perceived behavioral control. The integrating model's explanatory power is 83.2%. Athletes' knowledge is crucial in shaping a positive attitude, commitment, and perceived control, enhancing their intention to get the COVID-19 vaccine booster.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Wenpeng Zhan", + "author_inst": "Lingnan Normal University" + }, + { + "author_name": "Qianting Deng", + "author_inst": "South China Normal University" + }, + { + "author_name": "Van Bac Nguyen", + "author_inst": "National Taiwan University of Sport" + }, + { + "author_name": "Tran Phan Duc Anh", + "author_inst": "National Taiwan University of Sport" + }, + { + "author_name": "Phan Danh Na", + "author_inst": "National Taiwan University of Sport" + }, + { + "author_name": "An-Shin Shia", + "author_inst": "Lingnan Normal University" + }, + { + "author_name": "Gordon Chih Ming Ku", + "author_inst": "National Taiwan University of Sport" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, + { + "rel_doi": "10.1101/2023.11.13.23298463", + "rel_title": "A SOLUTION TO THE KERMACK AND MCKENDRICK INTEGRO-DIFFERENTIAL EQUATIONS WHICH ACCURATELY PROJECTS COVID-19 CASE DATA USING GOOGLE MOBILITY DATA AS AN INPUT", + "rel_date": "2023-11-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.13.23298463", + "rel_abs": "In this manuscript, we derive a closed form solution to the full Kermack and McKendrick integro-differential equations (Kermack and McKendrick 1927) which we call the KMES. We demonstrate the veracity of the KMES using the Google Residential Mobility Measure to accurately project case data from the Covid 19 pandemic and we derive many useful, but previously unknown, analytical expressions for characterizing and managing an epidemic. These include expressions for the viral load, the final size, the effective reproduction number, and the time to the peak in infections. The KMES can also be cast in the form of a step function system response to the input of new infections; and that response is the time series of total infections. Since the publication of Kermack and McKendricks seminal paper (1927), thousands of authors have utilized the Susceptible, Infected, and Recovered (SIR) approximations; expressions putatively derived from the integro-differential equations to model epidemic dynamics. Implicit in the use of the SIR approximation are the beliefs that there is no closed form solution to the integro-differential equations, and that the approximation is a special case which adequately reproduces the dynamics of the integro-differential equations mapped onto the physical world. However, the KMES demonstrates that the SIR approximations are not adequate representations of the integro-differential equations, and we therefore suggest that the KMES obsoletes the need for the SIR approximations by providing not only a new mathematical perspective, but a new understanding of epidemic dynamics.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Theodore G Duclos", + "author_inst": "Ted Duclos Advisors" + }, + { + "author_name": "Thomas Reichert", + "author_inst": "Entropy Research Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, + { + "rel_doi": "10.1101/2023.11.13.23298464", + "rel_title": "Assessing the Impact of Mask Mandates on SARS-CoV-2 Transmission: A Case Study of Utah", + "rel_date": "2023-11-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.13.23298464", + "rel_abs": "Background: Throughout the COVID-19 pandemic, the effectiveness of face masks mandates has been intensely debated. Many methods have been used to demonstrate mask effectiveness, including one that compares the change in reproduction number following implementing and removing face mask mandates. Methods: Using data from Utah, we calculated the effect of mask mandates (EFm) in each local health district from before and after three key mandates: the Salt Lake and Summit County (SLSC) mask mandates enacted; the Utah statewide mask mandate enacted; and the Utah statewide mandate was lifted. Results: We found that most counties had a reduction in the growth rate of cases following the mandates. There were reductions in EFm in many counties after the introduction of the SLSC mask mandates and a more widespread reduction in EFm across the state following the statewide mandate. Lifting the mandates, many counties across the states saw an increase in EFm. Conclusion: Our data show mask mandates were an effective way to reduce transmission both within the jurisdiction they were enacted and in neighboring jurisdictions. We provide evidence to support mask mandates as a way to prevent transmission to be better equipped to respond to future pandemics.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Alicia C Horn", + "author_inst": "University of Utah" + }, + { + "author_name": "Holly E Shoemaker", + "author_inst": "University of Utah" + }, + { + "author_name": "Lindsay T Keegan", + "author_inst": "University of Utah" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, + { + "rel_doi": "10.1101/2023.11.10.566587", + "rel_title": "Insights into B Cell and Antibody Kinetics Against SARS-CoV-2 Variants Using Mathematical Modelling", + "rel_date": "2023-11-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.10.566587", + "rel_abs": "B cells and antibodies are crucial in protecting against infections like SARS-CoV-2. However, antibody levels decline after infection or vaccination, reducing defences against future SARS-CoV-2 infections. To understand antibody production and decline, we developed a mathematical model that predicts germinal center B cell, long-lived plasma cell, memory B cell, and antibody dynamics. Our focus was on B cell activation and antibody generation following both primary and secondary SARS-CoV-2 infections. Aligning our model with clinical data, we adjusted antibody production rates for germinal center B cells and plasma B cells during primary and secondary infections. We also assessed antibody neutralization against Delta and Omicron variants post-primary and secondary exposure. Our findings showed reduced neutralization against Omicron due to its immune evasion. In primary and secondary exposures to Delta and Omicron, our predictions indicated enhanced antibody neutralization in the secondary response within a year of the primary response. We also explored waning immunity, demonstrating how B cell kinetics affect viral neutralization post-primary infection. This study enhances our understanding of humoral immunity to SARS-CoV-2 and can predict antibody dynamics post-infection or vaccination.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Suzan Farhang-Sardroodi", + "author_inst": "University of Manitoba" + }, + { + "author_name": "Xiaoyan Deng", + "author_inst": "University of Manitoba" + }, + { + "author_name": "Stephanie Portet", + "author_inst": "University of Manitoba" + }, + { + "author_name": "Julien Arino", + "author_inst": "University of Manitoba" + }, + { + "author_name": "Morgan Craig", + "author_inst": "University of Montreal" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "immunology" + }, + { + "rel_doi": "10.1101/2023.11.10.566576", + "rel_title": "The SARS-CoV-2 Omicron sub-variant BA.2.86 is attenuated in hamsters", + "rel_date": "2023-11-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.10.566576", + "rel_abs": "SARS-CoV-2 variants have emerged throughout the COVID-19 pandemic. There is a need to risk-assess newly emerged variants in near \"real-time\" to estimate their potential threat to public health. The recently emerged Omicron sub-variant BA.2.86 raised concerns as it carries a high number of mutations compared to its predecessors. Here, we assessed the virulence of BA.2.86 in hamsters. We compared the pathogenesis of BA.2.86 and BA.2.75, as the latter is one of the most virulent Omicron sub-variants in this animal model. Using digital pathology pipelines, we quantified the extent of pulmonary lesions measuring T cell and macrophage infiltrates, in addition to alveolar epithelial hyperplasia. We also assessed body weight loss, clinical symptoms, virus load in oropharyngeal swabs, and virus replication in the respiratory tract. Our data show that BA.2.86 displays an attenuated phenotype in hamsters, suggesting that it poses no greater risk to public health than its parental Omicron sub-variants.\n\nArticle summary lineThe newly emerged Omicron sub-variant BA.2.86 is attenuated in hamsters.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Vanessa Herder", + "author_inst": "MRC-University of Glasgow Centre for Virus Research" + }, + { + "author_name": "Diogo Correa Mendonca", + "author_inst": "MRC-University of Glasgow Centre for Virus Research" + }, + { + "author_name": "Nicole Upfold", + "author_inst": "MRC-University of Glasgow Centre for Virus Research" + }, + { + "author_name": "Wilhelm Furnon", + "author_inst": "MRC-University of Glasgow Centre for Virus Research" + }, + { + "author_name": "Karen Kerr", + "author_inst": "MRC-University of Glasgow Centre for Virus Research" + }, + { + "author_name": "Georgios Ilia", + "author_inst": "MRC-University of Glasgow Centre for Virus Research" + }, + { + "author_name": "Jay Allan", + "author_inst": "MRC-University of Glasgow Centre for Virus Research" + }, + { + "author_name": "Alex Sigal", + "author_inst": "Africa Health Research Institute, University of KwaZulu-Natal" + }, + { + "author_name": "Arvind H. Patel", + "author_inst": "MRC-University of Glasgow Centre for Virus Research" + }, + { + "author_name": "Massimo Palmarini", + "author_inst": "MRC-University of Glasgow Centre for Virus Research" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, + { + "rel_doi": "10.1101/2023.11.11.566634", + "rel_title": "Recreating the Biological Steps of Viral Infection on a Bioelectronic Platform to Profile Viral Variants of Concern", + "rel_date": "2023-11-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.11.566634", + "rel_abs": "Viral mutation rates frequently outpace the development of technologies used to detect and identify harmful variants; for SARS Coronavirus-2 (SARS-CoV-2), these are called variants of concern (VOC). Given the continual emergence of VOC, there is a critical need to develop platforms that can identify the presence of a virus and readily identify its propensity for infection. We present an electronic biomembrane sensing platform that recreates the multifaceted and sequential biological cues that give rise to distinct SARS-CoV-2 virus host cell entry pathways and reports the progression of entry steps of these pathways as electrical signals. Within these electrical signals, two necessary entry processes mediated by the viral Spike protein, virus binding and membrane fusion, can be distinguished. Remarkably, we find that closely related VOC exhibit distinct fusion signatures that correlate with trends reported in cell-based infectivity assays, allowing us to report quantitative differences in fusion characteristics among them that inform their infectivity potentials. This cell-free biomimetic infection platform also has a virus-free option that equally reports infectivity potential of the Spike proteins. We used SARS-CoV-2 as our prototype, but we anticipate that this platform will extend to other enveloped viruses and cell lines to quantifiably explore virus/host interactions. This advance should aid in faster determination of entry characteristics and fusogenicities of future VOC, necessary for rapid response.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Zhongmou Chao", + "author_inst": "Cornell University" + }, + { + "author_name": "Ekaterina Selivanovitch", + "author_inst": "Cornell University" + }, + { + "author_name": "Konstantinos Kallitsis", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Zixuan Lu", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Ambika Pachaury", + "author_inst": "Cornell University" + }, + { + "author_name": "R\u00f3is\u00edn Owens", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Susan Daniel", + "author_inst": "Cornell University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioengineering" + }, + { + "rel_doi": "10.1101/2023.11.10.566497", + "rel_title": "Single Nucleus RNA Sequencing of Remnant Kidney Biopsies and Urine Cell RNA Sequencing Reveal Cell Specific Markers of Covid-19 Acute Kidney Injury", + "rel_date": "2023-11-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.10.566497", + "rel_abs": "Acute kidney injury (AKI) in COVID-19 patients is associated with high mortality and morbidity. Critically ill COVID-19 patients are at twice the risk of in-hospital mortality compared to non-COVID AKI patients. We know little about the cell-specific mechanism in the kidney that contribute to worse clinical outcomes in these patients. New generation single cell technologies have the potential to provide insights into physiological states and molecular mechanisms in COVID-AKI. One of the key limitations is that these patients are severely ill posing significant risks in procuring additional biopsy tissue. We recently generated single nucleus RNA-sequencing data using COVID-AKI patient biopsy tissue as part of the human kidney atlas. Here we describe this approach in detail and report deeper comparative analysis of snRNAseq of 4 COVID-AKI, 4 reference, and 6 non-COVID-AKI biopsies. We also generated and analyzed urine transcriptomics data to find overlapping COVID-AKI-enriched genes and their corresponding cell types in the kidney from snRNA-seq data. We identified all major and minor cell types and states by using by using less than a few cubic millimeters of leftover tissue after pathological workup in our approach. Differential expression analysis of COVID-AKI biopsies showed pathways enriched in viral response, WNT signaling, kidney development, and cytokines in several nephron epithelial cells. COVID-AKI profiles showed a much higher proportion of altered TAL cells than non-COVID AKI and the reference samples. In addition to kidney injury and fibrosis markers indicating robust remodeling we found that, 17 genes overlap between urine cell COVID-AKI transcriptome and the snRNA-seq data from COVID-AKI biopsies. A key feature was that several of the distal nephron and collecting system cell types express these markers. Some of these markers have been previously observed in COVID-19 studies suggesting a common mechanism of injury and potentially the kidney as one of the sources of soluble factors with a potential role in disease progression.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Reetika Ghag", + "author_inst": "Washington University in St Louis" + }, + { + "author_name": "Madhurima Kaushal", + "author_inst": "Washington University in St. Louis" + }, + { + "author_name": "Gerald Nwanne", + "author_inst": "Washington University in St. Louis" + }, + { + "author_name": "Amanda Knoten", + "author_inst": "Washington University in St Louis" + }, + { + "author_name": "Krzysztof Kiryluk", + "author_inst": "Columbia University" + }, + { + "author_name": "Avi Rosenberg", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Steven Menez", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Serena M Bagnasco", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "C John Sperati", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Mohamed G Atta", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Joseph P Gaut", + "author_inst": "Washington University St. Louis" + }, + { + "author_name": "James C Williams Jr.", + "author_inst": "Indiana University" + }, + { + "author_name": "Tarek M El-Achkar", + "author_inst": "Indiana University" + }, + { + "author_name": "Lois J Arend", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Chirag R Parikh", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Sanjay Jain", + "author_inst": "Washington University in St Louis" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "genetics" + }, + { + "rel_doi": "10.1101/2023.11.12.23298174", + "rel_title": "Application of the Fluctuation Test to the data of Morbidity and Mortality by COVID-19 in China 2020-2023", + "rel_date": "2023-11-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.12.23298174", + "rel_abs": "In this work the Luria and Delbruck Fluctuation Test was applied to the data of Morbidity and Mortality by COVID-19 in China from January 2020 to August 2023. Three types of data were used: es.statista.com, datosmacro.expansion.com and larepublica.co without modification, but trying to avoid and justify the anomalies and inconsistencies observed. The methods originally used to establish the interactions of two populations were evaluated: the viral population with that of its host and the drift of both organisms. Only the fluctuations of the weekly Variance of daily increase of Cases (Morbidity) and of the weekly Variance of daily increase of Deaths (Mortality) were studied. The results showed that the Fluctuation Test is applicable to the selected data from China and other data from India, Japan and South Korea, used as controls. The study was separated into two periods: a first initial period from January 2020 to September 2021 and a second final period from October 2021 to August 2023. Results were obtained for Morbidity and Mortality that relate the fluctuations of the first with the fluctuations of the second. However, it was possible to detect some anomalies and uncertainties that were possibly derived from inconsistencies in the original data. A repeated fluctuation was observed in the boreal winter in January, February and March of each one of the year studied. A clear decrease in fluctuation was detected in that period in 2021 that could be attributed to the strict confinement during the quarantine in China between 2020 and 2021. Massive, extensive and intensive vaccinations failed to completely eliminate the most important fluctuations. In this work we tried to correlate the appearance of some virus variants with the fluctuations. The most relevant results of said correlation are presented. With the results of this work, the animal origin cannot be confirmed nor can the human or laboratory origin of the SARS CoV-2 virus that caused the initial emerging infection, be ruled out. However, it was concluded that this method could be used to search for clues about its origin. One of these keys is the comparison of the result of the first important fluctuation in the boreal winter of 2020 in each of the countries studied as controls: India, Japan and South Korea. The comparison of this result with the first fluctuation of China for that same period could give clues about the origin of the virus.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Anyi Y Lopez", + "author_inst": "PQM, Facultad de Farmacia y Bionalisis, ULA" + }, + { + "author_name": "Maria A Fernandez", + "author_inst": "PQM, Facultad de Farmacia y Bionalisis, ULA" + }, + { + "author_name": "Hilda C Grassi", + "author_inst": "Seccion de Biotecnologia, Instituto de Investigaciones, Facultad de Farmacia y Bioanalisis, ULA" + }, + { + "author_name": "Efren J Andrades", + "author_inst": "Seccion de Biotecnologia, Instituto de Investigaciones, Facultad de Farmacia y Bioanalisis, ULA" + }, + { + "author_name": "Jesus E Andrades", + "author_inst": "Departamento de Ordenacion de Cuencas, Facultad de Ciencias Forestales y Ambientales, ULA" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, + { + "rel_doi": "10.1101/2023.11.10.23298322", + "rel_title": "Synergistic Role of NK Cells and Monocytes in Promoting Atherogenesis in Severe COVID-19 Patients.", + "rel_date": "2023-11-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.10.23298322", + "rel_abs": "Clinical data demonstrate an increased predisposition to cardiovascular disease (CVD) following severe COVID-19 infection. This may be driven by a dysregulated immune response associated with severe disease. Monocytes and vascular tissue resident macrophages play a critical role in atherosclerosis, the main pathology leading to ischemic CVD. Natural killer (NK) cells are a heterogenous group of cells that are critical during viral pathogenesis and are known to be dysregulated during severe COVID-19 infection. Their role in atherosclerotic cardiovascular disease has recently been described. However, the contribution of their altered phenotypes to atherogenesis following severe COVID-19 infection is unknown. We demonstrate for the first time that during and after severe COVID-19, circulating proinflammatory monocytes and activated NK cells act synergistically to increase uptake of oxidized low-density lipoprotein (Ox-LDL) into vascular tissue with subsequent foam cell generation leading to atherogenesis despite recovery from acute infection. Our data provide new insights, revealing the roles of monocytes/macrophages, and NK cells in COVID-19-related atherogenesis.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Manuja Gunasena", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Mario Alles", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Yasasvi Wijewantha", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Will Mulhern", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Emily Bowman", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Janelle Gabriel", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Aaren Kettelhut", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Amrendra Kumar", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Krishanthi Weragalaarachchi", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Dhanuja Kasturiratna", + "author_inst": "Northern Kentucky University" + }, + { + "author_name": "Jeffrey C Horowitz", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Scott Scrape", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Sonal R Pannu", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Shan-Lu Liu", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Anna Vilgelm", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Saranga Wijeratne", + "author_inst": "Nationwide Children's Hospital" + }, + { + "author_name": "Joseph S Bednash", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Thorsten Demberg", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Nicholas T Funderburg", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Namal Liyanage", + "author_inst": "The Ohio State University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, + { + "rel_doi": "10.1101/2023.11.10.23298369", + "rel_title": "Clinical and Economic impact of updated Fall 2023 COVID-19 vaccines in the Immunocompromised Population in Canada", + "rel_date": "2023-11-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.10.23298369", + "rel_abs": "Background\n\nImmunocompromised (IC) individuals are at increased risk of COVID-19 infection-related severe outcomes. Moderna and Pfizer-BioNTech COVID-19 mRNA vaccines are available in Canada, and differences in vaccine effectiveness (VE) have been found between the two in IC individuals. The objective of this analysis was to compare the clinical and economic impact of a Moderna XBB.1.5 updated COVID-19 mRNA Fall 2023 vaccine to a Pfizer-BioNTech XBB.1.5 updated COVID-19 mRNA Fall 2023 vaccine in Canadian IC individuals aged [≥]18 years.\n\nMethodsA static decision-analytic model estimated the number of COVID-19 infections, hospitalizations, deaths, and resulting quality-adjusted life years (QALYs) over a one-year time horizon (September 2023-August 2024) in the Canadian IC adult population (n=894,580). Costs associated with COVID-19 infection were estimated from health care and societal perspectives. The predicted VE of the updated Moderna vaccine was based on prior variant versions, which were well-matched to the circulating variant. Pfizer-BioNTech VE was calculated based on a meta-analysis of comparative effectiveness between both vaccines (relative risk for Moderna vaccine: infection=0.85 [95%CI 0.75-0.97], hospitalization=0.88 [95%CI 0.79-0.97]). The model combined VE estimates with COVID-19 incidence and probability of COVID-19 related severe outcomes. Sensitivity analyses tested the impact of uncertainty surrounding incidence, hospitalization and mortality rates, costs, and QALYs.\n\nResultsGiven the expected higher VE against infection and hospitalizations with the Moderna Fall 2023 vaccine, its use is predicted to prevent an additional 2,411 infections (3.6%), 275 hospitalizations (3.7%), and 47 deaths (4.0%) compared to the Pfizer-BioNTech Fall 2023 vaccine, resulting in 330 QALYs gained, and savings of $7.4M in infection treatment costs, and $0.9M in productivity loss costs. Results were most sensitive to variations in VE parameters, specifically the relative risk of infection and hospitalizations between the vaccines, and waning rates.\n\nConclusionsIf the Moderna and Pfizer-BioNTech Fall 2023 vaccines protect against infection and hospitalizations similar to previous vaccines, using the Moderna Fall 2023 vaccine would result in substantial public health benefits in IC individuals, as well as provide health care and societal cost savings.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Amy Lee", + "author_inst": "Quadrant Health Economics" + }, + { + "author_name": "Kavisha Jayasundara", + "author_inst": "Moderna BioPharma Canada" + }, + { + "author_name": "Michele Kohli", + "author_inst": "Quadrant Health Economics Inc." + }, + { + "author_name": "Michael Maschio", + "author_inst": "Quadrant Health Economics" + }, + { + "author_name": "Kelly Fust", + "author_inst": "Quadrant Health Economics" + }, + { + "author_name": "Keya Joshi", + "author_inst": "Moderna, Inc." + }, + { + "author_name": "Nicolas Van de Velde", + "author_inst": "Moderna, Inc." + }, + { + "author_name": "Ekkehard Beck", + "author_inst": "Moderna, Inc." + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2023.11.09.23298266", "rel_title": "Post-Vaccination Syndrome: A Descriptive Analysis of Reported Symptoms and Patient Experiences After Covid-19 Immunization", "rel_date": "2023-11-10", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.09.23298266", - "rel_abs": "Introduction: A chronic post-vaccination syndrome (PVS) after covid-19 vaccination has been reported but has yet to be well characterized. Methods: We included 241 individuals aged 18 and older who self-reported PVS after covid-19 vaccination and who joined the online Yale Listen to Immune, Symptom and Treatment Experiences Now (LISTEN) Study from May 2022 to July 2023. We summarized their demographics, health status, symptoms, treatments tried, and overall experience. Results: The median age of participants was 46 years (interquartile range [IQR]: 38 to 56), with 192 (80%) identifying as female, 209 (87%) as non-Hispanic White, and 211 (88%) from the United States. Among these participants with PVS, 127 (55%) had received the BNT162b2 [Pfizer-BioNTech] vaccine, and 86 (37%) received the mRNA-1273 [Moderna] vaccine. The median time from the day of index vaccination to symptom onset was three days (IQR: 1 day to 8 days). The time from vaccination to symptom survey completion was 595 days (IQR: 417 to 661 days). The median Euro-QoL visual analogue scale score was 50 (IQR: 39 to 70). The five most common symptoms were exercise intolerance (71%), excessive fatigue (69%), numbness (63%), brain fog (63%), and neuropathy (63%). In the week before survey completion, participants reported feeling unease (93%), fearfulness (82%), and overwhelmed by worries (81%), as well as feelings of helplessness (80%), anxiety (76%), depression (76%), hopelessness (72%), and worthlessness (49%) at least once. Participants reported a median of 20 (IQR: 13 to 30) interventions to treat their condition. Conclusions: In this study, individuals who reported PVS after covid-19 vaccination had low health status, high symptom burden, and high psychosocial stress despite trying many treatments. There is a need for continued investigation to understand and treat this condition.", + "rel_abs": "IntroductionA chronic post-vaccination syndrome (PVS) after covid-19 vaccination has been reported but has yet to be well characterized.\n\nMethodsWe included 241 individuals aged 18 and older who self-reported PVS after covid-19 vaccination and who joined the online Yale Listen to Immune, Symptom and Treatment Experiences Now (LISTEN) Study from May 2022 to July 2023. We summarized their demographics, health status, symptoms, treatments tried, and overall experience.\n\nResultsThe median age of participants was 46 years (interquartile range [IQR]: 38 to 56), with 192 (80%) identifying as female, 209 (87%) as non-Hispanic White, and 211 (88%) from the United States. Among these participants with PVS, 127 (55%) had received the BNT162b2 [Pfizer-BioNTech] vaccine, and 86 (37%) received the mRNA-1273 [Moderna] vaccine. The median time from the day of index vaccination to symptom onset was three days (IQR: 1 day to 8 days). The time from vaccination to symptom survey completion was 595 days (IQR: 417 to 661 days). The median Euro-QoL visual analogue scale score was 50 (IQR: 39 to 70). The five most common symptoms were exercise intolerance (71%), excessive fatigue (69%), numbness (63%), brain fog (63%), and neuropathy (63%). In the week before survey completion, participants reported feeling unease (93%), fearfulness (82%), and overwhelmed by worries (81%), as well as feelings of helplessness (80%), anxiety (76%), depression (76%), hopelessness (72%), and worthlessness (49%) at least once. Participants reported a median of 20 (IQR: 13 to 30) interventions to treat their condition.\n\nConclusionsIn this study, individuals who reported PVS after covid-19 vaccination had low health status, high symptom burden, and high psychosocial stress despite trying many treatments. There is a need for continued investigation to understand and treat this condition.", "rel_num_authors": 20, "rel_authors": [ { @@ -100,7 +582,7 @@ "rel_date": "2023-11-10", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.09.23298305", - "rel_abs": "Background: The COVID-19 pandemic affected cancer screening, diagnosis and treatment pathways. This study examined the impact of the pandemic on incidence and trends of endocrine treatments in patients with breast or prostate cancer; and endocrine treatment-related side-effects. Methods: Population-based cohort study using UK primary care Clinical Practice Research Datalink (CPRD) GOLD database. There were 13,701 newly diagnosed breast cancer patients and 12,221 prostate cancer patients with [≥]1-year data availability since diagnosis between January 2017-June 2022. Incidence rates (IR) and incidence rate ratios (IRR) were calculated across multiple time periods before and after lockdown to examine the impact of changing social restrictions on endocrine treatments and treatment-related outcomes, including osteopenia, osteoporosis and bisphosphonate prescriptions. Results: In patients with breast cancer, aromatase inhibitor prescriptions increased during lockdown compared to pre-pandemic (IRR: 1.22 [95% Confidence Interval: 1.11-1.34]), followed by a decrease post-first lockdown (IRR: 0.79 [95%CI: 0.69-0.89]). In patients with prostate cancer, first-generation antiandrogen prescriptions increased compared to pre-pandemic (IRR: 1.23 [95% CI: 1.08-1.4]). For breast cancer patients on aromatase inhibitors, diagnoses of osteopenia, osteoporosis and bisphosphonate prescriptions were reduced across all lockdown periods compared to pre-pandemic (IRR range: 0.31-0.62). Conclusion: During the first two years of the pandemic, newly diagnosed breast and prostate cancer patients were prescribed more endocrine treatments compared to pre-pandemic, due to restrictions on hospital procedures replacing surgeries with bridging therapies. But breast cancer patients had fewer diagnoses of osteopenia and osteoporosis, and bisphosphonate prescriptions. These patients should be followed up in the coming years for signs of bone thinning. Evidence of poorer management of treatment-related side-effects will allow us to determine whether there is a need to better allocate resources to patients at high risk for bone-related complications.", + "rel_abs": "BackgroundThe COVID-19 pandemic affected cancer screening, diagnosis and treatment pathways. This study examined the impact of the pandemic on incidence and trends of endocrine treatments in patients with breast or prostate cancer; and endocrine treatment-related side-effects.\n\nMethodsPopulation-based cohort study using UK primary care Clinical Practice Research Datalink (CPRD) GOLD database. There were 13,701 newly diagnosed breast cancer patients and 12,221 prostate cancer patients with [≥]1-year data availability since diagnosis between January 2017-June 2022. Incidence rates (IR) and incidence rate ratios (IRR) were calculated across multiple time periods before and after lockdown to examine the impact of changing social restrictions on endocrine treatments and treatment-related outcomes, including osteopenia, osteoporosis and bisphosphonate prescriptions.\n\nResultsIn patients with breast cancer, aromatase inhibitor prescriptions increased during lockdown compared to pre-pandemic (IRR: 1.22 [95% Confidence Interval: 1.11-1.34]), followed by a decrease post-first lockdown (IRR: 0.79 [95%CI: 0.69-0.89]). In patients with prostate cancer, first-generation antiandrogen prescriptions increased compared to pre-pandemic (IRR: 1.23 [95% CI: 1.08-1.4]). For breast cancer patients on aromatase inhibitors, diagnoses of osteopenia, osteoporosis and bisphosphonate prescriptions were reduced across all lockdown periods compared to pre-pandemic (IRR range: 0.31-0.62).\n\nConclusionDuring the first two years of the pandemic, newly diagnosed breast and prostate cancer patients were prescribed more endocrine treatments compared to pre-pandemic, due to restrictions on hospital procedures replacing surgeries with bridging therapies. But breast cancer patients had fewer diagnoses of osteopenia and osteoporosis, and bisphosphonate prescriptions. These patients should be followed up in the coming years for signs of bone thinning. Evidence of poorer management of treatment-related side-effects will allow us to determine whether there is a need to better allocate resources to patients at high risk for bone-related complications.", "rel_num_authors": 10, "rel_authors": [ { @@ -155,7 +637,7 @@ "rel_date": "2023-11-10", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.10.23298290", - "rel_abs": "Abstract Introduction: The aim of this study was to assess the possible extent of bias due to violation of a core assumption (event-dependent exposures) when using self-controlled designs to analyse the association between COVID-19 vaccines and myocarditis. Methods: We used data from five European databases (Spain: BIFAP, FISABIO VID, and SIDIAP; Italy: ARS-Tuscany; England: CPRD Aurum) converted to the ConcePTION Common Data Model. Individuals who experienced both myocarditis and were vaccinated against COVID-19 between 1 September 2020 and the end of data availability in each country were included. We compared a self-controlled risk interval study (SCRI) using a pre-vaccination control window, an SCRI using a post-vaccination control window, a standard SCCS and an extension of the SCCS designed to handle violations of the assumption of event-dependent exposures. Results: We included 1,757 cases of myocarditis. In unadjusted analyses, agreement between study designs varied by vaccine brand. There was good agreement between all designs for AstraZeneca and Pfizer, but for Moderna we found harmful incidence rate ratios (IRR) using the standard and extended SCCS (standard SCCS: IRR = 3.12, 95%CI = 1.53, 6.40; extended SCCS: IRR = 2.43, 95%CI = 1.11, 5.33) compared with no association with the SCRIs (SCRI-pre: IRR = 0.60, 95%CI = 0.27, 1.33; SCRI-post: IRR = 0.86, 95%CI = 0.34, 2.19), although confidence intervals were wide. There was very good agreement between all designs for the unadjusted second dose analyses, confirming the known harmful association between the second dose of Moderna and Pfizer vaccines and myocarditis. Conclusions: In the context of the known association between COVID-19 vaccines and myocarditis, we have demonstrated that two forms of SCRI and two forms of SCCS led to largely comparable results, possibly because of limited violation of the assumption of event-dependent exposures.", + "rel_abs": "IntroductionThe aim of this study was to assess the possible extent of bias due to violation of a core assumption (event-dependent exposures) when using self-controlled designs to analyse the association between COVID-19 vaccines and myocarditis.\n\nMethodsWe used data from five European databases (Spain: BIFAP, FISABIO VID, and SIDIAP; Italy: ARS-Tuscany; England: CPRD Aurum) converted to the ConcePTION Common Data Model. Individuals who experienced both myocarditis and were vaccinated against COVID-19 between 1 September 2020 and the end of data availability in each country were included. We compared a self-controlled risk interval study (SCRI) using a pre-vaccination control window, an SCRI using a post-vaccination control window, a standard SCCS and an extension of the SCCS designed to handle violations of the assumption of event-dependent exposures.\n\nResultsWe included 1,757 cases of myocarditis. In unadjusted analyses, agreement between study designs varied by vaccine brand. There was good agreement between all designs for AstraZeneca and Pfizer, but for Moderna we found harmful incidence rate ratios (IRR) using the standard and extended SCCS (standard SCCS: IRR = 3.12, 95%CI = 1.53 - 6.40; extended SCCS: IRR = 2.43, 95%CI = 1.11 - 5.33) compared with no association with the SCRIs (SCRI-pre: IRR = 0.60, 95%CI = 0.27 - 1.33; SCRI-post: IRR = 0.86, 95%CI = 0.34 - 2.19), although confidence intervals were wide. There was very good agreement between all designs for the unadjusted second dose analyses, confirming the known harmful association between the second dose of Moderna and Pfizer vaccines and myocarditis.\n\nConclusionsIn the context of the known association between COVID-19 vaccines and myocarditis, we have demonstrated that two forms of SCRI and two forms of SCCS led to largely comparable results, possibly because of limited violation of the assumption of event-dependent exposures.", "rel_num_authors": 21, "rel_authors": [ { @@ -254,7 +736,7 @@ "rel_date": "2023-11-10", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.09.23298162", - "rel_abs": "Background In patients with COVID-19 requiring supplemental oxygen, dexamethasone reduces acute severity and improves survival, but longer-term effects are unknown. We hypothesised that systemic corticosteroid administration during acute COVID-19 would be associated with improved health-related quality of life (HRQoL) one year after discharge. Methods Adults admitted to hospital between February 2020 and March 2021 for COVID-19 and meeting current guideline recommendations for dexamethasone treatment were included using two prospective UK cohort studies. HRQoL, assessed by EQ-5D-5L utility index, pre-hospital and one year after discharge were compared between those receiving corticosteroids or not after propensity weighting for treatment. Secondary outcomes included patient reported recovery, physical and mental health status, and measures of organ impairment. Sensitivity analyses were undertaken to account for survival and selection bias. Findings In 1,888 participants included in the primary analysis, 1,149 received corticosteroids. There was no between-group difference in EQ-5D-5L utility index at one year (mean difference 0.004, 95% CI: -0.026 to 0.034, p = 0.77). A similar reduction in EQ-5D-5L was seen at one year between corticosteroid exposed and non-exposed groups (mean (SD) change -0.12 (0.22) vs -0.11 (0.22), p = 0.32). Overall, there were no differences in secondary outcome measures. After sensitivity analyses modelled using a larger cohort of 109,318 patients admitted to hospital with COVID-19, EQ-5D-5L utility index at one year remained similar between the two groups. Interpretation Systemic corticosteroids for acute COVID-19 have no impact on the large reduction in HRQoL one year after hospital discharge. Treatments to address this are urgently needed.", + "rel_abs": "BackgroundIn patients with COVID-19 requiring supplemental oxygen, dexamethasone reduces acute severity and improves survival, but longer-term effects are unknown. We hypothesised that systemic corticosteroid administration during acute COVID-19 would be associated with improved health-related quality of life (HRQoL) one year after discharge.\n\nMethodsAdults admitted to hospital between February 2020 and March 2021 for COVID-19 and meeting current guideline recommendations for dexamethasone treatment were included using two prospective UK cohort studies. HRQoL, assessed by EQ-5D-5L utility index, pre-hospital and one year after discharge were compared between those receiving corticosteroids or not after propensity weighting for treatment. Secondary outcomes included patient reported recovery, physical and mental health status, and measures of organ impairment. Sensitivity analyses were undertaken to account for survival and selection bias.\n\nFindingsIn 1,888 participants included in the primary analysis, 1,149 received corticosteroids. There was no between-group difference in EQ-5D-5L utility index at one year (mean difference 0.004, 95% CI: -0.026 to 0.034, p = 0.77). A similar reduction in EQ-5D-5L was seen at one year between corticosteroid exposed and non-exposed groups (mean (SD) change -0.12 (0.22) vs -0.11 (0.22), p = 0.32). Overall, there were no differences in secondary outcome measures. After sensitivity analyses modelled using a larger cohort of 109,318 patients admitted to hospital with COVID-19, EQ-5D-5L utility index at one year remained similar between the two groups.\n\nInterpretationSystemic corticosteroids for acute COVID-19 have no impact on the large reduction in HRQoL one year after hospital discharge. Treatments to address this are urgently needed.\n\nTake home messageSystemic corticosteroids given for acute COVID-19 do not affect health-related quality of life or other patient reported outcomes, physical and mental health outcomes, and organ function one year after hospital discharge", "rel_num_authors": 74, "rel_authors": [ { @@ -565,7 +1047,7 @@ "rel_date": "2023-11-10", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.10.23298350", - "rel_abs": "Objectives: In response to the COVID-19 pandemic, countries implemented various non-pharmaceutical interventions(NPIs). With this systematic review, we investigated the effectiveness of NPIs in mitigating SARS-CoV-2 transmission by assessing empirical evidence and data obtained through modelling studies. Design: We searched Medline(OVID) and EMBASE until 26 May 2022. The PICO framework was used to determine the eligibility of the studies. Populations were restricted to studies on humans, and there was no geographical limitation. The included articles assessed NPIs at the regional or national level as mitigation measures against SARS-CoV-2 transmission for human population without geographical limitation. Unmitigated SARS-CoV-2 transmission or the period before the implementation of the assessed NPI were used as the comparator. Main outcome measures: Outcome indicators were extracted and included COVID-19 cases, incidence and peaks, reproduction rate, growth rate, case mortality, and hospital and Intensive Care Unit admissions. Due to the heterogeneity between studies, statistical analysis was not possible and hence the results were presented narratively. Results: 49 studies were included; 21 based on empirical evidence and 28 modelling studies. Among the latter, the effectiveness of facemasks was evaluated in 11 studies, five assessed stay-at-home orders and five school closures. Regarding face mask use, the majority of studies presented a beneficial effect when appropriate social distancing measures could not be maintained. Restrictions on mass gatherings, stay-at-home-orders and lockdown measures were found to be effective in reducing SARS-CoV-2 transmission when timely and properly implemented. The results related to school closures were inconclusive. Conclusions: This systematic review assesses the effectiveness of NPIs in reducing SARS-CoV-2 transmission from January 2021 until May 2022. It suggests the importance of timely implementation and the optimised impact when implementing multiple NPIs in parallel. Continuous monitoring of the effectiveness of NPIs is required to determine the most suitable nature, time, and duration of the implemented NPIs.", + "rel_abs": "ObjectivesIn response to the COVID-19 pandemic, countries implemented various non-pharmaceutical interventions(NPIs). With this systematic review, we investigated the effectiveness of NPIs in mitigating SARS-CoV-2 transmission by assessing empirical evidence and data obtained through modelling studies.\n\nDesignWe searched Medline(OVID) and EMBASE until 26 May 2022. The PICO framework was used to determine the eligibility of the studies. Populations were restricted to studies on humans, and there was no geographical limitation. The included articles assessed NPIs at the regional or national level as mitigation measures against SARS-CoV-2 transmission for human population without geographical limitation. Unmitigated SARS-CoV-2 transmission or the period before the implementation of the assessed NPI were used as the comparator.\n\nMain outcome measuresOutcome indicators were extracted and included COVID-19 cases, incidence and peaks, reproduction rate, growth rate, case mortality, and hospital and Intensive Care Unit admissions. Due to the heterogeneity between studies, statistical analysis was not possible and hence the results were presented narratively.\n\nResults49 studies were included; 21 based on empirical evidence and 28 modelling studies. Among the latter, the effectiveness of facemasks was evaluated in 11 studies, five assessed stay-at-home orders and five school closures. Regarding face mask use, the majority of studies presented a beneficial effect when appropriate social distancing measures could not be maintained. Restrictions on mass gatherings, stay-at-home-orders and lockdown measures were found to be effective in reducing SARS-CoV-2 transmission when timely and properly implemented. The results related to school closures were inconclusive.\n\nConclusionsThis systematic review assesses the effectiveness of NPIs in reducing SARS-CoV-2 transmission from January 2021 until May 2022. It suggests the importance of timely implementation and the optimised impact when implementing multiple NPIs in parallel. Continuous monitoring of the effectiveness of NPIs is required to determine the most suitable nature, time, and duration of the implemented NPIs.\n\nWhat is already known on this topicPrior to this study, it was recognised that in response to the COVID-19 pandemic, various non-pharmaceutical interventions (NPIs) such as hygiene measures, face mask usage, travel restrictions, social distancing, and contact tracing were implemented worldwide. The scientific community has been assessing the effectiveness of these NPIs in mitigating the pandemics impact on public health and the economy.\n\nWhat this study addsThis systematic review contributes by presenting updated and comprehensive evidence regarding the effectiveness of NPIs as a means of mitigating SARS-CoV-2 transmission, using both real-world evidence and data obtained through modelling studies. The study affirms that the timely application of NPIs, including the use of face masks, stay-at-home orders, restrictions on mass gatherings, and school closures, substantially reduced COVID-19 cases and fatalities. It underscores the significance of employing multiple NPIs in tandem for heightened effectiveness within future respiratory pandemics. The review emphasises the necessity for ongoing assessment of NPI efficacy, taking into account factors such as public compliance, vaccination rates, and the prevalence of virus variants.\n\nHow this study might affect research, practice, or policyThe findings of this study carry various implications. Firstly, they inform policymakers about the critical importance of promptly implementing NPIs and employing them in combination to manage respiratory pandemics. Secondly, the results underscore the enduring relevance of NPIs even as pandemic vaccination campaigns progress. Thirdly, the study highlights the need for standardized methodologies for evaluating the effectiveness of NPIs. Lastly, this review can guide future public health strategies by offering valuable insights into the impact of different interventions on pandemic control.", "rel_num_authors": 10, "rel_authors": [ { @@ -620,7 +1102,7 @@ "rel_date": "2023-11-10", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.08.566276", - "rel_abs": "The Coronavirus disease 2019 (COVID19) pandemic caused by Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) is an ongoing threat to global public health. To this end, intense efforts are underway to develop reagents to aid in diagnostics, enhance preventative measures, and provide therapeutics for managing COVID-19. The recent emergence of SARS-CoV-2 Omicron variants with enhanced transmissibility, altered antigenicity, and significant escape of existing monoclonal antibodies and vaccines underlines the importance of the continued development of such agents. The SARS-CoV-2 spike protein and its receptor binding domain (RBD) are critical to viral attachment and host cell entry and are primary targets for antibodies elicited from both vaccination and natural infection. In this study, mice were immunized with two synthetic peptides (Pep 1 and Pep 2) within the RBD of the original Wuhan SARS-CoV-2, as well as the whole RBD as a recombinant protein (rRBD). Hybridomas were generated and a panel of three monoclonal antibodies, mAb CU-P1-1 against Pep 1, mAb CU-P2-20 against Pep 2, and mAb CU-28-24 against rRBD, were generated and further characterized. The monoclonal antibodies were shown through ELISA to be specific for each immunogen/antigen and to be reactive by immunoblotting against RBD. Monoclonal antibody CU-P1-1 has limited applicability other than in ELISA approaches and basic immunoblotting. Monoclonal antibody CU-P2-20 is shown to be favorable for ELISA, immunoblotting, and immunohistochemistry (IHC), however, not live virus neutralization. In contrast, mAb CU-28-24 is most effective at live virus neutralization as well as ELISA, immunoblotting, and IHC. Moreover, mAb CU-28-24 was active against rRBD proteins from Omicron variants B.2 and B.4/B5 as determined by ELISA, suggesting this mAb may neutralize live virus of these variants. Each of the immunoglobulin genes has been sequenced using Next Generation Sequencing, which allows the expression of respective recombinant proteins, thereby eliminating the need for long-term hybridoma maintenance. These hybridomas and related mAbs are now protected by Intellectual Property agreements with the Clemson University Research Foundation and are Patent Pending based on their unique amino acids within the complementary determining regions (CDRs).", + "rel_abs": "The Coronavirus disease 2019 (COVID19) pandemic caused by Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) is an ongoing threat to global public health. To this end, intense efforts are underway to develop reagents to aid in diagnostics, enhance preventative measures, and provide therapeutics for managing COVID-19. The recent emergence of SARS-CoV-2 Omicron variants with enhanced transmissibility, altered antigenicity, and significant escape of existing monoclonal antibodies and vaccines underlines the importance of the continued development of such agents. The SARS-CoV-2 spike protein and its receptor binding domain (RBD) are critical to viral attachment and host cell entry and are primary targets for antibodies elicited from both vaccination and natural infection. In this study, mice were immunized with two synthetic peptides (Pep 1 and Pep 2) within the RBD of the original Wuhan SARS-CoV-2, as well as the whole RBD as a recombinant protein (rRBD). Hybridomas were generated and a panel of three monoclonal antibodies, mAb CU-P1-1 against Pep 1, mAb CU-P2-20 against Pep 2, and mAb CU-28-24 against rRBD, were generated and further characterized. These mAbs were shown by ELISA to be specific for each immunogen/antigen. Monoclonal antibody CU-P1-1 has limited applicability other than in ELISA approaches and basic immunoblotting. Monoclonal antibody CU-P2-20 is shown to be favorable for ELISA, immunoblotting, and immunohistochemistry (IHC), however, not live virus neutralization. In contrast, mAb CU-28-24 is most effective at live virus neutralization as well as ELISA and IHC. Moreover, mAb CU-28-24 was active against rRBD proteins from Omicron variants B.2 and B.4/B5 as determined by ELISA, suggesting this mAb may neutralize live virus of these variants. Each of the immunoglobulin genes has been sequenced using Next Generation Sequencing, which allows the expression of respective recombinant proteins, thereby eliminating the need for long-term hybridoma maintenance. The synthetic peptide sequences, hybridomas, and related mAbs are now protected by Intellectual Property agreements with the Clemson University Research Foundation and are Patent Pending based on their unique amino acids within the complementary determining regions (CDRs).", "rel_num_authors": 6, "rel_authors": [ { @@ -653,13 +1135,91 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.11.10.23298376", + "rel_title": "Topic: Effect of Lockdown Of COVID-19 And The Impact On People Living In Enugu State, Nigeria", + "rel_date": "2023-11-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.10.23298376", + "rel_abs": "IntroductionWhen the coronavirus (COVID-19) pandemic struck, countries employed diverse strategies in the control of the virus aimed at preventing, detecting, controlling and mitigating the impact of the pandemic. Initially, there was no known cure for this viral infection so this stay-at-home necessitated the preventive measures to break the chain of transmission. This study aims to examine the different challenges people passed through as a result of this pandemic and the effect of the lockdown on people. This study will serve as the basis for future reference to know if this lockdown could be repeated in the face of another pandemic.\n\nMethodologyThe study was carried out in Enugu Metropolis, South East, Nigeria. This is a cross-sectional study among people living in Enugu State. Google forms were dispatched to adults from 18-65 years on social media or the internet. Data entry was to Excel, then to SPSS version 26 and analyzed with students t-test and Chi-square.\n\nResultsFrom the study, 35% said there were financial losses, some complained of poor recreation, 52% of people said there was loss of learning opportunities for their children due to school shutdown 23% had a reduction in their income with 35% losing their job, 57.9% of people said the crime rate increased, 26.6% had a mental breakdown, 45.1% of people had relationship/spousal problems and 64.1% of people lost someone during the COVID-19 lockdown and There were also some benefits of the lockdown like 70% said there was reduction in RTA, air pollution, introduction to remote working popularly known as \"working from home\" and 32% of people claimed it caused family bonding. In all, 73% of people said they would not want or support a repeat lockdown.\n\nConclusionThe impact of the lockdown on the residents of Enugu State was generally not a palatable experience. From this study, though some good things were achieved, it led to a number of irreversible crises. It also caused serious implications like a decline to access to healthcare, economic effects, political, social and cultural effects, educational impacts, an increase in crime rate, domestic violence, religious impact, and environmental effects. In future, a better method of approach is recommended.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Nwadiuto Chidinma Ojielo", + "author_inst": "University of Nigeria Teaching Hospital" + }, + { + "author_name": "Daniel Chinemerem Onwuliri", + "author_inst": "University of Nigeria Teaching Hospital" + }, + { + "author_name": "Augustine Onuh", + "author_inst": "University of Nigeria Teaching Hospital" + }, + { + "author_name": "Adaobi Ilo", + "author_inst": "University of Nigeria Teaching Hospital" + }, + { + "author_name": "Ngozi Rosemary Njeze", + "author_inst": "University of Nigeria" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, + { + "rel_doi": "10.1101/2023.11.10.23298337", + "rel_title": "Importations of SARS-CoV-2 lineages decline after nonpharmaceutical interventions in phylogeographic analyses", + "rel_date": "2023-11-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.10.23298337", + "rel_abs": "The onset of the SARS-CoV-2 pandemic marked a period of substantial challenges as the virus and its variants rapidly spread, placing enormous strain on both society and healthcare systems. Prior to the widespread availability of vaccines, non-pharmaceutical interventions such as reducing contacts, antigenic testing, or travel restrictions were the primary means of reducing viral transmission and case numbers, and quantifying the success of these measures is therefore key for future pandemic preparedness. Using SARS-CoV-2 genomes collected in systematic surveillance, we studied lineage importations for the third, pandemic wave in Germany, employing a large-scale Bayesian phylogenetic and phylogeographic analysis coupled to a longitudinal assessment of lineage importation dynamics over multiple sampling strategies. We evaluated the effect of twelve major nationwide nonpharmaceutical interventions (NPIs) on lineage importations and dissemination within the country. All NPIs were followed by reduced lineage importations, with the most substantial decreases seen for the provision of free rapid tests, the strengthening of regulations on mask-wearing in public transport and stores, as well as on internal movements and gatherings. Most SARS-CoV-2 lineages first appeared in the three states with the largest populations and most cases, and from there spread within the country. Importations began to rise before and peaked shortly after the Christmas holidays. Analysis of SARS-CoV-2 data revealed the substantial effects of free rapid tests and obligatory medical/surgical mask-wearing, suggesting these as key for pandemic preparedness, given their relatively few, negative socioeconomic effects. The approach quantifies the relationships between environmental factors at the host population level to viral lineage dissemination from genomic surveillance data, facilitating similar analyses of rapidly evolving pathogens in the future.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Sama Goliaei", + "author_inst": "Helmholtz Center for Infection Research" + }, + { + "author_name": "Mohammad-Hadi Foroughmand-Araabi", + "author_inst": "Helmholtz Center for Infection Research" + }, + { + "author_name": "Aideen Roddy", + "author_inst": "Helmholtz Center for Infection Research" + }, + { + "author_name": "Ariane Weber", + "author_inst": "Max-Planck Institute of Geoanthropology" + }, + { + "author_name": "Sanni Oeversti", + "author_inst": "Max-Planck Institute of Geoanthropology" + }, + { + "author_name": "Denise Kuehnert", + "author_inst": "Max Planck Institute of Geoanthropology" + }, + { + "author_name": "Alice Carolyn McHardy", + "author_inst": "Helmholtz Centre for Infection Research" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.11.08.23298274", "rel_title": "A Systematic Review of the Attitude, Beliefs, and Acceptance of COVID-19 Vaccine in the Western and Eastern Hemisphere.", "rel_date": "2023-11-09", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.08.23298274", - "rel_abs": "Background: The availability of an effective vaccine does not equate to its use; its effectiveness primarily depends on vaccine acceptance by the targeted population. Despite the rapid development and widespread access to the COVID-19 vaccine, herd immunity is yet to be achieved, with vaccine hesitancy as a major barrier. This study sought to systematically assess the beliefs, attitudes, and acceptance towards COVID-19 vaccines, including factors contributing to vaccination hesitancy in the Eastern and Western hemispheres. Methods: A comprehensive search of articles was conducted through Scopus, PubMed, Embase, CINAHL, Cochrane CENTRAL, and Web of Science databases for studies published from inception to May 2023 using the PRISMA guidelines. Results: Our search yielded 1154, of which 21 were eligible for inclusion. The rate of willingness or intention to vaccinate varied with the geographic region, from 12% in the USA to 93.9% in China. Four studies from the Western and two from Eastern regions reported a low acceptance rate (defined as <50%): USA (12%), Spain (48.3%), Switzerland (38.6%), Europe (multi-national, 31%), Nepal (38.3%), and Oman (43%). Overall, vaccine acceptance was low-to-moderate in the general population and healthcare workers (HCWs) in both Eastern and Western hemispheres except for China which reported high acceptance (defined as >75%) among the general population and HCWs. Demographic characteristics (female, younger age, and higher education) and non-demographic factors (knowledge about the COVID-19 vaccine and its development, history of influenza vaccination, perceived susceptibility or severity of infection, and the belief that vaccines are effective in controlling the pandemic were associate with high acceptance rates or intentions to take the COVID-19 vaccine. On the other hand, mistrust of the vaccine, its safety and effectiveness, disinformation or poor awareness of the vaccine, side effects concerns, belief in natural immunity, previous adverse experience with the vaccines, and distrust in the information sources about the COVID-19 pandemic were associated with vaccination hesitancy. Conclusion: For better acceptance, COVID-19 vaccination campaign strategies should be modeled based on regional political, economic, and social contexts.", + "rel_abs": "BackgroundThe availability of an effective vaccine does not equate to its use; its effectiveness primarily depends on vaccine acceptance by the targeted population. Despite the rapid development and widespread access to the COVID-19 vaccine, herd immunity is yet to be achieved, with vaccine hesitancy as a major barrier. This study sought to systematically assess the beliefs, attitudes, and acceptance towards COVID-19 vaccines, including factors contributing to vaccination hesitancy in the Eastern and Western hemispheres.\n\nMethodsA comprehensive search of articles was conducted through Scopus, PubMed, Embase, CINAHL, Cochrane CENTRAL, and Web of Science databases for studies published from inception to May 2023 using the PRISMA guidelines.\n\nResultsOur search yielded 1154, of which 21 were eligible for inclusion. The rate of willingness or intention to vaccinate varied with the geographic region, from 12% in the USA to 93.9% in China. Four studies from the Western and two from Eastern regions reported a low acceptance rate (defined as <50%): USA (12%), Spain (48.3%), Switzerland (38.6%), Europe (multi-national, 31%), Nepal (38.3%), and Oman (43%). Overall, vaccine acceptance was low-to-moderate in the general population and healthcare workers (HCWs) in both Eastern and Western hemispheres except for China which reported high acceptance (defined as >75%) among the general population and HCWs. Demographic characteristics (female, younger age, and higher education) and non-demographic factors (knowledge about the COVID-19 vaccine and its development, history of influenza vaccination, perceived susceptibility or severity of infection, and the belief that vaccines are effective in controlling the pandemic were associate with high acceptance rates or intentions to take the COVID-19 vaccine. On the other hand, mistrust of the vaccine, its safety and effectiveness, disinformation or poor awareness of the vaccine, side effects concerns, belief in natural immunity, previous adverse experience with the vaccines, and distrust in the information sources about the COVID-19 pandemic were associated with vaccination hesitancy.\n\nConclusionFor better acceptance, COVID-19 vaccination campaign strategies should be modeled based on regional political, economic, and social contexts.\n\nHighlightsO_LIThe willingness to accept COVID-19 vaccines was low-to-moderate in both hemispheres.\nC_LIO_LIHealthcare workers were as willing to vaccinate as the general population.\nC_LIO_LIVaccine hesitancy was associated with demographic and vaccine-specific factors.\nC_LI", "rel_num_authors": 3, "rel_authors": [ { @@ -721,7 +1281,7 @@ "rel_date": "2023-11-09", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.07.565953", - "rel_abs": "\"Succession\" refers to the process of certain species replacing others over time. It is of great significance for understanding the characteristics and evolution of ecosystems. This article compares the changes in school rooftop green areas before and after the COVID-19 epidemic (2019, 2023), and studies the situation of wild grass invading roofs during the three years of the epidemic, as well as the response of original rooftop plants to the invasion. The results showed that 1. invasive weeds were concentrated in 2 families and 4 species, forming a population advantage in most of the invaded planting boxes; 2. The succession has had a significant impact on the roof greening area; 2. Among the two cultivated plants (Phedimus aizoon (PA) and Sedum sarmentosum (SS)), SS was greatly affected, with the community almost disappearing, while PA was almost unaffected.", + "rel_abs": "\"Succession\" refers to the process of certain species replacing others over time. It is of great significance for understanding the characteristics and evolution of ecosystems. This article compares the changes in school rooftop green areas before and after the COVID-19 epidemic (2019, 2023), and studies the situation of wild grass invading roofs during the three years of the epidemic, as well as the response of original rooftop plants to the invasion. The results showed that: [circled1] invasive weeds were concentrated in 2 families and 4 species, forming a population advantage in most of the invaded planting boxes; [circled2] The succession has had a significant impact on the roof greening area; [circled3] Among the two cultivated plants (Phedimus aizoon (PA) and Sedum sarmentosum (SS)), SS was greatly affected, with the community almost disappearing, while PA was almost unaffected.", "rel_num_authors": 6, "rel_authors": [ { @@ -851,7 +1411,7 @@ "rel_date": "2023-11-09", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.08.566182", - "rel_abs": "Cross-species transmission of coronaviruses (CoVs) poses a serious threat to both animal and human health. Whilst the large RNA genome of CoVs shows relatively low mutation rates, recombination within genera is frequently observed and demonstrated. Companion animals are often overlooked in the transmission cycle of viral diseases; however, the close relationship of feline (FCoV) and canine CoV (CCoV) to human hCoV-229E, as well as their susceptibility to SARS-CoV-2 highlight their importance in potential transmission cycles. Whilst recombination between CCoV and FCoV of a large fragment spanning orf1b to M has been previously described, here we report the emergence of a novel, highly pathogenic FCoV-CCoV recombinant responsible for a rapidly spreading outbreak of feline infectious peritonitis (FIP), originating in Cyprus. The recombination, spanning spike, shows 97% sequence identity to the pantropic canine coronavirus CB/05. Infection is spreading fast and infecting cats of all ages. Development of FIP appears rapid and likely non-reliant on biotype switch. High sequence identity of isolates from cats in different districts of the island is strongly supportive of direct transmission. A deletion and several amino acid changes in spike, particularly the receptor binding domain, compared to other FCoV-2s, indicate changes to receptor binding and likely cell tropism.", + "rel_abs": "Cross-species transmission of coronaviruses (CoVs) poses a serious threat to both animal and human health1-3. Whilst the large RNA genome of CoVs shows relatively low mutation rates, recombination within genera is frequently observed and demonstrated4-7. Companion animals are often overlooked in the transmission cycle of viral diseases; however, the close relationship of feline (FCoV) and canine CoV (CCoV) to human hCoV-229E5,8, as well as their susceptibility to SARS-CoV-29 highlight their importance in potential transmission cycles. Whilst recombination between CCoV and FCoV of a large fragment spanning orf1b to M has been previously described5,10, here we report the emergence of a novel, highly pathogenic FCoV-CCoV recombinant responsible for a rapidly spreading outbreak of feline infectious peritonitis (FIP), originating in Cyprus11. The recombination, spanning spike, shows 97% sequence identity to the pantropic canine coronavirus CB/05. Infection is spreading fast and infecting cats of all ages. Development of FIP appears rapid and likely non-reliant on biotype switch12. High sequence identity of isolates from cats in different districts of the island is strongly supportive of direct transmission. A deletion and several amino acid changes in spike, particularly the receptor binding domain, compared to other FCoV-2s, indicate changes to receptor binding and likely cell tropism.", "rel_num_authors": 15, "rel_authors": [ { @@ -1032,7 +1592,7 @@ "rel_date": "2023-11-08", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.08.23297633", - "rel_abs": "SARS-CoV-2, the causal agent of the global COVID-19 pandemic, made its appearance at the end of 2019 and is still circulating in the population. The pandemic led to an urgent need for fast, reliable, and widely available testing. After December 2020, the emergence of new variants of SARS-CoV-2 led to additional challenges since new and existing tests had to detect variants to the same extent as the original Wuhan strain. When an antigen-based test is submitted to the Food and Drug Administration (FDA) for Emergency Use Authorization (EUA) consideration it is benchmarked against PCR comparator assays, which yield cycle threshold (CT) data as an indirect indicator of viral load--the lower the CT, the higher the viral load of the sample and the higher the CT, the lower the viral load. The FDA mandates that 10-20% of clinical samples used to evaluate the antigen test have to be low positive. Low positive, as defined by the FDA, are clinical samples in which the CT of the SARS-CoV-2 target gene is within 3 CT of the mean CT value of the approved comparator test's Limit of Detection (LOD). While all comparator tests are PCR-based, the results from different PCR assays used are not uniform. Results vary depending on assay platform, target gene, LOD and laboratory methodology. The emergence and dominance of the Omicron variant further challenged this approach as the fraction of low positive clinical samples dramatically increased as compared to earlier SARS-CoV-2 variants. This led to 20-40% of clinical samples having high CT values and therefore assays vying for an EUA were failing to achieve the 80% Percent Positive Agreement (PPA) threshold required. Here we describe the methods and statistical analyses used to establish a predefined cutoff, based on genome copies per ml (GE/ml) to classify samples as low positive (less than the cutoff GE/ml) or high positive (greater than the cutoff GE/mL). CT 30 for the E gene target using Cobas(R) SARS-CoV-2-FluA/B platform performed at TriCore Reference Laboratories, and this low positive cutoff value was used for two EUA authorizations. Using droplet digital PCR and methods described here, a value 49,447.72 was determined as the GE/ml equivalent for the low positive cutoff. The CT cutoff corresponding to 49447.72 GE/ml was determined across other platforms and laboratories. The methodology and statistical analysis described here can now be used for standardization of all comparators used for FDA submissions with a goal towards establishing uniform criteria for EUA authorization.", + "rel_abs": "SARS-CoV-2, the causal agent of the global COVID-19 pandemic, made its appearance at the end of 2019 and is still circulating in the population. The pandemic led to an urgent need for fast, reliable, and widely available testing. After December 2020, the emergence of new variants of SARS-CoV-2 led to additional challenges since new and existing tests had to detect variants to the same extent as the original Wuhan strain. When an antigen-based test is submitted to the Food and Drug Administration (FDA) for Emergency Use Authorization (EUA) consideration it is benchmarked against PCR comparator assays, which yield cycle threshold (CT) data as an indirect indicator of viral load - the lower the CT, the higher the viral load of the sample and the higher the CT, the lower the viral load. The FDA mandates that 10-20% of clinical samples used to evaluate the antigen test have to be low positive. Low positive, as defined by the FDA, are clinical samples in which the CT of the SARS-CoV-2 target gene is within 3 CT of the mean CT value of the approved comparator tests Limit of Detection (LOD). While all comparator tests are PCR-based, the results from different PCR assays used are not uniform. Results vary depending on assay platform, target gene, LOD and laboratory methodology. The emergence and dominance of the Omicron variant further challenged this approach as the fraction of low positive clinical samples dramatically increased as compared to earlier SARS-CoV-2 variants. This led to 20-40% of clinical samples having high CT values and therefore assays vying for an EUA were failing to achieve the 80% Percent Positive Agreement (PPA) threshold required. Here we describe the methods and statistical analyses used to establish a predefined cutoff, based on genome copies per ml (GE/ml) to classify samples as low positive (less than the cutoff GE/ml) or high positive (greater than the cutoff GE/mL). CT 30 for the E gene target using Cobas(R) SARS-CoV-2-FluA/B platform performed at TriCore Reference Laboratories, and this low positive cutoff value was used for two EUA authorizations. Using droplet digital PCR and methods described here, a value 49,447.72 was determined as the GE/ml equivalent for the low positive cutoff. The CT cutoff corresponding to 49447.72 GE/ml was determined across other platforms and laboratories. The methodology and statistical analysis described here can now be used for standardization of all comparators used for FDA submissions with a goal towards establishing uniform criteria for EUA authorization.\n\nMotivationThe motivation for this work was the need to establish a predefined cutoff based on genome copies per ml (GE/ml) rather than Ct, which can vary depending on the laboratory and assay used. A GE/ml-based threshold was necessary to define what constituted low positives\" for samples that were included in data sets submitted to the FDA for emergency use approval for SARS-CoV-2 antigen tests.", "rel_num_authors": 14, "rel_authors": [ { @@ -1103,7 +1663,7 @@ "rel_date": "2023-11-08", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.07.23297422", - "rel_abs": "Abstract Background: Children (<18 years old) were not initially considered significant sources of infection (SOIs) for SARS-CoV-2. Risk mitigation strategies were thus prioritized for adults, and vaccination was inaccessible for children until mid-2021. Emergence of novel variants led to significant increases in COVID-19 cases in both children and adults. Whether these emergence events and increased vulnerability of unvaccinated children had a synergistic effect resulting in increased caseloads in adults requires further exploration. Methods: A retrospective cohort study was conducted among 3,545 workers diagnosed with COVID-19. Case details were compiled during contact investigations. Variants of concern were identified following sequencing of biological samples collected through employer-based testing programs. Logistic regression was performed to compare the odds of having a child SOI based on the dominant variant in the workforce. Results: One-fourth (24.5%) of the cohort reported having a child in-residence; 11.2% identified a child as their SOI. In Alpha-dominant months, the odds of having a child SOI were 0.3, and the child SOI was likely older (5-17 years old). The odds of having a child SOI increased to 1.3 and 2.2 in Delta- and Omicron-dominant months, respectively. The odds of having younger child SOIs (<5 years old) were significantly higher in Omicron-dominant months. Conclusions: Children were highly likely to acquire the virus and posed a significant risk of transmission to their adult caretakers during Delta- and Omicron-dominant months. Without proper mitigation strategies in both the home and the workplace, child-associated transmission can threaten operations in the forms of staff shortages.", + "rel_abs": "BackgroundChildren (<18 years old) were not initially considered significant sources of infection (SOIs) for SARS-CoV-2. Risk mitigation strategies were thus prioritized for adults, and vaccination was inaccessible for children until mid-2021. Emergence of novel variants led to significant increases in COVID-19 cases in both children and adults. Whether these emergence events and increased vulnerability of unvaccinated children had a synergistic effect resulting in increased caseloads in adults requires further exploration.\n\nMethodsA retrospective cohort study was conducted among 3,545 workers diagnosed with COVID-19. Case details were compiled during contact investigations. Variants of concern were identified following sequencing of biological samples collected through employer-based testing programs. Logistic regression was performed to compare the odds of having a child SOI based on the dominant variant in the workforce.\n\nResultsOne-fourth (24.5%) of the cohort reported having a child in-residence; 11.2% identified a child as their SOI. In Alpha-dominant months, the odds of having a child SOI were 0.3, and the child SOI was likely older (5-17 years old). The odds of having a child SOI increased to 1.3 and 2.2 in Delta- and Omicron-dominant months, respectively. The odds of having younger child SOIs (<5 years old) were significantly higher in Omicron-dominant months.\n\nConclusionsChildren were highly likely to acquire the virus and posed a significant risk of transmission to their adult caretakers during Delta- and Omicron-dominant months. Without proper mitigation strategies in both the home and the workplace, child-associated transmission can threaten operations in the forms of staff shortages.\n\nWhat is already known on this topicIncreases in transmission trends related to SARs-CoV-2 Variants of Concern have been documented in the literature at the population level and in workplaces.\n\nWhat this study addsThis study looks more closely at the role that children played in transmission to adult workers, and therefore their potential to seed transmission outside of the home. This interface of transmission has been neglected in the literature but is key for future policy development.\n\nHow this study might affect research, practice, or policyTransmission of SARS-CoV-2 from children to their caretakers may cause significantly increased odds of infection in a worker population. This may have second order effects for staffing, particularly in workgroups with employees of childbearing age. Employers should consider this in the design of their policies for continuity of operations, telework, and leave.", "rel_num_authors": 11, "rel_authors": [ { @@ -1162,7 +1722,7 @@ "rel_date": "2023-11-08", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.07.23297764", - "rel_abs": "Objectives: Report a case series of new onset small fiber neuropathy (SFN) after COVID-19 treated with intravenous immunoglobulin (IVIG). SFN is a critical objective finding in long COVID and amenable to treatment. Methods: A retrospective chart review was conducted on patients seen in the NeuroCOVID Clinic at Yale who developed new-onset SFN after a documented COVID-19 illness. We documented demographics, symptoms, treatments, diagnostics, and clinical response to treatment. Results: Sixteen patients were diagnosed with length dependent or independent SFN on skin biopsy (median age 47, 75% female, 75% Caucasian). Among the nine patients tested for autoantibodies, six were positive for either trisulfated heparin disaccharide (TS-HDS) or fibroblast growth factor receptor 3 (FGFR3). Eight patients underwent treatment with IVIG and experience significant clinical improvement in their neuropathic symptoms. 92% of patients reported post-exertional malaise characteristic of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) and six patients underwent invasive cardiopulmonary exercise testing (iCPET), which demonstrated neurovascular dysregulation and dysautonomia consistent with ME/CFS. Discussion: Here we present preliminary evidence that SFN is responsive to treatment with IVIG and linked with neurovascular dysregulation and dysautonomia. A larger clinical trial is indicated to further demonstrate the clinical utility of IVIG in treating post-infectious small fiber neuropathy.", + "rel_abs": "ObjectivesReport a case series of new onset small fiber neuropathy (SFN) after COVID-19 treated with intravenous immunoglobulin (IVIG). SFN is a critical objective finding in long COVID and amenable to treatment.\n\nMethodsA retrospective chart review was conducted on patients seen in the NeuroCOVID Clinic at Yale who developed new-onset SFN after a documented COVID-19 illness. We documented demographics, symptoms, treatments, diagnostics, and clinical response to treatment.\n\nResultsSixteen patients were diagnosed with length dependent or independent SFN on skin biopsy (median age 47, 75% female, 75% Caucasian). Among the nine patients tested for autoantibodies, six were positive for either trisulfated heparin disaccharide (TS-HDS) or fibroblast growth factor receptor 3 (FGFR3). Eight patients underwent treatment with IVIG and experience significant clinical improvement in their neuropathic symptoms. 92% of patients reported post-exertional malaise characteristic of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) and six patients underwent invasive cardiopulmonary exercise testing (iCPET), which demonstrated neurovascular dysregulation and dysautonomia consistent with ME/CFS.\n\nDiscussionHere we present preliminary evidence that SFN is responsive to treatment with IVIG and linked with neurovascular dysregulation and dysautonomia. A larger clinical trial is indicated to further demonstrate the clinical utility of IVIG in treating post-infectious small fiber neuropathy.", "rel_num_authors": 4, "rel_authors": [ { @@ -1193,7 +1753,7 @@ "rel_date": "2023-11-08", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.07.23298178", - "rel_abs": "SARS-CoV-2 Omicron surged as a variant of concern (VOC) in late 2021. Subsequently, several distinct Omicron variants have appeared and overtaken each other. We combined variant frequencies from GISAID and infection estimates from a nowcasting model for each US state to estimate variant-specific infections, attack rates, and effective reproduction numbers (Rt). BA.1 rapidly emerged, and we estimate that it infected 47.7% of the US population between late 2021 and early 2022 before it was replaced by BA.2. We estimate that BA.5, despite a slower takeoff than BA.1, also infected 35.7% of the US population, persisting in circulation for nearly 6 months. Other Omicron variants - BA.2, BA.4, or XBB - infected 30.7% of the US population. We found a positive correlation between the state-level BA.1 attack rate and social vulnerability. Our findings reveal the complex interplay between viral evolution, population susceptibility, and social factors since Omicron emerged in the US.", + "rel_abs": "SARS-CoV-2 Omicron surged as a variant of concern (VOC) in late 2021. Subsequently, several distinct Omicron variants have appeared and overtaken each other. We combined variant frequencies from GISAID and infection estimates from a nowcasting model for each US state to estimate variant-specific infections, attack rates, and effective reproduction numbers (Rt). BA.1 rapidly emerged, and we estimate that it infected 47.7% of the US population between late 2021 and early 2022 before it was replaced by BA.2. We estimate that BA.5, despite a slower takeoff than BA.1, also infected 35.7% of the US population, persisting in circulation for nearly 6 months. Other Omicron variants - BA.2, BA.4, or XBB - infected 30.7% of the US population. We found a positive correlation between the state-level BA.1 attack rate and social vulnerability. Our findings reveal the complex interplay between viral evolution, population susceptibility, and social factors since Omicron emerged in the US.\n\nOne-Sentence SummaryFor each US state, we estimate Omicron variant-specific infections, attack rates, and effective reproduction numbers.", "rel_num_authors": 11, "rel_authors": [ { @@ -1252,7 +1812,7 @@ "rel_date": "2023-11-08", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.07.23297704", - "rel_abs": "Background Non-pharmaceutical interventions (NPIs) have been widely used to control the transmission of infectious diseases. However, the current research evidence on the policy mechanisms of NPIs is still limited. This study aims to systematically identify, describe, and evaluate the existing literature for the real-world effectiveness of NPIs in containing COVID-19 pandemic after the roll-out of coronavirus vaccines, in order to search for optimal strategies for implementing NPIs. Methods We conducted a comprehensive search of relevant studies from January 1, 2021, to June 4, 2023 in PubMed, Embase, Web of science and MedRxiv. Two authors independently assessed eligibility and extracted data. Risk of bias assessment tool was used to evaluate the study design, statistical methodology, and quality of reporting. Data were collected, synthesised and analyzed through quantitative and qualitative approaches. The findings were presented using summary tables and figures, including information on the target countries and regions of the study, types of NPIs, and evidence quality. Results The review included a total of seventeen studies that examined the real-world effectiveness of NPIs in containing the COVID-19 pandemic after the vaccine roll-out. These studies used five composite indicator that combined multiple NPIs and fourteen individual NPIs. The studies had an average quality assessment score of 13 (range: 10-16), indicating moderately high quality. Among the included studies, nine assessed the effectiveness of the composite indicator, with four of them also evaluating individual NPIs. Additionally, twelve studies investigated the effectiveness of individual NPIs. The most frequently evaluated individual NPIs were testing policy, restrictions on gathering, facial covering, and school closure. Workplace closures and stay-at-home requirements were also assessed. The effectiveness of NPIs varied depending on time frames, countries and regions. Conclusion In summary, the research evidence suggests that NPIs remain effective in curbing the spread of COVID-19 even after the roll-out of vaccines. Studies based on different contexts had different viewpoints or conclusions regarding the effectiveness of NPIs in containing the COVID-19 pandemic. Further research is needed to understand the policy mechanisms and address potential future challenges.", + "rel_abs": "BackgroundNon-pharmaceutical interventions (NPIs) have been widely used to control the transmission of infectious diseases. However, the current research evidence on the policy mechanisms of NPIs is still limited. This study aims to systematically identify, describe, and evaluate the existing literature for the real-world effectiveness of NPIs in containing COVID-19 pandemic after the roll-out of coronavirus vaccines, in order to search for optimal strategies for implementing NPIs.\n\nMethodsWe conducted a comprehensive search of relevant studies from January 1, 2021, to June 4, 2023 in PubMed, Embase, Web of science and MedRxiv. Two authors independently assessed eligibility and extracted data. Risk of bias assessment tool was used to evaluate the study design, statistical methodology, and quality of reporting. Data were collected, synthesised and analyzed through quantitative and qualitative approaches. The findings were presented using summary tables and figures, including information on the target countries and regions of the study, types of NPIs, and evidence quality.\n\nResultsThe review included a total of seventeen studies that examined the real-world effectiveness of NPIs in containing the COVID-19 pandemic after the vaccine roll-out. These studies used five composite indicator that combined multiple NPIs and fourteen individual NPIs. The studies had an average quality assessment score of 13 (range: 10-16), indicating moderately high quality. Among the included studies, nine assessed the effectiveness of the composite indicator, with four of them also evaluating individual NPIs. Additionally, twelve studies investigated the effectiveness of individual NPIs. The most frequently evaluated individual NPIs were testing policy, restrictions on gathering, facial covering, and school closure. Workplace closures and stay-at-home requirements were also assessed. The effectiveness of NPIs varied depending on time frames, countries and regions.\n\nConclusionIn summary, the research evidence suggests that NPIs remain effective in curbing the spread of COVID-19 even after the roll-out of vaccines. Studies based on different contexts had different viewpoints or conclusions regarding the effectiveness of NPIs in containing the COVID-19 pandemic. Further research is needed to understand the policy mechanisms and address potential future challenges.", "rel_num_authors": 4, "rel_authors": [ { @@ -1277,209 +1837,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2023.11.06.565765", - "rel_title": "Mucosal Adenoviral-vectored Vaccine Boosting Durably Prevents XBB.1.16 Infection in Nonhuman Primates", - "rel_date": "2023-11-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.06.565765", - "rel_abs": "Waning immunity and continued virus evolution have limited the durability of protection from symptomatic infection mediated by intramuscularly (IM)-delivered mRNA vaccines against COVID-19 although protection from severe disease remains high. Mucosal vaccination has been proposed as a strategy to increase protection at the site of SARS-CoV-2 infection by enhancing airway immunity, potentially reducing rates of infection and transmission. Here, we compared protection against XBB.1.16 virus challenge 5 months following IM or mucosal boosting in non-human primates (NHP) that had previously received a two-dose mRNA-1273 primary vaccine regimen. The mucosal boost was composed of a bivalent chimpanzee adenoviral-vectored vaccine encoding for both SARS-CoV-2 WA1 and BA.5 spike proteins (ChAd-SARS-CoV-2-S) and delivered either by an intranasal mist or an inhaled aerosol. An additional group of animals was boosted by the IM route with bivalent WA1/BA.5 spike-matched mRNA (mRNA-1273.222) as a benchmark control. NHP were challenged in the upper and lower airways 18 weeks after boosting with XBB.1.16, a heterologous Omicron lineage strain. Cohorts boosted with ChAd-SARS-CoV-2-S by an aerosolized or intranasal route had low to undetectable virus replication as assessed by levels of subgenomic SARS-CoV-2 RNA in the lungs and nose, respectively. In contrast, animals that received the mRNA-1273.222 boost by the IM route showed minimal protection against virus replication in the upper airway but substantial reduction of virus RNA levels in the lower airway. Immune analysis showed that the mucosal vaccines elicited more durable antibody and T cell responses than the IM vaccine. Protection elicited by the aerosolized vaccine was associated with mucosal IgG and IgA responses, whereas protection elicited by intranasal delivery was mediated primarily by mucosal IgA. Thus, durable immunity and effective protection against a highly transmissible heterologous variant in both the upper and lower airways can be achieved by mucosal delivery of a virus-vectored vaccine. Our study provides a template for the development of mucosal vaccines that limit infection and transmission against respiratory pathogens.", - "rel_num_authors": 47, - "rel_authors": [ - { - "author_name": "Matthew Gagne", - "author_inst": "Vaccine Research Center, NIAID, NIH; Bethesda, MD" - }, - { - "author_name": "Barbara J. Flynn", - "author_inst": "Vaccine Research Center, NIAID, NIH; Bethesda, MD" - }, - { - "author_name": "Shayne F. Andrew", - "author_inst": "Vaccine Research Center, NIAID, NIH; Bethesda, MD" - }, - { - "author_name": "Dillon R. Flebbe", - "author_inst": "Vaccine Research Center, NIAID, NIH; Bethesda, MD" - }, - { - "author_name": "Anna Mychalowych", - "author_inst": "Vaccine Research Center, NIAID, NIH; Bethesda, MD" - }, - { - "author_name": "Evan Lamb", - "author_inst": "Vaccine Research Center, NIAID, NIH; Bethesda, MD" - }, - { - "author_name": "Meredith E. Davis-Gardner", - "author_inst": "Emory University School of Medicine; Atlanta, GA" - }, - { - "author_name": "Matthew R. Burnett", - "author_inst": "Vaccine Research Center, NIAID, NIH; Bethesda, MD" - }, - { - "author_name": "Leonid A. Serebryannyy", - "author_inst": "Vaccine Research Center, NIAID, NIH; Bethesda, MD" - }, - { - "author_name": "Bob C. Lin", - "author_inst": "Vaccine Research Center, NIAID, NIH; Bethesda, MD" - }, - { - "author_name": "Laurent Pessaint", - "author_inst": "Bioqual, Inc; Rockville, MD" - }, - { - "author_name": "John-Paul M. Todd", - "author_inst": "Vaccine Research Center, NIAID, NIH; Bethesda, MD" - }, - { - "author_name": "Zohar E. Ziff", - "author_inst": "Vaccine Research Center, NIAID, NIH; Bethesda, MD" - }, - { - "author_name": "Erin Maule", - "author_inst": "Vaccine Research Center, NIAID, NIH; Bethesda, MD" - }, - { - "author_name": "Robin Carroll", - "author_inst": "Vaccine Research Center, NIAID, NIH; Bethesda, MD" - }, - { - "author_name": "Mursal Naisan", - "author_inst": "Vaccine Research Center, NIAID, NIH; Bethesda, MD" - }, - { - "author_name": "Yogita Jethmalani", - "author_inst": "Vaccine Research Center, NIAID, NIH; Bethesda, MD" - }, - { - "author_name": "James Brett Case", - "author_inst": "Washington University School of Medicine; St. Louis, MO" - }, - { - "author_name": "Igor P. Dmitriev", - "author_inst": "Washington University School of Medicine; St. Louis, MO" - }, - { - "author_name": "Elena A. Kashentseva", - "author_inst": "Washington University School of Medicine; St. Louis, MO" - }, - { - "author_name": "Baoling Ying", - "author_inst": "Washington University School of Medicine; St. Louis, MO" - }, - { - "author_name": "Alan Dodson", - "author_inst": "Bioqual, Inc; Rockville, MD" - }, - { - "author_name": "Katelyn Kouneski", - "author_inst": "Bioqual, Inc; Rockville, MD" - }, - { - "author_name": "Nicole A. Doria-Rose", - "author_inst": "Vaccine Research Center, NIAID, NIH; Bethesda, MD" - }, - { - "author_name": "Sijy O'Dell", - "author_inst": "Vaccine Research Center, NIAID, NIH; Bethesda, MD" - }, - { - "author_name": "Sucheta Godbole", - "author_inst": "Vaccine Research Center, NIAID, NIH; Bethesda, MD" - }, - { - "author_name": "Farida Laboune", - "author_inst": "Vaccine Research Center, NIAID, NIH; Bethesda, MD" - }, - { - "author_name": "Amy R. Henry", - "author_inst": "Vaccine Research Center, NIAID, NIH; Bethesda, MD" - }, - { - "author_name": "Josue Marquez", - "author_inst": "Vaccine Research Center, NIAID, NIH; Bethesda, MD" - }, - { - "author_name": "I-Ting Teng", - "author_inst": "Vaccine Research Center, NIAID, NIH; Bethesda, MD" - }, - { - "author_name": "Lingshu Wang", - "author_inst": "Vaccine Research Center, NIAID, NIH; Bethesda, MD" - }, - { - "author_name": "Qiong Zhou", - "author_inst": "Vaccine Research Center, NIAID, NIH; Bethesda, MD" - }, - { - "author_name": "Bushra Wali", - "author_inst": "Emory University School of Medicine; Atlanta, GA" - }, - { - "author_name": "Madison Ellis", - "author_inst": "Emory University School of Medicine; Atlanta, GA" - }, - { - "author_name": "Serge Zouantchangadou", - "author_inst": "Bioqual, Inc; Rockville, MD" - }, - { - "author_name": "Alex Van Ry", - "author_inst": "Bioqual, Inc; Rockville, MD" - }, - { - "author_name": "Mark G. Lewis", - "author_inst": "Bioqual, Inc; Rockville, MD" - }, - { - "author_name": "Hanne Andersen", - "author_inst": "Bioqual, Inc; Rockville, MD" - }, - { - "author_name": "Peter D. Kwong", - "author_inst": "Vaccine Research Center, NIAID, NIH; Bethesda, MD" - }, - { - "author_name": "David T. Curiel", - "author_inst": "Washington University School of Medicine; St. Louis, MO" - }, - { - "author_name": "Kathryn E. Foulds", - "author_inst": "Vaccine Research Center, NIAID, NIH; Bethesda, MD" - }, - { - "author_name": "Martha C. Nason", - "author_inst": "Biostatistics Research Branch, NIAID, NIH; Bethesda, MD" - }, - { - "author_name": "Mehul S. Suthar", - "author_inst": "Emory University School of Medicine; Atlanta, GA" - }, - { - "author_name": "Mario Roederer", - "author_inst": "Vaccine Research Center, NIAID, NIH; Bethesda, MD" - }, - { - "author_name": "Michael S. Diamond", - "author_inst": "Washington University School of Medicine; St. Louis, MO" - }, - { - "author_name": "Daniel C. Douek", - "author_inst": "Vaccine Research Center, NIAID, NIH; Bethesda, MD" - }, - { - "author_name": "Robert A. Seder", - "author_inst": "Vaccine Research Center, NIAID, NIH; Bethesda, MD" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.11.06.565781", "rel_title": "The \u03b1-dystroglycan N-terminus is a broad-spectrum antiviral agent against SARS-CoV-2 and enveloped viruses", @@ -1612,7 +1969,7 @@ "rel_date": "2023-11-08", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.07.566012", - "rel_abs": "The COVID-19 disease is an ongoing global health concern. Although vaccination provides some protection, people are still susceptible to re-infection. Ostensibly, certain populations or clinical groups may be more vulnerable. Factors causing these differences are unclear and whilst socioeconomic and cultural differences are likely to be important, human genetic factors could influence susceptibility. Experimental studies indicate SARS-CoV-2 uses innate immune suppression as a strategy to speed-up entry and replication into the host cell. Therefore, it is necessary to understand the impact of variants in immunity-associated human proteins on susceptibility to COVID-19. In this work, we analysed missense coding variants in several SARS-CoV-2 proteins and its human protein interactors that could enhance binding affinity to SARS-CoV-2. We curated a dataset of 19 SARS-CoV-2: human protein 3D-complexes, from the experimentally determined structures in the Protein Data Bank and models built using AlphaFold2-multimer, and analysed impact of missense variants occurring in the protein-protein interface region. We analysed 468 missense variants from human proteins and 212 variants from SARS-CoV-2 proteins and computationally predicted their impacts on binding affinities to SARS-CoV-2 proteins, using 3D-complexes. We predicted a total of 26 affinity-enhancing variants from 14 human proteins implicated in increased binding affinity to SARS-CoV-2. These include key-immunity associated genes (TOMM70, ISG15, IFIH1, IFIT2, RPS3, PALS1, NUP98, RAE1, AXL, ARF6, TRIMM, TRIM25) as well as important spike receptors (KREMEN1, AXL and ACE2). We report both common (e.g., Y13N in IFIH1) and rare variants in these proteins and discuss their likely structural and functional impact, using information on known and predicted functional sites. Potential mechanisms associated with immune suppression implicated by these variants are discussed. Occurrence of certain predicted affinity-enhancing variants should be monitored as they could lead to increased susceptibility and reduced immune response to SARS-CoV-2 infection in individuals/populations carrying them. Our analyses aid in understanding the potential impact of genetic variation in immunity-associated proteins on COVID-19 susceptibility and help guide drug-repurposing strategies.", + "rel_abs": "The COVID-19 disease is an ongoing global health concern. Although vaccination provides some protection, people are still susceptible to re-infection. Ostensibly, certain populations or clinical groups may be more vulnerable. Factors causing these differences are unclear and whilst socioeconomic and cultural differences are likely to be important, human genetic factors could influence susceptibility. Experimental studies indicate SARS-CoV-2 uses innate immune suppression as a strategy to speed-up entry and replication into the host cell. Therefore, it is necessary to understand the impact of variants in immunity-associated human proteins on susceptibility to COVID-19.\n\nIn this work, we analysed missense coding variants in several SARS-CoV-2 proteins and its human protein interactors that could enhance binding affinity to SARS-CoV-2. We curated a dataset of 19 SARS-CoV-2: human protein 3D-complexes, from the experimentally determined structures in the Protein Data Bank and models built using AlphaFold2-multimer, and analysed impact of missense variants occurring in the protein-protein interface region. We analysed 468 missense variants from human proteins and 212 variants from SARS-CoV-2 proteins and computationally predicted their impacts on binding affinities to SARS-CoV-2 proteins, using 3D-complexes.\n\nWe predicted a total of 26 affinity-enhancing variants from 14 human proteins implicated in increased binding affinity to SARS-CoV-2. These include key-immunity associated genes (TOMM70, ISG15, IFIH1, IFIT2, RPS3, PALS1, NUP98, RAE1, AXL, ARF6, TRIMM, TRIM25) as well as important spike receptors (KREMEN1, AXL and ACE2). We report both common (e.g., Y13N in IFIH1) and rare variants in these proteins and discuss their likely structural and functional impact, using information on known and predicted functional sites. Potential mechanisms associated with immune suppression implicated by these variants are discussed.\n\nOccurrence of certain predicted affinity-enhancing variants should be monitored as they could lead to increased susceptibility and reduced immune response to SARS-CoV-2 infection in individuals/populations carrying them. Our analyses aid in understanding the potential impact of genetic variation in immunity-associated proteins on COVID-19 susceptibility and help guide drug-repurposing strategies.", "rel_num_authors": 11, "rel_authors": [ { @@ -1828,7 +2185,7 @@ "rel_date": "2023-11-06", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.06.23298096", - "rel_abs": "Objectives: To explore the experience of accessing Long COVID community rehabilitation from the perspectives of people with Long COVID and General Practitioners (GPs). Design: Qualitative descriptive study employing one-to-one semi-structured virtual interviews analysed using the framework method. Setting: Four NHS Scotland territorial health boards. Participants: Eleven people with Long COVID (1 male, 10 female; aged 40-65 [mean 53], and 13 GPs (5 male, 8 female). Results: Four key themes were identified: i) The lived experience of Long COVID; ii) The challenges of an emergent and complex chronic condition; iii) Systemic challenges for Long COVID service delivery, and iv) Perceptions and experiences of Long COVID and its management, including rehabilitation. Conclusions: There are several patient, GP, and service-level barriers to accessing community rehabilitation for Long COVID. There is a need for greater understanding by the public, GPs, and other potential referrers of the role of community rehabilitation professionals in the management of Long COVID. There is also a need for community rehabilitation services to be well promoted and accessible to the people with Long COVID for whom they may be appropriate. Service providers need to consider availability and accessibility of Long COVID rehabilitation and ensure adequate interprofessional communication and collaboration to enhance the experience for people with Long COVID.", + "rel_abs": "ObjectivesTo explore the experience of accessing Long COVID community rehabilitation from the perspectives of people with Long COVID and General Practitioners (GPs).\n\nDesignQualitative descriptive study employing one-to-one semi-structured virtual interviews analysed using the framework method.\n\nSettingFour NHS Scotland territorial health boards.\n\nParticipantsEleven people with Long COVID (1 male, 10 female; aged 40-65 [mean 53], and 13 GPs (5 male, 8 female).\n\nResultsFour key themes were identified: i) The lived experience of Long COVID; ii) The challenges of an emergent and complex chronic condition; iii) Systemic challenges for Long COVID service delivery, and iv) Perceptions and experiences of Long COVID and its management, including rehabilitation.\n\nConclusionsThere are several patient, GP, and service-level barriers to accessing community rehabilitation for Long COVID. There is a need for greater understanding by the public, GPs, and other potential referrers of the role of community rehabilitation professionals in the management of Long COVID. There is also a need for community rehabilitation services to be well promoted and accessible to the people with Long COVID for whom they may be appropriate. Service providers need to consider availability and accessibility of Long COVID rehabilitation and ensure adequate interprofessional communication and collaboration to enhance the experience for people with Long COVID.\n\nStrengths and limitations of this studyO_LIThis is the first study to explore the issue of accessing Long COVID community rehabilitation from the perspectives of potential service users and referrers in the Scottish context.\nC_LIO_LIOne researcher conducted all interviews, ensuring consistency in their conduct\nC_LIO_LIData were analysed and interpreted by multiple researchers, including people with Long COVID\nC_LIO_LIThe small sample size, largely drawn from health boards with a similar approach to Long COVID rehabilitation, limits generalisability\nC_LI\n\nFunding statementThis work was supported by the Chief Scientist Office Scotland, grant number COV/LTE/20/29.", "rel_num_authors": 13, "rel_authors": [ { @@ -2233,6 +2590,61 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.11.04.565404", + "rel_title": "Dynamic gene expression analysis reveals distinct severity phases of immune and cellular dysregulation in COVID-19", + "rel_date": "2023-11-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.04.565404", + "rel_abs": "BackgroundCOVID-19 patients experience dynamic changes in immune and cellular function over time with potential clinical implications. However, there is insufficient research investigating, on a gene expression level, the mechanisms that become activated or suppressed over time as patients deteriorate or recover, which can inform use of repurposed and novel drugs as therapies.\n\nObjectiveTo investigate longitudinal changes in gene expression profiles throughout the COVID-19 disease timeline.\n\nMethodsThree-hundred whole blood samples from 128 adult patients were collected during hospitalization from COVID-19, with up to five samples per patient. Transcriptome sequencing (RNA-Seq), differential gene expression analysis and pathway enrichment was performed. Drug-gene set enrichment analysis was used to identify FDA-approved medications that could inhibit critical genes and proteins at each disease phase. Prognostic gene-expression signatures were generated using machine learning to distinguish 3 disease stages.\n\nResultsSamples were longitudinally grouped by clinical criteria and gene expression into six disease phases: Mild, Moderate, Severe, Critical, Recovery, and Discharge. Distinct mechanisms with differing trajectories during COVID-19 hospitalization were apparent. Antiviral responses peaked early in COVID-19, while heme metabolism pathways became active much later during disease. Adaptive immune dysfunction, inflammation, and metabolic derangements were most pronounced during phases with higher disease severity, while hemostatic abnormalities were elevated early and persisted throughout the disease course. Drug-gene set enrichment analysis predicted repurposed medications for potential use, including platelet inhibitors in early disease, antidiabetic medications for patients with increased disease severity, and dasatinib throughout the disease course. Disease phases could be categorized using specific gene signatures for prognosis and treatment selection. Disease phases were also highly correlated to previously developed sepsis endotypes, indicating that severity and disease timing were significant contributors to heterogeneity observed in sepsis and COVID-19.\n\nConclusionsHigher temporal resolution of longitudinal mechanisms in COVID-19 revealed multiple immune and cellular changes that were activated at different phases of COVID-19. Understanding how a patients gene expression profile changes over time can permit more accurate risk stratification of patients and provide time-dependent personalized treatments with repurposed medications. This creates an opportunity for timely intervention before patients transition to a more severe phase, potentially accelerating patients to recovery.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Andy An", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Arjun Baghela", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Peter Zhang", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Travis M Blimkie", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Jeff Gauthier", + "author_inst": "Laval University" + }, + { + "author_name": "Daniel E Kaufmann", + "author_inst": "Centre de Recherche du Centre Hospitalier de l'Universite de Montreal (CRCHUM)" + }, + { + "author_name": "Erica Acton", + "author_inst": "Simon Fraser University" + }, + { + "author_name": "Amy HY Lee", + "author_inst": "Simon Fraser University" + }, + { + "author_name": "Roger C Levesque", + "author_inst": "Laval University" + }, + { + "author_name": "Robert E.W. Hancock", + "author_inst": "University of British Columbia" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.11.03.565419", "rel_title": "Voltage-gated T-type calcium channel blockers reduce apoptotic body-mediated SARS-CoV-2 cell-to-cell spread and subsequent cytokine storm", @@ -2314,7 +2726,7 @@ "rel_date": "2023-11-06", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.02.565396", - "rel_abs": "Measures to control the COVID-19 pandemic such as antiviral therapy and vaccination have been challenged by ongoing virus evolution under antiviral and immune pressures. Understanding viral evolutionary dynamics is crucial for responding to SARS-CoV-2, and preparing for the next pandemic, by informing prediction of virus adaptation, public health strategies, and design of broadly effective therapies. Whole-genome sequencing (WGS) of SARS-CoV-2 during the pandemic enabled fine-grained studies of virus evolution in the human population. Serial passaging in vitro offers a controlled environment to investigate the emergence and persistence of genetic variants that may confer selective advantage. Nine virus lineages, including four \"variants of concern\" and three former \"variants under investigation\" as designated by the World Health Organisation, were chosen to investigate intra- and inter-lineage evolution through long-term serial passaging in Vero E6 cells. Viruses were sampled over at least 33 passages (range 33-100) and analysed using WGS to examine evolutionary dynamics and identify key mutations with implications for virus fitness, transmissibility, and immune evasion. All passages continued to replicate in culture, despite regular accumulation of mutations. There was evidence of convergent acquisition of mutations both across passage lines and compared with contemporaneous SARS CoV-2 clinical sequences from population studies. Some of these convergent mutations are hypothesised to be important in proliferation of SARS-CoV-2 lineages, such as by evading host immune responses (e.g. S:A67V, S:H655Y). Given these mutations arose in vitro, in the absence of a multicellular host immune response, this suggests virus genome mutation resulted from stochastic events, rather than immune-driven mutation. There was a regular gain and loss of low-frequency variants during serial passaging, but some became fixed in subsequent multiple passages, suggesting either a benefit of the mutation in vitro, or at least a lack of deleterious effect. Our findings reveal valuable insights into the evolution of SARS-CoV-2 by quantitatively investigating evolutionary dynamics of the virus over the greatest number of serial passages to date. Knowledge of these evolutionary trends will be useful for public health and the development of antiviral and vaccine measures to reduce the effects of SARS CoV-2 infection on the human population.", + "rel_abs": "Measures to control the COVID-19 pandemic such as antiviral therapy and vaccination have been challenged by ongoing virus evolution under antiviral and immune pressures. Understanding viral evolutionary dynamics is crucial for responding to SARS-CoV-2, and preparing for the next pandemic, by informing prediction of virus adaptation, public health strategies, and design of broadly effective therapies. Whole-genome sequencing (WGS) of SARS-CoV-2 during the pandemic enabled fine-grained studies of virus evolution in the human population. Serial passaging in vitro offers a controlled environment to investigate the emergence and persistence of genetic variants that may confer selective advantage.\n\nNine virus lineages, including four \"variants of concern\" and three former \"variants under investigation\" as designated by the World Health Organisation, were chosen to investigate intra- and inter-lineage evolution through long-term serial passaging in Vero E6 cells. Viruses were sampled over at least 33 passages (range 33-100) and analysed using WGS to examine evolutionary dynamics and identify key mutations with implications for virus fitness, transmissibility, and immune evasion. All passages continued to replicate in culture, despite regular accumulation of mutations. There was evidence of convergent acquisition of mutations both across passage lines and compared with contemporaneous SARS CoV-2 clinical sequences from population studies. Some of these convergent mutations are hypothesised to be important in proliferation of SARS-CoV-2 lineages, such as by evading host immune responses (e.g. S:A67V, S:H655Y). Given these mutations arose in vitro, in the absence of a multicellular host immune response, this suggests virus genome mutation resulted from stochastic events, rather than immune-driven mutation. There was a regular gain and loss of low-frequency variants during serial passaging, but some became fixed in subsequent multiple passages, suggesting either a benefit of the mutation in vitro, or at least a lack of deleterious effect. Our findings reveal valuable insights into the evolution of SARS-CoV-2 by quantitatively investigating evolutionary dynamics of the virus over the greatest number of serial passages to date. Knowledge of these evolutionary trends will be useful for public health and the development of antiviral and vaccine measures to reduce the effects of SARS CoV-2 infection on the human population.", "rel_num_authors": 10, "rel_authors": [ { @@ -3307,45 +3719,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.10.30.564766", - "rel_title": "Stability of DNA-Methylation Profiles of Biological Aging in Children and Adolescents", - "rel_date": "2023-11-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.30.564766", - "rel_abs": "Background and ObjectivesMethylation profile scores (MPSs) index biological aging and aging-related disease in adults and are cross-sectionally associated with social determinants of health in childhood. MPSs thus provide an opportunity to trace how aging-related biology responds to environmental changes in early life. Information regarding the stability of MPSs in early life is currently lacking.\n\nMethodWe use longitudinal data from children and adolescents ages 8-18 (N = 428, M age = 12.15 years) from the Texas Twin Project. Participants contributed two waves of salivary DNA-methylation data (mean lag = 3.94 years), which were used to construct four MPSs reflecting multi-system physiological decline and mortality risk (PhenoAgeAccel and GrimAgeAccel), pace of biological aging (DunedinPACE), and cognitive function (Epigenetic-g). Furthermore, we exploit variation among participants in whether they were exposed to the COVID-19 pandemic during the course of study participation, in order to test how a historical period characterized by environmental disruption might affect childrens aging-related MPSs.\n\nResultsAll MPSs showed moderate longitudinal stability (test-retest rs = 0.42, 0.44, 0.46, 0.51 for PhenoAgeAccel, GrimAgeAccel, and Epigenetic-g, and DunedinPACE, respectively). No differences in the stability of MPSs were apparent between those whose second assessment took place after the onset of the COVID-19 pandemic vs. those for whom both assessments took place prior to the pandemic.\n\nConclusionsAging-related DNA-methylation patterns are less stable in childhood than has been previously observed in adulthood. Further developmental research on the methylome is necessary to understand which environmental perturbations in childhood impact trajectories of biological aging and when children are most sensitive to those impacts.\n\nArticle SummaryMethylation profiles of biological aging are less stable in childhood than has been previously observed in adulthood.\n\nWhats Known on This SubjectMethylation profile scores (MPSs) index biological aging in adults and are cross-sectionally associated with social determinants of health in childhood. Aging-related MPSs in adulthood show very high test-retest stability but data on longitudinal stability of MPSs in childhood is sparse.\n\nWhat This Study AddsChildrens methylation profiles of biological aging are moderately stable across an approximately four-year period. Methylation profiles are less stable in childhood than in adulthood, suggesting that aging-related biology in childhood might be more responsive to environmental changes than in adulthood.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Abby J deSteiguer", - "author_inst": "University of Texas at Austin" - }, - { - "author_name": "Laurel Raffington", - "author_inst": "Max Planck Institute for Human Development" - }, - { - "author_name": "Aditi Sabhlok", - "author_inst": "University of Texas at Austin" - }, - { - "author_name": "Peter T Tanksley", - "author_inst": "University of Texas at Austin" - }, - { - "author_name": "Kathryn Paige Harden", - "author_inst": "University of Texas at Austin" - }, - { - "author_name": "Elliot M Tucker-Drob", - "author_inst": "University of Texas at Austin" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "developmental biology" - }, { "rel_doi": "10.1101/2023.10.30.564067", "rel_title": "Pervasive aggregation and depletion of host and viral proteins in response to cysteine-reactive electrophilic compounds", @@ -3442,7 +3815,7 @@ "rel_date": "2023-11-01", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.30.564631", - "rel_abs": "RationaleTNF inhibitors have shown promise in reducing mortality in hospitalized COVID-19 patients; one hypothesis explaining the limited clinical efficacy is patient heterogeneity in the TNF pathway.\n\nMethodsWe evaluated the effect of TNF inhibitors in a mouse model of LPS-induced acute lung injury. Using machine learning we attempted predictive enrichment of TNF signaling in patients with either ARDS or sepsis. We examined biological factors that drive heterogeneity in host responses to critical infection and their relation to clinical outcomes.\n\nResultsIn mice, LPS induced TNF-dependent neutrophilia, alveolar permeability and endothelial injury. In humans, TNF pathway activation was significantly increased in peripheral blood of patients with critical illnesses and associated with the presence of mature neutrophils across critical illnesses and several autoimmune conditions. Machine learning using a gene signature separated patients into 5 phenotypes; one was a hyper-inflammatory, interferon-associated phenotype enriched for increased TNF pathway activation and conserved across critical illnesses and autoimmune diseases. Cell subset profiles segregated severely ill patients into neutrophil-subset-dependent groups that were enriched for disease severity, demonstrating the importance of neutrophils in the immune response in critical illness.\n\nConclusionsTNF signaling and mature neutrophils are associated with a hyper-inflammatory phenotype of patients, shared across critical illness and autoimmune disease. This phenotyping provides a personalized medicine hypothesis to test anti-TNF therapy in severe respiratory illness.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC=\"FIGDIR/small/564631v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (36K):\norg.highwire.dtl.DTLVardef@198dd22org.highwire.dtl.DTLVardef@de00b8org.highwire.dtl.DTLVardef@10162bdorg.highwire.dtl.DTLVardef@1f995ff_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_abs": "RationaleTNF inhibitors have shown promise in reducing mortality in hospitalized COVID-19 patients; one hypothesis explaining the limited clinical efficacy is patient heterogeneity in the TNF pathway.\n\nMethodsWe evaluated the effect of TNF inhibitors in a mouse model of LPS-induced acute lung injury. Using machine learning we attempted predictive enrichment of TNF signaling in patients with either ARDS or sepsis. We examined biological factors that drive heterogeneity in host responses to critical infection and their relation to clinical outcomes.\n\nResultsIn mice, LPS induced TNF-dependent neutrophilia, alveolar permeability and endothelial injury. In humans, TNF pathway activation was significantly increased in peripheral blood of patients with critical illnesses and associated with the presence of mature neutrophils across critical illnesses and several autoimmune conditions. Machine learning using a gene signature separated patients into 5 phenotypes; one was a hyper-inflammatory, interferon-associated phenotype enriched for increased TNF pathway activation and conserved across critical illnesses and autoimmune diseases. Cell subset profiles segregated severely ill patients into neutrophil-subset-dependent groups that were enriched for disease severity, demonstrating the importance of neutrophils in the immune response in critical illness.\n\nConclusionsTNF signaling and mature neutrophils are associated with a hyper-inflammatory phenotype of patients, shared across critical illness and autoimmune disease. This phenotyping provides a personalized medicine hypothesis to test anti-TNF therapy in severe respiratory illness.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC=\"FIGDIR/small/564631v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (36K):\norg.highwire.dtl.DTLVardef@1e25724org.highwire.dtl.DTLVardef@c708bcorg.highwire.dtl.DTLVardef@10e7531org.highwire.dtl.DTLVardef@3014b8_HPS_FORMAT_FIGEXP M_FIG C_FIG", "rel_num_authors": 13, "rel_authors": [ { @@ -3967,6 +4340,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.10.27.564440", + "rel_title": "NK cell-monocyte crosstalk underlies NK cell activation in severe COVID-19", + "rel_date": "2023-10-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.27.564440", + "rel_abs": "NK cells in the peripheral blood of severe COVID-19 patients exhibit a unique profile characterized by activation and dysfunction. Previous studies have identified soluble factors, including type I interferon and TGF{beta}, that underlie this dysregulation. However, the role of cell-cell interactions in mediating changes in NK cell function during COVID-19 remains unclear. To address this question, we combined cell-cell communication analysis on existing single-cell RNA sequencing data with in vitro primary cell co-culture experiments to dissect the mechanisms underlying NK cell dysfunction in COVID-19. We found that NK cells are predicted to interact most strongly with monocytes and that this occurs via both soluble factors and direct interactions. To validate these findings, we performed in vitro co-cultures in which NK cells from healthy donors were incubated with monocytes from COVID-19+ or healthy donors. Co-culture of healthy NK cells with monocytes from COVID-19 patients recapitulated aspects of the NK cell phenotype observed in severe COVID-19, including decreased expression of NKG2D, increased expression of activation markers, and increased proliferation. When these experiments were performed in a transwell setting, we found that only CD56bright CD16- NK cells were activated in the presence of severe COVID-19 patient monocytes. O-link analysis of supernatants from transwell co-cultures revealed that cultures containing severe COVID-19 patient monocytes had significantly elevated levels of proinflammatory cytokines and chemokines as well as TGF{beta}. Collectively, these results demonstrate that interactions between NK cells and monocytes in the peripheral blood of COVID-19 patients contribute to NK cell activation and dysfunction in severe COVID-19.\n\nBACKGROUNDNatural killer (NK) cells are innate lymphocytes that are critical antiviral effectors. Because of their role in controlling acute viral infections, multiple studies have evaluated the role of NK cells in SARS-CoV-2 infection. Such studies revealed that NK cell phenotype and function are significantly altered by severe COVID-19; the peripheral NK cells of severe COVID-19 patients are highly activated and proliferative(1-5), with increased expression of cytotoxic molecules, Ki-67, and several surface markers of activation(3, 5-8). However, these NK cells also have dysfunctional cytotoxic responses to both tumor target cells(1, 2, 9, 10) and SARS-CoV-2-infected target cells(9, 10). Given that peripheral NK cells are thought to migrate to the lung during COVID-19(11-13), these results suggest that the NK cells of severe COVID-19 patients may be incapable of mounting a successful antiviral response to SARS-CoV-2 infection.\n\nAlthough the unique phenotype and dysfunctionality of NK cells in severe COVID-19 has been well-characterized, the processes underlying these phenomena have not. Only one study has conducted in vitro mechanistic experiments to identify a possible cause of NK cell dysfunction: Witkowski et al. identified serum-derived TGF{beta} as a suppressor of NK cell functionality in severe COVID-19 patients(9). However, this study did not identify the source of serum TGF{beta}. Additionally, given the high degree of complexity within the immune system, there are likely other causes of NK cell dysfunction in COVID-19 that have thus far remain unexplored. One such mechanism may be the myriad of interactions between NK cells and other peripheral immune cells. NK cells are known to interact with CD4 and CD8 T cells, dendritic cells, neutrophils, and macrophages/monocytes(14), which can prime NK cell cytotoxicity or induce tolerance. Previous work by our lab suggested the potential for NK cell-monocyte crosstalk in severe COVID-19 through the expression of ligands for NK cell activating receptors on the monocytes of these patients(3). Crosstalk between NK cells and monocytes plays a role in regulating the NK cell response to other infections, including HIV-1(15, 16), mouse(17) and human cytomegalovirus(18), and malaria(19) through mechanisms including secretion of NK cell-regulating cytokines by monocytes.\n\nIn this study, we used a combination of computational and in vitro methods to dissect the interactions between NK cells and monocytes in severe COVID-19. We utilized primary NK cells and monocytes from a large cohort of COVID-19 patients to demonstrate that co-culture of healthy NK cells with monocytes from severe COVID-19 donors can partially recapitulate the activated phenotype observed in the NK cells from COVID-19 patients. We then interrogated the mechanisms by which this activation occurs by performing NK cell-monocyte co-cultures in a transwell setting and using O-link to analyze the cytokines present in this system. Collectively, our work identifies monocytes as a driver of NK cell activation in severe COVID-19 and reveals interactions between NK cells and monocytes that may underlie this process.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Madeline J Lee", + "author_inst": "Stanford University" + }, + { + "author_name": "Izumi de los Rios Kobara", + "author_inst": "Stanford University" + }, + { + "author_name": "Trisha R Barnard", + "author_inst": "Stanford University" + }, + { + "author_name": "Xariana Vales Torres", + "author_inst": "Stanford University" + }, + { + "author_name": "Nicole H Tobin", + "author_inst": "David Geffen School of Medicine at UCLA" + }, + { + "author_name": "Kathie G Ferbas", + "author_inst": "David Geffen School of Medicine at UCLA" + }, + { + "author_name": "Anne W J Rimoin", + "author_inst": "University of California Los Angeles" + }, + { + "author_name": "Otto O Yang", + "author_inst": "David Geffen School of Medicine at UCLA" + }, + { + "author_name": "Grace M Aldrovandi", + "author_inst": "University of California Los Angeles" + }, + { + "author_name": "Aaron James Wilk", + "author_inst": "Stanford University" + }, + { + "author_name": "Jennifer Fulcher", + "author_inst": "University of California Los Angeles" + }, + { + "author_name": "Catherine A Blish", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.10.30.564680", "rel_title": "Characterization of Unique Pathological Features of COVID-Associated Coagulopathy: Studies with AC70 hACE2 Transgenic Mice Highly Permissive to SARS-CoV-2 Infection", @@ -4889,41 +5325,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2023.10.25.23297561", - "rel_title": "Changes in emergency department utilization in vulnerable populations after COVID-19 shelter in place orders", - "rel_date": "2023-10-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.25.23297561", - "rel_abs": "PurposeTo compare emergency department (ED) utilization and admission rates for patients with a history of mental health (MH), substance use disorder (SUD) and social determinants of health (SDOH) before and after implementing COVID-19s shelter-in-place (SIP) orders.\n\nMethodsThis was a retrospective, multicenter study leveraging electronic medical record data from 20 EDs across a large Midwest integrated healthcare system from 5/2/2019 to 12/31/2019 (pre-SIP) and from 5/2/2020 to 12/31/2020 (post-SIP). Diagnoses were documented in the patients medical records. Poisson and logistic regression models were used to evaluate ED utilization and admission rate changes.\n\nResults871,020 total ED encounters from 487,028 unique patients were captured. 2,572 (0.53%) patients had a documented Z code for SDOH. Patients with previously diagnosed MH or SUDs were more likely to seek ED care after the SIP orders were implemented (RR: 1.20, 95% CI: 1.18 - 1.22, p<0.001), as were patients with SDOH (RR: 2.37, 95% CI: 2.19 - 2.55, p<0.001). Patients with both previously diagnosed MH or SUD and a documented SDOH had even higher ED utilization (RR: 3.31, 95% CI: 2.83 - 3.88, p<0.001) than those with either condition alone. Patients with MH and SUDs (OR: 0.89, 95% CI: 0.86 - 0.92, p<0.001) or SDOH (OR: 0.67, 95% CI: 0.54, 0.83, p<0.001) were less likely to be admitted post-SIP orders while patients with a history of diseases of physiologic systems were more likely to be admitted.\n\nConclusionsVulnerable populations with a history of MH, SUD, and SDOH experienced increased ED utilization but a lower rate of hospital admissions after the implementation of SIP orders. The findings highlight the importance of addressing these needs to mitigate the impact of public health crises on these populations.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Philip Wang", - "author_inst": "Cleveland Clinic Lerner College of Medicine at Case Western Reserve University, EC-10 Cleveland Clinic, Cleveland, OH, USA" - }, - { - "author_name": "Akhil Anand", - "author_inst": "Department of Psychiatry and Psychology, Center for Behavioral Health, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA" - }, - { - "author_name": "James Bena", - "author_inst": "Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, Ohio" - }, - { - "author_name": "Shannon Morrison", - "author_inst": "Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, Ohio" - }, - { - "author_name": "Jeremy Weleff", - "author_inst": "Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2023.10.25.23297548", "rel_title": "The experiences and impact of the COVID-19 pandemic on Young Carers: practice implications and planning for future health emergencies", @@ -5629,6 +6030,261 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.10.26.23297581", + "rel_title": "Potential impact of annual vaccination with reformulated COVID-19 vaccines: lessons from the U.S. COVID-19 Scenario Modeling Hub", + "rel_date": "2023-10-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.26.23297581", + "rel_abs": "ImportanceCOVID-19 continues to cause significant hospitalizations and deaths in the United States. Its continued burden and the impact of annually reformulated vaccines remain unclear.\n\nObjectiveTo project COVID-19 hospitalizations and deaths from April 2023-April 2025 under two plausible assumptions about immune escape (20% per year and 50% per year) and three possible CDC recommendations for the use of annually reformulated vaccines (no vaccine recommendation, vaccination for those aged 65+, vaccination for all eligible groups).\n\nDesignThe COVID-19 Scenario Modeling Hub solicited projections of COVID-19 hospitalization and deaths between April 15, 2023-April 15, 2025 under six scenarios representing the intersection of considered levels of immune escape and vaccination. State and national projections from eight modeling teams were ensembled to produce projections for each scenario.\n\nSettingThe entire United States.\n\nParticipantsNone.\n\nExposureAnnually reformulated vaccines assumed to be 65% effective against strains circulating on June 15 of each year and to become available on September 1. Age and state specific coverage in recommended groups was assumed to match that seen for the first (fall 2021) COVID-19 booster.\n\nMain outcomes and measuresEnsemble estimates of weekly and cumulative COVID-19 hospitalizations and deaths. Expected relative and absolute reductions in hospitalizations and deaths due to vaccination over the projection period.\n\nResultsFrom April 15, 2023-April 15, 2025, COVID-19 is projected to cause annual epidemics peaking November-January. In the most pessimistic scenario (high immune escape, no vaccination recommendation), we project 2.1 million (90% PI: 1,438,000-4,270,000) hospitalizations and 209,000 (90% PI: 139,000-461,000) deaths, exceeding pre-pandemic mortality of influenza and pneumonia. In high immune escape scenarios, vaccination of those aged 65+ results in 230,000 (95% CI: 104,000-355,000) fewer hospitalizations and 33,000 (95% CI: 12,000-54,000) fewer deaths, while vaccination of all eligible individuals results in 431,000 (95% CI: 264,000-598,000) fewer hospitalizations and 49,000 (95% CI: 29,000-69,000) fewer deaths.\n\nConclusion and RelevanceCOVID-19 is projected to be a significant public health threat over the coming two years. Broad vaccination has the potential to substantially reduce the burden of this disease.\n\nKey pointsO_ST_ABSQuestionC_ST_ABSWhat is the likely impact of COVID-19 from April 2023-April 2025 and to what extent can vaccination reduce hospitalizations and deaths?\n\nFindingsUnder plausible assumptions about viral evolution and waning immunity, COVID-19 will likely cause annual epidemics peaking in November-January over the two-year projection period. Though significant, hospitalizations and deaths are unlikely to reach levels seen in previous winters. The projected health impacts of COVID-19 are reduced by 10-20% through moderate use of reformulated vaccines.\n\nMeaningCOVID-19 is projected to remain a significant public health threat. Annual vaccination can reduce morbidity, mortality, and strain on health systems.", + "rel_num_authors": 60, + "rel_authors": [ + { + "author_name": "Sung-mok Jung", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Sara L Loo", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Emily Howerton", + "author_inst": "The Pennsylvania State University" + }, + { + "author_name": "Lucie Contamin", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Claire P Smith", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Erica C Carcel\u00e9n", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Katie Yan", + "author_inst": "The Pennsylvania State University" + }, + { + "author_name": "Samantha J Bents", + "author_inst": "National Institutes of Health Fogarty International Center" + }, + { + "author_name": "Jessi Espino", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "John Levander", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Nicholas G Reich", + "author_inst": "University of Massachusetts Amherst" + }, + { + "author_name": "Joseph C Lemaitre", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Koji Sato", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Clifton D McKee", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Alison L Hill", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Matteo Chinazzi", + "author_inst": "Northeastern University" + }, + { + "author_name": "Jessica T Davis", + "author_inst": "Northeastern University" + }, + { + "author_name": "Kunpeng Mu", + "author_inst": "Northeastern University" + }, + { + "author_name": "Alessandro Vespignani", + "author_inst": "Northeastern University" + }, + { + "author_name": "Erik T Rosenstrom", + "author_inst": "North Carolina State University" + }, + { + "author_name": "Sebastian A Rodriguez-Cartes", + "author_inst": "North Carolina State University" + }, + { + "author_name": "Julie S Ivy", + "author_inst": "North Carolina State University and University of Michigan" + }, + { + "author_name": "Maria E Mayorga", + "author_inst": "North Carolina State University" + }, + { + "author_name": "Julie L Swann", + "author_inst": "North Carolina State University" + }, + { + "author_name": "Guido Espa\u00f1a", + "author_inst": "University of Notre Dame" + }, + { + "author_name": "Sean Cavany", + "author_inst": "University of Notre Dame" + }, + { + "author_name": "Sean M Moore", + "author_inst": "University of Notre Dame" + }, + { + "author_name": "Alex Perkins", + "author_inst": "University of Notre Dame" + }, + { + "author_name": "Shi Chen", + "author_inst": "University of North Carolina at Charlotte" + }, + { + "author_name": "Rajib Paul", + "author_inst": "University of North Carolina at Charlotte" + }, + { + "author_name": "Daniel Janies", + "author_inst": "University of North Carolina at Charlotte" + }, + { + "author_name": "Jean-Claude Thill", + "author_inst": "University of North Carolina at Charlotte" + }, + { + "author_name": "Ajitesh Srivastava", + "author_inst": "University of Southern California" + }, + { + "author_name": "Majd Al Aawar", + "author_inst": "University of Southern California" + }, + { + "author_name": "Kaiming Bi", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Shraddha Ramdas Bandekar", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Anass Bouchnita", + "author_inst": "University of Texas at El Paso" + }, + { + "author_name": "Spencer J Fox", + "author_inst": "University of Georgia" + }, + { + "author_name": "Lauren Ancel Meyers", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Przemyslaw Porebski", + "author_inst": "University of Virginia" + }, + { + "author_name": "Srinivasan Venkatramanan", + "author_inst": "University of Virginia" + }, + { + "author_name": "Aniruddha Adiga", + "author_inst": "University of Virginia" + }, + { + "author_name": "Bryan Lewis", + "author_inst": "University of Virginia" + }, + { + "author_name": "Brian Klahn", + "author_inst": "University of Virginia" + }, + { + "author_name": "Benjamin Hurt", + "author_inst": "University of Virginia" + }, + { + "author_name": "Jiangzhuo Chen", + "author_inst": "University of Virginia" + }, + { + "author_name": "Amanda Wilson", + "author_inst": "University of Virginia" + }, + { + "author_name": "Stefan Hoops", + "author_inst": "University of Virginia" + }, + { + "author_name": "Parantapa Bhattacharya", + "author_inst": "University of Virginia" + }, + { + "author_name": "Dustin Machi", + "author_inst": "University of Virginia" + }, + { + "author_name": "Joseph Outten", + "author_inst": "University of Virginia" + }, + { + "author_name": "Henning Mortveit", + "author_inst": "University of Virginia" + }, + { + "author_name": "Anil Vullikanti", + "author_inst": "University of Virginia" + }, + { + "author_name": "Madhav Marathe", + "author_inst": "University of Virginia" + }, + { + "author_name": "Harry Hochheiser", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Michael C Runge", + "author_inst": "U.S. Geological Survey Eastern Ecological Science Center" + }, + { + "author_name": "Katriona Shea", + "author_inst": "The Pennsylvania State University" + }, + { + "author_name": "Shaun Truelove", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "C\u00e9cile Viboud", + "author_inst": "National Institutes of Health Fogarty International Center" + }, + { + "author_name": "Justin Lessler", + "author_inst": "University of North Carolina at Chapel Hill" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.10.26.23297598", "rel_title": "Assessing the causal effect of air pollution on risk of SARS-CoV-2 infection", @@ -6774,7 +7430,7 @@ "rel_date": "2023-10-24", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.23.563669", - "rel_abs": "COVID-19 can result in neurological symptoms such as fever, headache, dizziness, and nausea. We evaluated whether the Calcitonin Gene-Related Peptide (CGRP) receptor antagonist, olcegepant, used in migraine treatment could mitigate acute neuroinflammatory and neurological responses to SARS-COV-2 infection. We infected wildtype C57BL/6J and 129/SvEv mice, and a 129 CGRP-null mouse line with a mouse-adapted SARS-CoV-2 virus, and evaluated the effect of CGRP receptor antagonism on the outcome of that infection. We determined that CGRP receptor antagonism provided protection from permanent weight loss in older (>12 m) C57BL/6J and 129 SvEv mice. We also observed acute fever and motion-induced dizziness in all older mice, regardless of treatment. However, in both wildtype mouse lines, CGRP antagonism reduced acute interleukin 6 (IL-6) levels by half, with virtually no IL-6 release in mice lacking CGRP. These findings suggest that blockage of CGRP signaling protects against acute IL-6 release and subsequent inflammatory events after SARS-CoV-2 infection.\n\nSignificance StatementCOVID-19 can cause neurological symptoms such as fever, headache, dizziness, and nausea. However, such neurological symptoms of SARS-CoV-2 infection have not been assessed in mouse models. Here, we infected two commonly used wildtype mice lines (C57BL/6 and 129S) with mouse-adapted SARS-CoV-2 - and demonstrated neurological signs that including motion-related dizziness. Further, we show that CGRP signaling blockade can reduce IL-6 release and reverse long-term weight loss associated with SARS-CoV-2 infection, without rescuing either fever and dizziness. These findings suggest that CGRP signaling blockade can be protective in acute SARS-CoV-2 infections, and raise the possibility that it may also impact long-term outcomes of infection.", + "rel_abs": "COVID-19 can result in neurological symptoms such as fever, headache, dizziness, and nausea. We evaluated whether the Calcitonin Gene-Related Peptide (CGRP) receptor antagonist, olcegepant, used in migraine treatment could mitigate acute neuroinflammatory and neurological responses to SARS-COV-2 infection. We infected wildtype C57BL/6J and 129/SvEv mice, and a 129 CGRP-null mouse line with a mouse-adapted SARS-CoV-2 virus, and evaluated the effect of CGRP receptor antagonism on the outcome of that infection. We determined that CGRP receptor antagonism provided protection from permanent weight loss in older (>12 m) C57BL/6J and 129 SvEv mice. We also observed acute fever and motion-induced dizziness in all older mice, regardless of treatment. However, in both wildtype mouse lines, CGRP antagonism reduced acute interleukin 6 (IL-6) levels by half, with virtually no IL-6 release in mice lacking CGRP. These findings suggest that blockage of CGRP signaling protects against acute IL-6 release and subsequent inflammatory events after SARS-CoV-2 infection.\n\nSignificance StatementCOVID-19 can cause neurological symptoms such as fever, headache, dizziness, and nausea. However, such neurological symptoms of SARS-CoV-2 infection have not been assessed in mouse models. Here, we infected two commonly used wildtype mice lines (C57BL/6 and 129S) with mouse-adapted SARS-CoV-2 - and demonstrated neurological signs that including motion-related dizziness. Further, we show that CGRP signaling blockade can reduce IL-6 release and reverse long-term weight loss associated with SARS-CoV-2 infection, without rescuing either fever and/or dizziness. These findings suggest that CGRP signaling blockade can be protective in acute SARS-CoV-2 infections, and raise the possibility that it may also impact long-term outcomes of infection.", "rel_num_authors": 10, "rel_authors": [ { @@ -6823,61 +7479,6 @@ "type": "new results", "category": "neuroscience" }, - { - "rel_doi": "10.1101/2023.10.23.563621", - "rel_title": "Heterotypic responses against nsp12/nsp13 from prior SARS-CoV-2 infection associates with lower subsequent endemic coronavirus incidence", - "rel_date": "2023-10-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.23.563621", - "rel_abs": "Immune responses from prior SARS-CoV-2 infection and COVID-19 vaccination do not prevent re-infections and may not protect against future novel coronaviruses (CoVs). We examined the incidence of and immune differences against human endemic CoVs (eCoV) as a proxy for response against future emerging CoVs. Assessment was among those with known SARS-CoV-2 infection, COVID-19 vaccination but no documented SARS-CoV-2 infection, or neither exposure. Retrospective cohort analyses suggest that prior SARS-CoV-2 infection, but not COVID-19 vaccination alone, protects against subsequent symptomatic eCoV infection. CD8+ T cell responses to the non-structural eCoV proteins, nsp12 and nsp13, were significantly higher in individuals with previous SARS-CoV-2 infection as compared to the other groups. The three groups had similar cellular responses against the eCoV spike and nucleocapsid, and those with prior spike exposure had lower eCoV-directed neutralizing antibodies. Incorporation of non-structural viral antigens in a future pan-CoV vaccine may improve protection against future heterologous CoV infections.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "David J Bean", - "author_inst": "Boston University Chobanian & Avedisian School of Medicine" - }, - { - "author_name": "Janet Monroe", - "author_inst": "Boston University Chobanian & Avedisian School of Medicine" - }, - { - "author_name": "Yan Mei Liang", - "author_inst": "Boston University Chobanian & Avedisian School of Medicine" - }, - { - "author_name": "Ella Borberg", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Yasmeen Senussi", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Zoe Swank", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Sujata Chalise", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "David Walt", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Janice Weinberg", - "author_inst": "Boston University School of Public Health" - }, - { - "author_name": "Manish Sagar", - "author_inst": "Boston University Chobanian & Avedisian School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.10.22.563481", "rel_title": "Microfluidic antibody profiling after repeated SARS-CoV-2 vaccination links antibody affinity and concentration to impaired immunity and variant escape in patients on anti-CD-20 therapy", @@ -6963,7 +7564,7 @@ "rel_date": "2023-10-24", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.23.563088", - "rel_abs": "Since it was proposed as a potential host-directed antiviral agent for SARS-CoV-2, the antiparasitic drug ivermectin has been investigated thoroughly in clinical trials, which have provided insufficient support for its clinical efficacy. To examine the potential for ivermectin to be repurposed as an antiviral agent, we therefore undertook a series of preclinical studies. Consistent with early reports, ivermectin decreased SARS-CoV-2 viral burden in in vitro models at low micromolar concentrations, five-to ten-fold higher than the reported toxic clinical concentration. At similar concentrations, ivermectin also decreased cell viability and increased biomarkers of cytotoxicity and apoptosis. Further mechanistic and profiling studies revealed that ivermectin nonspecifically perturbs membrane bilayers at the same concentrations where it decreases the SARS-CoV-2 viral burden, resulting in nonspecific modulation of membrane-based targets such as G-protein coupled receptors and ion channels. These results suggest that a primary molecular mechanism for the in vitro antiviral activity of ivermectin may be nonspecific membrane perturbation, indicating that ivermectin is unlikely to be translatable into a safe and effective antiviral agent. These results and experimental workflow provide a useful paradigm for performing preclinical studies on (pandemic-related) drug repurposing candidates.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=61 SRC=\"FIGDIR/small/563088v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (18K):\norg.highwire.dtl.DTLVardef@1ee9b50org.highwire.dtl.DTLVardef@16dca6org.highwire.dtl.DTLVardef@f03208org.highwire.dtl.DTLVardef@164b6fb_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG", + "rel_abs": "Since it was proposed as a potential host-directed antiviral agent for SARS-CoV-2, the antiparasitic drug ivermectin has been investigated thoroughly in clinical trials, which have provided insufficient support for its clinical efficacy. To examine the potential for ivermectin to be repurposed as an antiviral agent, we therefore undertook a series of preclinical studies. Consistent with early reports, ivermectin decreased SARS-CoV-2 viral burden in in vitro models at low micromolar concentrations, five-to ten-fold higher than the reported toxic clinical concentration. At similar concentrations, ivermectin also decreased cell viability and increased biomarkers of cytotoxicity and apoptosis. Further mechanistic and profiling studies revealed that ivermectin nonspecifically perturbs membrane bilayers at the same concentrations where it decreases the SARS-CoV-2 viral burden, resulting in nonspecific modulation of membrane-based targets such as G-protein coupled receptors and ion channels. These results suggest that a primary molecular mechanism for the in vitro antiviral activity of ivermectin may be nonspecific membrane perturbation, indicating that ivermectin is unlikely to be translatable into a safe and effective antiviral agent. These results and experimental workflow provide a useful paradigm for performing preclinical studies on (pandemic-related) drug repurposing candidates.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=61 SRC=\"FIGDIR/small/563088v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (18K):\norg.highwire.dtl.DTLVardef@1324fc9org.highwire.dtl.DTLVardef@143275org.highwire.dtl.DTLVardef@1fcaaa6org.highwire.dtl.DTLVardef@1277c62_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG", "rel_num_authors": 14, "rel_authors": [ { @@ -7475,6 +8076,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, + { + "rel_doi": "10.1101/2023.10.22.23297358", + "rel_title": "Proportion of cancer cases and deaths attributable to potentially modifiable risk factors in Peru prior to the COVID-19 pandemic", + "rel_date": "2023-10-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.22.23297358", + "rel_abs": "OBJECTIVETo estimate the fraction of cancer cases and deaths attributable to potentially modifiable risk factors in Peru in 2018, prior to the COVID-19 pandemic.\n\nMATERIAL AND METHODSAn ecological study was carried out using the prevalence of exposure of the Peruvian population to modifiable risk factors for cancer, relative risk of each risk factor, and number of cancer cases and deaths in 2018 as inputs. We used the Parkin formula with a Montecarlo statistical simulation model to calculate the population attributable fraction (PAF) and confidence intervals. The number of new cancer cases and deaths attributable to each risk factor was calculated by multiplying the number of cases and deaths in each sex by the PAF of each risk factor.\n\nRESULTS38.4% of new cases (34.4% in men and 41.8% in women) and 43.2% of deaths by cancer in Peru (43.1% in men and 43.2% in women) were attributable to modifiable risk factors. The number of cancers attributable was 25,591 (10,616 in men and 14,975 in women) and the number of deaths attributable to cancer was 14,922 (6,996 in men and 7,926 in women). The modifiable risk factors that caused a greater number of cases and deaths were HPV infection (4563 cases, 2410 deaths), current tobacco use (3387 cases, 2198 deaths), and Helicobacter pylori infection (2686 cases, 1874 deaths). The oncogenic infections made up the group of risk factors that presented a greater PAF (16.6% for cases, 19.1% for deaths) followed by other unhealthy lifestyle factors (14.1% for cases, 16.5% for deaths), tobacco (7.2% for cases, 7.3% for deaths) and ultraviolet radiation (0.5% for cases, 0.3% for deaths).\n\nCONCLUSIONPrior to the COVID-19 pandemic, a proportion of 38.4% of cancer cases and 43.2% of cancer deaths in Peru during 2018 were attributable to modifiable risk factors. Most preventable cancer cases and deaths are linked to oncogenic infections, primarily caused by HPV and Helicobacter pylori.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Jhony A. De La Cruz-Vargas", + "author_inst": "Instituto de Investigaciones en Ciencias Biomedicas, Universidad Ricardo Palma. Lima-Peru." + }, + { + "author_name": "Willy Ramos", + "author_inst": "Instituto de Investigaciones en Ciencias Biomedicas, Universidad Ricardo Palma. Lima-Peru." + }, + { + "author_name": "Willer D Chanduvi Puicon", + "author_inst": "Instituto de Investigaciones en Ciencias Biomedicas, Universidad Ricardo Palma. Lima-Peru." + }, + { + "author_name": "Lucy E. Correa-Lopez", + "author_inst": "Instituto de Investigaciones en Ciencias Biomedicas, Universidad Ricardo Palma. Lima-Peru." + }, + { + "author_name": "Nadia Guerrero", + "author_inst": "Instituto de Investigaciones en Ciencias Biomedicas, Universidad Ricardo Palma. Lima-Peru." + }, + { + "author_name": "Joan Loayza-Castro", + "author_inst": "Instituto de Investigaciones en Ciencias Biomedicas, Universidad Ricardo Palma. Lima-Peru." + }, + { + "author_name": "Irene M. Tami-Maury", + "author_inst": "The University of Texas Health Science Center at Houston. Houston, USA" + }, + { + "author_name": "Diego Venegas", + "author_inst": "Facultad de Ciencias e Ingenieria. Universidad Peruana Cayetano Heredia, Lima-Peru" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.10.22.23297069", "rel_title": "Post-COVID chronic neuropsychiatric symptoms persisting beyond one year from infection- a case-control study and network analysis", @@ -8685,61 +9333,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.10.09.23296726", - "rel_title": "XAV-19 a Glyco-Humanized polyclonal antibody targeting SARS-CoV-2 accelerates the recovery of mild to moderate COVID-19 patients and keeps its neutralizing activity against Omicron and its subvariants.", - "rel_date": "2023-10-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.09.23296726", - "rel_abs": "BackgroundXAV-19 is a glyco-humanized swine polyclonal antibody targeting SARS-CoV-2. The safety and clinical efficacy of XAV-19 was investigated in patients with a WHO score of 2 to 4 in the WHO 7-point ordinal scale. The activity of XAV-19 against Omicron and its subvariants was assessed in vitro.\n\nMethodsA phase II/III, multicentric randomized double-blind placebo-controlled, clinical trial was conducted to evaluate the safety and clinical efficacy of XAV-19 in inpatients with COVID-19 requiring or not oxygen therapy and outpatients not requiring oxygen (EUROXAV trial, NCT04928430). Most patients were not vaccinated. The primary endpoint was the proportion of patients with an aggravation of COVID-19 within 8 days after treatment. Binding and neutralization of Omicron or its subvariants by XAV-19 was investigated by ELISA or with a whole virus neutralization assay.\n\nResultsPatients received either 150mg of XAV-19 (N=139) or placebo (N=140). Low enrolment forced the premature trial termination. XAV-19 was well tolerated. No difference in the primary endpoint, nor in the proportion with an improvement at day 8 (secondary endpoint) was observed between the 2 groups. For patients not requiring oxygen therapy, XAV-19 reduced the time to improvement significantly (7 days vs 14 days p=0.0159). Neutralizing activity against Omicron and BA.2, BA2.12.1, BA.4/5 and BQ1.1 subvariants was shown in vitro.\n\nConclusionsXAV-19 did not reduce the aggravation in COVID-19 patients. While it did not bring any benefit to patients requiring oxygen, it reduced the time to improvement for patients not requiring oxygen (WHO score 2 or 3). These preliminary clinical data might indicate a therapeutic potential for patients with mild to moderate COVID-19 requiring supplementation with anti-SARS-CoV-2 neutralizing antibodies.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Garyfallia Poulakou", - "author_inst": "3rd Department of Internal Medicine, Medical School, Sotiria General Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece" - }, - { - "author_name": "Pierre-Joseph Royer", - "author_inst": "Xenothera" - }, - { - "author_name": "Nikolai Evgeniev", - "author_inst": "Complex Oncology Center, Department of Medical oncology, Russe, Bulgaria" - }, - { - "author_name": "Gwena\u00eblle Evanno", - "author_inst": "Xenothera" - }, - { - "author_name": "Fran\u00e7oise Shneiker", - "author_inst": "Xenothera" - }, - { - "author_name": "Anne-Genevi\u00e8ve Marcelin", - "author_inst": "Sorbonne Universit\u00e9 INSERM 1136, Institut Pierre Louis d'Epid\u00e9miologie et de Sant\u00e9 Publique, Assistance Publique-H\u00f4pitaux de Paris (AP-HP), Piti\u00e9 Salp\u00eatri\u00e8re Ho" - }, - { - "author_name": "Bernard Vanhove", - "author_inst": "Xenothera" - }, - { - "author_name": "Odile Duvaux", - "author_inst": "Xenothera" - }, - { - "author_name": "St\u00e9phane Marot", - "author_inst": "Sorbonne Universit\u00e9 INSERM 1136, Institut Pierre Louis d'Epid\u00e9miologie et de Sant\u00e9 Publique, Assistance Publique-H\u00f4pitaux de Paris (AP-HP), Piti\u00e9 Salp\u00eatri\u00e8re Ho" - }, - { - "author_name": "Vincent Calvez", - "author_inst": "Sorbonne Universit\u00e9 INSERM 1136, Institut Pierre Louis d'Epid\u00e9miologie et de Sant\u00e9 Publique, Assistance Publique-H\u00f4pitaux de Paris (AP-HP), Piti\u00e9 Salp\u00eatri\u00e8re Ho" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.10.18.23297204", "rel_title": "Excess deaths in China during SARS-CoV-2 viral waves in 2022-2023", @@ -9237,6 +9830,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2023.10.16.23297064", + "rel_title": "Trends in Nationally Notifiable Infectious Diseases in Humans and Animals During the COVID-19 Pandemic in South Korea", + "rel_date": "2023-10-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.16.23297064", + "rel_abs": "Non-pharmaceutical interventions (NPIs) were implemented to cope with the coronavirus disease 2019 (COVID-19) pandemic in South Korea. These interventions could also have affected other infectious diseases, but there have been no comprehensive studies regarding their impacts. This study examined trends in notifiable infectious diseases in both humans and animals during the COVID-19 pandemic. Autoregressive integrated moving average (ARIMA) models were developed for each disease using data from 2016 to 2019, and the incidences for 2020 to 2021 were predicted. Subsequently, the predicted numbers of cases were compared with actual observations. Our findings indicated a substantial reduction in human respiratory infectious diseases during implementation of NPIs. However, human gastrointestinal infectious diseases and livestock diseases did not show a significant decrease. The results revealed that the preventive effect sizes of NPIs varied among diseases and indicated the potential for side effects, suggesting that complementary interventions are needed to minimize these negative effects.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Taehee Chang", + "author_inst": "Institute of Health and Environment, Seoul National University, Seoul, Republic of Korea" + }, + { + "author_name": "Sung-il Cho", + "author_inst": "Department of Public Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea" + }, + { + "author_name": "Dae-sung Yoo", + "author_inst": "College of Veterinary Medicine, Chonnam National University, Gwangju, Republic of Korea" + }, + { + "author_name": "Kyung-Duk Min", + "author_inst": "College of Veterinary Medicine, Chungbuk National University, Republic of Korea" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.10.11.23296868", "rel_title": "Did long COVID increase road deaths in the U.S.?", @@ -10543,41 +11167,6 @@ "type": "new results", "category": "genetics" }, - { - "rel_doi": "10.1101/2023.10.11.561925", - "rel_title": "Sex-Specific Development of ssRNA Virus Receptor Gene Expression in the Human Brain", - "rel_date": "2023-10-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.11.561925", - "rel_abs": "Viral infection severity often varies with host factors such as age and sex. The pathogenesis of infections caused by a broad range of viruses, from neurotropic viruses like Rabies and Zika to respiratory viruses such as influenza and SARS-CoV-2, differ between the sexes and across the lifespan. Typically, older males are more susceptible to severe acute outcomes, while females are more vulnerable to the post-acute sequelae of infections. All of these complications can include neuroinflammation, stroke, cognitive dysfunction, and delirium. While these symptoms can be secondary to infection, recent studies suggest that even peripheral infections can lead to neuropathological changes in the brain. However, few studies have characterized the expression of viral receptors in the human brain or examined age- or sex-related differences in such expression. In this study, we used a publicly accessible transcriptomic database to assess the impact of age and sex on the expression of 67 viral host factor genes, associated with ten virus families. Analyzing data from 15 brain areas (n=33, F=14, M=19, age:4 mo-80 yrs), we determined the lifespan trajectory for each gene in each area via LOESS regressions. We used unsupervised hierarchical clustering to determine if a brain-wide pattern or virus family pattern can be detected. Using Dense-tSNE, a dimension-reduction and visualization technique, we discovered four distinct developmental trajectories, clustering the areas into two mixed-sex subcortical clusters and one each of male and female cortical clusters. Applying Differential Expression Sliding Window Analysis (DeSWAN), we identified the genes driving these age- and sex-related differences. Many sex differences were noted in childhood, potentially impacting the brains susceptibility to viral infections and underscoring a broader dimorphic organization of male and female brains. These insights contribute to our understanding of sex-specific responses to viral infections, offering the potential for more personalized treatment strategies.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Negeen Halabian", - "author_inst": "McMaster University" - }, - { - "author_name": "Leanne Monteiro", - "author_inst": "McMaster University" - }, - { - "author_name": "Lisa Jaiwei Li", - "author_inst": "McMaster University" - }, - { - "author_name": "Maheshwar Panday", - "author_inst": "McMaster University" - }, - { - "author_name": "Kathy Murphy", - "author_inst": "McMaster University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "neuroscience" - }, { "rel_doi": "10.1101/2023.10.12.23296938", "rel_title": "The impact of COVID-19 on non-communicable disease patients in sub-Saharan African countries: systematic review", @@ -11259,6 +11848,121 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.10.09.557914", + "rel_title": "SARS-CoV-2 antibodies cross-react and enhance dengue infection", + "rel_date": "2023-10-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.09.557914", + "rel_abs": "Dengue disease is highly prevalent in tropical and subtropical regions worldwide. However, its pathogenesis is still incompletely understood, particularly in comparison to other endemic viruses. Antibody-dependent enhancement (ADE) is a well-known phenomenon for dengue viruses. Given the recent surge in dengue cases and potential cross-reactivity with SARS-CoV-2 antibodies, this study explores the impact of anti-SARS-CoV-2 antibodies on DENV-2 infection.\n\nThe study assessed the cross-reactivity of SARS-CoV-2 antibodies with the DENV-2 Virus. Human convalescent plasma samples collected during different waves of COVID-19 and monoclonal and polyclonal antibodies raised against SARS-CoV-2 were examined for their potential to cause ADE of DENV-2 infection using cell-based assays. The study found that anti-SARS-CoV-2 antibodies acquired from natural infection in humans or through experimental immunization in animals were cross-reactive with DENV-2 and had the potential to enhance DENV-2 infection in K562 and U937 cells. In-silico and in-vitro studies indicated a strong interaction between SARS-CoV-2 antibodies and DENV-2 E-protein, providing a molecular basis for these findings. This study is the first to demonstrate that anti-SARS-CoV-2 antibodies can cross-react with DENV-2 and can enhance its infection through ADE. These findings have implications for SARS-CoV-2 vaccine development and deployment strategies in regions where dengue is endemic.\n\nSummaryAntibodies against SARS-CoV-2 (RBD and Spike) showed significant cross reactivity with DENV-2 (E protein). Also, anti-SARS-CoV-2-commercial antibodies, immunised animal sera and 46 human convalescent plasma samples (from different waves of pandemic) demonstrated antibody-dependent enhancement (ADE) of DENV-2 infection.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Kamini Jakhar", + "author_inst": "Translational Health Science and technology Institute, Faridabad" + }, + { + "author_name": "Sudipta Sonar", + "author_inst": "Translational Health Science and technology Institute, Faridabad" + }, + { + "author_name": "Gagandeep Singh", + "author_inst": "Translational Health Science and technology Institute, Faridabad" + }, + { + "author_name": "Tania Sarkar", + "author_inst": "Translational Health Science and technology Institute, Faridabad" + }, + { + "author_name": "Mahima Tiwari", + "author_inst": "Translational Health Science and technology Institute, Faridabad" + }, + { + "author_name": "Jaskaran Kaur", + "author_inst": "Translational Health Science and technology Institute, Faridabad" + }, + { + "author_name": "Deepak Kumar Rathore", + "author_inst": "Translational Health Science and technology Institute, Faridabad" + }, + { + "author_name": "Banwari Lal", + "author_inst": "Translational Health Science and technology Institute, Faridabad" + }, + { + "author_name": "Sandeep Kumar", + "author_inst": "Translational Health Science and technology Institute, Faridabad" + }, + { + "author_name": "Puneet Srivastav", + "author_inst": "Translational Health Science and technology Institute, Faridabad" + }, + { + "author_name": "Satendra Kumar", + "author_inst": "Translational Health Science and technology Institute, Faridabad" + }, + { + "author_name": "Vikas Phagna", + "author_inst": "Translational Health Science and technology Institute, Faridabad" + }, + { + "author_name": "Lokesh Kumar", + "author_inst": "Translational Health Science and technology Institute, Faridabad" + }, + { + "author_name": "Vishal Gupta", + "author_inst": "Translational Health Science and technology Institute, Faridabad" + }, + { + "author_name": "Pallavi Kshetrapal", + "author_inst": "Translational Health Science and technology Institute, Faridabad" + }, + { + "author_name": "Savita Singh", + "author_inst": "Translational Health Science and technology Institute, Faridabad" + }, + { + "author_name": "Nitya Wadhwa", + "author_inst": "Translational Health Science and technology Institute, Faridabad" + }, + { + "author_name": "Ramachandran Thiruvengadam", + "author_inst": "Translational Health Science and technology Institute, Faridabad" + }, + { + "author_name": "Sreevatsan Raghavan", + "author_inst": "Translational Health Science and technology Institute, Faridabad" + }, + { + "author_name": "Mudita Gosain", + "author_inst": "Translational Health Science and technology Institute, Faridabad" + }, + { + "author_name": "Tripti Shrivastava", + "author_inst": "Translational Health Science and technology Institute, Faridabad" + }, + { + "author_name": "Sankar Bhattacharyya", + "author_inst": "Translational Health Science and technology Institute, Faridabad" + }, + { + "author_name": "Jayanta Bhattacharya", + "author_inst": "Translational Health Science and technology Institute, Faridabad" + }, + { + "author_name": "Shailendra Asthana", + "author_inst": "Translational Health Science and technology Institute, Faridabad" + }, + { + "author_name": "Shailendra Mani", + "author_inst": "Translational Health Science and technology Institute, Faridabad" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.10.09.561498", "rel_title": "SHIFTR enables the unbiased and multiplexed identification of proteins bound to specific RNA regions in live cells", @@ -12413,69 +13117,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.10.06.23296657", - "rel_title": "The macroeconomic and epidemiological impacts of Covid-19 in Pakistan.", - "rel_date": "2023-10-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.06.23296657", - "rel_abs": "\"Coronavirus Disease 2019\" (C19) is a respiratory illness caused by \"new Coronavirus\" SARS-CoV-2. The C19 pandemic, which engulfed the world in 2021, also caused a national C19 epidemic in Pakistan, who responded with initial forced lockdowns (15-30 March 2020) and a subsequent switch to a smart lockdown strategy, and, by 31 December 2020, Pakistan had managed to limit confirmed cases and case fatalities to 482,506 (456 per 100,000) and 10,176 (4.8 per 100,000). The early switch to a smart lockdown strategy, and successful follow-up move to central coordination and effective communication and enforcement of Standard Operating Procedures, was motivated by a concern over how broad-based forced lockdowns would affect poor households and day-labour. The current study aims to investigate how the national Pakistan C19 epidemic would have unfolded under an uncontrolled baseline scenario and an alternative set of controlled non-pharmaceutical intervention (NPI) policy lockdown scenarios, including health and macroeconomic outcomes. We employ a dynamically-recursive version of the IFPRI Standard Computable General Equilibrium model framework (Lofgren, Lee Harris and Robinson 2002), and a, by now, well-established epidemiological transmission-dynamic model framework (Davies, Klepac et al 2020) using Pakistan-specific 5-year age-group contact matrices on four types of contact rates, including at home, at work, at school, and at other locations (Prem, Cook & Jit 2017), to characterize an uncontrolled spread of disease. Our simulation results indicate that an uncontrolled C19 epidemic, by itself, would have led to a 0.12% reduction in Pakistani GDP (-721mn USD), and a total of 0.65mn critically ill and 1.52mn severely ill C19 patients during 2020-21, while 405,000 Pakistani citizens would have lost their lives. Since the majority of case fatalities and symptomatic cases, respectively 345,000 and 35.9mn, would have occurred in 2020, the case fatality and confirmed case numbers, observed by 31. December 2020 represents an outcome which is far better than the alternative. Case fatalities by 31. December 2020 could possibly have been somewhat improved either via a more prolonged one-off 10 week forced lockdown (66% reduction) or a 1-month forced lockdown/2-months opening intermittent lockdown strategy (33% reduction), but both sets of strategies would have carried significant GDP costs in the order of 2.2%-6.2% of real GDP.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Henning Tarp Jensen", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Marcus R. Keogh-Brown", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Rosalind M Eggo", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Carl A. B. Pearson", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Sergio Torres-Rueda", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Maryam Huda", - "author_inst": "Aga Khan University" - }, - { - "author_name": "Muhammad Khalid", - "author_inst": "Ministry of National Health Services, Regulations & Coordination, Islamabad, Pakistan" - }, - { - "author_name": "Wahaj Sulfiqar", - "author_inst": "Ministry of National Health Services, Regulations & Coordination, Islamabad, Pakistan" - }, - { - "author_name": "- CMMID COVID-19 Working Group", - "author_inst": "-" - }, - { - "author_name": "Richard D. Smith", - "author_inst": "University of Exeter" - }, - { - "author_name": "Mark Jit", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Anna Vassall", - "author_inst": "London School of Hygiene & Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.10.04.560875", "rel_title": "Unveiling the antiviral capabilities of targeting Human Dihydroorotate Dehydrogenase against SARS-CoV-2", @@ -13088,7 +13729,7 @@ "rel_date": "2023-10-04", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.03.560722", - "rel_abs": "The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has led to significant global morbidity and mortality. A crucial viral protein, the non-structural protein 14 (nsp14), catalyzes the methylation of viral RNA and plays a critical role in viral genome replication and transcription. Due to the low mutation rate in the nsp region among various SARS-CoV-2 variants, nsp14 has emerged as a promising therapeutic target. However, discovering potential inhibitors remains a challenge. In this work, we introduce a computational pipeline for the rapid and efficient identification of potential nsp14 inhibitors by leveraging virtual screening and the NCI open compound collection, which contains 250,000 freely available molecules for researchers worldwide. The introduced pipeline provides a cost-effective and efficient approach for early-stage drug discovery by allowing researchers to evaluate promising molecules without incurring synthesis expenses. Our pipeline successfully identified seven promising candidates after experimentally validating only 40 compounds. Notably, we discovered NSC620333, a compound that exhibits a strong binding affinity to nsp14 with a dissociation constant of 427 {+/-} 84 nM. In addition, we gained new insights into the structure and function of this protein through molecular dynamics simulations. We identified new conformational states of the protein and determined that residues Phe367, Tyr368, and Gln354 within the binding pocket serve as stabilizing residues for novel ligand interactions. We also found that metal coordination complexes are crucial for the overall function of the binding pocket. Lastly, we present the solved crystal structure of the nsp14-MTase complexed with SS148, a potent inhibitor of methyltransferase activity at the nanomolar level (IC50 value of 70 {+/-} 6 nM). Our computational pipeline accurately predicted the binding pose of SS148, demonstrating its effectiveness and potential in accelerating drug discovery efforts against SARS-CoV-2 and other emerging viruses.", + "rel_abs": "The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has led to significant global morbidity and mortality. A crucial viral protein, the non-structural protein 14 (nsp14), catalyzes the methylation of viral RNA and plays a critical role in viral genome replication and transcription. Due to the low mutation rate in the nsp region among various SARS-CoV-2 variants, nsp14 has emerged as a promising therapeutic target. However, discovering potential inhibitors remains a challenge. In this work, we introduce a computational pipeline for the rapid and efficient identification of potential nsp14 inhibitors by leveraging virtual screening and the NCI open compound collection, which contains 250,000 freely available molecules for researchers worldwide. The introduced pipeline provides a cost-effective and efficient approach for early-stage drug discovery by allowing researchers to evaluate promising molecules without incurring synthesis expenses. Our pipeline successfully identified seven promising candidates after experimentally validating only 40 compounds. Notably, we discovered NSC620333, a compound that exhibits a strong binding affinity to nsp14 with a dissociation constant of 427 {+/-} 84 nM. In addition, we gained new insights into the structure and function of this protein through molecular dynamics simulations. We identified new conformational states of the protein and determined that residues Phe367, Tyr368, and Gln354 within the binding pocket serve as stabilizing residues for novel ligand interactions. We also found that metal coordination complexes are crucial for the overall function of the binding pocket. Lastly, we present the solved crystal structure of the nsp14-MTase complexed with SS148 (PDB:8BWU), a potent inhibitor of methyltransferase activity at the nanomolar level (IC50 value of 70 {+/-} 6 nM). Our computational pipeline accurately predicted the binding pose of SS148, demonstrating its effectiveness and potential in accelerating drug discovery efforts against SARS-CoV-2 and other emerging viruses.", "rel_num_authors": 26, "rel_authors": [ { @@ -13201,6 +13842,37 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2023.10.03.560739", + "rel_title": "Comparative single-cell analysis reveals IFN-\u03b3 as a driver of respiratory sequelae post COVID-19", + "rel_date": "2023-10-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.03.560739", + "rel_abs": "Post-acute sequelae of SARS-CoV-2 infection (PASC) represents an urgent public health challenge, with its impact resonating in over 60 million individuals globally. While a growing body of evidence suggests that dysregulated immune reactions may be linked with PASC symptoms, most investigations have primarily centered around blood studies, with few focusing on samples derived from post-COVID affected tissues. Further, clinical studies alone often provide correlative insights rather than causal relationships. Thus, it is essential to compare clinical samples with relevant animal models and conduct functional experiments to truly understand the etiology of PASC. In this study, we have made comprehensive comparisons between bronchoalveolar lavage fluid (BAL) single-cell RNA sequencing (scRNAseq) data derived from clinical PASC samples and relevant PASC mouse models. This revealed a strong pro-fibrotic monocyte-derived macrophage response in respiratory PASC (R-PASC) in both humans and mice, and abnormal interactions between pulmonary macrophages and respiratory resident T cells. IFN-{gamma} emerged as a key node mediating the immune anomalies in R-PASC. Strikingly, neutralizing IFN-{gamma} post the resolution of acute infection reduced lung inflammation, tissue fibrosis, and improved pulmonary gas-exchange function in two mouse models of R-PASC. Our study underscores the importance of performing comparative analysis to understand the root cause of PASC for developing effective therapies.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Jie Sun", + "author_inst": "University of Virginia" + }, + { + "author_name": "Chaofan Li", + "author_inst": "University of Virginia" + }, + { + "author_name": "Wei Qian", + "author_inst": "University of Virginia" + }, + { + "author_name": "Xiaoqin Wei", + "author_inst": "University of Virginia" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.10.04.560777", "rel_title": "mRNA vaccines encoding membrane-anchored receptor-binding domains of SARS-CoV-2 mutants induce strong humoral responses and can overcome immune imprinting", @@ -14251,109 +14923,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.09.29.23296330", - "rel_title": "Protection of second booster vaccinations and prior infection against SARS-CoV-2 in the UK SIREN healthcare worker cohort", - "rel_date": "2023-10-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.29.23296330", - "rel_abs": "BackgroundThe protection of fourth dose mRNA vaccination against SARS-CoV-2 is relevant to current global policy decisions regarding ongoing booster roll-out. We estimate the effect of fourth dose vaccination, prior infection, and duration of PCR positivity in a highly-vaccinated and largely prior-COVID-19 infected cohort of UK healthcare workers.\n\nMethodsParticipants underwent fortnightly PCR and regular antibody testing for SARS-CoV-2 and completed symptoms questionnaires. A multi-state model was used to estimate vaccine effectiveness (VE) against infection from a fourth dose compared to a waned third dose, with protection from prior infection and duration of PCR positivity jointly estimated.\n\nResults1,298 infections were detected among 9,560 individuals under active follow-up between September 2022 and March 2023. Compared to a waned third dose, fourth dose VE was 13.1% (95%CI 0.9 to 23.8) overall; 24.0% (95%CI 8.5 to 36.8) in the first two months post-vaccination, reducing to 10.3% (95%CI - 11.4 to 27.8) and 1.7% (95%CI -17.0 to 17.4) at 2-4 and 4-6 months, respectively. Relative to an infection >2 years ago and controlling for vaccination, 63.6% (95%CI 46.9 to 75.0) and 29.1% (95%CI 3.8 to 43.1) greater protection against infection was estimated for an infection within the past 0-6, and 6-12 months, respectively. A fourth dose was associated with greater protection against asymptomatic infection than symptomatic infection, whilst prior infection independently provided more protection against symptomatic infection, particularly if the infection had occurred within the previous 6 months. Duration of PCR positivity was significantly lower for asymptomatic compared to symptomatic infection.\n\nConclusionsDespite rapid waning of protection, vaccine boosters remain an important tool in responding to the dynamic COVID-19 landscape; boosting population immunity in advance of periods of anticipated pressure, such as surging infection rates or emerging variants of concern.\n\nFundingUK Health Security Agency, Medical Research Council, NIHR HPRU Oxford, and others.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Peter D Kirwan", - "author_inst": "MRC Biostatistics Unit, University of Cambridge" - }, - { - "author_name": "Victoria Jane Hall", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Sarah Foulkes", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Ashley Otter", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Katie Munro", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Dominic Sparkes", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Anna Howells", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Naomi Platt", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Jonathan Broad", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "David Crossman", - "author_inst": "School of Medicine, University of St Andrews" - }, - { - "author_name": "Chris Norman", - "author_inst": "Health and Care Research Wales" - }, - { - "author_name": "Dianne Corrigan", - "author_inst": "Northern Ireland Public Health Agency" - }, - { - "author_name": "Christopher H Jackson", - "author_inst": "MRC Biostatistics Unit, University of Cambridge" - }, - { - "author_name": "Michelle Cole", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Colin S Brown", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Ana Atti", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Jasmin Islam", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "- SIREN Study Group", - "author_inst": "" - }, - { - "author_name": "Anne Presanis", - "author_inst": "MRC Biostatistics Unit, University of Cambridge" - }, - { - "author_name": "Andre Charlett", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Daniela De Angelis", - "author_inst": "MRC Biostatistics Unit, University of Cambridge" - }, - { - "author_name": "Susan Hopkins", - "author_inst": "UK Health Security Agency" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.10.01.560357", "rel_title": "The TMPRSS2 non-protease domains regulating SARS-CoV-2 Spike in mediated virus entry", @@ -14807,7 +15376,7 @@ "rel_date": "2023-09-29", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.29.560084", - "rel_abs": "Antibodies play a central role in the immune defense against SARS-CoV-2. Strong evidence has shown that non-neutralizing antibodies (nnAbs) are important for anti-SARS-Cov-2 immunity through Fc-mediated effector functions. These nnAbs bind to epitopes that could be less subjected to mutations in the emerging variants. When protective, such nnAbs would constitute a more promising alternative to neutralizing mAbs (nAbs). Here, we show that six nnAbs retain binding to Omicron, while two nAbs do not. Furthermore, two of our nnAbs, which are protective in vivo, retained binding to XBB, XBB.1.5, and BQ.1.1. They appear to bind to conserved epitopes on the N-terminal and receptor binding domain (RBD), respectively. As a proof of concept, we show that these protective non-neutralizing antibodies retain potent Fc-mediated opsonic function against BQ.1.1 and XBB. We also show that the Fc-mediated function is further enhanced by expressing the antibodies in the IgG3 subclass and combining them into a dual antibody cocktail. Our work suggests that opsonizing nnAbs could be a viable strategy for anti-SARS-CoV-2 mAb therapies against current and future SARS-CoV-2 variants.", + "rel_abs": "Antibodies play a central role in the immune defense against SARS-CoV-2. There is substantial evidence supporting that Fc-mediated effector functions of anti-spike antibodies contribute to anti-SARS-Cov-2 immunity. We have previously shown that two non-neutralizing but opsonic mAbs, Ab81 and Ab94, are protective against lethal Wuhan SARS-CoV-2 infection in mice. The protective effect was comparable to a potent neutralizing antibody, Ab59. Here, we hypothesized that, unlike the neutralizing antibodies, non-neutralizing opsonic antibodies would have a higher likelihood of retaining their function to the mutated variants, potentially functioning as broadly protective mAbs. Most of the mutations on the SARS-CoV-2 variants cluster on neutralizing epitopes, leaving other epitopes unaltered. We observed that neutralizing antibodies lost binding to Omicron. In contrast, seven non-neutralizing opsonic antibodies retained nanomolar affinity towards Omicron, BA.2, BA.4, and BA.5. Focusing on the two protective non-neutralizing antibodies Ab81 and Ab94, we showed that they maintain their strong reactivity even to XBB, XBB1.5, and BQ1.1. In the case of Ab94, interestingly, it even has increased affinity towards all variants except for XBB, which is comparable to WT. Finally, we show that Ab94 and Ab81 have potent Fc-mediated functions in vitro against the XBB and BQ1.1 and that combining the mAbs in a cocktail further enhances the effect. These results show that protective non-neutralizing mAbs such as Ab94 and Ab81 can be a viable strategy for anti-SARS-CoV-2 mAb therapies against current and possibly future SARS-CoV-2 variants and that opsonic epitopes could have implications for vaccine design.", "rel_num_authors": 4, "rel_authors": [ { @@ -14851,6 +15420,49 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2023.09.28.560070", + "rel_title": "Curcumin and turmeric extract inhibited SARS-CoV-2 pseudovirus cell entry and Spike mediated cell fusion", + "rel_date": "2023-09-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.28.560070", + "rel_abs": "Turmeric extract (TE) with curcumin as its main active ingredient has been studied as a potential COVID-19 therapeutic. Curcumin has been studied in silico and in vitro against a naive SARS-CoV-2 virus, yet little is known about TEs impact on SARS-CoV-2 infection. Moreover, no study reveals the potentials of both curcumin and TE on the inhibition of SARS-CoV-2 cell-to-cell transmission. Here, we investigated the effects of both curcumin and TE on the inhibition of SARS-CoV-2 entry and cell-to-cell transmission using pseudovirus (PSV) and syncytia models. We performed PSV entry assay in 293T or 293 cells expressing hACE2. The cells were pretreated with curcumin or TE, then treated with PSV with or without the test samples. Next, we carried out syncytia assay by co-transfecting 293T cells with plasmids encoding Spike, hACE2, and TMPRSS2 to be treated with the test samples. The results showed that in PSV entry assay on 293T/hACE/TMPRSS2 cells, both curcumin and TE inhibited PSV entry at concentrations of 1 {micro}M and 10 {micro}M for curcumin and 1 {micro}g/ml and 10 {micro}g/ml for TE. Moreover, both curcumin and TE also reduced syncytia formation compared to control cells. Based on our study, both TE and curcumin are potential inhibitors of SARS-CoV-2 infection at entry points, either by direct or indirect infection models.\n\nGRAPHICAL ABSTRACT\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=165 SRC=\"FIGDIR/small/560070v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (29K):\norg.highwire.dtl.DTLVardef@1c4c732org.highwire.dtl.DTLVardef@1f1d9ddorg.highwire.dtl.DTLVardef@11678a9org.highwire.dtl.DTLVardef@4bccf0_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Endah Puji Puji Septisetyani", + "author_inst": "National Research and Innovation Agency" + }, + { + "author_name": "Dinda Lestari", + "author_inst": "Universitas Syiah Kuala" + }, + { + "author_name": "Komang Alit Paramitasari", + "author_inst": "National Research and Innovation Agency" + }, + { + "author_name": "Pekik Wiji Prasetyaningrum", + "author_inst": "National Research and Innovation Agency" + }, + { + "author_name": "Ria Fajarwati Kastian", + "author_inst": "National Research and Innovation Agency" + }, + { + "author_name": "Adi Santoso", + "author_inst": "National Research and Innovation Agency" + }, + { + "author_name": "Kartini Eriani", + "author_inst": "Universitas Syiah Kuala" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2023.09.28.23296264", "rel_title": "Endemic means change as SARS-CoV-2 evolves", @@ -15917,49 +16529,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.09.21.23295853", - "rel_title": "A Phase 2, randomized, double-blind, placebo-controlled multi-center trial sub-study for the clinical effects of paridiprubart treatment in hospitalized critically ill patients with COVID-19 ARDS", - "rel_date": "2023-09-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.21.23295853", - "rel_abs": "BackgroundCoronavirus disease 2019 (COVID-19) mortality is predominantly due to acute respiratory distress syndrome (ARDS). There are currently limited treatment options for ARDS, a life-threatening condition with different etiologies, secondary to inflammation-induced lung injury. Paridiprubart is a monoclonal antibody that inhibits Toll-like Receptor 4 (TLR4), a key player in ARDS pathophysiology.\n\nMethodsThis was a prespecified sub-study of a randomized, double-blind, placebo-controlled, Phase 2 trial evaluating the efficacy and safety of paridiprubart in COVID-19 patients with ARDS receiving invasive mechanical ventilation and additional organ support. Efficacy outcomes were 28- and 60-day all-cause mortality, and improvement in COVID-19 severity and ventilation-free days at 28-days post-treatment.\n\nResultsThirteen (13) and twenty (20) patients received paridiprubart and placebo, respectively. The groups were comparable for demographics and baseline parameters, except for higher kidney failure incidence and use of immune modulators and antivirals, and lower corticosteroids use in the paridiprubart group. Mortality at 28-days post-treatment was 7.7% (1/13) in the paridiprubart group versus 40.0% (8/20) for placebo (OR=0.125; 95% CI, 0.013-1.160; P=0.067; P[bootstrap]=0.011). 60-day mortality was 23.1% (3/13) in paridiprubart-treated patients and 45.0% (9/20) in placebo patients (OR=0.367; 95% CI, 0.077-1.749; P=0.208; P[bootstrap]=0.162). Mean survival time was 55.78 days for paridiprubart recipients compared to 41.44 days for placebo patients (HR=0.386; 95% CI, 0.077-1.436; P=0.156; P[bootstrap]=0.083). Although not statistically significant, results for other efficacy measures favored paridiprubart. Incidence of adverse events was similar in both groups.\n\nConclusionsIn COVID-19 patients with ARDS requiring invasive ventilation and organ support, paridiprubart was efficacious in preventing mortality and improving clinical outcomes, with no safety concerns.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Blair Gordon", - "author_inst": "Edesa Biotech Inc, Markham, Ontario, Canada" - }, - { - "author_name": "Fiona Allum", - "author_inst": "JSS Medical Research Inc, St-Laurent, Quebec, Canada" - }, - { - "author_name": "Michael Brooks", - "author_inst": "Edesa Biotech Inc, Markham, Ontario, Canada" - }, - { - "author_name": "Nishani Rajakulendran", - "author_inst": "Edesa Biotech Inc, Markham, Ontario, Canada" - }, - { - "author_name": "Emmanouil Rampakakis", - "author_inst": "JSS Medical Research Inc, St-Laurent, Quebec, Canada; Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada" - }, - { - "author_name": "John Sampalis", - "author_inst": "JSS Medical Research Inc, St-Laurent, Quebec, Canada; Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada" - }, - { - "author_name": "- EB05 Study Investigators", - "author_inst": "-" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2023.09.26.23295911", "rel_title": "Analysis of Potential Risk Factors of COVID-19 Based on Variants: Omicron, Delta, and Alpha", @@ -16541,6 +17110,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.09.24.23296056", + "rel_title": "Research ethics review during the COVID-19 pandemic An international study", + "rel_date": "2023-09-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.24.23296056", + "rel_abs": "Research ethics review committees (ERCs) worldwide faced daunting challenges during the COVID-19 pandemic. There was a need to balance rapid turnaround with rigorous evaluation of high-risk research protocols in the context of considerable uncertainty. This study explored the experiences and performance of ERCs during the pandemic.\n\nWe conducted an anonymous, cross-sectional, global online survey of chairs (or their delegates) of ERCs who were involved in the review of COVID-19-related research protocols after March 2020. The survey ran from October 2022 to February 2023 and consisted of 50 items, with opportunities for open text responses.\n\nTwo hundred and three participants [130 from high-income countries (HICs) and 73 from low-and middle-income countries (LMICs)] completed our survey. Respondents came from diverse entities and organizations from 48 countries (19 HICs and 29 LMICs) in all World Health Organization regions. Responses show little of the increased global funding for COVID-19 research was allotted to the operation of ERCs. Few ERCs had pre-existing internal policies to address operation during public health emergencies, but almost half used existing guidelines. Most ERCs modified existing procedures or designed and implemented new ones but had not evaluated the success of these changes. Participants overwhelmingly endorsed permanently implementing several of them. Few ERCs added new members but non-member experts were consulted; quorum was generally achieved. Collaboration among ERCs was infrequent, but reviews conducted by external ERCs were recognized and validated. Review volume increased during the pandemic, with COVID-19-related studies being prioritized. Most protocol reviews were reported as taking less than three weeks. One-third of respondents reported external pressure on their ERCs from different stakeholders to approve or reject specific COVID-19-related protocols.\n\nERC members faced significant challenges to keep their committees functioning during the pandemic. Our findings can inform ERC approaches towards future public health emergencies. To our knowledge, this is the first international, COVID-19-related study of its kind.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Fabio Salamanca-Buentello", + "author_inst": "Lunenfeld-Tanenbaum Research Institute" + }, + { + "author_name": "Rachel Katz", + "author_inst": "University of Toronto Institute for the History & Philosophy of Science & Technology" + }, + { + "author_name": "Diego S. Silva", + "author_inst": "The University of Sydney School of Public Health" + }, + { + "author_name": "Ross E.G. Upshur", + "author_inst": "University of Toronto Dalla Lana School of Public Health" + }, + { + "author_name": "Maxwell J. Smith", + "author_inst": "Western University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.09.22.559030", "rel_title": "Survey of white-footed mice in Connecticut, USA reveals low SARS-CoV-2 seroprevalence and infection with divergent betacoronaviruses", @@ -17142,7 +17746,7 @@ "rel_date": "2023-09-25", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.22.23295541", - "rel_abs": "Our understanding of the quality of cellular and humoral immunity conferred by COVID-19 vaccination alone versus vaccination plus SARS-CoV-2 breakthrough (BT) infection remains incomplete. While the current (2023) SARS-CoV-2 immune landscape of Canadians is complex, in late 2021 most Canadians had either just received a third dose of COVID-19 vaccine, or had received their two dose primary series and then experienced an Omicron BT. Herein we took advantage of this coincident timing to contrast cellular and humoral immunity conferred by three doses of vaccine versus two doses plus BT. Our results show that mild BT infection induces cell-mediated immune responses to variants comparable to an intramuscular vaccine booster dose. In contrast, BT subjects had higher salivary IgG and IgA levels against the Omicron Spike and enhanced reactivity to the ancestral Spike for the IgA isotype, which also reacted with SARS-CoV-1. Serum neutralizing antibody levels against the ancestral strain and the variants were also higher after BT infection. Our results support the need for mucosal vaccines to emulate the enhanced mucosal and humoral immunity induced by Omicron without exposing individuals to the risks associated with SARS-CoV-2 infection.\n\nONE SENTENCE SUMMARYOmicron breakthrough elicits cross-reactive systemic and mucosal immune responses in fully vaccinated adults.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC=\"FIGDIR/small/23295541v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (27K):\norg.highwire.dtl.DTLVardef@19842eaorg.highwire.dtl.DTLVardef@151376borg.highwire.dtl.DTLVardef@10d9006org.highwire.dtl.DTLVardef@16a9c4e_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_abs": "Our understanding of the quality of cellular and humoral immunity conferred by COVID-19 vaccination alone versus vaccination plus SARS-CoV-2 breakthrough (BT) infection remains incomplete. While the current (2023) SARS-CoV-2 immune landscape of Canadians is complex, in late 2021 most Canadians had either just received a third dose of COVID-19 vaccine, or had received their two dose primary series and then experienced an Omicron BT. Herein we took advantage of this coincident timing to contrast cellular and humoral immunity conferred by three doses of vaccine versus two doses plus BT. Our results show that mild BT infection induces cell-mediated immune responses to variants comparable to an intramuscular vaccine booster dose. In contrast, BT subjects had higher salivary IgG and IgA levels against the Omicron Spike and enhanced reactivity to the ancestral Spike for the IgA isotype, which also reacted with SARS-CoV-1. Serum neutralizing antibody levels against the ancestral strain and the variants were also higher after BT infection. Our results support the need for mucosal vaccines to emulate the enhanced mucosal and humoral immunity induced by Omicron without exposing individuals to the risks associated with SARS-CoV-2 infection.\n\nONE SENTENCE SUMMARYOmicron breakthrough elicits cross-reactive systemic and mucosal immune responses in fully vaccinated adults.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC=\"FIGDIR/small/23295541v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (27K):\norg.highwire.dtl.DTLVardef@11e2f95org.highwire.dtl.DTLVardef@c5ff92org.highwire.dtl.DTLVardef@10df6bforg.highwire.dtl.DTLVardef@1c2a760_HPS_FORMAT_FIGEXP M_FIG C_FIG", "rel_num_authors": 22, "rel_authors": [ { @@ -17815,45 +18419,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2023.09.21.23295894", - "rel_title": "Statistical analysis of three data sources for Covid-19 monitoring in Rhineland-Palatinate, Germany", - "rel_date": "2023-09-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.21.23295894", - "rel_abs": "In Rhineland-Palatinate, Germany, a system of three data sources has been established to track the Covid-19 pandemic. These sources are the number of Covid-19-related hospitalizations, the Covid-19 genecopies in wastewater, and the prevalence derived from a cohort study. This paper presents an extensive comparison of these parameters. It is investigated whether wastewater data and a cohort study can be valid surrogate parameters for the number of hospitalizations and thus serve as predictors for coming Covid-19 waves. We observe that this is possible in general for the cohort study prevalence, while the wastewater data suffer from a too large variability to make quantitative predictions by a purely data-driven approach. However, the wastewater data as well as the cohort study prevalence are able to detect hospitalizations waves in a qualitative manner. Furthermore, a detailed comparison of different normalization techniques of wastewater data is provided.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Maximilian Pilz", - "author_inst": "Fraunhofer Institute for Industrial Mathematics ITWM" - }, - { - "author_name": "Karl-Heinz Kuefer", - "author_inst": "Fraunhofer Institute for Industrial Mathematics ITWM" - }, - { - "author_name": "Jan Mohring", - "author_inst": "Fraunhofer Institute for Industrial Mathematics ITWM" - }, - { - "author_name": "Johanna Muench", - "author_inst": "Fraunhofer Institute for Industrial Mathematics ITWM" - }, - { - "author_name": "Jaroslaw Wlazlo", - "author_inst": "Fraunhofer Institute for Industrial Mathematics ITWM" - }, - { - "author_name": "Neele Leithaeuser", - "author_inst": "Fraunhofer Institute for Industrial Mathematics ITWM" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.09.20.23295832", "rel_title": "Targeted MRM-analysis of plasma proteins in frozen whole blood samples from patients with COVID-19", @@ -18519,6 +19084,85 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2023.09.18.558353", + "rel_title": "High-affinity binding to the SARS-CoV-2 spike trimer by a nanostructured, trivalent protein-DNA synthetic antibody", + "rel_date": "2023-09-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.18.558353", + "rel_abs": "Multivalency enables nanostructures to bind molecular targets with high affinity. Although antibodies can be generated against a wide range of antigens, their shape and size cannot be tuned to match a given target. DNA nanotechnology provides an attractive approach for designing customized multivalent scaffolds due to the addressability and programmability of the nanostructure shape and size. Here, we design a nanoscale synthetic antibody (\"nano-synbody\") based on a three-helix bundle DNA nanostructure with one, two, or three identical arms terminating in a mini-binder protein that targets the SARS-CoV-2 spike protein. The nano-synbody was designed to match the valence and distance between the three receptor binding domains (RBDs) in the spike trimer, in order to enhance affinity. The protein-DNA nano-synbody shows tight binding to the wild-type, Delta, and several Omicron variants of the SARS-CoV-2 spike trimer, with affinity increasing as the number of arms increases from one to three. The effectiveness of the nano-synbody was also verified using a pseudovirus neutralization assay, with the three-arm nanostructure inhibiting two Omicron variants against which the structures with only one or two arms are ineffective. The structure of the three-arm nano-synbody bound to the Omicron variant spike trimer was solved by negative-stain transmission electron microscopy reconstruction, and shows the protein-DNA nanostructure with all three arms attached to the RBD domains, confirming the intended trivalent attachment. The ability to tune the size and shape of the nano-synbody, as well as its potential ability to attach two or more different binding ligands, will enable the high-affinity targeting of a range of proteins not possible with traditional antibodies.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Yang Xu", + "author_inst": "Arizona State University" + }, + { + "author_name": "Rong Zheng", + "author_inst": "Arizona State University" + }, + { + "author_name": "Abhay Prasad", + "author_inst": "Arizona State University" + }, + { + "author_name": "Minghui Liu", + "author_inst": "Arizona State University" + }, + { + "author_name": "Zijian Wan", + "author_inst": "Arizona State University" + }, + { + "author_name": "Xiaoyan Zhou", + "author_inst": "Arizona State University" + }, + { + "author_name": "Ryan M. Porter", + "author_inst": "Arizona State University" + }, + { + "author_name": "Matthew Sample", + "author_inst": "Arizona State University" + }, + { + "author_name": "Erik Poppleton", + "author_inst": "Arizona State University" + }, + { + "author_name": "Jonah Procyk", + "author_inst": "Arizona State University" + }, + { + "author_name": "Hao Liu", + "author_inst": "Arizona State University" + }, + { + "author_name": "Yize Li", + "author_inst": "Arizona State University" + }, + { + "author_name": "Shaopeng Wang", + "author_inst": "Arizona State University" + }, + { + "author_name": "Hao Yan", + "author_inst": "Arizona State University" + }, + { + "author_name": "Petr Sulc", + "author_inst": "Arizona State University" + }, + { + "author_name": "Nicholas Stephanopoulos", + "author_inst": "Arizona State University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2023.09.15.557929", "rel_title": "Third dose COVID-19 mRNA vaccine enhances IgG4 isotype switching and recognition of Omicron subvariants by memory B cells after with mRNA but not adenovirus priming", @@ -19509,85 +20153,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.09.14.23295549", - "rel_title": "Enhanced production of eicosanoids in plasma and activation of DNA damage pathways in PBMCs are correlated with the severity of ancestral COVID-19 infection", - "rel_date": "2023-09-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.14.23295549", - "rel_abs": "BackgroundMany questions remain unanswered regarding the implication of lipid metabolites in severe SARS-CoV-2 infections. By re-analyzed sequencing data from the nasopharynx of a previously published cohort, we found that alox genes, involved in eicosanoid synthesis, were up-regulated in high WHO score patients, especially in goblet cells. Herein, we aimed to further understand the roles played by eicosanoids during severe SARS-CoV-2 infection.\n\nMethods and findingsWe performed a total fatty acid panel on plasma and bulk RNA-seq analysis on peripheral blood mononuclear cells (PBMCs) collected from 10 infected and 10 uninfected patients. Univariate comparison of lipid metabolites revealed that lipid metabolites were increased in SARS-CoV-2 patients including the lipid mediators Arachidonic Acid (AA) and Eicosapentaenoic Acid (EPA). AA, EPA and the fatty acids Docosahexaenoic acid (DHA) and Docosapentaenoic acid (DPA), were positively correlated to WHO disease severity score. Transcriptomic analysis demonstrated that COVID-19 patients can be segregated based on WHO scores. Ontology, KEGG and Reactome analysis identified pathways enriched for genes related to innate immunity, interactions between lymphoid and nonlymphoid cells, interleukin signaling and, cell cycling pathways.\n\nConclusionsOur study offers an association between nasopharynx mucosa eicosanoid genes expression, specific serum inflammatory lipids and, subsequent DNA damage pathways activation in PBMCs to severity of COVID-19 infection.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Jeffrey A. Tomalka", - "author_inst": "Emory University School of Medicine. Atlanta, GA, USA" - }, - { - "author_name": "Anna Owings", - "author_inst": "University of Mississippi Medical Center, Jackson, MS, USA" - }, - { - "author_name": "Michelle Galeas-Pena", - "author_inst": "Tulane University School of Medicine, New Orleans, LA, USA" - }, - { - "author_name": "Carly G.K. Ziegler", - "author_inst": "Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Tanya O. Robinson", - "author_inst": "The University of Mississippi Medical Center, Jackson, MS, USA" - }, - { - "author_name": "Thomas G. Wichman", - "author_inst": "The University of Mississippi Medical Center, Jackson, MS, USA" - }, - { - "author_name": "Hannah Laird", - "author_inst": "The University of Mississippi Medical Center, Jackson, MS, USA" - }, - { - "author_name": "Haley B. Williams", - "author_inst": "The University of Mississippi Medical Center, Jackson, MS, USA" - }, - { - "author_name": "Neha S. Dhaliwal", - "author_inst": "The University of Mississippi Medical Center, Jackson, MS, USA" - }, - { - "author_name": "Steven Everman", - "author_inst": "The University of Mississippi Medical Center, Jackson, MS, USA" - }, - { - "author_name": "Yousaf Zafar", - "author_inst": "The University of Mississippi Medical Center, Jackson, MS, USA" - }, - { - "author_name": "Alex Shalek", - "author_inst": "Harvard University, Boston, MA, USA" - }, - { - "author_name": "Bruce H. Horwitz", - "author_inst": "Boston Children's Hospital, Boston, MA, USA" - }, - { - "author_name": "Jose Ordovas-Montanes", - "author_inst": "Harvard University and MIT. Ragon Institute, Boston, MA, USA" - }, - { - "author_name": "Sarah C. Glover", - "author_inst": "Tulane University School of Medicine, New Orleans, LA, USA" - }, - { - "author_name": "Yann Gibert", - "author_inst": "Cancer Center and Research Institute. University of Mississippi Medical Center. Jackson, MS, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.09.13.23295114", "rel_title": "Assessing the impact of the Gamma variant on COVID-19 Patient admissions in a Southern Brazilian tertiary hospital - A comparison of dual pandemic phases", @@ -19688,7 +20253,7 @@ "rel_date": "2023-09-14", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.13.557622", - "rel_abs": "The long-term health effects of SARS-CoV-2, termed Post-Acute Sequelae of COVID-19 (PASC), are quickly evolving into a major public health concern, but the underlying cellular and molecular etiology remain poorly defined. There is growing evidence that PASC is linked to abnormal immune responses and/or poor organ recovery post-infection. However, the exact processes linking non-resolving inflammation, impaired tissue repair, and PASC are still unclear. In this report, we utilized a cohort of respiratory PASC patients with viral infection-mediated pulmonary fibrosis and a clinically relevant mouse model of post-viral lung sequelae to investigate the pathophysiology of respiratory PASC. Using a combination of imaging and spatial transcriptomics, we identified dysregulated proximal interactions between immune cells and epithelial progenitors unique to respiratory PASC but not acute COVID-19 or idiopathic pulmonary fibrosis (IPF). Specifically, we found a central role for lung-resident CD8+ T cell-macrophage interactions in maintaining Krt8hi transitional and ectopic Krt5+ basal cell progenitors, and the development of fibrotic sequelae after acute viral pneumonia. Mechanistically, CD8+ T cell derived IFN-{gamma} and TNF stimulated lung macrophages to chronically release IL-1{beta}, resulting in the abnormal accumulation of dysplastic epithelial progenitors in fibrotic areas. Notably, therapeutic neutralization of IFN-{gamma} and TNF, or IL-1{beta} after the resolution of acute infection resulted in markedly improved alveolar regeneration and restoration of pulmonary function. Together, our findings implicate a dysregulated immune-epithelial progenitor niche in driving respiratory PASC and identify potential therapeutic targets to dampen chronic pulmonary sequelae post respiratory viral infections including SARS-CoV-2.", + "rel_abs": "The long-term physiological consequences of SARS-CoV-2, termed Post-Acute Sequelae of COVID-19 (PASC), are rapidly evolving into a major public health concern. The underlying cellular and molecular etiology remain poorly defined but growing evidence links PASC to abnormal immune responses and/or poor organ recovery post-infection. Yet, the precise mechanisms driving non-resolving inflammation and impaired tissue repair in the context of PASC remain unclear. With insights from three independent clinical cohorts of PASC patients with abnormal lung function and/or viral infection-mediated pulmonary fibrosis, we established a clinically relevant mouse model of post-viral lung sequelae to investigate the pathophysiology of respiratory PASC. By employing a combination of spatial transcriptomics and imaging, we identified dysregulated proximal interactions between immune cells and epithelial progenitors unique to the fibroproliferation in respiratory PASC but not acute COVID-19 or idiopathic pulmonary fibrosis (IPF). Specifically, we found a central role for lung-resident CD8+ T cell-macrophage interactions in maintaining Krt8hi transitional and ectopic Krt5+ basal cell progenitors, thus impairing alveolar regeneration and driving fibrotic sequelae after acute viral pneumonia. Mechanistically, CD8+ T cell derived IFN-{gamma} and TNF stimulated lung macrophages to chronically release IL-1{beta}, resulting in the abnormal accumulation of dysplastic epithelial progenitors and fibrosis. Notably, therapeutic neutralization of IFN-{gamma} and TNF, or IL-1{beta} after the resolution of acute infection resulted in markedly improved alveolar regeneration and restoration of pulmonary function. Together, our findings implicate a dysregulated immune-epithelial progenitor niche in driving respiratory PASC. Moreover, in contrast to other approaches requiring early intervention, we highlight therapeutic strategies to rescue fibrotic disease in the aftermath of respiratory viral infections, addressing the current unmet need in the clinical management of PASC and post-viral disease.", "rel_num_authors": 8, "rel_authors": [ { @@ -20177,6 +20742,37 @@ "type": "new results", "category": "neuroscience" }, + { + "rel_doi": "10.1101/2023.09.12.557363", + "rel_title": "Identification of a Druggable Site on GRP78 at the GRP78-SARS-CoV-2 Interface and Compounds to Disrupt that Interface", + "rel_date": "2023-09-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.12.557363", + "rel_abs": "SARS-CoV-2, the virus that causes COVID-19, led to a global health emergency that claimed the lives of millions. Despite the widespread availability of vaccines, the virus continues to exist in the population in an endemic state which allows for the continued emergence of new variants. Most of the current vaccines target the spike glycoprotein interface of SARS-CoV-2, creating a selection pressure favoring viral immune evasion. Antivirals targeting other molecular interactions of SARS-CoV-2 can help slow viral evolution by providing orthogonal selection pressures on the virus. GRP78 is a host auxiliary factor that mediates binding of the SARS-CoV-2 spike protein to human cellular ACE2, the primary pathway of cell infection. As GRP78 forms a ternary complex with SARS-CoV-2 spike protein and ACE2, disrupting the formation of this complex is expected to hinder viral entry into host cells. Here, we developed a model of the GRP78-spike protein-ACE2 complex. We then used that model together with hot spot mapping of the GRP78 structure to identify the putative binding site for spike protein on GRP78. Next, we performed structure-based virtual screening of known drug/candidate drug libraries to identify binders to GRP78 that are expected to disrupt spike protein binding to the GRP78, and thereby preventing viral entry to the host cell. A subset of these compounds have previously been shown to have some activity against SARS-CoV-2. The identified hits are starting points for the further development of novel SARS-CoV-2 therapeutics, potentially serving as proof-of-concept for GRP78 as a potential drug target for other viruses.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Maria Lazou", + "author_inst": "Boston University" + }, + { + "author_name": "Jonathan R. Hutton", + "author_inst": "Boston University" + }, + { + "author_name": "Arijit Chakravarty", + "author_inst": "Fractal Therapeutics Inc." + }, + { + "author_name": "Diane Joseph-McCarthy", + "author_inst": "Boston University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2023.09.12.23295445", "rel_title": "Determinants of SARS-CoV-2 IgG response and decay in Canadian healthcare workers: a prospective cohort study.", @@ -20963,61 +21559,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.09.12.23295426", - "rel_title": "Prevalence of Long COVID-associated symptoms in adults with and without SARS-CoV-2 infection in Germany: Results of the population-based study: Corona Monitoring Nationwide 2021/22 (RKI-SOEP-2)", - "rel_date": "2023-09-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.12.23295426", - "rel_abs": "BackgroundControlled population-based studies on long-term health sequelae of SARS-CoV-2 can help to identify clinical signs specific to \"Long COVID\" and to evaluate this emerging public health challenge.\n\nAimTo examine prevalence differences of Long COVID-associated symptoms among adults with and without SARS-CoV-2 infection in Germany.\n\nMethodsThis population-based, retrospective study (11/2021-2/2022) included 7,683 working aged adults (18-65 years), a subset of the Corona Monitoring Nationwide study in Germany. Prior SARS-CoV-2 infection was defined based on self-reported PCR-confirmed infections and IgG-antibody dried blood spot testing. Participants answered a questionnaire including 19 common symptoms of Long COVID experienced in the six months preceding the survey. We estimated population-weighted prevalence of (1) individual symptoms, and (2) [≥]1 symptom, with and without impact on work ability, by infection status within strata of sex, age group, income and comorbidity. We calculated model-adjusted prevalence differences and the probability that symptoms among infected are attributable to infection.\n\nResults12 of 19 symptoms showed a significantly higher prevalence in infected than non-infected participants, including fatigue (27.5% versus 18.3%; p<0.001), concentration problems (22.2% vs. 13.1%; p<0.001), shortness of breath (15.6% vs. 7.5%; p<0.001), and smell and taste disorder (10% vs. 1.2%; p<0.001). [≥]1 symptom with impact on work ability was more prevalent following infection (16.0% vs. 12.2%; p=0.06) with a model-adjusted prevalence difference of 3.8% (95%-CI -0.5-8.0).\n\nConclusionWe observed a rather small excess prevalence attributable to SARS-CoV-2 infection. However, the absolute number of persons places great demands on the health care system and may affect economic productivity.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Christina Poethko-Mueller", - "author_inst": "Robert Koch Institut" - }, - { - "author_name": "Ana Ordonez-Cruickshank", - "author_inst": "Robert Koch Institute" - }, - { - "author_name": "Julia Nuebel", - "author_inst": "Robert Koch Institute" - }, - { - "author_name": "Giselle Sarganas", - "author_inst": "Robert Koch Institute" - }, - { - "author_name": "Antje Goesswald", - "author_inst": "Robert Koch Institute" - }, - { - "author_name": "Lorenz Schmid", - "author_inst": "Robert Koch Institute" - }, - { - "author_name": "Angelika Schaffrath Rosario", - "author_inst": "Robert Koch Institute" - }, - { - "author_name": "Jens Hoebel", - "author_inst": "Robert Koch Institute" - }, - { - "author_name": "Martin Schlaud", - "author_inst": "Robert Koch Institute" - }, - { - "author_name": "Christa Scheidt-Nave", - "author_inst": "Robert Koch Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.09.12.23295441", "rel_title": "Validation of Real-World Case Definitions for COVID-19 Diagnosis and Severe COVID-19 Illness Among Patients Infected with SARS-CoV-2: Translation of Clinical Trial Definitions to Real-World Settings", @@ -21907,6 +22448,37 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.09.08.556906", + "rel_title": "Brain infection by wild-type SARS-CoV-2 and the B.1.617.2 and B.1.1.529 variants of concern is a severe outcome in K18-hACE2 transgenic mice", + "rel_date": "2023-09-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.08.556906", + "rel_abs": "BackgroundSARS-CoV-2 is a respiratory virus with neurological complications including loss of smell and taste, headache, and confusion that can persist for months or longer. Severe neuronal cell damage has also been reported in some cases. The objective of this study was to compare the infectivity of Wild-type, Delta, and Omicron variants in transgenic mice that express the human angiotensin-converting enzyme 2 (hACE2) receptor under the control of the keratin 18 promoter (K18) and characterize the progression of infection and inflammatory response in the lung and brain of these animals.\n\nMethodsK18-hACE2 female mice were intranasally infected with Wild-type, Delta, or Omicron variants and euthanized either at 3 days post-infection (dpi) or at the humane endpoint. None of the animals infected with the Omicron variant reached the humane endpoint and were euthanized at day 8 dpi. Virological and immunological analyses were performed in the lungs, olfactory bulbs, medulla oblongata, and brains.\n\nResultsWe established that Wild-type, Delta, and Omicron infect the lung and brain of K18-hACE2 mice. At 3 dpi, mice infected with the Omicron variant show lower levels of viral RNA than those infected with Wild-type or Delta in the lung and brain. However, they still demonstrate upregulation of cytokines and chemokines, indicating that the Omicron variant can induce pulmonary and neuronal inflammation despite reduced viral proliferation after infection. At the humane endpoint/8dpi, there is a significant increase in viral RNA in mice infected with the Wild-type or Delta variant brains. However, viral RNA levels in Omicron-infected mice did not increase significantly as compared to 3dpi, and the expression of cytokines and chemokines in the brain, olfactory bulb, and medulla oblongata was downregulated, suggesting that infection by the Omicron variant results in attenuated neuroinflammation as compared with Wild-type and Delta.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Yicheng Yicheng He", + "author_inst": "University of Southern California" + }, + { + "author_name": "Jill E Henley", + "author_inst": "University of Southern California" + }, + { + "author_name": "Philip Sell", + "author_inst": "University of Southern California" + }, + { + "author_name": "Lucio Comai", + "author_inst": "University of Southern California" + } + ], + "version": "1", + "license": "cc_no", + "type": "confirmatory results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.09.08.556901", "rel_title": "The role of ion dissolution in metal and metal oxide surface inactivation of SARS-CoV-2", @@ -23065,81 +23637,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.09.07.23295190", - "rel_title": "Uncovering the implications of IFN-I in severe COVID-19 neutrophil inflammasome", - "rel_date": "2023-09-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.07.23295190", - "rel_abs": "The severity of COVID-19 is linked to excessive inflammation. Neutrophils represent a critical arm of the innate immune response and are major mediators of inflammation, but their role in COVID-19 pathophysiology remains poorly understood. We conducted transcriptomic profiling of neutrophils obtained from patients with mild and severe COVID-19, as well as from SARS-CoV-2 infected mice, in comparison to non-infected healthy controls. In addition, we investigated the inflammasome formation potential in neutrophils from patients and mice upon SARS-CoV-2 infection. Transcriptomic analysis of polymorphonuclear cells (PMNs), consisting mainly of mature neutrophils, revealed a striking type I interferon (IFN-I) gene signature in severe COVID-19 patients, contrasting with mild COVID-19 and healthy controls. Notably, low-density granulocytes (LDGs) from severe COVID-19 patients exhibited an immature neutrophil phenotype and lacked this IFN-I signature. Moreover, PMNs from severe COVID-19 patients showed heightened nigericin-induced caspase1 activation, but reduced responsiveness to exogenous inflammasome priming. Furthermore, IFN-I emerged as a priming stimulus for neutrophil inflammasomes, which was confirmed in a COVID-19 mouse model. These findings underscore the crucial role of neutrophil inflammasomes in driving inflammation during severe COVID-19, with mature neutrophils displaying heightened inflammasome activity and exhibiting a distinctive IFN-I gene signature. Altogether, these findings open promising avenues for targeted therapeutic interventions to mitigate the pathological processes associated with the disease.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Luz Eneida Cabrera", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Suvi T. Jokiranta", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Sanna M\u00e4ki", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Simo Miettinen", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Ravi Kant", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Lauri Kareinen", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Tarja Sironen", - "author_inst": "University of Helsinki/Medicum" - }, - { - "author_name": "Jukka-Pekka Pietil\u00e4", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Anu Kantele", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Eliisa Kek\u00e4l\u00e4inen", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Hanna Lindgren", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Pirkko Mattila", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Anja Kipar", - "author_inst": "University of Zurich/Vetsuisse faculty" - }, - { - "author_name": "Olli Vapalahti", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Tomas Strandin", - "author_inst": "Haartman Institute/University of Helsinki" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2023.09.06.23294696", "rel_title": "Predictors of SARS-CoV-2 anti-Spike IgG antibody levels following two COVID-19 vaccine doses among children and adults in the Canadian CHILD Cohort", @@ -23961,6 +24458,53 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.09.07.556634", + "rel_title": "The anti-SARS-CoV-2 BNT162b2 vaccine suppresses mithramycin-induced erythroid differentiation and expression of embryo-fetal globin genes in human erythroleukemia K562 cells", + "rel_date": "2023-09-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.07.556634", + "rel_abs": "The COVID-19 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) the ongoing coronavirus disease 2019 (COVID-19) pandemic. The SARS-CoV-2 Spike protein (S-protein) plays an important role in the early phase of SARS-CoV2 infection through efficient interaction with ACE2. The S-protein is produced by RNA-based COVID-19 vaccines, and has been hypothesized to be responsible for damaging cells of several tissues and for some important side effects of RNA-based COVID-19 vaccines. The aim of this study was to verify the effect of the BNT162b2 vaccine on erythroid differentiation of the human K562 cell line, that has been in the past intensively studied as a model system mimicking some steps of erythropoiesis. We found that the BNT162b2 vaccine suppresses mithramycin-induced erythroid differentiation of K562 cells. Reverse-transcription-PCR and Western blotting assays demonstrated that suppression of erythroid differentiation was associated with sharp inhibition of the expression of -globin and {gamma}-globin mRNA accumulation. Inhibition of accumulation of {zeta}-globin and {varepsilon}-globin mRNAs was also observed. In addition, we provide in silico studies suggesting a direct interaction between SARS-CoV-2 Spike protein and Hb Portland, that is the major hemoglobin produced by K562 cells. This study thus provides information suggesting the need of great attention on possible alteration of hematopoietic parameters following SARS-CoV-2 infection and/or COVID-19 vaccination.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Matteo Zurlo", + "author_inst": "University of Ferrara" + }, + { + "author_name": "Jessica Gasparello", + "author_inst": "University of Ferrara" + }, + { + "author_name": "Marco Verona", + "author_inst": "University of Padova" + }, + { + "author_name": "Chiara Papi", + "author_inst": "University of Ferrara" + }, + { + "author_name": "Lucia Carmela Cosenza", + "author_inst": "University of Ferrara" + }, + { + "author_name": "Alessia Finotti", + "author_inst": "University of Ferrara" + }, + { + "author_name": "Giovanni Marzaro", + "author_inst": "University of Padova" + }, + { + "author_name": "Roberto Gambari", + "author_inst": "University of Ferrara" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2023.09.05.23295085", "rel_title": "The potential clinical impact and cost-effectiveness of the updated COVID-19 mRNA Fall 2023 vaccines in the United States", @@ -24867,57 +25411,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2023.09.03.555867", - "rel_title": "Meisoindigo: An Effective Inhibitor of SARS-CoV-2 Main Protease Revealed by Yeast System", - "rel_date": "2023-09-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.03.555867", - "rel_abs": "The COVID-19 pandemic caused by SARS-CoV-2 has had a significant impact on global health and economy. Despite the availability of vaccines, their limited accessibility and vaccine hesitancy pose challenges in controlling the spread of the disease. Effective therapeutic strategies, including antiviral drugs, are needed to combat the future spread of new SARS- CoV-2 virus variants. The main protease (Mpro) is a critical therapeutic target for COVID-19 medicines, as its inhibition impairs viral replication. However, the use of substances that inhibit Mpro may induce selection pressure. Thus, it is vital to monitor viral resistance to known drugs and to develop new drugs. Here we have developed a yeast system for the identification of Mpro inhibitors as an alternative to costly and demanding high biosecurity procedures. The system is based on stable expression of Mpro and does not require selection media. Yeast can be cultured on a rich carbon source, providing rapid growth and screening results. The designed tool was subsequently used to screen the FDA-Approved Drug Library. Several chemicals with Mpro inhibitory properties were identified. We found that meisoindigo not previously known for its potential to inhibit Mpro, was highly effective. Our results may promote development of new derivatives with therapeutic properties against SARS-CoV-2 and other beta-coronaviruses.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Wojciech Grabi\u0144ski", - "author_inst": "Department of Bioenergetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Pozna\u0144, Poland." - }, - { - "author_name": "Anna Kici\u0144ska", - "author_inst": "Department of Bioenergetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Pozna\u0144, Poland." - }, - { - "author_name": "Ewa Kosicka", - "author_inst": "Department of Bioenergetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Pozna\u0144, Poland." - }, - { - "author_name": "Martyna Baranek-Grabi\u0144ska", - "author_inst": "Department of Bioenergetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Pozna\u0144, Poland." - }, - { - "author_name": "Ewelina D Hejenkowska", - "author_inst": "Department of Pediatrics, University of Virginia, Charlottesville, VA 22903, USA." - }, - { - "author_name": "Joanna Budzik", - "author_inst": "Department of Bioenergetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Pozna\u0144, Poland." - }, - { - "author_name": "Paulina \u015aliska", - "author_inst": "Department of Bioenergetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Pozna\u0144, Poland." - }, - { - "author_name": "Weronika \u015aliwi\u0144ska", - "author_inst": "Department of Bioenergetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Pozna\u0144, Poland." - }, - { - "author_name": "Andonis Karachitos", - "author_inst": "Department of Bioenergetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Pozna\u0144, Poland." - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2023.09.01.555815", "rel_title": "Antigenicity and infectivity characterization of SARS-CoV-2 BA.2.86", @@ -25495,6 +25988,117 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.09.01.555899", + "rel_title": "SARS-CoV-2 hijacks fragile X mental retardation proteins for efficient infection", + "rel_date": "2023-09-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.01.555899", + "rel_abs": "Viruses interact with numerous host factors to facilitate viral replication and to dampen antiviral defense mechanisms. We currently have a limited mechanistic understanding of how SARS-CoV-2 binds host factors and the functional role of these interactions. Here, we uncover a novel interaction between the viral NSP3 protein and the fragile X mental retardation proteins (FMRPs: FMR1 and FXR1-2). SARS-CoV-2 NSP3 mutant viruses preventing FMRP binding have attenuated replication in vitro and have delayed disease onset in vivo. We show that a unique peptide motif in NSP3 binds directly to the two central KH domains of FMRPs and that this interaction is disrupted by the I304N mutation found in a patient with fragile X syndrome. NSP3 binding to FMRPs disrupts their interaction with the stress granule component UBAP2L through direct competition with a peptide motif in UBAP2L to prevent FMRP incorporation into stress granules. Collectively, our results provide novel insight into how SARS-CoV-2 hijacks host cell proteins for efficient infection and provides molecular insight to the possible underlying molecular defects in fragile X syndrome.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Dimitriya Garvanska", + "author_inst": "University of Copenhagen" + }, + { + "author_name": "Rojelio E Alvarado", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Filip Mundt", + "author_inst": "Novo Nordisk Foundation Center for Protein Research" + }, + { + "author_name": "Emma Nilsson", + "author_inst": "Umeaa University" + }, + { + "author_name": "Josephine Duel", + "author_inst": "University of Copenhagen" + }, + { + "author_name": "Fabian Coscia", + "author_inst": "Max Delbruck Center" + }, + { + "author_name": "Richard Lindqvist", + "author_inst": "Umeaa University" + }, + { + "author_name": "Kumari Lokugamage", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Bryan Johnson", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Jessica A Plante", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Dorothea R. Morris", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Michelle N Vu", + "author_inst": "University of Texas Medical Branch at Galveston" + }, + { + "author_name": "Leah Estes", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Alyssa McLeland", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Jordyn Walker", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Patricia Crocquet-Valdes", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Blanca Lopez-Mendez", + "author_inst": "University of Copenhagen" + }, + { + "author_name": "Kenneth Plante", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "David H. Walker", + "author_inst": "The University of Texas Medical Branch at Galveston" + }, + { + "author_name": "Melanie B Weisser", + "author_inst": "University of Copenhagen" + }, + { + "author_name": "Anna K Overby", + "author_inst": "Umeaa university" + }, + { + "author_name": "Matthias Mann", + "author_inst": "University of Copenhagen" + }, + { + "author_name": "Vineet D Menachery", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Jakob Nilsson", + "author_inst": "University of Copenhagen" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.08.31.555625", "rel_title": "Differences in syncytia formation by SARS-CoV-2 variants modify host chromatin accessibility and cellular senescence via TP53", @@ -26573,49 +27177,6 @@ "type": "new results", "category": "ecology" }, - { - "rel_doi": "10.1101/2023.08.31.23294901", - "rel_title": "Association between pre-existing conditions and hospitalization, intensive care services and mortality from COVID-19, a cross sectional analysis of an international global health data repository", - "rel_date": "2023-08-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.31.23294901", - "rel_abs": "ObjectiveTo investigate the association between pre-existing conditions and hospitalization, need for intensive care services (ICU) and mortality due to COVID-19.\n\nMethodsWe used data on all cases recorded in the Global Health Data repository up to the 10th of March 2021 to carry out a cross-sectional analysis of associations between cardiovascular diseases (CVD), hypertension, diabetes, obesity, lung diseases and kidney disease and hospitalization, ICU admission and mortality due to COVID-19. The Global Health repository reported data from 137 countries, but only Brazil, Mexico and Cuba reported more than 10 COVID-19 cases in participants with preexisting conditions. We used multivariable logistic regression to compute adjusted odds ratios (aOR) of the three outcomes for each pre-existing condition in ten-year age groups from 0-9 years and up to 110-120 years.\n\nResultsThe Global Health repository held 25 900 000 records of confirmed cases of COVID-19, of which 2 900 000 cases were from Brazil, Mexico and Cuba. The overall adjusted odds of hospitalization for the selected pre-existing condition were; CVD (OR 1.7, 95%CI 1.7-1.7), hypertension (OR 1.5, 95%CI 1.4-1.5), diabetes (OR 2.2, 95%CI 2.1-2.2), obesity (OR 1.7, 95%CI 1.6-1.7), kidney disease (OR 5.5, 95%CI 5.2-5.7) and lung disease (OR 1.9, 95%CI 1.8-1.9). The overall adjusted odds of ICU admission for each pre-existing condition were; CVD (OR 2.1, 95%CI 1.8-2.4), hypertension (OR 1.3, 95%CI 1.2-1.4), diabetes (OR 1.7, 95%CI 1.5-1.8), obesity (OR 2.2, 95%%CI 2.1-2.4), kidney disease (OR 1.4, 95%CI 1.2-1.7) and lung disease (OR 1.1, 95%CI 0.9-1.3). The overall adjusted odds of mortality for each pre-existing condition were; CVD (OR 1.7, 95%CI 1.6-1.7), hypertension (OR 1.3, 95%CI 1.3-1.4), diabetes (OR 2.0, 95%CI 1.9-2.0), obesity (OR 1.9, 95%CI 1.8-2.0), kidney disease (OR 2.7, 95%CI 2.6-2.9) and lung disease (OR 1.6, 95%CI 1.5-1.7). The odds of each outcome were considerably larger in children and young adults with these preexisting conditions than for adults, especially for kidney disease, CVD, and diabetes.\n\nConclusionThis analysis of a global health repository confirms associations between pre-existing diseases and clinical outcomes of COVID-19. The odds of these outcomes are especially elevated in children and young adults with these preexisting conditions.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Basant Elsayed", - "author_inst": "Qatar University" - }, - { - "author_name": "Lina Altarawneh", - "author_inst": "Qatar University" - }, - { - "author_name": "Habib Farooqui", - "author_inst": "Qatar University" - }, - { - "author_name": "Giridhara Babu", - "author_inst": "Qatar University" - }, - { - "author_name": "Muhammad Naseem Khan", - "author_inst": "Qatar University" - }, - { - "author_name": "Suhail A. R. Doi", - "author_inst": "Qatar University" - }, - { - "author_name": "Tawanda Chivese", - "author_inst": "Qatar University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.08.30.23294839", "rel_title": "Vaccination status and re-infection among COVID patients admitted in COVID High Dependency Unit (HDU) of a tertiary hospital in Eastern Nepal: A cross-sectional study", @@ -27397,6 +27958,69 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.08.28.555062", + "rel_title": "Discovery of 2-amide-3-methylester thiophenes inhibiting SARS-CoV-2 ADP-ribosyl hydrolysing macrodomain and coronavirus replication", + "rel_date": "2023-08-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.28.555062", + "rel_abs": "The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has made it clear that further development of antiviral therapies will be needed to combat additional SARS-CoV-2 variants or novel CoVs. Here, we describe small molecule inhibitors for SARS-CoV-2 Mac1, which counters ADP-ribosylation mediated innate immune responses. The compounds inhibiting Mac1 were discovered through high-throughput screening (HTS) using a protein FRET-based competition assay and the best hit compound had an IC50 of 14 {micro}M. Three validated HTS hits have the same 2-amide-3-methylester thiophene scaffold and the scaffold was selected for structure-activity relationship (SAR) studies through commercial and synthesized analogs. We studied the compound binding mode in detail using X-ray crystallography and this allowed us to focus on specific features of the compound and design analogs. Compound 27 (MDOLL-0229) had an IC50 of 2.1 {micro}M and was generally selective for CoV Mac1 proteins after profiling for activity against a panel of viral and human ADP-ribose binding proteins. The improved potency allowed testing of its effect on virus replication and indeed, 27 inhibited replication of a mouse hepatitis virus, a prototype CoV. Compound 27 is the first Mac1 targeted small molecule demonstrated to inhibit coronavirus replication in a cell model. This, together with its well-defined binding mode, makes 27 a good candidate for further hit/lead-optimization efforts.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Sarah Wazir", + "author_inst": "University of Oulu" + }, + { + "author_name": "Tomi A. O. Parviainen", + "author_inst": "University of Oulu" + }, + { + "author_name": "Mirko M. Maksimainen", + "author_inst": "University of Oulu" + }, + { + "author_name": "Men Thi Hoai Duong", + "author_inst": "University of Oulu" + }, + { + "author_name": "Jessica J Pfannenstiel", + "author_inst": "University of Kansas" + }, + { + "author_name": "Daniel Cluff", + "author_inst": "University of Kansas" + }, + { + "author_name": "Sven T. Sowa", + "author_inst": "University of Oulu" + }, + { + "author_name": "Albert Galera-Prat", + "author_inst": "University of Oulu" + }, + { + "author_name": "Dana V Ferraris", + "author_inst": "McDaniel College" + }, + { + "author_name": "Anthony Fehr", + "author_inst": "University of Kansas" + }, + { + "author_name": "Juha P. Heiskanen", + "author_inst": "University of Oulu" + }, + { + "author_name": "Lari Lehti\u00f6", + "author_inst": "University of Oulu" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2023.08.29.555304", "rel_title": "A short sequence in the tail of SARS-CoV-2 envelope protein controls accessibility of its PDZ Binding Motif to the cytoplasm.", @@ -28603,45 +29227,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2023.08.21.554192", - "rel_title": "Gender differences in submission behavior exacerbate publication disparities in elite journals", - "rel_date": "2023-08-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.21.554192", - "rel_abs": "Women are particularly underrepresented in journals of the highest scientific impact, with substantial consequences for their careers. While a large body of research has focused on the outcome and the process of peer review, fewer articles have explicitly focused on gendered submission behavior and the explanations for these differences. In our study of nearly five thousand active authors, we find that women are less likely to report having submitted papers and, when they have, to submit fewer manuscripts, on average, than men. Women were more likely to indicate that they did not submit their papers (in general and their subsequently most cited papers) to Science, Nature, or PNAS because they were advised not to. In the aggregate, no statistically significant difference was observed between men and women in how they rated the quality of their work. Nevertheless, regardless of discipline, women were more likely than men to indicate that their \"work was not ground-breaking or sufficiently novel\" as a rationale for not submitting to one of the listed prestigious journals. Men were more likely than women to indicate that the \"work would fit better in a more specialized journal.\" We discuss the implications of these findings and interventions that can serve to mitigate the disparities caused by gendered differences in submission behavior.\n\nSignificancePublishing in high-impact scholarly journals has a significant effect on researchers careers. Our findings identify factors that affect submission to Science, Nature, and the Proceedings of the National Academy of Sciences of the United States of America (PNAS) and explore whether there is a relationship between gender and desk rejections or submission rates. We found no relationship between gender and reported desk rejection and a relationship between gender and reported submissions. Women were more likely than men to indicate that their \"work was not ground-breaking or sufficiently novel\" for the listed prestigious journals and that they were advised against submitting to these venues. Men were more likely to indicate that the \"work would fit better in a more specialized journal.\"", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Isabel Basson", - "author_inst": "Universite de Montreal" - }, - { - "author_name": "Chaoqun Ni", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Giovanna Badia", - "author_inst": "McGill University" - }, - { - "author_name": "Nathalie Tufenkji", - "author_inst": "McGill University" - }, - { - "author_name": "Cassidy R. Sugimoto", - "author_inst": "Georgia Tech" - }, - { - "author_name": "Vincent Lariviere", - "author_inst": "Universite de Montreal" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "scientific communication and education" - }, { "rel_doi": "10.1101/2023.08.21.553968", "rel_title": "Antibody Neutralization of Emerging SARS-CoV-2: EG.5.1 and XBC.1.6", @@ -29187,6 +29772,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2023.08.24.23294583", + "rel_title": "Rates of SARS-CoV-2 transmission between and into California state prisons", + "rel_date": "2023-08-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.24.23294583", + "rel_abs": "Correctional institutions are a crucial hotspot amplifying SARS-CoV-2 spread and disease disparity in the U.S. In the California state prison system, multiple massive outbreaks have been caused by transmission between prisons. Correctional staff are a likely vector for transmission into the prison system from surrounding communities. We used publicly available data to estimate the magnitude of flows to and between California state prisons, estimating rates of transmission from communities to prison staff and residents, among and between residents and staff within facilities, and between staff and residents of distinct facilities in the states 34 prisons through March 22, 2021. We use a mechanistic model, the Hawkes process, reflecting the dynamics of SARS-CoV-2 transmission, for joint estimation of transmission rates. Using nested models for hypothesis testing, we compared the results to simplified models (i) without transmission between prisons, and (ii) with no distinction between prison staff and residents. We estimated that transmission between different facilities staff is a significant cause of disease spread, and that staff are a vector of transmission between resident populations and outside communities. While increased screening and vaccination of correctional staff may help reduce introductions, large-scale decarceration remains crucially needed as more limited measures are not likely to prevent large-scale disease spread.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Preeti Dubey", + "author_inst": "Francis I. Proctor Foundation, University of California, San Francisco, Calif., USA" + }, + { + "author_name": "Christopher Hoover", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Phoebe Lu", + "author_inst": "Francis I. Proctor Foundation, University of California, San Francisco, Calif., USA" + }, + { + "author_name": "Seth Blumberg", + "author_inst": "Francis I. Proctor Foundation, University of California, San Francisco, Calif., USA" + }, + { + "author_name": "Travis C Porco", + "author_inst": "Francis I. Proctor Foundation, University of California, San Francisco, Calif., USA" + }, + { + "author_name": "Todd L Parsons", + "author_inst": "CNRS & Laboratoire de Probabilites, Statistique et Modelisation, Campus Pierre et Marie Curie, Sorbonne Universite, Paris, France" + }, + { + "author_name": "Lee Worden", + "author_inst": "UCSF" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.08.24.23294559", "rel_title": "Serological surveillance reveals a high exposure to SARS-CoV-2 and altered immune response among COVID-19 unvaccinated Cameroonian individuals", @@ -30101,125 +30729,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.08.22.554373", - "rel_title": "Potent and broadly neutralizing antibodies against sarbecoviruses induced by sequential COVID-19 vaccination", - "rel_date": "2023-08-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.22.554373", - "rel_abs": "The current SARS-CoV-2 variants strikingly evade all authorized monoclonal antibodies and threaten the efficacy of serum-neutralizing activity elicited by vaccination or prior infection, urging the need to develop antivirals against SARS-CoV-2 and related sarbecoviruses. Here, we identified both potent and broadly neutralizing antibodies from a five-dose vaccinated donor who exhibited cross-reactive serum neutralizing activity against diverse coronaviruses. Through single B cell sorting and sequencing followed by a tailor-made computational pipeline, we successfully selected 86 antibodies with potential cross-neutralizing ability from 684 antibody sequences. Among them, one potently neutralized all SARS-CoV-2 variants that arose prior to Omicron BA.5, and the other three could broadly neutralize all current SARS-CoV-2 variants of concern, SARS-CoV and their related sarbecoviruses (Pangolin-GD, RaTG13, WIV-1, and SHC014). Cryo-EM analysis demonstrates that these antibodies have diverse neutralization mechanisms, such as disassembling spike trimers, or binding to RBM or SD1 to affect ACE2 binding. In addition, prophylactic administration of these antibodies significantly protects nasal turbinate and lung infections against BA.1, XBB.1 and SARS-CoV viral challenge in golden Syrian hamsters, respectively. This study reveals the potential utility of computational process to assist screening cross-reactive antibodies, as well as the potency of vaccine-induced broadly neutralizing antibodies against current SARS-CoV-2 variants and related sarbecoviruses, offering promising avenues for the development of broad therapeutic antibody drugs.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Xiaoyu Zhao", - "author_inst": "Fudan University" - }, - { - "author_name": "Tianyi Qiu", - "author_inst": "Fudan University" - }, - { - "author_name": "Xiner Huang", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Qiyu Mao", - "author_inst": "Fudan University" - }, - { - "author_name": "Yajie Wang", - "author_inst": "Fudan University" - }, - { - "author_name": "Rui Qiao", - "author_inst": "Fudan University" - }, - { - "author_name": "Tiantian Mao", - "author_inst": "Tongji University" - }, - { - "author_name": "Yuan Wang", - "author_inst": "Tongji University" - }, - { - "author_name": "Jiayan Li", - "author_inst": "Fudan University" - }, - { - "author_name": "Cuiting Luo", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Chaemin Yoon", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Xun Wang", - "author_inst": "Fudan University" - }, - { - "author_name": "Chen Li", - "author_inst": "Fudan University" - }, - { - "author_name": "Yuchen Cui", - "author_inst": "Fudan University" - }, - { - "author_name": "Chaoyue Zhao", - "author_inst": "Fudan University" - }, - { - "author_name": "Minghui Li", - "author_inst": "Fudan University" - }, - { - "author_name": "Yanjia Chen", - "author_inst": "Fudan University" - }, - { - "author_name": "Guonan Cai", - "author_inst": "Fudan University" - }, - { - "author_name": "Wenye Geng", - "author_inst": "Fudan University" - }, - { - "author_name": "Zixin Hu", - "author_inst": "Fudan University" - }, - { - "author_name": "Jinglei Cao", - "author_inst": "Fudan University" - }, - { - "author_name": "Wenhong Zhang", - "author_inst": "Huashan Hospital, Fudan University" - }, - { - "author_name": "Zhiwei Cao", - "author_inst": "School of Life Sciences, Fudan University, Shanghai, China" - }, - { - "author_name": "Hin Chu", - "author_inst": "Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrativ" - }, - { - "author_name": "Lei Sun", - "author_inst": "Fudan University" - }, - { - "author_name": "Pengfei Wang", - "author_inst": "Fudan University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.08.23.554434", "rel_title": "SARS-CoV-2 Nsp13 is a viral RHIM protein promoting cell death linked to Z-RNA sensing and ZBP1-RIPK3 signaling", @@ -30821,6 +31330,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.08.19.23294314", + "rel_title": "Study of the protective OAS1 rs10774671-G allele against severe COVID-19 in Moroccans suggests a North African origin for Neanderthals", + "rel_date": "2023-08-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.19.23294314", + "rel_abs": "BackgroundThe clinical presentation of COVID-19 has shown high variability between individuals, which is partly due to genetic factors. The OAS1/2/3 cluster was found to be strongly associated with COVID-19 severity. We aimed to examine this locus for the occurrence of the critical variant, rs10774671, and its respective haplotype blocks within the Moroccan population.\n\nMethodsThe frequency of SNPs at the cluster of OAS immunity genes was assessed from an in-house database in 157 unrelated individuals of Moroccan origin. The OAS1 exon 6 was sequenced by Sangers method in 71 asymptomatic/mild and 74 moderate/severe individuals positive for SARS-CoV-2. Genotypic, allelic, and haplotype frequencies of three SNPs were compared between the two groups. Finally, males in our COVID-19 series were genotyped for the Berber-specific marker E-M81.\n\nResultsThe prevalence of the OAS1 rs10774671-G allele in present-day Moroccans was 40.4%, close to that of Europeans. However, it was found equally on both the Neanderthal GGG haplotype and the African GAC haplotype with a frequency of 20% each. These two haplotypes, and hence the rs10774671-G allele, were significantly associated with the protection against severe COVID-19 (p = 0.034, p = 0.041, and p = 0.008 respectively). Surprisingly, among Berber men, the African haplotype was absent while the prevalence of the Neanderthal haplotype was close to that of Europeans.\n\nConclusionThe protective rs10774671-G allele of OAS1 was found only in the Neanderthal haplotype in Berbers, the indigenous people of North Africa, suggesting that this region may have served as the stepping-stone for the passage of the hominids to the other continents.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Fatima Zohra El Youssfi", + "author_inst": "Mohammed V University of Rabat Faculty of Medicine and Pharmacy of Rabat: Universite Mohammed V de Rabat Faculte de Medecine et de Pharmacie de Rabat" + }, + { + "author_name": "Abbas Ermilo Haroun", + "author_inst": "Mohammed V University of Rabat Faculty of Medicine and Pharmacy of Rabat: Universite Mohammed V de Rabat Faculte de Medecine et de Pharmacie de Rabat" + }, + { + "author_name": "Chaimae Nebhani", + "author_inst": "Mohammed V University of Rabat Faculty of Medicine and Pharmacy of Rabat: Universite Mohammed V de Rabat Faculte de Medecine et de Pharmacie de Rabat" + }, + { + "author_name": "Jihane Belayachi", + "author_inst": "Mohammed V University of Rabat Faculty of Medicine and Pharmacy of Rabat: Universite Mohammed V de Rabat Faculte de Medecine et de Pharmacie de Rabat" + }, + { + "author_name": "Omar Askander", + "author_inst": "Mohammed VI Polytechnic University: Universite Mohammed VI Polytechnique" + }, + { + "author_name": "Elmostafa El Fahime", + "author_inst": "Centre National pour la Recherche Scientifique et Technique" + }, + { + "author_name": "Hakima Fares", + "author_inst": "Cheikh Zaid Hospital: Hopital Universitaire International Cheikh Zaid" + }, + { + "author_name": "Khalid Ennibi", + "author_inst": "H\u00f4pital Militaire d'Instruction Mohammed V: Hopital Militaire d'Instruction Mohammed V" + }, + { + "author_name": "Redouane Abouqal", + "author_inst": "Mohammed V University of Rabat Faculty of Medicine and Pharmacy of Rabat: Universite Mohammed V de Rabat Faculte de Medecine et de Pharmacie de Rabat" + }, + { + "author_name": "Rachid Razine", + "author_inst": "Mohammed V University of Rabat Faculty of Medicine and Pharmacy of Rabat: Universite Mohammed V de Rabat Faculte de Medecine et de Pharmacie de Rabat" + }, + { + "author_name": "Ahmed Bouhouche", + "author_inst": "Mohammed V University of Rabat Faculty of Medicine and Pharmacy of Rabat: Universite Mohammed V de Rabat Faculte de Medecine et de Pharmacie de Rabat" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2023.08.21.23293488", "rel_title": "Drivers and impact of the early silent invasion of SARS-CoV-2 Alpha", @@ -31959,37 +32527,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2023.08.17.23293589", - "rel_title": "Strategic use of SARS-CoV-2 wastewater concentration data could enhance, but not replace, high-resolution community prevalence survey programmes", - "rel_date": "2023-08-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.17.23293589", - "rel_abs": "Wastewater-based epidemiology (WBE) has been proposed as a tool for public health authorities to monitor community transmission of SARS-CoV-2 and other agents. Here, we review the utility of WBE for estimating SARS-CoV-2 prevalence using wastewater data from the Environmental Monitoring for Health Protection (EMHP) programme and prevalence data from the REal-time Assessment of Community Transmission-1 (REACT-1) study in England. Our analysis shows a temporally evolving relationship between wastewater and prevalence which limits the utility of WBE for estimating SARS-CoV-2 prevalence in high spatial resolution without a concurrent prevalence survey. We further characterise WBE for SARS-CoV-2 prevalence as i) vaccination-coverage-dependent and ii) variant-specific. Our work provides a gesopatial framework to map wastewater concentrations to public health boundaries, enabling public health authorities to interpret the relationship between wastewater and prevalence. We demonstrate that WBE can improve the cost efficiency and accuracy of community prevalence surveys which on their own may have incomplete geographic coverage or small sample sizes.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Cathal Mills", - "author_inst": "University of Oxford" - }, - { - "author_name": "Marc Chadeau-Hyam", - "author_inst": "Imperial College London School of Public Health" - }, - { - "author_name": "Paul L Elliott", - "author_inst": "Imperial College London School of Public Health" - }, - { - "author_name": "Christl A Donnelly", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.08.16.23294160", "rel_title": "Unraveling COVID-19: Descriptive Analytics in a Middle-Income Country, Paving the Path Forward", @@ -32519,6 +33056,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.08.14.23294060", + "rel_title": "Improving estimates of epidemiological quantities by combining reported cases with wastewater data: a statistical framework with applications to COVID-19 in Aotearoa New Zealand", + "rel_date": "2023-08-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.14.23294060", + "rel_abs": "BackgroundTimely and informed public health responses to infectious diseases such as COVID-19 necessitate reliable information about infection dynamics. The case ascertainment rate (CAR), the proportion of infections that are reported as cases, is typically much less than one and varies with testing practices and behaviours, making reported cases unreliable as the sole source of data. The concentration of viral RNA in wastewater samples provides an alternate measure of infection prevalence that is not affected by human behaviours. Here, we investigated how these two data sources can be combined to inform estimates of the instantaneous reproduction number, R, and track changes in the CAR over time.\n\nMethodsWe constructed a state-space model that we solved using sequential Monte Carlo methods. The observed data are the levels of SARS-CoV-2 in wastewater and reported case incidence. The hidden states that we estimate are R and CAR. Model parameters are estimated using the particle marginal Metropolis Hastings algorithm.\n\nFindingsWe analysed data from 1 January 2022 to 31 March 2023 from Aotearoa New Zealand. Our model estimates that R peaked at 2.76 (95% CrI 2.20, 3.83) around 18 February 2022 and the CAR peaked around 12 March 2022. Accounting for reduced CAR, we estimate that New Zealands second Omicron wave in July 2022 was similar in size to the first, despite fewer reported cases. We estimate that the CAR in the BA.5 Omicron wave in July 2022 was approximately 50% lower than in the BA.1/BA.2 Omicron wave in March 2022. The CAR in subsequent waves around November 2022 and April 2023 was estimated to be comparable to that in the second Omicron wave.\n\nInterpretationThis work on wastewater-based epidemiology (WBE) can be used to give insight into key epidemiological quantities. Estimating R, CAR, and cumulative number of infections provides useful information for planning public health responses and understanding the state of immunity in the population. This model is a useful disease surveillance tool, improving situational awareness of infectious disease dynamics in real-time, which may be increasingly useful as intensive pandemic surveillance programmes are wound down.\n\nFundingNew Zealand Ministry of Health, Department of Prime Minister and Cabinet, the Royal Society Te Ap[a]rangi, Imperial College London, and University of Oxford.\n\nResearch in ContextO_ST_ABSEvidence before this studyC_ST_ABSThere has been a substantial increase in the number of publications focusing on wastewater-based epidemiology (WBE) in recent years, particularly during the COVID-19 pandemic. We searched PubMed for \"wastewater based epidemiology\" and found fewer than 10 papers per year prior to 2014 with a drastic increase to 463 in 2022. Approximately 52% of the WBE publications are related to COVID-19 (\"wastewater based epidemiology\" AND (\"SARS-CoV-2\" OR \"COVID-19\")). Many studies have focused on detecting SARS-CoV-2 in wastewater systems but only 10 have estimated the reproduction number (\"wastewater based epidemiology\" AND (\"SARS-CoV-2\" OR \"COVID-19\") AND \"reproduction number\"). No previous work has combined WBE with reported case data to estimate (relative) case ascertainment rate (\"waste-water based epidemiology\" AND (\"SARS-CoV-2\" OR \"COVID-19\") AND \"case ascertainment rate\"). Previous work has estimated the reproduction number from reported cases assuming constant under-ascertainment but the issue of time-varying case ascertainment has not yet been addressed, except to demonstrate the effect of a pre-determined change in case ascertainment.\n\nAdded value of this studyWe present a model that, for the first time, enables reported case information to be combined with wastewater data to estimate epidemiology quantities. This work further demonstrates the utility of WBE; the reproduction number can be estimated in the absence of reported case information (although results are more reliable when case data are included), and wastewater data include information that, when combined with case data, can be used to estimate the time-varying relative case ascertainment rate.\n\nImplications of all the available evidenceIn order to make informed and timely public health decisions about infectious diseases, it is important to understand the number of infections in the community. WBE provides a useful source of data that is not impacted by time-varying testing practices. Wastewater data can be quantitatively combined with case information to better understand the state of an epidemic. In order to determine the absolute case ascertainment rate (rather than the relative rate calculated in this work), there is a need for infection prevalence surveys to calibrate model results against.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Leighton M Watson", + "author_inst": "University of Canterbury" + }, + { + "author_name": "Michael J Plank", + "author_inst": "University of Canterbury" + }, + { + "author_name": "Bridget Armstrong", + "author_inst": "Environmental Science and Research" + }, + { + "author_name": "Joanne Chapman", + "author_inst": "Environmental Science and Research" + }, + { + "author_name": "Joanne Hewitt", + "author_inst": "Environmental Science and Research" + }, + { + "author_name": "Helen Morris", + "author_inst": "Environmental Science and Research" + }, + { + "author_name": "Alvaro Orsi", + "author_inst": "Environmental Science and Research" + }, + { + "author_name": "Michael Bunce", + "author_inst": "Environmental Science and Research" + }, + { + "author_name": "Christl A. Donnelly", + "author_inst": "Imperial College London" + }, + { + "author_name": "Nicholas Steyn", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.08.11.23294002", "rel_title": "Evolution of Myocarditis Incidence at a Large Healthcare System Before and During COVID-19 Pandemic", @@ -33433,49 +34025,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2023.08.11.552988", - "rel_title": "PRIEST - Predicting viral mutations with immune escape capability of SARS-CoV-2 using temporal evolutionary information", - "rel_date": "2023-08-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.11.552988", - "rel_abs": "The dynamic evolution of the SARS-CoV-2 virus is largely driven by mutations in its genetic sequence, culminating in the emergence of variants with increased capability to evade host immune responses. Accurate prediction of such mutations is fundamental in mitigating pandemic spread and developing effective control measures. In this study, we introduce a robust and interpretable deep-learning approach called PRIEST. This innovative model leverages time-series viral sequences to foresee potential viral mutations. Our comprehensive experimental evaluations underscore PRIESTs proficiency in accurately predicting immune-evading mutations. Our work represents a substantial step forward in the utilization of deep-learning methodologies for anticipatory viral mutation analysis and pandemic response.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Gourab Saha", - "author_inst": "Bangladesh University of Engineering and Technology" - }, - { - "author_name": "Shashata Sawmya", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Arpita Saha", - "author_inst": "Bangladesh University of Engineering and Technology" - }, - { - "author_name": "Sadia Tasnim", - "author_inst": "Bangladesh University of Engineering and Technology" - }, - { - "author_name": "Md. Ajwad Akil", - "author_inst": "Bangladesh University of Engineering and Technology" - }, - { - "author_name": "M. Saifur Rahman", - "author_inst": "Bangladesh University of Engineering and Technology" - }, - { - "author_name": "M. Sohel Rahman", - "author_inst": "Bangladesh University of Engineering and Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2023.08.13.553144", "rel_title": "Mutational basis of serum cross-neutralization profiles elicited by infection or vaccination with SARS-CoV-2 variants", @@ -33961,6 +34510,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.08.11.23293975", + "rel_title": "Identifying facilitators and barriers to culturally responsive communication for racial, ethnic, sexual, and gender minoritized patients when screened for COVID-19 vaccinations: A Scoping Review Protocol", + "rel_date": "2023-08-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.11.23293975", + "rel_abs": "IntroductionRacial, ethnic, sexual, and gender minoritized groups are considered historically excluded groups and have been disproportionately affected by the coronavirus disease 2019 (COVID-19) pandemic. The influence of social determinants of health (SDOH), including access to screening and treatment, and other systemic and structural factors are largely responsible for these disparities. Primary care practitioner (PCP) competence in culturally responsive screening practices will be critical to reducing the impact of systemic and structural factors serving as barriers to screening and treatment. Correspondingly, improving the capacity of PCPs to communicate with patients in a culturally responsive manner may influence improved screening and treatment outcomes for minoritized groups related to COVID-19. This scoping literature review aims to determine the current breadth of literature on culturally responsive communication (CRC) in regard to COVID-19 vaccination screening for historically excluded, or minoritized groups. Results from this review will inform the development of a training series and social marketing campaign to improve PCPs capacity in CRC.\n\nObjectivesThis scoping literature review aims to analyze existing literature on culturally responsive COVID-19 vaccinations between PCPs and patients in the U.S., specifically for racial, ethnic, sexual, and gender minoritized groups. Results of this scoping review will inform the development of a training series and social marketing campaign to improve capacity of PCPs in this area. Additionally, the review will inform recommendations for future research.\n\nMaterials and MethodsThis scoping review will be performed following the framework of Arksey and OMalley and the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for scoping reviews (PRISMA-ScR). Relevant studies between the years 2019-2022 were identified using a rigorous search strategy across four databases: MEDLINE (via PubMed), Scopus, Cochrane (CENTRAL; via Wiley), and CINAHL (via EBSCO), using Boolean and Medical Subject Headings (MeSH) search terms. Studies will be uploaded to the data extraction tool, Covidence, to remove duplicates and perform a title/abstract screening, followed by a full-text screening.\n\nResultsThe data extraction and analysis phases of the scoping review are in progress. Data will be analyzed for themes related to culturally responsive COVID-19 screening practices in clinical encounters with the identified study populations. Results will be reported by theme and align to PRISMA-ScR guidelines.\n\nDiscussionTo our knowledge, this is the first study to use scoping methods to investigate the barriers and facilitators to CRC of COVID-19 vaccine screening for historically excluded communities in the U.S. The work and results from this research will be directly utilized for the development of nationally-accessible, continuing medical education materials to teach PCPs about CRC, as well as other materials to influence relevant policy changes within the healthcare landscape.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Nikhil Kalita", + "author_inst": "The George Washington University Milken Institute of Public Health" + }, + { + "author_name": "Patrick G Corr", + "author_inst": "The George Washington University School of Medicine and Health Sciences" + }, + { + "author_name": "Maranda C Ward", + "author_inst": "The George Washington University School of Medicine and Health Sciences" + }, + { + "author_name": "Julia Xavier", + "author_inst": "The George Washington University School of Medicine and Health Sciences" + }, + { + "author_name": "Paige McDonald", + "author_inst": "The George Washington University School of Medicine and Health Sciences" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "primary care research" + }, { "rel_doi": "10.1101/2023.08.10.552726", "rel_title": "Additive Manufacturing Leveraged Microfluidic Setup for Sample to Answer Colorimetric Detection of Pathogens", @@ -34727,141 +35311,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2023.08.07.23293778", - "rel_title": "Diabetes following SARS-CoV-2 infection: Incidence, persistence, and implications of COVID-19 vaccination. A cohort study of fifteen million people.", - "rel_date": "2023-08-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.07.23293778", - "rel_abs": "BackgroundType 2 diabetes (T2DM) incidence is increased after diagnosis of COVID-19. The impact of vaccination on this increase, for how long it persists, and the effect of COVID-19 on other types of diabetes remain unclear.\n\nMethodsWith NHS England approval, we studied diabetes incidence following COVID-19 diagnosis in pre-vaccination (N=15,211,471, January 2020-December 2021), vaccinated (N =11,822,640), and unvaccinated (N=2,851,183) cohorts (June-December 2021), using linked electronic health records. We estimated adjusted hazard ratios (aHRs) comparing diabetes incidence post-COVID-19 diagnosis with incidence before or without diagnosis up to 102 weeks post-diagnosis. Results were stratified by COVID-19 severity (hospitalised/non-hospitalised) and diabetes type.\n\nFindingsIn the pre-vaccination cohort, aHRS for T2DM incidence after COVID-19 (compared to before or without diagnosis) declined from 3.01 (95% CI: 2.76,3.28) in weeks 1-4 to 1.24 (1.12,1.38) in weeks 53-102. aHRS were higher in unvaccinated than vaccinated people (4.86 (3.69,6.41)) versus 1.42 (1.24,1.62) in weeks 1-4) and for hospitalised COVID-19 (pre-vaccination cohort 21.1 (18.8,23.7) in weeks 1-4 declining to 2.04 (1.65,2.51) in weeks 52-102), than non-hospitalised COVID-19 (1.45 (1.27,1.64) in weeks 1-4, 1.10 (0.98,1.23) in weeks 52-102). T2DM persisted for 4 months after COVID-19 for [~]73% of those diagnosed. Patterns were similar for Type 1 diabetes, though excess incidence did not persist beyond a year post-COVID-19.\n\nInterpretationElevated T2DM incidence after COVID-19 is greater, and persists longer, in hospitalised than non-hospitalised people. It is markedly less apparent post-vaccination. Testing for T2DM after severe COVID-19 and promotion of vaccination are important tools in addressing this public health problem.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed for population-based observational studies published between December 1st 2019 and July 12th 2023 examining associations between SARS-CoV-2 infection or COVID-19 diagnosis (search string: SARS-CoV-2 or COVID* or coronavirus*) and subsequent incident diabetes (search term: diabetes). Of nineteen relevant studies; eight had a composite outcome of diabetes types, six stratified by diabetes type and five pertained to type-1-diabetes (T1DM) only. We did not identify any studies relating to gestational or other types of diabetes. Eleven studies were from the US, three from the UK, two from Germany, one from Canada, one from Denmark and one from South Korea.\n\nMost studies described cumulative relative risks (for infection versus no infection) one to two years post-SARS-CoV-2 infection of 1.2 to 2.6, though four studies found no associations with T1DM after the post-acute period. All studies lacked the power to compare diabetes relative risk by type, severity, and vaccination status in population subgroups. One study examined relative risks by vaccination status, but this used a composite outcome of diabetes and hyperlipidaemia and was conducted in a predominantly white male population.\n\nTwo studies of T1DM found no evidence of elevated risk beyond 30 days after COVID-19 diagnosis, whilst two reported elevated risks at six months. Two studies of type 2 diabetes (T2DM) examined relative risks by time period post-infection: one study of US insurance claims reported a persistent association six months post-infection, whereas a large UK population-based study reported no associations after 12 weeks. However, the latter study used only primary care data, therefore COVID-19 cases were likely to have been under-ascertained.\n\nNo large studies have investigated the persistence of diabetes diagnosed following COVID-19; key to elucidating the role of stress/steroid-induced hyperglycaemia.\n\nAdded value of this studyThis study, which is the largest to address the question to date, analysed linked primary and secondary care health records with SARS-CoV-2 testing and COVID-19 vaccination data for 15 million people living in England. This enabled us to compare the elevation in diabetes incidence after COVID-19 diagnosis by diabetes type, COVID-19 severity and vaccination status, overall and in population subgroups. Importantly, excess diabetes incidence by time period since infection could also be quantified. Since healthcare in the UK is universal and free-at-the-point-of-delivery, almost the entire population is registered with primary care. Therefore the findings are likely to be generalisable.\n\nWe found that, before availability of COVID-19 vaccination, a COVID-19 diagnosis (vs. no diagnosis) was associated with increased T2DM incidence which remained elevated by approximately 30% beyond one year after diagnosis. Though still present (with around 30% excess incidence at eight weeks), these associations were substantially attenuated in unvaccinated compared with vaccinated people. Excess incidence was greater in people hospitalised with COVID-19 than those who were not hospitalised after diagnosis. T1DM incidence was elevated up to, but not beyond, a year post COVID-19. Around 73% of people diagnosed with incident T2DM after COVID-19 still had evidence of diabetes four months after infection.\n\nImplications of all the available evidenceThere is a 30-50% elevated T2DM incidence post-COVID-19, but we report the novel finding that there is elevated incidence beyond one-year post-diagnosis. Elevated T1DM incidence did not appear to persist beyond a year, which may explain why previous studies disagree. For the first time in a general-population dataset, we demonstrate that COVID-19 vaccination reduces, but does not entirely ameliorate, excess diabetes incidence after COVID-19. This supports a policy of universal vaccination and suggests that other public health activities, such as enhanced diabetes screening after severe COVID-19, may be warranted, particularly in unvaccinated people.", - "rel_num_authors": 30, - "rel_authors": [ - { - "author_name": "Kurt Taylor", - "author_inst": "University of Bristol" - }, - { - "author_name": "Sophie Eastwood", - "author_inst": "University College London" - }, - { - "author_name": "Venexia Walker", - "author_inst": "University of Bristol" - }, - { - "author_name": "Genevieve Cezard", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Rochelle Knight", - "author_inst": "University of Bristol" - }, - { - "author_name": "Marwa Al Arab", - "author_inst": "University of Bristol" - }, - { - "author_name": "Yinghui Wei", - "author_inst": "University of Plymouth" - }, - { - "author_name": "Elsie M F Horne", - "author_inst": "University of Bristol" - }, - { - "author_name": "Lucy Teece", - "author_inst": "University of Leicester" - }, - { - "author_name": "Harriet Forbes", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Alex Walker", - "author_inst": "University of Oxford" - }, - { - "author_name": "Louis Fisher", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jon Massey", - "author_inst": "University of Oxford" - }, - { - "author_name": "Lisa E M Hopcroft", - "author_inst": "University of Oxford" - }, - { - "author_name": "Tom Palmer", - "author_inst": "University of Bristol" - }, - { - "author_name": "Jose Cuitun Coronado", - "author_inst": "University of Bristol" - }, - { - "author_name": "Samantha Ip", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Simon Davy", - "author_inst": "University of Oxford" - }, - { - "author_name": "Iain Dillingham", - "author_inst": "University of Oxford" - }, - { - "author_name": "Caroline Morton", - "author_inst": "University of Oxford" - }, - { - "author_name": "Felix Greaves", - "author_inst": "National Institute for Health and Care Excellence" - }, - { - "author_name": "John MacLeod", - "author_inst": "University of Bristol" - }, - { - "author_name": "Ben Goldacre", - "author_inst": "University of Oxford" - }, - { - "author_name": "Angela Wood", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Nishi Chaturvedi", - "author_inst": "University College London" - }, - { - "author_name": "Jonathan A C Sterne", - "author_inst": "University of Bristol" - }, - { - "author_name": "Rachel Denholm", - "author_inst": "University of Bristol" - }, - { - "author_name": "- CONVALESCENCE Long-COVID study", - "author_inst": "-" - }, - { - "author_name": "- Longitudinal Health and Wellbeing and Data and Connectivity UK COVID-19 National Core Studies", - "author_inst": "-" - }, - { - "author_name": "- OpenSAFELY collaborative", - "author_inst": "-" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.08.07.23293304", "rel_title": "High-throughput detection of neutralizing antibodies to SARS-CoV-2 variants using flow cytometry", @@ -35355,6 +35804,61 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.08.07.552269", + "rel_title": "Purifying selection and adaptive evolution proximate to the zoonosis of SARS-CoV-1 and SARS-CoV-2", + "rel_date": "2023-08-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.07.552269", + "rel_abs": "Over the past two decades the pace of spillovers from animal viruses to humans has accelerated, with COVID-19 becoming the most deadly zoonotic disease in living memory. Prior to zoonosis, it is conceivable that the virus might largely be subjected to purifying selection, requiring no additional selective changes for successful zoonotic transmission. Alternatively, selective changes occurring in the reservoir species may coincidentally preadapt the virus for human-to-human transmission, facilitating spread upon cross-species exposure. Here we quantify changes in the genomes of SARS-CoV-2 and SARS-CoV-1 proximate to zoonosis to evaluate the selection pressures acting on the viruses. Application of molecular-evolutionary and population-genetic approaches to quantify site-specific selection within both SARS-CoV genomes revealed strong purifying selection across many genes at the time of zoonosis. Even in the viral surface-protein Spike that has been fast-evolving in humans, there is little evidence of positive selection proximate to zoonosis. Nevertheless, in SARS-CoV-2, NSP12, a core protein for viral replication, exhibited a region under adaptive selection proximate to zoonosis. Furthermore, in both SARS-CoV-1 and SARS-CoV-2, regions of adaptive selection proximate to zoonosis were found in ORF7a, a putative Major Histocompatibility Complex modulatory gene. These findings suggest that these replication and immunomodulatory proteins have played a previously underappreciated role in the adaptation of SARS coronaviruses to human hosts.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Jeffrey P Townsend", + "author_inst": "Yale University" + }, + { + "author_name": "Stephen Gaughran", + "author_inst": "Princeton University" + }, + { + "author_name": "Hayley B Hassler", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Jeffrey Nicholas Fisk", + "author_inst": "Yale University" + }, + { + "author_name": "Mofeed Nagib", + "author_inst": "Yale University" + }, + { + "author_name": "Yinfei Wu", + "author_inst": "Yale University" + }, + { + "author_name": "Yaning Wang", + "author_inst": "Yale University" + }, + { + "author_name": "Zheng Wang", + "author_inst": "Yale University" + }, + { + "author_name": "Alison P Galvani", + "author_inst": "Yale University" + }, + { + "author_name": "Alex Dornburg", + "author_inst": "University of North Carolina at Charlotte" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2023.08.07.552249", "rel_title": "phuEGO: A network-based method to reconstruct active signalling pathways from phosphoproteomics datasets", @@ -36269,109 +36773,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.07.31.23293337", - "rel_title": "Differential host responses within the upper respiratory tract and peripheral blood of children and adults with SARS-CoV-2 infection", - "rel_date": "2023-08-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.31.23293337", - "rel_abs": "Age is among the strongest risk factors for severe outcomes from SARS-CoV-2 infection. We sought to evaluate associations between age and both mucosal and systemic host responses to SARS-CoV-2 infection. We profiled the upper respiratory tract (URT) and peripheral blood transcriptomes of 201 participants (age range of 1 week to 83 years), including 137 non-hospitalized individuals with mild SARS-CoV-2 infection and 64 uninfected individuals. Among uninfected children and adolescents, young age was associated with upregulation of innate and adaptive immune pathways within the URT, suggesting that young children are primed to mount robust mucosal immune responses to exogeneous respiratory pathogens. SARS-CoV-2 infection was associated with broad induction of innate and adaptive immune responses within the URT of children and adolescents. Peripheral blood responses among SARS-CoV-2-infected children and adolescents were dominated by interferon pathways, while upregulation of myeloid activation, inflammatory, and coagulation pathways was observed only in adults. Systemic symptoms among SARS-CoV-2-infected subjects were associated with blunted innate and adaptive immune responses in the URT and upregulation of many of these same pathways within peripheral blood. Finally, within individuals, robust URT immune responses were correlated with decreased peripheral immune activation, suggesting that effective immune responses in the URT may promote local viral control and limit systemic immune activation and symptoms. These findings demonstrate that there are differences in immune responses to SARS-CoV-2 across the lifespan, including between young children and adolescents, and suggest that these varied host responses contribute to observed differences in the clinical presentation of SARS-CoV-2 infection by age.\n\nOne Sentence SummaryAge is associated with distinct upper respiratory and peripheral blood transcriptional responses among children and adults with SARS-CoV-2 infection.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Jillian H Hurst", - "author_inst": "Duke University School of Medicine" - }, - { - "author_name": "Aditya Mohan", - "author_inst": "Duke University School of Medicine" - }, - { - "author_name": "Trisha Dalapati", - "author_inst": "Duke University School of Medicine" - }, - { - "author_name": "Ian A. George", - "author_inst": "Duke University School of Medicine" - }, - { - "author_name": "Jhoanna N. Aquino", - "author_inst": "Duke University School of Medicine" - }, - { - "author_name": "Debra J. Lugo", - "author_inst": "Duke University School of Medicine" - }, - { - "author_name": "Trevor S. Pfeiffer", - "author_inst": "Duke University School of Medicine" - }, - { - "author_name": "Javier Rodriguez", - "author_inst": "Duke University School of Medicine" - }, - { - "author_name": "Alexandre T. Rotta", - "author_inst": "Duke University School of Medicine" - }, - { - "author_name": "Nicholas A. Turner", - "author_inst": "Duke University School of Medicine" - }, - { - "author_name": "Thomas W. Burke", - "author_inst": "Duke University School of Medicine" - }, - { - "author_name": "Micah T McClain", - "author_inst": "Duke University Medical Center" - }, - { - "author_name": "Ricardo Henao", - "author_inst": "Duke University" - }, - { - "author_name": "C. Todd DeMarco", - "author_inst": "Duke University School of Medicine" - }, - { - "author_name": "Raul Louzao", - "author_inst": "Duke University School of Medicine" - }, - { - "author_name": "Thomas N. Denny", - "author_inst": "Duke University School of Medicine" - }, - { - "author_name": "Kyle M. Walsh", - "author_inst": "DUKE UNIVERSITY" - }, - { - "author_name": "Zhaohui Xu", - "author_inst": "St. Jude Children's Research Hospital" - }, - { - "author_name": "Asuncion Mejias", - "author_inst": "St. Jude Children's Research Hospital" - }, - { - "author_name": "Octavio Ramilo", - "author_inst": "St. Jude Children's Research Hospital" - }, - { - "author_name": "Christopher W. Woods", - "author_inst": "Duke University School of Medicine" - }, - { - "author_name": "Matthew S Kelly", - "author_inst": "Duke University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.07.28.23293335", "rel_title": "Healthcare resource utilization and costs associated with COVID-19 among pediatrics managed in the community or hospital setting in England: a population-based cohort study", @@ -36893,6 +37294,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.08.02.23293519", + "rel_title": "Real-time epidemiological modelling during the COVID-19 emergency in Wales", + "rel_date": "2023-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.02.23293519", + "rel_abs": "The sudden outbreak of the COVID-19 pandemic presented governments, policy makers and health services with an unprecedented challenge of taking real-time decisions that could keep the disease under control with non-pharmaceutical interventions, while at the same time limit as much as possible severe consequences of a very strict lockdown. Mathematical modelling has proved to be a crucial element for informing those decisions. Here we report on the rapid development and application of the Swansea Model, a mathematical model of disease spread in real time, to inform policy decisions during the COVID-19 pandemic in Wales.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Michael Gravenor", + "author_inst": "Swansea University" + }, + { + "author_name": "Mark Dawson", + "author_inst": "Swansea University" + }, + { + "author_name": "Ed Bennett", + "author_inst": "Swansea University" + }, + { + "author_name": "Ben Thorpe", + "author_inst": "Swansea University" + }, + { + "author_name": "Carla White", + "author_inst": "Swansea University" + }, + { + "author_name": "Alma Rahat", + "author_inst": "Swansea University" + }, + { + "author_name": "Daniel Archambault", + "author_inst": "Swansea University" + }, + { + "author_name": "Noemi Picco", + "author_inst": "Swansea University" + }, + { + "author_name": "Gibin Powathil", + "author_inst": "Swansea University" + }, + { + "author_name": "Biagio Lucini", + "author_inst": "Swansea University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.08.02.23293563", "rel_title": "Post-acute health care costs following SARS-CoV-2 infection: A retrospective cohort study of among 531,182 matched adults", @@ -38043,33 +38499,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2023.08.01.551500", - "rel_title": "Recombinant Rotavirus Expressing the Glycosylated S1 Protein of SARS-CoV-2", - "rel_date": "2023-08-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.01.551500", - "rel_abs": "Reverse genetic systems have been used to introduce heterologous sequences into the rotavirus segmented double-stranded (ds)RNA genome, enabling the generation of recombinant viruses that express foreign proteins and possibly serve as vaccine vectors. Notably, insertion of SARS-CoV-2 sequences into the segment 7 (NSP3) RNA of simian SA11 rotavirus was previously shown to result in the production of recombinant viruses that efficiently expressed the N-terminal domain (NTD) and the receptor-binding domain (RBD) of the S1 region of the SARS-CoV-2 spike protein. However, efforts to generate a similar recombinant (r) SA11 virus that efficiently expressed full-length S1 were less successful. In this study, we describe modifications to the S1-coding cassette inserted in the segment 7 RNA that allowed recovery of second-generation rSA11 viruses that efficiently expressed the [~]120-kDa S1 protein. The [~]120-kDa S1 products were shown to be glycosylated, based on treatment with endoglycosidase H, which reduced the protein to a size of [~]80 kDa. Co-pulldown assays demonstrated that the [~]120-kDa S1 proteins had affinity for the human ACE2 receptor. Although all the second-generation rSA11 viruses expressed glycosylated S1 with affinity for the ACE receptor, only the S1 product of one virus (rSA11/S1f) was appropriately recognized by anti-S1 antibody, suggesting the rSA11/S1f virus expressed an authentic form of S1. Probably due to the presence of FLAG tags on their S1 signal peptides, the S1 products of the other viruses (rSA11/3fS1 and rSA11/3fS1-His) may have undergone defective glycosylation, impeding antibody binding. In summary, these results indicate that recombinant rotaviruses can serve as expression vectors of foreign glycosylated proteins, raising the possibility of generating rotavirus-based vaccines that can induce protective immune responses against enteric and mucosal viruses with glycosylated capsid components, including SARS-CoV-2.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Asha Ann Philip", - "author_inst": "Indiana University" - }, - { - "author_name": "Sannoong Hu", - "author_inst": "Indiana University" - }, - { - "author_name": "John T Patton", - "author_inst": "Indiana University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.07.28.550957", "rel_title": "Epigenetic liquid biopsies reveal elevated vascular endothelial cell turnover and erythropoiesis in asymptomatic COVID-19 patients", @@ -38843,6 +39272,157 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.07.27.23293177", + "rel_title": "Multimodal Molecular Imaging Reveals Tissue-Based T Cell Activation and Viral RNA Persistence for Up to Two Years Following COVID-19", + "rel_date": "2023-07-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.27.23293177", + "rel_abs": "The etiologic mechanisms of post-acute medical morbidities and unexplained symptoms (Long COVID) following SARS-CoV-2 infection are incompletely understood. There is growing evidence that viral persistence and immune dysregulation may play a major role. We performed whole-body positron emission tomography (PET) imaging in a cohort of 24 participants at time points ranging from 27 to 910 days following acute SARS-CoV-2 infection using a novel radiopharmaceutical agent, [18F]F-AraG, a highly selective tracer that allows for anatomical quantitation of activated T lymphocytes. Tracer uptake in the post-acute COVID group, which included those with and without Long COVID symptoms, was significantly higher compared to pre-pandemic controls in many anatomical regions, including the brain stem, spinal cord, bone marrow, nasopharyngeal and hilar lymphoid tissue, cardiopulmonary tissues, and gut wall. Although T cell activation tended to be higher in participants imaged closer to the time of the acute illness, tracer uptake was increased in participants imaged up to 2.5 years following SARS-CoV-2 infection. We observed that T cell activation in spinal cord and gut wall was associated with the presence of Long COVID symptoms. In addition, tracer uptake in lung tissue was higher in those with persistent pulmonary symptoms. Notably, increased T cell activation in these tissues was also observed in many individuals without Long COVID. Given the high [18F]F-AraG uptake detected in the gut, we obtained colorectal tissue for in situ hybridization SARS-CoV-2 RNA and immunohistochemical studies in a subset of participants with Long COVID symptoms. We identified cellular SARS-CoV-2 RNA in rectosigmoid lamina propria tissue in all these participants, ranging from 158 to 676 days following initial COVID-19 illness, suggesting that tissue viral persistence could be associated with long-term immunological perturbations.", + "rel_num_authors": 34, + "rel_authors": [ + { + "author_name": "Michael J Peluso", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Dylan M Ryder", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Robert Flavell", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Yingbing Wang", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Jelena Levi", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Brian H LaFranchi", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Tyler-Marie M Deveau", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Amanda M Buck", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Sadie E Munter", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Kofi A Asare", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Maya Aslam", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Walter Koch", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Gyula Szabo", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Rebecca Hoh", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Monika Deswal", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Antonio Rodriguez", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Melissa Buitrago", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Viva Tai", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Uttam Shrestha", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Scott Lu", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Sarah A Goldberg", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Thomas Dalhuisen", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Matthew S Durstenfeld", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Priscilla Y Hsue", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "J D Kelly", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Nitasha Kumar", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Jeffrey N Martin", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Aruna Gambhir", + "author_inst": "Cell Sight Technologies" + }, + { + "author_name": "Ma Somsouk", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Youngho Seo", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Steven G Deeks", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Zoltan G Laszik", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Henry F VanBrocklin", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Timothy J Henrich", + "author_inst": "University of California, San Francisco" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.07.30.551145", "rel_title": "Expansion of profibrotic monocyte-derived alveolar macrophages in patients with persistent respiratory symptoms and radiographic abnormalities after COVID-19", @@ -39969,53 +40549,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.07.26.23293191", - "rel_title": "Chronic Shedding of a SARS-CoV-2 Alpha Variant Lineage Q.3/Q.4 in Wastewater", - "rel_date": "2023-07-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.26.23293191", - "rel_abs": "Central Michigan University (CMU) participated in a state-wide SARS-CoV-2 wastewater monitoring program since 2021. Wastewater samples were collected from on-campus sites and nine off-campus wastewater treatment plants servicing small metropolitan and rural communities. SARS-CoV-2 genome copies were quantified using droplet digital PCR and results were reported to the health department. One rural, off-campus site consistently produced higher concentrations of SARS-CoV-2 genome copies. Samples from this site were sequenced and initially contained predominately Alpha variant lineage Q.3, which transitioned to lineage Q.4. Alpha variant lineage Q.3/Q.4 was detected at this site beginning in fall 2021 and continued until summer 2023. Mutational analysis of reconstructed genes revealed divergence from the Alpha variant lineage Q.3 clinical sequence over time, including numerous mutations in the surface glycoprotein RBD and NTD. We discuss the possibility that a chronic SARS-CoV-2 infection accumulated adaptive mutations that promoted long-term infection. This study reveals that small wastewater treatment plants can enhance resolution of rare events and facilitate reconstruction of viral genomes due to the relative lack of contaminating sequences.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Michael J Conway", - "author_inst": "Central Michigan University College of Medicine" - }, - { - "author_name": "Hannah Yang", - "author_inst": "Central Michigan University College of Medicine" - }, - { - "author_name": "Lauren A Revord", - "author_inst": "Central Michigan University College of Medicine" - }, - { - "author_name": "Avery S Ward", - "author_inst": "Central Michigan University College of Medicine" - }, - { - "author_name": "Jackson D Abel", - "author_inst": "Central Michigan University College of Medicine" - }, - { - "author_name": "Maggie R Williams", - "author_inst": "Central Michigan University School of Engineering & Technology" - }, - { - "author_name": "Rebecca L Uzarski", - "author_inst": "Central Michigan University Department of Biology and Herbert H. and Grace A. Dow College of Health" - }, - { - "author_name": "Elizabeth W Alm", - "author_inst": "Central Michigan University Department of Biology" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.07.25.550568", "rel_title": "Experimental infection of elk (Cervus canadensis) and mule deer (Odocoileus hemionus) with SARS-CoV-2", @@ -40653,6 +41186,49 @@ "type": "new results", "category": "pathology" }, + { + "rel_doi": "10.1101/2023.07.20.23292950", + "rel_title": "The Political Division toward COVID-19, Vaccines, Contact Tracing Apps, and A Future Pandemic Scenario in the United States: A Survey Result from A National Representative Sample", + "rel_date": "2023-07-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.20.23292950", + "rel_abs": "ObjectivesTo investigate the attitudes and behaviors of Americans concerning the COVID-19 pandemic, COVID-19 vaccines, COVID-19 tracing apps, and the actions they believe the government should take during a public health crisis, we designed and conducted a survey during the ongoing COVID-19 emergency.\n\nMethodsIn January 2022, we administered an online survey on Prolific Academic to 302 participants in the United States, a nationally demographic representative sample. To explore differences in attitudes and opinions among demographic subgroups, we employed several statistical tests, including Mann Whitney U tests, Kruskal-Wallis tests, and chi-squared tests.\n\nResultsOur survey results suggest that Americans opinions towards the COVID-19 pandemic are severely divided by their political views. There is strong partisan polarization in almost every COVID-19 related question in our survey.\n\nPolicy ImplicationsOur findings suggest that policy makers need to consider partisan polarization and the enormous impact it can have on peoples attitudes and behaviors during public health emergencies such as the COVID-19 pandemic. Public health experts need to consider how to convey scientific knowledge about a pandemic without allowing political views to dominate medical conversation.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Haijing Hao", + "author_inst": "Bentley University" + }, + { + "author_name": "Garrett Smith", + "author_inst": "Brigham Young University-Provo: Brigham Young University" + }, + { + "author_name": "Yunan Chen", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Mainack Mondal", + "author_inst": "Indian Institute of Technology Kharagpur" + }, + { + "author_name": "Po-Shen Loh", + "author_inst": "Carnegie Mellon University" + }, + { + "author_name": "Staci Smith", + "author_inst": "Brigham Young University-Provo: Brigham Young University" + }, + { + "author_name": "Xinru Page", + "author_inst": "Brigham Young University-Provo: Brigham Young University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2023.07.23.23293046", "rel_title": "Reactivation of herpesvirus type-6 and IgA/IgM-mediated responses to activin-A underpin Long COVID, including affective symptoms and chronic fatigue syndrome.", @@ -41563,49 +42139,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.07.19.23292289", - "rel_title": "Can computer simulation support strategic service planning? Modelling a large integrated mental health system on recovery from COVID-19", - "rel_date": "2023-07-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.19.23292289", - "rel_abs": "BackgroundCOVID-19 has had a significant impact on peoples mental health and mental health services. During the first year of the pandemic, existing demand was not fully met while new demand was generated, resulting in large numbers of people requiring support. To support mental health services to recover without being overwhelmed, it was important to know where services will experience increased pressure, and what strategies could be implemented to mitigate this.\n\nMethodsWe implemented a computer simulation model of patient flow through an integrated mental health service in Southwest England covering General Practice (GP), community-based talking therapies (IAPT), acute hospital care, and specialist care settings. The model was calibrated on data from 1 April 2019 to 1 April 2021. Model parameters included patient demand, service-level length of stay, and probabilities of transitioning to other care settings. We used the model to compare do nothing (baseline) scenarios to what if (mitigation) scenarios, including increasing capacity and reducing length of stay, for two future demand trajectories from 1 April 2021 onwards.\n\nResultsThe results from the simulation model suggest that, without mitigation, the impact of COVID-19 will be an increase in pressure on GP and specialist community based services by 50% and 50-100% respectively. Simulating the impact of possible mitigation strategies, results show that increasing capacity in lower-acuity services, such as GP, results in demand being shifted to other parts of the mental health system while decreasing length of stay in higher acuity services is insufficient to mitigate the impact of increased demand.\n\nConclusionIn capturing the interrelation of patient flow related dynamics between various mental health care settings, we demonstrate the value of computer simulation for assessing the impact of interventions on system flow.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Livia LP Pierotti", - "author_inst": "University of Bristol" - }, - { - "author_name": "Jennifer Cooper", - "author_inst": "University of Bristol" - }, - { - "author_name": "Charlotte James", - "author_inst": "University of Bristol" - }, - { - "author_name": "Rachel Denholm", - "author_inst": "University of Bristol" - }, - { - "author_name": "Kenah Cassels", - "author_inst": "Bristol, North Somerset and South Gloucestershire Integrated Care Board, UK National Health Service" - }, - { - "author_name": "Emma Gara", - "author_inst": "Bristol, North Somerset and South Gloucestershire Integrated Care Board, UK National Health Service" - }, - { - "author_name": "Richard Wood", - "author_inst": "Bristol, North Somerset and South Gloucestershire Integrated Care Board, UK National Health Service. HDR UK Southwest." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2023.07.19.23292810", "rel_title": "Several Mathematical Aspects on Daily Number of COVID-19 Infection Cases in Eight Southeast Asian Places", @@ -42143,6 +42676,105 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.07.19.549739", + "rel_title": "Design of SARS-CoV-2 protease inhibitors with improved affinity and reduced sensitivity to mutations", + "rel_date": "2023-07-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.19.549739", + "rel_abs": "Inhibitors of the SARS-CoV-2 main protease (Mpro) such as nirmatrelvir (NTV) and ensitrelvir (ETV) have proven effective in reducing the severity of COVID-19, but the presence of resistance-conferring mutations in sequenced viral genomes raises concerns about future drug resistance. Second-generation oral drugs that retain function on these mutants are thus urgently needed. We hypothesized that the covalent HCV protease inhibitor boceprevir (BPV) could serve as the basis for orally bioavailable drugs that inhibit SARS-CoV-2 Mpro more tightly than existing drugs. Performing structure-guided modifications of BPV, we developed a picomolar-affinity inhibitor, ML2006a4, with antiviral activity, oral pharmacokinetics, and therapeutic efficacy similar or superior to NTV. A crucial feature of ML2006a4 is a novel derivatization of the ketoamide reactive group that improves cell permeability and oral bioavailability. Finally, ML2006a4 is less sensitive to several mutations that cause resistance to NTV or ETV and occur in the natural SARS-CoV-2 population. Thus, anticipatory drug design can preemptively address potential resistance mechanisms.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Michael Westberg", + "author_inst": "Department of Chemistry, Aarhus University; Aarhus, Denmark" + }, + { + "author_name": "Yichi Su", + "author_inst": "Department of Neurobiology, Stanford University; Stanford, CA, USA" + }, + { + "author_name": "Xinzhi Zou", + "author_inst": "Department of Bioengineering, Stanford University; Stanford, CA, USA" + }, + { + "author_name": "Pinghan Huang", + "author_inst": "Department of Microbiology and Immunology, The University of Texas Medical Branch; Galveston, TX, USA" + }, + { + "author_name": "Arjun Rustagi", + "author_inst": "Department of Medicine, Stanford University; Stanford, CA, USA" + }, + { + "author_name": "Jaishree Garhyan", + "author_inst": "Stanford In Vitro Biosafety Level 3 Service Center, Stanford University; Stanford, CA, USA" + }, + { + "author_name": "Puja Bhavesh Patel", + "author_inst": "Stanford In Vitro Biosafety Level 3 Service Center, Stanford University; Stanford, CA, USA" + }, + { + "author_name": "Daniel Fernandez", + "author_inst": "Stanford ChEM-H, Macromolecular Structure Knowledge Center, Stanford University; Stanford, CA, USA" + }, + { + "author_name": "Yan Wu", + "author_inst": "Department of Bioengineering, Stanford University; Stanford, CA, USA" + }, + { + "author_name": "Lin Ning", + "author_inst": "Department of Neurobiology, Stanford University; Stanford, CA, USA" + }, + { + "author_name": "Aimee Beck", + "author_inst": "Department of Medicine, Stanford University; Stanford, CA, USA" + }, + { + "author_name": "Marwah Karim", + "author_inst": "Department of Medicine, Stanford University; Stanford, CA, USA" + }, + { + "author_name": "Chenzhou Hao", + "author_inst": "Department of Neurobiology, Stanford University; Stanford, CA, USA" + }, + { + "author_name": "Panatda Saenkham-Huntsinger", + "author_inst": "Department of Microbiology and Immunology, The University of Texas Medical Branch; Galveston, TX, USA" + }, + { + "author_name": "Vivian Tat", + "author_inst": "Department of Pathology, The University of Texas Medical Branch; Galveston, TX, USA" + }, + { + "author_name": "Aleksandra Drelich", + "author_inst": "Department of Microbiology and Immunology, The University of Texas Medical Branch; Galveston, TX, USA" + }, + { + "author_name": "Bi-Hung Peng", + "author_inst": "Department of Neuroscience, Cell Biology, and Anatomy, The University of Texas Medical Branch; Galveston, TX, USA" + }, + { + "author_name": "Shirit Einav", + "author_inst": "Department of Medicine, Stanford University; Stanford, CA, USA" + }, + { + "author_name": "Chien-Te K. Tseng", + "author_inst": "Department of Microbiology and Immunology, The University of Texas Medical Branch; Galveston, TX, USA" + }, + { + "author_name": "Catherine Blish", + "author_inst": "Department of Medicine, Stanford University; Stanford, CA, USA" + }, + { + "author_name": "Michael Z. Lin", + "author_inst": "Department of Neurobiology, Stanford University; Stanford, CA, USA" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.07.20.549884", "rel_title": "Induction of antiviral gene expression by cyclosporine A, but not inhibition of cyclophilin A or B, contributes to its restriction of human coronavirus 229E infection in a lung epithelial cell line", @@ -43065,65 +43697,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2023.07.17.23292762", - "rel_title": "Safety and immunogenicity of a heterologous booster with an RBD virus-like particle vaccine following two- or three-dose inactivated COVID-19 vaccine", - "rel_date": "2023-07-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.17.23292762", - "rel_abs": "BackgroundReduced protection against COVID-19 due to the waning vaccine-induced immunity over time and emergence of immune-evading SARS-CoV-2 variants of concern (VOCs) indicate the need for vaccine boosters. LYB001 is an innovative recombinant SARS-CoV-2 vaccine which displays a repetitive array of the Spike glycoproteins receptor binding domain (RBD) on a virus-like particle (VLP) vector to boost the immune system, produced using a Covalink plug-and-display protein binding technology.\n\nMethodsThe safety and immunogenicity of LYB001 as a heterologous booster at an interval of 6-12 months was assessed in 119 participants receiving a booster with (1) 30g LYB001 ((I-I-30L) or CoronaVac (I-I-C), (2) escalated dose of 60g LYB001 (I-I-60L) or CoronaVac in a ratio of 2:1 after two-dose primary series of inactivated COVID-19 vaccine in part 1 of this study, or (3) 30g LYB001 (I-I-I-30L) after three-dose primary series of inactivated COVID-19 vaccine in part 2 of this study.\n\nResultsA well-tolerated reactogenicity profile was observed for LYB001 as a heterologous booster, with adverse reactions predominantly being mild in severity and transient. The peak neutralizing antibody response was observed at 28 days after booster, with GMT (95%CI) against prototype SARS-CoV-2 being 1237.8 (747.2, 2050.6), 554.3 (374.6, 820.2), 181.9 (107.6, 307.6) and 1200.2 (831.5, 1732.3) in the I-I-30L, I-I-60L, I-I-C, and I-I-I-30L groups, respectively. LYB001 also elicited a cross-neutralizing antibody response against the BA.4/5 strain, dominant during the study period, with GMT being 201.1 (102.7, 393.7), 63.0 (35.1, 113.1), 29.2 (16.9, 50.3) and 115.3 (63.9, 208.1) at 28 days after booster in the I-I-30L, I-I-60L, I-I-C, and I-I-I-30L groups, respectively. Additionally, RBD-specific IFN-{gamma}, IL-2, IL-4 secreting T cells, as measured by ELISpot assay, dramatically increased (more than 10 times versus baseline) at 14 days after a single LYB001 booster.\n\nConclusionsOur data confirm the favorable safety and immunogenicity profile of the LYB001 vaccine when used as a heterologous booster, and support the continued clinical development of this promising candidate that utilize VLP platform to provide protection against COVID-19.\n\nTrial registrationhttps://www.clinicaltrials.gov (No. NCT05928455, https://www.clinicaltrials.gov/study/NCT05928455)", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Yan Liu", - "author_inst": "Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Xiaolan Yong", - "author_inst": "Chengdu Xinhua Hospital Affiliated to North Sichuan Medical College" - }, - { - "author_name": "Jun Liu", - "author_inst": "Chongqing Red Cross Hospital" - }, - { - "author_name": "Ying Zeng", - "author_inst": "Guangzhou Patronus Biotech Co. Ltd" - }, - { - "author_name": "Jing Nie", - "author_inst": "Chongqing Red Cross Hospital" - }, - { - "author_name": "Xuelian Cui", - "author_inst": "Chongqing Medleader Bio-Pharm Co., Ltd." - }, - { - "author_name": "Tao Wang", - "author_inst": "Chongqing Medleader Bio-Pharm Co., Ltd." - }, - { - "author_name": "Yilin Wang", - "author_inst": "Chongqing Medleader Bio-Pharm Co., Ltd." - }, - { - "author_name": "Yiyong Chen", - "author_inst": "Chongqing Medleader Bio-Pharm Co., Ltd." - }, - { - "author_name": "Wei Kang", - "author_inst": "Guangzhou Patronus Biotech Co. Ltd." - }, - { - "author_name": "Zhonghua Yang", - "author_inst": "Guangzhou Patronus Biotech Co. Ltd." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.07.17.23292426", "rel_title": "Intranasal lavage with hypochlorous acid safely reduces the symptoms in the ambulatory patient with COVID-19.", @@ -43729,6 +44302,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.07.13.23292421", + "rel_title": "Occupational dermatoses in health care personnel using PPE during the COVID pandemic.", + "rel_date": "2023-07-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.13.23292421", + "rel_abs": "BackgroundA sudden surge of occupation-associated dermatoses among the healthcare workers (HCWs) serving COVID-19 patients have been witnessed recently due to increased usage of PPE (PPE) kits and increased frequency of hygiene practices, with a significant impact on their quality of life and compromised efficacy at work. Hence, this study was conducted to measure the prevalence of occupational dermatoses among HCWs serving Covid-19 patients using PPE kits and hygiene practices and their impact on quality of life.\n\nMethodsHCWs of all cadres were screened for occupation-associated dermatoses. Cases with occupational dermatosis were further evaluated regarding using a PPE kit, and DLQI was calculated.\n\nResults19% of HCWs had dermatoses associated with PPE and hygiene practices. Hands were most affected, followed by the face, nasal bridge, and facial skin in contact with goggles. 48% had Mathias score >/= 4. Most cases had reported some impact on their quality of life. A significant association could be established between frequency of hand washing >/= 10 times/day with hand dermatitis (p=0.000).\n\nConclusionThe use of PPE has significantly raised cases of occupational dermatosis among HCWs. Repeated hand washing and hand sanitizer use has increased the incidence of hand dermatitis.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Dinesh Asati", + "author_inst": "All India Institute of Medical Sciences, Bhopal" + }, + { + "author_name": "Kapil Baheti", + "author_inst": "All India Institute of Medical Sciences, Bhopal" + }, + { + "author_name": "Maninder Kaur", + "author_inst": "All India Institute of Medical Sciences, Bhopal" + }, + { + "author_name": "Suman Patra", + "author_inst": "All India Institute of Medical Sciences, Bhopal" + }, + { + "author_name": "Kritika Singhal", + "author_inst": "All India Institute of Medical Sciences Bhopal" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "dermatology" + }, { "rel_doi": "10.1101/2023.07.14.23292649", "rel_title": "Early Biological Markers of Post-Acute Sequelae of SARS-CoV-2 Infection", @@ -44695,85 +45303,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.07.12.548617", - "rel_title": "The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2", - "rel_date": "2023-07-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.12.548617", - "rel_abs": "The emergence of SARS-CoV in 2002 and SARS-CoV-2 in 2019 has led to increased sampling of related sarbecoviruses circulating primarily in horseshoe bats. These viruses undergo frequent recombination and exhibit spatial structuring across Asia. Employing recombination-aware phylogenetic inference on bat sarbecoviruses, we find that the closest-inferred bat virus ancestors of SARS-CoV and SARS-CoV-2 existed just [~]1-3 years prior to their emergence in humans. Phylogeographic analyses examining the movement of related sarbecoviruses demonstrate that they traveled at similar rates to their horseshoe bat hosts and have been circulating for thousands of years in Asia. The closest-inferred bat virus ancestor of SARS-CoV likely circulated in western China, and that of SARS-CoV-2 likely circulated in a region comprising southwest China and northern Laos, both a substantial distance from where they emerged. This distance and recency indicate that the direct ancestors of SARS-CoV and SARS-CoV-2 could not have reached their respective sites of emergence via the bat reservoir alone. Our recombination-aware dating and phylogeographic analyses reveal a more accurate inference of evolutionary history than performing only whole-genome or single gene analyses. These results can guide future sampling efforts and demonstrate that viral genomic fragments extremely closely related to SARS-CoV and SARS-CoV-2 were circulating in horseshoe bats, confirming their importance as the reservoir species for SARS viruses.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Jonathan E Pekar", - "author_inst": "UC San Diego" - }, - { - "author_name": "Spyros Lytras", - "author_inst": "MRC - University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Mahan Ghafari", - "author_inst": "University of Oxford" - }, - { - "author_name": "Andrew F Magee", - "author_inst": "UC Los Angeles" - }, - { - "author_name": "Edyth Parker", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Jennifer L Havens", - "author_inst": "UC San Diego" - }, - { - "author_name": "Aris Katzourakis", - "author_inst": "University of Oxford Department of Zoology" - }, - { - "author_name": "Tetyana I Vasylyeva", - "author_inst": "UC San Diego" - }, - { - "author_name": "Marc A. Suchard", - "author_inst": "David Geffen School of Medicine at UCLA" - }, - { - "author_name": "Alice C Hughes", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Joseph Hughes", - "author_inst": "MRC-University of Glasgow" - }, - { - "author_name": "David L Robertson", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Simon Dellicour", - "author_inst": "Universit\u00e9 Libre de Bruxelles, KU Leuven" - }, - { - "author_name": "Michael Worobey", - "author_inst": "University of Arizona" - }, - { - "author_name": "Joel O Wertheim", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Philippe Lemey", - "author_inst": "KU Leuven" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2023.07.12.548725", "rel_title": "Endocytosis Inhibitors Block SARS-CoV-2 Pseudoparticle Infection of Mink Lung Epithelium", @@ -45311,6 +45840,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.07.08.23292128", + "rel_title": "Examination of Influenza A Infection Rate, Its Determinants, and Seasonal Influenza Vaccine Effectiveness in the Post-COVID-19 Pandemic Era", + "rel_date": "2023-07-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.08.23292128", + "rel_abs": "BackgroundIn the context of the COVID-19 pandemic, a pronounced wave of Influenza A occurred in the 2022/23 winter season under generally relaxed post-pandemic non-pharmaceutical preventive measures.\n\nAimThis study aimed to investigate the Influenza A infection rate, factors influencing its occurrence and seasonal Influenza vaccine effectiveness on seroconversion in the post-COVID-19 pandemic era.\n\nMethodsThe seroconversion of Anti-Influenza-A-Nucleoprotein/Matrix IgG was investigated in 402 healthcare workers (HCWs) during the winter season of 2022/2023 (23 May 2022 to 11 May 2023). The participants provided a serum sample and completed a study questionnaire both before and after the seasonal Influenza A wave (24 October 2022 to 8 January 2023). The levels of a vaccine-independent Anti-Influenza-A-Nucleoprotein/Matrix IgG were measured using the SERION ELISA classic Influenza A IgG assay, with a 2-fold increase as indicative of seroconversion after asymptomatic or symptomatic influenza infection.\n\nResultsAmong the participants, 20.6% (95% CI 17.0-24.9%; 83/402) showed seroconversion. The multivariate logistic regression analysis revealed that the age category of [≥] 45 years (p=0.03) and regular patient contact (p=0.02) significantly influenced seroconversion. However, the factors male gender, BMI, smoking, household size, seasonal Influenza vaccination, and SARS-CoV-2 infection during the Influenza A season were not significantly associated with seroconversion. The effectiveness of the 2022/23 seasonal Influenza vaccine on seroconversion induced by Influenza infection was 22.6% (95% CI -17.1-50.6%).\n\nConclusionDuring the initial Influenza A season following the COVID-19 pandemic, approximately 20% of HCWs contracted an Influenza A infection. This highlights a potential risk and a significant asymptomatic or symptomatic infection rate posing a theoretical risk for intrahospital transmission chains and nosocomial infections.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Isabell Wagenh\u00e4user", + "author_inst": "Infection Control and Antimicrobial Stewardship Unit, University Hospital W\u00fcrzburg, W\u00fcrzburg, Germany; Department of Internal Medicine I, University Hospital W\u00fc" + }, + { + "author_name": "Juliane Mees", + "author_inst": "Infection Control and Antimicrobial Stewardship Unit, University Hospital W\u00fcrzburg, W\u00fcrzburg, Germany" + }, + { + "author_name": "Julia Reusch", + "author_inst": "Infection Control and Antimicrobial Stewardship Unit, University Hospital W\u00fcrzburg, W\u00fcrzburg, Germany; Department of Internal Medicine I, University Hospital W\u00fc" + }, + { + "author_name": "Thi\u00ean-Tr\u00ed L\u00e2m", + "author_inst": "Institute for Hygiene and Microbiology, University of W\u00fcrzburg, W\u00fcrzburg, Germany" + }, + { + "author_name": "Alexandra Schubert-Unkmeir", + "author_inst": "Institute for Hygiene and Microbiology, University of W\u00fcrzburg, W\u00fcrzburg, Germany" + }, + { + "author_name": "Lukas B Krone", + "author_inst": "Department of Physiology, Anatomy and Genetics, Sir Jules Thorn Sleep and Circadian Neuroscience Institute, University of Oxford, Oxford, UK; Department of Neur" + }, + { + "author_name": "Anna Frey", + "author_inst": "Department of Internal Medicine I, University Hospital W\u00fcrzburg, W\u00fcrzburg, Germany" + }, + { + "author_name": "Oliver Kurzai", + "author_inst": "Institute for Hygiene and Microbiology, University of W\u00fcrzburg, W\u00fcrzburg, Germany; Leibniz Institute for Natural Product Research and Infection Biology - Hans-K" + }, + { + "author_name": "Stefan Frantz", + "author_inst": "Department of Internal Medicine I, University Hospital W\u00fcrzburg, W\u00fcrzburg, Germany" + }, + { + "author_name": "Lars D\u00f6lken", + "author_inst": "Institute for Virology and Immunobiology, University of W\u00fcrzburg, W\u00fcrzburg, Germany" + }, + { + "author_name": "Johannes Liese", + "author_inst": "Department of Paediatrics, University Hospital W\u00fcrzburg, W\u00fcrzburg, Germany" + }, + { + "author_name": "Alexander Gabel", + "author_inst": "Infection Control and Antimicrobial Stewardship Unit, University Hospital W\u00fcrzburg, W\u00fcrzburg, Germany" + }, + { + "author_name": "Nils Petri", + "author_inst": "Department of Internal Medicine I, University Hospital W\u00fcrzburg, W\u00fcrzburg, Germany" + }, + { + "author_name": "Manuel Krone", + "author_inst": "Infection Control and Antimicrobial Stewardship Unit, University Hospital W\u00fcrzburg, W\u00fcrzburg, Germany; Institute for Hygiene and Microbiology, University of W\u00fcr" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.07.11.548309", "rel_title": "Studies on the selectivity of the SARS-CoV-2 papain-like protease reveal the importance of the P2' proline of the viral polyprotein", @@ -45707,7 +46307,7 @@ "rel_date": "2023-07-09", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.08.23292389", - "rel_abs": "Antimicrobial peptides (AMPs) are a complex network of 10-100 amino acid sequence molecules, widely distributed in Nature. Even though more than 300 AMPs have been described in mammals, cathelicidins and defensins remain the most investigated to date.\n\nSome publications examined the role of AMPs in COVID-19, but the findings are preliminary and in vivo studies are still lacking. Here, we report the plasma levels of five AMPs (LL-37, -defensin 1, -defensin 3, {beta}-defensin 1 and {beta}-defensin 3) and five cytokines (tumor necrosis factor-, interleukin-1{beta}, interleukin-6, interleukin-10, interferon-{gamma} and monocyte chemoattractant protein-1), in 15 healthy volunteers, 36 COVID-19 patients without Acute Kidney Injury (AKI) and 17 COVID-19 patients with AKI, since AKI is a well-known marker of worse prognosis in Sars-CoV-2 infections.\n\nWe found increased levels of -defensin 1, -defensin 3 and {beta}-defensin 3, but not LL-37 or {beta}-defensin 3, in our COVID-19 population, when compared with the healthy controls, in conjunction with higher levels of interleukin-6, interleukin-10, interferon-{gamma} and monocyte chemoattractant protein-1, putting in evidence that these AMPs and cytokines may have an important role in the systemic inflammatory response and tissue damage that characterizes severe COVID-19.\n\nGraphic Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC=\"FIGDIR/small/23292389v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (45K):\norg.highwire.dtl.DTLVardef@1134bborg.highwire.dtl.DTLVardef@19cfaaborg.highwire.dtl.DTLVardef@10cf474org.highwire.dtl.DTLVardef@1851644_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_abs": "Antimicrobial peptides (AMPs) are a complex network of 10-100 amino acid sequence molecules, widely distributed in Nature. Even though more than 300 AMPs have been described in mammals, cathelicidins and defensins remain the most investigated to date.\n\nSome publications examined the role of AMPs in COVID-19, but the findings are preliminary and in vivo studies are still lacking. Here, we report the plasma levels of five AMPs (LL-37, -defensin 1, -defensin 3, {beta}-defensin 1 and {beta}-defensin 3) and five cytokines (tumor necrosis factor-, interleukin-1{beta}, interleukin-6, interleukin-10, interferon-{gamma} and monocyte chemoattractant protein-1), in 15 healthy volunteers, 36 COVID-19 patients without Acute Kidney Injury (AKI) and 17 COVID-19 patients with AKI, since AKI is a well-known marker of worse prognosis in Sars-CoV-2 infections.\n\nWe found increased levels of -defensin 1, -defensin 3 and {beta}-defensin 3, but not LL-37 or {beta}-defensin 3, in our COVID-19 population, when compared with the healthy controls, in conjunction with higher levels of interleukin-6, interleukin-10, interferon-{gamma} and monocyte chemoattractant protein-1, putting in evidence that these AMPs and cytokines may have an important role in the systemic inflammatory response and tissue damage that characterizes severe COVID-19.\n\nGraphic Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC=\"FIGDIR/small/23292389v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (45K):\norg.highwire.dtl.DTLVardef@56cb9dorg.highwire.dtl.DTLVardef@51bffaorg.highwire.dtl.DTLVardef@112e155org.highwire.dtl.DTLVardef@87b5da_HPS_FORMAT_FIGEXP M_FIG C_FIG", "rel_num_authors": 5, "rel_authors": [ { @@ -46445,41 +47045,6 @@ "type": "confirmatory results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2023.07.06.23292295", - "rel_title": "Spatio-temporal surveillance and early detection of SARS-CoV-2 variants of concern", - "rel_date": "2023-07-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.06.23292295", - "rel_abs": "The SARS-CoV-2 pandemic has been characterized by the repeated emergence of genetically distinct virus variants of increased transmissibility and immune evasion compared to pre-existing lineages. In many countries, their containment required the intervention of public health authorities and the imposition of control measures. While the primary role of testing is to identify infection, target treatment, and limit spread (through isolation and contact tracing), a secondary benefit is in terms of surveillance and the early detection of new variants. Here we study the spatial invasion and early spread of the Alpha, Delta, and Omicron (BA.1 and BA.2) variants in England from September 2020 to February 2022 using the random neighbourhood covering (RaNCover) method. This is a statistical technique for the detection of aberrations in spatial point processes, which we tailored here to community PCR (polymerase-chain-reaction) test data where the TaqPath kit provides a proxy measure of the switch between variants. Retrospectively, RaNCover detected the earliest signals associated with the four novel variants that led to large infection waves in England. With suitable data our method therefore has the potential to rapidly detect outbreaks of future SARS-CoV-2 variants, thus helping to inform targeted public health interventions.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Massimo Cavallaro", - "author_inst": "University of Warwick" - }, - { - "author_name": "Louise Dyson", - "author_inst": "University of Warwick" - }, - { - "author_name": "Michael J Tildesley", - "author_inst": "University of Warwick" - }, - { - "author_name": "Daniel Todkill", - "author_inst": "University of Warwick" - }, - { - "author_name": "Matt J Keeling", - "author_inst": "University of Warwick" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.07.06.23292296", "rel_title": "Long-term symptom profiles after COVID-19 vs other acute respiratory infections: a population-based observational study (COVIDENCE UK)", @@ -47097,6 +47662,49 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.07.03.547244", + "rel_title": "Lack of detection of SARS-CoV-2 in Wildlife from Kerala, India in 2020-21", + "rel_date": "2023-07-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.03.547244", + "rel_abs": "2.Spill over of SARs-CoV-2 into a variety of wild and domestic animals has been an ongoing feature of the human pandemic. The establishment of a new reservoir in white tailed deer in North America and increasing divergence of the viruses circulating in them from those circulating in the human population has highlighted the ongoing risk this poses for global health. Some parts of the world have seen more intensive monitoring of wildlife species for SARS-CoV-2 and related coronaviruses but there are still very large gaps in geographical and species-specific information. This paper reports negative results for SARS-CoV-2 PCR based testing using a pan coronavirus end point RDRP PCR and a Sarbecovirus specific E gene qPCR on lung and or gut tissue from wildlife from the Indian State of Kerala. These animals included: 121 Rhinolophus rouxii (Rufous Horsehoe Bat), 6 Rhinolophus bedommei (Lesser Woolly Horseshoe Bat), 15 Rossettus leschenaultii (Fulvous Fruit Bat), 47 Macaca radiata (Bonnet macaques), 35 Paradoxurus hermaphroditus (Common Palm Civet), 5 Viverricula indica (Small Indian Civet), 4 Herpestes edwardsii (Common Mongoose), 10 Panthera tigris (Bengal Tiger), 8 Panthera pardus fusca (Indian Leopard), 4 Prionailurus bengalensis (Leopard cats), 2 Felis chaus (Jungle cats), 2 Cuon alpinus (Wild dogs) and 1 Melursus ursinus (sloth bear).", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Arun Zachariah", + "author_inst": "Kerala Forests and Wildlife Department, Kerala, India" + }, + { + "author_name": "Sajesh P Krishnankutty", + "author_inst": "GeneSpec Pvt Ltd Kakkanad, Cochin, Kerala, India" + }, + { + "author_name": "Jishnu Manazhi", + "author_inst": "Kerala Forests and Wildlife Department, Kerala, India" + }, + { + "author_name": "Vishnu Omanakuttan", + "author_inst": "Kerala Forests and Wildlife Department, Kerala, India" + }, + { + "author_name": "Sam Santosh", + "author_inst": "SciGenom Research Foundation ,Kerala ,India" + }, + { + "author_name": "Adam Mark Blanchard", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Rachael E Tarlinton", + "author_inst": "University of Nottingham" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.07.02.547368", "rel_title": "Alternative cell entry mechanisms for SARS-CoV-2 and multiple animal viruses", @@ -48579,53 +49187,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.06.29.547094", - "rel_title": "Identification of side effects of COVID-19 drug candidates on embryogenesis using an integrated zebrafish screening platform", - "rel_date": "2023-06-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.29.547094", - "rel_abs": "Drug repurposing is an important strategy in COVID-19 treatment, but many clinically approved compounds have not been extensively studied in the context of embryogenesis, thus limiting their administration during pregnancy. Here we used the zebrafish embryo model organism to test the effects of 162 marketed drugs on cardiovascular development. Among the compounds used in the clinic for COVD-19 treatment, we found that Remdesivir led to reduced body size and heart functionality at clinically relevant doses. Ritonavir and Baricitinib showed reduced heart functionality and Molnupiravir and Baricitinib showed effects on embryo activity. Sabizabulin was highly toxic at concentrations only 5 times higher than Cmax and led to a mean mortality of 20% at Cmax. Furthermore, we tested if zebrafish could be used as a model to study inflammatory response in response to spike protein treatment and found that Remdesivir, Ritonavir, Molnupiravir, Baricitinib as well as Sabizabulin counteracted the inflammatory response related gene expression upon SARS-CoV-2 spike protein treatment. Our results show that the zebrafish allows to study immune-modulating properties of COVID-19 compounds and highlights the need to rule out secondary defects of compound treatment on embryogenesis. All results are available on a user friendly web-interface https://share.streamlit.io/alernst/covasc_dataapp/main/CoVasc_DataApp.py that provides a comprehensive overview of all observed phenotypic effects and allows personalized search on specific compounds or group of compounds. Furthermore, the presented platform can be expanded for rapid detection of developmental side effects of new compounds for treatment of COVID-19 and further viral infectious diseases.\n\nSummary statementA zebrafish screening platform assesses side effects on cardiovascular development and behavior of FDA approved drugs used in clinical practice to treat COVID-19 and their immune modulatory effect upon spike protein treatment.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Alexander Ernst", - "author_inst": "University of Bern" - }, - { - "author_name": "Indre Piragyte", - "author_inst": "University of Bern" - }, - { - "author_name": "Ayisha Marwa MP", - "author_inst": "University of Bern" - }, - { - "author_name": "Ngoc Dung Le", - "author_inst": "University of Bern" - }, - { - "author_name": "Denis Grandgirard", - "author_inst": "University of Bern" - }, - { - "author_name": "Stephen Leib", - "author_inst": "University of Bern" - }, - { - "author_name": "Andrew Oates", - "author_inst": "EPFL" - }, - { - "author_name": "Nadia Mercader", - "author_inst": "University of Bern" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "developmental biology" - }, { "rel_doi": "10.1101/2023.06.29.546792", "rel_title": "Human Immune Cell Epigenomic Signatures in Response to Infectious Diseases and Chemical Exposures", @@ -49471,6 +50032,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.06.28.23291997", + "rel_title": "The role of COVID-19 vaccines in preventing post COVID-19 thromboembolic and cardiovascular complications: a multinational cohort study", + "rel_date": "2023-06-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.28.23291997", + "rel_abs": "ImportanceThe overall effects of vaccination on the risk of cardiac, and venous and arterial thromboembolic complications following COVID-19 remain unclear.\n\nObjectiveWe studied the association between COVID-19 vaccination and the risk of acute and subacute COVID-19 cardiac and thromboembolic complications.\n\nDesignMultinational staggered cohort study, based on national vaccination campaign rollouts.\n\nSettingNetwork study using electronic health records from primary care records from the UK, primary care data linked to hospital data from Spain, and national insurance claims from Estonia.\n\nParticipantsAll adults with a prior medical history of [≥]180 days, with no history of COVID-19 or previous COVID-19 vaccination at the beginning of vaccine rollout were eligible.\n\nExposureVaccination status was used as a time-varying exposure. Vaccinated individuals were classified by vaccine brand according to the first dose received.\n\nMain OutcomesPost COVID-19 complications including myocarditis, pericarditis, arrhythmia, heart failure (HF), venous (VTE) and arterial thromboembolism (ATE) up to 1 year after SARS-CoV-2 infection.\n\nMeasuresPropensity Score overlap weighting and empirical calibration based on negative control outcomes were used to minimise bias due to observed and unobserved confounding, respectively. Fine-Gray models were fitted to estimate sub-distribution Hazard Ratios (sHR) for each outcome according to vaccination status. Random effect meta-analyses were conducted across staggered cohorts and databases.\n\nResultsOverall, 10.17 million vaccinated and 10.39 million unvaccinated people were included. Vaccination was consistently associated with reduced risks of acute (30-day) and subacute post COVID-19 VTE and HF: e.g., meta-analytic sHR 0.34 (95%CI, 0.27-0.44) and 0.59 (0.50-0.70) respectively for 0-30 days, sHR 0.58 (0.48 - 0.69) and 0.71 (0.59 - 0.85) respectively for 90-180 days post COVID-19. Additionally, reduced risks of ATE, myocarditis/pericarditis and arrhythmia were seen, but mostly in the acute phase (0-30 days post COVID-19).\n\nConclusionsCOVID-19 vaccination reduced the risk of post COVID-19 complications, including cardiac and thromboembolic outcomes. These effects were more pronounced for acute (1-month) post COVID-19 outcomes, consistent with known reductions in disease severity following breakthrough vs unvaccinated SARS-CoV-2 infection.\n\nRelevanceThese findings highlight the importance of COVID-19 vaccination to prevent cardiovascular outcomes after COVID-19, beyond respiratory disease.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSWhat is the impact of COVID-19 vaccination to prevent cardiac complications and thromboembolic events following a SARS-CoV-2 infection?\n\nFindingsResults from this multinational cohort study showed that COVID-19 vaccination reduced risk for acute and subacute COVID-19 heart failure, as well as venous and arterial thromboembolic events following SARS-CoV-2 infection.\n\nMeaningThese findings highlight yet another benefit of vaccination against COVID-19, and support the recommendations for COVID-19 vaccination even in people at high cardiovascular risk.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Nuria Mercade-Besora", + "author_inst": "Pharmaco- and Device Epidemiology Group, Health Data Sciences, Botnar Research Centre, NDORMS, University of Oxford, United Kingdom" + }, + { + "author_name": "Xintong Li", + "author_inst": "Pharmaco- and Device Epidemiology Group, Health Data Sciences, Botnar Research Centre, NDORMS, University of Oxford, United Kingdom" + }, + { + "author_name": "Raivo Kolde", + "author_inst": "Institute of Computer Science, University of Tartu, Tartu, Estonia" + }, + { + "author_name": "Nhung TH Trinh", + "author_inst": "Pharmacoepidemiology and Drug Safety Research Group, Department of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway" + }, + { + "author_name": "Maria T Sanchez-Santos", + "author_inst": "Pharmaco- and Device Epidemiology Group, Health Data Sciences, Botnar Research Centre, NDORMS, University of Oxford, United Kingdom" + }, + { + "author_name": "Wai Yi Man", + "author_inst": "Pharmaco- and Device Epidemiology Group, Health Data Sciences, Botnar Research Centre, NDORMS, University of Oxford, United Kingdom" + }, + { + "author_name": "Elena Roel", + "author_inst": "Fundacio Institut Universitari per a la recerca a l'Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain" + }, + { + "author_name": "Carlen Reyes", + "author_inst": "Fundacio Institut Universitari per a la recerca a l'Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain" + }, + { + "author_name": "Antonella Delmestri", + "author_inst": "Pharmaco- and Device Epidemiology Group, Health Data Sciences, Botnar Research Centre, NDORMS, University of Oxford, United Kingdom" + }, + { + "author_name": "Hedvig ME Nordeng", + "author_inst": "Pharmacoepidemiology and Drug Safety Research Group, Department of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway" + }, + { + "author_name": "Anneli Uuskula", + "author_inst": "Department of Family Medicine and Public Health, University of Tartu, Tartu, Estonia" + }, + { + "author_name": "Talita Duarte-Salles", + "author_inst": "Fundacio Institut Universitari per a la recerca a l'Atencio Primaria de Salut Jordi Gol i Gurina" + }, + { + "author_name": "Clara Prats", + "author_inst": "Department of Physics, Universitat Politecnica de Catalunya, Barcelona, Spain" + }, + { + "author_name": "Daniel Prieto-Alhambra", + "author_inst": "Pharmaco- and Device Epidemiology Group, Health Data Sciences, Botnar Research Centre, NDORMS, University of Oxford, United Kingdom" + }, + { + "author_name": "Annika M Jodicke", + "author_inst": "Pharmaco- and Device Epidemiology Group, Health Data Sciences, Botnar Research Centre, NDORMS, University of Oxford, United Kingdom" + }, + { + "author_name": "Marti Catala", + "author_inst": "Pharmaco- and Device Epidemiology Group, Health Data Sciences, Botnar Research Centre, NDORMS, University of Oxford, United Kingdom" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.06.23.23291828", "rel_title": "Growing inequities by immigration group among older adults: Population-based analysis of access to primary care and return to in-person visits during the COVID-19 pandemic in British Columbia, Canada.", @@ -50657,53 +51297,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2023.06.26.23291868", - "rel_title": "What works and for whom in treating depression in older adults in deprived communities in Brazil: Findings from a causal mediation analyses of the PROACTIVE trial that overlapped with the COVID-19 pandemic", - "rel_date": "2023-06-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.26.23291868", - "rel_abs": "BackgroundThe PROACTIVE trial was a task-shared, collaborative care, psychosocial intervention that was highly effective at improving recovery from depression in older adults in Brazil that overlapped with the COVID-19 pandemic. Here we investigate mediators of the interventions effectiveness.\n\nMethodsCausal mediation analysis using interventional indirect effects, decomposed the total effect of PROACTIVE on recovery from depression (PHQ-9<10), into multiple indirect effects including: dose of intervention (number of sessions and number of activities completed); social support measured through Luben Social Network Scale; perceived loneliness through the three-item UCLA questionnaire; conditions associated with frailty; and extra sessions offered to participants who did not respond to the intervention.\n\nFindingsOf the interventions total effect (difference in probability of recovery from depression between the intervention and control arms 0{middle dot}211 [bias-corrected 95% CI: 0{middle dot}139, 0{middle dot}274]): 14% was mediated through improved conditions associated with frailty 0{middle dot}030 [0{middle dot}003, 0{middle dot}065]); 6% through reduced loneliness (0{middle dot}013 [0{middle dot}001, 0{middle dot}028]); and 20% through attending extra sessions for participants who did not respond to the intervention (0{middle dot}042 [0{middle dot}007, 0{middle dot}105]).\n\nInterpretationOur findings emphasise the importance of a home-based intervention to improve depression outcomes where participants are encouraged to self-select activities to mitigate against loneliness and are referred to primary care to manage health issues relating to frailty. Importantly, our findings suggest that offering extra sessions to participants who did not respond to the intervention shows promise in ensuring a sustained recovery from depression.\n\nFundingSao Paulo Research Foundation and Joint Global Health Trials UK.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Nadine Seward", - "author_inst": "King's College London" - }, - { - "author_name": "Carina Akemi Nakamura", - "author_inst": "Universidade de Sao Paulo Faculdade de Medicina" - }, - { - "author_name": "Tim J Peters", - "author_inst": "University of Bristol Medical School" - }, - { - "author_name": "Wen Wei Low", - "author_inst": "Emory University" - }, - { - "author_name": "Dean McMillan", - "author_inst": "University of York Department of Health Sciences" - }, - { - "author_name": "Simon Gilbody", - "author_inst": "Mental Health and Addictions Research Group" - }, - { - "author_name": "Ricardo Araya", - "author_inst": "King's College London Institute of Psychiatry Psychology & Neuroscience" - }, - { - "author_name": "Marcia Scazufca", - "author_inst": "University of Sao Paulo" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.06.28.23291986", "rel_title": "The Role of VSL#3 in the Treatment of Fatigue and Other Symptoms in Long Covid-19 Syndrome: a Randomized, Double-blind, Placebo-controlled Pilot Study (DELong#3)", @@ -51301,6 +51894,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.06.26.23291921", + "rel_title": "Infoveillance study on the dynamic associations between CDC social media contents and epidemic measures during COVID-19", + "rel_date": "2023-06-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.26.23291921", + "rel_abs": "BackgroundHealth agencies have been widely adopting social media to disseminate important information, educate the public on emerging health issues, and understand public opinions. The Centers for Disease Control and Prevention (CDC) has been one of the leading agencies that utilizes social media platforms during the COVID-19 pandemic to communicate with the public and mitigate the disease in the United States. It is crucial to understand the relationships between CDCs social media communication and the actual epidemic metrics to improve public health agencies communication strategies during health emergencies.\n\nObjectiveThe aim of this study was to identify key topics in tweets posted by CDC during the pandemic, to investigate the temporal dynamics between these key topics and the actual COVID-19 epidemic measures, and to make recommendations for CDCs digital health communication strategies for future health emergencies.\n\nMethodsTwo types of data were collected: 1) a total of 17,524 COVID-19-related English tweets posted by the CDC between December 7, 2019 and January 15, 2022; 2) COVID-19 epidemic measures in the U.S. from the public GitHub repository of Johns Hopkins University from January 2020 to July 2022. Latent Dirichlet allocation (LDA) topic modeling was applied to identify key topics from all COVID-19-related tweets posted by CDC, and the final topics were determined by domain experts. Various multivariate time series analysis techniques were applied between each of the identified key topics and actual COVID-19 epidemic measures to quantify the dynamic associations between these two types of time series data.\n\nResultsFour major topics from CDCs COVID-19 tweets were identified: 1) information on prevention of health outcomes of COVID-19; 2) pediatric intervention and family safety; 3) updates of the epidemic situation of COVID-19; 4) research and community engagement to curb COVID-19. Multivariate analyses showed that there were significant variabilities of progression between CDCs topics and the actual COVID-19 epidemic measures. Some CDCs topics showed substantial associations with the COVID-19 measures over different time spans throughout the pandemic, expressing similar temporal dynamics between these two types of time series data.\n\nConclusionsOur study is the first to comprehensively investigate the dynamic associations between topics discussed by CDC on Twitter and the COVID-19 epidemic measures in the U.S. We identified four major topic themes via topic modeling and explored how each of these topics was associated with each major epidemic measure by performing various multivariate time series analyses. We recommend that it is critical for public health agencies, such as CDC, to disseminate and update timely and accurate information to the public and align major topics with the key epidemic measures over time. We suggest that social media can help public health agencies to inform the public on health emergencies and to mitigate them effectively.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Shuhua Yin", + "author_inst": "University of North Carolina at Charlotte" + }, + { + "author_name": "Shi Chen", + "author_inst": "University of North Carolina at Charlotte" + }, + { + "author_name": "Yaorong Ge", + "author_inst": "University of North Carolina at Charlotte" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2023.06.26.546514", "rel_title": "A pseudovirus-based method to dynamically mimic SARS-CoV-2-associated cell-to-cell fusion and transmission", @@ -52071,57 +52691,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.06.15.23291010", - "rel_title": "Effectiveness of a COVID-19 contact tracing app in a simulation model with indirect and informal contact tracing", - "rel_date": "2023-06-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.15.23291010", - "rel_abs": "During the COVID-19 pandemic, contact tracing was used to identify individuals who had been in contact with a confirmed case so that these contacted individuals could be tested and quarantined to prevent further spread of the SARS-CoV-2 virus. Many countries developed mobile apps to find these contacted individuals faster. We evaluate the epidemiological effectiveness of the Dutch app CoronaMelder, where we measure effectiveness as the reduction of the reproduction number R. To this end, we use a simulation model of SARS-CoV-2 spread and contact tracing, informed by data collected during the study period (December 2020 - March 2021) in the Netherlands. We show that the tracing app caused a clear but small reduction of the reproduction number, and the magnitude of the effect was found to be robust in sensitivity analyses. The app could have been more effective if more people had used it, and if time intervals between symptom onset and reporting of contacts would have been shorter. The model used is novel as it accounts for the clustered nature of social networks and as it accounts for cases informally alerting their contacts directly after symptom onset, without involvement of health authorities or a tracing app.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Ka Yin Leung", - "author_inst": "National Insitute of Public Health and the Environment" - }, - { - "author_name": "Esther Metting", - "author_inst": "University Medical Center Groningen" - }, - { - "author_name": "Wolfgang Ebbers", - "author_inst": "Erasmus University Rotterdam" - }, - { - "author_name": "Irene Veldhuijzen", - "author_inst": "National Institute of Public Health and the Environment" - }, - { - "author_name": "Stijn P Andeweg", - "author_inst": "National Institute for Public Health and the Environment" - }, - { - "author_name": "Guus Luijben", - "author_inst": "National Institute for Public Health and the Environment" - }, - { - "author_name": "Marijn de Bruin", - "author_inst": "National Institute for Public Health and the Environment, Radboud University Medical Centre" - }, - { - "author_name": "Jacco Wallinga", - "author_inst": "National Institute for Public Health and the Environment, Leiden University Medical Centre" - }, - { - "author_name": "Don Klinkenberg", - "author_inst": "National Institute for Public Health and the Environment" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.06.16.23291450", "rel_title": "High rates of SARS-CoV-2 infection in pregnant Ugandan women and association with stunting in infancy", @@ -52408,8 +52977,8 @@ "rel_date": "2023-06-20", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.16.23291515", - "rel_abs": "BACKGROUNDThe current understanding of the long-term effectiveness of the BNT162b2 vaccine across diverse U.S. pediatric populations is limited. Using data from the PEDSnet collaboration, we assessed the effectiveness of BNT162b2 against various strains of the SARS-CoV-2 virus.\n\nMETHODSWe emulated three target trials to assess the real-world effectiveness of BNT162b2: adolescents aged 12 to 20 years during the Delta variant period (Target trial 1), children aged 5 to 11 years (Target trial 2) and adolescents aged 12 to 20 years during the Omicron variant period (Target trial 3). The outcomes included documented infection, COVID-19 illness severity, admission to an intensive care unit (ICU), and two cardiac-related outcomes, myocarditis and pericarditis. We implemented a novel trial emulation pipeline accounting for possible misclassification bias in vaccine documentation in EHRs.\n\nRESULTSDuring the Delta period, the BNT162b2 vaccine demonstrated an overall effectiveness 98.4% against documented infection among adolescents, with no significant waning after receipt of the first dose. During the Omicron period, the overall effectiveness in preventing documented infection among children was estimated to be 74.3%. Higher levels of effectiveness of 75.5% and 84.9% were observed against moderate or severe COVID-19 and ICU admission with COVID-19, respectively. In the adolescent population, the overall effectiveness in preventing documented Omicron infection was 85.5%, with effectiveness of 84.8% against moderate or severe COVID-19, and 91.5% against ICU admission with COVID-19. The effectiveness of the BNT162b2 vaccine against the Omicron variant declined after 4 months following the first dose and then stabilized. Across all three cohorts, the risk of cardiac outcomes was approximately 65% to 85% lower in the vaccinated group than that of the unvaccinated group.\n\nCONCLUSIONSOur study suggests that BNT162b2 is effective for various COVID-19-related outcomes in children and adolescents during Delta and Omicron periods, with lower cardiac risk. Waning effectiveness indicates potential need for future revaccination.", - "rel_num_authors": 24, + "rel_abs": "Background: The efficacy of the BNT162b2 vaccine in pediatrics was assessed by randomized trials before the Omicron variant's emergence. The long-term durability of vaccine protection in this population during the Omicron period remains limited. Objective: To assess the effectiveness of BNT162b2 in preventing infection and severe diseases with various strains of the SARS-CoV-2 virus in previously uninfected children and adolescents. Design: Comparative effectiveness research accounting for underreported vaccination in three study cohorts: adolescents (12 to 20 years) during the Delta phase, children (5 to 11 years) and adolescents (12 to 20 years) during the Omicron phase. Setting: A national collaboration of pediatric health systems (PEDSnet). Participants: 77,392 adolescents (45,007 vaccinated) in the Delta phase, 111,539 children (50,398 vaccinated) and 56,080 adolescents (21,180 vaccinated) in the Omicron period. Exposures: First dose of the BNT162b2 vaccine vs. no receipt of COVID-19 vaccine. Measurements: Outcomes of interest include documented infection, COVID-19 illness severity, admission to an intensive care unit (ICU), and cardiac complications. The effectiveness was reported as (1-relative risk)*100% with confounders balanced via propensity score stratification. Results: During the Delta period, the estimated effectiveness of BNT162b2 vaccine was 98.4% (95% CI, 98.1 to 98.7) against documented infection among adolescents, with no significant waning after receipt of the first dose. An analysis of cardiac complications did not find an increased risk after vaccination. During the Omicron period, the effectiveness against documented infection among children was estimated to be 74.3% (95% CI, 72.2 to 76.2). Higher levels of effectiveness were observed against moderate or severe COVID-19 (75.5%, 95% CI, 69.0 to 81.0) and ICU admission with COVID-19 (84.9%, 95% CI, 64.8 to 93.5). Among adolescents, the effectiveness against documented Omicron infection was 85.5% (95% CI, 83.8 to 87.1), with 84.8% (95% CI, 77.3 to 89.9) against moderate or severe COVID-19, and 91.5% (95% CI, 69.5 to 97.6)) against ICU admission with COVID-19. The effectiveness of the BNT162b2 vaccine against the Omicron variant declined after 4 months following the first dose and then stabilized. The analysis revealed a lower risk of cardiac complications in the vaccinated group during the Omicron variant period. Limitations: Observational study design and potentially undocumented infection. Conclusions: Our study suggests that BNT162b2 was effective for various COVID-19-related outcomes in children and adolescents during the Delta and Omicron periods, and there is some evidence of waning effectiveness over time.", + "rel_num_authors": 28, "rel_authors": [ { "author_name": "Qiong Wu", @@ -52428,17 +52997,33 @@ "author_inst": "University of Pennsylvania" }, { - "author_name": "Jie Xu", - "author_inst": "University of Florida" + "author_name": "Jiajie Chen", + "author_inst": "University of Pennsylvania" }, { - "author_name": "Yishan Shen", + "author_name": "Yuqing Lei", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Yiwen Lu", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Yudong Wang", "author_inst": "University of Pennsylvania" }, { "author_name": "Lu Li", "author_inst": "University of Pennsylvania" }, + { + "author_name": "Yishan Shen", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Jie Xu", + "author_inst": "University of Florida" + }, { "author_name": "Charles Bailey", "author_inst": "The Children's Hospital of Philadelphia" @@ -52558,7 +53143,7 @@ "rel_date": "2023-06-20", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.15.23291472", - "rel_abs": "BackgroundThere are many COVID-19 vaccines currently available, however, Low- and middle-income countries (LMIC) still have large proportions of their populations unvaccinated. Decision-makers need to take decisions as of how best to allocate available vaccine (e.g. boosters or primary series vaccination, which age groups to target) but LMIC often lack the resources to undergo quantitative analyses of vaccine allocation, resulting and ad-hoc policies. We developed Covid19Vaxplorer (https://covid19vaxplorer.fredhutch.org/), a free, user-friendly online tool that simulates region-specific COVID-19 epidemics in conjunction with vaccination.\n\nMethodsWe developed an age-structured mathematical model of SARS-CoV-2 transmission and COVID-19 vaccination. The model considers vaccination with up to three different vaccine products, primary series and boosters. We simulate partial immunity derived from waning of natural infection and vaccination. The model is embedded in an an online tool that allows users in 183 regions in the world to compare several vaccination strategies simultaneously, adjusting parameters to their local epidemics, infrastructure and logistics, and reports cumulative number of deaths and epidemic curves.\n\nResultsWe provide two usage examples of Covid19Vaxplorer for vaccine allocation in Haiti and Afghanistan, which had as of Spring 2023 2% and 33% of their populations vaccinated, and show that in these examples, giving primary series vaccinations prevents more deaths than boosters. Covid19Vaxplorer is an online, free, user-friendly tool that facilitates evidence-based decision making for vaccine distribution.", + "rel_abs": "Background: There are many COVID-19 vaccines currently available, however, Low- and middle-income countries (LMIC) still have large proportions of their populations un- vaccinated. Decision-makers must decide how to effectively allocate available vaccines (e.g. boosters or primary series vaccination, which age groups to target) but LMIC often lack the resources to undergo quantitative analyses of vaccine allocation, resulting in ad- hoc policies. We developed Covid19Vaxplorer (https://covid19vaxplorer.fredhutch.org/), a free, user-friendly online tool that simulates region-specific COVID-19 epidemics in con- junction with vaccination with the purpose of providing public health officials worldwide with a tool for vaccine allocation planning and comparison. Methods: We developed an age-structured mathematical model of SARS-CoV-2 trans- mission and COVID-19 vaccination. The model considers vaccination with up to three different vaccine products, primary series and boosters. We simulated partial immunity de- rived from waning of natural infection and vaccination. The model is embedded in an online tool, Covid19Vaxplorer that was optimized for its ease of use. By prompting users to fill information through several windows to input local parameters (e.g. cumulative and cur- rent prevalence), epidemiological parameters (e.g basic reproduction number, current social distancing interventions), vaccine parameters (e.g. vaccine efficacy, duration of immunity) and vaccine allocation (both by age groups and by vaccination status). Covid19Vaxplorer connects the user to the mathematical model and simulates, in real time, region-specific epidemics. The tool then produces key outcomes including expected numbers of deaths, hospitalizations and cases, with the possibility of simulating several scenarios of vaccine allocation at once for a side-by-side comparison.", "rel_num_authors": 3, "rel_authors": [ { @@ -52707,8 +53292,8 @@ "rel_date": "2023-06-20", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.16.23291524", - "rel_abs": "We present Crykey, a computational tool for identifying SARS-CoV-2 cryptic mutations from wastewater. While previous exist for identifying cryptic mutations in specific regions of the SARS-CoV-2 genome, there is a need for computational tools capable of tracking cryptic mutations across the entire genome and at scale. Crykey fills this gap and leverages the co-occurrence of single nucleotide variants on the same read combined with variant frequency information. We evaluated Crykey on SARS-CoV-2 sequences from 3175 wastewater samples and more than 14000 clinical samples. Our results are threefold, we show: 1) Crykey can accurately identify cryptic lineages that are rare or missing in existing databases ; 2) the emergence of cryptic lineage can be related to increased transmission rates in the communities, and 3) some cryptic lineages in wastewater mirror intra-host low frequency co-occurring variants in individuals. In summary, Crykey facilitates rapid and comprehensive identification of SARS-CoV-2 cryptic mutations in wastewater samples.", - "rel_num_authors": 4, + "rel_abs": "We present Crykey, a computational tool for rapidly identifying cryptic mutations of SARS-CoV-2. Specifically, we identify co-occurring single nucleotide mutations on the same sequencing read, called linked-read mutations, that are rare or entirely missing in existing databases, and have the potential to represent novel cryptic lineages found in wastewater. While previous approaches exist for identifying cryptic linked-read mutations from specific regions of the SARS-CoV-2 genome, there is a need for computational tools capable of efficiently tracking cryptic mutations across the entire genome and for tens of thousands of samples and with increased scrutiny, given their potential to represent either artifacts or hidden SARS-CoV-2 lineages. Crykey fills this gap by identifying rare linked-read mutations that pass stringent computational filters to limit the potential for artifacts. We evaluate the utility of Crykey on >3,000 wastewater and >22,000 clinical samples; our findings are three-fold: i) we identify hundreds of cryptic mutations that cover the entire SARS-CoV-2 genome, ii) we track the presence of these cryptic mutations across multiple wastewater treatment plants and over a three years of sampling in Houston, and iii) we find a handful of cryptic mutations in wastewater mirror cryptic mutations in clinical samples and investigate their potential to represent real cryptic lineages. In summary, Crykey enables large-scale detection of cryptic mutations representing potential cryptic lineages in wastewater.", + "rel_num_authors": 7, "rel_authors": [ { "author_name": "Yunxi Liu", @@ -52718,6 +53303,18 @@ "author_name": "Nicolae Sapoval", "author_inst": "Department of Computer Science, Rice University, 6100 Main Street, Houston, TX 77005, USA" }, + { + "author_name": "Pilar Gallego-Garcia", + "author_inst": "CINBIO, Universidade de Vigo, 36310 Vigo, Spain" + }, + { + "author_name": "Laura Tomas", + "author_inst": "CINBIO, Universidade de Vigo, 36310 Vigo, Spain" + }, + { + "author_name": "David Posada", + "author_inst": "CINBIO, Universidade de Vigo, 36310 Vigo, Spain" + }, { "author_name": "Todd Treangen", "author_inst": "Department of Computer Science, Rice University, 6100 Main Street, Houston, TX 77005, USA" @@ -52923,6 +53520,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.06.14.23291320", + "rel_title": "Vagus nerve inflammation contributes to dysautonomia in COVID-19", + "rel_date": "2023-06-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.14.23291320", + "rel_abs": "Dysautonomia has substantially impacted acute COVID-19 severity as well as symptom burden after recovery from COVID-19 (long COVID), yet the underlying causes remain unknown. Here, we show that SARS-CoV-2 is detectable in postmortem vagus nerve specimen together with inflammatory cell infiltration derived primarily from monocytes. This is associated with a decreased respiratory rate in non-survivors of critical COVID-19. Our data suggest that SARS-CoV-2 induces vagus nerve inflammation followed by autonomic dysfunction.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Marcel Seungsu Woo", + "author_inst": "Institute of Neuroimmunology and Multiple Sclerosis, University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Mohsin Shafiq", + "author_inst": "Institute of Neuropathology, University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Antonia Fitzek", + "author_inst": "Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany" + }, + { + "author_name": "Matthias Dottermusch", + "author_inst": "Institute of Neuropathology, University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Hermann Altmeppen", + "author_inst": "Institute of Neuropathology, University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Behnam Mohammadi", + "author_inst": "Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany" + }, + { + "author_name": "Christina Mayer", + "author_inst": "Institute of Neuroimmunology and Multiple Sclerosis, University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Lukas Can Bal", + "author_inst": "Institute of Neuroimmunology and Multiple Sclerosis, University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Lukas Raich", + "author_inst": "Institute of Neuroimmunology and Multiple Sclerosis, University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Jakob Matschke", + "author_inst": "Institute of Neuropathology, University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Susanne Krasemann", + "author_inst": "Institute of Neuropathology, University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Susanne Pfefferle", + "author_inst": "Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Thomas Theo Seungsu Brehm", + "author_inst": "University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Marc Luetgehetmann", + "author_inst": "Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Julia Schaedler", + "author_inst": "Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Marylin M Addo", + "author_inst": "IUniversity Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Julian Schulze Zur Wiesch", + "author_inst": "University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Benjamin Ondruschka", + "author_inst": "Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Manuel A Friese", + "author_inst": "Institute of Neuroimmunology and Multiple Sclerosis, University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Markus Glatzel", + "author_inst": "University of Hamburg-Eppendorf" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2023.06.14.23291380", "rel_title": "A single blinded, phase IV, adaptive randomised control trial to evaluate the safety of coadministration of seasonal influenza and COVID-19 vaccines (The FluVID study)", @@ -53993,41 +54685,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, - { - "rel_doi": "10.1101/2023.06.12.544536", - "rel_title": "Defining the single base importance of human mRNAs and lncRNAs", - "rel_date": "2023-06-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.12.544536", - "rel_abs": "As the fundamental unit of a gene and its transcripts, nucleotides have enormous impacts on molecular function and evolution, and thus on phenotypes and diseases. Given that different nucleotides on one gene often exhibit diverse levels of effects, it is quite crucial to comprehensively and quantitatively measure the importance of each base on a gene transcript, however, tools are still not available. Here we proposed Base Importance Calculator (BIC), an algorithm to calculate the importance score of single bases based on sequence information of human mRNAs and long noncoding RNAs (lncRNAs). We then confirmed its power by applying BIC to three different tasks. Firstly, we revealed that BIC can effectively evaluate the pathogenicity of both genes and single bases by analyzing the BIC scores and the pathogenicity of single nucleotide variations (SNVs). Moreover, the BIC score in the Cancer Genome Atlas (TCGA) somatic mutations is able to predict the prognosis of some cancers. Finally, we show that BIC can also precisely predict the transmissibility of SARS-CoV-2. The above results indicate that BIC is a useful tool for evaluating the single base important of human mRNAs and lncRNAs.\n\nKey PointsO_LIBIC could measure the single base importance of human mRNAs and lncRNAs.\nC_LIO_LIBIC could be applied to many aspects including measuring the pathogenicity of SNVs and enhancing the ability of predicting cancer survival.\nC_LIO_LIBIC could predict the transmissibility of SARS-CoV-2\nC_LI", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Rui Fan", - "author_inst": "Peking University" - }, - { - "author_name": "Xiangwen Ji", - "author_inst": "Peking University" - }, - { - "author_name": "Jianwei Li", - "author_inst": "Institute of Computational Medicine, School of Artificial Intelligence, Hebei University of Technology, Tianjin, 300401, China" - }, - { - "author_name": "Qinghua Cui", - "author_inst": "Peking University" - }, - { - "author_name": "Chunmei Cui", - "author_inst": "School of Basic Medical Sciences, Peking University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2023.06.14.544985", "rel_title": "Inclusion of glycopeptides in hydrogen/deuterium exchange mass spectrometry analysis of SARS-CoV-2 spike ectodomain provides increased sequence coverage", @@ -54857,13 +55514,56 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.06.13.544745", + "rel_title": "SARS CoV-2 Envelope protein alters calcium signaling via SERCA interactions", + "rel_date": "2023-06-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.13.544745", + "rel_abs": "The clinical management of severe COVID-19 cases is not yet well resolved. Therefore, it is important to identify and characterize cell signaling pathways involved in virus pathogenesis that can be targeted therapeutically. Envelope (E) protein is a structural protein of the virus, which is known to be highly expressed in the infected host cell and is a key virulence factor, however, its role is poorly characterized. The E protein is a single-pass transmembrane protein that can assemble into a pentamer forming a viroporin, perturbing Ca2+ homeostasis. Because it is structurally similar to regulins such as, for example, phospholamban, that regulate the sarco/endoplasmic reticulum calcium ATPases (SERCA), we investigated whether the SARS-CoV-2 E protein affects the SERCA system as an exoregulin. Using FRET experiments we demonstrate that E protein can form oligomers with regulins, and thus can alter the monomer/multimer regulin ratio and consequently influence their interactions with SERCAs. We also confirmed that a direct interaction between E protein and SERCA2b results in a decrease in SERCA-mediated ER Ca2+ reload. Structural modeling and molecular dynamics of the complexes indicates an overlapping interaction site for E protein and endogenous regulins. Our results reveal novel links in the host-virus interaction network that play an important role in viral pathogenesis and may provide a new therapeutic target for managing severe inflammatory responses induced by SARS-CoV-2.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Blanka Berta", + "author_inst": "Semmelweis University" + }, + { + "author_name": "Hedvig Tordai", + "author_inst": "Semmelweis University" + }, + { + "author_name": "Gergely L Lukacs", + "author_inst": "McGill Univ" + }, + { + "author_name": "Bela Papp", + "author_inst": "Hopital Saint-Louis" + }, + { + "author_name": "Agnes Enyedi", + "author_inst": "Semmelweis University" + }, + { + "author_name": "Rita Padanyi", + "author_inst": "Semmelweis University" + }, + { + "author_name": "Tamas Hegedus", + "author_inst": "Semmelweis University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2023.06.13.543274", "rel_title": "Mycobiome analyses of critically ill COVID-19 patients suggests antifungal prophylaxis may be protective against A. fumigatus-associated mortality", "rel_date": "2023-06-13", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.13.543274", - "rel_abs": "RationaleCovid-associated pulmonary aspergillosis (CAPA) is a life-threatening complication in patients with severe COVID-19. Previously, acute respiratory distress syndrome in patients with COVID-19 has been associated with lung fungal dysbiosis, evidenced by reduced microbial diversity and Candida colonisation. Increased fungal burden in the lungs of critically ill COVID-19 patients is linked to prolonged mechanical ventilation and increased mortality. However, specific mycobiome signatures associated with severe COVID-19 in the context of survival and antifungal drug prophylaxis have not yet been determined and such knowledge could have an important impact on treatment.\n\nObjectivesTo understand the composition of the respiratory mycobiome in critically ill COVID-19 patients with and without CAPA, the impact of antifungal use and its role in patient outcome.\n\nMethodsWe performed a multi-national study of 39 COVID-19 patients in intensive care units (ICU) with and without CAPA. Respiratory mycobiome was profiled using ITS1 sequencing and Aspergillus fumigatus burden was further validated using qPCR. Fungal communities were investigated using alpha diversity, beta diversity, taxa prevalence and taxa abundances.\n\nResultsRespiratory mycobiomes were dominated by Candida and Aspergillus. There was no significant association with corticosteroid use or CAPA diagnosis and respiratory fungal communities. Increased A. fumigatus burden was associated with mortality. The use of antifungals at ICU admission was associated with an absence of A. fumigatus.\n\nConclusionsOur findings suggest that systemic antifungal treatment at ICU admission may be protective against A. fumigatus-associated mortality in CAPA.", + "rel_abs": "Rationale: COVID-19-associated pulmonary aspergillosis (CAPA) is a life-threatening complication in patients with severe COVID-19. Previously, acute respiratory distress syndrome in patients with COVID-19 has been associated with lung fungal dysbiosis, evidenced by reduced microbial diversity and Candida colonisation. Increased fungal burden in the lungs of critically ill COVID-19 patients is linked to prolonged mechanical ventilation and increased mortality. However, specific mycobiome signatures associated with severe COVID-19 in the context of survival and antifungal drug prophylaxis have not yet been determined and such knowledge could have an important impact on treatment. Objectives: To understand the composition of the respiratory mycobiome in critically ill COVID-19 patients with and without CAPA and the impact of antifungal use in patient outcome. Methods: We performed a multi-national study of 39 COVID-19 patients in intensive care units (ICU) with and without CAPA. Respiratory mycobiome was profiled using ITS1 sequencing and Aspergillus fumigatus burden was further validated using qPCR. Fungal communities were investigated using alpha diversity, beta diversity, taxa predominance and taxa abundances. Results: Respiratory mycobiomes of COVID-19 patients were dominated by Candida and Aspergillus. There was no significant association with corticosteroid use or CAPA diagnosis and respiratory fungal communities. Increased A. fumigatus burden was associated with mortality and, the use of azoles at ICU admission was linked with an absence of A. fumigatus. Conclusions: Our findings suggest that mould-active antifungal treatment at ICU admission may be linked with reduced A. fumigatus-associated mortality in severe COVID-19. However, further studies are warranted on this topic.", "rel_num_authors": 11, "rel_authors": [ { @@ -55823,53 +56523,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2023.06.08.23291008", - "rel_title": "Impact of COVID-19 Pandemic on Sleep Including HRV and Physical Activity as Mediators: A Causal ML Approach", - "rel_date": "2023-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.08.23291008", - "rel_abs": "Sleep quality is crucial to both mental and physical well-being. The COVID-19 pandemic, which has notably affected the populations health worldwide, has been shown to deteriorate peoples sleep quality. Numerous studies have been conducted to evaluate the impact of the COVID-19 pandemic on sleep efficiency, investigating their relationships using correlation-based methods. These methods merely rely on learning spurious correlation rather than the causal relations among variables. Furthermore, they fail to pinpoint potential sources of bias and mediators and envision counterfactual scenarios, leading to a poor estimation. In this paper, we develop a Causal Machine Learning method, which encompasses causal discovery and causal inference components, to extract the causal relations between the COVID-19 pandemic (treatment variable) and sleep quality (outcome) and estimate the causal treatment effect, respectively. We conducted a wearable-based health monitoring study to collect data, including sleep quality, physical activity, and Heart Rate Variability (HRV) from college students before and after the COVID-19 lockdown in March 2020. Our causal discovery component generates a causal graph and pinpoints mediators in the causal model. We incorporate the strongly contributing mediators (i.e., HRV and physical activity) into our causal inference component to estimate the robust, accurate, and explainable causal effect of the pandemic on sleep quality. Finally, we validate our estimation via three refutation analysis techniques. Our experimental results indicate that the pandemic exacerbates college students sleep scores by 8%. Our validation results show significant p-values confirming our estimation.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Elahe Khatibi", - "author_inst": "University of California, Irvine" - }, - { - "author_name": "Mahyar Abbasian", - "author_inst": "University of California at Irvine" - }, - { - "author_name": "Iman Azimi", - "author_inst": "University of California at Irvine" - }, - { - "author_name": "Sina Labbaf", - "author_inst": "UCI: University of California Irvine" - }, - { - "author_name": "Mohammad Feli", - "author_inst": "University of Turku" - }, - { - "author_name": "Jessica Borelli", - "author_inst": "University of California at Irvine" - }, - { - "author_name": "Nikil Dutt", - "author_inst": "University of California at Irvine" - }, - { - "author_name": "Amir Rahmani", - "author_inst": "University of California, Irvine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2023.06.09.23291202", "rel_title": "Trends in medication use after the onset of the COVID-19 pandemic in the Republic of Ireland: an interrupted time series study", @@ -56495,6 +57148,85 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.06.07.544133", + "rel_title": "Anti-Viral and Anti-Inflammatory Therapeutic Effect of RAGE-Ig Protein Against Multiple SARS-CoV-2 Variants of Concern Demonstrated in K18-hACE2 Mouse and Syrian Golden Hamster Models", + "rel_date": "2023-06-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.07.544133", + "rel_abs": "SignificanceSARS-CoV-2 Variants of Concern (VOCs) continue to evolve and re-emerge with chronic inflammatory long-COVID sequelae necessitating the development of anti-inflammatory therapeutic molecules. Therapeutic effects of the Receptor for Advanced Glycation End products (RAGE) were reported in many inflammatory diseases. However, a therapeutic effect of the RAGE in COVID-19 has not been reported. In the present study, we investigated whether and how the RAGE-Ig fusion protein would have an anti-viral and anti-inflammatory therapeutic effect in the COVID-19 system.\n\nMethodsThe protective therapeutic effect of RAGE-Ig was determined in vitro in K18-hACE2 transgenic mice and Syrian golden hamsters infected with six various VOCs of SARS-CoV-2. The underlying anti-viral mechanism of RAGE-Ig was determined in vitro in SARS-CoV-2-infected human lung epithelial cells (BEAS-2B).\n\nResultsFollowing treatment of K18-hACE2 mice and hamsters infected with various SARS-CoV-2 VOCs with RAGE-Ig, we demonstrated: (i) significant dose-dependent protection (i.e. greater survival, less weight loss, lower virus replication in the lungs); (ii) a reduction of inflammatory macrophages (F4/80+/Ly6C+) and neutrophils (CD11b+/Ly6G+) infiltrating the infected lungs; (iii) a RAGE-Ig dose-dependent increase in the expression of type I interferons (IFN-, and IFN-{beta}) and type III interferon (IFN{lambda}2) and a decrease in the inflammatory cytokines (IL-6 and IL-8) in SARS-CoV-2-infected human lung epithelial cells; and (iv) a dose-dependent decrease in the expression of CD64 (FcgR1) on monocytes and lung epithelial cells from symptomatic COVID-19 patients.\n\nConclusionOur pre-clinical findings revealed type I and III interferons-mediated anti-viral and anti-inflammatory therapeutic effects of RAGE-Ig protein against COVID-19 caused by multiple SARS-CoV-2 VOCs.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Nisha Dhanushkodi", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Swayam Prakash", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Afshana Quadiri", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Latifa Zayou", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Ruchi Srivastava", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Amin Mohammed Shaik", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Berfin Suzer", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Izabela Coimbra Ibraim", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Gary Landucci", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Delia F Tifrea", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Mahmoud Singer", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Leila Jamal", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Robert A Edwards", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Hawa Vahed", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Lawrence Brown", + "author_inst": "Galactica Pharmaceuticals, Inc., Villanova, PA 19085" + }, + { + "author_name": "LBACHIR BENMOHAMED", + "author_inst": "UC Irvine, School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.06.07.544062", "rel_title": "Single-cell RNA sequencing reveals HIF1A as a severity-sensitive immunological scar in circulating monocytes of convalescent comorbidity-free COVID-19 patients", @@ -57477,25 +58209,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2023.06.05.23290994", - "rel_title": "Mortality associated with influenza infections in France before and during the COVID-19 pandemic, and mortality associated with Omicron infections, including mortality for cardiovascular disease and for mental and behavioral disorders", - "rel_date": "2023-06-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.05.23290994", - "rel_abs": "BackgroundDuring the winter of 2022-2023, high rates of all-cause mortality, not seen since April 2020, were recorded in France, with excess all-cause mortality being related to the Omicron and influenza epidemics during that period. Moreover, that period saw a significant increase in the proportion of residents in long-term care facilities among cases of death in the population. Studies have found that increased influenza vaccination coverage in healthcare workers can result in a substantial reduction (up to 20%-30% during the course of select influenza seasons in the pre-pandemic period) in all-cause mortality in residents in nursing homes.\n\nMethodsWe applied the previously developed methodology to estimate the contribution of influenza infections to all-cause mortality in France for the 2014-2015 through the 2018-2019 influenza seasons, and the contribution of both SARS-CoV-2 and influenza infections to all-cause mortality between week 33, 2022 through week 12, 2023.\n\nResultsFor the 2014-2015 through the 2018-2019 seasons, influenza was associated with an average of 15654 (95% CI (13013,18340)) deaths, while between week 33, 2022 through week 12, 2023, we estimated 7851 (5213,10463) influenza-associated deaths and 32607 (20794,44496) SARS-CoV-2 associated deaths. The number of SARS-CoV-2-associated deaths during the Omicron epidemic was significantly higher than the number of deaths with COVID-19 listed on the death certificate or the hospitalization record - for example, between weeks 33-52 in 2022, we estimated 23983 (15307,32620) SARS-CoV-2-associated deaths in France, compared with 12811 deaths with COVID-19 listed on the death certificate, and 8639 in-hospital deaths with COVID-19 during the same period. Examination of US mortality data suggests a significant contribution of Omicron infections to mortality for cardiac disease and mental/behavioral disorders with COVID-19 not listed on the death certificate.\n\nConclusionsOur results suggest the need for boosting influenza vaccination coverage in different population groups (including healthcare workers, particularly nurse assistants for whom influenza vaccination coverage rates in France are low), as well as for wider use of influenza antiviral medications in influenza-related respiratory hospitalizations with different diagnoses (including pneumonia). Wider detection and treatment of Omicron infections, particularly in older individuals/persons with underlying health conditions such as cardiac disease and mental/behavioral disorders, and wider use of bivalent COVID-19 boosters would be needed in the event of the recrudescence of Omicron circulation in France.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Edward Goldstein", - "author_inst": "Massachusetts Eye and Ear Hospital, Harvard Medical School" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.06.03.543542", "rel_title": "Species and habitat specific changes in bird activity in an urban environment during Covid 19 lockdown", @@ -58041,6 +58754,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nutrition" }, + { + "rel_doi": "10.1101/2023.06.04.23290946", + "rel_title": "Association between sleep and seroconversion after vaccination with inactivated SARS-CoV-2 in pregnant women", + "rel_date": "2023-06-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.04.23290946", + "rel_abs": "To assess the association between sleep and seroconversion after receipt of two doses of inactivated severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) vaccines in pregnant women. The serum level of immunoglobulin (Ig)G antibodies against the nucleic acids of SARS-CoV-2 was measured. Logistic regression was used to analyze the association between sleep and seroconversion. After two doses of SARS-CoV-2 vaccine, 41.2% of the study cohort reached seroconversion. Analysis revealed that pregnant women with poor quality of sleep had a lower serum level of IgG antibodies (P = 0.008, 95%CI = 0.285-0.826) and that sleeping late at night (SLaN) may be a risk factor for a low serum level of IgG antibodies (P = 0.025, 95%CI = 0.436-0.946). Besides sleep, age and the time since vaccination were important influences on seroconversion. A stratified analysis revealed that the effects of sleep quality and SLaN on seroconversion occurred mainly in pregnant women aged <35 years. Thus, sleep quality and SLaN can affect the serum level of IgG antibodies in pregnant women after vaccination with inactivated SARS-CoV-2.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Xue Han", + "author_inst": "Guangdong Pharmaceutical University" + }, + { + "author_name": "Wenhan Yang", + "author_inst": "Guangdong Pharmaceutical University" + }, + { + "author_name": "Xi Zhang", + "author_inst": "Guangdong Pharmaceutical University" + }, + { + "author_name": "Baolan Chen", + "author_inst": "Guangdong Pharmaceutical University" + }, + { + "author_name": "Xi Fu", + "author_inst": "Guangdong Pharmaceutical University" + }, + { + "author_name": "Jitian Huang", + "author_inst": "Guangdong Pharmaceutical University" + }, + { + "author_name": "Yingxia Xu", + "author_inst": "Guangdong Pharmaceutical University" + }, + { + "author_name": "Yajie Gong", + "author_inst": "Guangdong Pharmaceutical University" + }, + { + "author_name": "Qingsong CHEN", + "author_inst": "Guangdong Pharmaceutical University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.06.02.23290867", "rel_title": "Comparative Analysis of Decision Trees on Two COVID-19 Symptom Datasets", @@ -59647,109 +60411,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2023.06.02.543298", - "rel_title": "Deep Phenotyping of the Lipidomic Response in COVID and non-COVID Sepsis", - "rel_date": "2023-06-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.02.543298", - "rel_abs": "Lipids may influence cellular penetrance by pathogens and the immune response that they evoke. Here we find a broad based lipidomic storm driven predominantly by secretory (s) phospholipase A2 (sPLA2) dependent eicosanoid production occurs in patients with sepsis of viral and bacterial origin and relates to disease severity in COVID-19. Elevations in the cyclooxygenase (COX) products of arachidonic acid (AA), PGD2 and PGI2, and the AA lipoxygenase (LOX) product, 12-HETE, and a reduction in the high abundance lipids, ChoE 18:3, LPC-O-16:0 and PC-O-30:0 exhibit relative specificity for COVID-19 amongst such patients, correlate with the inflammatory response and link to disease severity. Linoleic acid (LA) binds directly to SARS-CoV-2 and both LA and its di-HOME products reflect disease severity in COVID-19. AA and LA metabolites and LPC-O-16:0 linked variably to the immune response. These studies yield prognostic biomarkers and therapeutic targets for patients with sepsis, including COVID-19. An interactive purpose built interactive network analysis tool was developed, allowing the community to interrogate connections across these multiomic data and generate novel hypotheses.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Hu Meng", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Arjun Sengupta", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Emanuela Riccioti", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Antonijo Mr\u010dela", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Divij Mathew", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Liudmila Mazaleuskaya", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Soumita Ghosh", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Thomas Brooks", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Alexandra Turner", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Alessa Schanoski", - "author_inst": "Mount Sinai School of Medicine" - }, - { - "author_name": "Nicholas Lahens", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Ai Wen Tan", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Ashley Woolfork", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Greg Grant", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Katalin Susztak", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Andrew Letizia", - "author_inst": "Naval Medical researech Center" - }, - { - "author_name": "Stuart Sealfon", - "author_inst": "Mount Sinai School of Medicine" - }, - { - "author_name": "E. John Wherry", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Krysztof Laudanski", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Aalim Weljie", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Nuala Meyer", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Garret Fitzgerald", - "author_inst": "University of Pennsylvania" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "systems biology" - }, { "rel_doi": "10.1101/2023.05.31.543022", "rel_title": "Universal features of Nsp1-mediated translational shutdown by coronaviruses", @@ -60431,6 +61092,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2023.05.24.23290491", + "rel_title": "Association between lifestyle factors and weight in Japan university students during COVID-19 mild lockdown: a quantitative study", + "rel_date": "2023-05-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.24.23290491", + "rel_abs": "We investigated the lifestyle factors influencing weight gain in university students during restrictions (mild lockdown) imposed owing to the novel coronavirus disease pandemic in Japan. In this cross-sectional study, a questionnaire survey of Nagasaki University students undergoing health examinations was conducted in 2021. Students reporting [≥]3 kg weight gain were included in the weight gain group; the remaining students were in the non-weight gain group. Fishers exact test and binary logistic regression were performed to detect the associations between weight gain and each lifestyle factor. We included 3,059 respondents (response rate: 45.7%), and 9.5% respondents reported [≥]3 kg weight gain. The following factors were associated with weight gain (odds ratio, 95% confidence interval, p value from Fishers exact test): dining out for [≥]4 times/week (2.16 [1.40, 3.32], p = 8.7 x 10-4), gaming time of [≥]4 h/day (2.26 [1.45, 3.47], p = 2.4 x 10-4). Binary logistic regression among the four highest odds ratios showed that after adjusting for other factors frequently dining out and prolonged gaming time were significantly associated with weight gain. Prolonged gaming and frequently dining out were associated with weight gain in students during the mild lockdown.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Haruka Arimori", + "author_inst": "Nagasaki University Hospital: Nagasaki Daigaku Byoin" + }, + { + "author_name": "Norio Abiru", + "author_inst": "Nagasaki University Hospital: Nagasaki Daigaku Byoin" + }, + { + "author_name": "Shimpei Morimoto", + "author_inst": "Nagasaki University Graduate School of Biomedical Sciences: Nagasaki Daigaku Daigakuin Ishiyakugaku Sogo Kenkyuka" + }, + { + "author_name": "Tomoya Nishino", + "author_inst": "Nagasaki University: Nagasaki Daigaku" + }, + { + "author_name": "Atsushi Kawakami", + "author_inst": "Nagasaki University Hospital: Nagasaki Daigaku Byoin" + }, + { + "author_name": "Akie Kamada", + "author_inst": "Nagasaki University Hospital: Nagasaki Daigaku Byoin" + }, + { + "author_name": "Masakazu Kobayashi", + "author_inst": "Nagasaki University Hospital: Nagasaki Daigaku Byoin" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.05.29.542735", "rel_title": "Antibodies against SARS-CoV-2 control complement-induced inflammatory responses to SARS-CoV-2", @@ -62161,77 +62865,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.05.26.542489", - "rel_title": "SARS-CoV-2 lineage assignments using phylogenetic placement/UShER are superior to pangoLEARN machine learning method", - "rel_date": "2023-05-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.26.542489", - "rel_abs": "With the rapid spread and evolution of SARS-CoV-2, the ability to monitor its transmission and distinguish among viral lineages is critical for pandemic response efforts. The most commonly used software for the lineage assignment of newly isolated SARS-CoV-2 genomes is pangolin, which offers two methods of assignment, pangoLEARN and pUShER. PangoLEARN rapidly assigns lineages using a machine learning algorithm, while pUShER performs a phylogenetic placement to identify the lineage corresponding to a newly sequenced genome. In a preliminary study, we observed that pangoLEARN (decision tree model), while substantially faster than pUShER, offered less consistency across different versions of pangolin v3. Here, we expand upon this analysis to include v3 and v4 of pangolin, which moved the default algorithm for lineage assignment from pangoLEARN in v3 to pUShER in v4, and perform a thorough analysis confirming that pUShER is not only more stable across versions but also more accurate. Our findings suggest that future lineage assignment algorithms for various pathogens should consider the value of phylogenetic placement.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Adriano de Bernardi Schneider", - "author_inst": "University of California Santa Cruz" - }, - { - "author_name": "Michelle Su", - "author_inst": "New York City Public Health Laboratory, Department of Health and Mental Hygiene, New York, NY, USA" - }, - { - "author_name": "Angie S Hinrichs", - "author_inst": "Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA" - }, - { - "author_name": "Jade Wang", - "author_inst": "New York City Public Health Laboratory, Department of Health and Mental Hygiene, New York, NY, USA" - }, - { - "author_name": "Helly Amin", - "author_inst": "New York City Public Health Laboratory, Department of Health and Mental Hygiene, New York, NY, USA" - }, - { - "author_name": "John Bell", - "author_inst": "California Department of Public Health (CDPH), VRDL/COVIDNet, Richmond, CA 94804, USA" - }, - { - "author_name": "Debra A Wadford", - "author_inst": "California Department of Public Health (CDPH), VRDL/COVIDNet, Richmond, CA 94804, USA" - }, - { - "author_name": "\u00c1ine O'Toole", - "author_inst": "Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK" - }, - { - "author_name": "Emily Scher", - "author_inst": "Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK" - }, - { - "author_name": "Marc D Perry", - "author_inst": "Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA" - }, - { - "author_name": "Yatish Turakhia", - "author_inst": "Department of Electrical and Computer Engineering, University of California San Diego, San Diego, CA 92093, USA" - }, - { - "author_name": "Nicola De Maio", - "author_inst": "European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton CB10 1SD, United Kingdom" - }, - { - "author_name": "Scott Hughes", - "author_inst": "New York City Public Health Laboratory, Department of Health and Mental Hygiene, New York, NY, USA" - }, - { - "author_name": "Russ Corbett-Detig", - "author_inst": "Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2023.05.23.542024", "rel_title": "A Multi-Epitope/CXCL11 Prime/Pull Coronavirus Mucosal Vaccine Boosts the Frequency and the Function of Lung-Resident CD4+ and CD8+ Memory T Cells and Protects Against COVID-19-like Symptoms and Death Caused by SARS-CoV-2 infection", @@ -63029,6 +63662,53 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.05.24.542043", + "rel_title": "The impact of RSV/SARS-CoV-2 co-infection on clinical disease and viral replication: insights from a BALB/c mouse model", + "rel_date": "2023-05-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.24.542043", + "rel_abs": "RSV and SARS-CoV-2 are prone to co-infection with other respiratory viruses. In this study, we use RSV/SARS-CoV-2 co-infection to evaluate changes to clinical disease and viral replication in vivo. To consider the severity of RSV infection, effect of sequential infection, and the impact of infection timing, mice were co-infected with varying doses and timing. Compared with a single infection of RSV or SARS-CoV-2, the co-infection of RSV/SARS-CoV-2 and the primary infection of RSV followed by SARS-CoV-2 results in protection from SARS-CoV-2-induced clinical disease and reduces SARS-CoV-2 replication. Co-infection also augmented RSV replication at early timepoints with only the low dose. Additionally, the sequential infection of RSV followed by SARS-CoV-2 led to improved RSV clearance regardless of viral load. However, SARS-CoV-2 infection followed by RSV results in enhanced SARS-CoV-2-induced disease while protecting from RSV-induced disease. SARS-CoV-2/RSV sequential infection also reduced RSV replication in the lung tissue, regardless of viral load. Collectively, these data suggest that RSV and SARS-CoV-2 co-infection may afford protection from or enhancement of disease based on variation in infection timing, viral infection order, and/or viral dose. In the pediatric population, understanding these infection dynamics will be critical to treat patients and mitigate disease outcomes.\n\nAuthor SummaryInfants and young children are commonly affected by respiratory viral co-infections. While RSV and SARS-CoV-2 are two of the most prevalent respiratory viruses, their co-infection rate in children remains surprisingly low. In this study, we investigate the impact of RSV/SARS-CoV-2 co-infection on clinical disease and viral replication using an animal model. The findings indicate that RSV infection either simultaneously or prior to SARS-CoV-2 infection in mice protect against SARS-CoV-2-induced clinical disease and viral replication. On the other hand, infection with SARS-CoV-2 followed by RSV results in worsening of SARS-CoV-2-induced clinical disease, but also protection from RSV-induced clinical disease. These results highlight a protective role for RSV exposure, given this occurs before infection with SARS-CoV-2. This knowledge could help guide vaccine recommendations in children and sets a basis for future mechanistic studies.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=151 SRC=\"FIGDIR/small/542043v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (35K):\norg.highwire.dtl.DTLVardef@f37ec4org.highwire.dtl.DTLVardef@782a8org.highwire.dtl.DTLVardef@112f0f1org.highwire.dtl.DTLVardef@889107_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Dorothea R. Morris", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Yue Qu", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Kerrie S. Thomason", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Aline Haas de Mello", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Richard Preble", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Vineet D. Menachery", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Antonella Casola", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Roberto P. Garofalo", + "author_inst": "University of Texas Medical Branch" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.05.24.542061", "rel_title": "Computational insights on the destabilizing mutations in the binding site of 3CL-protease SARS-CoV-2 Omicron (VOC)", @@ -64175,45 +64855,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.05.18.23289533", - "rel_title": "Predicting the public health impact of bivalent vaccines and nirmatrelvir-ritonavir against COVID-19", - "rel_date": "2023-05-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.18.23289533", - "rel_abs": "BackgroundUptake of COVID-19 bivalent vaccines and oral medication nirmatrelvir-ritonavir (Paxlovid) has remained low across the United States. Assessing the public health impact of increasing uptake of these interventions in key risk groups can guide further public health resources and policy.\n\nMethodsThis modeling study used person-level data from the California Department of Public Health on COVID-19 cases, hospitalizations, deaths, and vaccine administration from July 23, 2022 to January 23, 2023. We modeled the impact of additional uptake of bivalent COVID-19 vaccines and nirmatrelvir-ritonavir during acute illness in different risk groups defined by age (50+, 65+, 75+ years) and vaccination status (everyone, primary series only, previously vaccinated). We predicted the number of averted COVID-19 cases, hospitalizations, and deaths and number needed to treat (NNT).\n\nResultsFor both bivalent vaccines and nirmatrelvir-ritonavir, the most efficient strategy (based on NNT) for averting severe COVID-19 was targeting the 75+ years group. We predicted that perfect coverage of bivalent boosters in the 75+ years group would avert 3,920 hospitalizations (95%UI: 2,491-4,882; 7.8% total averted; NNT 387) and 1,074 deaths (95%UI: 774-1,355; 16.2% total averted; NNT 1,410). Perfect uptake of nirmatrelvir-ritonavir in the 75+ years group would avert 5,644 hospitalizations (95%UI: 3,947-6,826; 11.2% total averted; NNT 11) and 1,669 deaths (95%UI: 1,053-2,038; 25.2% total averted; NNT 35).\n\nConclusionsThese findings suggest prioritizing uptake of bivalent boosters and nirmatrelvir-ritonavir among the oldest age groups would be efficient and have substantial public health impact in reducing the burden of severe COVID-19, but would not address the entire burden of severe COVID-19.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Hailey J Park", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Sophia T Tan", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Tom\u00e1s M Le\u00f3n", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Seema Jain", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Robert Schechter", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Nathan C Lo", - "author_inst": "University of California, San Francisco" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.05.16.23290033", "rel_title": "Viral rebound among patients receiving COVID-19 convalescent plasma for treatment of Covid-19 in Uganda.", @@ -64811,6 +65452,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.05.19.23290208", + "rel_title": "Assessing changes in incubation period, serial interval, and generation time of SARS-CoV-2 variants of concern: a systematic review and meta-analysis", + "rel_date": "2023-05-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.19.23290208", + "rel_abs": "BackgroundAfter the first COVID-19 wave caused by the ancestral lineage, the pandemic has been fueled from the continuous emergence of new SARS-CoV-2 variants. Understanding key time-to-event periods for each emerging variant of concern is critical as it can provide insights into the future trajectory of the virus and help inform outbreak preparedness and response planning. Here, we aim to examine how the incubation period, serial interval, and generation time have changed from the ancestral SARS-CoV-2 lineage to different variants of concern.\n\nMethodsWe conducted a systematic review and meta-analysis that synthesized the estimates of incubation period, serial interval, and generation time (both realized and intrinsic) for the ancestral lineage, Alpha, Beta, and Omicron variants of SARS-CoV-2.\n\nResultsOur study included 274 records obtained from 147 household studies, contact tracing studies or studies where epidemiological links were known. With each emerging variant, we found a progressive shortening of each of the analyzed key time-to-event periods. Specifically, we found that Omicron had the shortest pooled estimates for the incubation period (3.63 days, 95%CI: 3.25-4.02 days), serial interval (3.19 days, 95%CI: 2.95-3.43 days), and realized generation time (2.96 days, 95%CI: 2.54-3.38 days) whereas the ancestral lineage had the highest pooled estimates for each of them. We also observed shorter pooled estimates for the serial interval compared to the incubation period across the virus lineages. We found considerable heterogeneities (I2 > 80%) when pooling the estimates across different virus lineages, indicating potential unmeasured confounding from population factors (e.g., social behavior, deployed interventions).\n\nConclusionOur study supports the importance of conducting contact tracing and epidemiological investigations to monitor changes in SARS-CoV-2 transmission patterns. Our findings highlight a progressive shortening of the incubation period, serial interval, and generation time, which can lead to epidemics that spread faster, with larger peak incidence, and harder to control. We also consistently found a shorter serial interval than incubation period, suggesting that a key feature of SARS-CoV-2 is the potential for pre-symptomatic transmission. These observations are instrumental to plan for future COVID-19 waves.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Xiangyanyu Xu", + "author_inst": "Fudan University" + }, + { + "author_name": "Yanpeng Wu", + "author_inst": "Fudan University" + }, + { + "author_name": "Allisandra G. Kummer", + "author_inst": "Indiana University" + }, + { + "author_name": "Yuchen Zhao", + "author_inst": "Fudan University" + }, + { + "author_name": "Zexin Hu", + "author_inst": "Fudan University" + }, + { + "author_name": "Yan Wang", + "author_inst": "Fudan University" + }, + { + "author_name": "Hengcong Liu", + "author_inst": "Fudan University" + }, + { + "author_name": "Marco Ajelli", + "author_inst": "Department of Epidemiology and Biostatistics, Indiana University School of Public Health" + }, + { + "author_name": "Hongjie Yu", + "author_inst": "Fudan University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.05.17.541173", "rel_title": "Structure and function of the SIT1 proline transporter in complex with the COVID-19 receptor ACE2", @@ -66001,37 +66693,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.05.13.540576", - "rel_title": "A peptide derived from the SARS-CoV-2 S2-protein heptad-repeat-2 inhibits pseudoviral fusion at micromolar concentrations: Role of palmitic acid conjugation", - "rel_date": "2023-05-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.13.540576", - "rel_abs": "SARS-CoV-2 S protein-mediated fusion is thought to involve the interaction of the membrane-distal, or N-terminal heptad repeat (NHR) (\"HR1\") of the cleaved S2 segment of the protein, and the membrane-proximal, or C-terminal heptad repeat (CHR) (\"HR2\") regions of the protein. Following the observations of Xia et al (Xia S, Liu M, Wang C, Xu W, Lan Q, Feng S, Qi F, Bao L, Du L, Liu S, Qin C, Sun F, Shi Z, Zhu Y, Jiang S, Lu L. Cell Res. 2020b Apr;30(4):343-355), we examined the fusion inhibitory activity of a PEGylated HR2-derived peptide and its palmitoylated derivative, using a pseudovirus infection assay. The latter peptide caused a 76% reduction in fusion activity at 10 M. Our results suggest that small variations in peptide derivatization and differences in the membrane composition of pseudovirus preparations may affect the inhibitory potency of HR2-derived peptides.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Nejat D\u00fczg\u00fcne\u015f", - "author_inst": "University of the Pacific School of Dentistry" - }, - { - "author_name": "Zhihua Tao", - "author_inst": "BPS Bioscience, 6405 Mira Mesa Blvd, Suite 100, San Diego CA 92121, USA" - }, - { - "author_name": "Yuxia Zhang", - "author_inst": "BPS Bioscience, 6405 Mira Mesa Blvd, Suite 100, San Diego CA 92121, USA" - }, - { - "author_name": "Krzysztof Krajewski", - "author_inst": "Department of Biochemistry and Biophysics, 3057 Genetic Medicine, CB# 7260 University of North Carolina School of Medicine, Chapel Hill, NC 27599-7260, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.05.14.540726", "rel_title": "Metformin an anti-diabetic drug, possess ACE-2 receptor-SARS- Cov-2 RBD binding antagonist activity, anti-inflammatory and cytokine inhibitory properties suitable for treatment of COVID-19", @@ -66425,6 +67086,85 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.05.10.540101", + "rel_title": "Metabolic alterations unravel the materno fetal immune responses with disease severity in pregnant women infected with SARS-CoV-2", + "rel_date": "2023-05-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.10.540101", + "rel_abs": "BackgroundPregnancy being immune compromised state, COVID-19 disease poses high risk of premature delivery and threat to fetus. Plasma metabolome regulates immune cellular responses and we aimed to analyze the plasma secretome, metabolome and immune cells in COVID-19 positive pregnant mother and cord blood.\n\nMethodsCOVID-19 RT-PCR positive pregnant females (n=112) asymptomatic (n=82), or with mild (n=21) or moderate (n=9) disease and control healthy pregnant (n=10) females were included. Mothers blood and cord blood (n=80) was analysed for untargeted metabolome profiling and plasma cytokines by high-resolution mass spectrometry (MS) and multiplex cytokine bead array. Immune scan in mothers was done using flow cytometry.\n\nResultsIn asymptomatic SARS-CoV-2 infection, --the amino acid metabolic pathways such as glycine, serine, L-lactate and threonine metabolism was upregulated, riboflavin and tyrosine metabolism, downregulated. In mild to moderate disease, the pyruvate and NAD+ metabolism (energy metabolic pathways) were mostly altered. In addition to raised TNF-, IFN-, IFN-{gamma}, IL-6 cytokine storm, IL-9 was increased in both mothers and neonates. Pyruvate and NAD+ metabolic pathways along with IL-9 and IFN-{gamma} had impact on non-classical monocytes, increased CD4 T cells and B cells but depleted CD8+ T cells. Cord blood mimicked the mothers metabolomic profiles by showing altered valine, leucine, isoleucine, glycine, serine, threonine in asymptomatic and NAD+ and riboflavin metabolism in mild and moderate disease subjects.\n\nConclusionsOur results demonstrate a graduated immune-metabolomic interplay in mother and fetus in pregnant females with different degrees of severity of COVID-19 disease. IL-9 and IFN- {gamma} regulated pyruvate, lactate TCA metabolism and riboflavin metabolism with context to disease severity are hall marks of this materno-fetal metabolome.\n\nHighlightsO_LISARS-CoV-2 infection alters energy consumption metabolic pathways during pregnancy.\nC_LIO_LIPregnant women with mild to moderate COVID-19 show increased energy demands, and consume stored glucose by upregulating pyruvate and NAD+ metabolism.\nC_LIO_LIIncreased TNF- and IL-9 in mild COVID-19 disease involve TCA cycle to produce lactate and consume stored glucose by up regulating pyruvate and nicotinamide and nicotinate metabolism.\nC_LIO_LIWith mild to moderate disease, raised IL-9 and TNF-, decreased riboflavin pathway, exhaustion of T and B cells cause pathogenesis.\nC_LIO_LICord blood mimics the metabolic profile of mothers peripheral blood, SARS- CoV-2 infection reshapes immune-metabolic profiles of mother-infant dyad.\nC_LI\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=141 HEIGHT=200 SRC=\"FIGDIR/small/540101v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (36K):\norg.highwire.dtl.DTLVardef@657cc3org.highwire.dtl.DTLVardef@e1e76forg.highwire.dtl.DTLVardef@12153f2org.highwire.dtl.DTLVardef@10e5332_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Sandhya Hora", + "author_inst": "Institute of Liver and Biliary Sciences, New Delhi, India" + }, + { + "author_name": "Prabhjyoti Pahwa", + "author_inst": "Institute of Liver and Biliary Sciences, New Delhi, India" + }, + { + "author_name": "Hamda Siddqui", + "author_inst": "Institute of Liver and Biliary Sciences, New Delhi, India" + }, + { + "author_name": "Anoushka Saxena", + "author_inst": "Institute of Liver and Biliary Sciences, New Delhi, India" + }, + { + "author_name": "Minal Kashyap", + "author_inst": "Lok Nayak Jai Prakash Hospital, New Delhi, India" + }, + { + "author_name": "Jayesh Kumar Sevak", + "author_inst": "Institute of Liver and Biliary Sciences, New Delhi, India" + }, + { + "author_name": "Ravinder Singh", + "author_inst": "Institute of Liver and Biliary Sciences, New Delhi, India" + }, + { + "author_name": "Maryam Javed", + "author_inst": "Institute of Liver and Biliary Sciences, New Delhi, India" + }, + { + "author_name": "Pushpa Yadav", + "author_inst": "Institute of Liver and Biliary Sciences, New Delhi, India" + }, + { + "author_name": "Pratibha Kale", + "author_inst": "Institute of Liver and Biliary Sciences, New Delhi" + }, + { + "author_name": "Gayatri Ramakrishna", + "author_inst": "Institute of Liver and Biliary Sciences, New Delhi" + }, + { + "author_name": "Asmita Rathore", + "author_inst": "Lok Nayak Jai Prakash Hospital, New Delhi, India" + }, + { + "author_name": "Jaswinder Singh Maras", + "author_inst": "Institute of Liver and Biliary Sciences, New Delhi, India" + }, + { + "author_name": "Shakun Tyagi", + "author_inst": "Lok Nayak Jai Prakash Hospital, New Delhi, India" + }, + { + "author_name": "Shiv Kumar Sarin", + "author_inst": "Institute of Liver and Biliary Sciences, New Delhi, India" + }, + { + "author_name": "Nirupama Trehanpati", + "author_inst": "Institute of Liver and Biliary Sciences, New Delhi, India" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.05.10.540228", "rel_title": "D614G and Omicron SARS-CoV-2 variant spike proteins differ in the effects of N-glycan modifications on spike expression, virus infectivity, and neutralization by some therapeutic antibodies", @@ -67575,49 +68315,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.05.09.23289735", - "rel_title": "The New Normal: Delayed Peak SARS-CoV-2 Viral Loads Relative to Symptom Onset and Implications for COVID-19 Testing Programs", - "rel_date": "2023-05-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.09.23289735", - "rel_abs": "BackgroundEarly in the COVID-19 pandemic, peak viral loads coincided with symptom onset. We hypothesized that in a highly immune population, symptom onset might occur earlier in infection, coinciding with lower viral loads.\n\nMethodsWe assessed SARS-CoV-2 and influenza A viral loads relative to symptom duration in recently-tested adults. Symptomatic participants [≥]16y presenting to testing sites in Georgia (4/2022-4/2023; Omicron variant predominant) provided symptom duration. Nasal swab samples were tested by the Xpert Xpress SARS-CoV-2/Flu/RSV assay and Ct values recorded. Nucleoprotein concentrations in SARS-CoV-2 PCR-positive samples were measured by Single Molecule Array. To estimate hypothetical antigen rapid diagnostic test (Ag RDT) sensitivity on each day after symptom onset, percentages of individuals with Ct value [≤]30 or [≤]25 were calculated.\n\nResultsOf 621 SARS-CoV-2 PCR-positive individuals (64.1% women, median 40.9y), 556/621 (89.5%) had a history of vaccination, natural infection, or both. By both Ct value and antigen concentration measurements, median viral loads rose from the day of symptom onset and peaked on the fourth day. Ag RDT sensitivity estimates were 35.7-71.4% on the first day, 63.9-78.7% on the third day, and 78.6-90.6% on the fourth day of symptoms.\n\nIn 74 influenza A PCR-positive individuals (55.4% women; median 35.0y), median influenza viral loads peaked on the second day of symptoms.\n\nConclusionsIn a highly immune adult population, median SARS-CoV-2 viral loads peaked on the fourth day of symptoms. Influenza A viral loads peaked soon after symptom onset. These findings have implications for ongoing use of Ag RDTs for COVID-19 and influenza.\n\nKey PointsIn a highly immune adult population, median SARS-CoV-2 viral loads by cycle threshold and antigen measurements peaked on the fourth day of symptoms, with implications for testing practice. In contrast, viral loads for influenza A peaked soon after symptom onset.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Jennifer Frediani", - "author_inst": "Emory University School of Nursing" - }, - { - "author_name": "Richard Parsons", - "author_inst": "Emory University School of Nursing" - }, - { - "author_name": "Kaleb Benjamin McLendon", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "Adrianna Westbrook", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "Wilbur A. Lam", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "Greg Martin", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "Nira R Pollock", - "author_inst": "Boston Children's Hospital" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.05.08.539897", "rel_title": "Evolving spike-protein N-glycosylation in SARS-CoV-2 variants", @@ -68199,6 +68896,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.05.08.23289659", + "rel_title": "Emergency department visits and boarding for pediatric patients with suicidality before and during the COVID-19 pandemic", + "rel_date": "2023-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.08.23289659", + "rel_abs": "ObjectiveTo quantify the increase in pediatric patients presenting to the emergency department with suicidality before and during the COVID-19 pandemic, and the subsequent impact on emergency department length of stay and boarding.\n\nMethodsThis retrospective cohort study from June 1, 2016, to October 31, 2022, identified patients presenting to the emergency department with suicidality using ICD-10 codes. Number of emergency department encounters for suicidality, demographic characteristics of patients with suicidality, and emergency department length of stay were compared before and during the COVID-19 pandemic. Unobserved components models were used to describe monthly counts of emergency department encounters for suicidality.\n\nResultsThere were 179,736 patient encounters to the emergency department during the study period, 6,168 (3.4%) for suicidality. There were, on average, more encounters for suicidality each month during the COVID-19 pandemic than before the COVID-19 pandemic. A time series unobserved components model demonstrated an initial drop in encounters for suicidality in April and May of 2020, followed by an increase starting in July 2020. The average length of stay for patients that boarded in the emergency department with a diagnosis of suicidality was 37.4 hours longer during the COVID-19 pandemic compared to before the COVID-19 pandemic.\n\nConclusionsThe number of encounters for suicidality among pediatric patients and the emergency department length of stay for psychiatry boarders has increased during the COVID-19 pandemic. There is a need for acute care mental health services and solutions to emergency department capacity issues.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Amy R Zipursky", + "author_inst": "Boston Children's Hospital" + }, + { + "author_name": "Karen L Olson", + "author_inst": "Boston Children's Hospital" + }, + { + "author_name": "Louisa Bode", + "author_inst": "Boston Children's Hospital" + }, + { + "author_name": "Alon Geva", + "author_inst": "Boston Children's Hospital" + }, + { + "author_name": "James Jones", + "author_inst": "Boston Children's Hospital" + }, + { + "author_name": "Kenneth D Mandl", + "author_inst": "Boston Children's Hospital" + }, + { + "author_name": "Andrew McMurry", + "author_inst": "Boston Children's Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2023.05.05.23289209", "rel_title": "Vaccine effectiveness of BNT162b2 mRNA Covid-19 Vaccine in Children below 5 Years in German Primary Care", @@ -69133,33 +69873,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2023.05.03.23289478", - "rel_title": "COVID-19 risk variant associations with chromatin remodelling, DNA maintenance and surfactant genes are infection dependent in the lung", - "rel_date": "2023-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.03.23289478", - "rel_abs": "During viral infection the structure of host chromatin is modified. It is generally assumed that these chromatin modifications will affect variant-gene mapping, and therefore gene expression. What is not clear is how limitations imposed by host germline risk affect the expression changes that occur with infection induced chromatin remodelling. Critically, this lack of information extends to how germline variants associated with severe SARS-CoV-2 impact on tissue-specific gene expression changes in response to infection-induced chromatin conformation changes. Here we combined temporal chromatin conformation data from SARS-CoV-2 stimulated cells with a lung spatial-eQTL gene expression analysis to contextualise the functional effects and contributions of germline risk on the severe phenotypes observed in SARS-CoV-2. We identify changes in lung-specific SARS-CoV-2 risk variant-gene mapping across the infection time course. Our results provide evidence for infection-induced chromatin remodelling that impacts the regulation of genes associated with the severity of SARS-CoV-2 infection. The gene targets we identified are functionally involved in host chromatin modifications and maintenance and the expression of these genes is amplified by SARS-CoV-2-induced epigenetic remodelling. The effect of this remodelling includes transcriptional changes to gene targets such as SMARCA4, NCOR1, DNMT1, DNMT3a, DAXX, and PIAS4, all critical components of epigenetic control mechanisms and SARS-CoV-2 antiviral activity, along with several genes involved in surfactant metabolism. We show how severe-phenotype-associated eQTLs form and break in an infection time-course-dependent manner that mimics positive feedback loops connecting germline variation with the process of viral infection and replication. Our results provide a novel bridge between existing COVID-19 epigenetic research and demonstrate the critical role of epigenomics in understanding SARS-CoV-2-risk-associated gene regulation in the lung.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Rachel K Jaros", - "author_inst": "University of Auckland" - }, - { - "author_name": "Evgeniia Golovina", - "author_inst": "University of Auckland, Liggins Institute" - }, - { - "author_name": "Justin M O'Sullivan", - "author_inst": "The University of Auckland" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2023.05.03.23289435", "rel_title": "Improved access to diabetic retinopathy screening through primary care-based teleophthalmology during the COVID-19 pandemic", @@ -69945,6 +70658,221 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.04.27.23289234", + "rel_title": "Researching COVID to enhance recovery (RECOVER) autopsy study protocol: Rationale, objectives, and design", + "rel_date": "2023-05-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.27.23289234", + "rel_abs": "ImportanceSARS-CoV-2 infection can result in ongoing, relapsing, or new symptoms or organ dysfunction after the acute phase of infection, termed Post-Acute Sequelae of SARS-CoV-2 (PASC), or long COVID. The characteristics, prevalence, trajectory and mechanisms of PASC are poorly understood. The objectives of the Researching COVID to Enhance Recovery (RECOVER) Tissue Pathology Study (RECOVER-Pathology) are to: (1) characterize prevalence and types of organ injury/disease and pathology occurring with PASC; (2) characterize the association of pathologic findings with clinical and other characteristics; (3) define the pathophysiology and mechanisms of PASC, and possible mediation via viral persistence; and (4) establish a post-mortem tissue biobank and post-mortem brain imaging biorepository.\n\nMethodsRECOVER-Pathology is a cross-sectional study of decedents dying at least 15 days following initial SARS-CoV-2 infection. Eligible decedents must meet WHO criteria for suspected, probable, or confirmed infection and must be aged 18 years or more at the time of death. Enrollment occurs at 7 sites in four U.S. states and Washington, DC. Comprehensive autopsies are conducted according to a standardized protocol within 24 hours of death; tissue samples are sent to the PASC Biorepository for later analyses. Data on clinical history are collected from the medical records and/or next of kin. The primary study outcomes include an array of pathologic features organized by organ system. Casual inference methods will be employed to investigate associations between risk factors and pathologic outcomes.\n\nDiscussionRECOVER-Pathology is the largest autopsy study addressing PASC among US adults. Results of this study are intended to elucidate mechanisms of organ injury and disease and enhance our understanding of the pathophysiology of PASC.\n\nClinicaltrials.gov number: NCT05292274", + "rel_num_authors": 50, + "rel_authors": [ + { + "author_name": "Andrea B. Troxel", + "author_inst": "NYU Grossman School of Medicine: New York University School of Medicine" + }, + { + "author_name": "Marie-Abele C. Bind", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Thomas J. Flotte", + "author_inst": "Mayo Clinic Rochester" + }, + { + "author_name": "Carlos Cordon-Cardo", + "author_inst": "Mount Sinai Health System" + }, + { + "author_name": "Lauren A. Decker", + "author_inst": "University of New Mexico Health Sciences Center" + }, + { + "author_name": "Aloke V. Finn", + "author_inst": "CVPath Institute Inc" + }, + { + "author_name": "Robert F. Padera", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "R. Ross Reichard", + "author_inst": "Mayo Clinic Rochester" + }, + { + "author_name": "James R. Stone", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Natalie L. Adolphi", + "author_inst": "University of New Mexico School of Medicine" + }, + { + "author_name": "Faye Victoria C. Casimero", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "John F. Crary", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jamie Elifritz", + "author_inst": "University of New Mexico - Albuquerque: The University of New Mexico" + }, + { + "author_name": "Arline Faustin", + "author_inst": "New York University Grossman School of Medicine" + }, + { + "author_name": "Saikat Kumar B. Ghosh", + "author_inst": "CVPath Institute Inc" + }, + { + "author_name": "Amanda Krausert", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Maria Martinez-Lage", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Jonathan Melamed", + "author_inst": "NYU Langone Hospital - Long Island" + }, + { + "author_name": "Roger A. Mitchell Jr.", + "author_inst": "Howard University College of Medicine" + }, + { + "author_name": "Barbara A. Sampson", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Alan C. Seifert", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Aylin Simsir", + "author_inst": "New York University Grossman School of Medicine" + }, + { + "author_name": "Cheryle Adams", + "author_inst": "Howard University College of Medicine" + }, + { + "author_name": "Stephanie Haasnoot", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Stephanie Hafner", + "author_inst": "Mayo Clinic Rochester" + }, + { + "author_name": "Michelle A. Siciliano", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Brittany Vallejos", + "author_inst": "University of New Mexico - Albuquerque: The University of New Mexico" + }, + { + "author_name": "Phoebe Del Boccio", + "author_inst": "New York University Grossman School of Medicine" + }, + { + "author_name": "Michelle F. Lamendola-Essel", + "author_inst": "New York University Grossman School of Medicine" + }, + { + "author_name": "Chloe E. Young", + "author_inst": "New York University Grossman School of Medicine" + }, + { + "author_name": "Deepshikha Kewlani", + "author_inst": "New York University Grossman School of Medicine" + }, + { + "author_name": "Precious A. Akinbo", + "author_inst": "New York University Grossman School of Medicine" + }, + { + "author_name": "Brendan Parent", + "author_inst": "New York University Grossman School of Medicine" + }, + { + "author_name": "Alicia Chung", + "author_inst": "New York University Grossman School of Medicine" + }, + { + "author_name": "Teresa C. Cato", + "author_inst": "New York University Grossman School of Medicine" + }, + { + "author_name": "Praveen C. Mudumbi", + "author_inst": "New York University Grossman School of Medicine" + }, + { + "author_name": "Shari Esquenazi-Karonika", + "author_inst": "New York University Grossman School of Medicine" + }, + { + "author_name": "Marion J. Wood", + "author_inst": "New York University Grossman School of Medicine" + }, + { + "author_name": "James Chan", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Jonathan Monteiro", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Daniel J. Shinnick", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Tanayott Thaweethai", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Amber N. Nguyen", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Megan L. Fitzgerald", + "author_inst": "Patient-Led Research Collaborative" + }, + { + "author_name": "Alice A. Perlowski", + "author_inst": "Blooming Magnolia" + }, + { + "author_name": "Lauren E. Stiles", + "author_inst": "Stony Brook University Renaissance School of Medicine" + }, + { + "author_name": "Moira L. Paskett", + "author_inst": "NYU Langone Hospital - Long Island" + }, + { + "author_name": "Stuart D. Katz", + "author_inst": "New York University Grossman School of Medicine" + }, + { + "author_name": "Andrea S. Foulkes", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "- RECOVER Initiative", + "author_inst": "-" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "pathology" + }, { "rel_doi": "10.1101/2023.05.03.23289084", "rel_title": "Effect of Nirmatrelvir/Ritonavir (Paxlovid) on Hospitalization among Adults with COVID-19: an EHR-based Target Trial Emulation from N3C", @@ -71559,61 +72487,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.04.28.23289261", - "rel_title": "Mediators of monocyte chemotaxis and matrix remodeling are associated with the development of fibrosis in patients with COVID-19", - "rel_date": "2023-05-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.28.23289261", - "rel_abs": "Acute respiratory distress syndrome (ARDS) has a fibroproliferative phase that may be followed by pulmonary fibrosis. This has been described in patients with COVID-19 pneumonia, but the underlying mechanisms have not been completely defined. We hypothesized that protein mediators of tissue remodeling and monocyte chemotaxis are elevated in the plasma and endotracheal aspirates of critically ill patients with COVID-19 who subsequently develop radiographic fibrosis.\n\nWe enrolled COVID-19 patients admitted to the ICU who had hypoxemic respiratory failure, were hospitalized and alive for at least 10 days, and had chest imaging done during hospitalization (n = 119). Plasma was collected within 24h of ICU admission and at 7d. In mechanically ventilated patients, endotracheal aspirates (ETA) were collected at 24h and 48-96h. Protein concentrations were measured by immunoassay. We tested for associations between protein concentrations and radiographic evidence of fibrosis using logistic regression adjusting for age, sex, and APACHE score.\n\nWe identified 39 patients (33%) with features of fibrosis. Within 24h of ICU admission, plasma proteins related to tissue remodeling (MMP-9, Amphiregulin) and monocyte chemotaxis (CCL-2/MCP-1, CCL-13/MCP-4) were associated with the subsequent development of fibrosis whereas markers of inflammation (IL-6, TNF-) were not. After 1 week, plasma MMP-9 increased in patients without fibrosis. In ETAs, only CCL-2/MCP-1 was associated with fibrosis at the later timepoint.\n\nThis cohort study identifies proteins of tissue remodeling and monocyte recruitment that may identify early fibrotic remodeling following COVID-19. Measuring changes in these proteins over time may allow for early detection of fibrosis in patients with COVID-19.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Sarah E Holton", - "author_inst": "University of Washington" - }, - { - "author_name": "Mallorie Mitchem", - "author_inst": "Benaroya Research Institute at Virginia Mason" - }, - { - "author_name": "Sudhakar Pipavath", - "author_inst": "University of Washington Department of Radiology" - }, - { - "author_name": "Eric D. Morrell", - "author_inst": "University of Washington School of Medicine" - }, - { - "author_name": "Pavan K. Bhatraju", - "author_inst": "University of Washington School of Medicine" - }, - { - "author_name": "Jessica A. Hamerman", - "author_inst": "Benaroya Research Institute at Virginia Mason" - }, - { - "author_name": "Cate Speake", - "author_inst": "Benaroya Research Institute at Virginia Mason" - }, - { - "author_name": "Uma Malhotra", - "author_inst": "Virginia Mason Franciscan Health" - }, - { - "author_name": "Mark M. Wurfel", - "author_inst": "University of Washington School of Medicine" - }, - { - "author_name": "Carmen Mikacenic", - "author_inst": "Benaroya Research Institute at Virginia Mason" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2023.04.27.23289205", "rel_title": "Characterization and Resistance to Mutation of a Single-Channel Multiplex PCR Assay for SARS-CoV-2", @@ -72351,6 +73224,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.04.27.23289109", + "rel_title": "Why are different estimates of the effective reproductive number so different? A case study on COVID-19 in Germany", + "rel_date": "2023-04-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.27.23289109", + "rel_abs": "The effective reproductive number Rt has taken a central role in the scientific, political, and public discussion during the COVID-19 pandemic, with numerous real-time estimates of this quantity routinely published. Disagreement between estimates can be substantial and may lead to confusion among decision-makers and the general public. In this work, we compare different estimates of the national-level effective reproductive number of COVID-19 in Germany in 2020 and 2021. We consider the agreement between estimates from the same method but published at different time points (within-method agreement) as well as retrospective agreement across different approaches (between-method agreement). Concerning the former, estimates from some methods are very stable over time and hardly subject to revisions, while others display considerable fluctuations. To evaluate between-method agreement, we reproduce the estimates generated by different groups using a variety of statistical approaches, standardizing analytical choices to assess how they contribute to the observed disagreement. These analytical choices include the data source, data pre-processing, assumed generation time distribution, statistical tuning parameters, and various delay distributions. We find that in practice, these auxiliary choices in the estimation of Rt may affect results at least as strongly as the selection of the statistical approach. They should thus be communicated transparently along with the estimates.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Elisabeth Brockhaus", + "author_inst": "Karlsruhe Institute of Technology" + }, + { + "author_name": "Daniel Wolffram", + "author_inst": "Karlsruhe Institute of Technology" + }, + { + "author_name": "Tanja Stadler", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Michael Osthege", + "author_inst": "Forschungszentrum Juelich, RWTH Aachen University" + }, + { + "author_name": "Tanmay Mitra", + "author_inst": "Helmholtz Centre for Infection Research, Braunschweig" + }, + { + "author_name": "Jonas M. Littek", + "author_inst": "Karlsruhe Institute of Technology" + }, + { + "author_name": "Anna J. Klesen", + "author_inst": "Karlsruhe Institute of Technology" + }, + { + "author_name": "Ekaterina Krymova", + "author_inst": "ETH Zurich and EPFL Lausanne" + }, + { + "author_name": "Jana S. Huisman", + "author_inst": "ETH Zurich and Massachusetts Institute of Technology" + }, + { + "author_name": "Stefan Heyder", + "author_inst": "Technische Universitaet Ilmenau" + }, + { + "author_name": "Laura M. Helleckes", + "author_inst": "Forschungszentrum Juelich and RWTH Aachen University" + }, + { + "author_name": "Matthias an der Heiden", + "author_inst": "Robert Koch Institute, Berlin" + }, + { + "author_name": "Sebastian Funk", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Sam Abbott", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Johannes Bracher", + "author_inst": "Karlsruhe Institute of Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.04.27.23289229", "rel_title": "State and County-Level Factors Associated with the Effectiveness of Stay-At-Home Orders Issued in the United States in Response to COVID-19", @@ -73549,41 +74497,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.04.24.23288115", - "rel_title": "Anxiety due to Long COVID is partially driven by activation of the tryptophan catabolite (TRYCAT) pathway", - "rel_date": "2023-04-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.24.23288115", - "rel_abs": "This study examines whether activation of the tryptophan catabolite (TRYCAT) pathway is associated with anxiety symptoms due to Long COVID. We selected 90 participants, 60 Long COVID patients and 30 individuals without any symptoms following acute CIVID-19 infection. Using cluster analysis and the Hamilton Anxiety Rating scale (HAMA) score, the pure HAMA anxiety score, serum tryptophan (TRP) and kynurenine (KYN), the KYN/TRP ratio (all measured during Long COVID), and oxygen saturation (SpO2) (measured during the acute phase of COVID-19), we were able to classify Long COVID patients into two distinct clusters with an adequate silhouette cohesion and separation index (0.58): cluster 1 (n=61) and cluster 2 (n=29). Cluster 2 patients had lower SpO2 and TRP levels, as well as higher KYN, KYN/TRP ratio, and HAMA scores than cluster 1. Regression analysis revealed that the KYN/TRP ratio explained 14.4% of the variance in the HAMA score (F=14.81, df=1/88, p=0.001). In addition, regression analysis revealed that SpO2 partially explained the variance in serum TRP (r=0.396, p=0.005), KYN/TRP ratio (r=-0.248, p=0.018), and the HAMA score (r=-0.279, p=0.008). The current data imply that decreased SpO2 during the acute phase of COVID-19 infection is predictive of anxiety caused by Long COVID. Our data reveal that around 32% of Long COVID patients have elevated IDO activity in association with elevated anxiety.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Hussein Al-Hakeim", - "author_inst": "Universit of Kufa" - }, - { - "author_name": "Anwar Khairi Abed", - "author_inst": "university of kufa" - }, - { - "author_name": "Abbas F. Almulla", - "author_inst": "Chulalongkorn university" - }, - { - "author_name": "Shatha Rouf Moustafa", - "author_inst": "Hawler Medical University" - }, - { - "author_name": "Michael F. Maes", - "author_inst": "Chulalongkorn University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2023.04.20.23288904", "rel_title": "Aerosol Jet Printing Enabled Dual-Function Electrochemical and Colorimetric Biosensor for SARS-CoV-2 Detection", @@ -74157,6 +75070,173 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2023.04.13.23288227", + "rel_title": "Human SARS-CoV-2 challenge resolves local and systemic response dynamics", + "rel_date": "2023-04-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.13.23288227", + "rel_abs": "The COVID-19 pandemic is an ongoing global health threat, yet our understanding of the cellular disease dynamics remains limited. In our unique COVID-19 human challenge study we used single cell genomics of nasopharyngeal swabs and blood to temporally resolve abortive, transient and sustained infections in 16 seronegative individuals challenged with preAlpha-SARS-CoV-2. Our analyses revealed rapid changes in cell type proportions and dozens of highly dynamic cellular response states in epithelial and immune cells associated with specific timepoints or infection status. We observed that the interferon response in blood precedes the nasopharynx, and that nasopharyngeal immune infiltration occurred early in transient but later in sustained infection, and thus correlated with preventing sustained infection. Ciliated cells showed an acute response phase, upregulated MHC class II while infected, and were most permissive for viral replication, whilst nasal T cells and macrophages were infected non-productively. We resolve 54 T cell states, including acutely activated T cells that clonally expanded while carrying convergent SARS-CoV-2 motifs. Our novel computational pipeline (Cell2TCR) identifies activated antigen-responding clonotype groups and motifs in any dataset. Together, we show that our detailed time series data (covid19cellatlas.org) can serve as a \"Rosetta stone\" for the epithelial and immune cell responses, and reveals early dynamic responses associated with protection from infection.", + "rel_num_authors": 38, + "rel_authors": [ + { + "author_name": "Rik G H Lindeboom", + "author_inst": "Wellcome Sanger Institute, Cambridge, CB10 1SA, UK; The Netherlands Cancer Institute, Amsterdam, the Netherlands" + }, + { + "author_name": "Kaylee B Worlock", + "author_inst": "UCL Respiratory, Division of Medicine, University College London, London, WC1E 6JF UK" + }, + { + "author_name": "Lisa M Dratva", + "author_inst": "Wellcome Sanger Institute, Cambridge, CB10 1SA, UK" + }, + { + "author_name": "Masahiro Yoshida", + "author_inst": "UCL Respiratory, Division of Medicine, University College London, London, WC1E 6JF UK" + }, + { + "author_name": "David Scobie", + "author_inst": "Division of Infection and Immunity, University College London, London WC1E 6BT" + }, + { + "author_name": "Helen R Wagstaffe", + "author_inst": "Department of Infectious Disease, Imperial College London, London" + }, + { + "author_name": "Laura Richardson", + "author_inst": "Wellcome Sanger Institute, Cambridge, CB10 1SA, UK" + }, + { + "author_name": "Anna L Wilbrey-Clark", + "author_inst": "Wellcome Sanger Institute, Cambridge, CB10 1SA, UK" + }, + { + "author_name": "Josephine L Barnes", + "author_inst": "UCL Respiratory, Division of Medicine, University College London, London, WC1E 6JF UK" + }, + { + "author_name": "Krzysztof Polanski", + "author_inst": "Wellcome Sanger Institute, Cambridge, CB10 1SA, UK" + }, + { + "author_name": "Jessica Allen-Hyttinen", + "author_inst": "UCL Respiratory, Division of Medicine, University College London, London, WC1E 6JF UK" + }, + { + "author_name": "Puja Mehta", + "author_inst": "UCL Respiratory, Division of Medicine, University College London, London, WC1E 6JF UK" + }, + { + "author_name": "Dinithi Sumanaweera", + "author_inst": "Wellcome Sanger Institute, Cambridge, CB10 1SA, UK" + }, + { + "author_name": "Jacqueline M Boccacino", + "author_inst": "Wellcome Sanger Institute, Cambridge, CB10 1SA, UK" + }, + { + "author_name": "Waradon Sungnak", + "author_inst": "Wellcome Sanger Institute, Cambridge, CB10 1SA, UK; Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; Integrative Com" + }, + { + "author_name": "Ni Huang", + "author_inst": "Wellcome Sanger Institute, Cambridge, CB10 1SA, UK" + }, + { + "author_name": "Lira Mamanova", + "author_inst": "Wellcome Sanger Institute, Cambridge, CB10 1SA, UK" + }, + { + "author_name": "Rakeshlal Kapuge", + "author_inst": "Wellcome Sanger Institute, Cambridge, CB10 1SA, UK" + }, + { + "author_name": "Liam Bolt", + "author_inst": "Wellcome Sanger Institute, Cambridge, CB10 1SA, UK" + }, + { + "author_name": "Elena Prigmore", + "author_inst": "Wellcome Sanger Institute, Cambridge, CB10 1SA, UK" + }, + { + "author_name": "Ben Killingley", + "author_inst": "Department of Infectious Diseases, University College London Hospital, London, UK" + }, + { + "author_name": "Mariya Kalinova", + "author_inst": "hVIVO, London, UK" + }, + { + "author_name": "Maria Mayer", + "author_inst": "hVIVO, London, UK" + }, + { + "author_name": "Alison Boyers", + "author_inst": "hVIVO, London, UK" + }, + { + "author_name": "Alex Mann", + "author_inst": "hVIVO, London, UK" + }, + { + "author_name": "Vitor H Teixeira", + "author_inst": "UCL Respiratory, Division of Medicine, University College London, London, WC1E 6JF UK" + }, + { + "author_name": "Sam M Janes", + "author_inst": "UCL Respiratory, Division of Medicine, University College London, London, WC1E 6JF UK" + }, + { + "author_name": "Rachel C Chambers", + "author_inst": "UCL Respiratory, Division of Medicine, University College London, London, WC1E 6JF UK" + }, + { + "author_name": "Muzlifah Haniffa", + "author_inst": "Wellcome Sanger Institute, Cambridge, CB10 1SA, UK" + }, + { + "author_name": "Andrew Catchpole", + "author_inst": "hVIVO, London, UK" + }, + { + "author_name": "Robert S Heyderman", + "author_inst": "Division of Infection and Immunity, University College London, London WC1E 6BT" + }, + { + "author_name": "Mahdad Noursadeghi", + "author_inst": "Division of Infection and Immunity, University College London, London WC1E 6BT" + }, + { + "author_name": "Benny Chain", + "author_inst": "Division of Infection and Immunity, University College London, London WC1E 6BT" + }, + { + "author_name": "Andreas Mayer", + "author_inst": "Division of Infection and Immunity, University College London, London WC1E 6BT" + }, + { + "author_name": "Kerstin B Meyer", + "author_inst": "Wellcome Sanger Institute, Cambridge, CB10 1SA, UK" + }, + { + "author_name": "Christopher Chiu", + "author_inst": "Department of Infectious Disease, Imperial College London, London" + }, + { + "author_name": "Marko Z Nikoli\u0107", + "author_inst": "UCL Respiratory, Division of Medicine, University College London, London, WC1E 6JF UK" + }, + { + "author_name": "Sarah A Teichmann", + "author_inst": "Wellcome Sanger Institute, Cambridge, CB10 1SA, UK" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.04.22.537917", "rel_title": "SARS-CoV-2 Nonstructural Proteins 3 and 4 tune the Unfolded Protein Response", @@ -75423,149 +76503,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.04.18.23288720", - "rel_title": "COVID-19 illness severity and 2-year prevalence of physical symptoms: an observational study in Iceland, Sweden, Norway and Denmark", - "rel_date": "2023-04-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.18.23288720", - "rel_abs": "BackgroundPersistence of physical symptoms after SARS-CoV-2 infection is a major public health concern, although evidence from large observational studies remain scarce. We aimed to assess the prevalence of physical symptoms in relation to acute illness severity up to more than 2-years after diagnosis of COVID-19.\n\nMethodsThis multinational study included 64 880 adult participants from Iceland, Sweden, Denmark, and Norway with self-reported data on COVID-19 and physical symptoms from April 2020 to August 2022. We compared the prevalence of 15 physical symptoms, measured by the Patient Health Questionnaire (PHQ-15), among individuals with or without a confirmed COVID-19 diagnosis, by acute illness severity, and by time since diagnosis. We additionally assessed the change in symptoms in a subset of Swedish adults with repeated measures, before and after COVID-19 diagnosis.\n\nFindingsDuring up to 27 months of follow-up, 22 382 participants (34.5%) were diagnosed with COVID-19. Individuals who were diagnosed with COVID-19, compared to those not diagnosed, had an overall 37% higher prevalence of severe physical symptom burden (PHQ-15 score [≥] 15, adjusted prevalence ratio [PR] 1.37 [95% confidence interval [CI] 1.23-1.52]). The prevalence was associated with acute COVID-19 severity: individuals bedridden for seven days or longer presented with the highest prevalence (PR 2.25[1.85-2.74]), while individuals never bedridden presented with similar prevalence as individuals not diagnosed with COVID-19 (PR 0.92 [0.68-1.24]). The prevalence was statistically significantly elevated among individuals diagnosed with COVID-19 for eight of the fifteen measured symptoms: shortness of breath, chest pain, dizziness, heart racing, headaches, low energy/fatigue, trouble sleeping, and back pain. The analysis of repeated measurements rendered similar results as the main analysis.\n\nInterpretationThese data suggest an elevated prevalence of some, but not all, physical symptoms during up to more than 2 years after diagnosis of COVID-19, particularly among individuals suffering a severe acute illness.\n\nFundingThis work was mainly supported by grants from NordForsk (COVIDMENT, grant number 105668 and 138929) and Horizon2020 (CoMorMent, 847776). See Acknowledgements for further details on funding.\n\nResearch in contextO_ST_ABSEvidence before the studyC_ST_ABSAs the majority of the global population has contracted COVID-19, persistence of physical symptoms after SARS-CoV-2 infection (Long COVID or post COVID-19 condition) has become a major public health concern. We searched PubMed for studies assessing physical symptoms after COVID-19, published by March 22, 2023. The search term was (physical symptoms after covid) AND LitCLONGCOVID [Pubmed filter]. We reviewed 82 studies, after excluding those not on humans or not published in English. High prevalence of multiple physical symptoms, mainly fatigue, shortness of breath, headache, muscle and chest pain, has been reported, mostly based on small samples of hospitalized patients confined to three to six months after diagnosis. A comprehensive assessment of long-term prevalence of physical symptoms beyond six months after diagnosis and among non-hospitalized patients is lacking.\n\nAdded value of this studyWe included 64 880 participants from the general population of four Nordic countries, of whom 22 382 had been diagnosed with COVID-19 up to 2 years earlier (<1% hospitalized due to COVID-19). Individuals diagnosed with COVID-19 reported a 37% higher prevalence of overall severe physical symptom burden compared to individuals not diagnosed with COVID-19. We found that shortness of breath, chest pain, dizziness, headaches, and low energy/fatigue were particularly increased among individuals with COVID-19 diagnosis. Individuals bedridden for seven days or more during the acute illness phase (9.6% of the patients) showed the greatest and most persistent elevation in prevalence of severe physical symptoms while individuals not bedridden during the acute COVID-19 illness showed no increase in prevalence of physical symptoms compared to those not diagnosed.\n\nImplications of the available evidenceOur findings provide timely and valuable evidence to demonstrate the constitution of Long COVID and the long-term health consequences after recovery from COVID-19 in the general population. The long-term risk of severe physical symptom burden is distinctly associated with acute illness severity, highlighting the importance of sustained monitoring of physical symptoms among the group of patients who suffered severe acute illness course.", - "rel_num_authors": 32, - "rel_authors": [ - { - "author_name": "Qing Shen", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Emily E. Joyce", - "author_inst": "karolinska institutet" - }, - { - "author_name": "Omid V. Ebrahimi", - "author_inst": "University of Oslo" - }, - { - "author_name": "Maria Didriksen", - "author_inst": "Copenhagen University Hospital, Rigshospitalet" - }, - { - "author_name": "Aniko Lovik", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Karen Sol Savarsdottir", - "author_inst": "University of Iceland" - }, - { - "author_name": "Ingibjorg Magnusdottir", - "author_inst": "University of Iceland" - }, - { - "author_name": "Dorte Helenius Mikkelsen", - "author_inst": "Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Copenhagen, Denmark; The Lundbeck Foundation Initiative for Integrat" - }, - { - "author_name": "Anna Bara Unnarsdottir", - "author_inst": "University of Iceland" - }, - { - "author_name": "Arna Hauksdottir", - "author_inst": "University of Iceland" - }, - { - "author_name": "Asle Hoffart", - "author_inst": "Modum Bad Research Institute" - }, - { - "author_name": "Anna Kahler", - "author_inst": "Karolinska Insitutet" - }, - { - "author_name": "Edda Bjork Thordardottir", - "author_inst": "University of Iceland" - }, - { - "author_name": "Elias Eythorsson", - "author_inst": "Landspitali National University Hospital of Iceland" - }, - { - "author_name": "Emma M. Frans", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Gunnar Tomasson", - "author_inst": "University of Iceland" - }, - { - "author_name": "Helga Ask", - "author_inst": "University of Oslo" - }, - { - "author_name": "Hronn Hardardottir", - "author_inst": "Landspitali National University Hospital of Iceland" - }, - { - "author_name": "Johanna Jakobsdottir", - "author_inst": "University of Iceland" - }, - { - "author_name": "Kelli Lehto", - "author_inst": "University of Tartu" - }, - { - "author_name": "Li Lu", - "author_inst": "University of Oslo" - }, - { - "author_name": "Ole Andreassen", - "author_inst": "Oslo University Hospital and University of Oslo" - }, - { - "author_name": "Patrick Sullivan", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Runolfur Palsson", - "author_inst": "Landspitali-The National University Hospital" - }, - { - "author_name": "Christian Erikstrup", - "author_inst": "Aarhus University Hospital" - }, - { - "author_name": "Sisse Rye Ostrowski", - "author_inst": "Copenhagen University Hospital" - }, - { - "author_name": "Thomas Werge", - "author_inst": "Mental Health Services Capital Region of Denmark" - }, - { - "author_name": "Thor Aspelund", - "author_inst": "University of Iceland" - }, - { - "author_name": "Ole B. V. Pedersen", - "author_inst": "University of Copenhagen" - }, - { - "author_name": "Sverre Urnes Johnson", - "author_inst": "University of Oslo" - }, - { - "author_name": "Fang Fang", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Unnur Valdimarsdottir", - "author_inst": "University of Iceland" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.04.17.23288710", "rel_title": "COVID-19 testing avoidance among patients with cardiovascular disease", @@ -76419,6 +77356,57 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.04.18.537373", + "rel_title": "An ex vivo human precision-cut lung slice platform provides insight into SARS-CoV-2 pathogenesis and antiviral drug efficacy", + "rel_date": "2023-04-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.04.18.537373", + "rel_abs": "COVID-19 has claimed millions of lives since the emergence of SARS-CoV-2, and lung disease appears the primary cause of the death in COVID-19 patients. However, the underlying mechanisms of COVID-19 pathogenesis remain elusive, and there is no existing model where the human disease can be faithfully recapitulated and conditions for the infection process can be experimentally controlled. Herein we report the establishment of an ex vivo human precision-cut lung slice (hPCLS) platform for studying SARS-CoV-2 pathogenicity and innate immune responses, and for evaluating the efficacy of antiviral drugs against SARS-CoV-2. We show that while SARS-CoV-2 continued to replicate during the course of infection of hPCLS, infectious virus production peaked within 2 days, and rapidly declined thereafter. Although most proinflammatory cytokines examined were induced by SARS-CoV-2 infection, the degree of induction and types of cytokines varied significantly among hPCLS from individual donors, reflecting the heterogeneity of human populations. In particular, two cytokines (IP-10 and IL-8) were highly and consistently induced, suggesting a role in the pathogenesis of COVID-19. Histopathological examination revealed focal cytopathic effects late in the infection. Transcriptomic and proteomic analyses identified molecular signatures and cellular pathways that are largely consistent with the progression of COVID-19 in patients. Furthermore, we show that homoharringtonine, a natural plant alkaloid derived from Cephalotoxus fortunei, not only inhibited virus replication but also production of pro-inflammatory cytokines, and ameliorated the histopathological changes of the lungs caused by SARS-CoV-2 infection, demonstrating the usefulness of the hPCLS platform for evaluating antiviral drugs.\n\nSIGNIFICANCEHere we established an ex vivo human precision-cut lung slice platform for assessing SARS-CoV-2 infection, viral replication kinetics, innate immune response, disease progression, and antiviral drugs. Using this platform, we identified early induction of specific cytokines, especially IP-10 and IL-8, as potential predictors for severe COVID-19, and uncovered a hitherto unrecognized phenomenon that while infectious virus disappears at late times of infection, viral RNA persists and lung histopathology commences. This finding may have important clinical implications for both acute and post-acute sequelae of COVID-19. This platform recapitulates some of the characteristics of lung disease observed in severe COVID-19 patients and is therefore a useful platform for understanding mechanisms of SARS-CoV-2 pathogenesis and for evaluating the efficacy of antiviral drugs.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Xuming Zhang", + "author_inst": "University of Arkansas for Medical Sciences" + }, + { + "author_name": "Roger D Pechous", + "author_inst": "University of Arkansas for Medical Sciences" + }, + { + "author_name": "Priyangi A. Malaviarachchi", + "author_inst": "University of Arkansas for Medical Sciences" + }, + { + "author_name": "Srijon K Banerjee", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Stephanie Byrum", + "author_inst": "University of Arkansas for Medical Sciences" + }, + { + "author_name": "Duah Alkam", + "author_inst": "University of Arkansas for Medical Sciences" + }, + { + "author_name": "Alireza Ghaffarieh", + "author_inst": "University of Arkansas for Medical Sciences" + }, + { + "author_name": "Richard C Kurten", + "author_inst": "University of Arkansas for Medical Sciences" + }, + { + "author_name": "Joshua L. Kennedy", + "author_inst": "University of Arkansas for Medical Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.04.17.23288637", "rel_title": "Post-COVID-19 syndrome and insulin resistance 20 months after a mild COVID-19", @@ -77529,57 +78517,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.04.15.23288553", - "rel_title": "Effect of nasal carriage of Bacillus species on COVID-19 severity: A cross-sectional study", - "rel_date": "2023-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.15.23288553", - "rel_abs": "Intranasal sprays containing Bacillus species are being researched for treating viral respiratory tract infections. The aim of this study was to assess the relationship between the nasal carriage of Bacillus and COVID-19 severity. This was a cross-sectional study that collected nasopharyngeal samples from adults 18 years and above visiting two COVID-19 testing centers in Lagos, Nigeria between September 2020 and September 2021. Bacillus species were cultured from the respiratory samples and confirmed using molecular methods. The dependent variable was COVID-19 status classified as negative, asymptomatic, mild, or severe. The independent variable was the nasal carriage of Bacillus species. Multinomial regression analysis was done to determine the association between nasal carriage of Bacillus and COVID-19 severity after adjusting for age, sex, and co-morbidity status. About 388 participants were included in the study with a mean (standard deviation) age of 40.05 (13.563) years. The majority (61.1%) of the participants were male, 100 (25.8%) had severe COVID-19, 130 (33.5%) had pre-existing comorbidity, and 76 (19.6%) had Bacillus cultured from their nasopharyngeal specimen. Bacillus species presence was significantly associated with higher odds of severe COVID-19 compared to having a negative COVID-19 status. However, the presence of Bacillus species was significantly associated with lower odds of severe COVID-19 compared to having a mild COVID-19 status. The study suggests that nasal carriage of Bacillus species may substantially impact the clinical course of COVID-19. This study supports the exploration of Bacillus species in the prevention and management of viral respiratory tract infections.\n\nIMPORTANCEWith the introduction of intranasal spray containing Bacillus species for the treatment of viral respiratory tract infections, such as COVID-19 and respiratory syncytial virus, identifying the association between the nasal carriage of Bacillus species and COVID-19 susceptibility and severity will help further substantiate the investigation of these bacteria for COVID-19 prevention and treatment. This study evaluated the association between the carriage of Bacillus species in the nasopharyngeal tract and COVID-19 severity and found that the presence of Bacillus species in the nasopharynx may significantly impact the clinical course of COVID-19.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Muinah Adenike Fowora", - "author_inst": "Nigerian Institute of Medical Research" - }, - { - "author_name": "Adenike Aiyedogbon", - "author_inst": "Nigerian Institute of Medical Research" - }, - { - "author_name": "Ibilola Omolopo", - "author_inst": "Nigerian Institute of Medical Research" - }, - { - "author_name": "Ahmed Oluwasegun Tajudeen", - "author_inst": "Nigerian Institute of Medical Research" - }, - { - "author_name": "Abdul-Lateef Olanlege", - "author_inst": "Infectious Disease Hospital, Lagos" - }, - { - "author_name": "Adefunke Abioye", - "author_inst": "Infectious Diseases Hospital, Lagos" - }, - { - "author_name": "Grace Bosede Akintunde", - "author_inst": "Nigerian Institute of Medical Research" - }, - { - "author_name": "Morenike Oluwatoyin Folayan", - "author_inst": "Obafemi Awolowo University" - }, - { - "author_name": "Babatunde Salako", - "author_inst": "Nigerian Institute of Medical Research" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.04.11.23288130", "rel_title": "Clinical Performance of BD Veritor\u2122 Assay Across SARS-CoV-2 Variants", @@ -78089,6 +79026,101 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2023.04.13.535896", + "rel_title": "SARS-CoV-2 spike antigen-specific B cell and antibody responses in pre-vaccination period COVID-19 convalescent males and females with or without post-covid condition", + "rel_date": "2023-04-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.04.13.535896", + "rel_abs": "BackgroundFollowing SARS-CoV-2 infection a significant proportion of convalescent individuals develop the post-COVID condition (PCC) that is characterized by wide spectrum of symptoms encompassing various organs. Even though the underlying pathophysiology of PCC is not known, detection of viral transcripts and antigens in tissues other than lungs raise the possibility that PCC may be a consequence of aberrant immune response to the viral antigens. To test this hypothesis, we evaluated B cell and antibody responses to the SARS-CoV-2 antigens in PCC patients who experienced mild COVID-19 disease during the pre-vaccination period of COVID-19 pandemic.\n\nMethodsThe study subjects included unvaccinated male and female subjects who developed PCC or not (No-PCC) after clearing RT-PCR confirmed mild COVID-19 infection. SARS-CoV-2 D614G and omicron RBD specific B cell subsets in peripheral circulation were assessed by flow cytometry. IgG, IgG3 and IgA antibody titers toward RBD, spike and nucleocapsid antigens in the plasma were evaluated by ELISA.\n\nResultsThe frequency of the B cells specific to D614G-RBD were comparable in convalescent groups with and without PCC in both males and females. Notably, in females with PCC, the anti-D614G RBD specific double negative (IgD-CD27-) B cells showed significant correlation with the number of symptoms at acute of infection. Anti-spike antibody responses were also higher at 3 months post-infection in females who developed PCC, but not in the male PCC group. On the other hand, the male PCC group also showed consistently high anti-RBD IgG responses compared to all other groups.\n\nConclusionsThe antibody responses to the spike protein, but not the RBD-specific B cell responses diverge between convalescent males and females, and those who develop PCC or not. Our findings suggest that sex-related factors may also be involved in the development of PCC via modulating antibody responses to the SARS-CoV-2 antigens.\n\nShort SummaryPost-COVID Condition (PCC) is lingering illness that afflicts a significant proportion of COVID-19 patients from three months after clearing SARS-CoV-2 infection. Therapy for PCC is only palliative and the underlying disease mechanisms are unclear. The wide spectrum of PCC symptoms that can affect different organs and the detection of viral components in tissues distant from lungs raise the possibility that PCC may be associated with aberrant immune response due to presence of viral antigens. Therefore, we studied B cell and antibody responses to the spike and nucleoprotein antigens in PCC patients who cleared mild SARS-CoV-2 infection during the pre-vaccination COVID-19 pandemic period. We observed divergent patterns of immune reactivity to the spike protein in PCC males and females at different times post-infection, suggesting that the immune responses in PCC may also be influenced by sex-related factors.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Marc-Andre Limoges", + "author_inst": "University of Sherbrooke" + }, + { + "author_name": "Akouavi Julite Irmine Quenum", + "author_inst": "University of Sherbrooke" + }, + { + "author_name": "Mohammad Mobarak H Chowdhury", + "author_inst": "University of Sherbrooke" + }, + { + "author_name": "Fjolla Rexhepi", + "author_inst": "University of Sherbrooke" + }, + { + "author_name": "Mozhdeh Namvarpour", + "author_inst": "University of Sherbrooke" + }, + { + "author_name": "Sara Ali Akbari", + "author_inst": "University of Sherbrooke" + }, + { + "author_name": "Christine Rioux-Perreault", + "author_inst": "University of Sherbrooke" + }, + { + "author_name": "Madhuparna Nandi", + "author_inst": "University of Sherbrooke" + }, + { + "author_name": "Jean-Francois Lucier", + "author_inst": "University of Sherbrooke" + }, + { + "author_name": "Samuel Lemaire-Paquette", + "author_inst": "University of Sherbrooke" + }, + { + "author_name": "Lakshmanane Premkumar", + "author_inst": "The University of North Carolina at Chapel Hill" + }, + { + "author_name": "Yves Durocher", + "author_inst": "National Research Council Canada" + }, + { + "author_name": "Andre Cantin", + "author_inst": "University of Sherbrooke" + }, + { + "author_name": "Simon Levesque", + "author_inst": "University of Sherbrooke" + }, + { + "author_name": "Alfredo Menendez", + "author_inst": "University of Sherbrooke" + }, + { + "author_name": "Isabelle J. Dionne", + "author_inst": "University of Sherbrooke" + }, + { + "author_name": "Subburaj Ilangumaran", + "author_inst": "University of Sherbrooke" + }, + { + "author_name": "Hugues Allard-Chamard", + "author_inst": "University of Sherbrooke" + }, + { + "author_name": "Alain Piche", + "author_inst": "University of Sherbrooke" + }, + { + "author_name": "Sheela Ramanathan", + "author_inst": "University of Sherbrooke" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.04.12.536590", "rel_title": "Evaluation of mRNA-LNP and adjuvanted protein SARS-CoV-2 vaccines in a maternal antibody mouse model", @@ -79478,41 +80510,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2023.04.10.23288358", - "rel_title": "Global surveillance of novel SARS-CoV-2 variants", - "rel_date": "2023-04-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.10.23288358", - "rel_abs": "Earlier global detection of novel SARS-CoV-2 variants gives governments more time to respond. However, few countries can implement timely national surveillance resulting in gaps in monitoring. The UK implemented large-scale community and hospital surveillance, but experience suggests it may be faster to detect new variants through testing UK arrivals for surveillance. We developed simulations of the emergence and importation of novel variants with a range of infection hospitalisation rates (IHR) to the UK. We compared time taken to detect the variant though testing arrivals at UK borders, hospital admissions, and the general community. We found that sampling 10-50% of arrivals at UK borders could confer a speed advantage of 3.5-6 weeks over existing community surveillance, and 1.5-5 weeks (depending on IHR) over hospital testing. We conclude that directing limited global capacity for surveillance to highly connected ports could speed up global detection of novel SARS-CoV-2 variants.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Selina Patel", - "author_inst": "University College London & UK Health Security Agency" - }, - { - "author_name": "Fergus Cumming", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Carl Mayers", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Andre Charlett", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Steven Riley", - "author_inst": "UK Health Security Agency & Imperial College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.04.07.23288262", "rel_title": "COVID-19 Vaccine Uptake And Its Associated Factors among general population In Basmaia City in Baghdad 2022", @@ -80118,6 +81115,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.04.05.23288195", + "rel_title": "Comparative Effectiveness of mRNA-1273 and BNT162b2 COVID-19 Vaccines in Immunocompromised Individuals: A Systematic Review and Meta-Analysis Using the GRADE Framework", + "rel_date": "2023-04-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.05.23288195", + "rel_abs": "IntroductionDespite representing only 3% of the US population, immunocompromised (IC) individuals account for nearly half of the COVID-19 breakthrough hospitalizations. IC individuals generate a lower immune response following vaccination in general, and the US CDC recommended a third dose of either mRNA-1273 or BNT162b2 COVID-19 vaccines as part of their primary series. Influenza vaccine trials have shown that increasing dosage could improve effectiveness in IC populations. The objective of this systematic literature review and pairwise meta-analysis was to evaluate the clinical effectiveness of mRNA-1273 (50 or 100 mcg/dose) versus BNT162b2 (30 mcg/dose) in IC populations using the GRADE framework.\n\nMethodsThe systematic literature search was conducted in the World Health Organization COVID-19 Research Database. Studies were included in the pairwise meta-analysis if they reported comparisons of mRNA-1273 and BNT162b2 in IC individuals [≥]18 years of age; outcomes of interest were SARS-CoV-2 infection, hospitalization due to COVID-19, and mortality due to COVID-19. Risk ratios (RR) were pooled across studies using random-effects meta-analysis models. Outcomes were also analyzed in subgroups of patients with cancer, autoimmune disease, and solid organ transplant. Risk of bias was assessed for randomized and observational studies using the Risk of Bias 2 tool and the Newcastle-Ottawa Scale, respectively. Evidence was evaluated using the GRADE framework.\n\nResultsOverall, 22 studies were included in the pairwise meta-analysis. Compared with BNT162b2, mRNA-1273 was associated with significantly reduced risk of SARS-CoV-2 infection (RR 0.87, 95% CI 0.79-0.96; P=0.0054; I2=61.9%), COVID-19-associated hospitalization (RR 0.83, 95% CI 0.76-0.90; P<0.0001; I2=0%), and COVID-19-associated mortality (RR 0.62, 95% CI 0.43-0.89; P=0.011; I2=0%) in IC populations. Results were consistent across subgroups. Because of sample size limitations, relative effectiveness of COVID-19 mRNA vaccines in IC populations cannot be studied in randomized trials and evidence certainty among comparisons was type 3 (low) and 4 (very low), reflecting potential biases in observational studies.\n\nConclusionThis GRADE meta-analysis based on a large number of consistent observational studies showed that the mRNA-1273 COVID-19 vaccine is associated with improved clinical effectiveness in IC populations compared with BNT162b2.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Xuan Wang", + "author_inst": "ICON plc" + }, + { + "author_name": "Katrin Haeussler", + "author_inst": "ICON plc" + }, + { + "author_name": "Anne Spellman", + "author_inst": "Data Health Ltd" + }, + { + "author_name": "Leslie Phillips", + "author_inst": "Data-Driven LLC" + }, + { + "author_name": "Allison Ramiller", + "author_inst": "Data-Driven LLC" + }, + { + "author_name": "Mary Bausch-Jurken", + "author_inst": "Moderna, Inc." + }, + { + "author_name": "Pawana Sharma", + "author_inst": "ICON plc" + }, + { + "author_name": "Anna Krivelyova", + "author_inst": "ICON plc" + }, + { + "author_name": "Sonam Vats", + "author_inst": "ICON plc" + }, + { + "author_name": "Nicolas Van de Velde", + "author_inst": "Moderna, Inc." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.04.05.23288196", "rel_title": "Incidence of Symptoms Associated with Post-Acute Sequelae of SARS-CoV-2 infectionin Non-Hospitalized Vaccinated Patients Receiving Nirmatrelvir-Ritonavir", @@ -81404,37 +82456,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.03.31.23287964", - "rel_title": "A nationwide multistate analysis estimating the rates and risks of transferring critically ill COVID-19 patients during the Delta and Omicron waves in Germany", - "rel_date": "2023-04-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.31.23287964", - "rel_abs": "BackgroundThe spread of several SARS-CoV-2 variants of concern (VOC) led to increasing numbers of patients with coronavirus disease 2019 (COVID-19) in German intensive care units (ICU), resulting in capacity shortages and even transfers of COVID-19 ICU patients between federal states in late 2021. Comprehensive evidence on the impact of predominant VOC, in this case Delta and Omicron, on inter-hospital transfers of COVID-19 ICU patients remains scarce.\n\nMethodsA retrospective cohort study was conducted from July 01, 2021 until May 31, 2022 using nationwide reimbursement inpatient count data of COVID-19 ICU patients and weekly sequence data of VOC in Germany. A multivariable Poisson regression analysis was performed to estimate incidence rates and incidence rate ratios (IRR) for competing events of transfer, discharge and death, adjusted for VOC infection, age group and sex. For corresponding risk estimation, a multistate model for the clinical trajectory in ICU was applied.\n\nResultsOmicron versus Delta infection yielded estimated adjusted IRR of 1.23 (95% CI, 1.16 - 1.30) for transfer, 2.27 (95% CI, 2.20 - 2.34), for discharge and 0.98 (95% CI, 0.94 - 1.02) for death. For death in ICU, estimated adjusted IRR increased progressively with age up to 4.09 (95% CI, 3.74 - 4.47) for those 90 years and older. COVID-19 ICU patients with Omicron infection were at comparatively higher estimated risk of discharge, whereas the estimated risk of transfer and death were higher for those with Delta infection.\n\nConclusionsInter-hospital transfers and discharges occurred more frequently in COVID-19 ICU patients with Omicron infection than in those with Delta infection, who in turn had a higher estimated risk of death. Age emerges as a relevant determinant for fatal clinical trajectories in COVID-19 ICU patients and imposes close therapeutic care.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Matth\u00e4us Lottes", - "author_inst": "Robert Koch Institute, Department of Methods Development, Research Infrastructure and Information Technology" - }, - { - "author_name": "Marlon Grodd", - "author_inst": "Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center - University of Freiburg" - }, - { - "author_name": "Linus Grabenhenrich", - "author_inst": "Robert Koch Institute, Department of Methods Development, Research Infrastructure and Information Technology" - }, - { - "author_name": "Martin Wolkewitz", - "author_inst": "Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center - University of Freiburg" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2023.04.01.23287538", "rel_title": "Trends in weight gain recorded in English primary care before and during the Coronavirus-19 pandemic: an observational cohort study using the OpenSAFELY platform", @@ -82008,6 +83029,117 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2023.03.30.534980", + "rel_title": "Spatiotemporally organized immunomodulatory response to SARS-CoV-2 virus in primary human broncho-alveolar epithelia", + "rel_date": "2023-03-31", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.03.30.534980", + "rel_abs": "The COVID-19 pandemic continues to be a health crisis with major unmet medical needs. The early responses from airway epithelial cells, the first target of the virus regulating the progression towards severe disease, are not fully understood. Primary human air-liquid interface cultures representing the broncho-alveolar epithelia were used to study the kinetics and dynamics of SARS-CoV-2 variants infection. The infection measured by nucleoprotein expression, was a late event appearing between day 4-6 post infection for Wuhan-like virus. Other variants demonstrated increasingly accelerated timelines of infection. All variants triggered similar transcriptional signatures, an \"early\" inflammatory/immune signature preceding a \"late\" type I/III IFN, but differences in the quality and kinetics were found, consistent with the timing of nucleoprotein expression. Response to virus was spatially organized: CSF3 expression in basal cells and CCL20 in apical cells. Thus, SARS-CoV-2 virus triggers specific responses modulated over time to engage different arms of immune response.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Diana Cadena Castaneda", + "author_inst": "The Jackson Laboratory for Genomic Medicine" + }, + { + "author_name": "Sonia Jangra", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Marina Yurieva", + "author_inst": "The Jackson Laboratory for Genomic Medicine" + }, + { + "author_name": "Jan Martinek", + "author_inst": "The Jackson Laboratory for Genomic Medicine" + }, + { + "author_name": "Megan Callender", + "author_inst": "The Jackson Laboratory for Genomic Medicine" + }, + { + "author_name": "Matthew Coxe", + "author_inst": "The Jackson Laboratory for Genomic Medicine" + }, + { + "author_name": "Angela Choi", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Juan Garcia-Bernalt Diego", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jianan Lin", + "author_inst": "The Jackson Laboratory for Genomic Medicine, Farmington" + }, + { + "author_name": "Te-Chia Wu", + "author_inst": "The Jackson Laboratory for Genomic Medicine" + }, + { + "author_name": "Florentina Marches", + "author_inst": "The Jackson Laboratory for Genomic Medicine" + }, + { + "author_name": "Damien Chaussabel", + "author_inst": "The Jackson Laboratory for Genomic Medicine" + }, + { + "author_name": "Peter Yu", + "author_inst": "Hartford HealthCare Cancer Institute" + }, + { + "author_name": "Andrew Salner", + "author_inst": "Hartford HealthCare Cancer Institute" + }, + { + "author_name": "Gabrielle Aucello", + "author_inst": "The Jackson Laboratory for Genomic Medicine" + }, + { + "author_name": "Jonathan Koff", + "author_inst": "Adult Cystic Fibrosis Program, Yale University" + }, + { + "author_name": "Briana Hudson", + "author_inst": "Nanostring Technologies, Translational Sciences" + }, + { + "author_name": "Sarah E. Church", + "author_inst": "Nanostring Technologies, Translational Sciences" + }, + { + "author_name": "Kara Gorman", + "author_inst": "Nanostring Technologies, Translational Sciences" + }, + { + "author_name": "Esperanza Anguiano", + "author_inst": "Nanostring Technologies, Translational Sciences" + }, + { + "author_name": "Adolfo Garcia-Sastre", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Adam Williams", + "author_inst": "The Jackson Laboratory for Genomic Medicine" + }, + { + "author_name": "Michael Schotsaert", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Karolina Palucka", + "author_inst": "The Jackson Laboratory For Genomic Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.03.31.535072", "rel_title": "Explicit Modelling of Antibody Levels for Infectious Disease Simulations in the Context of SARS-CoV-2", @@ -83009,149 +84141,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2023.03.27.23287773", - "rel_title": "mTOR inhibition improves the formation of functional T cell memory following COVID-19 vaccination of kidney transplant recipients", - "rel_date": "2023-03-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.27.23287773", - "rel_abs": "Inadequate immune response to vaccination is a long-standing problem faced by immunosuppressed kidney transplant recipients (KTRs), requiring novel strategies to improve vaccine efficacy. In this study, the potential of mechanistic target of rapamycin inhibitors (mTORi) to improve T cell responses to COVID-19 vaccination was investigated. Following primary vaccination with adenoviral (ChAdOx1) or mRNA (BNT162b2) COVID-19 vaccines, KTRs receiving rapamycin demonstrated T cell responses greater than those of healthy individuals, characterized by increased frequencies of vaccine-specific central memory, effector memory and TEMRA T cells, in both the CD4+ and CD8+ compartments. Relative to standard-of-care triple therapy, mTORi-based therapy was associated with a 12-fold greater functional T cell response to primary vaccination of KTRs. The use of rapamycin to augment T cell responses to COVID-19 booster (third dose) vaccination was next investigated in a randomized, controlled trial. Immunosuppression modification with rapamycin was feasible and well-tolerated, but did not improve vaccine-specific T cell responses in this cohort. To understand the parameters for effective use of rapamycin as a vaccine adjuvant, mice were treated with rapamycin before primary or booster vaccination with ancestral and/or Omicron COVID-19 vaccines. Supporting the findings from KTRs, significant enhancement of functional and stem-like memory T cell responses was observed when rapamycin was administered from the time of primary, rather than booster, vaccination. Collectively, a positive effect of mTOR inhibitors on vaccine-induced T cell immunity against COVID-19 in humans was demonstrated.\n\nOne Sentence SummaryRapamycin use at the time of primary COVID-19 vaccination augments the formation of functional, vaccine-specific T cell memory in immunosuppressed kidney transplant recipients.", - "rel_num_authors": 32, - "rel_authors": [ - { - "author_name": "Griffith Boord Perkins", - "author_inst": "Royal Adelaide Hospital" - }, - { - "author_name": "Matthew J Tunbridge", - "author_inst": "Royal Adelaide Hospital" - }, - { - "author_name": "Cheng Sheng Chai", - "author_inst": "University of Adelaide" - }, - { - "author_name": "Christopher Martin Hope", - "author_inst": "University of Adelaide" - }, - { - "author_name": "Arthur Eng Lip Yeow", - "author_inst": "Basil Hetzel Institute for Translational Health Research" - }, - { - "author_name": "Tania Salehi", - "author_inst": "Royal Adelaide Hospital" - }, - { - "author_name": "Julian J Singer", - "author_inst": "Royal Prince Alfred Hospital" - }, - { - "author_name": "Bree Shi", - "author_inst": "Royal Prince Alfred Hospital" - }, - { - "author_name": "Makutiro Masavuli", - "author_inst": "Basil Hetzel Institute for Translational Health Research" - }, - { - "author_name": "Zelalem Mekonnen", - "author_inst": "Basil Hetzel Institute for Translational Health Research" - }, - { - "author_name": "Pablo Garcia-Valtanen", - "author_inst": "Universidad Miguel Hernandez" - }, - { - "author_name": "Svjetlana Kireta", - "author_inst": "Royal Adelaide Hospital" - }, - { - "author_name": "Julie K Johnston", - "author_inst": "Royal Adelaide Hospital" - }, - { - "author_name": "Christopher J Drogemuller", - "author_inst": "Royal Adelaide Hospital" - }, - { - "author_name": "Beatrice Z Sim", - "author_inst": "Peter MacCallum Cancer Centre" - }, - { - "author_name": "Shane M Spencer", - "author_inst": "The Queen Elizabeth Hospital" - }, - { - "author_name": "Benedetta Sallustio", - "author_inst": "The Queen Elizabeth Hospital" - }, - { - "author_name": "Iain Comerford", - "author_inst": "University of Adelaide" - }, - { - "author_name": "George Bouras", - "author_inst": "Basil Hetzel Institute for Translational Health Research" - }, - { - "author_name": "Daniela Weiskopf", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Alessandro Sette", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Anupriya Aggarwal", - "author_inst": "University of New South Wales Kirby Institute" - }, - { - "author_name": "Anouschka Akerman", - "author_inst": "University of New South Wales Kirby Institute" - }, - { - "author_name": "Vanessa Milogiannakis", - "author_inst": "University of New South Wales Kirby Institute" - }, - { - "author_name": "Stuart G Turville", - "author_inst": "University of New South Wales Kirby Institute" - }, - { - "author_name": "Plinio R Hurtado", - "author_inst": "Royal Adelaide Hospital" - }, - { - "author_name": "Tracey Ying", - "author_inst": "Royal Prince Alfred Hospital" - }, - { - "author_name": "Pravin Hissaria", - "author_inst": "Royal Adelaide Hospital" - }, - { - "author_name": "Simon C Barry", - "author_inst": "Women's and Children's Hospital" - }, - { - "author_name": "Steven J Chadban", - "author_inst": "Royal Prince Alfred Hospital" - }, - { - "author_name": "Branka Grubor-Bauk", - "author_inst": "Basil Hetzel Institute for Translational Health Research" - }, - { - "author_name": "Toby Coates", - "author_inst": "Royal Adelaide Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "transplantation" - }, { "rel_doi": "10.1101/2023.03.28.23287762", "rel_title": "Early real world evidence on the relative SARS-COV-2 vaccine effectiveness of bivalent COVID-19 booster doses: a rapid review.", @@ -83629,6 +84618,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2023.03.27.23287793", + "rel_title": "Timing and magnitude of the next wave of COVID-19 in China:lessons from 189 countries and territories", + "rel_date": "2023-03-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.27.23287793", + "rel_abs": "Because of the fading immunity to COVID-19 and continuous evolution of the SARS-CoV-2 Omicron variants, the next epidemic wave of COVID-19 is inevitable. The Omicron variant has been the cause of several waves of the COVID-19 epidemics in the majority of countries. Thus, lessons from other countries may provide guidance regarding the timing and magnitude of the next COVID-19 wave of the pandemic in China. In this study, the COVID-19 surveillance data from 189 countries that experienced two or more waves of the SARS-CoV-2 Omicron variant were analysed. The median peak timing between the first and second/third waves of the SARS-CoV-2 Omicron variant was 164/243 days. The peaks of the second and third waves were much lower than that of the first wave. The median relative peaks of the second and third compared with the first waves were 14.5% and 11.2%, respectively. The time window between the peak timings of the first and second waves showed no significant rank correlation with the five socioeconomic factors included in this study. However, the relative peak of the second wave increased significantly with gross domestic product per capita (P<0.001), urbanisation rate (P=0.003), population density (P=0.007), and proportion of older adults >65 years (P<0.001), although decreased significantly with the proportion of 0-14 teenagers (P<0.001). In summary, the historical situations and progression of COVID-19 outbreaks in other countries may inform the risk assessment of incoming outbreaks in mainland China; however, the timing and magnitude of the next COVID-19 wave may also be influenced by several unknown factors, including rapid viral evaluation of SARS-CoV-2", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Beidi Niu", + "author_inst": "School of Public Health, Zhejiang University, Hangzhou City, Zhejiang Province, China" + }, + { + "author_name": "Shuyi Ji", + "author_inst": "School of Public Health, Zhejiang University, Hangzhou City, Zhejiang Province, China" + }, + { + "author_name": "Shi Zhao", + "author_inst": "School of Public Health, Zhejiang University, Hangzhou City, Zhejiang Province, China" + }, + { + "author_name": "Hao Lei", + "author_inst": "School of Public Health, Zhejiang University, Hangzhou City, Zhejiang Province, China and School of Public Health, Zhejiang University, Hangzhou City, Zhejiang " + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.03.29.23287591", "rel_title": "Coronavirus pathogenesis in mice explains the SARS-CoV-2 multi-organ spread by red blood cell hitch-hiking", @@ -84635,37 +85655,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2023.03.24.23287683", - "rel_title": "Used paper tissues for pathogen identification in acute respiratory infection.", - "rel_date": "2023-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.24.23287683", - "rel_abs": "We investigated the potential of used paper tissues as a non-invasive sampling method for the diagnosis of acute respiratory infections. The method allowed the identification and typing of respiratory pathogens in symptomatic individuals, as well as in collective samples taken at a community level. The collection of used paper tissues could therefore be useful in epidemiological surveillance for SARS-CoV-2 and other respiratory pathogens such as influenzavirus, respiratory syncytial virus, entero/rhinoviruses and Streptococcus pneumoniae.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Annabel Rector", - "author_inst": "Rega Institute, KU Leuven" - }, - { - "author_name": "Mandy Bloemen", - "author_inst": "Rega Institute, KU Leuven" - }, - { - "author_name": "Marc Van Ranst", - "author_inst": "UZ Leuven / KU Leuven" - }, - { - "author_name": "Elke Wollants", - "author_inst": "KU Leuven Rega Institute" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.03.24.23287700", "rel_title": "The potential contribution of vaccination uptake to occupational differences in risk of SARS-CoV-2: Analysis of the ONS COVID-19 Infection Survey", @@ -85447,6 +86436,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rheumatology" }, + { + "rel_doi": "10.1101/2023.03.22.533798", + "rel_title": "Distribution of nematocytes differs in two types of gonophores in hydrozoan Sarsia lovenii.", + "rel_date": "2023-03-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.03.22.533798", + "rel_abs": "Hydrozoan cnidarians are widely known for a diversity of life cycles. While some hydrozoan polyps produce medusae, in most species the gonophore remains attached to the polyp. Little is known about the mechanisms behind the loss of the medusal stage in hydrozoans. Hydrozoan Sarsia lovenii is a promising model for studying this issue. It is a polymorphic species with several haplogroups. One haplogroup produces attached eumedusoids and the other one buds free-swimming medusae. Here, we compared patterns of cell proliferation and distribution of nematocytes in medusoids, medusa buds and medusae of S. lovenii.\n\nCell proliferation is absent from exumbrella of late medusa buds and medusae, but presumably i-cells proliferate in exumbrella of medusoids. In exumbrella of medusoids, we also observed evenly distributed nematocytes with capsules and expression of late nematogenesis-associated gene, Nowa. Nematocyte capsules and Nowa expression were also observed in exumbrella of medusa bud, but we did not detect prominent Nowa signal in the bell of developed medusa. It is also known that abundance of exumbrellar nematocysts signs immaturity in medusae of Sarsia genus. Our data demonstrate that nematocyte distribution and associated gene expression in medusoids resemble medusa buds rather than developed medusae. Thus, sexually mature medusoids exhibit juvenile somatic characters, demonstrating signs of neoteny.\n\nResearch highlightsHydrozoan Sarsia lovenii has attached eumedusoids and free-swimming medusae. The distribution of nematocytes in eumedusoids resembles that in medusa buds. This may indicate neoteny of eumedusoids.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Alexandra Vetrova", + "author_inst": "Koltzov Institute of Developmental Biology RAS" + }, + { + "author_name": "Andrey Prudkovsky", + "author_inst": "Lomonosov Moscow State University" + }, + { + "author_name": "Stanislav V Kremnyov", + "author_inst": "Lomonosov Moscow State University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "zoology" + }, { "rel_doi": "10.1101/2023.03.16.23287365", "rel_title": "Estimating the Impact of Pre-Exposure Prophylaxis (PrEP) on Mortality in COVID-19 Patients: A Causal Inference Approach", @@ -86301,37 +87317,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2023.03.21.23287519", - "rel_title": "Endemic-epidemic modelling of school closure to prevent spread of COVID-19 in Switzerland", - "rel_date": "2023-03-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.21.23287519", - "rel_abs": "The coronavirus disease 2019 (COVID-19) pandemic disrupted daily life and changes to routines were made in accordance with public health regulations. In 2020, nonpharmaceutical interventions were put in place to reduce exposure to and spread of the disease. The goal of this work was to quantify the effect of school closure during the first year of COVID-19 pandemic in Switzerland. This allowed us to determine the usefulness of school closures as a pandemic countermeasure for emerging coronaviruses in the absence of pharmaceutical interventions. The use of multivariate endemic-epidemic modelling enabled us to analyse disease spread between age groups which we believe is a necessary inclusion in any model seeking to achieve our goal. Sophisticated time-varying contact matrices encapsulating four different contact settings were included in our complex statistical modelling approach to reflect the amount of school closure in place on a given day. Using the model, we projected case counts under various transmission scenarios (driven by implemented social distancing policies). We compared these counterfactual scenarios against the true levels of social distancing policies implemented, where schools closed in the spring and reopened in the autumn. We found that if schools had been kept open, the vast majority of additional cases would be expected among primary school-aged children with a small fraction of cases percolating into other age groups following the contact matrix structure. Under this scenario where schools were kept open, the cases were highly concentrated among the youngest age group. In the scenario where schools had remained closed, most reduction would also be expected in the lowest age group with less effects seen in other groups.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Maria Bekker-Nielsen Dunbar", - "author_inst": "Epidemiology, Biostatistics and Prevention Institute, University of Zurich" - }, - { - "author_name": "Felix Hofmann", - "author_inst": "Epidemiology, Biostatistics and Prevention Institute, University of Zurich" - }, - { - "author_name": "Sebastian Meyer", - "author_inst": "Institute of Medical Informatics, Biometry, and Epidemiology, Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg" - }, - { - "author_name": "Leonhard Held", - "author_inst": "Epidemiology, Biostatistics and Prevention Institute, University of Zurich" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.03.20.23287264", "rel_title": "Nasopharyngeal Angiotensin Converting Enzyme 2 (ACE2) Expression as a Risk-Factor for SARS-CoV-2 Transmission in Concurrent Hospital Associated Outbreaks", @@ -86965,6 +87950,69 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.03.19.533317", + "rel_title": "Analysis of spike protein variants evolved in a novel mouse model of persistent SARS-CoV-2 infection", + "rel_date": "2023-03-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.03.19.533317", + "rel_abs": "SARS-CoV-2 mutation rates have increased over time, resulting in the emergence of several variants of concern. Persistent infection is assumed to be involved in the evolution of the variants; however, there is currently no animal model to recapitulate persistent infection. We established a novel model of persistent infection using xenografts of Calu-3 human lung cancer cells in immunocompromised mice. After infection with wild-type SARS-CoV-2, viruses were found in the tumor tissues for up to 30 days and acquired various mutations, predominantly in the spike (S) protein, some of which increased while others fluctuated for 30 days. Three isolated viral clones with defined mutations produced higher virus titers than the wild-type virus in Calu-3 cells without cytotoxic effects. In K18-hACE2 mice, the variants were less lethal than the wild-type virus. Infection with each variant induced production of cross-reactive antibodies to the receptor binding domain of wild-type S protein and provided protective immunity against subsequent challenge with wild-type virus. These results suggest that most of the SARS-CoV-2 variants acquired mutations promoting host adaptation in the Calu-3 xenograft mice. This model can be used in the future to further study persistent SARS-CoV-2 infection.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Dongbum Kim", + "author_inst": "Hallym University" + }, + { + "author_name": "Jinsoo Kim", + "author_inst": "Hallym University" + }, + { + "author_name": "Minyoung Kim", + "author_inst": "Hallym University" + }, + { + "author_name": "Heedo Park", + "author_inst": "Korea University" + }, + { + "author_name": "Sony Maharjan", + "author_inst": "Hallym University" + }, + { + "author_name": "Kyeongbin Baek", + "author_inst": "Hallym University" + }, + { + "author_name": "Bo Min Kang", + "author_inst": "Hallym University" + }, + { + "author_name": "Suyeon Kim", + "author_inst": "Hallym University" + }, + { + "author_name": "Sangkyu Park", + "author_inst": "Chungbuk National University" + }, + { + "author_name": "Man-Seong Park", + "author_inst": "Korea University" + }, + { + "author_name": "Younghee Lee", + "author_inst": "Chungbuk National University" + }, + { + "author_name": "Hyung-Joo Kwon", + "author_inst": "Hallym University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.03.19.23287460", "rel_title": "Data-driven control of airborne infection risk and energy use in buildings", @@ -88294,33 +89342,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.03.13.23287198", - "rel_title": "Importation of Alpha and Delta variants during the SARS-CoV-2 epidemic in Switzerland: phylogenetic analysis and intervention scenarios", - "rel_date": "2023-03-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.13.23287198", - "rel_abs": "The SARS-CoV-2 pandemic has led to the emergence of various variants of concern (VoCs) that are associated with increased transmissibility, immune evasion, or differences in disease severity. The emergence of VoCs fueled interest in understanding the potential impact of travel restrictions and surveillance strategies to prevent or delay the early spread of VoCs. We performed phylogenetic analyses and mathematical modeling to study the importation and spread of the VoCs Alpha and Delta in Switzerland in 2020 and 2021. Using a phylogenetic approach, we estimated 383-1,038 imports of Alpha and 455-1,347 imports of Delta into Switzerland. We then used the results from the phylogenetic analysis to parameterize a dynamic transmission that accurately described the subsequent spread of Alpha and Delta. We modeled different counterfactual intervention scenarios to quantify the potential impact of border closures and surveillance of travelers on the spread of Alpha and Delta. We found that implementing border closures after the announcement of VoCs would have been of limited impact to mitigate the spread of VoCs. In contrast, increased surveillance of travelers could prove to be an effective measure for delaying the spread of VoCs in situations where their severity remains unclear. Our study shows how phylogenetic analysis in combination with dynamic transmission models can be used to estimate the number of imported SARS-CoV-2 variants and the potential impact of different intervention scenarios to inform the public health response during the pandemic.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Martina Reichmuth", - "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Emma B Hodcroft", - "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland; Swiss Institute of Bioinformatics, Basel, Switzerland; Multidisciplinary Cen" - }, - { - "author_name": "Christian L Althaus", - "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland; Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, " - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.03.16.23287322", "rel_title": "Serial SARS-CoV-2 antibody titers in vaccinated dialysis patients: prevalence of unrecognized infection and duration of seroresponse", @@ -89146,6 +90167,93 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.03.15.532878", + "rel_title": "The highly conserved stem-loop II motif is dispensable for SARS-CoV-2", + "rel_date": "2023-03-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.03.15.532878", + "rel_abs": "The stem-loop II motif (s2m) is a RNA structural element that is found in the 3 untranslated region (UTR) of many RNA viruses including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Though the motif was discovered over twenty-five years ago, its functional significance is unknown. In order to understand the importance of s2m, we created viruses with deletions or mutations of the s2m by reverse genetics and also evaluated a clinical isolate harboring a unique s2m deletion. Deletion or mutation of the s2m had no effect on growth in vitro, or growth and viral fitness in Syrian hamsters in vivo. We also compared the secondary structure of the 3 UTR of wild type and s2m deletion viruses using SHAPE-MaP and DMS-MaPseq. These experiments demonstrate that the s2m forms an independent structure and that its deletion does not alter the overall remaining 3UTR RNA structure. Together, these findings suggest that s2m is dispensable for SARS-CoV-2.\n\nIMPORTANCERNA viruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contain functional structures to support virus replication, translation and evasion of the host antiviral immune response. The 3 untranslated region of early isolates of SARS-CoV-2 contained a stem-loop II motif (s2m), which is a RNA structural element that is found in many RNA viruses. This motif was discovered over twenty-five years ago, but its functional significance is unknown. We created SARS-CoV-2 with deletions or mutations of the s2m and determined the effect of these changes on viral growth in tissue culture and in rodent models of infection. Deletion or mutation of the s2m element had no effect on growth in vitro, or growth and viral fitness in Syrian hamsters in vivo. We also observed no impact of the deletion on other known RNA structures in the same region of the genome. These experiments demonstrate that the s2m is dispensable for SARS-CoV-2.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Hongbing Jiang", + "author_inst": "Third Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Astha Joshi", + "author_inst": "Washington University in St. Louis School of Medicine" + }, + { + "author_name": "Tianyu Gan", + "author_inst": "Washington University in St Louis Department of Molecular Microbiology" + }, + { + "author_name": "Andrew B Janowski", + "author_inst": "Washington University in St. Louis" + }, + { + "author_name": "Chika Fujii", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Traci L Bricker", + "author_inst": "Washington University in St. Louis School of Medicine" + }, + { + "author_name": "Tamarand Darling", + "author_inst": "Washington University in St. Louis School of Medicine" + }, + { + "author_name": "Houda H. Harastani", + "author_inst": "Washington University in St. Louis School of Medicine" + }, + { + "author_name": "Kuljeet Seehra", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Hongwei Chen", + "author_inst": "Third Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Stephen Tahan", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Ana Jung", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Binita Febles", + "author_inst": "Washington University in St Louis Department of Molecular Microbiology" + }, + { + "author_name": "Joshua A Blatter", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Scott Handley", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Bijal A Parikh", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "David Wang", + "author_inst": "Washington University in St Louis School of Medicine" + }, + { + "author_name": "Adrianus C Boon", + "author_inst": "Washington University in St Louis School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.03.15.529513", "rel_title": "Modelling the viral dynamics of the SARS-CoV-2 Delta and Omicron variants in different cell types", @@ -90192,57 +91300,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2023.03.15.532439", - "rel_title": "Changes in Environmental Stress over COVID-19 Pandemic Likely Contributed to Failure to Replicate Adiposity Phenotype Associated with Krtcap3", - "rel_date": "2023-03-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.03.15.532439", - "rel_abs": "We previously identified Keratinocyte-associated protein 3, Krtcap3, as an obesity-related gene in female rats where a whole-body Krtcap3 knock-out (KO) led to increased adiposity compared to wild-type (WT) controls when fed a high-fat diet (HFD). We sought to replicate this work to better understand the function of Krtcap3 but were unable to reproduce the adiposity phenotype. In the current work, WT female rats ate more compared to WT in the prior study, with corresponding increases in body weight and fat mass, while there were no changes in these measures in KO females between the studies. The prior study was conducted before the COVID-19 pandemic, while the current study started after initial lock-down orders and was completed during the pandemic with a generally less stressful environment. We hypothesize that the environmental changes impacted stress levels and may explain the failure to replicate our results. Analysis of corticosterone (CORT) at euthanasia showed a significant study by genotype interaction where WT had significantly higher CORT relative to KO in Study 1, with no differences in Study 2. These data suggest that decreasing Krtcap3 expression may alter the environmental stress response to influence adiposity. We also found that KO rats in both studies, but not WT, experienced a dramatic increase in CORT after their cage mate was removed, suggesting a separate connection to social behavioral stress. Future work is necessary to confirm and elucidate the finer mechanisms of these relationships, but these data indicate the possibility of Krtcap3 as a novel stress gene.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Alexandria M Szalanczy", - "author_inst": "Wake Forest University School of Medicine" - }, - { - "author_name": "Gina Giorgio", - "author_inst": "Wake Forest University School of Medicine" - }, - { - "author_name": "Emily Goff", - "author_inst": "Wake Forest University School of Medicine" - }, - { - "author_name": "Ozzie Seshie", - "author_inst": "Wake Forest University School of Medicine" - }, - { - "author_name": "Michael Grzybowski", - "author_inst": "Medical College of Wisconsin" - }, - { - "author_name": "Jason Klotz", - "author_inst": "Medical College of Wisconsin" - }, - { - "author_name": "Aron M Geurts", - "author_inst": "Medical College of Wisconsin" - }, - { - "author_name": "Eva E Redei", - "author_inst": "Northwestern University Feinberg School of Medicine" - }, - { - "author_name": "Leah C Solberg Woods", - "author_inst": "Wake Forest University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2023.03.12.23287049", "rel_title": "The cost of primary care consultations associated with long COVID in non-hospitalised patients: a retrospective cohort study using UK primary care data", @@ -90796,6 +91853,61 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.03.13.532347", + "rel_title": "Resolving the developmental mechanisms of coagulation abnormalities characteristic of SARS-CoV2 based on single-cell transcriptome analysis", + "rel_date": "2023-03-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.03.13.532347", + "rel_abs": "The COVID-19 outbreak caused by the SARS-CoV-2 virus has developed into a global health emergency. In addition to causing respiratory symptoms following SARS-CoV-2 infection, COVID-19-associated coagulopathy (CAC) is the main cause of death in patients with severe COVID-19. In this study, we performed single-cell sequencing analysis of the right ventricular free wall tissue from healthy donors, patients who died in the hypercoagulable phase of CAC, and patients in the fibrinolytic phase of CAC. Among these, we collected 61,187 cells, which were enriched in 24 immune cell subsets and 13 cardiac-resident cell subsets. We found that in response to SARS-CoV-2 infection, CD9highCCR2highmonocyte-derived mo promoted hyperactivation of the immune system and initiated the extrinsic coagulation pathway by activating CXCR-GNB/G-PI3K-AKT. This sequence of events is the main process contributing the development of coagulation disorders subsequent to SARS-CoV-2 infection. In the characteristic coagulation disorder caused by SARS-CoV-2, excessive immune activation is accompanied by an increase in cellular iron content, which in turn promotes oxidative stress and intensifies intercellular competition. This induces cells to alter their metabolic environment, resulting in an increase in sugar uptake, such as that via the glycosaminoglycan synthesis pathway, in CAC coagulation disorders. In addition, high levels of reactive oxygen species generated in response elevated iron levels promote the activation of unsaturated fatty acid metabolic pathways in endothelial cell subgroups, including vascular endothelial cells. This in turn promotes the excessive production of the toxic peroxidation by-product malondialdehyde, which exacerbates both the damage caused to endothelial cells and coagulation disorders.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Xizi Luo", + "author_inst": "Jilin University" + }, + { + "author_name": "Nan Zhang", + "author_inst": "Jilin University" + }, + { + "author_name": "Yuntao Liu", + "author_inst": "Shandong University" + }, + { + "author_name": "Beibei Du", + "author_inst": "Jilin University" + }, + { + "author_name": "Xuan Wang", + "author_inst": "Jilin University" + }, + { + "author_name": "Tianxu Zhao", + "author_inst": "Jilin University" + }, + { + "author_name": "Bingqiang Liu", + "author_inst": "Shandong University" + }, + { + "author_name": "Shishun Zhao", + "author_inst": "Jilin University" + }, + { + "author_name": "Jiazhang Qiu", + "author_inst": "Jilin University" + }, + { + "author_name": "Guoqing Wang", + "author_inst": "Jilin University" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.03.11.532212", "rel_title": "In vitro comparison of SARS-CoV-2 variants", @@ -91738,57 +92850,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.03.08.23287004", - "rel_title": "Medium-term scenarios of COVID-19 as a function of immune uncertainties and chronic disease", - "rel_date": "2023-03-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.08.23287004", - "rel_abs": "As the SARS-CoV-2 trajectory continues, the longer-term immuno-epidemiology of COVID-19, the dynamics of Long COVID, and the impact of escape variants are important outstanding questions. We examine these remaining uncertainties with a simple modelling framework that accounts for multiple (antigenic) exposures via infection or vaccination. If immunity (to infection or Long COVID) accumulates rapidly with the valency of exposure, we find that infection levels and the burden of Long COVID are markedly reduced in the medium term. More pessimistic assumptions on host adaptive immune responses illustrate that the longer term burden of COVID-19 may be elevated for years to come. However, we also find that these outcomes could be mitigated by the eventual introduction of a vaccine eliciting robust (i.e. durable, transmission-blocking and/or evolution-proof) immunity. Overall, our work stresses the wide range of future scenarios that still remain, the importance of collecting real world epidemiological data to identify likely outcomes, and the crucial need for the development of a highly effective transmission-blocking, durable, and broadly-protective vaccine.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Chadi M Saad-Roy", - "author_inst": "University of California Berkeley" - }, - { - "author_name": "Sinead E Morris", - "author_inst": "Columbia University" - }, - { - "author_name": "Rachel E Baker", - "author_inst": "Brown University" - }, - { - "author_name": "Jeremy Farrar", - "author_inst": "The Wellcome Trust" - }, - { - "author_name": "Andrea L Graham", - "author_inst": "Princeton University" - }, - { - "author_name": "Simon A Levin", - "author_inst": "Princeton University" - }, - { - "author_name": "Caroline E Wagner", - "author_inst": "McGill University" - }, - { - "author_name": "C. Jessica E. Metcalf", - "author_inst": "Princeton University" - }, - { - "author_name": "Bryan M Grenfell", - "author_inst": "Princeton University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.03.09.23287043", "rel_title": "Integrated analyses of single-cell RNA-seq public data reveal the gene regulatory network landscape of respiratory epithelial and peripheral immune cells in COVID-19 patients", @@ -92746,6 +93807,57 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.03.08.531833", + "rel_title": "Generation of a SARS-CoV-2 reverse genetics system and novel human lung cell lines that exhibit high virus-induced cytopathology", + "rel_date": "2023-03-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.03.08.531833", + "rel_abs": "The global COVID-19 pandemic continues with an increasing number of cases worldwide and the emergence of new SARS-CoV-2 variants. In our study, we have developed novel tools with applications for screening antivirals, identifying virus-host dependencies, and characterizing viral variants. Using reverse genetics, we rescued SARS-CoV-2 Wuhan1 (D614G variant) wild type (WTFL) and reporter virus (NLucFL) using molecular BAC clones. The replication kinetics, plaque morphology and titers were comparable between rescued molecular clones and a clinical isolate (VIDO-01 strain), thus providing confidence that the rescued viruses can be used as effective replication tools. Furthermore, the reporter SARS-CoV-2 NLucFL virus exhibited robust luciferase values over the time course of infection and was used to develop a rapid antiviral assay using remdesivir as proof-of-principle. In addition, as a tool to study lung-relevant virus-host interactions, we established novel human lung cell lines that support SARS-CoV-2 infection with high virus-induced cytopathology. Six lung cell lines (NCI-H23, A549, NCI-H1703, NCI-H520, NCI-H226, and HCC827) and HEK293T cells, were transduced to stably express ACE2 and tested for their ability to support virus infection. A549ACE2 B1 and HEK293TACE2 A2 cell lines exhibited more than 70% virus-induced cell death and a novel lung cell line NCI-H23ACE2 A3 showed about [~]99% cell death post-infection. These cell lines are ideal for assays relying on live-dead selection and are currently being used in CRISPR knockout and activation screens in our lab.\n\nImportanceWe used a reverse genetics system to generate a wild type as well as a nanoluciferase-expressing reporter clone of SARS-CoV-2. The reporter virus allows for rapid transient replication assays and high throughput screens by detection of virus replication using luciferase assays. In addition, the reverse genetic system can be used to generate mutant viruses to study phenotypes of variant mutations. Additionally, unique human lung cell lines supporting SARS-CoV-2 replication will aid in studying the virus in a lung-relevant environment and based on high cytopathology induced in some cell lines, will be useful for screens that rely on virus-induced cell death for selection. Our study aims to enhance and contribute to the current replication tools available to study SARS-CoV-2 by providing rapid methods, virus clones and novel lung cell lines.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Juveriya Qamar Khan", + "author_inst": "University of Saskatchewan" + }, + { + "author_name": "Megha Rohamare", + "author_inst": "University of Saskatchewan" + }, + { + "author_name": "Karthic Rajamanickam", + "author_inst": "University of Saskatchewan" + }, + { + "author_name": "Kalpana K Bhanumathy", + "author_inst": "University of Saskatchewan" + }, + { + "author_name": "Jocelyne Lew", + "author_inst": "University of Saskatchewan" + }, + { + "author_name": "Anil Kumar", + "author_inst": "University of Saskatchewan" + }, + { + "author_name": "Darryl Falzarano", + "author_inst": "University of Saskatchewan" + }, + { + "author_name": "Franco Vizeacoumar", + "author_inst": "University of Saskatchewan" + }, + { + "author_name": "Joyce A Wilson", + "author_inst": "University of Saskatchewan" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2023.03.07.23286904", "rel_title": "The impact of signal variability on epidemic growth rate estimation from wastewater surveillance data", @@ -93420,45 +94532,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.03.07.23286938", - "rel_title": "The impact of public-initiated COVID-19 risk communication on individual NPI practices", - "rel_date": "2023-03-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.07.23286938", - "rel_abs": "BackgroundNon-Pharmaceutical Interventions (NPI) are the most widely recognized public health measures practiced globally to prevent the spread of Covid-19 transmission. The effectiveness of NPIs is dependent on the type, a combination of applied interventions, and the level of compliance of the NPIs. The expected outcome of behavioral practices varies relative to the behavioral intervention duration.\n\nObjectivesThis study aimed to assess the trend of community compliance to NPIs and with its level of variation with the place of residence and sociodemographic characteristics of people.\n\nMethodsA weekly non-participatory field survey on an individuals NPI practice was observed from October 2020 to July 2021, for a total of 39 weeks. The survey covered all the regions; 14 regional and capital cities. Data collection for the 3 NPI behaviors (mask use, hand hygiene, and physical distance was and managed weekly at eight public service locations using the Open Data Kit (ODK) tool.\n\nResultsMore than 180,000 individuals were observed for their NPI practice; on average 5,000 observations in a week. About 43% of the observation was made from Addis Ababa, 56% were male participants and the middle age group (18-50 years) accounts for 75%. The overall level of NPI compliance had a peak around the 26th - 30th weeks then decline the rest of the weeks. Respiratory hygiene had the highest compliance whereas hand hygiene had the least 41% and 4%, respectively. There was a significant difference between capital city and regional city residents by their level of NPI compliance. Females comply more than males, and individuals had increased NPI compliance while at the bank service and workplaces compared to while in the transport services at p<0.001.\n\nConclusionThe overall community compliance with NPI practice showed a declining trend in Ethiopia but increased compliance was also observed following the implementation of government-initiated public measures. Therefore, public-initiated risk communication and public advocacy programs for the prevention of Covid-19 should be strengthened.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Yifokire Tefera Zele", - "author_inst": "Addis Ababa University Department of Community Health: Addis Ababa University School of Public Health" - }, - { - "author_name": "Abera Kumie", - "author_inst": "Addis Ababa University Department of Community Health: Addis Ababa University School of Public Health" - }, - { - "author_name": "Damen Hailemariam", - "author_inst": "Addis Ababa University Department of Community Health: Addis Ababa University School of Public Health" - }, - { - "author_name": "Samson Wakuma", - "author_inst": "Addis Ababa University Department of Community Health: Addis Ababa University School of Public Health" - }, - { - "author_name": "Teferi Abegaz", - "author_inst": "Addis Ababa University Department of Community Health: Addis Ababa University School of Public Health" - }, - { - "author_name": "Shibabaw Yirsaw", - "author_inst": "Addis Ababa University Department of Community Health: Addis Ababa University School of Public Health" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.03.06.23286834", "rel_title": "SARS-CoV-2 viral replication persists in the human lung for several weeks after onset of symptomatic severe COVID-19 and is associated with attenuated pulmonary immunity and variant-specific clinical sequalae", @@ -94272,6 +95345,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2023.03.05.23286816", + "rel_title": "Modelling the association between neutralizing antibody levels and SARS-CoV-2 viral dynamics : implications to define correlates of protection against infection", + "rel_date": "2023-03-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.05.23286816", + "rel_abs": "BackgroundWhile anti-SARS-CoV-2 antibody kinetics have been well described in large populations of vaccinated individuals, we still poorly understand how they evolve during a natural infection and how this impacts viral clearance.\n\nMethodsFor that purpose, we analyzed the kinetics of both viral load and neutralizing antibody levels in a prospective cohort of individuals during acute infection by Alpha variant.\n\nResultsUsing a mathematical model, we show that the progressive increase in neutralizing antibodies leads to a shortening of the half-life of both infected cells and infectious viral particles. We estimated that the neutralizing activity reached 90% of its maximal level within 8 days after symptoms onset and could reduce the half-life of both infected cells and infectious virus by a 6-fold factor, thus playing a key role to achieve rapid viral clearance. Using this model, we conducted a simulation study to predict in a more general context the protection conferred by the existence of pre-existing neutralization, due to either vaccination or prior infection. We predicted that a neutralizing activity, as measured by ED50 >103, could reduce by 50% the risk of having viral load detectable by standard PCR assays and by 99% the risk of having viral load above the threshold of cultivable virus.\n\nConclusionsThis threshold value for the neutralizing activity could be used to identify individuals with poor protection against disease acquisition.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Guillaume Lingas", + "author_inst": "Inserm" + }, + { + "author_name": "Delphine Planas", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "H\u00e9l\u00e8ne P\u00e9r\u00e9", + "author_inst": "Assistance Publique - H\u00f4pitaux de Paris" + }, + { + "author_name": "Darragh Duffy", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Isabelle Staropoli", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Fran\u00e7oise Porrot", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Florence Guivel-Benhassine", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Nicolas Chapuis", + "author_inst": "Universit\u00e9 Paris Descartes" + }, + { + "author_name": "Camille Gobeaux", + "author_inst": "Assistance Publique - H\u00f4pitaux de Paris" + }, + { + "author_name": "David Veyer", + "author_inst": "Assistance Publique - H\u00f4pitaux de Paris" + }, + { + "author_name": "Constance Delaugerre", + "author_inst": "Assistance Publique - H\u00f4pitaux de Paris" + }, + { + "author_name": "J\u00e9r\u00f4me Le Goff", + "author_inst": "Assistance Publique - H\u00f4pitaux de Paris" + }, + { + "author_name": "Prunelle Getten", + "author_inst": "Assistance Publique - H\u00f4pitaux de Paris" + }, + { + "author_name": "J\u00e9r\u00f4me Hadjadj", + "author_inst": "Assistance Publique - H\u00f4pitaux de Paris" + }, + { + "author_name": "Ad\u00e8le Bellino", + "author_inst": "Assistance Publique - H\u00f4pitaux de Paris" + }, + { + "author_name": "B\u00e9atrice Parfait", + "author_inst": "Assistance Publique - H\u00f4pitaux de Paris" + }, + { + "author_name": "Jean-Marc Treluyer", + "author_inst": "Assistance Publique - H\u00f4pitaux de Paris" + }, + { + "author_name": "Olivier Schwartz", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Jeremie Guedj", + "author_inst": "Inserm" + }, + { + "author_name": "Solen Kern\u00e9is", + "author_inst": "Assistance Publique - H\u00f4pitaux de Paris" + }, + { + "author_name": "Benjamin Terrier", + "author_inst": "Assistance Publique - H\u00f4pitaux de Paris" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.03.04.531078", "rel_title": "Tau protein aggregation associated with SARS-CoV-2 main protease", @@ -95294,49 +96466,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.03.03.23286761", - "rel_title": "Molnupiravir's real-world effectiveness in COVID-19 non-hospitalized patients at high risk of severe disease: a single-center study", - "rel_date": "2023-03-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.03.23286761", - "rel_abs": "ObjectiveTo assess the real-world effectiveness of molnupiravir (MOL) in reducing the need for hospitalization in at-risk, non-hospitalized patients with confirmed COVID-19.\n\nMethodsA single-center, non-randomized, observational retrospective study of non-hospitalized patients with confirmed COVID-19 treated at the Clinic for Infectious and Tropical Diseases, University Clinical Center in Belgrade, Serbia.\n\nResultsBetween December 15th, 2021, and February 15th, 2022, 320 patients were eligible for inclusion in the study. Of these, 165 received treatment with molnupiravir (51.6%), while both groups were similar in gender and age distribution. The treatment group had a higher proportion of vaccination (75.2% vs. 51%, p<0.001) but was similar to the control group in terms of multiple comorbidity predomination (65.5% vs. 65.2%, p 0.956). The majority of patients who received MOL didnt require hospitalization (92.7 vs. 24.5%, p<0.001) and needed oxygen supplementation less frequently than those in the control group (0.6% vs. 31%, p<0.001). During the follow-up period of 12.12{+/-}3.5 days, none of the patients on MOL were admitted to the Intensive Care Unit (vs. 10.3%, p<0.001). Molnupiravir significantly reduced the risk of hospitalization by 97.9% (HR 0.021, p<0.001).\n\nConclussionOur study has proven the effectiveness of molnupiravir in preventing hospitalization in a population at risk for developing severe forms of COVID-19.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Ivana Gmizic", - "author_inst": "Clinic for Infectious and Tropical Diseases, University Clinical Center of Serbia, Belgrade, Serbia" - }, - { - "author_name": "Nevena Todorovic", - "author_inst": "Clinic for Infectious and Tropical Diseases, University Clinical Center of Serbia, Belgrade, Serbia" - }, - { - "author_name": "Milos Sabanovic", - "author_inst": "Clinic for Infectious and Tropical Diseases, University Clinical Center of Serbia, Belgrade, Serbia" - }, - { - "author_name": "Natalija Kekic", - "author_inst": "Clinic for Infectious and Tropical Diseases, University Clinical Center of Serbia, Belgrade, Serbia" - }, - { - "author_name": "Nikola Boskovic", - "author_inst": "Clinic for Cardiology, University clinical center of Serbia, Belgrade, Serbia" - }, - { - "author_name": "Ivana Milosevic", - "author_inst": "Clinic for Infectious and Tropical Diseases, University Clinical Center of Serbia, Belgrade, Serbia. Faculty of Medicine, University of Belgrade, Belgrade, Serb" - }, - { - "author_name": "Goran Stevanovic", - "author_inst": "Clinic for Infectious and Tropical Diseases, University Clinical Center of Serbia, Belgrade, Serbia. Faculty of Medicine, University of Belgrade, Belgrade, Serb" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.03.02.23286561", "rel_title": "Bivalent booster effectiveness against severe COVID-19 outcomes in Finland, September 2022 - January 2023", @@ -95930,6 +97059,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2023.02.28.23286515", + "rel_title": "Association between spironolactone use and COVID-19 outcomes in population-scale claims data: a retrospective cohort study", + "rel_date": "2023-03-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.28.23286515", + "rel_abs": "BackgroundSpironolactone has been proposed as a potential modulator of SARS-CoV-2 cellular entry. We aimed to measure the effect of spironolactone use on the risk of adverse outcomes following COVID-19 hospitalization.\n\nMethodsWe performed a retrospective cohort study of COVID-19 outcomes for patients with or without exposure to spironolactone, using population-scale claims data from the Komodo Healthcare Map. We identified all patients with a hospital admission for COVID-19 in the study window, defining treatment status based on spironolactone prescription orders. The primary outcomes were progression to respiratory ventilation or mortality during the hospitalization. Odds ratios (OR) were estimated following either 1:1 propensity score matching (PSM) or multivariable regression. Subgroup analysis was performed based on age, gender, body mass index (BMI), and dominant SARS-CoV-2 variant.\n\nFindingsAmong 898,303 eligible patients with a COVID-19-related hospitalization, 16,324 patients (1.8%) had a spironolactone prescription prior to hospitalization. 59,937 patients (6.7%) met the ventilation endpoint, and 26,515 patients (3.0%) met the mortality endpoint. Spironolactone use was associated with a significant reduction in odds of both ventilation (OR 0.82; 95% CI: 0.75-0.88; p < 0.001) and mortality (OR 0.88; 95% CI: 0.78-0.99; p = 0.033) in the PSM analysis, supported by the regression analysis. Spironolactone use was associated with significantly reduced odds of ventilation for all age groups, men, women, and non-obese patients, with the greatest protective effects in younger patients, men, and non-obese patients.\n\nInterpretationSpironolactone use was associated with a protective effect against ventilation and mortality following COVID-19 infection, amounting to up to 64% of the protective effect of vaccination against ventilation and consistent with an androgen-dependent mechanism. The findings warrant initiation of large-scale randomized controlled trials to establish a potential therapeutic role for spironolactone in COVID-19 patients.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Henry C. Cousins", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Russ B. Altman", + "author_inst": "Stanford University School of Medicine" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.03.02.23286698", "rel_title": "A novel approach for estimating vaccine efficacy for infections with multiple disease outcomes: application to a COVID-19 vaccine trial", @@ -97048,81 +98200,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.03.01.530431", - "rel_title": "Bulk RNA-Sequencing of small airway cell cultures from IPF and post-COVID lung fibrosis patients illustrates disease signatures and differential responses to TGF-\u03b21 treatment", - "rel_date": "2023-03-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.03.01.530431", - "rel_abs": "IPF is a condition in which an injury to the lung leads to the accumulation of scar tissue. This fibrotic tissue reduces lung compliance and impairs gas exchange. Studies have shown that infection with COVID-19 significantly worsens the clinical outcomes of IPF patients. The exact etiology of IPF is unknown, but recent evidence suggests that the distal small airways, (those having a diameter less than 2 mm in adults), play a role in the early pathogenesis of IPF. TGF-{beta}1 is a main driver of fibrosis in a variety of tissues; the binding of TGF-{beta}1 to its receptor triggers a signaling cascade that results in inflammatory signaling, accumulation of collagen and other components of the extracellular matrix, and immune system activation. This study aimed to investigate possible mechanisms that contribute to worsening lung fibrosis in IPF patients after being diagnosed with COVID-19, with a particular focus on the role of TGF-{beta}1. Small airway cell cultures derived from IPF and post-COVID-19 IPF patient transplant tissues were submitted for RNA-sequencing and differential gene expression analysis. The genetic signatures for each disease state were determined by comparing the differentially expressed genes present in the cells cultured under control conditions to cells cultured with TGF-{beta}1. The genes shared between the culture conditions laid the framework for determining the genetic signatures of each disease. Our data found that genes associated with pulmonary fibrosis appeared to be more highly expressed in the post-COVID fibrosis samples, under both control and TGF-{beta}1-treated conditions. A similar trend was noted for genes involved in the TGF-{beta}1 signaling pathway; the post-COVID fibrosis cell cultures seemed to be more responsive to treatment with TGF-{beta}1. Gene expression analysis, RT-PCR, and immunohistochemistry confirmed increased levels of BMP signaling in the IPF small airway cell cultures. These findings suggest that TGF-{beta}1 signaling in IPF small airway cells could be inhibited by BMP signaling, leading to the differences in genetic signatures between IPF and post-COVID fibrosis.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Katie Uhl", - "author_inst": "Michigan State University" - }, - { - "author_name": "Shreya Paithankar", - "author_inst": "Michigan State University" - }, - { - "author_name": "Dmitry Leshchiner", - "author_inst": "Michigan State University" - }, - { - "author_name": "Tara Jager", - "author_inst": "Corewell Health West" - }, - { - "author_name": "Mohamed Abdelgied", - "author_inst": "Michigan State University" - }, - { - "author_name": "Kaylie Tripp", - "author_inst": "Michigan State University" - }, - { - "author_name": "Angela Peraino", - "author_inst": "Corewell Health West" - }, - { - "author_name": "Maximiliano Kakazu", - "author_inst": "Corewell Health West" - }, - { - "author_name": "Cameron Lawson", - "author_inst": "Corewell Health West" - }, - { - "author_name": "David Chesla", - "author_inst": "Corewell Health West" - }, - { - "author_name": "Jeremy Prokop", - "author_inst": "Michigan State University" - }, - { - "author_name": "Bin Chen", - "author_inst": "Michigan State University" - }, - { - "author_name": "Edward Murphy", - "author_inst": "Corewell Health West" - }, - { - "author_name": "Reda Girgis", - "author_inst": "Corewell Health West" - }, - { - "author_name": "Xiaopeng Li", - "author_inst": "Michigan State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2023.02.28.530489", "rel_title": "Coarse-Grained Molecular Simulations and Ensemble-Based Mutational Profiling of Protein Stability in the Different Functional Forms of the SARS-CoV-2 Spike Trimers : Balancing Stability and Adaptability in BA.1, BA.2 and BA.2.75 Variants", @@ -97752,6 +98829,37 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2023.02.25.530000", + "rel_title": "Rapid resistance profiling of SARS-CoV-2 protease inhibitors", + "rel_date": "2023-02-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.25.530000", + "rel_abs": "Resistance to nirmatrelvir (Paxlovid) has been shown by multiple groups and may already exist in clinical SARS-CoV-2 isolates. Here a panel of SARS-CoV-2 main protease (Mpro) variants and a robust cell-based assay are used to compare the resistance profiles of nirmatrelvir, ensitrelvir, and FB2001. The results reveal distinct resistance mechanisms (\"fingerprints\") and indicate that these next-generation drugs have the potential to be effective against nirmatrelvir-resistant variants and vice versa.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Seyed Arad Moghadasi", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Rayhan Biswas", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Daniel A Harki", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Reuben Harris", + "author_inst": "University of Texas Health San Antonio" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.02.24.23286187", "rel_title": "Coping with drug resistant tuberculosis alongside COVID-19 and other stressors in Zimbabwe: a qualitative study.", @@ -98862,65 +99970,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2023.02.23.529833", - "rel_title": "Machine learning on large scale perturbation screens for SARS-CoV-2 host factors identifies \u03b2-catenin/CBP inhibitor PRI-724 as a potent antiviral", - "rel_date": "2023-02-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.23.529833", - "rel_abs": "Expanding antiviral treatment options against SARS-CoV-2 remains crucial as the virus evolves rapidly and drug resistant strains have emerged. Broad spectrum host-directed antivirals (HDA) are promising therapeutic options, however the robust identification of relevant host factors by CRISPR/Cas9 or RNA interference screens remains challenging due to low consistency in the resulting hits.\n\nTo address this issue, we employed machine learning based on experimental data from knockout screens and a drug screen. As gold standard, we assembled perturbed genes reducing virus replication or protecting the host cells. The machines based their predictions on features describing cellular localization, protein domains, annotated gene sets from Gene Ontology, gene and protein sequences, and experimental data from proteomics, phospho-proteomics, protein interaction and transcriptomic profiles of SARS-CoV-2 infected cells.\n\nThe models reached a remarkable performance with a balanced accuracy of 0.82 (knockout based classifier) and 0.71 (drugs screen based classifier), suggesting patterns of intrinsic data consistency. The predicted host dependency factors were enriched in sets of genes particularly coding for development, morphogenesis, and neural related processes. Focusing on development and morphogenesis-associated gene sets, we found {beta}-catenin to be central and selected PRI-724, a canonical {beta}-catenin/CBP disruptor, as a potential HDA. PRI-724 limited infection with SARS-CoV-2 variants, SARS-CoV-1, MERS-CoV and IAV in different cell line models. We detected a concentration-dependent reduction in CPE development, viral RNA replication, and infectious virus production in SARS-CoV-2 and SARS-CoV-1-infected cells. Independent of virus infection, PRI-724 treatment caused cell cycle deregulation which substantiates its potential as a broad spectrum antiviral. Our proposed machine learning concept may support focusing and accelerating the discovery of host dependency factors and the design of antiviral therapies.\n\nAuthors summaryDrug resistance to pathogens is a well-known phenomenon which was also observed for SARS-CoV-2. Given the gradually increasing evolutionary pressure on the virus by herd immunity, we attempted to enlarge the available antiviral repertoire by focusing on host proteins that are usurped by viruses. The identification of such proteins was followed within several high throughput screens in which genes are knocked out individually. But, so far, these efforts led to very different results. Machine learning helps to identify common patterns and normalizes independent studies to their individual designs. With such an approach, we identified genes that are indispensable during embryonic development, i.e., when cells are programmed for their specific destiny. Shortlisting the hits revealed {beta}-catenin, a central player during development, and PRI-724, which inhibits the interaction of {beta}-catenin with cAMP responsive element binding (CREB) binding protein (CBP). In our work, we confirmed that the disruption of this interaction impedes virus replication and production. In A549-AT cells treated with PRI-724, we observed cell cycle deregulation which might contribute to the inhibition of virus infection, however the exact underlying mechanisms needs further investigation.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Maximilian Alexander Kelch", - "author_inst": "Johann Wolfgang Goethe-Universit\u00e4t Frankfurt am Main: Goethe-Universitat Frankfurt am Main" - }, - { - "author_name": "Antonella Loren Vera-Guapi", - "author_inst": "Johann Wolfgang Goethe-Universit\u00e4t Frankfurt am Main: Goethe-Universitat Frankfurt am Main" - }, - { - "author_name": "Thomas Beder", - "author_inst": "Universit\u00e4tsklinikum Schleswig-Holstein Campus Kiel: Universitatsklinikum Schleswig-Holstein Campus Kiel" - }, - { - "author_name": "Marcus Oswald", - "author_inst": "Universit\u00e4tsklinikum Jena: Universitatsklinikum Jena" - }, - { - "author_name": "Alicia Hiemisch", - "author_inst": "Jena University Hospital: Universitatsklinikum Jena" - }, - { - "author_name": "Nina Beil", - "author_inst": "Universit\u00e4t Heidelberg: Universitat Heidelberg" - }, - { - "author_name": "Piotr Wajda", - "author_inst": "Universit\u00e4t Heidelberg: Universitat Heidelberg" - }, - { - "author_name": "Sandra Ciesek", - "author_inst": "Klinikum der Johann Wolfgang Goethe-Universit\u00e4t Frankfurt: Klinikum der Johann Wolfgang Goethe-Universitat Frankfurt" - }, - { - "author_name": "Holger Erfle", - "author_inst": "Universit\u00e4t Heidelberg: Universitat Heidelberg" - }, - { - "author_name": "Tuna Toptan", - "author_inst": "Goethe University Frankfurt: Goethe-Universitat Frankfurt am Main" - }, - { - "author_name": "Rainer K\u00f6nig", - "author_inst": "Jena University Hospital: Universitatsklinikum Jena" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.02.15.23285880", "rel_title": "Has the COVID-19 pandemic ended or not? opinions from the public in the U.S.", @@ -99742,6 +100791,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "otolaryngology" }, + { + "rel_doi": "10.1101/2023.02.17.23285959", + "rel_title": "A comprehensive survey on the beliefs, perceptions, and clinical manifestations of pre and post Covid-19 vaccinations among physiotherapy students in the United Arab Emirates", + "rel_date": "2023-02-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.17.23285959", + "rel_abs": "BackgroundThe World Health Organization has defined Coronavirus Disease (COVID-19) as an infectious pandemic, caused by a newly discovered SARS-CoV-2 virus. Students relied heavily on the internet, social media, parents, and friends, in addition to medical advice for information on its presentation, complications, prevention, and management. It is evident from the literature that healthcare professionals including students who play an important role in the healthcare system may be lacking important information on COVID-19 vaccinations. Thus, the study aims to identify and compare the pre-post covid-19 vaccination-related essential information among Physical Therapy university students.\n\nMethodsA cross-sectional survey was conducted among physiotherapy university students in the United Arab Emirates using a self-administrated structured questionnaire. The questionnaire comprised three sections covering beliefs, perceptions, and clinical manifestations of the pre and post-COVID-19 vaccination. The survey was shared with more than 300 students through email and social platforms during the time between January 2022 till December 2022.\n\nResultsThe majority of the physiotherapy students believed the vaccines to be safe (71.3%) due to multiple reasons while others did not believe in the effectiveness of the vaccine (28.7%). Some students did report unusual symptoms (painful periods, hair loss, forgetfulness) after the vaccine (10%). Similar findings were reported for family members as well (14%). Students had a positive perception of the vaccine and reported willingness to take it even if not mandatory (68%).\n\nConclusionSome students did believe in the safety of the vaccine due to multiple reasons while some did not due to fear of long-term side effects and personal choices. The finding of the study could be useful to create confidence as well as awareness among physiotherapy students as they are often invited to aid during medical pandemics such as Covid 19. Also, higher rates of vaccination among healthcare professionals will impart higher acceptance in the medical organization due to safety guidelines. This could also help to counsel other students against fear and apprehension towards the vaccination of such kind in the future.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Shaikha AlMheiri", + "author_inst": "GMU: Gulf Medical University" + }, + { + "author_name": "Animesh Hazari", + "author_inst": "GMU: Gulf Medical University" + }, + { + "author_name": "Praveen Kumar", + "author_inst": "GMU: Gulf Medical University" + }, + { + "author_name": "Sampath Kumar", + "author_inst": "GMU: Gulf Medical University" + }, + { + "author_name": "Srilatha Girish", + "author_inst": "GMU: Gulf Medical University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2023.02.17.23286079", "rel_title": "Surface sampling for SARS-CoV-2 in workplace outbreak settings in the UK, 2021-22.", @@ -100732,33 +101816,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.02.14.23285818", - "rel_title": "An empirical analysis of lay media coverage on influenza prevention pre- and post-COVID 19: Mask recommendations were previously rare, now ubiquitous.", - "rel_date": "2023-02-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.14.23285818", - "rel_abs": "ImportanceConsistent, evidence-based communication is critical to building trust and maintaining credibility of public health agencies.\n\nObjectiveTo identify any significant changes in the mainstream medias presentation of public health advice for flu prevention before and after the COVID-19 pandemic.\n\nDesign, Setting, and ParticipantsA systematic search in Factiva of top ten U.S. newspapers by circulation, using two search periods, 2018-2019 and 2021-2022. Articles with flu prevention advice were identified, abstracted for media outlet, reporter, date. Articles were coded for the specific advice provided.\n\nMain Measure(s)Number of recommendations for flu prevention, frequency of each recommendation; percent of recommendations aligned with CDC guidelines for each period. Changes in frequency of each recommendation. Differences determined using 2-proportion Z-tests, p-value 0.05 significance.\n\nResults128 articles with 244 recommendations for pre-COVID period; 122 articles with 296 recommendations post-COVID. 96.3% of recommendations in alignment with CDC guidelines pre-COVID. 63.9% of recommendations in alignment with CDC during post-COVID timeframe. Percentage of articles with advice to mask for flu increased by 1,494.8% (p=<0.00001). 14.5% decline in percentage of articles advising flu vaccine (p=0.002). 495.5% increase in percentage of articles recommending social distancing (p=0.001). 1,368.9% increase in percentage articles recommending increased ventilation (p=0.0004).Advice to cover cough/sneeze declined by 52.8% (p=0.041); advice to disinfect surfaces declined by 76.7% (p=0.038).\n\nConclusions and RelevanceExpert advice on flu prevention as presented in top 10 U.S. newspapers changed significantly during the COVID-19 pandemic. The strategies discussed more frequently are not currently recommended by CDC. This is relevant information for public health leaders as they address ongoing issues of trust and credibility.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSAre there significant differences between the mainstream medias presentation of expert advice for flu prevention before and after the COVID-19 pandemic?\n\nFindingsA systematic search of the top ten U.S. newspapers by circulation found that the percentage of total articles with advice to use a face mask for flu prevention increased by 1,494.8% from the pre-to post-COVID period, while the percentage of total articles advising a flu vaccine decreased by 14.5%. Other significant findings include an increase in advice to social distance (494.5%), an increase in advice to improve ventilation (1,368.9%), a decline in advice to cover your cough (58.2%) and a decline in advice to disinfect surfaces (76.7%). The strategies discussed more frequently are not currently recommended by Centers for Disease Control (CDC) for flu prevention.\n\nMeaningSignificant changes in public health advice on flu prevention, as presented by high-circulation U.S. newspapers, occurred during the COVID-19 pandemic, resulting in less consistency with CDC recommendations for flu prevention.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Vinay Prasad", - "author_inst": "UCSF" - }, - { - "author_name": "Elissa Brown", - "author_inst": "University of Washington" - }, - { - "author_name": "Alyson Haslam", - "author_inst": "UCSF" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.02.21.23286181", "rel_title": "Associations between SARS-CoV-2 infection and incidence of new chronic condition diagnoses: a systematic review", @@ -101256,6 +102313,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.02.20.529306", + "rel_title": "Recognition and Cleavage of Human tRNA Methyltransferase TRMT1 by the SARS-CoV-2 Main Protease", + "rel_date": "2023-02-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.20.529306", + "rel_abs": "The SARS-CoV-2 main protease (Mpro) is critical for the production of functional viral proteins during infection and, like many viral proteases, can also target host proteins to subvert their cellular functions. Here, we show that the human tRNA methyltransferase TRMT1 can be recognized and cleaved by SARS-CoV-2 Mpro. TRMT1 installs the N2,N2-dimethylguanosine (m2,2G) modification on mammalian tRNAs, which promotes global protein synthesis and cellular redox homeostasis. We find that Mpro can cleave endogenous TRMT1 in human cell lysate, resulting in removal of the TRMT1 zinc finger domain required for tRNA modification activity in cells. Evolutionary analysis shows that the TRMT1 cleavage site is highly conserved in mammals, except in Muroidea, where TRMT1 may be resistant to cleavage. In primates, regions outside the cleavage site with rapid evolution could indicate adaptation to ancient viral pathogens. We determined the structure of a TRMT1 peptide in complex with Mpro, revealing a substrate binding conformation distinct from the majority of available Mpro-peptide complexes. Kinetic parameters for peptide cleavage showed that the TRMT1(526-536) sequence is cleaved with comparable efficiency to the Mpro-targeted nsp8/9 viral cleavage site. Mutagenesis studies and molecular dynamics simulations together indicate that kinetic discrimination occurs during a later step of Mpro-mediated proteolysis that follows substrate binding. Our results provide new information about the structural basis for Mpro substrate recognition and cleavage that could help inform future therapeutic design and raise the possibility that proteolysis of human TRMT1 during SARS-CoV-2 infection suppresses protein translation and oxidative stress response to impact viral pathogenesis.\n\nSignificance StatementViral proteases can strategically target human proteins to manipulate host biochemistry during infection. Here, we show that the SARS-CoV-2 main protease (Mpro) can specifically recognize and cleave the human tRNA methyltransferase enzyme TRMT1, which installs a modification on human tRNAs that is critical for protein translation. Our structural and functional analysis of the Mpro-TRMT1 interaction shows how the flexible Mpro active site engages a conserved sequence in TRMT1 in an uncommon binding mode to catalyze its cleavage and inactivation. These studies provide new insights into substrate recognition by SARS-CoV-2 Mpro that could inform future antiviral therapeutic design and suggest that proteolysis of TRMT1 during SARS-CoV-2 infection may disrupt tRNA modification and host translation to impact COVID-19 pathogenesis or phenotypes.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Angel D'Oliviera", + "author_inst": "University of Delaware" + }, + { + "author_name": "Xuhang Dai", + "author_inst": "New York University" + }, + { + "author_name": "Saba Mottaghinia", + "author_inst": "CIRI, Centre International de Recherche en Infectiologie" + }, + { + "author_name": "Evan P Geissler", + "author_inst": "University of Delaware" + }, + { + "author_name": "Lucie Etienne", + "author_inst": "CIRI, Centre International de Recherche en Infectiologie" + }, + { + "author_name": "Yingkai Zhang", + "author_inst": "New York University" + }, + { + "author_name": "Jeffrey S Mugridge", + "author_inst": "University of Delaware" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2023.02.20.23286191", "rel_title": "Longitudinal dynamics of Streptococcus pneumoniae carriage and SARS-CoV-2 infection in households with children.", @@ -102278,57 +103378,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.02.17.23286074", - "rel_title": "Rapidly Adaptable Multiplexed Yeast Surface Display Serological Assay for Immune Escape Screening of SARS-CoV-2 Variants", - "rel_date": "2023-02-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.17.23286074", - "rel_abs": "With numerous variations in the Spike protein, including concentrated mutations in the receptor-binding domain (RBD), the SARS-CoV-2 Omicron variant significantly shifted in the trajectory of the COVID-19 pandemic. To understand individual patient risk profiles in the face of rapidly emerging variants, there is an interest in sensitive serological tests capable of analyzing patient IgG response to multiple variants in parallel. Here, we present a serological test based on yeast surface display and serum biopanning that characterizes immune profiles against SARS-CoV-2 RBD variants. We used this yeast-based multi-variant serology method to examine IgG titers from 30 serum samples derived from COVID-19-convalescent and vaccinated individuals in Switzerland and assessed the relative affinity of polyclonal serum IgG for Wuhan (B lineage), Delta (B.1.617.2 lineage), and Omicron (B.1.1.529 lineage) RBD domains. We validated and benchmarked our system against a commercial lateral flow assay and showed strong concordance. Our assay demonstrates that serum IgGs from patients recovered from severe COVID-19 between March-June 2021 bound tightly to both original Wuhan and Delta RBD variants, but became indistinguishable from background when assayed against Omicron, representing an affinity loss of >10-20 fold. Our yeast immunoassay is easily tailored and parallelized with newly emerging RBD variants.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Joanan Lopez-Morales", - "author_inst": "University of Basel and ETH Zurich" - }, - { - "author_name": "Rosario Vanella", - "author_inst": "University of Basel and ETH Zurich" - }, - { - "author_name": "Tamara Utzinger", - "author_inst": "University of Basel" - }, - { - "author_name": "Valentin Schittny", - "author_inst": "University of Basel" - }, - { - "author_name": "Julia Hirsiger", - "author_inst": "University of Basel" - }, - { - "author_name": "Michael Osthoff", - "author_inst": "University Hospital Basel" - }, - { - "author_name": "Christoph T. Berger", - "author_inst": "University of Basel" - }, - { - "author_name": "Yakir Guri", - "author_inst": "University Hospital Basel" - }, - { - "author_name": "Michael A. Nash", - "author_inst": "University of Basel / ETH Zurich" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.02.17.23286083", "rel_title": "Prevalence of anti-SARS-CoV-2 antibodies in people attending the two main Goma markets in the eastern Democratic Republic of Congo", @@ -102858,6 +103907,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.02.15.23285963", + "rel_title": "On the Impact of Mass Screening for SARS-CoV-2 through Self-Testing in Greece", + "rel_date": "2023-02-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.15.23285963", + "rel_abs": "The emergence of COVID-19 stressed country health systems up to the point of triggering compulsory public health interventions to flatten the epidemic curve. Most of the interventions during the first year of the pandemic were non-pharmaceutical and aimed to reduce the contact rate of the people, which reduced the transmission rate of all respiratory pathogens, but had a large social and financial burden. SARS-CoV-2 specific interventions included screening, that is testing of asymptomatic people, which was largely facilitated by the availability of self-testing lateral flow antigen detection devices. The importance of self-testing interventions in controlling COVID-19 epidemic is not well-documented. We study as a paradigm-model the self-testing COVID-19 mass screening program that was implemented in Greece, involving large, susceptible populations taking tests routinely and pre-emptively so as to enable early detection of infections. Using a novel compartmental model we quantify the effectiveness of the program in curbing the COVID-19 pandemic. Conservative estimates indicate that the program reduced the reproductive number by 4%, hospital admissions by 25% and deaths by 20%, which translated into approximately 20,000 averted hospitalizations and 2,000 averted deaths between April-December 2021. Self-testing mass screening programs are efficient interventions with minimal social and financial burden, thus they are invaluable tools to be considered in pandemic preparedness.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Samuel Gilmour", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Spyros Sapounas", + "author_inst": "National Public Health Organization in Greece" + }, + { + "author_name": "Kimon Drakopoulos", + "author_inst": "University of Southern California" + }, + { + "author_name": "Patrick Jaillet", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Gkikas Magiorkinis", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Nikolaos Trichakis", + "author_inst": "Massachusetts Institute of Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.02.15.23285941", "rel_title": "Underreporting of SARS-CoV-2 infections during the first wave of the 2020 COVID-19 epidemic in Finland - Bayesian inference based on a series of serological surveys", @@ -104336,57 +105424,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.02.13.528341", - "rel_title": "SARS-CoV-2 Neutralizing Antibodies After Bivalent vs. Monovalent Booster", - "rel_date": "2023-02-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.13.528341", - "rel_abs": "Bivalent mRNA vaccine boosters expressing Omicron BA.5 spike and ancestral D614G spike were introduced to attempt to boost waning antibody titers and broaden coverage against emerging SARS-CoV-2 lineages. Previous reports showed that peak serum neutralizing antibody (NAb) titers against SARS-CoV-2 variants following bivalent booster were similar to peak titers following monovalent booster. It remains unknown whether these antibody responses would diverge over time. We assessed serum virus-neutralizing titers in 41 participants who received three monovalent mRNA vaccine doses followed by bivalent booster, monovalent booster, or BA.5 breakthrough infection at one month and three months after the last vaccine dose or breakthrough infection using pseudovirus neutralization assays against D614G and Omicron subvariants (BA.2, BA.5, BQ.1.1, and XBB.1.5). There was no significant difference at one month and three months post-booster for the two booster cohorts. BA.5 breakthrough patients exhibited significantly higher NAb titers at three months against all Omicron subvariants tested compared against monovalent and bivalent booster cohorts. There was a 2-fold drop in mean NAb titers in the booster cohorts between one and three month time points, but no discernible waning of titers in the BA.5 breakthrough cohort over the same period. Our results suggest that NAb titers after boosting with one dose of bivalent mRNA vaccine are not higher than boosting with monovalent vaccine. Perhaps inclusion of D614G spike in the bivalent booster exacerbates the challenge posed by immunological imprinting. Hope remains that a second bivalent booster could induce superior NAb responses against emerging variants.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Qian Wang", - "author_inst": "Columbia University Vagelos College of Physicians and Surgeons" - }, - { - "author_name": "Anthony D Bowen", - "author_inst": "Columbia University Vagelos College of Physicians and Surgeons" - }, - { - "author_name": "Anthony R Tam", - "author_inst": "Queen Mary Hospital, University of Hong Kong" - }, - { - "author_name": "Riccardo Valdez", - "author_inst": "University of Michigan" - }, - { - "author_name": "Emily Stoneman", - "author_inst": "University of Michigan" - }, - { - "author_name": "Ian A Mellis", - "author_inst": "Columbia University Vagelos College of Physicians and Surgeons" - }, - { - "author_name": "Aubree Gordon", - "author_inst": "University of Michigan" - }, - { - "author_name": "Lihong Liu", - "author_inst": "Columbia University Vagelos College of Physicians and Surgeons" - }, - { - "author_name": "David D Ho", - "author_inst": "Columbia University Vagelos College of Physicians and Surgeons" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.02.13.528349", "rel_title": "Propylene glycol inactivates respiratory viruses and prevents airborne transmission", @@ -105020,6 +106057,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.02.10.23285780", + "rel_title": "Low Antibody Titers Demonstrate Significantly Increased Rate of SARS-CoV-2 Infection in a Highly Vaccinated Population from the National Basketball Association", + "rel_date": "2023-02-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.10.23285780", + "rel_abs": "SARS-CoV-2 antibody titers may serve as a correlate for immunity and could inform optimal booster timing. The relationship between antibody titer and protection from infection was evaluated in 2,323 vaccinated individuals from the National Basketball Association who had antibody levels measured from 9/12/2021--12/31/2021. Cox-proportional hazards models were used to estimate risk of infection within 90-days of serologic testing by titer level (<250, 250-800, and >800 AU/mL) and individuals were censored on date of booster receipt. The cohort was 78.2% male, 68.1% aged [≤] 40 years, and 56.4% vaccinated (primary series) with the Pfizer-BioNTech mRNA vaccine. Among the 2,248 individuals not yet boosted at testing, those with titers <250 AU/mL (adj HR: 2.4; 95% CI: 1.5, 3.7) and 250-800 800 AU/mL (adj HR: 1.5; 95% CI: 0.98, 2.4) had greater infection risk compared to those with titers >800 AU/mL. Serologic titers could inform individual COVID-19 risk and booster scheduling.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Caroline Tai", + "author_inst": "IQVIA" + }, + { + "author_name": "Miriam J Haviland", + "author_inst": "IQVIA" + }, + { + "author_name": "Stephen M Kissler", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Rachel M Lucia", + "author_inst": "IQVIA" + }, + { + "author_name": "Michael Merson", + "author_inst": "Duke University" + }, + { + "author_name": "Lisa L Maragakis", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "David D Ho", + "author_inst": "Columbia University" + }, + { + "author_name": "Deverick J Anderson", + "author_inst": "Duke University" + }, + { + "author_name": "John DiFiori", + "author_inst": "Hospital for Special Surgery and National Basketball Association" + }, + { + "author_name": "Nathan D Grubaugh", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Yonatan H Grad", + "author_inst": "Harvard T. H. Chan School of Public Health" + }, + { + "author_name": "Christina DeFilippo Mack", + "author_inst": "IQVIA" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.02.10.527914", "rel_title": "The disordered N-terminal tail of SARS CoV-2 Nucleocapsid protein forms a dynamic complex with RNA", @@ -105882,57 +106982,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.02.07.23285620", - "rel_title": "Resilience and social support improve mental health and quality of life in patients with post-COVID-19 syndrome", - "rel_date": "2023-02-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.07.23285620", - "rel_abs": "The effects of post-COVID-19 syndrome on patients life are significant. As there is no prior study available, we investigated the impact of resilience and social support on anxiety, depression, and quality of life among patients with post-COVID-19 syndrome. We conducted a cross-sectional study with a convenience sample. The measures included demographic and clinical characteristics of patients, the Brief Resilience Scale, the Multidimensional Scale of Perceived Social Support, the Patient Health Questionnaire-4, and the EuroQol-5D-3L. Multivariable analysis identified that resilience and social support reduced anxiety and depression among our patients. Also, we found a significant positive relationship between resilience and social support, and quality of life. In conclusion, our findings suggest that resilience and social support can be protective by reducing anxiety and depression, and improving quality of life among patients with post-COVID-19 syndrome. Policy makers should develop and implement healthcare management programs to provide psychological support to these patients.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Petros A Galanis", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Aglaia Katsiroumpa", - "author_inst": "Faculty of Nursing, National and Kapodistrian University of Athens" - }, - { - "author_name": "Irene Vraka", - "author_inst": "P. & A. Kyriakou Children Hospital" - }, - { - "author_name": "Katerina Kosiara", - "author_inst": "Faculty of Nursing, National and Kapodistrian University of Athens" - }, - { - "author_name": "Olga Siskou", - "author_inst": "University of Piraeus" - }, - { - "author_name": "Olympia Konstantakopoulou", - "author_inst": "Faculty of Nursing, National and Kapodistrian University of Athens" - }, - { - "author_name": "Theodoros Katsoulas", - "author_inst": "Faculty of Nursing, National and Kapodistrian University of Athens" - }, - { - "author_name": "Parisis Gallos", - "author_inst": "Faculty of Nursing, National and Kapodistrian University of Athens" - }, - { - "author_name": "Daphne Kaitelidou", - "author_inst": "Faculty of Nursing, National and Kapodistrian University of Athens" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2023.02.08.23285645", "rel_title": "Mental health, gender, and care-seeking behavior during the COVID-19 pandemic in Sweden: An exploratory study", @@ -106646,6 +107695,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.02.09.23285716", + "rel_title": "Divergence of wastewater SARS-CoV-2 and reported laboratory-confirmed COVID-19 incident case data coincident with wide-spread availability of at-home COVID-19 antigen tests", + "rel_date": "2023-02-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.09.23285716", + "rel_abs": "Concentrations of SARS-CoV-2 RNA in wastewater settled solids from publicly owned treatment works (POTWs) historically correlated strongly with laboratory confirmed incident COVID-19 case data. With the increased availability of at-home antigen tests since late 2021 and early 2022, laboratory test availability and test seeking behavior has decreased. In the United States, the results from at-home antigen tests are not typically reportable to public health agencies and thus are not counted in case reports. As a result, the number of reported laboratory-confirmed incident COVID-19 cases has decreased dramatically, even during times of increased test positivity rates and wastewater concentrations of SARS-CoV-2 RNA. Herein, we tested whether the correlative relationship between wastewater concentrations of SARS-CoV-2 RNA and reported laboratory-confirmed COVID-19 incidence rate has changed since 1 May 2022, a point in time immediately before the onset of the BA.2/BA.5 surge, the first surge to begin after at-home antigen test availability was high in the region. We used daily data from three POTWs in the Greater San Francisco Bay Area of California, USA for the analysis. We found that although there is a significant positive association between wastewater measurements and incident rate data collected after 1 May 2022, the parameters describing the relationship are different than those describing the relationship between the data collected prior to 1 May 2022. If laboratory test seeking or availability continues to change, the relationship between wastewater and reported case data will continue to change. Results suggests that, assuming SARS-CoV-2 RNA shedding remains relatively stable among those infected with the virus as different variants emerge, that wastewater concentrations of SARS-CoV-2 RNA can be used to estimate COVID-19 cases as they would have been during the time when laboratory testing availability and test seeking behavior were at a high (here, before 1 May 2022) using the historical relationship between SARS-CoV-2 RNA and COVID-19 case data.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Alexandria Boehm", + "author_inst": "Stanford University" + }, + { + "author_name": "Marlene K Wolfe", + "author_inst": "Emory University" + }, + { + "author_name": "Bradley White", + "author_inst": "Verily Life Sciences" + }, + { + "author_name": "Bridgette Hughes", + "author_inst": "Verily Life Sciences" + }, + { + "author_name": "Dorothea Duong", + "author_inst": "Verily Life Sciences" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.02.10.528032", "rel_title": "SARS-CoV-2 NSP5 Antagonizes the MHC II Antigen Presentation Pathway by Hijacking Histone Deacetylase 2", @@ -107680,37 +108764,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.02.07.527372", - "rel_title": "Counterintuitive effect of antiviral therapy on influenza A-SARS-CoV-2 coinfection due to viral interference", - "rel_date": "2023-02-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.07.527372", - "rel_abs": "The resurgence of influenza and continued circulation of SARS-CoV-2 raise the question of how these viruses interact in a co-exposed host. Here we studied virus-virus and host-virus interactions during influenza A virus (IAV) -SARS-CoV-2 coinfection using differentiated cultures of the human airway epithelium. Coexposure to IAV enhanced the tissue antiviral response during SARS-CoV-2 infection and suppressed SARS-CoV-2 replication. Oseltamivir, an antiviral targeting influenza, reduced IAV replication during coinfection but also reduced the antiviral response and paradoxically restored SARS-CoV-2 replication. These results highlight the importance of diagnosing coinfections and compel further study of how coinfections impact the outcome of antiviral therapy.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Nagarjuna R. Cheemarla", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Valia T. Mihaylova", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Timothy A. Watkins", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Ellen F. Foxman", - "author_inst": "Yale University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.02.08.23285651", "rel_title": "Individual costs and societal benefits of interventions during the COVID-19 pandemic", @@ -108420,6 +109473,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.02.02.23285386", + "rel_title": "Addressing a climate emergency amidst the COVID-19 pandemic: A mixed-methods study on a hospital evacuation during the 2021 European floods", + "rel_date": "2023-02-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.02.23285386", + "rel_abs": "IntroductionIn July 2021, several European countries were affected by severe floods with water levels of the river Meuse reaching a record high. VieCuri Medical Center (Venlo, the Netherlands) is a hospital located directly adjacent to this river, and in response to the flood threat it was decided to completely evacuate the hospital. The aim of this study was to explore the decision-making process of this emergent evacuation.\n\nMethodsA mixed-method approach was used. Qualitative data were collected through semi-structured interviews with 11 key participants closely involved in the evacuation. Quantitative data on the patients that were admitted at the time of the evacuation decision were collected, and included 30-day mortality, 7-day readmission rates and Charlson Comorbidity Index.\n\nResultsThree themes were constructed from the interviews: risk-assessment, COVID-19 experience and collaboration. Participants highlighted the role of previous experiences from the COVID-19 pandemic. The use of a national patient coordination center enabled to rapidly assess capacity of potential destination hospitals. Furthermore, the hospitals preparedness for evacuation could be improved by a thorough analysis of locoregional hazards and preparing for loss of regional healthcare capacity. Findings unrelated to decision-making included the inefficiency of large-scale ambulance dispatches and the expansion of business continuity plans. No patients died unanticipated during this hospital evacuation or within 30 days.\n\nConclusionExperiences of the COVID-19 pandemic and the availability of a national patient coordination center were found to be decisive in performing this evacuation. This allowed for the swift identification of available capacity in appropriate destination hospitals.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Willemijn van der Wal", + "author_inst": "VieCuri Medical Center" + }, + { + "author_name": "Dennis Barten", + "author_inst": "VieCuri Medical Center" + }, + { + "author_name": "Linsay Ketelings", + "author_inst": "Food Claims Center, Maastricht University" + }, + { + "author_name": "Frits van Osch", + "author_inst": "VieCuri Medical Center" + }, + { + "author_name": "Madhura Rao", + "author_inst": "Food Claims Center, Maastricht University" + }, + { + "author_name": "Luc Mortelmans", + "author_inst": "ZNA Antwerpen" + }, + { + "author_name": "Joost Bierens", + "author_inst": "Vrije Universiteit Brussel" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "emergency medicine" + }, { "rel_doi": "10.1101/2023.02.04.23285479", "rel_title": "Understanding the Impact of Social Engagement Activities, Health Protocol Maintenance, and Social Interaction on Depression During Covid-19 Pandemic Among Older Americans", @@ -109426,25 +110522,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.02.01.526736", - "rel_title": "Omicron's Intrinsic Gene-Gene Interactions Jumped Away from Earlier SARS-CoV-2 Variants and Gene Homologs between Humans and Animals", - "rel_date": "2023-02-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.01.526736", - "rel_abs": "Omicron and its subvariants have become the predominant SARS-CoV-2 variants worldwide. The Omicrons basic reproduction number (R0) has been close to 20 or higher. However, it is not known what caused such an extremely high R0. This work aims to find an explanation for such high R0 Omicron infection. We found that Omicrons intrinsic gene-gene interactions jumped away from earlier SARS-CoV-2 variants which can be fully described by a miniature set of genes reported in our earlier work. We found that the gene PTAFR (Platelet Activating Factor Receptor) is highly correlated with Omicron variants, and so is the gene CCNI (Cyclin I), which is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, and frog. The combination of PTAFR and CCNI can lead to a 100% accuracy of differentiating Omicron COVID-19 infection and COVID-19 negative. We hypothesize that Omicron variants were potentially jumped from COVID-19-infected animals back to humans. In addition, there are also several other two-gene interactions that lead to 100% accuracy. Such observations can explain Omicrons fast-spread reproduction capability as either of those two-gene interactions can lead to COVID-19 infection, i.e., multiplication of R0s leads to a much higher R0. At the genomic level, PTAFR, CCNI, and several other genes identified in this work rise to Omicron druggable targets and antiviral drugs besides the existing antiviral drugs.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Zhengjun Zhang", - "author_inst": "University of Wisconsin" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2023.02.03.526970", "rel_title": "Epidemic patterns of emerging variants with dynamical social distancing", @@ -110194,6 +111271,165 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.01.31.23285306", + "rel_title": "Immunogenicity of the BA.1 and BA.4/5 Bivalent Boosts: A Brief Report of Preliminary Results from the COVAIL Randomized Clinical Trial", + "rel_date": "2023-02-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.31.23285306", + "rel_abs": "In a randomized clinical trial, we compare early neutralizing antibody responses after boosting with bivalent SARS-CoV-2 mRNA vaccines based on either BA.1 or BA.4/BA.5 Omicron spike protein combined with wildtype spike. Responses against SARS-CoV-2 variants exhibited the greatest reduction in titers against currently circulating Omicron subvariants for both bivalent vaccines.", + "rel_num_authors": 36, + "rel_authors": [ + { + "author_name": "Angela R Branche", + "author_inst": "University of Rochester" + }, + { + "author_name": "Nadine Rouphael", + "author_inst": "Emory University Hope Clinic" + }, + { + "author_name": "Cecilia Losada", + "author_inst": "Emory University Hope Clinic" + }, + { + "author_name": "Lindsey R Baden", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Evan J Anderson", + "author_inst": "Emory University Children's Center" + }, + { + "author_name": "Annie F Luetkemeyer", + "author_inst": "Zuckerberg San Francisco General Hospital UCSF" + }, + { + "author_name": "David J Diemert", + "author_inst": "George Washington University" + }, + { + "author_name": "Patricia L Winokur", + "author_inst": "University of Iowa" + }, + { + "author_name": "Rachel M Presti", + "author_inst": "Washington University" + }, + { + "author_name": "Angelica C Kottkamp", + "author_inst": "NYU Langone Manhattan" + }, + { + "author_name": "Ann R Falsey", + "author_inst": "University of Rochester" + }, + { + "author_name": "Sharon E Frey", + "author_inst": "Saint Louis University" + }, + { + "author_name": "Richard Rupp", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Martin Backer", + "author_inst": "NYU Langone Long Island" + }, + { + "author_name": "Richard M Novak", + "author_inst": "University of Illinois at Chicago" + }, + { + "author_name": "Emmanuel B Walter", + "author_inst": "Duke University" + }, + { + "author_name": "Lisa A Jackson", + "author_inst": "Kaiser Permanente Washington Health" + }, + { + "author_name": "Susan J Little", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Lily C Immergluck", + "author_inst": "Morehouse School of Medicine" + }, + { + "author_name": "Siham M Mahgoub", + "author_inst": "Howard University Hospital" + }, + { + "author_name": "Jennifer A Whitaker", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Tara M Babu", + "author_inst": "University of Washington" + }, + { + "author_name": "Paul A Goepfert", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Dahlene N Fusco", + "author_inst": "Tulane University" + }, + { + "author_name": "Robert L Atmar", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Chris M Posavad", + "author_inst": "Fred Hutchinson Cancer Center and University of Washington" + }, + { + "author_name": "Antonia Netzl", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Derek J Smith", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Kalyani Telu", + "author_inst": "The Emmes Company" + }, + { + "author_name": "Jinjian Mu", + "author_inst": "The Emmes Company" + }, + { + "author_name": "Mat Matkowski", + "author_inst": "The Emmes Company" + }, + { + "author_name": "Mamodikoe Makhene", + "author_inst": "Division of Microbiology and Infectious Diseases, NIAID, NIH" + }, + { + "author_name": "Sonja Crandon", + "author_inst": "Division of Microbiology and Infectious Diseases, NIAID, NIH" + }, + { + "author_name": "David C Montefiori", + "author_inst": "Duke University School of Medicine" + }, + { + "author_name": "Paul C Roberts", + "author_inst": "Division of Microbiology and Infectious Diseases, NIAID, NIH" + }, + { + "author_name": "John H Beigel", + "author_inst": "Division of Microbiology and Infectious Diseases, NIAID, NIH" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.02.01.23284949", "rel_title": "Determinants of COVID-19 vaccine uptake in the Netherlands: an ecological analysis", @@ -111196,157 +112432,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pain medicine" }, - { - "rel_doi": "10.1101/2023.01.28.23285133", - "rel_title": "Systems biological assessment of the temporal dynamics of immunity to a viral infection in the first weeks and months of life", - "rel_date": "2023-01-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.28.23285133", - "rel_abs": "The dynamics of innate and adaptive immunity to infection in infants remain obscure. Here, we used a multi-omics approach to perform a longitudinal analysis of immunity to SARS-CoV-2 infection in infants and young children in the first weeks and months of life by analyzing blood samples collected before, during, and after infection with Omicron and Non-Omicron variants. Infection stimulated robust antibody titers that, unlike in adults, were stably maintained for >300 days. Antigen-specific memory B cell (MCB) responses were durable for 150 days but waned thereafter. Somatic hypermutation of V-genes in MCB accumulated progressively over 9 months. The innate response was characterized by upregulation of activation markers on blood innate cells, and a plasma cytokine profile distinct from that seen in adults, with no inflammatory cytokines, but an early and transient accumulation of chemokines (CXCL10, IL8, IL-18R1, CSF-1, CX3CL1), and type I IFN. The latter was strongly correlated with viral load, and expression of interferon-stimulated genes (ISGs) in myeloid cells measured by single-cell transcriptomics. Consistent with this, single-cell ATAC-seq revealed enhanced accessibility of chromatic loci targeted by interferon regulatory factors (IRFs) and reduced accessibility of AP-1 targeted loci, as well as traces of epigenetic imprinting in monocytes, during convalescence. Together, these data provide the first snapshot of immunity to infection during the initial weeks and months of life.", - "rel_num_authors": 34, - "rel_authors": [ - { - "author_name": "Florian Wimmers", - "author_inst": "Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA; Department of Molecular Medicine, Interfaculty Institute for Bioc" - }, - { - "author_name": "Allison R Burrell", - "author_inst": "Department of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Environmental and Public Health Sciences, D" - }, - { - "author_name": "Yupeng Feng", - "author_inst": "Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA" - }, - { - "author_name": "Hong Zheng", - "author_inst": "Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA; Center for Biomedical Informatics Research, Department of Medicin" - }, - { - "author_name": "Prabhu S Arunachalam", - "author_inst": "Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA" - }, - { - "author_name": "Mengyun Hu", - "author_inst": "Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA" - }, - { - "author_name": "Sara Spranger", - "author_inst": "Department of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA" - }, - { - "author_name": "Lindsay Nyhoff", - "author_inst": "Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine" - }, - { - "author_name": "Devyani Joshi", - "author_inst": "Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine" - }, - { - "author_name": "Meera Trisal", - "author_inst": "Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA" - }, - { - "author_name": "Mayanka Awasthi", - "author_inst": "Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, 20993, USA" - }, - { - "author_name": "Lorenza Bellusci", - "author_inst": "Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, 20993, USA." - }, - { - "author_name": "Usama Ashraf", - "author_inst": "Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA; Department of Medicine, Division of Infectious Diseases, Stanford" - }, - { - "author_name": "Sangeeta Kowli", - "author_inst": "Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA; Department of Microbiology and Immunology, Stanford University Sc" - }, - { - "author_name": "Katherine C Konvinse", - "author_inst": "Department of Pediatrics, Stanford University School of Medicine, Stanford University, Stanford, CA, USA" - }, - { - "author_name": "Emily Yang", - "author_inst": "Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA; Department of Medicine, Division of Immunology and Rheumatology, " - }, - { - "author_name": "Michael Blanco", - "author_inst": "Stanford Genomics Service Center, Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA" - }, - { - "author_name": "Kathryn Pellegrini", - "author_inst": "Yerkes National Primate Research Center, Atlanta, GA, USA" - }, - { - "author_name": "Gregory Tharp", - "author_inst": "Yerkes National Primate Research Center, Atlanta, GA, USA" - }, - { - "author_name": "Thomas Hagan", - "author_inst": "Department of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati Colleg" - }, - { - "author_name": "R Sharon Chinthrajah", - "author_inst": "Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA 94305, USA" - }, - { - "author_name": "Alba Grifoni", - "author_inst": "Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA" - }, - { - "author_name": "Alessandro Sette", - "author_inst": "Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infect" - }, - { - "author_name": "Kari C Nadeau", - "author_inst": "Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA 94305, USA" - }, - { - "author_name": "David B Haslam", - "author_inst": "Department of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati Colleg" - }, - { - "author_name": "Steven E Bosinger", - "author_inst": "Yerkes National Primate Research Center, Atlanta, GA, USA; Department of Pathology, Emory University School of Medicine, Atlanta, GA, USA" - }, - { - "author_name": "Jens Wrammert", - "author_inst": "Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine" - }, - { - "author_name": "Holden T Maecker", - "author_inst": "Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA; Department of Microbiology and Immunology, Stanford University Sc" - }, - { - "author_name": "Paul J Utz", - "author_inst": "Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA; Department of Medicine, Division of Immunology and Rheumatology, " - }, - { - "author_name": "Taia T Wang", - "author_inst": "Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA; Department of Medicine, Division of Infectious Diseases, Stanford" - }, - { - "author_name": "Surender Khurana", - "author_inst": "Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, 20993, USA" - }, - { - "author_name": "Purvesh Khatri", - "author_inst": "Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA; Center for Biomedical Informatics Research, Department of Medicin" - }, - { - "author_name": "Mary A Staat", - "author_inst": "Department of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati Colleg" - }, - { - "author_name": "Bali Pulendran", - "author_inst": "Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA; Department of Microbiology and Immunology, Stanford University Sc" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.01.29.23285159", "rel_title": "Probable transmission of SARS-CoV-2 from an African lion to zoo employees", @@ -111888,6 +112973,157 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2023.01.29.23285160", + "rel_title": "High number of SARS-CoV-2 persistent infections uncovered through genetic analysis of samples from a large community-based surveillance study", + "rel_date": "2023-01-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.29.23285160", + "rel_abs": "Persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections may act as viral reservoirs that could seed future outbreaks 1-5, give rise to highly divergent lineages 6-8, and contribute to cases with post-acute Coronavirus disease 2019 (COVID-19) sequelae (Long Covid) 9,10. However, the population prevalence of persistent infections, their viral load kinetics, and evolutionary dynamics over the course of infections remain largely unknown. We identified 381 infections lasting at least 30 days, of which 54 lasted at least 60 days. These persistently infected individuals had more than 50% higher odds of self-reporting Long Covid compared to the infected controls, and we estimate that 0.09-0.5% of SARS-CoV-2 infections can become persistent and last for at least 60 days. In nearly 70% of the persistent infections we identified, there were long periods during which there were no consensus changes in virus sequences, consistent with prolonged presence of non-replicating virus. Our findings also suggest reinfections with the same major lineage are rare and that many persistent infections are characterised by relapsing viral load dynamics. Furthermore, we found a strong signal for positive selection during persistent infections, with multiple amino acid substitutions in the Spike and ORF1ab genes emerging independently in different individuals, including mutations that are lineage-defining for SARS-CoV-2 variants, at target sites for several monoclonal antibodies, and commonly found in immunocompromised patients 11-14. This work has significant implications for understanding and characterising SARS-CoV-2 infection, epidemiology, and evolution.", + "rel_num_authors": 34, + "rel_authors": [ + { + "author_name": "Mahan Ghafari", + "author_inst": "University of Oxford" + }, + { + "author_name": "Matthew Hall", + "author_inst": "University of Oxford" + }, + { + "author_name": "Tanya Golubchik", + "author_inst": "University of Oxford" + }, + { + "author_name": "Daniel Ayoubkhani", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Thomas House", + "author_inst": "University of Manchester" + }, + { + "author_name": "George MacIntyre-Cockett", + "author_inst": "University of Oxford" + }, + { + "author_name": "Helen Fryer", + "author_inst": "University of Oxford" + }, + { + "author_name": "Laura Thomson", + "author_inst": "University of Oxford" + }, + { + "author_name": "Anel Nurtay", + "author_inst": "University of Oxford" + }, + { + "author_name": "David Buck", + "author_inst": "University of Oxford" + }, + { + "author_name": "Angie Green", + "author_inst": "University of Oxford" + }, + { + "author_name": "Amy Trebes", + "author_inst": "University of Oxford" + }, + { + "author_name": "Paolo Piazza", + "author_inst": "University of Oxford" + }, + { + "author_name": "Lorne J Lonie", + "author_inst": "University of Oxford" + }, + { + "author_name": "Ruth Studley", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Emma Rourke", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Darren Smith", + "author_inst": "Northumbria University" + }, + { + "author_name": "Matthew Bashton", + "author_inst": "Northumbria University" + }, + { + "author_name": "Andrew Nelson", + "author_inst": "Northumbria University" + }, + { + "author_name": "Matthew Crown", + "author_inst": "Northumbria University" + }, + { + "author_name": "Clare McCann", + "author_inst": "Northumbria University" + }, + { + "author_name": "Gregory R Young", + "author_inst": "Northumbria University" + }, + { + "author_name": "Rui Andre Nunes de Santos", + "author_inst": "Northumbria University" + }, + { + "author_name": "Zack Richards", + "author_inst": "Northumbria University" + }, + { + "author_name": "Adnan Tariq", + "author_inst": "Northumbria University" + }, + { + "author_name": "Roberto Cahuantzi", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "- Wellcome Sanger Institute COVID-19 Surveillance Team", + "author_inst": "-" + }, + { + "author_name": "- COVID-19 Infection Survey Group", + "author_inst": "-" + }, + { + "author_name": "- The COVID-19 Genomics UK (COG-UK) consortium", + "author_inst": "-" + }, + { + "author_name": "Jeff Barrett", + "author_inst": "Wellcome Sanger Institute" + }, + { + "author_name": "Christophe Fraser", + "author_inst": "University of Oxford" + }, + { + "author_name": "David Bonsall", + "author_inst": "University of Oxford" + }, + { + "author_name": "Sarah Walker", + "author_inst": "University of Oxford" + }, + { + "author_name": "Katrina A Lythgoe", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.01.27.23285032", "rel_title": "Geotemporal analysis of COVID-19 in the Dominican Republic 2020-2021", @@ -113026,37 +114262,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2023.01.25.23284999", - "rel_title": "Prevalence, perceptions and factors influencing COVID-19 vaccines uptake among nurses in fako division, Cameroon", - "rel_date": "2023-01-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.25.23284999", - "rel_abs": "BackgroundSince December 2019, the world has watched the rapid growth of a new pandemic, the COVID-19, a novel pandemic causing death and disruption of normal life. This COVID-19 continues to spread and poses serious threats to public health throughout the world. Even though vaccines are available, there is no guarantee of critical population vaccination, as there still exist stiff resistance to the uptake of the currently available vaccines.\n\nPurposeTo assess nurses perceptions regarding the uptake of COVID-19 vaccines, determine the proportion of nurses vaccinated, as well as the associated factors influencing the uptake of COVID-19 vaccines, so as to alert decision makers on the possible limitations associated with the uptake of the vaccines in the nursing population in Fako Division, Cameroon.\n\nMethodsThis was a mixed method quantitative and qualitative study conducted in Fako Division. A multistage random sampling technique was employed to enroll participants into the study. We collected quantitative data from consented nurses through the use of a structured questionnaire from April 06th to June 2nd, 2022, and qualitative data from nurse leaders through focused-group discussion from June 3rd to 23rd, 2022. In the quantitative phase, we performed descriptive and inferential statistics using the SPSS Version 23.0 and in the qualitative phase, we performed a thematic content analyses and transcription.\n\nResultsIn the quantitative phase, we had more females 131(66.5%), and nurses aged 26-40years 90(45.7%). Most nurses worked in the maternity 49(24.9%). In the qualitative phase, 20(76.9%) were females. Regarding nurses perceptions of COVID-19 vaccines uptake, 133(67.5%) nurses had positive perceptions, and 26(07.6%) had \"No trust\" in the vaccines. Most nurses 109(55.3%) had not been vaccinated. Negative factors reported by nurses included the belief that the vaccines were dangerous and could cause death 120(60.9%) and 32(16.2%) said no one can influence them to change their minds about taking the vaccines. In the qualitative phase, a majority of the nurse leaders 15(57.7%) wished that COVID-19 vaccination should continue, but with accompanying research to eliminate side effects. It was observed that a majority of the nurse leaders 16(61.5%) had been vaccinated. The respondents reported some factors (belief factors, social influence and lack of knowledge), which had negatively influenced them from taking the COVID-19 vaccines.\n\nConclusionNurses perceived high relevance for the COVID-19 vaccines while a majority of the nurse leaders perceived that the COVID-19 vaccines are not safe, ineffective with numerous side effects, has a magnetic effect, politically motivated with bad faith, and has the possibility to cause infections. Furthermore, most nurses had not been vaccinated, but a majority of nurse leaders were reported to have taken a COVID-19 vaccine. Several negative factors including belief, social influence and religious factors were reported to have contributed to the lower uptake of the COVID-19 vaccines amongst nurses and nurse leaders in Fako division, Cameroon.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Niba Clinton Ambe", - "author_inst": "University of Buea Faculty of Health Sciences" - }, - { - "author_name": "Achidi Eric Akum", - "author_inst": "University of Buea" - }, - { - "author_name": "Nkemayim Florence Binwi", - "author_inst": "University of Buea Faculty of Health Sciences" - }, - { - "author_name": "Palle John Ngunde", - "author_inst": "University of Buea Faculty of Health Sciences" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "nursing" - }, { "rel_doi": "10.1101/2023.01.25.23284428", "rel_title": "Primary care coding activity related to the use of online consultation systems or remote consulting: an analysis of 53 million peoples' health records using OpenSAFELY", @@ -113690,6 +114895,77 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.01.26.525770", + "rel_title": "Infection of equine bronchial epithelial cells with a SARS-CoV-2 pseudovirus", + "rel_date": "2023-01-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.26.525770", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of COVID-19, can infect animals by binding to the angiotensin-converting enzyme 2 (ACE2). Equine infection appears possible due to high homology ({approx}97%) between human and equine ACE2, evidence of in vitro infection in cell lines expressing equine ACE2, and evidence of seroconversion in horses after exposure to persons infected with SARS-CoV-2. Our objective was to examine susceptibility of cultured primary equine bronchial epithelial cells (EBECs) to a SARS-CoV-2 pseudovirus relative to human bronchial epithelial cells (HBECs; positive control). ACE2 expression in EBECs detected by immunofluorescence, western immunoblotting, and flow cytometry was lower in EBECs than in HBECs. EBECs were transduced with a lentivirus pseudotyped with the SARS-CoV-2 spike protein that binds to ACE2 and expresses the enhanced green fluorescent protein (eGFP) as a reporter. Cells were co-cultivated with the pseudovirus at a multiplicity of infection of 0.1 for 6 hours, washed, and maintained in media. After 96 hours, eGFP expression in EBECs was demonstrated by fluorescence microscopy, and mean {Delta} Ct values from quantitative PCR were significantly (P < 0.0001) higher in HBECs (8.78) than HBECs (3.24) indicating lower infectivity in EBECs. Equine respiratory tract cells were susceptible to infection with a SARS-CoV-2 pseudovirus. Lower replication efficiency in EBECs suggests that horses are unlikely to be an important zoonotic host of SARS-CoV-2, but viral mutations could render some strains more infectious to horses. Serological and virological monitoring of horses in contact with persons shedding SARS-CoV-2 is warranted.\n\nIMPORTANCEThis study provides the first published evidence for SARS-CoV-2 pseudovirus infection in equine airway epithelial cells, which were less susceptible to infection than cells of human origin. This was presumably due to lower ACE2 expression in equine cells, lower viral affinity for equine ACE2, or both. Our results are important considering recent evidence for asymptomatic seroconversion in horses following exposure to COVID-19 positive humans, despite this lower susceptibility, and increased affinity of viral variants of concern for equine ACE2 compared to ancestral strains. Thus, there is great need to better characterize SARS-CoV-2 susceptibility in horses for the benefit of veterinary and human health.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Rebecca M. Legere", + "author_inst": "Texas A & M University School of Veterinary Medicine and Biomedical Sciences" + }, + { + "author_name": "Angelica R. Allegro", + "author_inst": "Texas A & M University School of Veterinary Medicine and Biomedical Sciences" + }, + { + "author_name": "Yvonne Affram", + "author_inst": "Texas A & M University" + }, + { + "author_name": "Bibiana Petri da Silveira", + "author_inst": "Texas A & M University School of Veterinary Medicine and Biomedical Sciences" + }, + { + "author_name": "Jennifer L. Fridley", + "author_inst": "Texas A & M University School of Veterinary Medicine and Biomedical Sciences" + }, + { + "author_name": "Kelsey M. Wells", + "author_inst": "Texas A & M Health Science Center" + }, + { + "author_name": "Numan Oezguen", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Robert C. Burghardt", + "author_inst": "Texas A & M University School of Veterinary Medicine and Biomedical Sciences" + }, + { + "author_name": "Gus A. Wright", + "author_inst": "Texas A & M University School of Veterinary Medicine and Biomedical Sciences" + }, + { + "author_name": "Jeroen Pollet", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Angela I. Bordin", + "author_inst": "Texas A & M University School of Veterinary Medicine and Biomedical Sciences" + }, + { + "author_name": "Paul de Figueiredo", + "author_inst": "Texas A & M Health Science Center" + }, + { + "author_name": "Julian L. Leibowitz", + "author_inst": "Texas A & M Health Science Center" + }, + { + "author_name": "Noah D. Cohen", + "author_inst": "Texas A & M University School of Veterinary Medicine and Biomedical Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.01.23.23284848", "rel_title": "Acute tubulointerstitial nephritis with or without uveitis: a novel form of post-acute COVID-19 syndrome in children", @@ -114956,41 +116232,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.01.18.22277474", - "rel_title": "COVID-19 isolation and quarantine orders in Berlin-Reinickendorf (Germany): How many, how long and to whom?", - "rel_date": "2023-01-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.18.22277474", - "rel_abs": "Isolating COVID-19 cases and quarantining their close contacts can prevent COVID-19 transmissions but also inflict harm. We analysed isolation and quarantine orders by the local public health agency in Berlin-Reinickendorf (Germany) and their dependence on the recommendations by the Robert Koch Institute, the national public health institute. Between 3 March 2020 and 18 December 2021 the local public health agency ordered 24603 isolations and 45014 quarantines (mean contacts per case 1.9). More days of quarantine per 100 inhabitants were ordered for children than for adults: 4.1 for children aged 0-6, 5.2 for children aged 7-17, 0.9 for adults aged 18-64 and 0.3 for elderly aged 65-110. The mean duration for isolation orders was 10.2 and for quarantine orders 8.2 days. We calculated a delay of 4 days between contact and quarantine order. 3484 of contact persons were in quarantine when they developed an infection. Our study quantifies isolation and quarantine orders, shows that children had been ordered to quarantine more than adults and that there were fewer school days lost to isolation or quarantine as compared to school closures. Our results indicate that the recommendations of the Robert Koch Institute had an influence on isolation and quarantine duration as well as contact identification and that the local public health agency was not able to provide rigorous contact tracing, as the mean number of contacts was lower than expected.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Jakob Schumacher", - "author_inst": "Robert Koch Institut" - }, - { - "author_name": "Lisa Kuehne", - "author_inst": "Leibniz-Institute for Prevention Research an Epidemiology - BIPS" - }, - { - "author_name": "Sophia Bruessermann", - "author_inst": "Leibniz Institutefor Prevention Research and Epidemiology - BIPS" - }, - { - "author_name": "Benjamin Geisler", - "author_inst": "Fraunhofer Institute for Digital Medicine - MEVIS" - }, - { - "author_name": "Sonja Jaeckle", - "author_inst": "Fraunhofer Institute for Digital Medicine - MEVIS" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.01.23.525275", "rel_title": "Genome-wide CRISPR screens identify noncanonical translation factor eIF2A as an enhancer of SARS-CoV-2 programmed -1 ribosomal frameshifting", @@ -115620,6 +116861,37 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2023.01.22.23284879", + "rel_title": "Delirium in a Young Predominantly Hispanic Population with COVID-19", + "rel_date": "2023-01-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.22.23284879", + "rel_abs": "PurposeTo study a primarily Hispanic population of adults younger than 65 to determine if COVID-19 patients with a concurrent delirium diagnosis had worse clinical outcomes in terms of hospital stay, ventilation and mortality, than those without a delirium diagnosis.\n\nMethodsAfter approval by the appropriate Institutional Review Board, a retrospective cohort study was performed looking at demographics, vital statistics, and clinical outcomes of patients aged 18-65 admitted to a hospital in the United States - Mexico border region with COVID-19 between March 1 and June 30, 2020. Data were analyzed using Fishers exact test, or an unpaired t-test where appropriate, and a univariate analysis was performed to establish relative risk. Confidence intervals were set at 95% and p values [≤]0.05 were considered significant.\n\nResults133 patients with confirmed COVID-19 diagnoses (58% men, 92% Hispanic) were included. Mean age was 50.5 with a standard deviation of 11.7 years (range 20-65 years). The prevalence of delirium was 6%. Fifty percent of delirium patients died during hospitalization compared to 15% of patients without delirium. Patients with delirium were found to spend more days hospitalized, in the intensive care unit, and intubated than their counterparts without delirium. Delirium was associated with increased risk of being placed on mechanical ventilation (RR 3.91, 95% CI 1.46--10.41, p value 0.006).\n\nConclusionsDelirium was associated with worse COVID-19 outcomes independent of age. COVID-19 patients need to be actively assessed for signs of delirium and appropriate precautionary measures should be implemented. Proper documentation of delirium is key to continue learning about the incidence of delirium in COVID-19 patients.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Kelsey C Talkington", + "author_inst": "TTUHSC El Paso Paul L Foster School of Medicine" + }, + { + "author_name": "Luis A Alvarado", + "author_inst": "TTUHSC El Paso Biostatistics and Epidemiology Consulting Laboratory" + }, + { + "author_name": "Christopher A Castaneda", + "author_inst": "TTUHSC El Paso Department of Psychiatry" + }, + { + "author_name": "Silvina B Tonarelli", + "author_inst": "TTUHSC El Paso Department of Psychiatry" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2023.01.22.23284880", "rel_title": "COVision: Convolutional Neural Network for the Differentiation of COVID-19 from Common Pulmonary Conditions using CT Scans", @@ -116718,33 +117990,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "surgery" }, - { - "rel_doi": "10.1101/2023.01.20.23284600", - "rel_title": "COVID-19 and Mental Health in China: Effects of Personality and Demographics", - "rel_date": "2023-01-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.20.23284600", - "rel_abs": "China was the first country affected by the COVID-19 virus and it reacted strongly in the first months of 2020. This paper presents new evidence on the deterioration in mental health in China between 2018 and 2020. Using two waves of the China Family Panel Studies (CFPS) we can follow the same individuals pre and during the pandemic periods. We find clear evidence of a moderate level of mental health deterioration between 2018 and 2020. The prevalence of severe cases of depression, measured using an eight-item version of the common CES-D scale, increased from 6.33% in 2018 to 7.54% in 2020; quantifiable as around a 19% increase. This deterioration is higher for individuals who are subject to strict lockdowns, about 0.3 symptoms more on average, and it is stronger among those who already reported symptoms of depression in the 2018 wave of data. The effects we find are larger for individuals with more open personalities: one standard deviation of the Openness trait corresponds to 0.08 more symptoms, while more Neurotic individuals do not seem to be more affected. Younger cohorts and individuals with lower levels of education are more affected. Males seem slightly more affected than females, although this difference is statistically non-significant.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Xiao Zhang", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Michele Battisti", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Eugenio Proto", - "author_inst": "University of Glasgow" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2023.01.16.23284626", "rel_title": "High proportion of Ugandans with pre-pandemic SARS-CoV-2 cross-reactive CD4+ and CD8+ T-cell responses", @@ -117410,6 +118655,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.01.18.23284739", + "rel_title": "Effectiveness of Vaccination and Previous Infection Against Omicron Infection and Severe Outcomes in Children Under 12 Years of Age", + "rel_date": "2023-01-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.18.23284739", + "rel_abs": "BackgroundData on the protection conferred by Covid-19 vaccination and previous SARS-CoV-2 infection against omicron infection and severe outcomes in children can inform prevention strategies.\n\nMethodsWe obtained vaccination records and clinical outcomes for 1,368,721 North Carolina residents 11 years of age or younger from October 29, 2021 to January 6, 2023. We used Cox regression to estimate the time-varying effects of primary and booster vaccination and previous infection on the risks of omicron infection, hospitalization, and death.\n\nResultsFor children 5-11 years of age, the effectiveness of primary vaccination against infection was 59.9% (95% confidence interval [CI], 58.5 to 61.2), 33.7% (95% CI, 32.6 to 34.8), and 14.9% (95% CI, 12.3 to 17.5) at 1, 4 and 10 months after the first dose; the effectiveness of a monovalent or bivalent booster dose after 1 month was 24.4% (95% CI, 14.4 to 33.2) or 76.7% (95% CI, 45.7 to 90.0); and the effectiveness of omicron infection against reinfection was 79.9% (95% CI, 78.8 to 80.9) and 53.9% (95% CI, 52.3 to 55.5) after 3 and 6 months, respectively. For children 0-4 years of age, the effectiveness of primary vaccination against infection was 63.8% (95% CI, 57.0 to 69.5) and 58.1% (95% CI, 48.3 to 66.1) at 2 and 5 months after the first dose, and the effectiveness of omicron infection against reinfection was 77.3% (95% CI, 75.9 to 78.6) and 64.7% (95% CI, 63.3 to 66.1) after 3 and 6 months, respectively. For both age groups, vaccination and previous infection had better effectiveness against hospitalization and death than against infection.\n\nConclusionsCovid-19 vaccination was effective against omicron infection and severe outcomes in children under the age of 12 years, although the effectiveness decreased over time. Bivalent boosters were more effective than monovalent boosters. Immunity acquired via omicron infection was very high and waned gradually over time.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Danyu Lin", + "author_inst": "University of North Carolina" + }, + { + "author_name": "Yangjianchen Xu", + "author_inst": "University of North Carolina" + }, + { + "author_name": "Yu Gu", + "author_inst": "University of North Carolina" + }, + { + "author_name": "Donglin Zeng", + "author_inst": "University of North Carolina" + }, + { + "author_name": "Bradford Wheeler", + "author_inst": "North Carolina Department of Health and Human Services" + }, + { + "author_name": "Hayley Young", + "author_inst": "North Carolina Department of Health and Human Services" + }, + { + "author_name": "Zack Moore", + "author_inst": "North Carolina Department of Health and Human Services" + }, + { + "author_name": "Shadia Sunny", + "author_inst": "CDC Foundation at North Carolina Department of Health and Human Services" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.01.18.524660", "rel_title": "SARS-CoV-2 Omicron XBB.1.5 may be a cautionary variant by in silico study", @@ -118536,57 +119828,6 @@ "type": "new results", "category": "neuroscience" }, - { - "rel_doi": "10.1101/2023.01.17.524254", - "rel_title": "Higher Angiotensin I Converting Enzyme 2 (ACE2) levels in the brain of individuals with Alzheimer's disease.", - "rel_date": "2023-01-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.17.524254", - "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a major cause of death in the elderly. Cognitive decline due to Alzheimers disease (AD) is frequent in the geriatric population disproportionately affected by the COVID-19 pandemic. Interestingly, central nervous system (CNS) manifestations have been reported in SARS-CoV-2-infected patients. In this study, we investigated the levels of Angiotensin I Converting Enzyme 2 (ACE2), the main entry receptor of SARS-COV-2 in cells, in postmortem parietal cortex samples from two independent AD cohorts, totalling 142 persons. Higher concentrations of ACE2 protein and mRNA were found in individuals with a neuropathological diagnosis of AD compared to age-matched healthy control subjects. Brain levels of soluble ACE2 were inversely associated with cognitive scores (p = 0.02), markers of pericytes (PDGFR{beta}, p=0.02 and ANPEP, p = 0.007) and caveolin1 (p = 0.03), but positively correlated with soluble amyloid-{beta} peptides (A{beta}) concentrations (p = 0.01) and insoluble phospho- tau (S396/404, p = 0.002). No significant differences in ACE2 were observed in the 3xTgAD mouse model of tau and A{beta} neuropathology. Results from immunofluorescence and Western blots showed that ACE2 protein is mainly localized in neurons in the human brain but predominantly in microvessels in the mouse brain. The present data show that an AD diagnosis is associated with higher levels of soluble ACE2 in the human brain, which might contribute to a higher risk of CNS SARS-CoV-2 infection.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Louise Reveret", - "author_inst": "Centre de recherche du CHU de Quebec - Universite Laval (CHUL)" - }, - { - "author_name": "Manon Leclerc", - "author_inst": "Centre de recherche du CHU de Quebec - Universite Laval (CHUL)" - }, - { - "author_name": "vincent Emond", - "author_inst": "Centre de recherche du CHU de Quebec - Universite Laval (CHUL)" - }, - { - "author_name": "Andreanne Loiselle", - "author_inst": "Centre de recherche du CHU de Quebec - Universite Laval (CHUL)" - }, - { - "author_name": "Bourassa Philippe", - "author_inst": "Centre de recherche du CHU de Quebec - Universite Laval (CHUL)" - }, - { - "author_name": "Cyntia Tremblay", - "author_inst": "Centre de recherche du CHU de Quebec - Universite Laval (CHUL)" - }, - { - "author_name": "David A Bennett", - "author_inst": "Rush University Medical Center" - }, - { - "author_name": "Sebastien S. Hebert", - "author_inst": "Laval University" - }, - { - "author_name": "Frederic S. Calon", - "author_inst": "Centre de recherche du CHU de Quebec - Universite Laval (CHUL)" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "neuroscience" - }, { "rel_doi": "10.1101/2023.01.18.524384", "rel_title": "Cell division tracing combined with single-cell transcriptomics reveals new cell types and differentiation paths in the regenerating mouse lung", @@ -119284,6 +120525,53 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.01.16.524178", + "rel_title": "Enhanced transmissibility, infectivity and immune resistance of the SARS-CoV-2 Omicron XBB.1.5 variant", + "rel_date": "2023-01-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.16.524178", + "rel_abs": "In 2022, we have elucidated the characteristics of a variety of newly emerging SARS-CoV-2 Omicron subvariants. At the end of 2022, the XBB.1.5 variant, an descendant of XBB.1 that acquired the S:F486P substitution, emerged and is rapidly spreading in the USA and is the latest variant of concern. Although the features of XBB.1.5 was already reported by another group as a preprint, we think multiple and independent evaluations important, and these reports are crucial for sustained global health. In this study, our epidemic dynamics analysis revealed that the relative effective reproduction number (Re) of XBB.1.5 is more than 1.2-fold greater than that of the parental XBB.1, and XBB.1.5 is outcompeting BQ.1.1, the predominant lineage in the USA as of December 2022. Our data suggest that XBB.1.5 will rapidly spread worldwide in the near future. Yeast surface display assay and pseudovirus assay respectively showed that the ACE2 binding affinity and infectivity of XBB.1.5 is 4.3-fold and 3.3-fold higher than those of XBB.1, respectively. Moreover, neutralization assay revealed that XBB.1.5 is robustly resistant to BA.2 breakthrough infection sera (41-fold versus B.1.1, 20-fold versus BA.2) and BA.5 breakthrough infection sera (32-fold versus B.1.1, 9.5-fold versus BA.5), respectively. Because the immune resistance of XBB.1.5 is comparable to that of XBB.1, our results suggest that XBB.1.5 is the most successful XBB lineage as of January 2023 by acquiring the S:F486P substitution to augment ACE2 binding affinity without losing remarkable immune resistance, which leads to greater transmissibility.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Keita Uriu", + "author_inst": "University of Tokyo" + }, + { + "author_name": "Jumpei Ito", + "author_inst": "The Institute of Medical Science, The University of Tokyo" + }, + { + "author_name": "Jiri Zahradnik", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Shigeru Fujita", + "author_inst": "University of Tokyo" + }, + { + "author_name": "Yusuke Kosugi", + "author_inst": "University of Tokyo" + }, + { + "author_name": "Gideon Schreiber", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "- The Genotype to Phenotype Japan (G2P-Japan) Consortium", + "author_inst": "" + }, + { + "author_name": "Kei Sato", + "author_inst": "Institute of Medical Science, The University of Tokyo" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.01.16.524211", "rel_title": "The emergence of goblet inflammatory or ITGB6hi nasal progenitor cells determines age-associated SARS-CoV-2 pathogenesis", @@ -120466,33 +121754,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2023.01.13.23284305", - "rel_title": "Burden, Causation, and Particularities of long-COVID in African populations: A rapid systematic review", - "rel_date": "2023-01-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.13.23284305", - "rel_abs": "BackgroundThe global estimated prevalence of long COVID-19 is 43%, and the most common symptoms found globally are fatigue, confusion, or lack of confusion, and dyspnea, with prevalence rates of 23%, 14%, and 13%, respectively. However, long COVID still lacks an overall review in African populations. The aim of this review was to determine the prevalence of long COVID, its most common symptoms, comorbidities, and pathophysiological mechanisms.\n\nMethodsA systematic review of long COVID in African populations was conducted. The random effects model was used to calculate the pooled prevalence rates (95% CI). If the results could not be pooled, a narrative synthesis was performed.\n\nResultsWe included 14 studies from 7 African countries, totaling 6,030 previously SARS-CoV-2 infected participants and 2,954 long COVID patients. Long COVID had a pooled prevalence of 41% [26%-56%]. Fatigue, dyspnea, and confusion or lack of concentration were the most common symptoms, with prevalence rates (95% CI) of 41% [26%-56%], 25% [12%-38%], and 40% [12%-68%], respectively. Long COVID was associated with advanced age, being female, more than three long COVID symptoms in the acute phase, initial fatigue and dyspnea, post-recovery stress, sadness, and sleep disturbances, and loss of appetite at symptoms onset, mild, moderate, and severe, pre-existing obesity, hypertension, diabetes mellitus, and the presence of any chronic illness (P [≤]0.05). According to our review, high micro clot and platelet poor plasma (PPP) viscosity explain the pathophysiology of long COVID.\n\nConclusionLong COVID prevalence in Africa was comparable to the global prevalence. However, the prevalence of the most common symptoms was higher in Africa. Comorbidities associated with long COVID may lead to additional complications in African populations due to hypercoagulation and thrombosis.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Peter S Nyasulu", - "author_inst": "Stellenbosch University" - }, - { - "author_name": "Jacques L Tamuzi", - "author_inst": "Stellenbosch University" - }, - { - "author_name": "Rajiv T Erasmus", - "author_inst": "Stellenbosch University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.01.10.523518", "rel_title": "Anthracyclines inhibit SARS-CoV-2 infection", @@ -121146,6 +122407,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.01.11.523616", + "rel_title": "Intranasal mRNA-LNP vaccination protects hamsters from SARS-CoV-2 infection", + "rel_date": "2023-01-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.11.523616", + "rel_abs": "Intranasal vaccination represents a promising approach for preventing disease caused by respiratory pathogens by eliciting a mucosal immune response in the respiratory tract that may act as an early barrier to infection and transmission. This study investigated immunogenicity and protective efficacy of intranasally administered messenger RNA (mRNA)-lipid nanoparticle (LNP) encapsulated vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Syrian golden hamsters. Intranasal mRNA-LNP vaccination systemically induced spike-specific binding (IgG and IgA) and neutralizing antibodies with similar robustness to intramuscular controls. Additionally, intranasal vaccination decreased viral loads in the respiratory tract, reduced lung pathology, and prevented weight loss after SARS-CoV-2 challenge. This is the first study to demonstrate successful immunogenicity and protection against respiratory viral infection by an intranasally administered mRNA-LNP vaccine.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Gabriela Baldeon Vaca", + "author_inst": "Moderna, Inc." + }, + { + "author_name": "Michelle Meyer", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Ana Cadete", + "author_inst": "Moderna, Inc." + }, + { + "author_name": "Chiaowen Joyce Hsiao", + "author_inst": "Moderna, Inc." + }, + { + "author_name": "Anne Golding", + "author_inst": "Moderna, Inc." + }, + { + "author_name": "Albert Jeon", + "author_inst": "Moderna, Inc." + }, + { + "author_name": "Eric Jacquinet", + "author_inst": "Moderna, Inc." + }, + { + "author_name": "Emily Azcue", + "author_inst": "Moderna, Inc." + }, + { + "author_name": "Chenxia Monica Guan", + "author_inst": "Moderna, Inc." + }, + { + "author_name": "Xavier Sanchez-Felix", + "author_inst": "Moderna, Inc." + }, + { + "author_name": "Colette A. Pietzsch", + "author_inst": "University of Texas Medical Branch; Galveston National Laboratory" + }, + { + "author_name": "Chad E. Mire", + "author_inst": "University of Texas Medical Branch; Galveston National Laboratory" + }, + { + "author_name": "Matthew A. Hyde", + "author_inst": "University of Texas Medical Branch; Galveston National Laboratory" + }, + { + "author_name": "Margaret E. Comeaux", + "author_inst": "University of Texas Medical Branch; Galveston National Laboratory" + }, + { + "author_name": "Julie M. Williams", + "author_inst": "University of Texas Medical Branch; Galveston National Laboratory" + }, + { + "author_name": "Jean C. Sung", + "author_inst": "Moderna, Inc." + }, + { + "author_name": "Andrea Carfi", + "author_inst": "Moderna, Inc." + }, + { + "author_name": "Darin K. Edwards", + "author_inst": "Moderna, Inc." + }, + { + "author_name": "Alexander Bukreyev", + "author_inst": "University of Texas Medical Branch at Galveston" + }, + { + "author_name": "Kapil Bahl", + "author_inst": "Moderna, Inc." + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.01.11.523649", "rel_title": "Vectored Immunoprophylaxis and Treatment of SARS-CoV-2 Infection", @@ -122088,69 +123444,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.01.09.23284367", - "rel_title": "Validation of a MALDI-TOF MS method for SARS-CoV-2 detection on the Bruker Biotyper and nasopharyngeal swabs. A Brazil - UK collaborative study.", - "rel_date": "2023-01-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.09.23284367", - "rel_abs": "We had developed a MALDI-TOF mass spectrometry method for detection of SARS-CoV-2 virus in saliva-gargle samples using Shimadzu MALDI-TOF mass spectrometers in the UK. This was validated in the USA to CLIA-LDT standards for asymptomatic infection detection remotely via sharing protocols, shipping key reagents, video conference and data exchange. In Brazil, more so than in the UK and USA, there is a need to develop non-PCR dependent rapid affordable SARS-CoV-2 infection screening tests, which also identify variant SARS-CoV-2 and other virus infections. Travel restrictions necessitated remote collaboration with validation on the available Clinical MALDI-TOF - the Bruker Biotyper (microflex(R) LT/SH) - and on nasopharyngeal swab samples, as salivary gargle samples were not available. The Bruker Biotyper was shown to be almost log10^3 more sensitive at detection of high molecular weight spike proteins. A protocol for saline swab soaks out was developed and duplicate swab samples collected in Brazil were analysed by MALDI-TOF MS. The swab collected sample spectra varied from that of gargle-saliva in three additional mass peaks in the mass region expected for IgG heavy chains and human serum albumin. A subset of clinical samples with additional high mass, probably Spike-related proteins, were also found. Spectral data comparisons and analysis, subjected to machine learning algorithms in order to resolve RT-qPCR positive from RT-qPCR negative swab samples, showed a 78% agreement with RT-qPCR scoring for SARS-CoV-2 infection.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Otavio von Ameln Lovison Sr.", - "author_inst": "Federal University of Rio Grande do Sul" - }, - { - "author_name": "Raminta Grigaite", - "author_inst": "Map Sciences Ltd, The iLab, Priory Park, Bedford UK, MK44 3RZ" - }, - { - "author_name": "Fabiana Carolina Zempulski Volpato", - "author_inst": "Laboratorio de Pesquisa em Resistencia Bacteriana (LABRESIS); Hospital de Clinicas de Porto Alegre , RS, Brazil" - }, - { - "author_name": "Jason Kruse Iles", - "author_inst": "Map Sciences Ltd, The iLab, Priory Park, Bedford UK, MK44 3RZ" - }, - { - "author_name": "Jonathan Lacey", - "author_inst": "Map Sciences Ltd, The iLab, Priory Park, Bedford UK, MK44 3RZ" - }, - { - "author_name": "Fabiano Barreto", - "author_inst": "Laboratorio Federal de Defesa Agropecuaria; RS, Brazil" - }, - { - "author_name": "Sai Rahul Pandiri", - "author_inst": "Map Sciences Ltd, The iLab, Priory Park, Bedford UK, MK44 3RZ" - }, - { - "author_name": "Lisiane da Luz Rocha Balzan", - "author_inst": "Grupo Exame, DASA, RS, Brazil" - }, - { - "author_name": "Vlademir Vicente Cantarelli", - "author_inst": "Universidade Federal de Ciencias da Saude de Porto Alegre, RS, Brazil; Universidade FEEVALE, RS, Brazil" - }, - { - "author_name": "Afonso Luis Barth", - "author_inst": "Hospital de Clinicas de Porto Alegre" - }, - { - "author_name": "Andreza Francisco Martins", - "author_inst": "Universidade Federal do Rio Grande do Sul" - }, - { - "author_name": "Raymond Kruse Iles", - "author_inst": "MAP Sciences" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.01.09.23284380", "rel_title": "Effectiveness of an eHealth Intervention for Reducing Psychological Distress and Increasing COVID-19 Knowledge and Protective Behaviors among Ethnoracially Diverse Sexual and Gender Minority Adults: A Quasi-experimental Study (#SafeHandsSafeHearts)", @@ -122660,6 +123953,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2023.01.06.23284259", + "rel_title": "Degree of immunoglobulin kappa light chain glycosylation of anti-spike SARS CoV-2 antibodies correlates with COVID-19 severity.", + "rel_date": "2023-01-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.06.23284259", + "rel_abs": "Glycosylation of antibodies and the effects this has on inflammatory responses has concentrated predominately on the study of glycosylation moieties found in the Fc region of heavy chains. Light chain glycosylation and their ratios are relatively understudied. Nevertheless, variable glycosylation and ratio of {kappa} and {lambda} light chains have been associated with worse prognosis in myeloma and in tissue deposition - amyloidosis.\n\nThe {kappa} & {lambda} light chains, of antibodies binding to SARS-CoV2 nucleocapsid and spike protein were analysed, using MALDI-ToF MS, in respect to their intensity, ratios, glycosylation patterns and any pattern changes correlating with COVID-19 severity. The molecular masses and signal intensity of {kappa} and {lambda} glycosylated and non-glycosylated light chains were measured for immunoglobulins isolated from plasma of sero-positive and sero-negative health care workers (HCW), and convalescent patients who had suffered from acute respiratory distress syndrome (ARDS).\n\nOverall, there was no significant changes in {kappa} to {lambda} ratio of total IgG (via protein G capture) antibodies between the groups. A non-statistically significant trend towards {lambda} light chains was found in antibodies against SARS CoV-2 Nucleocapsid and Spike proteins. However, detailed analysis of the molecular forms found a significant increase and bias towards un-glycosylated light chains and in particular un-glycosylated {kappa} light chains, in antibodies against SAR-CoV-2 spike protein, from convalescent COVID-ARDS patients.\n\nHere we have demonstrated a bias towards un-glycosylated {kappa} chains in anti-spike antibodies in those who suffered from ARDS as a result of SARS-CoV2 infection 3 months after recovery. How this relates to the immunopathology of COVID-19 requires further study.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Raminta Grigaite", + "author_inst": "MAPSciences Ltd" + }, + { + "author_name": "Jason K Iles", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Stephen Harding", + "author_inst": "Bindingsite group" + }, + { + "author_name": "Roshani Patel", + "author_inst": "Bindingsite Group" + }, + { + "author_name": "Gregg Wallis", + "author_inst": "Bindingsite group" + }, + { + "author_name": "Raymond Kruse Iles", + "author_inst": "MAP Sciences" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.01.06.23284202", "rel_title": "Long Covid symptoms and diagnosis in primary care: a cohort study using structured and unstructured data in The Health Improvement Network primary care database", @@ -123798,45 +125130,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.01.03.23284126", - "rel_title": "Can Koreans be 'FREE' from mask wearing?: Advanced mathematical model can suggest the idea", - "rel_date": "2023-01-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.03.23284126", - "rel_abs": "BackgroundIt was found that more than half of the population in Korea had a prior COVID-19 infection. In 2022, most nonpharmaceutical interventions, except mask-wearing indoors, had been lifted. Discussions about easing the indoor mask mandate are ongoing.\n\nMethodsWe developed an age-structured compartmental model that distinguishes vaccination history, prior infection, and medical staff from the rest of the population. Contact patterns among hosts were separated based on age and location. We simulated scenarios with the lifting of the mask mandate all at once or sequentially according to the locations. Furthermore, we investigated the impact of a new variant assuming that it has higher transmissibility and risk of breakthrough infection.\n\nFindingsWe found that the peak size of administered severe patients might not exceed 1,100 when the mask mandate is lifted everywhere, and 800 if the mask mandate only remains in the hospital. If the mask mandate is lifted in a sequence (except hospital), then the peak size of administered severe patients did not exceed 650. Moreover, if the new variant have both of higher transmissibility and immune reduction therefore the effective reproductive number of the new variant is approximately 3 times higher than the current variant, additional interventions may be needed to keep the administered severe patients from exceeding 2,000, which is the critical level we set.\n\nInterpretationOur findings showed that the lifting of the mask mandate, except in hospitals, would be applicable more manageable if it is implemented sequentially. Considering a new variant, we found that depending on the population immunity and transmissibility of the variant, wearing masks and other interventions may be necessary for controlling the disease.\n\nFundingThis paper is supported by the Korea National Research Foundation (NRF) grant funded by the Korean government (MEST) (NRF-2021M3E5E308120711). This paper is also supported by the Korea National Research Foundation (NRF) grant funded by the Korean government (MEST) (NRF-2021R1A2C100448711). This research was also supported by a fund (2022-03-008) by Research of Korea Disease Control and Prevention Agency.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSThere are numerous studies in modelling transmission dynamics of COVID-19 variants but only a few published works tackle the lifting of mask mandate considering the omicron variant, although these studies did not consider unreported cases, variants, and waning immunity. Furthermore, there is no age-structured modeling study which investigated the effect of lifting mask mandate considering high immune state of the population, contributed by both of natural infection and vaccination.\n\nAdded value of this studyOur mathematical model considered key factors such as vaccine status, age structure, medical staff, prior infection, and unreported cases to study the COVID-19 epidemic in Korea. Updated data and variant-specific parameters were used in the model. Contact patterns in the household, school, work, hospital and other places are considered separately to make the model applicable to the mask mandate issue. Seasonality and scenarios on possible future variants are also included in this study.\n\nImplications of all the available evidenceWith mask wearing as one of the remaining non-pharmaceutical interventions in Korea and other countries, this study proposes strategies for lifting the mask mandates while ensuring that cases remain manageable. A variant-dependent factor is incorporated into the model so that policymakers could prepare proactive intervention policies against future variants.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Youngsuk Ko", - "author_inst": "Department of Mathematics, Konkuk University, Seoul, Korea" - }, - { - "author_name": "Victoria May Mendoza", - "author_inst": "Department of Mathematics, Konkuk University, Seoul, Korea" - }, - { - "author_name": "Renier Mendoza", - "author_inst": "Department of Mathematics, Konkuk University, Seoul, Korea" - }, - { - "author_name": "Yu Bin Seo", - "author_inst": "Division of Infectious Disease, Department of Internal Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Korea" - }, - { - "author_name": "Jacob Lee", - "author_inst": "Division of Infectious Disease, Department of Internal Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Korea" - }, - { - "author_name": "Eunok Jung", - "author_inst": "Department of Mathematics, Konkuk University, Seoul, Korea" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.01.05.23284214", "rel_title": "The impact of the COVID-19 pandemic on Antipsychotic Prescribing in individuals with autism, dementia, learning disability, serious mental illness or living in a care home: A federated analysis of 59 million patients primary care records in situ using OpenSAFELY", @@ -124482,6 +125775,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.01.05.522964", + "rel_title": "Comparison of SARS-CoV-2 entry inhibitors based on ACE2 receptor or engineered Spike-binding peptides", + "rel_date": "2023-01-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.05.522964", + "rel_abs": "With increasing resistance of SARS-CoV-2 variants to antibodies, there is interest in developing entry inhibitors that target essential receptor binding regions of the viral Spike protein and thereby present a high bar for viral resistance. Such inhibitors can be derivatives of the viral receptor, ACE2, or peptides engineered to interact specifically with the receptor-binding pocket. We compared the efficacy of a series of both types of entry inhibitors, constructed as fusions to an antibody Fc domain. Such a design can increase protein stability and act to both neutralize free virus and recruit effector functions to clear infected cells. We tested the reagents against prototype variants of SARS-CoV-2, using both Spike pseudotyped VSV vectors and viral plaque assays. These analyses revealed that an optimized ACE2 derivative could neutralize all variants we tested with high efficacy. In contrast, the Spike-binding peptides had varying activities against different variants, with resistance observed for the Spike proteins from Beta, Gamma and Omicron. The resistance mapped to mutations at Spike residues K417 and N501 and could be overcome for one of the peptides by linking two copies in tandem, effectively creating a tetrameric reagent in the Fc fusion. Finally, both the optimized ACE2 and tetrameric peptide inhibitors provided some protection to human ACE2 transgenic mice challenged with the SARS-CoV-2 Delta variant, which typically causes death in this model within 7-9 days.\n\nImportanceThe increasing resistance of SARS-CoV-2 variants to therapeutic antibodies has highlighted the need for new treatment options, especially in individuals who do not respond to vaccination. Receptor decoys that block viral entry are an attractive approach because of the presumed high bar to developing viral resistance. Here, we compare two entry inhibitors based on derivatives of the ACE2 receptor or engineered peptides that bind to the receptor binding pocket of the SARS-CoV-2 Spike protein. In each case, the inhibitors were fused to immunoglobulin Fc domains, which can further enhance therapeutic properties, and compared for activity against different SARS-CoV-2 variants. Potent inhibition against multiple SARS-CoV-2 variants was demonstrated in vitro, and even relatively low single doses of optimized reagents provided some protection in mouse models, confirming their potential as an alternative to antibody therapies.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "George Nicholas Llewellyn", + "author_inst": "University of Southern California" + }, + { + "author_name": "Hsu-Yu Chen", + "author_inst": "University of Southern California" + }, + { + "author_name": "Geoffrey L. Rogers", + "author_inst": "University of Southern California" + }, + { + "author_name": "Xiaoli Huang", + "author_inst": "University of Southern California" + }, + { + "author_name": "Philip Sell", + "author_inst": "University of Southern California" + }, + { + "author_name": "Jill E Henley", + "author_inst": "University of Southern California" + }, + { + "author_name": "Paula M. Cannon", + "author_inst": "University of Southern California" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.01.06.522977", "rel_title": "Omicron Spike Protein Is Vulnerable to Reduction", @@ -126132,69 +127468,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.12.30.22283726", - "rel_title": "Attitudes towards booster, testing and isolation, and their impact on COVID-19 response in winter 2022/2023 in France, Belgium, and Italy", - "rel_date": "2023-01-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.30.22283726", - "rel_abs": "European countries are focusing on testing, isolation, and boosting strategies to counter the 2022/2023 winter surge due to Omicron subvariants. However, widespread pandemic fatigue and limited compliance potentially undermine mitigation efforts. To establish a baseline for interventions, we ran a multicountry survey to assess respondents willingness to receive booster vaccination and comply with testing and isolation mandates. The vast majority of survey participants (N=4,594) was willing to adhere to testing (>91%) and rapid isolation (>88%) across the three countries. Pronounced differences emerged in the declared senior adherence to booster vaccination (73% in France, 94% in Belgium, 86% in Italy). Next, we inferred the vaccine-induced population immunity profile at the winter start from prior vaccination data, immunity waning, and declared booster uptake. Integrating survey and estimated immunity data in a branching process epidemic spreading model, we evaluated the effectiveness and costs of current protocols in France, Belgium, and Italy to manage the winter wave. Model results estimate that testing and isolation protocols would confer significant benefit in reducing transmission (17-24%) with declared adherence. Achieving a mitigating level similar to the French protocol, the Belgian protocol would require 30% fewer tests and avoid the long isolation periods of the Italian protocol (average of 6 days vs. 11). A cost barrier to test would significantly decrease adherence in France and Belgium, undermining protocols effectiveness. Simpler mandates for isolation may increase awareness and actual compliance, reducing testing costs, without compromising mitigation. High booster vaccination uptake remains key for the control of the winter wave.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Giulia de Meijere", - "author_inst": "Gran Sasso Science Institute and Istituto Sistemi Complessi (ISC-CNR)" - }, - { - "author_name": "Eugenio Valdano", - "author_inst": "Institut Pierre Louis d'\u00c9pid\u00e9miologie et de Sant\u00e9 Publique" - }, - { - "author_name": "Claudio Castellano", - "author_inst": "Istituto Sistemi Complessi (ISC-CNR) and Centro Ricerche Enrico Fermi" - }, - { - "author_name": "Marion Debin", - "author_inst": "Institut Pierre Louis d'\u00c9pid\u00e9miologie et de Sant\u00e9 Publique" - }, - { - "author_name": "Charly Kengne-Kuetche", - "author_inst": "Institut Pierre Louis d'\u00c9pid\u00e9miologie et de Sant\u00e9 Publique" - }, - { - "author_name": "Cl\u00e9ment Turbelin", - "author_inst": "Institut Pierre Louis d'\u00c9pid\u00e9miologie et de Sant\u00e9 Publique" - }, - { - "author_name": "Harold No\u00ebl", - "author_inst": "Sant\u00e9 Publique France" - }, - { - "author_name": "Joshua S Weitz", - "author_inst": "Georgia Institute of Technology and \u00c9cole Normale Sup\u00e9rieure" - }, - { - "author_name": "Daniela Paolotti", - "author_inst": "Institute for Scientific Interchange" - }, - { - "author_name": "Lisa Hermans", - "author_inst": "Hasselt University" - }, - { - "author_name": "Niel Hens", - "author_inst": "Hasselt University and University of Antwerp" - }, - { - "author_name": "Vittoria Colizza", - "author_inst": "Institut Pierre Louis d'\u00c9pid\u00e9miologie et de Sant\u00e9 Publique" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.01.02.23284119", "rel_title": "Participant Demographics and Testing Trends: A Community Pandemic Response Program", @@ -126816,6 +128089,41 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2023.01.04.522629", + "rel_title": "In vivo activity of Sotrovimab against BQ.1.1 Omicron sublineage", + "rel_date": "2023-01-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.04.522629", + "rel_abs": "The successive emergence of SARS-CoV-2 Omicron variants has completely changed the modalities of use of therapeutic monoclonal antibodies. Recent in vitro studies indicated that only Sotrovimab has maintained partial activity against BQ.1.1 and XBB.1. In the present study, we used the hamster model to determine whether Sotrovimab retains antiviral activity against these Omicron variants in vivo. Our results show that at exposures consistent with those observed in humans, Sotrovimab remains active against BQ.1.1 and XBB.1, although for BQ.1.1 the efficacy is lower than that observed against the first globally dominant Omicron sublineages BA.1 and BA.2.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Jean-Selim Driouich", + "author_inst": "Aix-Marseille University - INSERM - IRD" + }, + { + "author_name": "Ornellie Bernadin", + "author_inst": "Aix Marseille University - INSERM - IRD" + }, + { + "author_name": "Franck Touret", + "author_inst": "Aix Marseille University - INSERM - IRD" + }, + { + "author_name": "Xavier de Lamballerie", + "author_inst": "Aix Marseille University - INSERM - IRD" + }, + { + "author_name": "Antoine Nougairede", + "author_inst": "Aix Marseille University - INSERM - IRD" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.01.01.22284075", "rel_title": "The illusion of personal health decisions for infectious disease management: disease spread in social contact networks", @@ -128074,25 +129382,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.12.30.22283949", - "rel_title": "On temporal changes in the role of different age groups in propagating the Omicron epidemic waves in England", - "rel_date": "2022-12-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.30.22283949", - "rel_abs": "BackgroundThere is limited information on the role of individuals in different age groups in the spread of infection during the Omicron epidemics, especially ones beyond the winter epidemic wave in 2021-2022. COVID-19 booster vaccination in England during the Autumn 2022 was restricted to persons aged over 50y, and persons in clinical risk groups.\n\nMethodsWe used previously developed methodology to evaluate the role of individuals in different age groups in propagating the Spring, Summer, and Autumn waves of the Omicron epidemic in England. This methodology utilizes the relative risk (RR) statistic that measures the change in the proportion of cases in each age group among all COVID-19 cases in the population before the peak of an epidemic wave vs. after the peak of an epidemic wave. Higher values for the RR statistic represent age groups that experienced a disproportionate depletion of susceptible individuals during the ascent of the epidemic (due to increased contact rates and/or susceptibility to infection).\n\nResultsFor the 2022 Spring wave, the highest RR estimate belonged to children aged 5-9y (RR=2.05 (95%CI (2.02,2.08)), followed by children aged 10-14y (RR=1.68 (1.66,1.7)) and children aged 0-4y (RR=1.38 (1.36,1.41)). For the Summer wave, the highest RR estimates belonged to persons aged 20-34y: (RR=1.09 (1.07,1.12) in aged 20-24y, RR=1.09 (1.07,1.11) in aged 25-29y, RR=1.09(1.07,1.11) in aged 30-34y). For the Autumn wave, the highest RR estimates belonged to those aged 70-74y (RR=1.10 (1.07,1.14)), followed by adults aged 35-39y (RR=1.09 (1.06,1.12)), adults aged 40-44y (RR=1.09 (1.06,1.12)), and adults aged 65-69y (RR=1.08 (1.05,1.11)).\n\nConclusionsAs time progressed, the greatest relative roles in propagating different waves of the Omicron epidemic in England shifted from school-age children to younger adults to adults aged 35-44y and 65-74y. Extending booster vaccination to all adults, and possibly to children should help limit the spread of Omicron infections in the community.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Edward Goldstein", - "author_inst": "Massachusetts Eye and Ear Hospital, Harvard Medical School" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.12.24.22283920", "rel_title": "COVID-19 in Cambodia: Epidemiology, Response, and Lessons Learned, 27 January 2020 to 30 June 2022", @@ -128774,6 +130063,69 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.12.28.22283971", + "rel_title": "Outcomes After Percutaneous Tracheostomy in Patients with COVID-19: A Single-Center Series of 377 Cases", + "rel_date": "2022-12-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.28.22283971", + "rel_abs": "IntroductionThe COVID 19 pandemic was highlighted by a rise in hospital admissions secondary to respiratory decompensation. This was accompanied by an increase in ICU admissions, endotracheal intubation and mechanical ventilation. As a consequence, tracheostomies became essential in preventing complications of prolonged intubation and to facilitate weaning from sedation and mechanical ventilation. With the lack of international consensus on tracheostomy technique and optimal timing, we present our experience with 377 percutaneous tracheostomies performed on critically ill COVID 19 patients.\n\nObjectiveTo report the outcomes of critically ill patients with COVID-19 who underwent percutaneous tracheostomy during a period of 24 months.\n\nMethodsA retrospective single-center electronic chart review was performed on all ICU patients who underwent percutaneous tracheostomy after respiratory failure secondary to COVID-19 between March 2020 to March 2022.\n\nResultsA total of 377 percutaneous tracheostomies were performed. The mean duration between intubation and percutaneous tracheostomy was 17.4 days (3-61). The study included 222 males (59%) and 155 females (41%).\n\nThe mean age of patients was 56.2 years (17-94), with a mean BMI was 31.3 (14-68).\n\nThe commonest comorbidities among patients were diabetes mellitus (50%) and hypertension (48%).\n\nComplications were encountered in 85 cases (23%), with the commonest overall complication being minor bleeding.\n\n203 patients (54%) were weaned from sedation. The mean duration between tracheostomy and weaning from sedation was 7.5 days (1 - 47 days). 156 patients (41%) were weaned from MV. The mean duration between tracheostomy and weaning from MV was 12.9 days (1 - 58 days). There was a total of 236 (63%) deaths reported during the period of this study.\n\nNo deaths were attributable to the surgical procedure.\n\nConclusionPercutaneous tracheostomy can be safely performed in patients with COVID-19. With lack of conclusive objective data regarding the optimal timing for tracheostomy, we recommend that tracheostomy be performed as soon as possible after the 7th day endotracheal intubation.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Abdullah Alshukry", + "author_inst": "Ministry of Health Kuwait" + }, + { + "author_name": "Abdulrazzaq Alhindi", + "author_inst": "Dasman Institute" + }, + { + "author_name": "Majdah Alzuabi", + "author_inst": "Ministry of Health Kuwait" + }, + { + "author_name": "Seema Husain", + "author_inst": "Ministry of Health Kuwait" + }, + { + "author_name": "Mohammad Tarakmeh", + "author_inst": "Ministry of Health Kuwait" + }, + { + "author_name": "Shaima Alqattan", + "author_inst": "Ministry of Health Kuwait" + }, + { + "author_name": "Abdullah Al Bader", + "author_inst": "Ministry of Health Kuwait" + }, + { + "author_name": "Ali Alhabib", + "author_inst": "Ministry of Health Kuwait" + }, + { + "author_name": "Yaseen Ali", + "author_inst": "Ministry of Health Kuwait" + }, + { + "author_name": "Fahd Al-Mulla", + "author_inst": "Dasman Diabetes Institute" + }, + { + "author_name": "Hamad Ali", + "author_inst": "Kuwait University" + }, + { + "author_name": "Mohammad Bu Abbas", + "author_inst": "Ministry of Health Kuwait" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "otolaryngology" + }, { "rel_doi": "10.1101/2022.12.30.22284063", "rel_title": "Effectiveness of Sotrovimab in Preventing COVID-19-related Hospitalizations or Deaths Among U.S. Veterans", @@ -129788,29 +131140,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2022.12.24.22283874", - "rel_title": "A second update on mapping the human genetic architecture of COVID-19", - "rel_date": "2022-12-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.24.22283874", - "rel_abs": "Investigating the role of host genetic factors in COVID-19 severity and susceptibility can inform our understanding of the underlying biological mechanisms that influence adverse outcomes and drug development1,2. Here we present a second updated genome-wide association study (GWAS) on COVID-19 severity and infection susceptibility to SARS-CoV-2 from the COVID-19 Host Genetic Initiative (data release 7). We performed a meta-analysis of up to 219,692 cases and over 3 million controls, identifying 51 distinct genome-wide significant loci--adding 28 loci from the previous data release2. The increased number of candidate genes at the identified loci helped to map three major biological pathways involved in susceptibility and severity: viral entry, airway defense in mucus, and type I interferon.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "- The COVID-19 Host Genetics Initiative", - "author_inst": "" - }, - { - "author_name": "Andrea Ganna", - "author_inst": "University of Helsinki" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2022.12.25.22283942", "rel_title": "Study COVID-19 Severity of Patients Admitted to Emergency Room (ER) with Chest X-ray Images", @@ -130532,6 +131861,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.12.22.22283858", + "rel_title": "Methodological approaches to optimize multiplex oral fluid SARS-CoV-2 IgG assay performance and correlation with serologic and neutralizing antibody responses", + "rel_date": "2022-12-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.22.22283858", + "rel_abs": "BackgroundOral fluid (hereafter, saliva) is a non-invasive and attractive alternative to blood for SARS-CoV-2 IgG testing; however, the heterogeneity of saliva as a matrix poses challenges for immunoassay performance.\n\nObjectivesTo optimize performance of a magnetic microparticle-based multiplex immunoassay (MIA) for SARS-CoV-2 IgG measurement in saliva, with consideration of: i) threshold setting and validation across different MIA bead batches; ii) sample qualification based on salivary total IgG concentration; iii) calibration to U.S. SARS-CoV-2 serological standard binding antibody units (BAU); and iv) correlations with blood-based SARS-CoV-2 serological and neutralizing antibody (nAb) assays.\n\nMethodsThe salivary SARS-CoV-2 IgG MIA included 2 nucleocapsid (N), 3 receptor-binding domain (RBD), and 2 spike protein (S) antigens. Gingival crevicular fluid (GCF) swab saliva samples were collected before December, 2019 (n=555) and after molecular test-confirmed SARS-CoV-2 infection from 113 individuals (providing up to 5 repeated-measures; n=398) and used to optimize and validate MIA performance (total n=953). Combinations of IgG responses to N, RBD and S and total salivary IgG concentration (g/mL) as a qualifier of nonreactive samples were optimized and validated, calibrated to the U.S. SARS-CoV-2 serological standard, and correlated with blood-based SARS-CoV-2 IgG ELISA and nAb assays.\n\nResultsThe sum of signal to cutoff (S/Co) to all seven MIA SARS-CoV-2 antigens and disqualification of nonreactive saliva samples with [≤]15 g/mL total IgG led to correct classification of 62/62 positives (sensitivity [Se]=100.0%; 95% confidence interval [CI]=94.8%, 100.0%) and 108/109 negatives (specificity [Sp]=99.1%; 95% CI=97.3%, 100.0%) at 8-million beads coupling scale and 80/81 positives (Se=98.8%; 95% CI=93.3%, 100.0%] and 127/127 negatives (Sp=100%; 95% CI=97.1%, 100.0%) at 20-million beads coupling scale. Salivary SARS-CoV-2 IgG crossed the MIA cutoff of 0.1 BAU/mL on average 9 days post-COVID-19 symptom onset and peaked around day 30. Among n=30 matched saliva and plasma samples, salivary SARS-CoV-2 MIA IgG levels correlated with corresponding-antigen plasma ELISA IgG (N: {rho}=0.67, RBD: {rho}=0.76, S: {rho}=0.82; all p<0.0001). Correlations of plasma SARS-CoV-2 nAb assay area under the curve (AUC) with salivary MIA IgG (N: {rho}=0.68, RBD: {rho}=0.78, S: {rho}=0.79; all p<0.0001) and with plasma ELISA IgG (N: {rho}=0.76, RBD: {rho}=0.79, S: {rho}=0.76; p<0.0001) were similar.\n\nConclusionsA salivary SARS-CoV-2 IgG MIA produced consistently high Se (>98.8%) and Sp (>99.1%) across two bead coupling scales and correlations with nAb responses that were similar to blood-based SARS-CoV-2 IgG ELISA data. This non-invasive salivary SARS-CoV-2 IgG MIA could increase engagement of vulnerable populations and improve broad understanding of humoral immunity (kinetics and gaps) within the evolving context of booster vaccination, viral variants and waning immunity.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Nora Pisanic", + "author_inst": "Bloomberg School of Public Health, Johns Hopkins University" + }, + { + "author_name": "Annukka A. R. Antar", + "author_inst": "School of Medicine, Johns Hopkins University" + }, + { + "author_name": "Kate L Kruczynski", + "author_inst": "Bloomberg School of Public Health, Johns Hopkins University" + }, + { + "author_name": "Magdielis Gregory Rivera", + "author_inst": "Bloomberg School of Public Health, Johns Hopkins University" + }, + { + "author_name": "Santosh Dhakal", + "author_inst": "Bloomberg School of Public Health, Johns Hopkins University" + }, + { + "author_name": "Kristoffer Spicer", + "author_inst": "Bloomberg School of Public Health, Johns Hopkins University" + }, + { + "author_name": "Pranay R. Randad", + "author_inst": "Bloomberg School of Public Health, Johns Hopkins University" + }, + { + "author_name": "Andrew Pekosz", + "author_inst": "Bloomberg School of Public Health, Johns Hopkins University" + }, + { + "author_name": "Sabra L Klein", + "author_inst": "Bloomberg School of Public Health, Johns Hopkins University" + }, + { + "author_name": "Michael J. Betenbaugh", + "author_inst": "Whiting School of Engineering, Johns Hopkins University" + }, + { + "author_name": "Barbara Detrick", + "author_inst": "School of Medicine, Johns Hopkins University" + }, + { + "author_name": "William Clarke", + "author_inst": "School of Medicine, Johns Hopkins University" + }, + { + "author_name": "David L Thomas", + "author_inst": "School of Medicine, Johns Hopkins University" + }, + { + "author_name": "Yukari C Manabe", + "author_inst": "School of Medicine, Johns Hopkins University" + }, + { + "author_name": "Christopher D Heaney", + "author_inst": "Bloomberg School of Public Health, Johns Hopkins University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.12.23.22283899", "rel_title": "US Public Opinion as to Whether \"The Pandemic is Over,\" September to October 2022", @@ -131830,137 +133234,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.12.21.22283654", - "rel_title": "Unbiased single cell spatial analysis localises inflammatory clusters of immature neutrophils-CD8 T cells to alveolar progenitor cells in fatal COVID-19 lungs", - "rel_date": "2022-12-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.21.22283654", - "rel_abs": "Single cell spatial interrogation of the immune-structural interactions in COVID -19 lungs is challenging, mainly because of the marked cellular infiltrate and architecturally distorted microstructure. To address this, we developed a suite of mathematical tools to search for statistically significant co-locations amongst immune and structural cells identified using 37-plex imaging mass cytometry. This unbiased method revealed a cellular map interleaved with an inflammatory network of immature neutrophils, cytotoxic CD8 T cells, megakaryocytes and monocytes co-located with regenerating alveolar progenitors and endothelium. Of note, a highly active cluster of immature neutrophils and cytotoxic CD8 T cells, was found spatially linked with alveolar progenitor cells, and temporally with the diffuse alveolar damage stage. These findings provide new insights into how immune cells interact in the lungs of severe COVID-19 disease. We provide our pipeline [Spatial Omics Oxford Pipeline (SpOOx)] and visual-analytical tool, Multi-Dimensional Viewer (MDV) software, as a resource for spatial analysis.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=190 HEIGHT=200 SRC=\"FIGDIR/small/22283654v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (58K):\norg.highwire.dtl.DTLVardef@f1332forg.highwire.dtl.DTLVardef@1576abcorg.highwire.dtl.DTLVardef@208c84org.highwire.dtl.DTLVardef@e93975_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 29, - "rel_authors": [ - { - "author_name": "Praveen Weeratunga", - "author_inst": "University of Oxford" - }, - { - "author_name": "Laura Denney", - "author_inst": "University of Oxford" - }, - { - "author_name": "Joshua A Bull", - "author_inst": "University of Oxford" - }, - { - "author_name": "Emmanouela Repapi", - "author_inst": "University of Oxford" - }, - { - "author_name": "Martin Sergeant", - "author_inst": "University of Oxford" - }, - { - "author_name": "Rachel Etherington", - "author_inst": "University of Oxford" - }, - { - "author_name": "Chaitanya Vuppusetty", - "author_inst": "University of Oxford" - }, - { - "author_name": "Gareth D.H. Turner", - "author_inst": "Oxford University Hospitals NHS Foundation Trust, UK" - }, - { - "author_name": "Colin Clelland", - "author_inst": "Anatomic Pathology, Weill Cornell Medical College, Doha, Qatar" - }, - { - "author_name": "Amy Cross", - "author_inst": "University of Oxford" - }, - { - "author_name": "Fadi Issa", - "author_inst": "University of Oxford" - }, - { - "author_name": "Carlos Eduardo de Andrea", - "author_inst": "Navarra Institute for Health Research, Pamplona, Spain" - }, - { - "author_name": "Ignacio Melero Bermejo", - "author_inst": "Navarra Institute for Health Research, Pamplona, Spain" - }, - { - "author_name": "David Sims", - "author_inst": "University of Oxford" - }, - { - "author_name": "Simon McGowan", - "author_inst": "University of Oxford" - }, - { - "author_name": "Yasemin-Xiomara Zurke", - "author_inst": "University of Oxford" - }, - { - "author_name": "David J Ahern", - "author_inst": "University of Oxford" - }, - { - "author_name": "Eddie C Gamez", - "author_inst": "University of Oxford" - }, - { - "author_name": "Justin Whalley", - "author_inst": "University of Oxford" - }, - { - "author_name": "Duncan Richards", - "author_inst": "University of Oxford" - }, - { - "author_name": "Paul Klenerman", - "author_inst": "University of Oxford" - }, - { - "author_name": "Claudia Monaco", - "author_inst": "University of Oxford" - }, - { - "author_name": "Irina A. Udalova", - "author_inst": "University of Oxford" - }, - { - "author_name": "Tao Dong", - "author_inst": "University of Oxford" - }, - { - "author_name": "Graham Ogg", - "author_inst": "University of Oxford" - }, - { - "author_name": "Julian Knight", - "author_inst": "University of Oxford" - }, - { - "author_name": "Helen M. Byrne", - "author_inst": "University of Oxford" - }, - { - "author_name": "Stephen Taylor", - "author_inst": "University of Oxford" - }, - { - "author_name": "Ling-Pei Ho", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2022.12.22.521201", "rel_title": "Enhanced neutralization escape to therapeutic monoclonal antibodies by SARS-CoV-2 Omicron sub-lineages", @@ -132438,6 +133711,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.12.21.22283793", + "rel_title": "Collective Intelligent Strategy for Improved Segmentation of COVID-19 from CT", + "rel_date": "2022-12-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.21.22283793", + "rel_abs": "The devastation caused by the coronavirus pandemic makes it imperative to design automated techniques for a fast and accurate detection. We propose a novel non-invasive tool, using deep learning and imaging, for delineating COVID-19 infection in lungs. The Ensembling Attention-based Multi-scaled Convolution network (EAMC), employing Leave-One-Patient-Out (LOPO) training, exhibits high sensitivity and precision in outlining infected regions along with assessment of severity. The Attention module combines contextual with local information, at multiple scales, for accurate segmentation. Ensemble learning integrates heterogeneity of decision through different base classifiers. The superiority of EAMC, even with severe class imbalance, is established through comparison with existing state-of-the-art learning models over four publicly-available COVID-19 datasets. The results are suggestive of the relevance of deep learning in providing assistive intelligence to medical practitioners, when they are overburdened with patients as in pandemics. Its clinical significance lies in its unprecedented scope in providing low-cost decision-making for patients lacking specialized healthcare at remote locations.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Surochita Pal Das", + "author_inst": "Indian Statistical Institute" + }, + { + "author_name": "Sushmita Mitra", + "author_inst": "Indian Statistical Institute" + }, + { + "author_name": "B. Uma Shankar", + "author_inst": "Indian Statistical Institute" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2022.12.22.22283763", "rel_title": "\"Side effects of Vero cell vaccination against Covid-19 among medical students of Nepalgunj Medical College\"-A Post Vaccination survey", @@ -133424,33 +134724,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "endocrinology" }, - { - "rel_doi": "10.1101/2022.12.16.22283591", - "rel_title": "Modeling a traffic light warning system for acute respiratory infections", - "rel_date": "2022-12-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.16.22283591", - "rel_abs": "The high morbidity of acute respiratory infections constitutes a crucial global health burden. In particular, for SARS-CoV-2, non-pharmaceutical intervention geared to enforce social distancing policies, vaccination, and treatments will remain an essential part of public health policies to mitigate and control disease outbreaks. However, the implementation of mitigation measures directed to increase social distancing when the risk of contagion is a complex enterprise because of the impact of NPI on beliefs, political views, economic issues, and, in general, public perception. The way of implementing these mitigation policies studied in this work is the so-called traffic-light monitoring system that attempts to regulate the application of measures that include restrictions on mobility and the size of meetings, among other non-pharmaceutical strategies. Balanced enforcement and relaxation of measures guided through a traffic-light system that considers public risk perception and economic costs may improve the public health benefit of the policies while reducing their cost. We derive a model for the epidemiological traffic-light policies based on the best response for trigger measures driven by the risk perception of people, instant reproduction number, and the prevalence of a hypothetical acute respiratory infection. With numerical experiments, we evaluate and identify the role of appreciation from a hypothetical controller that could opt for protocols aligned with the cost due to the burden of the underlying disease and the economic cost of implementing measures. As the world faces new acute respiratory outbreaks, our results provide a methodology to evaluate and develop traffic light policies resulting from a delicate balance between health benefits and economic implications.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Saul Diaz-Infante", - "author_inst": "Universidad de Sonora" - }, - { - "author_name": "M. Adrian Acuna-Zegarra", - "author_inst": "Universidad de Sonora" - }, - { - "author_name": "Jorge X. Velasco-Hernandez", - "author_inst": "Universidad Nacional Autonoma de Mexico" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.12.19.22283681", "rel_title": "Tracking the COVID-19 vaccine equity, distribution, and cases in the global south", @@ -134088,6 +135361,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.12.19.22283704", + "rel_title": "Outcomes in Patients with Acute Hypoxemic Respiratory Failure Secondary to COVID-19 Treated with Noninvasive Respiratory Support versus Invasive Mechanical Ventilation", + "rel_date": "2022-12-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.19.22283704", + "rel_abs": "PurposeThe goal of this study was to compare noninvasive respiratory support to invasive mechanical ventilation as the initial respiratory support in COVID-19 patients with acute hypoxemic respiratory failure.\n\nMethodsAll patients admitted to a large healthcare network with acute hypoxemic respiratory failure associated with COVID-19 and requiring respiratory support were eligible for inclusion. We compared patients treated initially with noninvasive respiratory support (noninvasive positive pressure ventilation by facemask or high flow nasal oxygen) with patients treated initially with invasive mechanical ventilation. The primary outcome was time-to-in-hospital death analyzed using an inverse probability of treatment weighted Cox model adjusted for potential confounders. Secondary outcomes included unweighted and weighted assessments of mortality, lengths-of-stay (intensive care unit and hospital) and time-to-intubation.\n\nResultsOver the study period, 2354 patients met inclusion criteria. Nearly half (47%) received invasive mechanical ventilation first and 53% received initial noninvasive respiratory support. There was an overall 38% in-hospital mortality (37% for invasive mechanical ventilation and 39% for noninvasive respiratory support). Initial noninvasive respiratory support was associated with an increased hazard of death compared to initial invasive mechanical ventilation (HR: 1.61, p < 0.0001, 95% CI: 1.33 - 1.94). However, patients on initial noninvasive respiratory support also experienced an increased hazard of leaving the hospital sooner, but the hazard ratio waned with time (HR: 0.97, p < 0.0001, 95% CI: 0.96 - 0.98).\n\nConclusionThese data show that the COVID-19 patients with acute hypoxemic respiratory failure initially treated with noninvasive respiratory support had an increased hazard of in-hospital death.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Julia Fisher", + "author_inst": "University of Arizona" + }, + { + "author_name": "Vignesh Subbian", + "author_inst": "University of Arizona" + }, + { + "author_name": "Patrick Essay", + "author_inst": "University of Arizona" + }, + { + "author_name": "Sarah Pungitore", + "author_inst": "University of Arizona" + }, + { + "author_name": "Edward Bedrick", + "author_inst": "The University of Arizona Mel and Enid Zuckerman College of Public Health" + }, + { + "author_name": "Jarrod Mosier", + "author_inst": "University of Arizona" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2022.12.19.521064", "rel_title": "Different B cell activation patterns in asymptomatic and symptomatic COVID-19 patients", @@ -135558,45 +136870,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.12.17.22283625", - "rel_title": "Effectiveness of the Coronavirus Disease 2019 (COVID-19) Bivalent Vaccine", - "rel_date": "2022-12-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.17.22283625", - "rel_abs": "BackgroundThe purpose of this study was to evaluate whether a bivalent COVID-19 vaccine protects against COVID-19.\n\nMethodsEmployees of Cleveland Clinic in employment when the bivalent COVID-19 vaccine first became available, were included. Cumulative incidence of COVID-19 over the following 26 weeks was examined. Protection provided by vaccination (analyzed as a time-dependent covariate) was evaluated using Cox proportional hazards regression, with change in dominant circulating lineages over time accounted for by time-dependent coefficients. The analysis was adjusted for the pandemic phase when the last prior COVID-19 episode occurred, and the number of prior vaccine doses.\n\nResultsAmong 51017 employees, COVID-19 occurred in 4424 (8.7%) during the study. In multivariable analysis, the bivalent vaccinated state was associated with lower risk of COVID-19 during the BA.4/5 dominant (HR, .71; 95% C.I., .63-.79) and the BQ dominant (HR, .80; 95% C.I., .69-.94) phases, but decreased risk was not found during the XBB dominant phase (HR, .96; 95% C.I., .82-.1.12). Estimated vaccine effectiveness (VE) was 29% (95% C.I., 21%-37%), 20% (95% C.I., 6%-31%), and 4% (95% C.I., -12%-18%), during the BA.4/5, BQ, and XBB dominant phases, respectively. Risk of COVID-19 also increased with time since most recent prior COVID-19 episode and with the number of vaccine doses previously received.\n\nConclusionsThe bivalent COVID-19 vaccine given to working-aged adults afforded modest protection overall against COVID-19 while the BA.4/5 lineages were the dominant circulating strains, afforded less protection when the BQ lineages were dominant, and effectiveness was not demonstrated when the XBB lineages were dominant.\n\nSummaryAmong 51017 working-aged Cleveland Clinic employees, the bivalent COVID-19 vaccine was 29% effective in preventing infection while the BA.4/5 lineages were dominant, and 20% effective while the BQ lineages were. Effectiveness was not demonstrated when the XBB lineages were dominant.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Nabin K. Shrestha", - "author_inst": "Cleveland Clinic" - }, - { - "author_name": "Patrick C Burke", - "author_inst": "Cleveland Clinic" - }, - { - "author_name": "Amy S Nowacki", - "author_inst": "Cleveland Clinic" - }, - { - "author_name": "James F Simon", - "author_inst": "Cleveland Clinic" - }, - { - "author_name": "Amanda Hagen", - "author_inst": "Cleveland Clinic" - }, - { - "author_name": "Steven M Gordon", - "author_inst": "Cleveland Clinic" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.12.18.22283646", "rel_title": "Association between SARS-CoV-2 Infection and Select Symptoms and Conditions 31 to 150 Days After Testing among Children and Adults", @@ -136210,6 +137483,169 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.12.16.22283578", + "rel_title": "Higher dose corticosteroids in hospitalised COVID-19 patients with hypoxia but not requiring ventilatory support (RECOVERY): a randomised, controlled, open-label, platform trial", + "rel_date": "2022-12-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.16.22283578", + "rel_abs": "BackgroundLow-dose corticosteroids have been shown to reduce mortality for hypoxic COVID-19 patients requiring oxygen or ventilatory support (non-invasive mechanical ventilation, invasive mechanical ventilation or extra-corporeal membrane oxygenation). We evaluated the use of a higher dose of corticosteroids in this patient group.\n\nMethodsThis randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]) is assessing multiple possible treatments in patients hospitalised for COVID-19. Eligible and consenting adult patients with clinical evidence of hypoxia (i.e. receiving oxygen or with oxygen saturation <92% on room air) were randomly allocated (1:1) to either usual care with higher dose corticosteroids (dexamethasone 20 mg once daily for 5 days followed by 10 mg once daily for 5 days or until discharge if sooner) or usual standard of care alone (which includes dexamethasone 6 mg once daily for 10 days or until discharge if sooner). The primary outcome was 28-day mortality. On 11 May 2022, the independent Data Monitoring Committee recommended stopping recruitment of patients receiving no oxygen or simple oxygen only to this comparison due to safety concerns. We report the results for these participants only. Recruitment of patients receiving ventilatory support continues. The RECOVERY trial is registered with ISRCTN (50189673) and clinicaltrials.gov (NCT04381936).\n\nFindingsBetween 25 May 2021 and 12 May 2022, 1272 COVID-19 patients with hypoxia and receiving no oxygen (1%) or simple oxygen only (99%) were randomly allocated to receive usual care plus higher dose corticosteroids versus usual care alone (of whom 87% received low dose corticosteroids during the follow-up period). Of those randomised, 745 (59%) were in Asia, 512 (40%) in the UK and 15 (1%) in Africa. 248 (19%) had diabetes mellitus. Overall, 121 (18%) of 659 patients allocated to higher dose corticosteroids versus 75 (12%) of 613 patients allocated to usual care died within 28 days (rate ratio [RR] 1{middle dot}56; 95% CI 1{middle dot}18-2{middle dot}06; p=0{middle dot}0020). There was also an excess of pneumonia reported to be due to non-COVID infection (10% vs. 6%; absolute difference 3.7%; 95% CI 0.7-6.6) and an increase in hyperglycaemia requiring increased insulin dose (22% vs. 14%; absolute difference 7.4%; 95% CI 3.2-11.5).\n\nInterpretationIn patients hospitalised for COVID-19 with clinical hypoxia but requiring either no oxygen or simple oxygen only, higher dose corticosteroids significantly increased the risk of death compared to usual care, which included low dose corticosteroids. The RECOVERY trial continues to assess the effects of higher dose corticosteroids in patients hospitalised with COVID-19 who require non-invasive ventilation, invasive mechanical ventilation or extra-corporeal membrane oxygenation.\n\nFundingUK Research and Innovation (Medical Research Council) and National Institute of Health and Care Research (Grant ref: MC_PC_19056), and Wellcome Trust (Grant Ref: 222406/Z/20/Z).", + "rel_num_authors": 37, + "rel_authors": [ + { + "author_name": "Peter W Horby", + "author_inst": "Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom" + }, + { + "author_name": "Jonathan R Emberson", + "author_inst": "MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" + }, + { + "author_name": "Buddha Basnyat", + "author_inst": "OUCRU-Nepal, Patan Academy of Health Sciences, Kathmandu, Nepal" + }, + { + "author_name": "Mark Campbell", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" + }, + { + "author_name": "Leon Peto", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" + }, + { + "author_name": "Guilherme Pessoa-Amorim", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" + }, + { + "author_name": "Natalie Staplin", + "author_inst": "MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" + }, + { + "author_name": "Raph L Hamers", + "author_inst": "Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia" + }, + { + "author_name": "John Amuasi", + "author_inst": "Kumasi Center for Collaborative Research in Tropic Medicine, Kumasi, Ghana" + }, + { + "author_name": "Jeremy Nel", + "author_inst": "Division of Infectious Diseases, Department of Medicine, University of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Evelyne Kestelyn", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom" + }, + { + "author_name": "Manisha Rawal", + "author_inst": "Sukraraj Tropical and Infectious Disease Hospital, Kathmandu, Nepal" + }, + { + "author_name": "Roshan Kumar Jha", + "author_inst": "Medicine Department, Nepal Armed Police Force Hospital, Chandragiri, Kathmandu, Nepal" + }, + { + "author_name": "Nguyen Thanh Phong", + "author_inst": "Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Uun Samardi", + "author_inst": "RSUP Dr Hasan Sadikin Hospital, Bandung, West Java, Indonesia" + }, + { + "author_name": "Damodar Paudel", + "author_inst": "Department of Medicine, Nepal Police Hospital, Maharajgunj, Kathmandu, Nepal" + }, + { + "author_name": "Pham Ngoc Thach", + "author_inst": "National Hospital for Tropical Diseases, Hanoi, Vietnam" + }, + { + "author_name": "Nasronudin Nasronudin", + "author_inst": "University of Airlangga Teaching Hospital, Surabaya, Indonesia" + }, + { + "author_name": "Emma Stratton", + "author_inst": "University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, United Kingdom" + }, + { + "author_name": "Louise Mew", + "author_inst": "Milton Keynes University Hospital, Milton Keynes, United Kingdom" + }, + { + "author_name": "Rahuldeb Sarkar", + "author_inst": "Faculty of Life Sciences and Medicine, King's College, London, United Kingdom" + }, + { + "author_name": "J Kenneth Baillie", + "author_inst": "Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom" + }, + { + "author_name": "Maya H Buch", + "author_inst": "Centre for Musculoskeletal Research, University of Manchester, Manchester, United Kingdom" + }, + { + "author_name": "Jeremy N Day", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom" + }, + { + "author_name": "Saul N Faust", + "author_inst": "NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, " + }, + { + "author_name": "Thomas Jaki", + "author_inst": "Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom" + }, + { + "author_name": "Katie Jeffery", + "author_inst": "Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom" + }, + { + "author_name": "Edmund Juszczak", + "author_inst": "School of Medicine, University of Nottingham, Nottingham, United Kingdom" + }, + { + "author_name": "Marian Knight", + "author_inst": "National Perinatal Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" + }, + { + "author_name": "Wei Shen Lim", + "author_inst": "Respiratory Medicine Department, Nottingham University Hospitals NHS Foundation Trust, Nottingham, United Kingdom" + }, + { + "author_name": "Marion Mafham", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" + }, + { + "author_name": "Alan Montgomery", + "author_inst": "School of Medicine, University of Nottingham, Nottingham, United Kingdom" + }, + { + "author_name": "Andrew Mumford", + "author_inst": "School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom" + }, + { + "author_name": "Kathryn Rowan", + "author_inst": "Intensive Care National Audit and Research Centre, London, United Kingdom" + }, + { + "author_name": "Guy Thwaites", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom" + }, + { + "author_name": "Richard Haynes", + "author_inst": "MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" + }, + { + "author_name": "Martin J Landray", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.12.16.22283251", "rel_title": "Sustained reductions in life-threatening invasive bacterial diseases during the first two years of the COVID-19 pandemic: analyses of prospective surveillance data from 30 countries participating in the IRIS Consortium", @@ -137116,69 +138552,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2022.12.16.520799", - "rel_title": "Surface-modified measles vaccines encoding oligomeric, fusion-stabilized SARS-CoV-2 spike glycoproteins bypass measles seropositivity, boosting neutralizing antibody responses to omicron and historical variants.", - "rel_date": "2022-12-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.16.520799", - "rel_abs": "Serum titers of SARS-CoV-2 neutralizing antibodies (nAb) correlate well with protection from symptomatic COVID-19, but decay rapidly in the months following vaccination or infection. In contrast, measles-protective nAb titers are life-long after measles vaccination, possibly due to persistence of the live-attenuated virus in lymphoid tissues. We therefore sought to generate a live recombinant measles vaccine capable of driving high SARS-CoV-2 nAb responses. Since previous clinical testing of a live measles vaccine encoding a SARS-CoV-2 spike glycoprotein resulted in suboptimal anti-spike antibody titers, our new vectors were designed to encode prefusion-stabilized SARS-CoV-2 spike glycoproteins, trimerized via an inserted peptide domain and displayed on a dodecahedral miniferritin scaffold. Additionally, to circumvent the blunting of vaccine efficacy by preformed anti-measles antibodies, we extensively modified the measles surface glycoproteins. Comprehensive in vivo mouse testing demonstrated potent induction of high titer nAb in measles-immune mice and confirmed the significant incremental contributions to overall potency afforded by prefusion stabilization, trimerization, and miniferritin-display of the SARS-CoV-2 spike glycoprotein, and vaccine resurfacing. In animals primed and boosted with a MeV vaccine encoding the ancestral SARS-CoV-2 spike, high titer nAb responses against ancestral virus strains were only weakly cross-reactive with the omicron variant. However, in primed animals that were boosted with a MeV vaccine encoding the omicron BA.1 spike, antibody titers to both ancestral and omicron strains were robustly elevated and the passive transfer of serum from these animals protected K18-ACE2 mice from infection and morbidity after exposure to BA.1 and WA1/2020 strains. Our results demonstrate that antigen engineering can enable the development of potent measles-based SARS-CoV-2 vaccine candidates.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Miguel Angel Munoz Alia", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Rebecca A. Nace", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Baskar Balakrishnan", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Lianwen Zhang", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Nandakumar Packiriswamy", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Gagandeep Singh", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Ignacio Mena", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Riya Narjari", - "author_inst": "Imanis Life Sciences" - }, - { - "author_name": "Rianna Vandergaast", - "author_inst": "Imanis Life Sciences" - }, - { - "author_name": "Adolfo Garcia-Sastre", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Michael Schotsaert", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Stephen J. Russell", - "author_inst": "Mayo Clinic" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.12.16.520599", "rel_title": "Cholesterol and ceramide facilitate SARS-CoV-2 Spike protein-mediated membrane fusion", @@ -137828,6 +139201,81 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.12.12.22283341", + "rel_title": "Severe Acute Respiratory Syndrome Coronavirus 2 detection in induced sputum of asthmatic patients using saliva sampling device", + "rel_date": "2022-12-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.12.22283341", + "rel_abs": "Since the beginning of the severe acute respiratory syndrome coronavirus 2 pandemic, the potential contamination of the induced sputum obtained from asthmatic patients in routine is a question of concern. The goal of this study was to assess this contamination using a saliva sample collection device. One hundred seventy-five sputum samples of asthmatic patients without fever were tested. We did not identify any positive PCR on sputum samples from asthmatic patients reporting chronic/episodic respiratory symptoms similar to what is seen in case of COVID-19. This technique was useful to evaluate the contamination of sputum samples generated during the pandemic.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Catherine Moermans", + "author_inst": "CHU Liege" + }, + { + "author_name": "Sara Gerday", + "author_inst": "ULiege" + }, + { + "author_name": "Noemie Bricmont", + "author_inst": "ULiege" + }, + { + "author_name": "Romane Bonhiver", + "author_inst": "Uliege" + }, + { + "author_name": "Florence Schleich", + "author_inst": "CHU Liege" + }, + { + "author_name": "Julien GUIOT", + "author_inst": "CHU Liege" + }, + { + "author_name": "Makon-Sebastien Njock", + "author_inst": "CHU Liege" + }, + { + "author_name": "Monique Henket", + "author_inst": "CHU Liege" + }, + { + "author_name": "Francoise Guissard", + "author_inst": "CHU Liege" + }, + { + "author_name": "Virginie Paulus", + "author_inst": "CHU Liege" + }, + { + "author_name": "Emmanuel Di Valentin", + "author_inst": "ULiege" + }, + { + "author_name": "Frederic Minner", + "author_inst": "ULiege" + }, + { + "author_name": "Laurent Gillet", + "author_inst": "ULiege" + }, + { + "author_name": "Fabrice Bureau", + "author_inst": "ULiege" + }, + { + "author_name": "Renaud Louis", + "author_inst": "CHU Liege" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2022.12.12.22283200", "rel_title": "COVID-19 Vaccination in Pregnancy: The Impact of Multimorbidity and Smoking Status on Vaccine Hesitancy, a Cohort Study of 25,111 Women in Wales, UK", @@ -139133,33 +140581,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2022.12.08.22283241", - "rel_title": "Estimating the epidemic reproduction number from temporally aggregated incidence data: a statistical modelling approach and software tool", - "rel_date": "2022-12-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.08.22283241", - "rel_abs": "BackgroundThe time-varying reproduction number (Rt) is an important measure of epidemic transmissibility; it can directly inform policy decisions and the optimisation of control measures. EpiEstim is a widely used software tool that uses case incidence and the serial interval (SI, time between symptoms in a case and their infector) to estimate Rt in real-time. The incidence and the SI distribution must be provided at the same temporal resolution, which limits the applicability of EpiEstim and other similar methods, e.g. for pathogens with a mean SI shorter than the frequency of incidence reporting.\n\nMethodsWe use an expectation-maximisation algorithm to reconstruct daily incidence from temporally aggregated data, from which Rt can then be estimated using EpiEstim. We assess the validity of our method using an extensive simulation study and apply it to COVID-19 and influenza data. The method is implemented in the opensource R package EpiEstim.\n\nFindingsFor all datasets, the influence of intra-weekly variability in reported data was mitigated by using aggregated weekly data. Rt estimated on weekly sliding windows using incidence reconstructed from weekly data was strongly correlated with estimates from the original daily data. The simulation study revealed that Rt was well estimated in all scenarios and regardless of the temporal aggregation of the data. In the presence of weekend effects, Rt estimates from reconstructed data were more successful at recovering the true value of Rt than those obtained from reported daily data.\n\nInterpretationRt can be successfully recovered from aggregated data, and estimation accuracy can even be improved by smoothing out administrative noise in the reported data.\n\nFundingMRC doctoral training partnership, MRC centre for global infectious disease analysis, the NIHR HPRU in Modelling and Health Economics, and the Academy of Medical Sciences Springboard, funded by the AMS, Wellcome Trust, BEIS, the British Heart Foundation and Diabetes UK.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Rebecca K Nash", - "author_inst": "Imperial College London" - }, - { - "author_name": "Anne Cori", - "author_inst": "Imperial College London" - }, - { - "author_name": "Pierre Nouvellet", - "author_inst": "Imperial College London; University of Sussex" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.12.10.22283287", "rel_title": "Reduced mortality among COVID-19 ICU patients after treatment with HemoClear convalescent plasma in Suriname", @@ -139937,6 +141358,61 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2022.12.13.520266", + "rel_title": "A Photonic Resonator Interferometric Scattering Microscope for Label-free Detection of Nanometer-Scale Objects with Digital Precision in Point-of-Use Environments", + "rel_date": "2022-12-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.13.520266", + "rel_abs": "Label-free detection and digital counting of nanometer-scaled objects such as nanoparticles, viruses, extracellular vesicles, and protein molecules enable a wide range of applications in cancer diagnostics, pathogen detection, and life science research. The contrast of interferometric scattering microscopy is amplified through a photonic crystal surface, upon which scattered light from an object combines with illumination from a monochromatic plane wave source. The use of a photonic crystal substrate for interference scattering microscopy results in reduced requirements for high-intensity lasers or oil-immersion objectives, thus opening a pathway toward instruments that are more suitable for environments outside the optics laboratory. Here, we report the design, implementation, and characterization of a compact Photonic Resonator Interferometric Scattering Microscope (PRISM) designed for point-of-use environments and applications. The instrument incorporates two innovative elements that facilitate operation on a desktop in ordinary laboratory environments by users that do not have optics expertise. First, because scattering microscopes are extremely sensitive to vibration, we incorporated an inexpensive but effective solution of suspending the instruments main components from a rigid metal framework using elastic bands, resulting in an average of 28.7 dBV reduction in vibration amplitude compared to an office desk. Second, an automated focusing module based on the principle of total internal reflection maintains the stability of image contrast over time and spatial position, facilitating automated data collection. In this work, we characterize the systems performance by measuring the contrast from gold nanoparticles with diameters in the 10-40 nm range and by observing various biological analytes, including HIV virus, SARS-CoV-2 virus, exosomes, and ferritin protein.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Leyang Liu", + "author_inst": "University of Illinois at Urbana-Champaign" + }, + { + "author_name": "Joseph Tibbs", + "author_inst": "University of Illinois at Urbana-Champaign" + }, + { + "author_name": "Nantao Li", + "author_inst": "University of Illinois at Urbana-Champaign" + }, + { + "author_name": "Amanda Bacon", + "author_inst": "University of Illinois at Urbana-Champaign" + }, + { + "author_name": "Skye Shephard", + "author_inst": "University of Illinois at Urbana-Champaign" + }, + { + "author_name": "Hankeun Lee", + "author_inst": "University of Illinois at Urbana-Champaign" + }, + { + "author_name": "Neha Chauhan", + "author_inst": "University of Illinois at Urbana-Champaign" + }, + { + "author_name": "Utkan Demirci", + "author_inst": "Stanford University" + }, + { + "author_name": "Xing Wang", + "author_inst": "University of Illinois at Urbana-Champaign" + }, + { + "author_name": "Brian T Cunningham", + "author_inst": "University of Illinois at Urbana-Champaign" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2022.12.12.520110", "rel_title": "Long COVID: G Protein-Coupled Receptors (GPCRs) responsible for persistent post-COVID symptoms", @@ -140827,57 +142303,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.12.07.519488", - "rel_title": "High-resolution app data reveal sustained increases in recreational fishing effort in Europe during and after COVID-19 lockdowns", - "rel_date": "2022-12-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.07.519488", - "rel_abs": "It is manifest that COVID-19 lockdowns extensively impacted human interactions with natural ecosystems. One example is recreational fishing, an activity which involves nearly 1 in 10 people in developed countries. Fishing licence sales and direct observations at popular angling locations suggest that recreational fishing effort increased substantially during lockdowns. However, the extent and duration of this increase remain largely unknown due to a lack of objective data. We used four years (2018 to 2021) of anonymous, high-resolution data from a personal fish-finder device to explore the impact of COVID-19 lockdowns on recreational fishing effort in four European countries (Lithuania, the Czech Republic, Denmark, and Germany). We show that device use and, by extension, angling effort increased 1.2-3.8 fold during March-May 2020 and remained elevated even at the end of 2021 in all countries except Denmark. Fishing during the first lockdown also became more frequent during weekdays. Statistical models with the full set of fixed (weekdays, lockdown, population) and random (season, year, administrative unit) factors typically explained 50-70% of the variation, suggesting that device use and angling effort were relatively consistent and predictable through space and time. Our study demonstrates that recreational fishing behaviour can change substantially and rapidly in response to societal shifts, with profound ecological, human well-being and economic implications. We also show the potential of angler devices and smartphone applications to supply data for high-resolution fishing effort analysis and encourage more extensive science and industry collaborations to take advantage of this information.\n\nSignificance statementRecreational fishing is a popular and widespread activity with ecological, social and economic impacts, though problematic to assess and manage due to a paucity of information regarding effort and catch. Here, we use high-resolution data from a personal angler sonar device to show how the COVID-19 pandemic changed angler behaviour and fishing effort across Europe. We demonstrate that angling effort doubled and remained higher at the end of 2021 than before the first lockdowns. Such rapid and profound changes could have significant consequences for aquatic ecosystems, possibly requiring new management approaches. We encourage the adoption of novel data from angler devices, citizen science, and more active science-industry collaborations to improve recreational fishing assessment and management.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Asta Audzijonyte", - "author_inst": "Nature Research Centre, Akademijos 2, Vilnius, Lithuania; Institute for Marine and Antarctic Studies, University of Tasmania, Australia" - }, - { - "author_name": "Fernando Mateos Gonzalez", - "author_inst": "Nature Research Centre, Akademijos 2, Vilnius, Lithuania; ALKA Wildlife, Liderovice, Czech Republic" - }, - { - "author_name": "Justas Dainys", - "author_inst": "Nature research centre" - }, - { - "author_name": "Casper Gundelund", - "author_inst": "Section of Freshwater Fisheries and Ecology, Technical University of Denmark, Denmark" - }, - { - "author_name": "Christian Skov", - "author_inst": "Section of Freshwater Fisheries and Ecology, Technical University of Denmark, Denmark" - }, - { - "author_name": "J. Tyrell DeWeber", - "author_inst": "Institute of Inland Fisheries, Im Konigwald 2, Potsdam, Germany" - }, - { - "author_name": "Paul Anthony Venturelli", - "author_inst": "Department of Biology, Ball State University, Muncie 47306, IN, USA" - }, - { - "author_name": "Vincentas Vienozinskis", - "author_inst": "Deeper, LT-10312 Vilnius, Lithuania" - }, - { - "author_name": "Carl Smith", - "author_inst": "Nature Research Centre, Akademijos 2, Vilnius, Lithuania; Department of Ecology and Vertebrate Zoology, University of Lodz, Lodz, Poland; Institute of Vertebrat" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "ecology" - }, { "rel_doi": "10.1101/2022.12.08.22283265", "rel_title": "Mental health self-care during the COVID-19 pandemic: a prospective cohort study in Australia", @@ -141467,6 +142892,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.11.29.22282864", + "rel_title": "Effect of BNT162b2 antigen dosage on protection against SARS-CoV-2 omicron infection", + "rel_date": "2022-12-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.29.22282864", + "rel_abs": "BackgroundCoronavirus Disease 2019 (COVID-19) vaccine antigen dosage may affect protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, but direct evidence to quantify this effect is lacking.\n\nMethodsA matched, retrospective, cohort study that emulated a randomized control trial was conducted in Qatar between February 3, 2022 and November 8, 2022, to provide a head-to-head, controlled comparison of protection induced by two antigen dosages of the BNT162b2 vaccine. The study compared incidence of omicron infection in the national cohort of adolescents 12 years of age who received the two-dose primary-series of the 30-{micro}g BNT162b2 vaccine to that in the national cohort of adolescents 11 years of age who received the two-dose primary-series of the pediatric 10-{micro}g BNT162b2 vaccine. Associations were estimated using Cox proportional-hazard regression models.\n\nResultsAmong adolescents with no record of prior infection, cumulative incidence of infection was 6.0% (95% CI: 4.9-7.3%) for the 30-{micro}g cohort and 7.2% (95% CI: 6.1-8.5%) for the 10-{micro}g cohort, 210 days after the start of follow-up. Incidence during follow-up was dominated by omicron subvariants including, consecutively, BA.1/BA.2, BA.4/BA.5, BA.2.75*, and XBB. The adjusted hazard ratio comparing incidence of infection in the 30-{micro}g cohort to the 10-{micro}g cohort was 0.77 (95% CI: 0.60-0.98). Corresponding relative effectiveness was 23.4% (95% CI: 1.6-40.4%). Relative effectiveness was -3.3% (95% CI: -68.0-27.5%) among adolescents with a record of prior infection.\n\nConclusionsThree-fold higher BNT162b2 dosage was associated with [~]25% higher protection against infection in infection-naive adolescents of similar age. These findings may inform design of future COVID-19 vaccines and boosters for persons of different age groups.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Hiam Chemaitelly", + "author_inst": "Weill Cornell Medicine-Qatar" + }, + { + "author_name": "Houssein Ayoub", + "author_inst": "Qatar University" + }, + { + "author_name": "Peter V. Coyle", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Patrick Tang", + "author_inst": "Sidra Medicine" + }, + { + "author_name": "HADI M. YASSINE", + "author_inst": "Qatar University" + }, + { + "author_name": "Asmaa Althani", + "author_inst": "Qatar University" + }, + { + "author_name": "Hebah A. Al-Khatib", + "author_inst": "Qatar University" + }, + { + "author_name": "Mohammad R. Hasan", + "author_inst": "Sidra Medicine" + }, + { + "author_name": "Zaina Al-Kanaani", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Einas Al-Kuwari", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Andrew Jeremijenko", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Anvar Hassan Kaleeckal", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Ali Nizar Latif", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Riyazuddin Mohammad Shaik", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Hanan F. Abdul-Rahim", + "author_inst": "Qatar University" + }, + { + "author_name": "Gheyath K. Nasrallah", + "author_inst": "Qatar University" + }, + { + "author_name": "Mohamed Ghaith Al-Kuwari", + "author_inst": "Primary Health Care Corporation" + }, + { + "author_name": "Hamad Eid Al-Romaihi", + "author_inst": "MoPH: Ministry of Public Health Qatar" + }, + { + "author_name": "Adeel A Butt", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Mohamed H. Al-Thani", + "author_inst": "MoPH: Ministry of Public Health Qatar" + }, + { + "author_name": "Abdullatif Al-Khal", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Roberto Bertollini", + "author_inst": "MoPH: Ministry of Public Health Qatar" + }, + { + "author_name": "Laith J Abu-Raddad", + "author_inst": "Weill Cornell Medicine-Qatar" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.12.08.519588", "rel_title": "Atlas-scale single-cell multi-sample multi-condition data integration using scMerge2", @@ -142537,89 +144069,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "sports medicine" }, - { - "rel_doi": "10.1101/2022.12.01.22282987", - "rel_title": "Factors Associated with Long Covid Symptoms in an Online Cohort Study", - "rel_date": "2022-12-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.01.22282987", - "rel_abs": "ImportanceProlonged symptoms following SARS-CoV-2 infection, or Long COVID, is common, but few prospective studies of Long COVID risk factors have been conducted.\n\nObjectiveTo determine whether sociodemographic factors, lifestyle, or medical history preceding COVID-19 or characteristics of acute SARS-CoV-2 infection are associated with Long COVID.\n\nDesignCohort study with longitudinal assessment of symptoms before, during, and after SARS-CoV-2 infection, and cross-sectional assessment of Long COVID symptoms using data from the COVID-19 Citizen Science (CCS) study.\n\nSettingCCS is an online cohort study that began enrolling March 26, 2020. We included data collected between March 26, 2020, and May 18, 2022.\n\nParticipantsAdult CCS participants who reported a positive SARS-CoV-2 test result (PCR, Antigen, or Antibody) more than 30 days prior to May 4, 2022, were surveyed.\n\nExposuresAge, sex, race/ethnicity, education, employment, socioeconomic status/financial insecurity, self-reported medical history, vaccination status, time of infection (variant wave), number of acute symptoms, pre-COVID depression, anxiety, alcohol and drug use, sleep, exercise.\n\nMain OutcomePresence of at least 1 Long COVID symptom greater than 1 month after acute infection. Sensitivity analyses were performed considering only symptoms beyond 3 months and only severe symptoms.\n\nResults13,305 participants reported a SARS-CoV-2 positive test more than 30 days prior, 1480 (11.1% of eligible) responded to a survey about Long COVID symptoms, and 476 (32.2% of respondents) reported Long COVID symptoms (median 360 days after infection).\n\nRespondents mean age was 53 and 1017 (69%) were female. Common Long COVID symptoms included fatigue, reported by 230/476 (48.3%), shortness of breath (109, 22.9%), confusion/brain fog (108, 22.7%), headache (103, 21.6%), and altered taste or smell (98, 20.6%). In multivariable models, number of acute COVID-19 symptoms (OR 1.30 per symptom, 95%CI 1.20-1.40), lower socioeconomic status/financial insecurity (OR 1.62, 95%CI 1.02-2.63), pre-infection depression (OR 1.08, 95%CI 1.01-1.16), and earlier variants (OR 0.37 for Omicron compared to ancestral strain, 95%CI 0.15-0.90) were associated with Long COVID symptoms.\n\nConclusions and RelevanceVariant wave, severity of acute infection, lower socioeconomic status and pre-existing depression are associated with Long COVID symptoms.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSWhat are the patterns of symptoms and risk factors for Long COVID among SARS-CoV-2 infected individuals?\n\nFindingsPersistent symptoms were highly prevalent, especially fatigue, shortness of breath, headache, brain fog/confusion, and altered taste/smell, which persisted beyond 1 year among 56% of participants with symptoms; a minority of participants reported severe Long COVID symptoms. Number of acute symptoms during acute SARS-CoV-2 infection, financial insecurity, pre-existing depression, and infection with earlier variants are associated with prevalent Long COVID symptoms independent of vaccination, medical history, and other factors.\n\nMeaningSeverity of acute infection, SARS-CoV-2 variant, and financial insecurity and depression are associated with Long COVID symptoms.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Matthew S Durstenfeld", - "author_inst": "Division of Cardiology at ZSFG and Department of Medicine, UCSF" - }, - { - "author_name": "Michael J Peluso", - "author_inst": "Division of HIV, Infectious Disease, & Global Medicine, UCSF" - }, - { - "author_name": "Noah D Peyser", - "author_inst": "Division of Cardiology, Department of Medicine, UCSF" - }, - { - "author_name": "Feng Lin", - "author_inst": "Department of Epidemiology and Biostatistics, UCSF" - }, - { - "author_name": "Sara J Knight", - "author_inst": "Division of Epidemiology, Department of Internal Medicine, University of Utah" - }, - { - "author_name": "Audrey Djibo", - "author_inst": "CVS Health Clinical Trial Services" - }, - { - "author_name": "Rasha Khatib", - "author_inst": "Advocate Aurora Research Institute" - }, - { - "author_name": "Heather Kitzman", - "author_inst": "Baylor Scott and White Health and Wellness Center" - }, - { - "author_name": "Emily O'Brien", - "author_inst": "Department of Population Health Sciences, Duke University School of Medicine" - }, - { - "author_name": "Natasha Williams", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Carmen Isasi", - "author_inst": "Department of Epidemiology & Population Health, Albert Einstein College of Medicine" - }, - { - "author_name": "John Kornak", - "author_inst": "Department of Epidemiology and Biostatistics, UCSF" - }, - { - "author_name": "Thomas W Carton", - "author_inst": "Louisiana Public Health Institute" - }, - { - "author_name": "Jeffrey E Olgin", - "author_inst": "Division of Cardiology, Department of Medicine, UCSF" - }, - { - "author_name": "Mark J Pletcher", - "author_inst": "Department of Epidemiology and Biostatistics, UCSF" - }, - { - "author_name": "Gregory M Marcus", - "author_inst": "Division of Cardiology, Department of Medicine, UCSF" - }, - { - "author_name": "Alexis L Beatty", - "author_inst": "Department of Epidemiology and Biostatistics, UCSF; Division of Cardiology, Department of Medicine, UCSF" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.12.02.22281853", "rel_title": "Quantifying individual-level heterogeneity in infectiousness and susceptibility through household studies", @@ -143337,6 +144786,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.12.04.22283067", + "rel_title": "Enhancing the sensitivity of rapid antigen detection test (RADT) of different SARS-CoV-2 variants and lineages using fluorescence-labeled antibodies and a fluorescent meter", + "rel_date": "2022-12-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.04.22283067", + "rel_abs": "RT-qPCR is considered the gold standard for diagnosis of COVID-19; however, it is laborious, time-consuming, and expensive. RADTs have evolved recently as relatively inexpensive methods to address these shortcomings, but their performance for detecting different SARS-COV-2 variants remains limited. RADT test performance could be enhanced using different antibody labeling and signal detection techniques. Here, we aimed to evaluate the performance of two Wondfo antigen RADTs for detecting different SARS-CoV-2 variants: (i) the conventional colorimetric RADT (Ab-conjugated with gold beads); and (ii) the new Finecare RADT (Ab-coated fluorescent beads). Finecare is a meter used for the detection of a fluorescent signal. 187 frozen nasopharyngeal swabs collected in Universal transport (UTM) that are RT-qPCR positive for different SARS-CoV-2 variants were selected, including 60 Alpha, 59 multiple Delta, and 108 multiple Omicron variants. 60 flu and 60 RSV-positive samples were included as negative controls (total sample number=349). The conventional RADT showed sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of 62.4% (95%CI: 54-70), 100% (95%CI: 97-100), 100% (95%CI: 100-100), and 58% (95%CI: 49-67) respectively. These measurements were enhanced using the Finecare RADT: sensitivity, specificity, PPV, and NPV were 92.6% (95%CI: 89.08-92.3), 96% (95%CI: 96-99.61), 98% (95%CI: 89-92.3), and 85% (95%CI: 96-99.6) respectively. The sensitivity of both RADTs could be greatly underestimated because nasopharyngeal swab samples collected UTM and stored at -80 {degrees}C were used. Despite that, our results indicate that the Finecare RADT is appropriate for clinical laboratory and community-based surveillance due to its high sensitivity and specificity.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Gheyath Nasrallah", + "author_inst": "Qatar University" + }, + { + "author_name": "Fatma Ali", + "author_inst": "Qatar University" + }, + { + "author_name": "Salma Younes", + "author_inst": "Qatar University" + }, + { + "author_name": "Hebah AlKhatib", + "author_inst": "Qatar University" + }, + { + "author_name": "Asmaa Althani", + "author_inst": "Qatar University" + }, + { + "author_name": "HADI M. YASSINE", + "author_inst": "Qatar University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.12.01.22283006", "rel_title": "SARS-CoV-2 infection- induced seroprevalence among children and associated risk factors during pre- and omicron-dominant wave, from January 2021 through November 2022, Thailand: Longitudinal study", @@ -144455,49 +145943,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2022.12.05.519140", - "rel_title": "Cyclic lipopeptides as membrane fusion inhibitors against SARS-CoV-2: new tricks for old dogs", - "rel_date": "2022-12-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.05.519140", - "rel_abs": "With the resurgence of the coronavirus pandemic, the repositioning of FDA-approved drugs against coronovirus and finding alternative strategies for antiviral therapy are both important. We previously identified the viral lipid envelope as a potential target for the prevention and treatment of SARS-CoV-2 infection with plant alkaloids [1]. Here, we investigated the effects of eleven cyclic lipopeptides (CLPs), including well-known antifungal and antibacterial compounds, on the liposome fusion triggered by calcium, polyethylene glycol 8000, and a fragment of SARS-CoV-2 fusion peptide (816-827) by calcein release assays. Differential scanning microcalorimetry of the gel-to-liquid-crystalline and lamellar-to-inverted hexagonal phase transitions and confocal fluorescence microscopy demonstrated the relation of the fusion inhibitory effects of CLPs to alterations in lipid packing, membrane curvature stress and domain organization. The effects of the compounds were evaluated in an in vitro Vero-based cell model, and aculeacin A, anidulafugin, iturin A, and mycosubtilin attenuated the cytopathogenicity of SARS-CoV-2 without specific toxicity.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Egor V. Shekunov", - "author_inst": "Institute of Cytology of Russian Academy of Sciences" - }, - { - "author_name": "Polina Z. Zlodeeva", - "author_inst": "Institute of Cytology of Russian Academy of Sciences" - }, - { - "author_name": "Svetlana S. Efimova", - "author_inst": "Institute of Cytology of Russian Academy of Sciences" - }, - { - "author_name": "Anna A. Muryleva", - "author_inst": "Saint-Petersburg Pasteur Institute of Epidemiology and Microbiology" - }, - { - "author_name": "Vladimir V. Zarubaev", - "author_inst": "Saint-Petersburg Pasteur Institute of Epidemiology and Microbiology" - }, - { - "author_name": "Alexander V. Slita", - "author_inst": "Saint-Petersburg Pasteur Institute of Epidemiology and Microbiology" - }, - { - "author_name": "Olga S. Ostroumova", - "author_inst": "Institute of Cytology of Russian Academy of Sciences" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2022.12.02.22283026", "rel_title": "Healthcare in England was affected by the COVID-19 pandemic across the pancreatic cancer pathway: a cohort study using OpenSAFELY-TPP", @@ -145115,6 +146560,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2022.11.30.22282954", + "rel_title": "Battle of Polio eradication in the Western Pacific Region in the transition to COVID-19 endemicity", + "rel_date": "2022-12-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.30.22282954", + "rel_abs": "The Polio eradication campaign has been set back substantially since 2020 due to the COVID-19 pandemic. Recent detections of poliovirus transmission in multiple high-income countries suggest suboptimal population immunity in many parts of the world even though polio vaccination has been included in routine childhood immunization for decades. We reviewed polio vaccination schedules and vaccine uptake in the Western Pacific Region countries and assessed the potential shortfall in population immunity against polio resurgence across these populations. In addition, we conducted a repeated cross-sectional study between 2021 and 2022 in the Western Pacific Region to understand factors contributing to polio vaccine hesitancy. Our results reveal potential shortfalls in population immunity against polio in Western Pacific Region and provide insights into how vaccination programs and campaigns can be strengthened to ensure continual progress towards polio eradication.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Ruobing Mei", + "author_inst": "Laboratory for Data Discovery of Health" + }, + { + "author_name": "Shirley L. L. Kwok", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Eric H. Y. Lau", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Tiffany H. K. Lo", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Joseph T. Wu", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Leesa K. Lin", + "author_inst": "Laboratory of Data Discovery for Health" + }, + { + "author_name": "Kathy Leung", + "author_inst": "The University of Hong Kong" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.12.02.22282981", "rel_title": "Protection of hybrid immunity against SARS-CoV-2 reinfection and severe COVID-19 during periods of Omicron variant predominance in Mexico", @@ -146417,41 +147905,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2022.11.30.518473", - "rel_title": "DAPTEV: Deep aptamer evolutionary modelling for COVID-19 drug design", - "rel_date": "2022-11-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.30.518473", - "rel_abs": "Typical drug discovery and development processes are costly, time consuming and often biased by expert opinion. Aptamers are short, single-stranded oligonucleotides (RNA/DNA) that bind to target proteins and other types of biomolecules. Compared with small-molecule drugs, aptamers can bind to their targets with high affinity (binding strength) and specificity (uniquely interacting with the target only). The conventional development process for aptamers utilizes a manual process known as Systematic Evolution of Ligands by Exponential Enrichment (SELEX), which is costly, slow, dependent on library choice and often produces aptamers that are not optimized. To address these challenges, in this research, we create an intelligent approach, named DAPTEV, for generating and evolving aptamer sequences to support aptamer-based drug discovery and development. Using the COVID-19 spike protein as a target, our computational results suggest that DAPTEV is able to produce structurally complex aptamers with strong binding affinities.\n\nAuthor summaryCompared with small-molecule drugs, aptamer drugs are short RNAs/DNAs that can specifically bind to targets with high strength. With the interest of discovering novel aptamer drugs as an alternative to address the long-lasting COVID-19 pandemic, in this research, we developed an artificial intelligence (AI) framework for the in silico design of novel aptamer drugs that can prevent the SARS-CoV-2 virus from entering human cells. Our research is valuable as we explore a novel approach for the treatment of SARS-CoV-2 infection and the AI framework could be applied to address future health crises.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Cameron Andress", - "author_inst": "Brock University Faculty of Mathematics and Science" - }, - { - "author_name": "Kalli Kappel", - "author_inst": "Eli and Edythe L. Broad Institute of Harvard and MIT: Broad Institute" - }, - { - "author_name": "Miroslava Cuperlovic-Culf", - "author_inst": "National Research Centre Canada Digital Technologies Research Centre" - }, - { - "author_name": "Hongbin Yan", - "author_inst": "Brock University" - }, - { - "author_name": "Yifeng Li", - "author_inst": "Brock University Faculty of Mathematics and Science" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2022.11.29.22282857", "rel_title": "Vaccine hesitancy, reactogenicity and immunogenicity of BNT162b2 and CoronaVac in pediatric patients with neuromuscular diseases", @@ -147005,6 +148458,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.11.29.22282913", + "rel_title": "Clinical, imaging, serological, and histopathological features of pulmonary post-acute sequelae after mild COVID-19 (PASC)", + "rel_date": "2022-11-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.29.22282913", + "rel_abs": "BackgroundA significant proportion of patients experience prolonged pulmonary, cardiocirculatory or neuropsychiatric symptoms after Coronavirus disease 2019 (COVID-19), termed post-acute sequelae of COVID (PASC). Lung manifestations of PASC include cough, dyspnea on exertion and persistent radiologic abnormalities and have been linked to viral persistence, ongoing inflammation and immune dysregulation. So far, there is limited data on lung histopathology and tissue-based immune cell subtyping in PASC.\n\nMethods51 unvaccinated patients (median age, 40 years; 43% female) with a median of 17 weeks (range, 2-55 weeks) after mild SARS-CoV-2 infection (without hospitalization) underwent full clinical evaluation including high-resolution computed tomography (HR-CT) and transbronchial biopsy. We used RT-PCR/FISH and immunohistochemistry (nucleocapsid/spike/CD3/CD4/CD8) for residual SARS-CoV-2 detection and T lymphocyte subtyping, respectively. We assessed interstitial fibrosis and macrophage profiles by transmission electron microscopy (TEM) and immunofluorescence multiplex staining, while cytokine profiling in bronchoalveolar lavage (BAL) fluid was performed by legendplex immunoassay.\n\nResultsDyspnea on exertion was the leading symptom of pulmonary PASC in our cohort. In 16% and 42.9% of patients, FEV1 and MEF50 were [≤] 80% and 35.3% showed low attenuation volume (LAV) in >5% of lung area, in line with airflow obstruction. There was a significant correlation between oxygen pulse and time since COVID (p=0.009). Histopathologically, PASC manifested as organizing pneumonia (OP), fibrinous alveolitis and increased CD4+ T cell infiltrate predominantly around airways (bronchiolitis), while the residual virus components were detectable in only a single PASC patient (2%). T cell infiltrates around small airways were inversely correlated with time since COVID, however, this trend failed to reach statistical significance. We identified discrete interstitial fibrosis and a pro-fibrotic macrophage subtype (CD68/CD163/S100A9) as well as significantly elevated interleukin 1{beta} in BAL fluid from PASC patients (p=0.01), but H-scores for fibrotic macrophage population did not correlate with severity of clinical symptoms or T cell infiltration.\n\nInterpretationWe show decreased FEV1/MEF50 and increased LAV in line with obstructive lung disease due to CD4+ T cell-predominant bronchiolitis as well as evidence of pro-fibrotic signaling in a subset of unvaccinated PASC patients. Since our results point towards self-limiting inflammation of small airways without detectable viral reservoirs, it remains unclear whether pulmonary symptoms in PASC are SARS-CoV-2-specific or represent a general response to viral infection. Still, evidence of pro-fibrotic signaling should warrant clincal follow-up and further research into possible long-time fibrotic remodeling in PASC patients.\n\nKey pointsO_LIDyspnea on exertion is the leading clinical manifestation of PASC in the lung\nC_LIO_LIa minority of pts have significantly impaired lung function (FVC/TLC[≤]80% or DLCO[≤]70%) in spiroergometry and/or radiologic abnormalities, oxygen pulse seems to normalize over time\nO_LI16% and 42.9% of pts have FEV1 and MEF50[≤]80% and 35.3% have LAV>5% of lung area, in line with airflow obstruction due to bronchiolitis\nC_LI\nC_LIO_LIResidual virus was not detectable in the lung tissue of all but one PASC patient (2%)\nC_LIO_LIHistologically, PASC may manifest as T cell-mediated bronchiolitis, OP and fibrinous alveolitis\nC_LIO_LIThere is evidence of fibrotic remodeling (ultrastructural interstitial fibrosis, pro-fibrotic macrophage subpopulation, pro-fibrotic cytokine IL-1{beta} in BAL) but this did not correlate with the degree of T cell infiltrate/bronchiolitis\nC_LI", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Daniel Gagiannis", + "author_inst": "Bundeswehrkrankenhaus Ulm" + }, + { + "author_name": "Carsten Hackenbroch", + "author_inst": "Bundeswehrkrankenhaus Ulm" + }, + { + "author_name": "Annika Czech", + "author_inst": "Bundeswehrkrankenhaus Ulm" + }, + { + "author_name": "Anna Lindner", + "author_inst": "Bundeswehrkrankenhaus Ulm" + }, + { + "author_name": "Nathalie Maag", + "author_inst": "Bundeswehrkrankenhaus Ulm" + }, + { + "author_name": "Wilhelm Bloch", + "author_inst": "German Sport University Cologne" + }, + { + "author_name": "Fabian Zech", + "author_inst": "University of Ulm" + }, + { + "author_name": "Frank Kirchhoff", + "author_inst": "University of Ulm" + }, + { + "author_name": "Sonja Djudjaj", + "author_inst": "RWTH Aachen University" + }, + { + "author_name": "Saskia E von Stillfried", + "author_inst": "RWTH Aachen University" + }, + { + "author_name": "Roman Buelow", + "author_inst": "RWTH Aachen University" + }, + { + "author_name": "Peter Boor", + "author_inst": "RWTH Aachen University" + }, + { + "author_name": "Konrad Steinestel", + "author_inst": "Bundeswehrkrankenhaus Ulm" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2022.11.27.518117", "rel_title": "Fc-gamma receptor-dependent antibody effector functions are required for vaccine protection against infection by antigenic variants of SARS-CoV-2", @@ -148843,6 +150363,53 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.11.28.518195", + "rel_title": "Highly potent antisense oligonucleotides (ASOs) targeting the SARS-CoV-2 RNA genome", + "rel_date": "2022-11-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.28.518195", + "rel_abs": "Currently the world is dealing with the third outbreak of the human-infecting coronavirus with potential lethal outcome, cause by a member of the Nidovirus family, the SARS-CoV-2. The severe acute respiratory syndrome coronavirus (SARS-CoV-2) has caused the last worldwide pandemic. Successful development of vaccines highly contributed to reduce the severeness of the COVID-19 disease. To establish a control over the current and newly emerging coronaviruses of epidemic concern requires development of substances able to cure severely infected individuals and to prevent virus transmission. Here we present a therapeutic strategy targeting the SARS-CoV-2 RNA using antisense oligonucleotides (ASOs) and identify locked nucleic acid gapmers (LNA gapmers) potent to reduce by up to 96% the intracellular viral load in vitro. Our results strongly suggest promise of our preselected ASOs for further development as therapeutic or prophylactic anti-viral agents.\n\nOne sentence summaryASOs (LNA gapmers) targeting the SARS-CoV-2 RNA genome have been effective in viral RNA (load) reduction in vitro.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Vita Dauksaite", + "author_inst": "Department of Internal Medicine (Nephrology), Leiden University Medical Center, Leiden, the Netherlands" + }, + { + "author_name": "Ali Tas", + "author_inst": "Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands" + }, + { + "author_name": "Falk Wachowius", + "author_inst": "Hybridize Therapeutics, Leiden, the Netherlands" + }, + { + "author_name": "Anouk Spruit", + "author_inst": "Dutch Center for RNA Therapeutics, LUMC, Leiden, the Netherlands" + }, + { + "author_name": "Martijn van Hemert", + "author_inst": "Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands" + }, + { + "author_name": "Eric Snijder", + "author_inst": "Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands" + }, + { + "author_name": "Eric P. van der Veer", + "author_inst": "Hybridize Therapeutics, Leiden, the Netherlands" + }, + { + "author_name": "Anton Jan van Zonneveld", + "author_inst": "Department of Internal Medicine (Nephrology), Leiden University Medical Center, Leiden, the Netherlands" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2022.11.24.517882", "rel_title": "SARS-CoV-2 Spike Protein Induces Hemagglutination: Implications for COVID-19 Morbidities and Therapeutics and for Vaccine Adverse Effects", @@ -150042,37 +151609,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.11.24.22282691", - "rel_title": "User feedback on the NHS Test & Trace Service during COVID-19: the use of machine learning to analyse free-text data from 37,914 UK adults", - "rel_date": "2022-11-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.24.22282691", - "rel_abs": "ObjectivesThe UK governments approach to the pandemic relies on a test, trace and isolate strategy, mainly implemented via the digital NHS Test & Trace Service. Feedback on user experience is central to the successful development of public-facing services. As the situation dynamically changes and data accumulate, interpretation of feedback by humans becomes time-consuming and unreliable. The specific objectives were to 1) evaluate a human-in-the-loop machine learning technique based on structural topic modelling in terms of its serviceability in the analysis of vast volumes of free-text data, 2) generate actionable themes that can be used to increase user satisfaction of the Service.\n\nMethodsWe evaluated an unsupervised Topic Modelling approach, testing models with 5-40 topics and differing covariates. Two human coders conducted thematic analysis to interpret the topics. We identified a Structural Topic Model with 25 topics and metadata as covariates as the most appropriate for acquiring insights.\n\nResultsResults from analysis of feedback by 37,914 users from May 2020 to March 2021 highlighted issues with the Service falling within three major themes: multiple contacts and incompatible contact method and incompatible contact method, confusion around isolation dates and tracing delays, complex and rigid system.\n\nConclusionsStructural Topic Modelling coupled with thematic analysis was found to be an effective technique to rapidly acquire user insights. Topic modelling can be a quick and cost-effective method to provide high quality, actionable insights from free-text feedback to optimize public health services.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Paulina Bondaronek", - "author_inst": "University College London" - }, - { - "author_name": "Trisevgeni Papakonstantinou", - "author_inst": "Office for Health Improvement & Disparities, Department of Health and Social Care" - }, - { - "author_name": "Chryssa Stefanidou", - "author_inst": "Office for Health Improvement & Disparities, Department of Health and Social Care" - }, - { - "author_name": "Tim Chadborn", - "author_inst": "Office for Health Improvement & Disparities, Department of Health and Social Care" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.11.23.22282684", "rel_title": "The dynamic relationship between COVID-19 cases and SARS-CoV-2 wastewater concentrations across time and space: considerations for model training data sets", @@ -150857,6 +152393,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.11.21.22282600", + "rel_title": "Susceptibility-Weighted Magnetic Resonance Imaging Highlights Brain Alterations in COVID Recovered Patients.", + "rel_date": "2022-11-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.21.22282600", + "rel_abs": "The increasing number of reports of mild to severe psychological, behavioral, and cognitive sequelae in COVID-19 survivors motivates a need for a thorough assessment of the neurological effects of the disease. In this regard, we have conducted a neuroimaging study to understand the neurotropic behavior of the coronavirus. We hypothesize that the COVID recovered subjects have developed alterations in the brain which can be measured through susceptibility differences in various regions of brain when compared to healthy controls (HCs). Hence we performed our investigations on susceptibility weighted imaging (SWI) volumes. Fatigue, being of the most common symptoms of Long COVID has also been studied in this work. SWI volumes of 46 COVID and 30 HCs were included in this study. The COVID patients were imaged within six months of their recovery. We performed unpaired two-sample t-test over the pre-processed SWI volumes of both the groups and multiple linear regression was performed to observe group differences and correlation of fatigue with SWI values. The group analysis showed that COVID recovered subjects had significantly higher susceptibility imaging values in regions of the frontal lobe and the brain stem. The clusters obtained in the frontal lobe primarily show differences in the white matter regions. The COVID group also demonstrated significantly higher fatigue levels than the HC group. The regression analysis on the COVID group yielded clusters in anterior cingulate gyrus and midbrain which exhibited negative correlations with fatigue scores. This study suggests an association of Long COVID with prolonged effects on the brain and also indicates the viability of SWI modality for analysis of post-COVID symptoms.\n\nHighlightsO_LISusceptibility weighted imaging is used for neuroimaging study of Long COVID.\nC_LIO_LIA group-level study is performed to analyze the effects of COVID on the brain.\nC_LIO_LICOVID survivors showed susceptibility differences in the frontal lobe and brainstem.\nC_LIO_LIAnalyzed the relationship between MRI data of COVID survivors and fatigue scores.\nC_LI", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Sapna S Mishra", + "author_inst": "Indian Institute of Technology Delhi" + }, + { + "author_name": "Rakibul Hafiz", + "author_inst": "New Jersey Institute of Technology" + }, + { + "author_name": "Rohit Misra", + "author_inst": "Indian Institute of Technology Delhi" + }, + { + "author_name": "Tapan Kumar Gandhi", + "author_inst": "Indian Institute of Technology Delhi" + }, + { + "author_name": "Alok Prasad", + "author_inst": "Irene Hospital" + }, + { + "author_name": "Vidur Mahajan", + "author_inst": "Mahajan Imaging Center" + }, + { + "author_name": "Bharat B. Biswal", + "author_inst": "New Jersey Institute of Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2022.11.21.22282601", "rel_title": "Cost of In-patient Management of Covid-19 Patients in a Tertiary Hospital in Kuwait", @@ -151780,77 +153359,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.11.20.517271", - "rel_title": "Paxlovid-like nirmatrelvir/ritonavir fails to block SARS-CoV-2 transmission in ferrets", - "rel_date": "2022-11-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.20.517271", - "rel_abs": "Despite the continued spread of SARS-CoV-2 and emergence of variants of concern (VOC) that are capable of escaping preexisting immunity, therapeutic options are underutilized. In addition to preventing severe disease in high-risk patients, antivirals may contribute to interrupting transmission chains. The FDA has granted emergency use authorizations for two oral drugs, molnupiravir and paxlovid. Initial clinical trials suggested an efficacy advantage of paxlovid, giving it a standard-of-care-like status in the United States. However, recent retrospective clinical studies suggested a more comparable efficacy of both drugs in preventing complicated disease and case-fatalities in older adults. For a direct efficacy comparison under controlled conditions, we assessed potency of both drugs against SARS-CoV-2 in two relevant animal models; the Roborovski dwarf hamster model for severe COVID-19 in high-risk patients and the ferret model of upper respiratory tract disease and transmission. After infection of dwarf hamsters with VOC omicron, paxlovid and molnupiravir were efficacious in mitigating severe disease and preventing death. However, a pharmacokinetics-confirmed human equivalent dose of paxlovid did not significantly reduce shed SARS-CoV-2 titers in ferrets and failed to block virus transmission to untreated direct-contact ferrets, whereas transmission was fully suppressed in a group of animals treated with a human-equivalent dose of molnupiravir. Prophylactic administration of molnupiravir to uninfected ferrets in direct contact with infected animals blocked productive SARS-CoV-2 transmission, whereas all contacts treated with prophylactic paxlovid became infected. These data confirm retrospective reports of similar therapeutic benefit of both drugs for older adults, and reveal that treatment with molnupiravir, but not paxlovid, may be suitable to reduce the risk of SARS-CoV-2 transmission.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Robert Cox", - "author_inst": "Georgia State University" - }, - { - "author_name": "Carolin M Lieber", - "author_inst": "Georgia State University" - }, - { - "author_name": "Josef D Wolf", - "author_inst": "Georgia State University" - }, - { - "author_name": "Amirhossein Karimi", - "author_inst": "Georgia State University" - }, - { - "author_name": "Nicole A.P. Lieberman", - "author_inst": "University of Washington" - }, - { - "author_name": "Zachary M Sticher", - "author_inst": "Emory University" - }, - { - "author_name": "Pavitra Roychoudhury", - "author_inst": "University of Washington" - }, - { - "author_name": "Meghan K Andrews", - "author_inst": "Emory University" - }, - { - "author_name": "Rebecca E Krueger", - "author_inst": "Emory University" - }, - { - "author_name": "Michael G Natchus", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "George R Painter", - "author_inst": "Emory University" - }, - { - "author_name": "Alexander Kolykhalov", - "author_inst": "Emory University" - }, - { - "author_name": "Alexander L Greninger", - "author_inst": "University of Washington" - }, - { - "author_name": "Richard K Plemper", - "author_inst": "Georgia State University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.11.18.517156", "rel_title": "SARS-CoV-2 exposure in Norwegian rats (Rattus norvegicus) from New York City", @@ -152667,6 +154175,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2022.11.15.22282328", + "rel_title": "Efficacy of the wild-type/Omicron BA.1 bivalent vaccine as the second booster dose against Omicron BA.2 and BA.5", + "rel_date": "2022-11-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.15.22282328", + "rel_abs": "IntroductionIn addition to the original monovalent vaccines available for SARS-CoV-2, bivalent vaccines covering wild-type (WT) and Omicron BA.1 are also available. However, there is a lack of real-world data on the effectiveness of bivalent vaccines as second boosters on the dominant Omicron sublineages, including BA.2 and BA.5.\n\nMethodsThis prospective longitudinal cohort study was conducted at Toyama University Hospital, a tertiary medical center in Japan. Participants (n = 565) who received the first booster vaccination were followed up until 2 weeks after the second booster dose of the monovalent mRNA-1273 (WT group, n = 168) and bivalent BNT162b2 (WT+BA.1 group, n = 23) vaccines. Participants with previous SARS-CoV-2 infections were excluded from the study. Anti-receptor-binding domain (RBD) antibody levels and neutralizing activity were measured. Vaccine-related symptoms were also assessed using a questionnaire after the second booster dose.\n\nResultsThe anti-RBD antibody levels after the second booster dose in the WT and WT+BA.1 group were similar (median [inter quartile], 26262.0 [16951.0-38137.0] U/mL vs. 24840.0 [14828.0-41460.0] U/mL, respectively). Although the neutralization activity of the pooled sera of the WT+BA.1 group was the lowest against BA.5, the activities against BA.2 and BA.5 were higher than those of the WT group in both pseudotyped and live virus assays. Vaccine-related symptoms, including systemic and local symptoms, were strongly correlated with anti-RBD antibody levels and neutralizing titers with significant differences.\n\nConclusionThe second booster dose of the bivalent (WT/Omicron BA.1) vaccine induced higher neutralizing activity against BA.2 and BA.5 than that of the original monovalent vaccine.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Hitoshi Kawasuji", + "author_inst": "Toyama University Graduate School of Medicine and Pharmaceutical Science" + }, + { + "author_name": "Yoshitomo Morinaga", + "author_inst": "University of Toyama" + }, + { + "author_name": "Hideki Tani", + "author_inst": "Toyama Institute of Health" + }, + { + "author_name": "Yumiko Saga", + "author_inst": "Toyama Institute of Health" + }, + { + "author_name": "Hiroshi Yamada", + "author_inst": "University of Toyama" + }, + { + "author_name": "Yoshihiro Yoshida", + "author_inst": "University of Toyama" + }, + { + "author_name": "Yusuke Takegoshi", + "author_inst": "University of Toyama" + }, + { + "author_name": "Makito Kaneda", + "author_inst": "University of Toyama" + }, + { + "author_name": "Yushi Murai", + "author_inst": "University of Toyama" + }, + { + "author_name": "Kou Kimoto", + "author_inst": "University of Toyama" + }, + { + "author_name": "Akitoshi Ueno", + "author_inst": "University of Toyama" + }, + { + "author_name": "Yuki Miyajima", + "author_inst": "University of Toyama" + }, + { + "author_name": "Kentaro Nagaoka", + "author_inst": "University of Toyama" + }, + { + "author_name": "Chikako Ono", + "author_inst": "University of Toyama" + }, + { + "author_name": "Yoshiharu Matsuura", + "author_inst": "University of Toyama" + }, + { + "author_name": "Hideki Niimi", + "author_inst": "University of Toyama" + }, + { + "author_name": "Yoshihiro Yamamoto", + "author_inst": "University of Toyama" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2022.11.16.22282346", "rel_title": "The CANDID Study: impact of COVID-19 on critical care nurses and organisational outcomes: implications for the delivery of critical care services. A questionnaire study before and during the pandemic.", @@ -153594,53 +155185,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.11.17.22282466", - "rel_title": "Hospital length of stay throughout bed pathways and factors affecting this time: a non-concurrent cohort study of Colombia COVID-19 patients and an unCoVer network project", - "rel_date": "2022-11-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.17.22282466", - "rel_abs": "Predictions of hospital beds occupancy depends on hospital admission rates and the length of stay (LoS) according to bed type (hospital and intensive care unit beds). The objective of this study was to describe the LoS of COVID-19 hospital patients in Colombia during 2020-2021. Accelerated failure time models were used to estimate the LoS distribution according to each bed type and throughout each bed pathway. Acceleration factors and 95% confidence intervals were calculated to measure the effect on LoS of the outcome, sex, age, admission period during the epidemic (i.e., epidemic waves, peaks or valleys, and before/after vaccination period), and patients geographic origin. Most of the admitted COVID-19 patients occupied just hospital bed. Recovered patients spent more time in the hospital and intensive care unit than deceased patients. Men had longer LoS than women. In general, the LoS increased with age. Finally, the LoS varied along epidemic waves. It was lower in epidemic valleys than peaks, and became shorter after vaccinations began in Colombia than before. Our study highlights the necessity of analyzing local data on hospital admission rates and LoS to design strategies to prioritize hospital beds resources during the current and future pandemics.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Lina Marcela Ruiz Galvis", - "author_inst": "University of Antioquia: Universidad de Antioquia" - }, - { - "author_name": "Carlos Andres Perez Aguirre", - "author_inst": "National University of Colombia Medellin: Universidad Nacional de Colombia Sede Medellin" - }, - { - "author_name": "Juan Pablo Perez Bedoya", - "author_inst": "University of Antioquia: Universidad de Antioquia" - }, - { - "author_name": "Oscar Ignacio Mendoza Cardozo", - "author_inst": "University of Antioquia: Universidad de Antioquia" - }, - { - "author_name": "No\u00ebl Christopher Barengo", - "author_inst": "Florida International University College of Medicine: Florida International University Herbert Wertheim College of Medicine" - }, - { - "author_name": "Juan Pablo Sanchez Escudero", - "author_inst": "University of Antioquia: Universidad de Antioquia" - }, - { - "author_name": "Jonathan Cardona Jimenez", - "author_inst": "Pascual Bravo University Institution: Institucion Universitaria Pascual Bravo" - }, - { - "author_name": "Paula Andrea Diaz Valencia", - "author_inst": "University of Antioquia: Universidad de Antioquia" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.11.16.22282387", "rel_title": "Comprative evaluation of Advanced Oxidation Processes (AOPs) for reducing SARS-CoV-2 viral load from campus sewage water", @@ -154281,6 +155825,89 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2022.11.17.516898", + "rel_title": "Improved Neutralization of Omicron BA.4/5, BA.4.6, BA.2.75.2, BQ.1.1, and XBB.1 with Bivalent BA.4/5 Vaccine", + "rel_date": "2022-11-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.17.516898", + "rel_abs": "The BNT162b2 bivalent BA.4/5 COVID-19 vaccine has been authorized to mitigate COVID-19 due to current Omicron and potentially future variants. New sublineages of SARS-CoV-2 Omicron continue to emerge and have acquired additional mutations, particularly in the spike protein, that may lead to improved viral fitness and immune evasion. The present study characterized neutralization activities against new Omicron sublineages BA.4.6, BA.2.75.2, BQ.1.1, and XBB.1 after a 4th dose (following three doses of BNT162b2) of either the original monovalent BNT162b2 or the bivalent BA.4/5 booster in individuals >55 years of age. For all participants, the 4th dose of monovalent BNT162b2 vaccine induced a 3.0x, 2.9x, 2.3x, 2.1x, 1.8x, and 1.5x geometric mean neutralizing titer fold rise (GMFR) against USA/WA1-2020 (a strain isolated in January 2020), BA.4/5, BA.4.6, BA.2.75.2, BQ.1.1, and XBB.1, respectively; the bivalent vaccine induced 5.8x, 13.0x, 11.1x, 6.7x, 8.7x, and 4.8x GMFRs. For individuals without SARS-CoV-2 infection history, BNT162b2 monovalent induced 4.4x, 3.0x, 2.5x, 2.0x, 1.5x, and 1.3x GMFRs, respectively; the bivalent vaccine induced 9.9x, 26.4x, 22.2x, 8.4x, 12.6x, and 4.7x GMFRs. These data suggest the bivalent BA.4/5 vaccine is more immunogenic than the original BNT162b2 monovalent vaccine against circulating Omicron sublineages, including BQ.1.1 that is becoming prevalent globally.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Jing Zou", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Chaitanya Kurhade", + "author_inst": "The University of Texas Medical Branch at Galveston" + }, + { + "author_name": "Sohil Patel", + "author_inst": "Pfizer Vaccine Research and Development, Pfizer Ltd, Hurley, UK" + }, + { + "author_name": "Nicholas Kitchin", + "author_inst": "Pfizer Vaccine Research and Development, Pfizer Ltd, Hurley, UK" + }, + { + "author_name": "Mark Cutler", + "author_inst": "Pfizer Vaccine Research and Development, Pearl River, New York, USA" + }, + { + "author_name": "David Cooper", + "author_inst": "Pfizer Vaccine Research and Development, Pearl River, New York, USA" + }, + { + "author_name": "Qi Yang", + "author_inst": "Pfizer Vaccine Research and Development, Pearl River, New York, USA" + }, + { + "author_name": "Hui Cai", + "author_inst": "Pfizer Vaccine Research and Development, Pearl River, New York, USA" + }, + { + "author_name": "Alexander Muik", + "author_inst": "BioNTech, Mainz, Germany" + }, + { + "author_name": "Ying Zhang", + "author_inst": "Pfizer Vaccine Research and Development, Pearl River, New York, USA" + }, + { + "author_name": "Dung-Yang Lee", + "author_inst": "Pfizer Vaccine Research and Development, Pearl River, New York, USA" + }, + { + "author_name": "Ugur Sahin", + "author_inst": "BioNTech" + }, + { + "author_name": "Annaliesa S. Anderson", + "author_inst": "Pfizer Vaccine Research and Development, Pearl River, New York, USA" + }, + { + "author_name": "William C. Gruber", + "author_inst": "Pfizer Vaccine Research and Development, Pearl River, New York, USA" + }, + { + "author_name": "Xuping Xie", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Kena A. Swanson", + "author_inst": "Pfizer Vaccine Research and Development, Pearl River, New York, USA" + }, + { + "author_name": "Pei-Yong Shi", + "author_inst": "University of Texas Medical Branch" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.11.11.516239", "rel_title": "Efficient SARS-CoV-2 detection utilizing chitin-immobilized nanobodies synthesized in Ustilago maydis", @@ -155256,93 +156883,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.11.08.22282084", - "rel_title": "Successful Detection of Delta and Omicron Variants of SARS-CoV-2 by Veterinary Diagnostic Laboratory Participants in an Interlaboratory Comparison Exercise", - "rel_date": "2022-11-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.08.22282084", - "rel_abs": "BackgroundSince the beginning of the COVID-19 pandemic veterinary diagnostic laboratories have tested diagnostic samples for SARS-CoV-2 not only in animals, but in over five million human samples. An evaluation of the performance of those laboratories is needed using blinded test samples to ensure that laboratories report reliable data to the public. This interlaboratory comparison exercise (ILC3) builds on two prior exercises to assess whether veterinary diagnostic laboratories can detect Delta and Omicron variants spiked in canine nasal matrix or viral transport medium.\n\nMethodsInactivated Delta variant at levels of 25 to 1,000 copies per 50 L of nasal matrix were prepared for participants by the ILC organizer, an independent laboratory, for blinded analysis. Omicron variant at 1,000 copies per 50 L of transport medium was also included. Feline infectious peritonitis virus (FIPV) RNA was used as a confounder for specificity assessment. A total of 14 test samples were prepared for each participant. Participants used their routine diagnostic procedures for RNA extraction and real-time RT-PCR. Results were analyzed according to International Organization for Standardization (ISO) 16140 - 2:2016.\n\nResultsThe overall results showed 93% detection for Delta and 97% for Omicron at 1,000 copies per 50 L (22-200 copies per reaction). The overall specificity was 97% for blank samples and 100% for blank samples with FIPV. No differences in Ct values were significant for samples with the same virus levels between N1 and N2 markers, nor between the two variants.\n\nConclusionsThe results indicated that all ILC3 participants were able to detect both Delta and Omicron variants. The canine nasal matrix did not significantly affect SARS-CoV-2 detection.\n\nImpact StatementEnsuring accurate detection methods for SARS-CoV-2 is critical as veterinary diagnostic labs are testing both human and animal samples. This exercise used blinded test samples and provided high confidence in the sensitivity of methods in twenty-nine laboratories for detection of SARS-CoV-2 variants while addressing the impact of sample matrix. Importantly, the results indicated that variants and matrix do not impact detection results. Additionally, this article examined decision-making criteria for Ct cut-off values from different laboratories and encouraged them to review and potentially reassess their criteria to improve future performance. This knowledge will lead to higher confidence in laboratory detection of current and new SARS-CoV-2 variants and aid in establishing reasonable cut-off parameters for these diagnostics tests.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Kaiping Deng", - "author_inst": "Division of Food Processing Science and Technology, U.S. Food and Drug Administration" - }, - { - "author_name": "Sarah M. Nemser", - "author_inst": "Center for Veterinary Medicine, U.S. Food and Drug Administration" - }, - { - "author_name": "Kirstin Frost", - "author_inst": "QuoData Quality & Statistics" - }, - { - "author_name": "Laura B. Goodman", - "author_inst": "College of Veterinary Medicine, Cornell University" - }, - { - "author_name": "Hon S. Ip", - "author_inst": "National Wildlife Health Center, U.S. Geological Survey" - }, - { - "author_name": "Mary Lea Killian", - "author_inst": "National Veterinary Services Laboratory, National Animal and Plant Health Inspection Service, U.S. Department of Agriculture" - }, - { - "author_name": "Jodie Ulaszek", - "author_inst": "Institute for Food Safety and Health, Illinois Institute of Technology" - }, - { - "author_name": "Shannon Kiener", - "author_inst": "Division of Food Processing Science and Technology, U.S. Food and Drug Administration" - }, - { - "author_name": "Matthew Kmet", - "author_inst": "Division of Food Processing Science and Technology, U.S. Food and Drug Administration" - }, - { - "author_name": "Steffen Uhlig", - "author_inst": "QuoData Quality & Statistics" - }, - { - "author_name": "Karina Hettwer", - "author_inst": "QuoData Quality & Statistics" - }, - { - "author_name": "Bertrand Colson", - "author_inst": "QuoData Quality & Statistics" - }, - { - "author_name": "Kapil Nichani", - "author_inst": "QuoData Quality & Statistics" - }, - { - "author_name": "Anja Schlierf", - "author_inst": "QuoData Quality & Statistics" - }, - { - "author_name": "Andriy Tkachenko", - "author_inst": "Center for Veterinary Medicine, U.S. Food and Drug Administration" - }, - { - "author_name": "Megan R. Miller", - "author_inst": "Center for Veterinary Medicine, U.S. Food and Drug Administration" - }, - { - "author_name": "Ravinder Reddy", - "author_inst": "Division of Food Processing Science and Technology, U.S. Food and Drug Administration" - }, - { - "author_name": "Gregory H. Tyson", - "author_inst": "Center for Veterinary Medicine, U.S. Food and Drug Administration" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.11.08.22282069", "rel_title": "Protection against infection with the Omicron BA.5 subvariant among people with previous SARS-CoV-2 infection - surveillance results from southern Sweden, June to August 2022", @@ -156055,6 +157595,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2022.11.05.22281734", + "rel_title": "Long-term experience with rapid air filtration (6 to 15 air changes per hour) in a K-5 elementary school using HEPA and Do-It-Yourself (DIY) air purifiers during the COVID-19 pandemic", + "rel_date": "2022-11-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.05.22281734", + "rel_abs": "On May 12, 2023 CDC recommended 5 air changes per hour (5 ACH) and in July 2021 California (CDPH) recommended 6 to 12 ACH to reduce long-range, aerosol transmission of COVID-19 and other pathogens in classrooms. EPA recommends MERV 13+ DIY air cleaners for temporary use during wildfires, and a recent EPA study reported inconsistent usage in homes due to excessive noise generated by the DIY air cleaners. Questions also remain about wear and tear including how long filters retain their filtration properties and need to be replaced. Herein we report real-world experience from daily usage of 47 HEPA and 60 MERV 16 DIY air cleaners in a California elementary school during two academic school years from spring 2021 through fall of 2023 across 16 classrooms, a library, an auditorium, a lunchroom, and in a hallway. Three to six purifiers were needed in classrooms to meet 6 to 12 ACH. Teachers reported noise generated by MERV 16 DIY purifiers on lowest fan speed as acceptable for classroom use. Filtration efficiency at 0.3 m (most penetrating particle size) for DIY air cleaners with 5\" MERV 16 filters used in the classrooms averaged 77% after six months (1st batch in February 2022) compared to 92% for newly installed filters (2nd batch in October 2022). Follow up testing on both batches of filters after an additional academic year (June 2023) showed only slight changes in average filtration efficiency. Portable air cleaners (HEPA and DIY) averaged and estimated 10 ACH (6-15 ACH) across the 16 classrooms demonstrating feasibility and unit economics of meeting CDPH targets per classroom for $200-$650 with DIY versus $600-$12,000 with the HEPA models used. In one 9000 cubic foot classroom with 7 air purifiers, air exchange rate was measured using ambient aerosols at 18 ACH from air purifiers (within 20% of ACH estimated based on CADR of purifiers) and 7 ACH from HVAC for a combined total of 25 ACH. Based on this long-term experience, specific recommendations for enhancing and improving CDCs web page \"Ventilation in Buildings\" include: (1) recommended operation of MERV 13+ DIY at their low speed for low noise, cost-effective air cleaning (2) electro-mechanical safety especially in relation to power outlets (3) an open-source procedure known as the \"spike test\" using ambient aerosols to verify ACH in a room, like the Portacount for mask fit testing. Spike testing can become the basis for ACH certification or verification in any room without generating aerosol contaminants (e.g. salt water, smoke, tracers which may be unsafe or disallowed indoors).", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Devabhaktuni Srikrishna", + "author_inst": "Patient Knowhow, Inc." + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.11.08.22282042", "rel_title": "Arrayed Imaging Reflectometry monitoring of anti-viral antibody production throughout vaccination and breakthrough Covid-19", @@ -157286,45 +158845,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.11.04.22281828", - "rel_title": "Outcome Of Total Surgical Debridement Of Covid Associated Skull base Mucormycosis Based on a New Surgical Staging System: Evidence From A Cohort Study.", - "rel_date": "2022-11-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.04.22281828", - "rel_abs": "PurposeTo propose a surgical staging system with management protocol for post-covid Rhino-Orbito-Cerebral Mucormycosis (ROCM) with central skull base osteomyelitis.\n\nMethodsA prospective cohort study of post-covid ROCM patients between May 2021 and January 2022. Patients were assessed radiologically and staged from I to V. Follow up period was 6 to 18 months and the surgical outcome was assessed.\n\nResultsTotal of 193 patients (129 primary and 64 revision). Maxilla was found to be the epicenter of anterior disease (69.3%) and pterygoid wedge, the epicenter of posterior disease (85.6%). More than 65% of our patients, at the time of presentation, presented with ROCM with involvement of the central skull base. Intracranial disease was noted in 13.9% of patients and the mortality rate was 6.2 %.\n\nConclusionThis staging system provides a systematic step-by-step protocol for the management of ROCM, with emphasis on meticulous disease clearance at the central skull base.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Lekshmy R Kurup", - "author_inst": "Royal Pearl Hospital, Trichy" - }, - { - "author_name": "Harshita Singh", - "author_inst": "Royal Pearl Hospital, Trichy, India" - }, - { - "author_name": "Shilpee Sharma", - "author_inst": "Royal Pearl Hospital,Trichy,India" - }, - { - "author_name": "Puya Dehgani-Mobaraki", - "author_inst": "Associazione Naso Sano, Italy, India" - }, - { - "author_name": "Asiya Kamber Zaidi", - "author_inst": "Associazione Naso Sano, Italy" - }, - { - "author_name": "T Narayanan Janakiram", - "author_inst": "Royal Pearl Hospital, Trichy, India" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "otolaryngology" - }, { "rel_doi": "10.1101/2022.11.04.22281946", "rel_title": "Sentiments and Emotions for Vaccination in 2021: An International Comparison Study", @@ -158041,6 +159561,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.11.09.22282151", + "rel_title": "Galectin approach to lower covid transmission - Drug Development for clinical use", + "rel_date": "2022-11-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.09.22282151", + "rel_abs": "BackgroundSARS-CoV-2 vaccines play an important role in reducing disease severity, hospitalization, and death, although they failed to prevent the transmission of SARS-CoV-2 variants. Therefore, an effective inhibitor of galectin-3 (Gal-3) could be used to treat and prevent transmission of COVID-19. ProLectin-M (PL-M), a Gal-3 antagonist, has been shown to interact with Gal-3 and thus prevent cellular entry of SARS-CoV-2 in previous studies.\n\nAimThe present study aimed to further evaluate the therapeutic effect of PL-M tablets in 34 subjects with COVID-19 disease, in addition to determining the mechanism of PL-M in preventing SARS-CoV-2 cell entry by NMR studies.\n\nMethodsThe efficacy of PL-M was evaluated in a randomized, double-blind, placebo-controlled clinical study in patients with mild to moderately severe COVID-19. Primary endpoints included changes in absolute RT-PCR Ct values of the nucleocapsid and open reading frame (ORF) genes from baseline to days 3 and 7. The incidence of adverse events, changes in blood biochemistry, inflammatory biomarkers, and levels of antibodies against COVID-19 were also evaluated as part of the safety evaluation. In vitro 1H-15N HSQC NMR spectroscopy studies were also performed to determine the interactions of PL-M with Gal-3 and the S1 spike protein of SARS-CoV-2.\n\nResultsPL-M treatment significantly (p = 0.001) increased RT-PCR cycle counts for N and ORF genes on days 3 (Ct values 32.09 and 30.69 {+/-} 3.38, respectively) and 7 (Ct values 34.91 {+/-} 0.39 and 34.85 {+/-} 0.61, respectively) compared to placebo. On day 3, 14 subjects in the PL-M group had cycle counts for the N gene above the cut-off of 29 (target cycle count 29), while on day 7 all subjects had cycle counts above the cut-off. Ct values in placebo subjects were consistently less than 29, and no placebo subjects were RT-PCR negative, until day 7. 1H-15N HSQC NMR spectroscopy revealed that PL-M specifically binds Gal-3 in the same way as the structurally similar NTD of the SARS-CoV-2 S1 subunit.\n\nConclusionPL-M is safe and effective for clinical use in reducing viral load and promoting rapid viral clearance in COVID-19 patients by inhibiting SARS-CoV-2 entry into cells through inhibition of Gal-3.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "ALBEN Sigamani", + "author_inst": "CARMEL Research Consultancy Private Limited, Bengaluru, Karnataka 560025, India." + }, + { + "author_name": "Kevin H Mayo", + "author_inst": "Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church Street, Minneapolis, MN 55455, USA." + }, + { + "author_name": "Hana Chen-Walden", + "author_inst": "Pharmalectin India Pvt. Ltd., Rangareddy, Telangana 500039, India." + }, + { + "author_name": "Surender Reddy", + "author_inst": "Department of Pulomonology, ESIC Medical college and Hospital, Sanath Nagar, Hyderabad, Telangana 500038, India." + }, + { + "author_name": "David Platt", + "author_inst": "Pharmalectin India Pvt. Ltd., Rangareddy, Telangana 500039, India." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.11.09.22282142", "rel_title": "Assessing the Effect of Selective Serotonin Reuptake Inhibitors in the Prevention of Post-Acute Sequelae of COVID-19", @@ -158928,69 +160483,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.11.04.22281927", - "rel_title": "COVID-19 (Omicron strain) hospital admissions from a virtual ward: who required further care?", - "rel_date": "2022-11-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.04.22281927", - "rel_abs": "BackgroundThe COVID-19 virtual ward was created to provide care for people at home with COVID-19. Only a small proportion required hospital admission during their care. Given this was a new model of care, little was known about the clinical characteristics and outcomes of patients requiring admission to hospital from the virtual ward platform.\n\nAimA retrospective observational study with the aim to characterise hospital admission volume, patient epidemiology, clinical characteristics and outcome form a virtual ward in the setting of an Omicron BA.1 and BA.2 outbreak.\n\nMethodsA retrospective observational study was performed for all virtual ward patients admitted from 1st January 2022 to 25th March 2022. Patients had to be at least 16 years old to be included. Epidemiological, clinical and laboratory data was reviewed on all patients who required admission to hospital. This was analysed to describe this patient cohort.\n\nResultsA total of 7021 patients were cared for on the virtual ward over the study period with 473 referred to hospital for assessment. Twenty-six (0.4%) patients were admitted to hospital during their care on the ward. Twenty-two (84.6%) admissions were COVID-19 related. Fifty three percent of the hospitalised patients were fully vaccinated, and 11 had received prior therapeutics for COVID-19 in the community. There was one ICU admission, and one in-hospital mortality. Shortness of breath was the most common reason for escalation to hospital. Chest pain was the second most common reason and the most common diagnosis after investigation was non-cardiac chest pain that spontaneously resolved.\n\nConclusionsFew patients required admission from the virtual ward in the setting of the Omicron variant (BA.1, BA.2) as a direct result of COVID-19 disease and virtual ward care. Shortness of breath and chest pain were the most common symptoms driving further clinical care.\n\nWhat does this paper add to the literature?This paper describes the patient cohort with COVID-19 (Omicron variant) who are unable to be cared for by the virtual model of care and required escalation for hospital admission. It assists in health service planning in the setting of large numbers of cases.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Ian Robert Mackay", - "author_inst": "Royal Brisbane and Women's Hospital" - }, - { - "author_name": "Megan W France", - "author_inst": "Metro North Health" - }, - { - "author_name": "Duncan McAuley", - "author_inst": "Royal Brisbane and Women's Hospita" - }, - { - "author_name": "Sean Wing", - "author_inst": "Royal Brisbane and Women's Hospital" - }, - { - "author_name": "Mary Wheeldon", - "author_inst": "Royal Brisbane and Women's Hospital" - }, - { - "author_name": "Susan Britton", - "author_inst": "Royal Brisbane and Women's Hospital" - }, - { - "author_name": "Catherine Todd", - "author_inst": "Metro North Hospital and Health Service" - }, - { - "author_name": "Alexandra Pitiris", - "author_inst": "Metro North Hospital and Health Service" - }, - { - "author_name": "Leah Barrett-Beck", - "author_inst": "Royal Brisbane and Women's Hospital" - }, - { - "author_name": "Elizabeth Rushbrook", - "author_inst": "Metro North Hospital and Health Service" - }, - { - "author_name": "Cameron J Bennett", - "author_inst": "Royal Brisbane and Women's Hospital" - }, - { - "author_name": "Kate McCarthy", - "author_inst": "Royal Brisbane and Women's Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.11.06.22281986", "rel_title": "LMIC-PRIEST: Derivation and validation of a clinical severity score for acutely ill adults with suspected COVID-19 in a middle-income setting", @@ -159555,6 +161047,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.11.06.22281979", + "rel_title": "Systematic review of the prevalence of Long Covid", + "rel_date": "2022-11-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.06.22281979", + "rel_abs": "BackgroundLong Covid occurs in those infected with SARSCoV2 whose symptoms persist or develop beyond the acute phase. We conducted a systematic review to determine the prevalence of persistent symptoms, functional disability or pathological changes in adults or children at least 12 weeks post- infection.\n\nMethodsWe searched key registers and databases from 1st January 2020 to 2nd r 2021, limited to publications in English and studies with at least 100 participants. Studies where all participants were critically ill were excluded. Long Covid was extracted as prevalence of at least one symptom or pathology, or prevalence of the most common symptom or pathology, at 12 weeks or later. Heterogeneity was quantified in absolute terms and as a proportion of total variation and explored across pre-defined subgroups (PROSPERO ID CRD42020218351).\n\nResults120 studies in 130 publications were included. Length of follow-up varied between 12 weeks - 12 months. Few studies had low risk of bias. All complete and subgroup analyses except one had I2 [≥] 90%, with prevalence of persistent symptoms range of 0% - 93% (pooled estimate 42.1%, 95% prediction interval : 6.8% to 87.9%). Studies using routine healthcare records tended to report lower prevalence of persistent symptoms/pathology than self-report. However, studies systematically investigating pathology in all participants at follow up tended to report the highest estimates of all three. Studies of hospitalised cases had generally higher estimates than community- based studies.\n\nConclusionsThe way in which Long Covid is defined and measured affects prevalence estimation. Given the widespread nature of SARSCoV2 infection globally, the burden of chronic illness is likely to be substantial even using the most conservative estimates.\n\nFunding this systematic review received no specific funding.\n\nKey pointsIn a systematic review of 130 publications, prevalence estimates of Long Covid (>12 weeks) after SARSCoV2 infection differed according to how persistent symptoms/pathology were identified and measured, and ranged between 0% - 93% (pooled estimate 42.1%, 95% prediction interval: 6.8% to 87.9%).", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Mirembe C Woodrow", + "author_inst": "School of Primary Care, Population Sciences and Medical Education, Faculty of Medicine, The University of Southampton, Southampton, UK" + }, + { + "author_name": "Charles Carey", + "author_inst": "Manchester University NHS Foundation Trust and The University of Manchester, UK" + }, + { + "author_name": "Nida Ziauddeen", + "author_inst": "School of Primary Care, Population Sciences and Medical Education, Faculty of Medicine, The University of Southampton, Southampton, UK" + }, + { + "author_name": "Rebecca Thomas", + "author_inst": "The University of Liverpool, Liverpool, UK" + }, + { + "author_name": "Athena Akrami", + "author_inst": "Sainsbury Wellcome Centre, University College London, London, UK" + }, + { + "author_name": "Vittoria Lutje", + "author_inst": "Cochrane Infectious Diseases Group, Liverpool, UK" + }, + { + "author_name": "Darren C Greenwood", + "author_inst": "School of Medicine, University of Leeds, UK" + }, + { + "author_name": "Nisreen A Alwan", + "author_inst": "School of Primary Care, Population Sciences and Medical Education, Faculty of Medicine, University of Southampton, Southampton, UK" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.11.07.22282029", "rel_title": "Changes in Alcohol Consumption during the COVID-19 Pandemic: Evidence from Wisconsin", @@ -160606,29 +162145,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2022.11.02.22276012", - "rel_title": "Estimating the gendered impact of COVID-19", - "rel_date": "2022-11-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.02.22276012", - "rel_abs": "The extent of gendered COVID-19 impact remains undetermined for the lack of sex-disaggregated data. The prevailing view puts males nearly twice as impacted as females. Globally, access to resources and their usage are gendered- mostly favoring males. Gender gaps widen during natural/man-made calamities and pandemics. Modeling estimates of impact for top 70 countries reporting >300 sex-disaggregated COVID-19 deaths (>80% of total), indicates average mortality sex (male:female) ratio (COVID-MSR) of 1.37{+/-}0.30 (95% confidence interval:1.30-1.44; range:0.85-2.47) against prevalent pre-pandemic MSR of 1.79{+/-}0.41 (1.70-1.89; range:0.93-2.99). Contrary to the prevailing view, widened gender gaps globally increased female mortality by 19.57{+/-}21.16% (14.62%-24.88%; range: -22.46 to +68.50%) causing an estimated 22.03% excess deaths (360 thousand by 30 December 2021). Identification of factors favoring gendered impacts is needed for equitable pandemic management.\n\nOne-Sentence Summary Missing Females in COVID-19?", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Samer Singh", - "author_inst": "Banaras Hindu University" - }, - { - "author_name": "Rakesh K Singh", - "author_inst": "Banaras Hindu University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.11.02.22281834", "rel_title": "Unsupervised clustering of SARS-CoV-2 positive hospitalized patients identifies six endophenotypes of COVID-19 and points to FGFR and SHC4-signaling in acute respiratory distress syndrome", @@ -161241,6 +162757,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.10.31.22281719", + "rel_title": "BIOLOGICAL RHYTHMS IN COVID-19 VACCINE EFFECTIVENESS", + "rel_date": "2022-11-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.31.22281719", + "rel_abs": "ImportanceCircadian rhythms affect fundamental immune processes, but how this translates to clinical outcomes like real-world vaccine effectiveness is unclear.\n\nObjectiveTo examine associations between Coronavirus Infectious Disease 2019 (COVID-19) vaccination timing and effectiveness.\n\nDesign, Setting, and ParticipantsRetrospective cohort study of database records from Maccabi Healthcare Services (MHS), a major Israeli Health Maintenance Organization (HMO). We included all individuals over 12 with at least one timestamped vaccine dose and no documented COVID-19 infection prior to completing the initial 2-dose immunization series (n=1,515,754, 99.2% receiving BNT162b2). Database records spanned December 19, 2020, to April 25, 2022, encompassing two spikes in COVID infection dominated by the delta (B.1.617.2) and omicron (B.1.1.529) SARS-CoV-2 variants.\n\nMain Outcomes and MeasuresOutcomes included COVID-19 breakthrough infection and COVID-19 associated emergency department (ED) visits. Our main comparison was between patients vaccinated exclusively during morning hours (8:00-11:59), afternoon (12:00-15:59), or evening hours (16:00-19:59). We employed Cox multivariate regression to adjust for differences in age, sex, and co-morbidities.\n\nResultsBreakthrough infections differed based on vaccination time, with lowest rates associated with late morning to early afternoon, and highest rates with evening vaccination. Vaccination timing remained significant after adjustment for patient age, sex, and co-morbidities (HR=0.88 afternoon vs. evening, [95% CI 0.87-0.90]). Results were consistent in patients who received the basic two-dose vaccine series and who received booster doses. The relationship between COVID-19 immunization time and breakthrough infection risk was sinusoidal, consistent with a biological rhythm in vaccine effectiveness. Vaccination timing altered breakthrough infection risk by 8.6-25% in our cohort, depending on patient age and dose number. The benefits of daytime vaccination were concentrated in younger and elderly patients. In contrast to breakthrough infections, COVID-19 related ED visits correlated with age and medical comorbidities but not with time of vaccination.\n\nConclusions and RelevanceWe report a significant association between the time of COVID-19 vaccination and its clinical effectiveness in terms of breakthrough infection. These data have implications for mass vaccination programs.\n\nKEY POINTS\n\nQuestionDoes the time of day patients receive their COVID-19 vaccinations influence their clinical benefit?\n\nFindingsIn this population-level cohort study that included 1,515,754 individuals aged 12 and over, COVID-19 vaccination during the late morning to early afternoon was associated with fewer breakthrough infections compared to other times. Vaccination timing altered breakthrough infection risk by 8.6-25%, depending on patient age and dose number.\n\nMeaningPrioritizing children and the elderly for late morning to early afternoon immunization could improve the effectiveness of mass vaccinations against COVID-19, and potentially other infectious diseases.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Guy Hazan", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Or Duek", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Hillel Alapi", + "author_inst": "Maccabitech Institute for Research and Innovation, Maccabi Healthcare Services" + }, + { + "author_name": "Huram Mok", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Alex Ganniger", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Elaine Ostendorf", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Carrie Gierasch", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Gabriel Chodick", + "author_inst": "Maccabitech Institute for Research and Innovation, Maccabi Healthcare Services" + }, + { + "author_name": "David Greenberg", + "author_inst": "Ben-Gurion University of the Negev" + }, + { + "author_name": "Jeffrey A Haspel", + "author_inst": "Washington University School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.11.01.22281810", "rel_title": "Impact of SARS-CoV-2 on the microbiota of pregnant women and their infants", @@ -161938,20 +163509,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2022.10.28.22281671", - "rel_title": "An implementation framework to improve the transparency and reproducibility of computational models of infectious diseases", - "rel_date": "2022-11-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.28.22281671", - "rel_abs": "Computational models of infectious diseases have become valuable tools for research and the public health response against epidemic threats. The reproducibility of computational models has been limited, undermining the scientific process and possibly trust in modeling results and related response strategies, such as vaccination. We translated published reproducibility guidelines from a wide range of scientific disciplines into an implementation framework for improving reproducibility of infectious disease computational models. The framework comprises twenty-two elements that should be described, grouped into six categories: computational environment, analytical software, model description, model implementation, data, and experimental protocol. The framework can be used by scientific communities to develop actionable tools for sharing computational models in a reproducible way.", - "rel_num_authors": 0, - "rel_authors": null, - "version": "1", - "license": "", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.10.30.22281713", "rel_title": "Safety and Immunogenicity of a Booster SARS-Cov-2 Vaccination in Patients with Chronic Liver Disease", @@ -162542,6 +164099,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.10.28.22281657", + "rel_title": "Potential risk polarization for acute myocardial infarction during the COVID-19 pandemic: Single-center experiences in Osaka, Japan", + "rel_date": "2022-10-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.28.22281657", + "rel_abs": "This study compared the time course and outcomes of acute myocardial infarction, including mechanical complications and hospital mortality, before and after the coronavirus disease 2019 (COVID-19) pandemic at a regional core hospital in South Osaka, Japan. Moreover, it identified predictors for hospital mortality and mechanical complications. In total, 503 patients who underwent emergency percutaneous coronary intervention between January 2011 and December 2021 at our institution were examined retrospectively. The time course of acute myocardial infarction, mechanical complications, and mortality rate before and after the COVID-19 emergency declaration were compared. Overall, 426 patients with ST-segment elevation myocardial infarction and 77 patients with non-ST-segment elevation myocardial infarction were identified. For patients with ST-segment elevation myocardial infarction, the onset-to-door time was longer (181 vs. 156 min, P = 0.001) and mechanical complications were worse (7.8% vs. 2.6%, P = 0.025) after the emergency declaration of COVID-19 than before the pandemic. Age, low ejection fraction, out-of-hospital cardiac arrest, and mechanical complications were identified as independent risk factors for hospital mortality among patients with ST-segment elevation myocardial infarction, using multivariable analysis. Post-declaration, age, walk-ins, referrals, and intra-aortic balloon pump use were independent predictors of mechanical complications among patients with ST-segment elevation myocardial infarction. Onset-to-door time and mechanical complication rate increased after the COVID-19 declaration among patients with ST-segment elevation myocardial infarction. Arrival by walk-in and a referral that caused treatment delay were identified as independent risk factors for mechanical complication, in addition to age, use of intra-aortic balloon pump, and post-declaration of COVID-19. Therefore, the risks posed by the COVID-19 pandemic might have a polarization tendency resulting from the relief or worsening of cardiac symptoms.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Masato Furui", + "author_inst": "Fukuoka University Hospital: Fukuoka Daigaku Byoin" + }, + { + "author_name": "Kenji Kawajiri", + "author_inst": "Matsubara Tokushukai Hospital" + }, + { + "author_name": "Takeshi Yoshida", + "author_inst": "Matsubara Tokushukai Hospital" + }, + { + "author_name": "Bunpachi Kakii", + "author_inst": "Matsubara Tokushukai Hopital" + }, + { + "author_name": "Norikazu Oshiro", + "author_inst": "Matsubara Tokushukai Hospital" + }, + { + "author_name": "Mai Asanuma", + "author_inst": "Matsubara Tokushukai Hospital" + }, + { + "author_name": "Hiroaki Nishioka", + "author_inst": "Matsubara Tokushukai Hospital" + }, + { + "author_name": "Hideichi Wada", + "author_inst": "Fukuoka University: Fukuoka Daigaku" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2022.10.28.22281660", "rel_title": "Seroprevalence, seroconversion, and seroreversion of infection-induced SARS-CoV-2 antibodies among a cohort of children and adolescents in Montreal, Canada", @@ -163797,61 +165401,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.10.26.22281547", - "rel_title": "Contribution of genetics and lifestyle to the risk of major cardiovascular and thromboembolic complications following COVID-19", - "rel_date": "2022-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.26.22281547", - "rel_abs": "Clinical determinants for cardiovascular and thromboembolic (CVE) complications of COVID-19 are well-understood, but the roles of genetics and lifestyle remain unknown. We performed a prospective cohort study using UK Biobank, including 25,335 participants with confirmed SARS-CoV-2 infection between March 1, 2020, and September 3, 2021. Outcomes were hospital-diagnosed atrial fibrillation (AF), coronary artery disease (CAD), ischemic stroke (ISS), and venous thromboembolism (VTE) within 90 days post-infection. Heritable risk was represented by validated polygenic risk scores (PRSs). Lifestyle was defined by a composite of nine variables. We estimated adjusted hazard ratios (aHR) and confidence intervals (CI) using Cox proportional hazards models. In the COVID-19 acute phase, PRSs linearly predicted a higher risk of AF (aHR 1.52 per standard deviation increase, 95% CI 1.39 to 1.67), CAD (1.59, 1.40 to 1.81), and VTE (1.30, 1.11 to 1.53), but not ISS (0.92, 0.64 to 1.33). A healthy lifestyle was associated with a substantially lower risk of post-COVID-19 AF (0.70, 0.53 to 0.92), CAD (0.64, 0.44 to 0.91), and ISS (0.28, 0.12 to0.64), but not VTE (0.82, 0.48 to 1.39), compared with an unhealthy lifestyle. No evidence for interactions between genetics and lifestyle was found. Our results demonstrated that population genetics and lifestyle considerably influence cardiovascular complications following COVID-19, with implications for future personalised thromboprophylaxis and healthy lifestyle campaigns to offset the elevated cardiovascular disease burden imposed by the ongoing pandemic.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Junqing Xie", - "author_inst": "NDORMS, University of Oxford" - }, - { - "author_name": "yuliang feng", - "author_inst": "NDORMS, University of Oxford" - }, - { - "author_name": "Danielle Newby", - "author_inst": "University of Oxford" - }, - { - "author_name": "Bang Zheng", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Qi Feng", - "author_inst": "The University of Oxford" - }, - { - "author_name": "Albert Prats-Uribe", - "author_inst": "University of Oxford" - }, - { - "author_name": "Chunxiao Li", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Nicholas J. Wareham", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Roger Paredes", - "author_inst": "Infectious Diseases Department and irsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Catalonia, Spain" - }, - { - "author_name": "DANIEL PRIETO-ALHAMBRA", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.10.26.22281446", "rel_title": "The genomic epidemiology of SARS-CoV-2 variants of concern in Kenya", @@ -164696,6 +166245,141 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.10.24.22281399", + "rel_title": "Integrated SARS-CoV-2 serological and virological screening across an acute fever surveillance platform to monitor temporal changes in anti-spike antibody levels and risk of infection during sequential waves of variant transmission - Dominican Republic, March 2021 to August 2022", + "rel_date": "2022-10-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.24.22281399", + "rel_abs": "The global SARS-CoV-2 immune landscape and population protection against emerging variants is largely unknown. We assessed SARS-CoV-2 antibody changes in the Dominican Republic and implications for immunological protection against variants of concern. Between March 2021 and August 2022, 2,300 patients with undifferentiated febrile illnesses were prospectively enrolled. Sera was tested for total anti-spike antibodies and simultaneously collected nasopharyngeal samples for acute SARS-CoV-2 infection with RT-PCR. Geometric mean anti-spike titers increased from 6.6 BAU/ml (95% CI 5.1-8.7) to 1,332 BAU/ml (1055-1,682). Multivariable binomial odds ratios for acute SARS-CoV-2 infection were 0.55 (0.40-0.74), 0.38 (0.27-0.55), and 0.27 (0.18-0.40) for the second, third, and fourth versus the first anti-S quartile, with similar findings by viral strain. Integrated serological and virological screening can leverage existing acute fever surveillance platforms to monitor population-level immunological markers and concurrently characterize implications for emergent variant transmission in near real-time.", + "rel_num_authors": 30, + "rel_authors": [ + { + "author_name": "Eric James Nilles", + "author_inst": "Brigham and Women's Hospital, Harvard Medical School, Harvard Humanitarian Initiative" + }, + { + "author_name": "Michael de St. Aubin", + "author_inst": "Brigham and Women's Hospital. Harvard Humanitarian Initiative" + }, + { + "author_name": "Devan Dumas", + "author_inst": "Brigham and Womens Hospital. Harvard Humanitarian Initiative" + }, + { + "author_name": "William Duke", + "author_inst": "Pedro Henriquez Urena National University, Santo Domingo, Dominican Republic" + }, + { + "author_name": "Marie Caroline Etienne", + "author_inst": "Brigham and Womens Hospital" + }, + { + "author_name": "Gabriela Abdalla", + "author_inst": "Brigham and Womens Hospital" + }, + { + "author_name": "Petr Jarolim", + "author_inst": "Brigham and Womens Hospital. Harvard Medical School." + }, + { + "author_name": "Timothy Oasan", + "author_inst": "Brigham and Womens Hospital" + }, + { + "author_name": "Salome Garnier", + "author_inst": "Brigham and Womens Hospital, Harvard Humanitarian Initiative" + }, + { + "author_name": "Naomi Iihoshi", + "author_inst": "Brigham and Womens Hospital" + }, + { + "author_name": "Beatriz Lopez", + "author_inst": "US Centers for Disease Control and Prevention" + }, + { + "author_name": "Lucia De la Cruz", + "author_inst": "Ministry of Health and Social Assistance, Santo Domingo, Dominican Republic" + }, + { + "author_name": "Yosanly Cornelio Puello", + "author_inst": "Ministry of Health and Social Assistance, Santo Domingo, Dominican Republic" + }, + { + "author_name": "Margaret Baldwin", + "author_inst": "Brigham and Womens Hospital, Boston, MA, USA, Harvard Humanitarian Initiative, Cambridge, MA, USA" + }, + { + "author_name": "Kathryn W Roberts", + "author_inst": "Brigham and Womens Hospital, Boston, MA, USA. Harvard Humanitarian Initiative, Cambridge, MA, USA" + }, + { + "author_name": "Farah Pena", + "author_inst": "Ministry of Health and Social Assistance, Santo Domingo, Dominican Republic" + }, + { + "author_name": "Kara Durski", + "author_inst": "Brigham and Womens Hospital, Boston, MA, USA. Harvard Humanitarian Initiative, Cambridge, MA, USA." + }, + { + "author_name": "Isaac Miguel Sanchez", + "author_inst": "Ministry of Health and Social Assistance, Santo Domingo, Dominican Republic" + }, + { + "author_name": "Sarah M Gunter", + "author_inst": "Baylor College of Medicine and Texas Childrens Hospital, Houston, USA" + }, + { + "author_name": "Alexander R Kneubehl", + "author_inst": "Baylor College of Medicine and Texas Childrens Hospital, Houston, TX, USA" + }, + { + "author_name": "Kristy O Murray", + "author_inst": "Baylor College of Medicine and Texas Childrens Hospital, Houston, TX, USA" + }, + { + "author_name": "Allison Lino", + "author_inst": "Baylor College of Medicine and Texas Childrens Hospital, Houston, TX, USA" + }, + { + "author_name": "Sarah Strobel", + "author_inst": "Baylor College of Medicine and Texas Childrens Hospital, Houston, TX, USA" + }, + { + "author_name": "Amado Baez Baez", + "author_inst": "Pedro Henriquez Urena National University, Santo Domingo, Dominican Republic. Office of the Presidency, Santo Domingo, Dominican Republic." + }, + { + "author_name": "Colleen Lau", + "author_inst": "University of Queensland" + }, + { + "author_name": "Adam J Kucharski", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Emily Zielinski Gutierrez", + "author_inst": "Centers for Disease Control and Prevention, Central America Regional Office, Guatemala City, Guatemala" + }, + { + "author_name": "Ronald Skewes-Ramm", + "author_inst": "Ministry of Health and Social Assistance, Santo Domingo, Dominican Republic" + }, + { + "author_name": "Marietta Vasquez", + "author_inst": "Yale School of Medicine, New Haven, CT, USA" + }, + { + "author_name": "Cecilia Then Paulino", + "author_inst": "Ministry of Health and Social Assistance, Santo Domingo, Dominican Republic" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.10.24.22281482", "rel_title": "The pervasive association between political ideology and COVID-19 vaccine uptake in Brazil: an ecologic study", @@ -165751,69 +167435,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.10.21.22281239", - "rel_title": "Development of criteria for cognitive dysfunction in post-COVID syndrome: the IC-CoDi-COVID approach", - "rel_date": "2022-10-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.21.22281239", - "rel_abs": "BackgroundWe aimed to develop objective criteria for cognitive dysfunction associated with the post-COVID syndrome.\n\nMethodsFour hundred and four patients with post-COVID syndrome from two centers were evaluated with comprehensive neuropsychological batteries. The International Classification for Cognitive Disorders in Epilepsy (IC-CoDE) framework was adapted and implemented. A complementary data-driven approach based on unsupervised machine-learning clustering algorithms was also used to evaluate the optimal classification and cutoff points.\n\nResultsAccording to the developed criteria, 41.2% and 17.3% of the sample were classified as having at least one cognitive domain impaired using -1 and -1.5 standard deviations as cutoff points. Attention/processing speed was the most frequently impaired domain. There were no differences in base rates of cognitive impairment between the two centers. Clustering analysis revealed two clusters according to the severity of cognitive impairment, but there was no difference in cognitive profiles. Cognitive impairment was associated with younger age and lower education levels, but not hospitalization.\n\nConclusionsWe propose a harmonization of the criteria to define and classify cognitive impairment in the post-COVID syndrome. These criteria may be extrapolated to other neuropsychological batteries and settings, contributing to the diagnosis of cognitive deficits after COVID-19 and facilitating multicenter studies to guide biomarker investigation and therapies.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Jordi A Matias-Guiu", - "author_inst": "Hospital Clinico San Carlos" - }, - { - "author_name": "Elena Herrera", - "author_inst": "Universidad de Oviedo" - }, - { - "author_name": "Maria Gonzalez-Nosti", - "author_inst": "Universidad de Oviedo" - }, - { - "author_name": "Kamini Krishnan", - "author_inst": "Department of Neurology, Cleveland Clinic, Cleveland, OH, USA." - }, - { - "author_name": "Cristina Delgado-Alonso", - "author_inst": "Hospital Clinico San Carlos" - }, - { - "author_name": "Maria Diez-Cirarda", - "author_inst": "Hospital Clinico San Carlos" - }, - { - "author_name": "Miguel Yus", - "author_inst": "Hospital Clinico San Carlos" - }, - { - "author_name": "Alvaro Martinez-Petit", - "author_inst": "Universidad Politecnica de Madrid" - }, - { - "author_name": "Josue Pagan", - "author_inst": "Universidad Politecnica de Madrid" - }, - { - "author_name": "Jose Luis Ayala", - "author_inst": "Universidad Complutense de Madrid" - }, - { - "author_name": "Robyn Busch", - "author_inst": "University of Wisconsin" - }, - { - "author_name": "Bruce P Hermann", - "author_inst": "University of Wisconsin" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2022.10.22.22281221", "rel_title": "Rare predicted loss-of-function variants of type I IFN immunity genes are associated with critical COVID-19", @@ -167174,6 +168795,193 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.10.21.513237", + "rel_title": "Computationally restoring the potency of a clinical antibody against SARS-CoV-2 Omicron subvariants", + "rel_date": "2022-10-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.21.513237", + "rel_abs": "The COVID-19 pandemic underscored the promise of monoclonal antibody-based prophylactic and therapeutic drugs1-3, but also revealed how quickly viral escape can curtail effective options4, 5. With the emergence of the SARS-CoV-2 Omicron variant in late 2021, many clinically used antibody drug products lost potency, including EvusheldTM and its constituent, cilgavimab4, 6. Cilgavimab, like its progenitor COV2-2130, is a class 3 antibody that is compatible with other antibodies in combination4 and is challenging to replace with existing approaches. Rapidly modifying such high-value antibodies with a known clinical profile to restore efficacy against emerging variants is a compelling mitigation strategy. We sought to redesign COV2-2130 to rescue in vivo efficacy against Omicron BA.1 and BA.1.1 strains while maintaining efficacy against the contemporaneously dominant Delta variant. Here we show that our computationally redesigned antibody, 2130-1-0114-112, achieves this objective, simultaneously increases neutralization potency against Delta and many variants of concern that subsequently emerged, and provides protection in vivo against the strains tested, WA1/2020, BA.1.1, and BA.5. Deep mutational scanning of tens of thousands pseudovirus variants reveals 2130-1-0114-112 improves broad potency without incurring additional escape liabilities. Our results suggest that computational approaches can optimize an antibody to target multiple escape variants, while simultaneously enriching potency. Because our approach is computationally driven, not requiring experimental iterations or pre-existing binding data, it could enable rapid response strategies to address escape variants or pre-emptively mitigate escape vulnerabilities.", + "rel_num_authors": 43, + "rel_authors": [ + { + "author_name": "Thomas A Desautels", + "author_inst": "Lawrence Livermore National Laboratory" + }, + { + "author_name": "Kathryn T Arrildt", + "author_inst": "Lawrence Livermore National Laboratory" + }, + { + "author_name": "Adam T Zemla", + "author_inst": "Lawrence Livermore National Laboratory" + }, + { + "author_name": "Edmond Y Lau", + "author_inst": "Lawrence Livermore National Laboratory" + }, + { + "author_name": "Fangqiang Zhu", + "author_inst": "Lawrence Livermore National Laboratory" + }, + { + "author_name": "Dante Ricci", + "author_inst": "Lawrence Livermore National Laboratory" + }, + { + "author_name": "Stephanie Cronin", + "author_inst": "Vanderbilt Vaccine Center" + }, + { + "author_name": "Seth Zost", + "author_inst": "Vanderbilt Vaccine Center" + }, + { + "author_name": "Elad Binshtein", + "author_inst": "Vanderbilt Vaccine Center" + }, + { + "author_name": "Suzanne M Scheaffer", + "author_inst": "Washington University in St. Louis" + }, + { + "author_name": "Bernadeta Dadonaite", + "author_inst": "Fred Hutchinson Cancer Center" + }, + { + "author_name": "Brenden K Petersen", + "author_inst": "Lawrence Livermore National Laboratory" + }, + { + "author_name": "Taylor B Engdahl", + "author_inst": "Vanderbilt Vaccine Center" + }, + { + "author_name": "Elaine Chen", + "author_inst": "Vanderbilt Vaccine Center" + }, + { + "author_name": "Laura S Handal", + "author_inst": "Vanderbilt Vaccine Center" + }, + { + "author_name": "Lynn Hall", + "author_inst": "Vanderbilt Vaccine Center" + }, + { + "author_name": "John W Goforth", + "author_inst": "Lawrence Livermore National Laboratory" + }, + { + "author_name": "Denis Vashchenko", + "author_inst": "Lawrence Livermore National Laboratory" + }, + { + "author_name": "Sam Nguyen", + "author_inst": "Lawrence Livermore National Laboratory" + }, + { + "author_name": "Dina R Weilhammer", + "author_inst": "Lawrence Livermore National Laboratory" + }, + { + "author_name": "Jacky Kai-Yin Lo", + "author_inst": "Lawrence Livermore National Laboratory" + }, + { + "author_name": "Bonnee Rubinfeld", + "author_inst": "Lawrence Livermore National Laboratory" + }, + { + "author_name": "Edwin A Saada", + "author_inst": "Lawrence Livermore National Laboratory" + }, + { + "author_name": "Tracy Weisenberger", + "author_inst": "Lawrence Livermore National Laboratory" + }, + { + "author_name": "Tek-Hyung Lee", + "author_inst": "Lawrence Livermore National Laboratory" + }, + { + "author_name": "Bradley Whitener", + "author_inst": "Washington University in St. Louis" + }, + { + "author_name": "James B Case", + "author_inst": "Washington University in St. Louis" + }, + { + "author_name": "Alexander Ladd", + "author_inst": "Lawrence Livermore National Laboratory" + }, + { + "author_name": "Mary S Silva", + "author_inst": "Lawrence Livermore National Laboratory" + }, + { + "author_name": "Rebecca M Haluska", + "author_inst": "Lawrence Livermore National Laboratory" + }, + { + "author_name": "Emilia A Grzesiak", + "author_inst": "Lawrence Livermore National Laboratory" + }, + { + "author_name": "Christopher G Earnhart", + "author_inst": "Joint Program Executive Office for Chemical, Biological, Radiological, and Nuclear Defense, US Department of Defense" + }, + { + "author_name": "Svetlana A Hopkins", + "author_inst": "Joint Research & Development, Inc." + }, + { + "author_name": "Thomas W Bates", + "author_inst": "Lawrence Livermore National Laboratory" + }, + { + "author_name": "Larissa B Thackray", + "author_inst": "Washington University in St. Louis" + }, + { + "author_name": "Brent W Segelke", + "author_inst": "Lawrence Livermore National Laboratory" + }, + { + "author_name": "Antonietta Maria Lillo", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Shankar Sundaram", + "author_inst": "Lawrence Livermore National Laboratory" + }, + { + "author_name": "Jesse D Bloom", + "author_inst": "Fred Hutchinson Cancer Center" + }, + { + "author_name": "Michael S Diamond", + "author_inst": "Washington University in St. Louis" + }, + { + "author_name": "James E Crowe Jr.", + "author_inst": "Vanderbilt Vaccine Center" + }, + { + "author_name": "Robert H Carnahan", + "author_inst": "Vanderbilt Vaccine Center" + }, + { + "author_name": "Daniel M Faissol", + "author_inst": "Lawrence Livermore National Laboratory" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.10.22.22281373", "rel_title": "Comparative Effectiveness of Dexamethasone in Treatment of Hospitalized COVID-19 Patients during the First Year of the Pandemic: The N3C Data Repository", @@ -168061,77 +169869,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.10.19.22281248", - "rel_title": "Dynamics of non-household contacts during the COVID-19 pandemic in 2020 and 2021 in the Netherlands", - "rel_date": "2022-10-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.19.22281248", - "rel_abs": "The COVID-19 pandemic was in 2020 and 2021 for a large part mitigated by reducing contacts in the general population. To monitor how these contacts changed over the course of the pandemic in the Netherlands, a longitudinal survey was conducted where participants reported on their at-risk contacts every two weeks, as part of the European CoMix survey. The survey included 1659 participants from April to August 2020 and 2514 participants from December 2020 to September 2021. We categorized the number of unique contacted persons excluding household members, reported per participant per day into six activity levels, defined as 0, 1, 2, 3-4, 5-9 and 10 or more reported contacts. After correcting for age, vaccination status, risk status for severe outcome of infection, and frequency of participation, activity levels increased over time, coinciding with relaxation of COVID-19 control measures.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Jantien A. Backer", - "author_inst": "National Institute for Public Health and the Environment" - }, - { - "author_name": "Laurens Bogaardt", - "author_inst": "National Institute for Public Health and the Environment" - }, - { - "author_name": "Philippe Beutels", - "author_inst": "University of Antwerp" - }, - { - "author_name": "Pietro Coletti", - "author_inst": "Hasselt University" - }, - { - "author_name": "John Edmunds", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Amy Gimma", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Cheyenne C.E. van Hagen", - "author_inst": "National Institute for Public Health and the Environment" - }, - { - "author_name": "Niel Hens", - "author_inst": "Hasselt University and University of Antwerp" - }, - { - "author_name": "Christopher I Jarvis", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Eric R.A. Vos", - "author_inst": "National Institute for Public Health and the Environement (RIVM)" - }, - { - "author_name": "James Wambua", - "author_inst": "University of Hasselt" - }, - { - "author_name": "Denise Wong", - "author_inst": "National Institute for Public Health and the Environment" - }, - { - "author_name": "Kevin van Zandvoort", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Jacco Wallinga", - "author_inst": "National Institute for Public Health and the Environment; Leiden University Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.10.20.22281313", "rel_title": "Parental Preferences and Reasons for COVID-19 Vaccination Among Their Children", @@ -168800,6 +170537,329 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2022.10.19.512927", + "rel_title": "Global landscape of the host response to SARS-CoV-2 variants reveals viral evolutionary trajectories", + "rel_date": "2022-10-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.19.512927", + "rel_abs": "A series of SARS-CoV-2 variants of concern (VOCs) have evolved in humans during the COVID-19 pandemic--Alpha, Beta, Gamma, Delta, and Omicron. Here, we used global proteomic and genomic analyses during infection to understand the molecular responses driving VOC evolution. We discovered VOC-specific differences in viral RNA and protein expression levels, including for N, Orf6, and Orf9b, and pinpointed several viral mutations responsible. An analysis of the host response to VOC infection and comprehensive interrogation of altered virus-host protein-protein interactions revealed conserved and divergent regulation of biological pathways. For example, regulation of host translation was highly conserved, consistent with suppression of VOC replication in mice using the translation inhibitor plitidepsin. Conversely, modulation of the host inflammatory response was most divergent, where we found Alpha and Beta, but not Omicron BA.1, antagonized interferon stimulated genes (ISGs), a phenotype that correlated with differing levels of Orf6. Additionally, Delta more strongly upregulated proinflammatory genes compared to other VOCs. Systematic comparison of Omicron subvariants revealed BA.5 to have evolved enhanced ISG and proinflammatory gene suppression that similarly correlated with Orf6 expression, effects not seen in BA.4 due to a mutation that disrupts the Orf6-nuclear pore interaction. Our findings describe how VOCs have evolved to fine-tune viral protein expression and protein-protein interactions to evade both innate and adaptive immune responses, offering a likely explanation for increased transmission in humans.\n\nOne sentence summarySystematic proteomic and genomic analyses of SARS-CoV-2 variants of concern reveal how variant-specific mutations alter viral gene expression, virus-host protein complexes, and the host response to infection with applications to therapy and future pandemic preparedness.", + "rel_num_authors": 77, + "rel_authors": [ + { + "author_name": "Mehdi Bouhaddou", + "author_inst": "UCSF" + }, + { + "author_name": "Ann-Kathrin Reuschl", + "author_inst": "University College London" + }, + { + "author_name": "Benjamin J. Polacco", + "author_inst": "UCSF" + }, + { + "author_name": "Lucy G. Thorne", + "author_inst": "University College London" + }, + { + "author_name": "Manisha R. Ummadi", + "author_inst": "UCSF" + }, + { + "author_name": "Chengjin Ye", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Romel Rosales Ramirez", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Adrian Pelin", + "author_inst": "UCSF" + }, + { + "author_name": "Jyoti Batra", + "author_inst": "UCSF" + }, + { + "author_name": "Gwendolyn M. Jang", + "author_inst": "UCSF" + }, + { + "author_name": "Jiewei Xu", + "author_inst": "UCSF" + }, + { + "author_name": "Jack M. Moen", + "author_inst": "UCSF" + }, + { + "author_name": "Alicia L. Richards", + "author_inst": "UCSF" + }, + { + "author_name": "Yuan Zhou", + "author_inst": "UCSF" + }, + { + "author_name": "Bhavya Harjai", + "author_inst": "UCSF" + }, + { + "author_name": "Erica Stevenson", + "author_inst": "UCSF" + }, + { + "author_name": "Ajda Rojc", + "author_inst": "UCSF" + }, + { + "author_name": "Roberta Ragazzini", + "author_inst": "Francis Crick Institute" + }, + { + "author_name": "Matthew V.X. Whelan", + "author_inst": "University College London" + }, + { + "author_name": "Wilhelm Furnon", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Giuditta De Lorenzo", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Vanessa Cowton", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Abdullah M. Syed", + "author_inst": "Gladstone Institutes" + }, + { + "author_name": "Alison Ciling", + "author_inst": "Gladstone Institutes" + }, + { + "author_name": "Noa Deutsch", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Daniel Pirak", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Giulia Dowgier", + "author_inst": "University College London" + }, + { + "author_name": "Dejan Mesner", + "author_inst": "University College London" + }, + { + "author_name": "Jane L. Turner", + "author_inst": "University College London" + }, + { + "author_name": "Briana L. McGovern", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "M. Luis Rodriguez", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Rocio Leiva-Rebollo", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Alistair S. Dunham", + "author_inst": "Wellcome Sanger Institute" + }, + { + "author_name": "Xiaofang Zhong", + "author_inst": "UCSF" + }, + { + "author_name": "Manon Eckhardt", + "author_inst": "UCSF" + }, + { + "author_name": "Andrea Fossati", + "author_inst": "UCSF" + }, + { + "author_name": "Nicholas Liotta", + "author_inst": "UCSF" + }, + { + "author_name": "Thomas Kehrer", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Anastasija Cupic", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Magda Rutkowska", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Nacho Mena", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Sadaf Aslam", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Alyssa Hoffert", + "author_inst": "UCSF" + }, + { + "author_name": "Helene Foussard", + "author_inst": "UCSF" + }, + { + "author_name": "John Pham", + "author_inst": "Synthego" + }, + { + "author_name": "Molly Lyons", + "author_inst": "Synthego" + }, + { + "author_name": "Laura Donahue", + "author_inst": "Synthego" + }, + { + "author_name": "Aliesha Griffin", + "author_inst": "Synthego" + }, + { + "author_name": "Rebecca Nugent", + "author_inst": "Synthego" + }, + { + "author_name": "Kevin Holden", + "author_inst": "Synthego" + }, + { + "author_name": "Robert Deans", + "author_inst": "Synthego" + }, + { + "author_name": "Pablo Aviles", + "author_inst": "Pharmamar" + }, + { + "author_name": "Jose Antonio Lopez-Martin", + "author_inst": "Pharmamar" + }, + { + "author_name": "Jose M. Jimeno", + "author_inst": "Pharmamar" + }, + { + "author_name": "Kirsten Obernier", + "author_inst": "UCSF" + }, + { + "author_name": "Jacqueline M. Fabius", + "author_inst": "UCSF" + }, + { + "author_name": "Margaret Soucheray", + "author_inst": "UCSF" + }, + { + "author_name": "Ruth Huttenhain", + "author_inst": "UCSF" + }, + { + "author_name": "Irwin Jungreis", + "author_inst": "MIT" + }, + { + "author_name": "Manolis Kellis", + "author_inst": "MIT" + }, + { + "author_name": "Ignacia Echeverria", + "author_inst": "UCSF" + }, + { + "author_name": "Kliment Verba", + "author_inst": "UCSF" + }, + { + "author_name": "Paola Bonfanti", + "author_inst": "University College London" + }, + { + "author_name": "Pedro Beltrao", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Roded Sharan", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Jennifer A. Doudna", + "author_inst": "Gladstone Institutes" + }, + { + "author_name": "Luis Martinez-Sobrido", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Arvind Patel", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Massimo Palmarini", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Lisa Miorin", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Kris White", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Danielle L. Swaney", + "author_inst": "UCSF" + }, + { + "author_name": "Adolfo Garcia-Sastre", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Clare Jolly", + "author_inst": "University College London" + }, + { + "author_name": "Lorena Zuliani-Alvarez", + "author_inst": "UCSF" + }, + { + "author_name": "Greg J. Towers", + "author_inst": "University College London" + }, + { + "author_name": "Nevan J. Krogan", + "author_inst": "UCSF" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "systems biology" + }, { "rel_doi": "10.1101/2022.10.21.513200", "rel_title": "A systems approach evaluating the impact of SARS-CoV-2 variant of concern mutations on CD8+ T cell responses", @@ -169843,29 +171903,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.10.18.22280274", - "rel_title": "Estimating LFT and qPCR test-sensitivity over time since infection from a human challenge study", - "rel_date": "2022-10-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.18.22280274", - "rel_abs": "Testing has been central to global policy throughout the SARS-CoV-2 pandemic. Understanding how test sensitivity changes after exposure is crucial for the interpretation of test outcomes and the design of testing-based interventions. Using data from a human challenge study, we derive temporal test sensitivity profiles for lateral flow tests (LFT), quantitative polymerase chain reaction (qPCR) tests and viable virus, measured by focus-forming assay (FFA). The median time to detectability was 2 days (throat swab) and 3 days (nasal) for qPCR and 4 days for LFT (both swabs), and there was strong positive correlation between first LFT positive and first FFA positive for both throat (p=0.00019) and nasal (p=0.00032) swabs, supporting the use of LFTs as a method of detecting infectiousness. Peak LFT sensitivity was 82.4% (67.0%-91.8%) for throat samples, occurring 6 days post-exposure and 93.3% (85.1%-98.0%) for nasal, 7 days post-exposure. These temporal profiles provide quantification of the mean behaviour of these tests and individual-based variability and could inform a framework for investigating future testing-based interventions.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Emma Louise Davis", - "author_inst": "Mathematics Institute, University of Warwick, UK, CV4 7AL" - }, - { - "author_name": "Deirdre Hollingsworth", - "author_inst": "Big Data Institute, University of Oxford" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.10.18.22280199", "rel_title": "Fatigue presentation, severity, and related outcomes 12 weeks post-COVID-19 hospitalization", @@ -170966,6 +173003,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.10.13.22281036", + "rel_title": "SARS-CoV-2 vaccine and increased myocarditis mortality risk: A population based comparative study in Japan", + "rel_date": "2022-10-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.13.22281036", + "rel_abs": "ObjectiveTo investigate the association between SARS-CoV-2 vaccination and myocarditis death\n\nDesignPopulation based comparative mortality study\n\nSettingJapan\n\nParticipantsVaccinated population was 99 834 543 individuals aged 12 years and older who have been received SARS-CoV-2 vaccine once or twice by 14 February 2022. Reference population was defined persons aged 10 years and older from 2017 to 2019.\n\nMain outcome measuresThe primary outcome was myocarditis death, defined as the case with \"myocarditis\" for primary cause of death and with onset 28 days or less after vaccination disclosed on 11 November 2022. Myocarditis mortality rate ratio (MMRR) of the SARS-CoV-2 vaccinated to the reference population by 10-year age group and standardised mortality ratio (SMR) were calculated. Mortality odds ratios (MORs) by 10-year age group were also calculated for supplementary analysis. Healthy vaccine effect-adjusted MMRRs (adMMRRs) or adjusted SMR (adSMR) were calculated by dividing MMRRs or SMR by 0.24 respectively.\n\nResultsNumber of myocarditis death which met the inclusion criteria were 32 cases. MMRR (95% confidence interval) was 4.03 (0.77 to 13.60) in 20s, 7.80 (2.85 to 18.56) in 30s, respectively. SMR of myocarditis was 1.69 (1.18 to 2.42) for overall vaccinated population, 1.35 (0.84 to 2.55) for those 60 years or older. Estimated adMMRRs and adSMR were about 4 times higher than the MMRRs and SMR. Pooled MOR for myocarditis were 148.49 (89.18 to 247.25).\n\nConclusionSARS-CoV-2 vaccination was associated with higher risk of myocarditis death, not only in young adults but also in all age groups including the elderly. Considering healthy vaccinee effect, the risk may be 4 times or higher than the apparent risk of myocarditis death. Underreporting should also be considered. Based on this study, risk of myocarditis following SARS-CoV-2 vaccination may be more serious than that reported previously.\n\nSUMMARY BOXESO_ST_ABSALREADY KNOWN ON THIS TOPICC_ST_ABSThere are many epidemiological studies showing increased myocarditis incidence after SARS-CoV-2 vaccination. There are also some case reports of fulminant myocarditis after receiving SARS-CoV-2 vaccine. However, no epidemiological studies focusing the association between vaccination and myocarditis death.\n\nWHAT THIS STUDY ADDSMyocarditis mortality rate ratios (MMRRs) and their 95% confidence intervals (95% CIs) after receiving SARS-CoV-2 vaccine compared with that in the reference population (previous 3 years) were higher not only in young adults (highest in the 30s with MMRR of 7.80) but also in the elderly. Standardised mortality ratio (SMR) for myocarditis was 1.35 (0.84 to 2.55) for those 60 years or older and 1.69 (1.18 to 2.42) in overall age. The risk of myocarditis mortality in the SARS-CoV-2 vaccinated population may be 4 times or higher than the apparent MMRRs considering healthy vaccinee effect. Unreported post-vaccination deaths should also be considered as suggested by the extremely high myocarditis mortality odds ratio (148.49; 89.18 to 247.25).", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Sintaroo Watanabe", + "author_inst": "Japan Marine United Corporation" + }, + { + "author_name": "Rokuro Hama", + "author_inst": "Non-profit Organization \"Japan Institute of Pharmacovigilance (Med Check)\"" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.10.17.512569", "rel_title": "N6-Adenosine Methylation of SARS-CoV-2 5-UTR Regulates Translation", @@ -172081,41 +174141,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "sexual and reproductive health" }, - { - "rel_doi": "10.1101/2022.10.14.22281094", - "rel_title": "\"How about me giving blood for the COVID vaccine and not being able to get vaccinated?\" A cognitive interview study on understanding of and agreement with broad consent for future use with cohort participants and guardians in Colombia and Nicaragua", - "rel_date": "2022-10-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.14.22281094", - "rel_abs": "Informed consent (IC) is key to generating and maintaining research participants trust and upholding the ethical principle of autonomy. Broad consent for future use, wherein researchers ask participants for permission to share participant-level data and samples collected within the study for purposes loosely related to the study objectives, is central to enabling ethical data and sample reuse. Ensuring that participants understand broad consent-related language is key in maintaining trust in the study itself and in public health research generally. Therefore, we conducted 52 cognitive interviews with the help of semi-structured interview guides to explore cohort research participants understanding of the broad consent-related language in the University of California at Berkeley template IC form for biomedical research with participants from long-standing infectious disease cohort studies in Nicaragua and Colombia. After the first round of interviews, we used participants explanations to modify the broad consent-related language in the IC template and consequently re-evaluated participants understanding of and agreement with the new consent form. Participants generally supported data and sample sharing but expressed concerns about the intentions of for-profit groups as well as misuse of data or samples. Moreover, they felt uncomfortable not receiving information about incidental findings and results from future studies. Cohort participants did not understand abstract concepts including the collection and reuse of genetic data in either version of the IC. Trust in the research team and the belief that data and sample sharing could lead to new scientific insights and improved treatments were key to participant support for data and sample sharing. The study findings and research participants language to describe broad consent provide essential insights for researchers who want to include broad consent and ethics review committees (ERCs) working to ensure research is conducted in keeping with the ethical principle of respect for persons.\n\nAuthor SummaryThis is the first study to apply cognitive interviewing to evaluate participants understanding of broad consent. We found that cohort participants did not well understand the broad consent-related language in the UCB template IC. When broad consent was reworded with language from the community, difficult to process concepts, like genetic studies, were better understood. Many ethics review committees (ERCs) and universities require researchers to use a template when consenting participants for participation in biomedical research. Our finding that key concepts in the broad consent section of the template, including genetic studies and sample collection, were not well understood suggests that ERCs must allow researchers flexibility to alter IC template language to ensure participant understanding. While, like many ERCs, the University of California at Berkeley (UCB) recommends that researchers not communicate incidental findings, participants did not understand that incidental findings would not be shared and universally wanted to learn about incidental findings. Participants generally believed in the utility of data and sample reuse but expressed concerns about reuse by commercial groups and wanted to better understand who and what the future users were. Participants did not mention privacy as a concern in data and sample sharing. Informing participants about incidental findings and future uses and users is an important part of maintaining trust in data and sample sharing.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Lauren Maxwell", - "author_inst": "UniversitatsKlinikum Heidelberg" - }, - { - "author_name": "Jackeline Bravo Chamorro", - "author_inst": "Universidad Industrial de Santander" - }, - { - "author_name": "Luz Leegstra", - "author_inst": "UniversitatsKlinikum Heidelberg" - }, - { - "author_name": "Harold Suazo Laguna", - "author_inst": "Sustainable Sciences Institute" - }, - { - "author_name": "Mar\u00eda Consuelo Miranda Montoya", - "author_inst": "Universidad Industrial de Santander" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "medical ethics" - }, { "rel_doi": "10.1101/2022.10.16.22281144", "rel_title": "Rapid quantitative electrochemical detection of SARS-CoV-2 antibodies in plasma and dried blood spot samples", @@ -172620,6 +174645,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nursing" }, + { + "rel_doi": "10.1101/2022.10.13.22280980", + "rel_title": "Stability of SARS-CoV-2 spike antigens against mutations", + "rel_date": "2022-10-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.13.22280980", + "rel_abs": "Modern health care needs preventive vaccines and therapeutic treatments with stability against pathogen mutations to cope with current and future viral infections. At the beginning of the COVID-19 pandemic, our analytic and predictive tool identified a set of eight short SARS-CoV-2 S-spike protein epitopes that had the potential to persistently avoid mutation. Here a combination of genetic, Systems Biology and protein structure analyses confirm the stability of our identified epitopes against viral mutations. Remarkably, this research spans the whole period of the pandemic, during which 93.9% of the eight peptides remained invariable in the globally predominant 43 circulating variants, including Omicron. Likewise, the selected epitopes are conserved in 97% of all 1,514 known SARS-CoV-2 lineages. Finally, experimental analyses performed with these short peptides showed their specific immunoreactivity. This work opens a new perspective on the design of next-generation vaccines and antibody therapies that will remain reliable against future pathogen mutations.\n\nHighlightsO_LIOur novel method predicts SARS-CoV-2 epitopes that are stable against future mutations\nC_LIO_LIGenetic analyses (performed 2 years after epitopes were identified) validate the stability of the identified peptides\nC_LIO_LIThese epitopes remained invariable in 97% of all 1,514 known SARS-CoV-2 lineages\nC_LIO_LI93.9% of such peptides were conserved in the 43 variants of most interest, including Omicron\nC_LI\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=166 SRC=\"FIGDIR/small/22280980v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (45K):\norg.highwire.dtl.DTLVardef@a9cb10org.highwire.dtl.DTLVardef@152a16corg.highwire.dtl.DTLVardef@1e3cea5org.highwire.dtl.DTLVardef@113ec06_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Ildefonso Martinez De la Fuente", + "author_inst": "Department of Nutrition, CEBAS-CSIC Institute, Espinardo University Campus, Murcia, 30100, Spain." + }, + { + "author_name": "Iker Malaina", + "author_inst": "Department of Mathematics, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, 48940, Spain." + }, + { + "author_name": "Maria Fedetz", + "author_inst": "Department of Cell Biology and Immunology, Lopez-Neyra Institute of Parasitology and Biomedicine, CSIC, Granada, 18016, Spain." + }, + { + "author_name": "Maksymilian Chruszcz", + "author_inst": "Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA." + }, + { + "author_name": "Gontzal Grandes", + "author_inst": "Biocruces-Bizkaia Health Research Institute, Barakaldo, 48903, Spain." + }, + { + "author_name": "Oleg Targoni", + "author_inst": "Cellular Technology Ltd, Cleveland, OH, 44122, USA." + }, + { + "author_name": "Antonio A. Lozano-Perez", + "author_inst": "Departamento de Biotecnologia, Genomica y Mejora Vegetal, Instituto Murciano de Investigacion y Desarrollo Agrario y Medioambiental (IMIDA), 30150, La Alberca (" + }, + { + "author_name": "Eyal Shteyer", + "author_inst": "The Juliet Keidan Institute of Pediatric Gastroenterology Hepatology and Nutrition, Shaare Zedek Medical Center, The Hebrew University School of Medicine, Jerus" + }, + { + "author_name": "Ami Ben Ya'akov", + "author_inst": "The Juliet Keidan Institute of Pediatric Gastroenterology Hepatology and Nutrition, Shaare Zedek Medical Center, The Hebrew University School of Medicine, Jerus" + }, + { + "author_name": "Agustin Gomez de la Camara", + "author_inst": "Department of Clinical Research, Hospital 12 de Octubre, Av. Cordoba, Madrid, Spain" + }, + { + "author_name": "Alberto M. Borobia", + "author_inst": "Clinical Pharmacology Department, La Paz University Hospital (IdiPAZ). Universidad Autonoma de Madrid, 28029, Spain." + }, + { + "author_name": "Jose Carrasco-Pujante", + "author_inst": "Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of the Basque Country, UPV/EHU, Leioa, 48940, Spain." + }, + { + "author_name": "Jose Ignacio Pijoan", + "author_inst": "Biocruces-Bizkaia Health Research Institute, Barakaldo, 48903, Spain." + }, + { + "author_name": "Carlos Bringas", + "author_inst": "Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of the Basque Country, UPV/EHU, Leioa, 48940, Spain." + }, + { + "author_name": "Gorka Perez-Yarza", + "author_inst": "Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of the Basque Country, UPV/EHU, Leioa, 48940, Spain." + }, + { + "author_name": "Alberto Ouro", + "author_inst": "NeuroAging Laboratory Group (NEURAL), Clinical Neurosciences Research Laboratories (LINCs), Health Research Institute of Santiago de Compostela (IDIS), 15706, S" + }, + { + "author_name": "Michael J. Crawford", + "author_inst": "Department of Biomedical Sciences, University of Windsor, Windsor Ontario, N9B 3P4, Canada." + }, + { + "author_name": "Varda Shoshan-Barmatz", + "author_inst": "Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University, Beer-Sheva, 84105, Israel." + }, + { + "author_name": "Vladimir Zhurov", + "author_inst": "Department of Biology University of Western Ontario, Ontario N6A5B7. Canada." + }, + { + "author_name": "Jose I. Lopez", + "author_inst": "Biocruces-Bizkaia Health Research Institute, Barakaldo, 48903, Spain." + }, + { + "author_name": "Shira Knafo", + "author_inst": "Department of Physiology and Cell Biology, Faculty of Health Sciences, and The National Institute for Biotechnology in the Negev, Ben-Gurion University of the N" + }, + { + "author_name": "Magdalena Tary-Lehmann", + "author_inst": "Cellular Technology Ltd, Cleveland, OH, 44122, USA." + }, + { + "author_name": "Toni Gabaldon", + "author_inst": "Barcelona Supercomputing Centre (BSC-CNS), Life Sciences Department, Jordi Girona 29, 08034 Barcelona, Spain." + }, + { + "author_name": "Miodrag Grbic", + "author_inst": "Department of Biology University of Western Ontario, Ontario N6A5B7. Canada." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.10.13.22280957", "rel_title": "Serology assays used in SARS-CoV-2 seroprevalence surveys worldwide: a systematic review and meta-analysis of assay features, testing algorithms, and performance", @@ -174011,33 +176147,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.10.12.511994", - "rel_title": "Reduction of RBD Binding Affinity to Glycosylated ACE2 is Entropic in Origin", - "rel_date": "2022-10-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.12.511994", - "rel_abs": "The spike protein in the virus SARS-CoV-2 (the causative agent of COVID-19) recognizes the host cell by binding to the peptidase domain (PD) of the extracellular enzyme Angiotensin-converting Enzyme 2 (ACE2). A variety of carbohydrates could be attached to the six asparagines in the PD, resulting in a heterogeneous population of ACE2 glycoforms. Experiments have shown that the binding affinity of glycosylated and deglycosylated ACE2 to the virus is virtually identical. In most cases, the reduction in glycan size correlates with stronger binding, which suggests that volume exclusion, and hence entropic forces, determine the binding affinity. Here, we quantitatively test the entropy-based hypothesis by developing a lattice model for the complex between ACE2 and the SARS-CoV-2 spike protein Receptor-binding Domain (RBD). Glycans are treated as branched polymers with only volume exclusion, which we justify using all atom molecular dynamics simulations in explicit water. We show that the experimentally measured changes in the ACE2-RBD dissociation constants for a variety of engineered ACE2 glycoforms are well accounted for by our theory, thus affirming that ACE2 glycans have only a weak, entropic effect on RBD binding.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Mauro Mugnai", - "author_inst": "Georgetown University" - }, - { - "author_name": "Sucheol Shin", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Dave Thirumalai", - "author_inst": "The University of Texas at Austin" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2022.10.13.512054", "rel_title": "Combination of the parent analogue of Remdesivir (GS-441524) and Molnupiravir results in a markedly potent antiviral effect in SARS-CoV-2 infected Syrian hamsters", @@ -174726,6 +176835,61 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2022.10.12.22280990", + "rel_title": "Post-acute symptoms four months after SARS-CoV-2 infection during the Omicron period: a nationwide Danish questionnaire study", + "rel_date": "2022-10-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.12.22280990", + "rel_abs": "BackgroundPost-acute symptoms are not uncommon after SARS-CoV-2 infection with pre-Omicron variants. How the Omicron variant and COVID-19 booster vaccination influences the risk of post-acute symptoms is less clear.\n\nObjectivesTo evaluate the effects of the Omicron variant and COVID-19 booster vaccination on post-acute symptoms, four months after infection with SARS-CoV-2.\n\nMethodsA nationwide Danish questionnaire study comprising 44,004 individuals aged 15 years or older with outcomes on post-acute symptoms and new-onset general health problems, four months after testing. Risk differences (RDs) were estimated by comparing Omicron -cases to controls, Omicron to Delta -cases, and Omicron vaccinated cases with three to -two doses, adjusted for age, sex, BMI, self-reported chronic diseases, Charlson comorbidity index, healthcare occupation, and vaccination status.\n\nResultsFour months after testing for SARS-CoV-2 during the Omicron period, the largest RD comparing Omicron cases to controls was observed for memory issues (RD=7.2%, 95% CI: 6.4 to 8.1). Compared to cases from the Delta period, Omicron cases reported reduced risks of post-acute dysosmia (RD=-15.5%, 95% CI: -17.5 to -13.4) and dysgeusia (RD=-11.8%, 95% CI: -13.9 to -9.8). Cases vaccinated with three doses prior to Omicron infection reported reduced risk of 13/26 post-acute symptoms and of 4/5 new-onset general health problems, compared to those vaccinated with two doses.\n\nConclusionsCases infected during the Omicron period experienced substantial post-acute symptoms and new-onset health problems, four months after testing, although milder than Delta cases. Booster vaccination was associated with fewer post-acute symptoms and new-onset health problems, four months after Omicron infection, compared to two doses of COVID-19 vaccine.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Lampros Spiliopoulos", + "author_inst": "Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark" + }, + { + "author_name": "Anna Irene Vedel S\u00f8rensen", + "author_inst": "Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark" + }, + { + "author_name": "Peter Bager", + "author_inst": "Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark, and Department of Infectious Disease Epidemiology and Prevention, Statens Seru" + }, + { + "author_name": "Nete Munk Nielsen", + "author_inst": "Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark, and Focused Research Unit in Neurology, Department of Neurology, Hospital of S" + }, + { + "author_name": "J\u00f8rgen Vinsl\u00f8v Hansen", + "author_inst": "Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark" + }, + { + "author_name": "Anders Koch", + "author_inst": "Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark, and Department of Public Health, Global Health Sectio" + }, + { + "author_name": "Inger Kristine Meder", + "author_inst": "Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark" + }, + { + "author_name": "Poul Videbech", + "author_inst": "Centre for Neuropsychiatric Depression Research, Mental Health Centre Glostrup, Glostrup, Denmark, and University of Copenhagen, Copenhagen, Denmark" + }, + { + "author_name": "Steen Ethelberg", + "author_inst": "Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark, and Department of Public Health, Global Health Sectio" + }, + { + "author_name": "Anders Hviid", + "author_inst": "Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark, and Pharmacovigilance Research Centre, Department of Drug Design and Pharmacol" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.10.11.511764", "rel_title": "SARS-CoV2 associated secretion of nanoLuciferase reports on virus and Virus-Like Particle production", @@ -175933,105 +178097,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2022.10.09.22280886", - "rel_title": "Cohort Profile: The Danish National Cohort Study of Effectiveness and Safety of SARS-CoV-2 vaccines (ENFORCE)", - "rel_date": "2022-10-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.09.22280886", - "rel_abs": "PurposeThe ENFORCE cohort is a national Danish prospective cohort of adults who received a Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine as part of the Danish National SARS-CoV-2 vaccination program. It was designed to investigate the long-term effectiveness, safety and durability of SARS-CoV-2 vaccines used in Denmark.\n\nParticipantsA total of 6943 adults scheduled to receive a SARS-CoV-2 vaccine in the Danish COVID-19 Vaccination Program were enrolled in the study prior to their first vaccination. Participants will be followed for a total of two years with five predetermined follow-up visits and additional visits in relation to any booster vaccination. Serology measurements are performed after each study visit. T-cell immunity is evaluated at each study visit for a subgroup of 699 participants. Safety information is collected from participants at visits following each vaccination. Data on hospital admissions, diagnoses, deaths and SARS-CoV-2 polymerase chain reaction (PCR) results are collected from national registries throughout the study period. The median age of participants was 64 years (IQR 53-75), 56.6% were females and 23% were individuals with an increased risk of a serious course of COVID-19. A total of 340 (4.9%) participants tested positive for SARS-CoV-2 spike IgG at baseline.\n\nFindings to dateResults have been published on risk factors for humoral hyporesponsiveness and non-durable response to SARS-CoV-2 vaccination, the risk of breakthrough infections at different levels of SARS-CoV-2 spike IgG by viral variant, and on the antibody neutralizing capacity against different SARS-CoV-2 variants following primary and booster vaccinations.\n\nFuture plansThe ENFORCE cohort will continuously generate studies investigating immunological response, effectiveness, safety and durability of the SARS-CoV-2 vaccines.\n\nRegistrationclinicaltrials.gov identifier: NCT04760132.\n\nStrengths and limitations- The ENFORCE study combines repeated detailed SARS-CoV-2 specific immunological measurements prior to, and throughout the course of SARS-CoV-2 vaccination, with register-based follow-up of safety data and microbiological test results.\n- The ENFORCE cohort includes a large proportion of elderly participants and participants with concomitant diseases.\n- The three vaccine groups display a high degree of variation in demographic factors and distribution across risk groups, due to the prioritization of specific vaccines to risk groups during the primary roll out of the SARS-CoV-2 vaccination program.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Nina B Staerke", - "author_inst": "Aarhus University Hospital" - }, - { - "author_name": "Joanne Reekie", - "author_inst": "Center of Excellence for Health Immunity and Infections, Copenhagen" - }, - { - "author_name": "Isik S Johansen", - "author_inst": "Odense University Hospital" - }, - { - "author_name": "Henrik Nielsen", - "author_inst": "Aalborg University Hospital" - }, - { - "author_name": "Thomas Benfield", - "author_inst": "Copenhagen University Hospital, Amager and Hvidovre" - }, - { - "author_name": "Lothar Wiese", - "author_inst": "Zealand University Hospital, Roskilde" - }, - { - "author_name": "Ole S Soegaard", - "author_inst": "Aarhus University Hospital" - }, - { - "author_name": "Martin Tolstrup", - "author_inst": "Aarhus University Hospital" - }, - { - "author_name": "Kasper K Iversen", - "author_inst": "Herlev Hospital" - }, - { - "author_name": "Britta Tarp", - "author_inst": "Silkeborg Regional Hospital" - }, - { - "author_name": "Fredrikke D Larsen", - "author_inst": "Aarhus University Hospital" - }, - { - "author_name": "Lykke Larsen", - "author_inst": "Odense University Hospital" - }, - { - "author_name": "Susan O Lindvig", - "author_inst": "Odense University Hospital" - }, - { - "author_name": "Inge K Holden", - "author_inst": "Odense University Hospital" - }, - { - "author_name": "Mette B Iversen", - "author_inst": "Zealand University Hospital, Roskilde" - }, - { - "author_name": "Lene S Knudsen", - "author_inst": "Zealand University Hospital, Roskilde" - }, - { - "author_name": "Kamille Fogh", - "author_inst": "Herlev Hospital, Herlev" - }, - { - "author_name": "Marie Louise Jakobsen", - "author_inst": "Center of Excellence for Health, Immunity and Infections, Copenhagen" - }, - { - "author_name": "Anna Traytel", - "author_inst": "Center of Excellence for Health, Immunity and Infections, Copenhagen" - }, - { - "author_name": "Lars Oestergaard", - "author_inst": "Aarhus University Hospital" - }, - { - "author_name": "Jens Lundgren", - "author_inst": "Center of Excellence for Health, Immunity and Infections, Copenhagen" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.10.07.22280814", "rel_title": "Pre-pandemic humoral immunity to SARS-CoV-2 in Africa: systematic review and meta-analysis", @@ -176872,6 +178937,65 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.10.07.22280732", + "rel_title": "Psychophysiologic symptom relief therapy (PSRT) for post-acute sequelae of COVID-19: a non-randomized interventional study", + "rel_date": "2022-10-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.07.22280732", + "rel_abs": "ObjectiveTo determine if psychophysiologic symptom relief therapy (PSRT) will reduce symptom burden in patients suffering from post-acute sequelae of COVID-19 (PASC) who had mild/moderate acute COVID-19 disease without objective evidence of organ injury.\n\nPatients and MethodsTwenty-three adults under the age of 60 with PASC for at least 12 weeks following COVID-19 infection were enrolled in an interventional cohort study conducted via virtual platform between May 18, 2021 and August 7, 2022. Participants received PSRT during a 13 week (approximately 44 hour) course. Participants were administered validated questionnaires at baseline and at 4, 8, and 13 weeks. The primary outcome was change in somatic symptoms from baseline, measured using the Somatic Symptom Scale-8 (SSS-8).\n\nResultsThe median duration of symptoms prior to joining the study was 267 days (IQR: 144, 460). The mean SSS-8 score of the cohort decreased from baseline by 8.5 (95% CI: 5.7-11.4), 9.4 (95% CI: 6.9-11.9), and 10.9 (95% CI: 8.3-13.5) at 4, 8, and 13 weeks respectively (all p<0.001). Participants also experienced statistically significant improvements across secondary outcomes including changes in dyspnea, fatigue, and pain (all p<0.001).\n\nConclusionPSRT may effectively decrease symptom burden in patients suffering from PASC without evidence of organ injury. The study was registered on clinicaltrials.gov (NCT 04854772).", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Michael W Donnino", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Patricia Howard", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Shivani Mehta", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Jeremy Silverman", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Maria J Cabrera", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Jolin B Yamin", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Lakshman Balaji", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Rebecca Tolin", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Katherine M Berg", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Robert Edwards", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Anne V Grossestreuer", + "author_inst": "Beth Israel Deaconess Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.10.07.22280607", "rel_title": "Comparison of COVID-19 Antigen Rapid Test (Oral Fluid) and Real-Time RT-PCR in the laboratory diagnosis of SARS-CoV-2 infection", @@ -177831,73 +179955,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.10.07.511324", - "rel_title": "Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets.", - "rel_date": "2022-10-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.07.511324", - "rel_abs": "The infection and replication cycle of all viruses depend on interactions between viral and host proteins. Each of these protein-protein interactions is therefore a potential drug target. These host-virus interactions often involve a disordered protein region on one side of the interface and a folded protein domain on the other. Here, we used proteomic peptide phage display (ProP-PD) to identify peptides from the intrinsically disordered regions of the human proteome that bind to folded protein domains encoded by the SARS-CoV-2 genome. Eleven folded domains of SARS-CoV-2 proteins were found to bind peptides from human proteins. Of 281 high/medium confidence peptides, 23 interactions involving eight SARS-CoV-2 protein domains were tested by fluorescence polarization, and binding was observed with affinities spanning the whole micromolar range. The key specificity determinants were established for six of these domains, two based on ProP-PD and four by alanine scanning SPOT arrays. Finally, two cell-penetrating peptides, targeting Nsp9 and Nsp16, respectively, were shown to function as inhibitors of viral replication. Our findings demonstrate how high-throughput peptide binding screens simultaneously provide information on potential host-virus interactions and identify ligands with antiviral properties.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Filip Mihalic", - "author_inst": "Uppsala University" - }, - { - "author_name": "Caroline Benz", - "author_inst": "Uppsala University" - }, - { - "author_name": "Eszter Kassa", - "author_inst": "Uppsala University" - }, - { - "author_name": "Richard Lindqvist", - "author_inst": "Umea University" - }, - { - "author_name": "Leandro Simonetti", - "author_inst": "Uppsala University" - }, - { - "author_name": "Raviteja Inturi", - "author_inst": "Uppsala University" - }, - { - "author_name": "Hanna Aronsson", - "author_inst": "Uppsala University" - }, - { - "author_name": "Eva Andersson", - "author_inst": "Uppsala University" - }, - { - "author_name": "Celestine N Chi", - "author_inst": "Uppsala University" - }, - { - "author_name": "Norman E Davey", - "author_inst": "The Institute of Cancer Research" - }, - { - "author_name": "Anna K Overby", - "author_inst": "Umea university" - }, - { - "author_name": "Per Jemth", - "author_inst": "Uppsala University" - }, - { - "author_name": "Ylva Ivarsson", - "author_inst": "Uppsala University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2022.10.07.510750", "rel_title": "Upregulation of CD55 complement regulator in distinct PBMC subpopulations of COVID-19 patients is associated with suppression of interferon responses.", @@ -178542,6 +180599,33 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.10.04.510830", + "rel_title": "SARS-CoV-2 infection alkalinizes the ERGIC and lysosomes through the viroporin activity of the viral envelope protein", + "rel_date": "2022-10-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.04.510830", + "rel_abs": "The coronavirus SARS-CoV-2, the agent of the deadly COVID-19 pandemic, is an enveloped virus propagating within the endocytic and secretory organelles of host mammalian cells. Enveloped viruses modify the ionic homeostasis of organelles to render their intra-luminal milieu permissive for viral entry, replication, and egress. Here, we show that infection of Vero E6 cells with the delta variant of the SARS-CoV-2 alkalinizes the endoplasmic reticulum-Golgi intermediate compartment (ERGIC) as well as lysosomes, mimicking the effect of inhibitors of vacuolar proton ATPases. We further show the envelope protein of SARS-CoV-2 accumulates in the ERGIC when expressed in mammalian cells and selectively dissipates the ERGIC pH. This viroporin effect is not associated with acute cellular toxicity but is prevented by mutations within the channel pore of E. We conclude that the envelope protein acts as a proton channel in the ERGIC to mitigate the acidity of this intermediate compartment. The altered pH homeostasis of the ERGIC likely contributes to the virus fitness and pathogenicity, making the E channel an attractive drug target for the treatment of COVID-19.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Wen-An Want", + "author_inst": "University of Geneva" + }, + { + "author_name": "Amado Carreras Sureda", + "author_inst": "University of Geneva" + }, + { + "author_name": "Nicolas Demaurex", + "author_inst": "University of Geneva" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "physiology" + }, { "rel_doi": "10.1101/483867", "rel_title": "Optimal metabolic states in cells", @@ -179865,77 +181949,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.10.04.510352", - "rel_title": "Distinct phenotype of SARS-CoV-2 Omicron BA.1 in human primary cells but no increased host range in cell lines of putative mammalian reservoir species", - "rel_date": "2022-10-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.04.510352", - "rel_abs": "SARS-CoV-2s genetic plasticity has led to several variants of concern (VOCs). Here we studied replicative capacity for seven SARS-CoV-2 isolates (B.1, Alpha, Beta, Gamma, Delta, Zeta, and Omicron BA.1) in primary reconstituted airway epithelia (HAE) and lung-derived cell lines. Furthermore, to investigate the host range of Delta and Omicron compared to ancestral SARS-CoV-2, we assessed replication in 17 cell lines from 11 non-primate mammalian species, including bats, rodents, insectivores and carnivores. Only Omicrons phenotype differed in vitro, with rapid but short replication and efficient production of infectious virus in nasal HAEs, in contrast to other VOCs, but not in lung cell lines. No increased infection efficiency for other species was observed, but Delta and Omicron infection efficiency was increased in A549 cells. Notably replication in A549 and Calu3 cells was lower than in nasal HAE. Our results suggest better adaptation of VOCs towards humans, without an extended host range.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Manel Essaidi-Laziosi", - "author_inst": "University of Geneva" - }, - { - "author_name": "Francisco Javier Perez Rodriguez", - "author_inst": "University Hospital of Geneva" - }, - { - "author_name": "Catia Alvarez", - "author_inst": "University of Geneva" - }, - { - "author_name": "Pascale Sattonnet-Roche", - "author_inst": "University Hospital of Geneva" - }, - { - "author_name": "Giulia Torriani", - "author_inst": "University of Geneva" - }, - { - "author_name": "Meriem Bekliz", - "author_inst": "University of Geneva" - }, - { - "author_name": "Kenneth Adea", - "author_inst": "University of Geneva" - }, - { - "author_name": "Matthias Lenk", - "author_inst": "Friedrich-Loeffler-Institute" - }, - { - "author_name": "Wolfgang Preiser", - "author_inst": "Stellenbosch University - Tygerberg Campus: Stellenbosch University Faculty of Medicine and Health Sciences" - }, - { - "author_name": "Tasnim Suliman", - "author_inst": "University of the Western Cape, Cape Town, South Africa" - }, - { - "author_name": "Marcel A Muller", - "author_inst": "Charite Universitatsmedizin Berlin" - }, - { - "author_name": "Christian Drosten", - "author_inst": "Charite Universitatsmedizin" - }, - { - "author_name": "Laurent Kaiser", - "author_inst": "University Hospital of Geneva" - }, - { - "author_name": "Isabella Eckerle", - "author_inst": "University of Geneva" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.10.04.510658", "rel_title": "A neonatal mouse model characterizes transmissibility of SARS-CoV-2 variants and reveals a role for ORF8", @@ -180748,6 +182761,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.10.03.507132", + "rel_title": "Biophysical characterisation of the structure of a SARS-CoV-2 self-amplifying - RNA (saRNA) vaccine", + "rel_date": "2022-10-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.03.507132", + "rel_abs": "The current SARS-Covid-2 pandemic has led to an acceleration of messenger - ribonucleic acid (mRNA) vaccine technology. The development of production processes for these large mRNA molecules, especially self-amplifying mRNA (saRNA) has required concomitant development of analytical characterisation techniques. Characterising the purity, shape and structure of these biomolecules is key to their successful performance as drug products. This paper describes the biophysical characterisation of the Imperial College London Self-amplifying viral RNA vaccine (IMP-1) developed for SARS-CoV-2. A variety of analytical techniques have been used to characterise the IMP-1 RNA molecule. In this paper we use UV spectroscopy, dynamic light scattering (DLS), size-exclusion chromatography small angle scattering (SEC-SAXS) and circular dichroism (CD) to determine key biophysical attributes of IMP-1. Each technique provides important information about the concentration, size, shape, structure and purity of the molecule.\n\nStatement of significanceThis paper is highly significant as it provides a prescient biophysical characterisation of an efficacious Sars-Cov-2 vaccine self-amplifying (sa)RNA molecule. RNA vaccines have been a major scientific breakthrough of the Covid-19 pandemic. saRNA is a further development of conventional mRNA vaccines, amplifying the RNA of interest in the cell, allowing the vaccine to be administered at lower dosages. These new biologics are distinct from previous biologics and have required distinct analytical characterisation. The analytics described herein provide detailed information on the size, shape, and structure of the RNA molecule. This paper is therefore an important step in characterising large saRNA biological relevant molecules.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Daniel Paul Myatt", + "author_inst": "Centre for Process Innovation" + }, + { + "author_name": "Lewis Wharram", + "author_inst": "Centre for Process Innovation" + }, + { + "author_name": "Charlotte Graham", + "author_inst": "Centre for Process Innovation" + }, + { + "author_name": "John Liddell", + "author_inst": "Centre for Process Innovation" + }, + { + "author_name": "Harvey Branton", + "author_inst": "Centre for Process Innovation" + }, + { + "author_name": "Claire Pizzey", + "author_inst": "Diamond Light Source Ltd" + }, + { + "author_name": "Nathan Cowieson", + "author_inst": "Diamond Light Source Ltd" + }, + { + "author_name": "Robert Rambo", + "author_inst": "Diamond Light Source Ltd" + }, + { + "author_name": "Robin Shattock", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2022.10.01.510442", "rel_title": "SARS-CoV-2 spike protein induces endothelial dysfunction in 3D engineered vascular networks", @@ -182019,29 +184083,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.09.30.510283", - "rel_title": "Novel and simple simulation method to design and development of antisense template", - "rel_date": "2022-09-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.30.510283", - "rel_abs": "Antisense technology is emerging as potential therapeutics against lethal infections. Basically, Antisense-mRNA complex inhibits the protein translation of pathogens and thus it is used for treatment. Based on previous online tools and literatures and difficulties for designing antisense template, finding high conserved regions from large number of long sequences, by taking all those factors in consideration, we proposed new innovative offline target simulation methods i.e. Deletion of unwanted region from viral sequence alignment (DURVA) and Most frequent region (MFR) for designing and developing antisense template from large number of long sequence or genomic data. Based on current pandemic crisis and long genomic sequence of SARS-CoV-2, we chose coronavirus for simulation. Initially, we hypothesized that DURVA-MFR would find stable region from large annotated sequencing data. As per Chan et.al. guidelines for antisense designing and development, we designed couple of algorithms and python scripts to process the data of approximately 30kbp sequence length and 1Gb file size in short turnaround time. The steps involved were as: 1) Simplifying whole genome sequence in single line; 2) Deletion of unwanted region from Virus sequence alignment(DURVA); 3)Most frequent antisense target region(MFR) and 4)Designing and development of antisense template. This simulation method is identifying most frequent regions between 20-30bp long, GC count[≥]10. Our study concluded that targets were highly identical with large population and similar with high number of remaining sequences. In addition, designed antisense sequences were stable and each sequence is having tighter binding with targets. After studying each parameter, here we suggested that our proposed method would be helpful for finding best antisense against all present and upcoming lethal infection.The initial design of this logic was published in Indian Patent Office Journal No.08/2021withApplication number202121005964A.\n\nSimple summaryThe antisense development is state of the art for modern therapeutics. There are number of online soft-wares and open sources for designing of antisense template. But all other tools did not consider frequency as major factor for designing antisense. Also; all sources excepting our simulation approach does not process large file or long sequences. Therefore; we designed an offline innovative simulation method which deletes the unwanted region from sequences and stores the data which are fulfilled antisense criteria. Further; the calculation of frequency from these short listed target regions; the most frequent region is desire antisense target and further antisense template will be designed according to Watson-Crick model. This article explained all information about how our new approach is best for designing antisense template against SARS-CoV-2 and many lethal infectious viruses etc.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Devendra Deo", - "author_inst": "Medgenome Labs" - }, - { - "author_name": "Nawaj Shaikh", - "author_inst": "Society for Health Allied Research and Education India" - } - ], - "version": "1", - "license": "cc_by", - "type": "confirmatory results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2022.09.29.510149", "rel_title": "The SARS-CoV-2 mutation landscape is shaped before replication starts", @@ -182578,6 +184619,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "addiction medicine" }, + { + "rel_doi": "10.1101/2022.09.29.510112", + "rel_title": "A linear SARS-CoV-2 DNA vaccine candidate reduces virus shedding in ferrets", + "rel_date": "2022-09-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.29.510112", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), has caused more than 600 million cases and over 6 million deaths worldwide. Vaccination has been the main strategy used to contain the spread of the virus, and to avoid hospitalizations and deaths. Currently, there are two mRNA-based and one adenovirus vectored vaccines approved and available for use in the U.S. population. The versatility, low cost and rapid-to-manufacture attributes of DNA vaccines are important advantages over other platforms. However, DNA vaccination must meet higher efficiency levels for use in humans. Importantly, in vivo DNA delivery combined with electroporation (EP) has been successfully used in the veterinary field. Here we evaluated the safety, immunogenicity and protective efficacy of a novel linear SARS-CoV-2 DNA vaccine candidate for delivered by intramuscular injection followed by electroporation (Vet-ePorator) in ferrets. The results demonstrated that the linear SARS-CoV-2 DNA vaccine candidate did not cause unexpected side effects, and was able to elicit neutralizing antibodies and T cell responses using a low dose of the linear DNA construct in prime-boost regimen, and significantly reduced shedding of infectious SARS-CoV-2 through oral and nasal secretions in a ferret model.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Mathias Martins", + "author_inst": "Cornell University" + }, + { + "author_name": "Gabriela M. do Nascimento", + "author_inst": "Cornell University College of Veterinary Medicine" + }, + { + "author_name": "Antonella Conforti", + "author_inst": "Evvivax" + }, + { + "author_name": "Jessica C.G. Noll", + "author_inst": "Cornell University" + }, + { + "author_name": "Joseph A. Impellizeri", + "author_inst": "Veterinary Oncology Services" + }, + { + "author_name": "Elisa Sanches", + "author_inst": "Veterinary Oncology Services" + }, + { + "author_name": "Bettina Wagner", + "author_inst": "Cornell University College of Veterinary Medicine" + }, + { + "author_name": "Lucia Lione", + "author_inst": "Takis Biotech" + }, + { + "author_name": "Erika Salvatori", + "author_inst": "Takis Biotech" + }, + { + "author_name": "Eleonora Pinto", + "author_inst": "Takis Biotech" + }, + { + "author_name": "Mirco Compagnone", + "author_inst": "Neomatrix Biotech" + }, + { + "author_name": "Brian Viscount", + "author_inst": "Applied DNA Sciences" + }, + { + "author_name": "James Hayward", + "author_inst": "Applied DNA Sciences" + }, + { + "author_name": "Clay Shorrock", + "author_inst": "Applied DNA Sciences" + }, + { + "author_name": "Luigi Aurisicchio", + "author_inst": "Evvivax Biotech" + }, + { + "author_name": "Diego G. Diel", + "author_inst": "Cornell University College of Veterinary Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.09.29.510004", "rel_title": "Sensitivity of diffusion-tensor and correlated diffusion imaging to white-matter microstructural abnormalities: application in COVID-19", @@ -183817,65 +185937,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.09.27.22280404", - "rel_title": "Presentation of long COVID and associated risk factors in a mobile health study", - "rel_date": "2022-09-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.27.22280404", - "rel_abs": "BackgrounThe Covid Collab study was a citizen science mobile health research project set up in June 2020 to monitor COVID-19 symptoms and mental health through questionnaire self-reports and passive wearable device data.\n\nMethodsUsing mobile health data, we consider whether a participant is suffering from long COVID in two ways. Firstly, by whether the participant has a persistent change in a physiological signal commencing at a diagnosis of COVID-19 that last for at least twelve weeks. Secondly, by whether a participant has self-reported persistent symptoms for at least twelve weeks. We assess sociodemographic and wearable-based risk factors for the development of long COVID according to the above two categorisations.\n\nFindingsPersistent changes to physiological signals measured by commercial fitness wearables, including heart rate, sleep, and activity, are visible following a COVID-19 infection and may help differentiate people who develop long COVID. Anxiety and depression are significantly and persistently affected at a group level following a COVID-19 infection. We found the level of activity undertaken in the year prior to illness was protective against long COVID and that symptoms of depression before and during the acute illness may be a risk factor.\n\nInterpretationMobile health and wearable devices may prove to be a useful resource for tracking recovery and presence of long-term sequelae to COVID-19. Mental wellbeing is significantly negatively effected on average for an extended period of time following a COVID-19 infection.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Callum Stewart", - "author_inst": "Department of Health Informatics and Biostatistics, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, UK" - }, - { - "author_name": "Yatharth Ranjan", - "author_inst": "Department of Health Informatics and Biostatistics, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, UK" - }, - { - "author_name": "Pauline Conde", - "author_inst": "Department of Health Informatics and Biostatistics, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, UK" - }, - { - "author_name": "Shaoxiong Sun", - "author_inst": "Department of Health Informatics and Biostatistics, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, UK" - }, - { - "author_name": "Zulqarnain Rashid", - "author_inst": "Department of Health Informatics and Biostatistics, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, UK" - }, - { - "author_name": "Heet Sankesara", - "author_inst": "Department of Health Informatics and Biostatistics, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, UK" - }, - { - "author_name": "Nicholas Cummins", - "author_inst": "Department of Health Informatics and Biostatistics, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, UK" - }, - { - "author_name": "Petroula Laiou", - "author_inst": "Department of Health Informatics and Biostatistics, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, UK" - }, - { - "author_name": "Xi Bai", - "author_inst": "Department of Health Informatics and Biostatistics, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, UK" - }, - { - "author_name": "Richard Dobson", - "author_inst": "Department of Health Informatics and Biostatistics, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, UK" - }, - { - "author_name": "Amos Folarin", - "author_inst": "Department of Health Informatics and Biostatistics, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, UK" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2022.09.27.22280419", "rel_title": "Comparison Of New and emerging SARS-CoV-2 variant Transmissibility through Active Contact Testing. A comparative cross-sectional household seroprevalence study.", @@ -184536,6 +186597,45 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.09.26.22280357", + "rel_title": "Impact of the COVID-19 restrictions on the epidemiology of Cryptosporidium spp. in England and Wales, 2015-2021A time-series analysis", + "rel_date": "2022-09-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.26.22280357", + "rel_abs": "BackgroundIn England and Wales, cryptosporidiosis cases peak in spring and autumn, usually associated with zoonotic and environmental exposures (Cryptosporidium parvum, spring/autumn) and with overseas travel and water-based activities (Cryptosporidium hominis, autumn). Restrictions to control the COVID-19 pandemic prevented social mixing and access to swimming pools and restaurants for many months. Foreign travel from the UK also reduced by 74% in 2020. However, these restrictions potentially increased environmental exposures as people sought alternative countryside activities locally. To inform and strengthen surveillance programmes, we investigated the impact of COVID-19 restrictions on the epidemiology of C. hominis and C. parvum cases.\n\nMethodsCryptosporidium-positive stools, with case demographic data, are referred routinely for genotyping to the national Cryptosporidium Reference Unit (CRU). Cases were extracted from the CRU database (01 January 2015 to 31 December 2021). We defined two periods for pre- and post-COVID-19 restrictions implementation corresponding to the first UK-wide lockdown on 23 March 2020: \"pre-restrictions\" between week 1, 2015 and week 12, 2020, and \"post restrictions-implementation\" between week 13, 2020 and week 52, 2021. We conducted an interrupted time-series analysis, assessing differences in C. parvum and C. hominis incidence, trends and periodicity between these periods using negative binomial regression with linear-splines and interactions.\n\nResultsThere were 21,304 cases between 01 January 2015 and 31 December 2021 (C. parvum = 12,246; C. hominis = 9,058). Post restrictions-implementation incidence of C. hominis dropped by 97.5% (95%CI: 95.4%-98.6%; p<0.001). The decreasing incidence-trend observed pre-restrictions (IRR=0.9976; 95%CI: 0.9969-0.9982; p<0.001) was not observed post restrictions-implementation (IRR=1.0081; 95%CI: 0.9978-1.0186; p=0.128) due to lack of cases. No periodicity change was observed post restrictions-implementation. Where recorded, 22% of C. hominis cases had travelled abroad. There was also a strong social gradient, with those who lived in deprived areas experiencing a higher proportion of cases. This gradient did not exist post restrictions-implementation, but the effect was exacerbated for the most deprived: 27.2% of cases from the most deprived decile compared to 12.7% in the pre-restrictions period. For C. parvum, post restrictions-implementation incidence fell by 49.0% (95%CI: 38.4%-58.3%; p<0.001). There was no pre-restrictions incidence-trend (IRR=1.0003; 95%CI: 0.9997-1.0009; p=0.322) but a slight increasing incidence-trend existed post restrictions-implementation (IRR=1.0071; 95%CI: 1.0038-1.0104; p<0.001). A periodicity change was observed for C. parvum post restrictions-implementation, peaking one week earlier in spring and two weeks later in autumn. Where recorded, 8% of C. parvum cases had travelled abroad. The social gradient observed for C. parvum was inverse to that for C. hominis, and was stable pre-restrictions and post restrictions-implementation.\n\nConclusionC. hominis cases were almost entirely arrested post restrictions-implementation, reinforcing that foreign travel is a major driver of seeding infections. Increased hand-hygiene, reduced social mixing, limited access to swimming pools and limited foreign travel affected incidence of most gastrointestinal (GI) pathogens, including Cryptosporidium, in the same period. C. parvum incidence fell sharply but recovered throughout the post restrictions-implementation period, back to pre-restrictions levels by the end of 2021; this is consistent with relaxation of restrictions, reduced compliance and increased countryside use. The effect on our results of changes in health-seeking behaviours, healthcare access and diagnostic laboratory practices post restrictions-implementation is uncertain, but it is likely that access to GPs and specimen referral rate to CRU decreased. Future exceedance reporting for C. hominis should exclude the post restrictions-implementation period but retain it for C. parvum (except the first six weeks post restrictions-implementation where the incidence fell sharply). Advice on infection prevention and control should be improved for people with GI symptoms, including returning travellers, to ensure hand hygiene and appropriate swimming pool avoidance.\n\nData summaryCryptosporidium is a notifiable agent in the UK which diagnostic laboratories must report to local health protection teams. Submission of Cryptosporidium-positive stools to the CRU is voluntary, but allows characterisation of the species. We used these data, where the specimen originated from English and Welsh diagnostic laboratories, to describe the epidemiology of Cryptosporidium spp. between 2015 and 2021.\n\nImpact statementCryptosporidium infections in industrialised countries can cause serious disease and lead to complicated and lasting sequelae, especially in the immunocompromised. Even in the general population, as well as long term gastrointestinal upset, joint pain, headache and eye pain have also been identified more frequently following cryptosporidiosis (1). There is an established association between cryptosporidiosis and colorectal cancer, although no conclusive evidence regarding causality in either direction (2-5). There has never been such a dramatic reduction in international travel in the modern era than during the COVID-19 pandemic, which is a key driver of C. hominis infections. Conversely, pressure on outdoor amenities has rarely been higher, which posed an increase in the likelihood of infection and cross-contamination for C. parvum infections. There have been few time-series analyses of cryptosporidiosis; in order to inform and strengthen surveillance programmes, we aimed to assess if there was a significant change to the epidemiology of C. parvum and C. hominis during the COVID-19 pandemic.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "James Adamson", + "author_inst": "Public Health Wales" + }, + { + "author_name": "Rachel Chalmers", + "author_inst": "Public Health Wales" + }, + { + "author_name": "Daniel Rhys Thomas", + "author_inst": "Public Health Wales" + }, + { + "author_name": "Krstin Elwin", + "author_inst": "Public Health Wales" + }, + { + "author_name": "Guy Robinson", + "author_inst": "Public Health Wales" + }, + { + "author_name": "Alicia Barrasa", + "author_inst": "UK Health Security Agency" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.09.26.22280233", "rel_title": "Impact of COVID-19 pandemic on the incidence of suicidal behaviors: a retrospective analysis of integrated electronic health records in a 7.5-million population", @@ -185855,153 +187955,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.09.23.22280285", - "rel_title": "Dimethyl fumarate in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial", - "rel_date": "2022-09-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.23.22280285", - "rel_abs": "BackgroundDimethyl fumarate (DMF) is an anti-inflammatory drug that has been proposed as a treatment for patients hospitalised with COVID-19\n\nMethodsThis randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), is assessing multiple possible treatments in patients hospitalised for COVID-19. In this initial assessment of DMF, performed at 27 UK hospitals, eligible and consenting adults were randomly allocated (1:1) to either usual standard of care alone or usual standard of care plus DMF 120mg twice daily for 2 days followed by 240mg twice daily for 8 days, or until discharge if sooner. The primary outcome was clinical status on day 5 measured on a seven-point ordinal scale, assessed using a proportional odds model. Secondary outcomes were time to sustained improvement in clinical status, time to discharge, day 5 peripheral blood oxygenation, day 5 C-reactive protein, and improvement in day 10 clinical status. The trial is registered with ISRCTN (50189673) and clinicaltrials.gov (NCT04381936).\n\nFindingsBetween 2 March 2021 and 18 November 2021, 713 patients were enrolled in the DMF evaluation, of whom 356 were randomly allocated to receive usual care plus DMF, and 357 to usual care alone. 95% of patients were receiving corticosteroids as part of routine care. There was no evidence of a beneficial effect of DMF on clinical status at day 5 (common odds ratio of unfavourable outcome 1.12; 95% CI 0.85-1.46; p=0.42). There was no significant effect of DMF on any secondary outcome. As expected, DMF caused flushing and gastrointestinal symptoms, each in around 6% of patients, but no new adverse effects were identified.\n\nInterpretationIn adults hospitalised with COVID-19, DMF was not associated with an improvement in clinical outcomes.\n\nFundingUK Research and Innovation (Medical Research Council) and National Institute of Health Research (Grant ref: MC_PC_19056).", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "- RECOVERY Collaborative Group", - "author_inst": "" - }, - { - "author_name": "Peter W Horby", - "author_inst": "Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom" - }, - { - "author_name": "Leon Peto", - "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" - }, - { - "author_name": "Natalie Staplin", - "author_inst": "MRC Population Health Research Unit, University of Oxford, Oxford, United Kingdom" - }, - { - "author_name": "Mark Campbell", - "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" - }, - { - "author_name": "Guilherme Pessoa-Amorim", - "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" - }, - { - "author_name": "Marion Mafham", - "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" - }, - { - "author_name": "Jonathan R Emberson", - "author_inst": "MRC Population Health Research Unit, University of Oxford, Oxford, United Kingdom" - }, - { - "author_name": "Richard Stewart", - "author_inst": "Milton Keynes University Hospital NHS Foundation Trust" - }, - { - "author_name": "Benjamin Prudon", - "author_inst": "North Tees and Hartlepool NHS Foundation Trust" - }, - { - "author_name": "Alison Uriel", - "author_inst": "Manchester University NHS Foundation Trust" - }, - { - "author_name": "Christopher A Green", - "author_inst": "University Hospitals Birmingham NHS Foundation Trust" - }, - { - "author_name": "Devesh J Dhasmana", - "author_inst": "Victoria Hospital Kirkcaldy, NHS Fife" - }, - { - "author_name": "Flora Malein", - "author_inst": "Liverpool University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Jaydip Majumdar", - "author_inst": "Mid Cheshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Paul Collini", - "author_inst": "Sheffield Teaching Hospitals NHS Foundation Trust" - }, - { - "author_name": "Jack Shurmer", - "author_inst": "Bolton NHS Foundation Trust" - }, - { - "author_name": "Bryan Yates", - "author_inst": "Northumbria Healthcare NHS Foundation Trust" - }, - { - "author_name": "J Kenneth Baillie", - "author_inst": "Roslin Institute, University of Edinburgh" - }, - { - "author_name": "Maya H Buch", - "author_inst": "Centre for Musculoskeletal Research, University of Manchester, Manchester, United Kingdom" - }, - { - "author_name": "Jeremy N Day", - "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam" - }, - { - "author_name": "Saul N Faust", - "author_inst": "NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University of Southampton, Southampton, United Kingdom" - }, - { - "author_name": "Thomas Jaki", - "author_inst": "University of Regensburg, Germany" - }, - { - "author_name": "Katie Jeffery", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Edmund Juszczak", - "author_inst": "School of Medicine, University of Nottingham, Nottingham, United Kingdom" - }, - { - "author_name": "Marian Knight", - "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" - }, - { - "author_name": "Wei Shen Lim", - "author_inst": "School of Medicine, University of Nottingham, Nottingham, United Kingdom" - }, - { - "author_name": "Alan Montgomery", - "author_inst": "School of Medicine, University of Nottingham, Nottingham, United Kingdom" - }, - { - "author_name": "Andrew Mumford", - "author_inst": "School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom" - }, - { - "author_name": "Kathryn Rowan", - "author_inst": "Intensive Care National Audit & Research Centre, London, United Kingdom" - }, - { - "author_name": "Guy Thwaites", - "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam" - }, - { - "author_name": "Richard Haynes", - "author_inst": "MRC Population Health Research Unit, University of Oxford, Oxford, United Kingdom" - }, - { - "author_name": "Martin Landray", - "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.09.23.22280279", "rel_title": "Determinants of self-reported health status during COVID-19 lockdown among surveyed Ecuadorian population: a cross sectional study", @@ -187238,6 +189191,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.09.22.509123", + "rel_title": "Generation and functional analysis of defective viral genomes during SARS-CoV-2 infection", + "rel_date": "2022-09-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.22.509123", + "rel_abs": "Defective viral genomes (DVGs) have been identified in many RNA viruses as a major factor influencing antiviral immune response and viral pathogenesis. However, the generation and function of DVGs in SARS-CoV-2 infection are less known. In this study, we elucidated DVG generation in SARS-CoV-2 and its relationship with host antiviral immune response. We observed DVGs ubiquitously from RNA-seq datasets of in vitro infections and autopsy lung tissues of COVID-19 patients. Four genomic hotspots were identified for DVG recombination and RNA secondary structures were suggested to mediate DVG formation. Functionally, bulk and single cell RNA-seq analysis indicated the IFN stimulation of SARS-CoV-2 DVGs. We further applied our criteria to the NGS dataset from a published cohort study and observed significantly higher DVG amount and frequency in symptomatic patients than that in asymptomatic patients. Finally, we observed unusually high DVG frequency in one immunosuppressive patient up to 140 days after admitted to hospital due to COVID-19, first-time suggesting an association between DVGs and persistent viral infections in SARS-CoV-2. Together, our findings strongly suggest a critical role of DVGs in modulating host IFN responses and symptom development, calling for further inquiry into the mechanisms of DVG generation and how DVGs modulate host responses and infection outcome during SARS-CoV-2 infection.\n\nImportanceDefective viral genomes (DVGs) are ubiquitously generated in many RNA viruses, including SARS-CoV-2. Their interference activity to full-length viruses and IFN stimulation provide them the potential for novel antiviral therapies and vaccine development. SARS-CoV-2 DVGs are generated through the recombination of two discontinuous genomic fragments by viral polymerase complex and the recombination is also one of the major mechanisms for the emergence of new coronaviruses. Focusing on the generation and function of SARS-CoV-2 DVGs, these studies identify new hotspots for non-homologous recombination and strongly suggest that the secondary structures within viral genomes mediate the recombination. Furthermore, these studies provide the first evidence for IFN stimulation activity of de novo DVGs during natural SARS-CoV-2 infection. These findings set up the foundation for further mechanism studies of SARS-CoV-2 recombination and provide the evidence to harness DVGs immunostimulatory potential in the development of vaccine and antivirals for SARS-CoV-2.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Terry Zhou", + "author_inst": "University of Rochester" + }, + { + "author_name": "Nora J. Gilliam", + "author_inst": "University of Rochester" + }, + { + "author_name": "Sizhen Li", + "author_inst": "Oregon State University" + }, + { + "author_name": "Simone Spaudau", + "author_inst": "University of Rochester Medical Center" + }, + { + "author_name": "Raven Osborn", + "author_inst": "University of Rochester" + }, + { + "author_name": "Christopher S Anderson", + "author_inst": "University of Rochester" + }, + { + "author_name": "Thomas J. Mariani", + "author_inst": "University of Rochester" + }, + { + "author_name": "Juilee Thakar", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Stephen Dewhurst", + "author_inst": "University of Rochester" + }, + { + "author_name": "David H Mathews", + "author_inst": "University of Rochester Medical Center" + }, + { + "author_name": "Liang Huang", + "author_inst": "Oregon State University" + }, + { + "author_name": "Yan Sun", + "author_inst": "The University of Rochester Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.09.22.508962", "rel_title": "Pharmacological inhibition of bromodomain and extra-terminal proteins induces NRF-2-mediated inhibition of SARS-CoV-2 replication and is subject to viral antagonism", @@ -188313,29 +190329,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.09.22.509013", - "rel_title": "Evolution of new variants of SARS-COV-2 during the pandemic: mutation limited or selection limited?", - "rel_date": "2022-09-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.22.509013", - "rel_abs": "The recent pandemic caused by SARS-Cov-2 has witnessed an evolving succession of variants of the virus. While the phenomenon of invasion by immunity evading variants is known for other viruses such as influenza, the dynamics of the ecological and evolutionary process in the succession is little known. Since during the Covid-19 pandemic, large scale epidemiological data were collected and made available in the public domain, it is possible to seek answers to a number of evolutionary questions, which will also have public health implications. We list multiple alternative hypotheses about the origin and invasion of the variants and evaluate them in the light of epidemiological data. Our analysis shows that invasion by novel variants is selection limited and not mutation limited. Further novel variants are not the necessary and sufficient causes of the repeated waves during the pandemic. Rather there is substantial overlap between the conditions leading to a wave and those favoring selection of a partial immune evading variant. This is likely to lead to an association between invasion by new variant and the rise of a new wave. But the association is not sufficiently strong and does not support a causal role of the new variant. The dynamics of interaction between epidemiological processes and selection on viral variants have many public health implications that can guide future policies for effective control of infectious epidemics.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Srashti Bajpai", - "author_inst": "School of Biology, MIT World Peace University, Pune, India" - }, - { - "author_name": "Milind Watve", - "author_inst": "Independent Researcher" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2022.09.21.508960", "rel_title": "Host specific sensing of coronaviruses and picornaviruses by the CARD8 inflammasome", @@ -189196,6 +191189,37 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2022.09.21.508832", + "rel_title": "PepGM: A probabilistic graphical model for taxonomic inference of viral proteome samples with associated confidence scores", + "rel_date": "2022-09-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.21.508832", + "rel_abs": "MotivationInferring taxonomy in mass spectrometry-based shotgun proteomics is a complex task. In multi-species or viral samples of unknown taxonomic origin, the presence of proteins and corresponding taxa must be inferred from a list of identified peptides which is often complicated by protein homology: many proteins do not only share peptides within a taxon but also between taxa. However, correct taxonomic identification is crucial when identifying different viral strains with high sequence homology - considering, e.g., the different epidemiological characteristics of the various strains of SARS-CoV-2. Additionally, many viruses mutate frequently, further complicating the correct assignment of virus proteomic samples.\n\nResultsWe present PepGM, a probabilistic graphical for the taxonomic assignment of virus proteomic samples with strain-level resolution and associated confidence scores. PepGM combines the results of a standard proteomic database search algorithm with belief propagation to calculate the marginal distributions, and thus confidence score, for potential taxonomic assignments. We demonstrate the performance of PepGM using several publicly available virus proteomic datasets, showing its strain-level resolution performance. In two out of eight cases, the taxonomic assignments were only correct on species level, which PepGM clearly indicates by lower confidence scores.\n\nAvailability and ImplementationPepGM is written in Python and embedded into a Snakemake workflow. Its is available at https://github.com/BAMeScience/PepGM", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Tanja Holstein", + "author_inst": "Federal Institute for Materials Research, VIB-UGent Center for Medical Biotechnology and Department of Biomolecular Medicine, Ghent University" + }, + { + "author_name": "Franziska Kistner", + "author_inst": "Federal Institute for Materials Research" + }, + { + "author_name": "Lennart Martens", + "author_inst": "VIB-UGent Center for Medical Biotechnology and Department of Biomolecular Medicine, Ghent University" + }, + { + "author_name": "Thilo Muth", + "author_inst": "Federal Institute for Materials Research" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.09.21.508870", "rel_title": "Association of polymorphisms of IL-6 pathway genes (IL6, IL6R and IL6ST) with COVID-19 severity in an Amazonian population.", @@ -190347,49 +192371,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.09.17.22280043", - "rel_title": "Lung remodeling regions in long-term Covid-19 feature basal epithelial cell reprogramming", - "rel_date": "2022-09-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.17.22280043", - "rel_abs": "Respiratory viruses, including SARS-CoV-2, can trigger chronic lung disease that persists and even progresses after expected clearance of infectious virus. To gain an understanding of this process, we examined a series of consecutive fatal cases of Covid-19 that came to autopsy at 27-51 d after hospital admission. In each patient, we identify a stereotyped bronchiolar-alveolar pattern of lung remodeling with basal epithelial cell hyperplasia and mucinous differentiation. Remodeling regions also feature macrophage infiltration and apoptosis and a marked depletion of alveolar type 1 and 2 epithelial cells. This entire pattern closely resembles findings from an experimental model of post-viral lung disease that requires basal-epithelial stem cell growth, immune activation, and differentiation. The present results thereby provide evidence of possible basal epithelial cell reprogramming in long-term Covid-19 as well and thereby a pathway for explaining and correcting lung dysfunction in this type of disease.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Kangyun Wu", - "author_inst": "Washington University St. Louis" - }, - { - "author_name": "Yong Zhang", - "author_inst": "Washington University St. Louis" - }, - { - "author_name": "Stephen R Austin", - "author_inst": "Washington University St. Louis" - }, - { - "author_name": "Huqing Yin Declue", - "author_inst": "Washington University St. Louis" - }, - { - "author_name": "Derek E Byers", - "author_inst": "Washington University St. Louis" - }, - { - "author_name": "Erika C Crouch", - "author_inst": "Washington University St. Louis" - }, - { - "author_name": "Michael J Holtzman", - "author_inst": "Washington University St Louis" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2022.09.16.22279736", "rel_title": "Comparison of a prototype SARS-CoV-2 lateral flow immunoassay with the BinaxNOW\u2122 COVID-19 Antigen CARD", @@ -191086,6 +193067,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.09.15.22279948", + "rel_title": "Differential contagiousness of respiratory disease across the United States", + "rel_date": "2022-09-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.15.22279948", + "rel_abs": "The initial contagiousness of a communicable disease within a given population is quantified by the basic reproduction number, denoted R0. The value of R0 gives the expected number of new cases generated by an infectious person in a wholly susceptible population and depends on both pathogen and population properties. On the basis of compartmental models that reproduce Coronavirus Disease 2019 (COVID-19) surveillance data, we estimated region-specific R0 values for 280 of 384 metropolitan statistical areas (MSAs) in the United States (US), which account for 95% of the US population living in urban areas and 82% of the total population. Our estimates range from 1.9 to 7.7 and quantify the relative susceptibilities of regional populations to spread of respiratory diseases.\n\nOne-Sentence SummaryInitial contagiousness of Coronavirus Disease 2019 varied over a 4-fold range across urban areas of the United States.\n\nLA-UR-22-29514", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Abhishek Mallela", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Yen Ting Lin", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "William S Hlavacek", + "author_inst": "Los Alamos National Laboratory" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.09.13.22279837", "rel_title": "Hospital contact patterns and vulnerability to SARS-CoV-2 outbreaks", @@ -192285,97 +194293,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.09.15.22279897", - "rel_title": "Angiotensin 1-7 in severe COVID-19 patients: a phase 1 clinical trial", - "rel_date": "2022-09-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.15.22279897", - "rel_abs": "BackgroundThe coronavirus-related disease (COVID-19) is mainly characterized by a respiratory involvement, with few available therapeutics for critically cases. The renin-angiotensin system (RAS) has a relevant role in the pathogenesis of COVID-19, as the virus enter hosts cells via the angiotensin-converting enzyme 2 (ACE2) and RAS disequilibrium promote inflammation and fibrosis. Exogenous angiotensin-(1-7) might modulate RAS in COVID-19 patients; however, no data on its safety are available in this setting.\n\nMethodsThis investigator-initiated, open label, phase I clinical trial was conducted to test the safety of intravenous administration of Angiotensin-(1-7) in severe COVID-19 patients admitted in two intensive care units (ICU) in Belo Horizonte, Brazil. In addition to standard of care, intravenous administration of Angiotensin-(1-7) was started at 5 mcg/Kg*day and increased to 10 mcg/Kg*day after 24 hours and continued for a maximum of 7 days or until ICU discharge. The rate of serious adverse events (SAEs) served as the primary outcome of the study.\n\nResultsBetween August and December 2020, 28 patients were included (mean age of 55.8{+/-}12.0 years). All but one patient underwent dose escalation after 24 hours and 8 (28.5%) received the treatment until day 7. No significant differences in mean blood pressure and heart rate were observed before and after the initiation of the drug. During the period of intervention, 5/28 (17.8%) patients required vasopressors, 4 at low dose norepinephrine (i.e. <0.05 mcg/kg*min), while one patient required higher doses because of septic shock. One patient presented with sinus bradycardia, which was considered possibly related to the study drug and resolved after discontinuation. Six patients (21.4%) died before ICU discharge.\n\nConclusionsIntravenous infusion of Angiotensin-(1-7) up to 10 mcg/Kg*day was safe in severe COVID-19 patients and could represent a potential therapeutic strategy in this setting.\n\nTrial RegistrationRegistro Brasileiro de Ensaios Clinicos, UTN code: U1111-1255-7167, registered on 08/05/2020; ClinicalTrials.gov Identifier: NCT04633772; retrospectively registered on November 18 2020", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Ana Luiza Valle Martins", - "author_inst": "Federal University of Minas Gerais, Belo Horizonte, Brasil" - }, - { - "author_name": "Filippo Annoni", - "author_inst": "Hopital Erasme, Universite' libre de Bruxelles" - }, - { - "author_name": "Filipe Alex da Silva", - "author_inst": "Federal University of Minas Gerais, Belo Horizonte, Brasil" - }, - { - "author_name": "Lucas Bolais-Ramos", - "author_inst": "Federal University of Minas Gerais, Belo Horizonte, Brasil" - }, - { - "author_name": "Gisele Capanema de Oliveira", - "author_inst": "Federal University of Minas Gerais, Belo Horizonte, Brasil" - }, - { - "author_name": "Alana Helen dos Santos Matos", - "author_inst": "Federal University of Minas Gerais, Belo Horizonte, Brasil" - }, - { - "author_name": "Maria Cecilia Jardim Heyden", - "author_inst": "Federal University of Minas Gerais, Belo Horizonte, Brasil" - }, - { - "author_name": "Beatriz Dias Pinheiro", - "author_inst": "Federal University of Minas Gerais, Belo Horizonte, Brasil" - }, - { - "author_name": "Natalia Abdo Rodrigues", - "author_inst": "Federal University of Minas Gerais, Belo Horizonte, Brasil" - }, - { - "author_name": "Danilo Augusto Alves Pereira", - "author_inst": "Federal University of Minas Gerais, Belo Horizonte, Brasil" - }, - { - "author_name": "Mirella Monique Lana Diniz", - "author_inst": "Federal University of Minas Gerais, Belo Horizonte, Brasil" - }, - { - "author_name": "Thuanny Granato Fonseca Silva", - "author_inst": "Federal University of Minas Gerais, Belo Horizonte, Brasil" - }, - { - "author_name": "Alexandre Carvalho Cardoso", - "author_inst": "Federal University of Minas Gerais, Belo Horizonte, Brasil" - }, - { - "author_name": "Juliana Carvalho Martins", - "author_inst": "Federal University of Minas Gerais, Belo Horizonte, Brasil" - }, - { - "author_name": "Daisy Motta-Santos", - "author_inst": "Federal University of Minas Gerais, Belo Horizonte, Brasil" - }, - { - "author_name": "Maria Jose Campagnole-Santos", - "author_inst": "Federal University of Minas Gerais, Belo Horizonte, Brasil" - }, - { - "author_name": "Thiago Verano-Braga", - "author_inst": "Federal University of Minas Gerais, Belo Horizonte, Brasil" - }, - { - "author_name": "Fabio Silvio Taccone", - "author_inst": "Hopital Erasme, Universite' Libre de Bruxelles" - }, - { - "author_name": "Robson A S Santos", - "author_inst": "Federal University of Minas Gerais, Belo Horizonte, Brasil" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2022.09.11.22279831", "rel_title": "The impact of COVID-19 on population cancer screening programs in Australia: modelled evaluations for breast, bowel and cervical cancer", @@ -193168,6 +195085,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2022.09.15.22279970", + "rel_title": "Severe fatigue as symptom of long COVID is characterized by increased expression of inflammatory genes in monocytes, increased serum pro-inflammatory cytokines, and increased CD8+ T-lymphocytes. A putative dysregulation of the immune-brain axis, the coagulation process, and auto-inflammation to explain the diversity of long COVID symptoms", + "rel_date": "2022-09-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.15.22279970", + "rel_abs": "BackgroundA significant proportion of patients with SARS-CoV-2 infection develops long COVID with fatigue as one of the most disabling symptoms. We performed clinical and immunologic profiling of fatigued and non-fatigued long COVID patients and age and gender matched healthy controls (HCs).\n\nMethodsWe included 37 long COVID patients with and 36 without severe fatigue and assessed inflammation-related monocyte gene expression, serum levels of inflammatory cytokines, and leukocyte and lymphocyte subsets 3-6 months after hospital discharge, and followed clinical symptoms up to one year.\n\nResultsLong COVID with fatigue represented a severe variant with many symptoms (median 9 [IQR 5.0-10.0] symptoms) and signs of cognitive failure (41%) and depression (>24%). Symptoms persisted up to one year follow-up. Fatigued patients showed increased expression of inflammatory genes in monocytes, increased serum IL-6, TNF-, galectin-9, and CXCL10, and increased CD8+ T-lymphocytes compared to HCs.\n\nNon-fatigued long COVID patients were arbitrarily divided in those with moderately severe disease (4 [2.5-5.0] symptoms, primarily impaired fitness, n=25) and those with mild disease (1 [1.0-2.0] symptom, n=11). Symptoms in non-fatigued long COVID patients persisted up to one year follow-up. Moderately severe patients showed reduced CD45RO- naive CD4+ T-lymphocytes and CD25+FOXP3+ regulatory CD4+ T-lymphocytes and limited monocyte and serum (galectin-9) inflammation. Mild patients showed monocyte and serum (IL-6, galectin-9) inflammation and decreased CD4+ T-lymphocyte subsets (T-helper 1 cells).\n\nConclusionLong COVID with fatigue is associated with many concurrent and persistent symptoms up to one year after hospitalization and with clear signs of low grade inflammation and increased CD8+ T-lymphocytes. We showed that long COVID is a clinical and immunologic heterogeneous disorder. Diagnostic tools and personalized therapies combatting the diverse immune abnormalities might be required to alleviate the persisting disabling complaints of the patients.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Julia C Berentschot", + "author_inst": "Erasmus MC, University Medical Center Rotterdam, The Netherlands." + }, + { + "author_name": "Hemmo A Drexhage", + "author_inst": "Erasmus MC, University Medical Center Rotterdam, The Netherlands." + }, + { + "author_name": "Daniel A Aynekulu Mersha", + "author_inst": "Erasmus MC, University Medical Center Rotterdam, The Netherlands." + }, + { + "author_name": "Annemarie JM Wijkhuijs", + "author_inst": "Erasmus MC, University Medical Center Rotterdam, The Netherlands." + }, + { + "author_name": "Corine H GeurtsvanKessel", + "author_inst": "Erasmus MC, University Medical Center Rotterdam, The Netherlands." + }, + { + "author_name": "Marion PG Koopmans", + "author_inst": "Erasmus MC, University Medical Center Rotterdam, The Netherlands." + }, + { + "author_name": "Jolanda Voermans", + "author_inst": "Erasmus MC, University Medical Center Rotterdam, The Netherlands." + }, + { + "author_name": "Majanka H Heijenbrok-Kal", + "author_inst": "Erasmus MC, University Medical Center Rotterdam, The Netherlands." + }, + { + "author_name": "L. Martine Bek", + "author_inst": "Erasmus MC, University Medical Center Rotterdam, The Netherlands." + }, + { + "author_name": "Gerard M Ribbers", + "author_inst": "Erasmus MC, University Medical Center Rotterdam, The Netherlands." + }, + { + "author_name": "Rita JG van den Berg-Emons", + "author_inst": "Erasmus MC, University Medical Center Rotterdam, The Netherlands." + }, + { + "author_name": "Joachim GJV Aerts", + "author_inst": "Erasmus MC, University Medical Center Rotterdam, The Netherlands." + }, + { + "author_name": "Willem A Dik", + "author_inst": "Erasmus MC, University Medical Center Rotterdam, The Netherlands." + }, + { + "author_name": "Merel E Hellemons", + "author_inst": "Erasmus MC, University Medical Center Rotterdam, The Netherlands." + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.09.13.22279543", "rel_title": "A Cross-Sectional Study of Quantitative CT Measurements Associated with the Diffusion Capacity of the Lung in Recovered COVID-19 Patients with Clear Chest CTs", @@ -194151,57 +196139,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, - { - "rel_doi": "10.1101/2022.09.13.22279908", - "rel_title": "Real-World Effectiveness of Nirmatrelvir/Ritonavir in Preventing Hospitalization Among Patients With COVID-19 at High Risk for Severe Disease in the United States: A Nationwide Population-Based Cohort Study", - "rel_date": "2022-09-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.13.22279908", - "rel_abs": "ObjectivesThe aim of this analysis was to describe nirmatrelvir/ritonavir real-world effectiveness in preventing hospitalization among high-risk US COVID-19 patients during SARS-CoV-2 Omicron predominance.\n\nDesignAn ongoing population-based cohort study with retrospective and prospective collection of electronic healthcare data in the United States.\n\nMethodsData for this analysis were collected from the US Optum(R) de-identified COVID-19 Electronic Health Record (EHR) dataset during December 22, 2021-June 8, 2022. Key eligibility criteria for inclusion in the database analysis were [≥]12-years-old; positive SARS-CoV-2 test, COVID-19 diagnosis, or nirmatrelvir/ritonavir prescription; and high risk of severe COVID-19 based on demographic/clinical characteristics. Potential confounders between groups were balanced using propensity score matching (PSM). Immortal time bias was addressed.\n\nOutcome measuresHospitalization rates within 30 (primary analysis) or 15 (sensitivity analysis) days from COVID-19 diagnosis overall and within subgroups were evaluated.\n\nResultsBefore PSM, the nirmatrelvir/ritonavir group (n=2811) was less racially diverse, older, and had higher COVID-19 vaccination rates and a greater number of comorbidities than the non-nirmatrelvir/ritonavir group (n=194,542). Baseline characteristics were well balanced across groups (n=2808 and n=10,849, respectively) after PSM. Incidence of hospitalization (95% CI) within 30 days was 1.21% (0.84%-1.69%) for the nirmatrelvir/ritonavir group and 6.94% (6.03%-7.94%) for the non-nirmatrelvir/ritonavir group, with a hazard ratio (95% CI) of 0.16 (0.11-0.22; 84% relative risk reduction). Incidence within 15 days was 0.78% (0.49%-1.18%) for the nirmatrelvir/ritonavir group and 6.54% (5.65%-7.52%) for the non-nirmatrelvir/ritonavir group; hazard ratio 0.11 (0.07-0.17; 89% relative risk reduction). Nirmatrelvir/ritonavir was effective in African American patients (hazard ratio, 0.35 [0.15-0.83]; 65% relative risk reduction). Relative risk reductions were comparable with overall results across ages and among vaccinated patients.\n\nConclusionsReal-world nirmatrelvir/ritonavir effectiveness against hospitalization during the Omicron era supports EPIC-HR efficacy among high-risk patients. Future research should confirm these early real-world results and address limitations.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Xiaofeng Zhou", - "author_inst": "Pfizer Inc." - }, - { - "author_name": "Scott P Kelly", - "author_inst": "Pfizer Inc" - }, - { - "author_name": "Caihua Liang", - "author_inst": "Pfizer Inc." - }, - { - "author_name": "Ling Li", - "author_inst": "Pfizer Inc" - }, - { - "author_name": "Rongjun Shen", - "author_inst": "Pfizer Inc." - }, - { - "author_name": "Heidi Leister-Tebbe", - "author_inst": "Pfizer.Inc" - }, - { - "author_name": "Steven G Terra", - "author_inst": "Pfizer Inc." - }, - { - "author_name": "Michael Gaffney", - "author_inst": "Pfizer Inc." - }, - { - "author_name": "Leo J Russo", - "author_inst": "Pfizer Inc." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.09.13.22279833", "rel_title": "The Effects of Long COVID-19, its Severity, and the Need for Immediate Attention: Analysis of Clinical Trials and Twitter data", @@ -194922,6 +196859,113 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2022.09.13.507852", + "rel_title": "IL-10 suppresses T cell expansion while promoting tissue-resident memory cell formation during SARS-CoV-2 infection in rhesus macaques", + "rel_date": "2022-09-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.13.507852", + "rel_abs": "The pro- and anti-inflammatory pathways that determine the balance of inflammation and viral control during SARS-CoV-2 infection are not well understood. Here we examine the roles of IFN{gamma} and IL-10 in regulating inflammation, immune cell responses and viral replication during SARS-CoV-2 infection of rhesus macaques. IFN{gamma} blockade tended to decrease lung inflammation based on 18FDG-PET/CT imaging but had no major impact on innate lymphocytes, neutralizing antibodies, or antigen-specific T cells. In contrast, IL-10 blockade transiently increased lung inflammation and enhanced accumulation of virus-specific T cells in the lower airways. However, IL-10 blockade also inhibited the differentiation of virus-specific T cells into airway CD69+CD103+ TRM cells. While virus-specific T cells were undetectable in the nasal mucosa of all groups, IL-10 blockade similarly reduced the frequency of total TRM cells in the nasal mucosa. Neither cytokine blockade substantially affected viral load and infection ultimately resolved. Thus, in the macaque model of mild COVID-19, the pro- and anti-inflammatory effects of IFN{gamma} and IL-10 have no major role in control of viral replication. However, IL-10 has a key role in suppressing the accumulation of SARS-CoV-2-specific T cells in the lower airways, while also promoting TRM at respiratory mucosal surfaces.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Christine E. Nelson", + "author_inst": "NIH/NIAID" + }, + { + "author_name": "Taylor W. Foreman", + "author_inst": "NIH/NIAID" + }, + { + "author_name": "Keith D. Kauffman", + "author_inst": "NIH/NIAID" + }, + { + "author_name": "Shunsuke Sakai", + "author_inst": "NIH/NIAID" + }, + { + "author_name": "Sydnee T. Gould", + "author_inst": "University of California, Berkley" + }, + { + "author_name": "Joel D. Fleegle", + "author_inst": "NIH/NIAID" + }, + { + "author_name": "Felipe Gomez", + "author_inst": "NIH/NIAID" + }, + { + "author_name": "- NIAID/DIR Tuberculosis Imaging Program", + "author_inst": "-" + }, + { + "author_name": "Cyril Le Nouen", + "author_inst": "NIH/NIAID" + }, + { + "author_name": "Xueqiao Liu", + "author_inst": "NIH/NIAID" + }, + { + "author_name": "Tracey L. Burdette", + "author_inst": "NIH/NIAID" + }, + { + "author_name": "Nicole L. Garza", + "author_inst": "NIH/NIAID" + }, + { + "author_name": "Bernard A. P. Lafont", + "author_inst": "NIH/NIAID" + }, + { + "author_name": "Kelsie Brooks", + "author_inst": "NIH/NIAID" + }, + { + "author_name": "Cecilia S. Lindestam Arlehamn", + "author_inst": "La Jolla Institute for Immunology" + }, + { + "author_name": "Daniela Weiskopf", + "author_inst": "La Jolla Institute For Allergy & Immunology" + }, + { + "author_name": "Alessandro Sette", + "author_inst": "La Jolla Institute for Allergy & Immunology" + }, + { + "author_name": "Heather D. Hickman", + "author_inst": "NIH/NIAID" + }, + { + "author_name": "Ursula J. Buchholz", + "author_inst": "NIH/NIAID" + }, + { + "author_name": "Reed F. Johnson", + "author_inst": "NIH/NIAID" + }, + { + "author_name": "Jason M. Brenchley", + "author_inst": "NIH/NIAID" + }, + { + "author_name": "Laura E. Via", + "author_inst": "NIH/NIAID" + }, + { + "author_name": "Daniel L. Barber", + "author_inst": "NIH/NIAID" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.09.12.505486", "rel_title": "High throughput Bioluminescent assay to characterize and monitor the activity of SARS-CoV-2 Methyltransferases", @@ -196129,85 +198173,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2022.09.07.22279668", - "rel_title": "LEAF- 4L6715 enhances oxygenation in patients with acute respiratory distress syndrome (ARDS) due to severe COVID-19: Final results of a phase I/II clinical trial", - "rel_date": "2022-09-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.07.22279668", - "rel_abs": "LEAF-4L6715 is a liposomal formulation encapsulating transcrocetin (TC) developed to enhance the diffusion of oxygen in the body. Here, we report the final results of the phase I/II clinical trial (NCT04378920; EUDRACT2020-001393-30) initiated to identify an optimal regimen and to assess the activity of TC in the context of acute respiratory distress syndrome (ARDS). More specifically, LEAF-4L6715 was developed to treat patients with ARDS due to severe SARS-CoV-2 infection who have a ratio of partial arterial pressure to inspired fraction of oxygen (PaO2/FiO2 ratio) <200 treated with artificial ventilation support in an intensive care unit.\n\nA total of 37 patients were treated (across 6 dosing cohorts) with LEAF-4L6715 given as an intravenous infusion for over 90 minutes. The dose of LEAF-4L6715 was increased until the transaminase levels were elevated and 4 grade 3 events occurred among 8 patients. The recommended dosage was determined to be a fixed concentration of 300 mg administered every 12 hours. An improvement in the PaO2/FiO2 ratio and SOFA score was observed. The overall 28-day survival rate of 81%.\n\nThis study identified the recommended dose for LEAF 4L6715 and the dose-limiting toxicity and showed an overall favorable risk/benefit profile. These preliminary findings are promising for the activity of LEAF-4L6715 but will require confirmation in a randomized phase III trial.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Paul-Michel Mertes", - "author_inst": "University Hospital of Strasbourg, France" - }, - { - "author_name": "Xavier Delabranche", - "author_inst": "Institut de Cancerologie Strasbourg Europe, Strasbourg, France" - }, - { - "author_name": "Pierre Coliat", - "author_inst": "Institut de Cancerologie Strasbourg Europe" - }, - { - "author_name": "Anne-Claude Roche", - "author_inst": "University Hospital of Strasbourg, France" - }, - { - "author_name": "Olivier Collange", - "author_inst": "University Hospital of Strasbourg, France" - }, - { - "author_name": "Manon Voegelin", - "author_inst": "Institut de Cancerologie Strasbourg Europe, Strasbourg, France" - }, - { - "author_name": "Alexandre Bernard", - "author_inst": "Institut de Cancerologie Strasbourg Europe, Strasbourg, France" - }, - { - "author_name": "Navreet Dhindsa", - "author_inst": "LEAF4Life, Inc. Woburn, MA, USA" - }, - { - "author_name": "Hannah Xu", - "author_inst": "LEAF4Life, Inc. Woburn, MA, USA" - }, - { - "author_name": "Bolin Geng", - "author_inst": "LEAF4Life, Inc. Woburn, MA, USA" - }, - { - "author_name": "Clet Niyikiza", - "author_inst": "LEAF4Life, Inc. Woburn, MA, USA" - }, - { - "author_name": "Victor Moyo", - "author_inst": "LEAF4Life, Inc. Woburn, MA, USA" - }, - { - "author_name": "Claire Bourbon", - "author_inst": "Plateforme de chimie Biologique integrative de Strasbourg (PCBIS), UAR 3286 CNRS/Universite de Strasbourg, Institut du Medicament de Strasbourg (IMS), Illkirch-" - }, - { - "author_name": "Pascal Villa", - "author_inst": "Plateforme de chimie Biologique integrative de Strasbourg (PCBIS), UAR 3286 CNRS/Universite de Strasbourg, Institut du Medicament de Strasbourg (IMS), Illkirch-" - }, - { - "author_name": "Alexandre Detappe", - "author_inst": "Institut de Cancerologie Strasbourg Europe, Strasbourg, France" - }, - { - "author_name": "Xavier Pivot", - "author_inst": "Institut de Cancerologie Strasbourg Europe, Strasbourg, France" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2022.09.06.22279656", "rel_title": "The Relationship Between Symptoms and Job Loss among Japanese Workers During the COVID-19 Pandemic: A Prospective Cohort Study", @@ -197180,6 +199145,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.09.07.22279669", + "rel_title": "SARS-CoV-2 seroprevalence on the north coast of Peru: A cross-sectional study after the first wave", + "rel_date": "2022-09-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.07.22279669", + "rel_abs": "BackgroundThe devastating repercussions of COVID-19 were felt in developing nations like Peru. However, few studies have been conducted in these countries. To make good decisions about public health, it is important to understand how the disease is spread in our area.\n\nMethodology/Principal findingsAn observational, cross-sectional study was performed between November 11th and November 30th, 2020. In Puerto Pizarro, one out of every four homes was invited to participate in a systematic randomized sampling. Individuals were screened for the qualitative detection of anti-SARS-CoV-2 nucleocapsid (N) protein antibodies and anti-SARS-CoV-2 spike RBD with a rapid chromatographic immunoassay. An adult of legal age was selected, and an additional molecular test (RT-PCR) was taken to look for active COVID-19 cases.\n\nConclusions/SignificanceThis study shows an adjusted seroprevalence of 24.72% posterior to the first wave of COVID-19 in Tumbes. When adjusted by participant characteristics, women had higher adjusted seroprevalence compared to men (213/356 vs 143/356 [28.01 % vs 21.18 %], p=0.005). More than 20% of IgG seropositive cases belong to the age group under 16 years old. Asymptomatic individuals with recent infections were 66.3% (IgM and IgM/IgG) across all age groups. No association between positive seroprevalence and water supply, water resources, or sanitation services was found. The information is relevant to the Ministry of Healths establishment of a regional program of COVID-19 control and strategic interventions, targeting vulnerable groups and improving vaccination campaigns.\n\nAuthor summaryCOVID-19 had devastating effects on developing countries such as Peru. Its crucial to understand the diseases underlying distribution in our region to create useful dynamics that engage the population in prevention measures. We performed an observational, cross-sectional study between November 11th and November 30th, 2020, in Puerto Pizarro. One out of every four houses was invited to participate, and individuals were screened for the qualitative detection of anti-SARS-CoV-2 antibodies (IgG and IgM) with a rapid test. This study shows an adjusted seroprevalence of 24.72% posterior to the first wave of COVID-19 in Tumbes. Women had a higher adjusted seroprevalence compared to men (213/356 vs 143/356 [28.01 % vs 21.18 %], p=0.005). More than 20% of IgG seropositive cases belong to the age group under 16 years old. Asymptomatic individuals with recent infections were 66.3% (IgM and IgM/IgG) across all age groups. Community participation in epidemiological surveillance strategies is crucial to establish a future follow-up cohort and evaluate the medium-term sequelae of this disease.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Luz M. Moyano", + "author_inst": "Universidad Cesar Vallejo Piura" + }, + { + "author_name": "Angie K. Toledo", + "author_inst": "Universidad Peruana Cayetano Heredia" + }, + { + "author_name": "Jenny Chirinos", + "author_inst": "Universidad Peruana Cayetano Heredia" + }, + { + "author_name": "Percy Mc Quen Vilchez Barreto", + "author_inst": "Universidad Peruana Cayetano Heredia" + }, + { + "author_name": "Sofia Cavalcanti", + "author_inst": "Hospital Amistad Peru Corea Santa Rosa II-2, Piura, Peru" + }, + { + "author_name": "Ricardo Gamboa", + "author_inst": "Universidad Peruana Cayetano Heredia" + }, + { + "author_name": "John Ypanaque", + "author_inst": "Universidad Nacional de Tumbes" + }, + { + "author_name": "Mauro Meza", + "author_inst": "Universidad Nacional de Tumbes" + }, + { + "author_name": "Sheila Noriega", + "author_inst": "Direcci\u00f3n Regional de Salud de Tumbes" + }, + { + "author_name": "Victor Herrera", + "author_inst": "Direcci\u00f3n Regional de Salud de Tumbes" + }, + { + "author_name": "Edgar Bazan", + "author_inst": "Universidad Cesar Vallejo Piura" + }, + { + "author_name": "Alexandra Requena", + "author_inst": "Universidad Nacional de Tumbes" + }, + { + "author_name": "Henry Silva", + "author_inst": "Universidad Nacional de Tumbes" + }, + { + "author_name": "Harold Burgos", + "author_inst": "Direcci\u00f3n Regional de Salud de Tumbes" + }, + { + "author_name": "Franco Le\u00f3n-Jimenez", + "author_inst": "Universidad Norbert Wiener" + }, + { + "author_name": "- Group of Neuroepidemiology and Science of Life of Peru", + "author_inst": "-" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.09.08.22278709", "rel_title": "Are primary care virtual visits associated with higher emergency department use? A cross-sectional analysis from Ontario, Canada", @@ -198179,29 +200223,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2022.09.08.22279714", - "rel_title": "A cross-sectional study of low birth satisfaction among Iranian postpartum women during COVID-19 epidemics fifth wave", - "rel_date": "2022-09-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.08.22279714", - "rel_abs": "BackgroundBirth dissatisfaction may increase the risk for postpartum depression and requests for an elective cesarean for the next birth. The outbreak of COVID-19 pandemic has had a considerable impact on the healthcare systems and their users in many aspects. We investigated predictors of birth satisfaction in a sample of Iranian postpartum women during the COVID-19 epidemics fifth wave.\n\nMethodsThis cross-sectional study was conducted on 601 postpartum women admitted to postpartum wards of Mobini maternity hospital using a convenience sampling method between 2 Aug and 18 September 2021. We collected data on socio-demographic, obstetric, labor and birth, and psychological variables. We used the general linear model and multiple linear regression analyses to determine predictors of birth satisfaction.\n\nResultsThe mean birth satisfaction score was 28.6{+/-}7.3. The percentages of mothers who gave birth by elective and emergency cesarean were 19.5% and 10.8%, respectively. Overall predictors of birth satisfaction were emergency cesarean [-7.463(-9.310, -5.616), instrumental birth [-3.571(-6.907, -0.235)], episiotomy [-2.227 (-3.591, -0.862)], Entonox analgesia [-1.548(-2.726, -0.371)], Well-being score < 50 [-1.812(-3.146, -0.478)], fear of COVID-19 [-1.216(-2.288,, -0.144)], low satisfaction with pregnancy -2.539(-3.952, -1.127) and low satisfaction with spouses support [-2.419(-4.598, -0.240)].\n\nConclusionsDuring the pandemic, fear of COVID-19, low level of well-being, low satisfaction with pregnancy and low satisfaction with spouses support as well as womens experience of emergency cesarean, instrumental birth, episiotomy, and Entonox analgesia, are exerting negative influences on birth satisfaction. To improve birth satisfaction and thus maternal mental health interventions to lower fear of contracting COVID-19 and reduce rates of episiotomy, emergency cesarean, and instrumental birth are recommended.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Forough Mortazavi", - "author_inst": "Sabzevar University of Medical Sciences" - }, - { - "author_name": "Maryam Mehrabadi", - "author_inst": "Sabzevar University of Medical Sciences" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "obstetrics and gynecology" - }, { "rel_doi": "10.1101/2022.09.09.507250", "rel_title": "Mucosal vaccination for SARS-CoV-2 elicits superior systemic T central memory function and cross-neutralizing antibodies against variants of concern", @@ -198906,6 +200927,129 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.09.02.22279542", + "rel_title": "Targeting ATP2B1 impairs PI3K/Akt/Fox-O3 signaling and reduces SARS-COV-2 replication in vivo.", + "rel_date": "2022-09-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.02.22279542", + "rel_abs": "ATP2B1 is a known regulator of calcium (Ca2+) cellular export and homeostasis. Diminished levels of extra- or intra-cellular Ca2+ content have been suggested to block SARS-CoV-2 replication. Here, we demonstrate that a newly nontoxic caloxin-derivative compound (PI-7) inhibits ATP2B1, reduces the extra- and intra-cellular Ca2+ levels and impairs SARS-CoV-2 replication and propagation (VOCs: Delta and Omicron 2), as also measured by inhibition of syncytia in vitro. Furthermore, a FOXO3 transcriptional site of regulation of expression at the 5 end of the ATP2B1 locus, together with a rare homozygous intronic variant in the ATP2B1 locus (rs11337717; chr12:89643729, T>C), are shown to be associated with severity of COVID19 (symptomatic versus asymptomatic patients). Here, we identify the mechanism of action during SARS-CoV-2 infection, which involves the PI3K/Akt signaling pathway, inactivation of FOXO3 (i.e., phosphorylation), and inhibition of transcriptional control of both membrane and reticulum Ca2+ pumps (ATP2B1 and ATP2A1 [i.e., SERCA1], respectively). The pharmacological action of compound PI-7 on sustaining both ATP2B1 and ATP2A1 expression reduces the intracellular cytoplasmic Ca2+ pool and thus negatively influences SARS-CoV-2 replication and propagation. As compound PI-7 shows a lack of toxicity, its prophylactic use as a therapy against the COVID19 pandemic is here proposed.\n\nIn briefDe Antonellis et al. shows the importance of the Ca2+ channel pump ATP2B1 in the regulation of extracellular and intracellular Ca2+ levels that positively influence SARS-CoV-2 replication in human cells. Our study identifies the mechanism of action of SARS-CoV-2 in the regulation of the expression of ATP2B1 and ATP2A1 loci during infection via FOXO3 transcriptional factor. Furthermore, a small caloxin-derivative molecule (compound PI-7) can inhibit ATP2B1 activity, thus resulting in SARS-CoV-2 impairment. In further support, we have identified a genetic variant within the noncoding upstream region of ATP2B1 in symtomatic patients affected by severe COVID19, thus indicating this polymorphism as a genetic predisposition factor to SARS-CoV-2 infection.\n\nHighlightsO_LIAn anti-viral model of network of action for ATP2B1 against SARS-CoV-2 at the intracellular level that involves the PI3K/Akt signaling pathway, inactivation (i.e., phosphorylation) of FOXO3 and its transcriptional control, and inhibition of both membrane and reticulum Ca2+ pumps (i.e., ATP2B1, ATP2A1, respectively).\nC_LIO_LIA new drug and its lack of toxicity \"compound PI-7\", thus envisioning both preventive and therapeutic applications in patients with COVID-19.\nC_LIO_LIThe specificity of action in the context of Ca2+ homeostasis is one of the strategies that coronaviruses (including SARS-CoV-2 and any new VOC, including Omicron 2) use to infect host cells and promote organ dysfunction.\nC_LIO_LITherapeutic applications for compound PI-7 against all other viruses belonging to the Coronoviridae family (e.g., SARS-CoV, MERS-CoV), and against the main families of positive sense ssRNA viruses from other hosts (e.g., Nidovirales), as these are all Ca2+ dependent.\nC_LIO_LIIdentification of a rare homozygous intronic variant in the ATP2B1 locus (rs11337717; chr12:89643729, T>C) that is associated with severity of COVID19 (i.e., symptomatic versus asymptomatic patients). This variant can be used as a marker to identify those patients that might show severe COVID19 following their SARS-COV-2 infection.\nC_LI", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Paqualino de Antonellis", + "author_inst": "Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), Federico II University of Naples, Naples, Italy" + }, + { + "author_name": "Veronica Ferrucci", + "author_inst": "Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), Federico II University of Naples, Naples, Italy" + }, + { + "author_name": "Francesca Bibbo", + "author_inst": "Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), Federico II University of Naples, Naples, Italy" + }, + { + "author_name": "Fatemeh Asadzadeh", + "author_inst": "Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), Federico II University of Naples, Naples, Italy" + }, + { + "author_name": "Francesca Gorini", + "author_inst": "Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), Federico II University of Naples, Naples, Italy" + }, + { + "author_name": "Angelo Boccia", + "author_inst": "CEINGE, Biotecnologie Avanzate, Naples, Italy" + }, + { + "author_name": "Carmen Sorice", + "author_inst": "CEINGE, Biotecnologie Avanzate, Naples, Italy" + }, + { + "author_name": "Roberto Siciliano", + "author_inst": "CEINGE, Biotecnologie Avanzate, Naples, Italy" + }, + { + "author_name": "Roberta Russo", + "author_inst": "Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), Federico II University of Naples, Naples, Italy" + }, + { + "author_name": "Immacolata Andolfo", + "author_inst": "Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), Federico II University of Naples, Naples, Italy" + }, + { + "author_name": "Vito Alessandro Lasorsa", + "author_inst": "CEINGE, Biotecnologie Avanzate, Naples, Italy" + }, + { + "author_name": "Sueva Cantalupo", + "author_inst": "CEINGE, Biotecnologie Avanzate, Naples, Italy" + }, + { + "author_name": "Giovanni Paolella", + "author_inst": "Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), Federico II University of Naples, Naples, Italy" + }, + { + "author_name": "Giovanna Fusco", + "author_inst": "Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute 2, 80055, Naples, Italy" + }, + { + "author_name": "Maurizio Viscardi", + "author_inst": "Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute 2, 80055, Naples, Italy" + }, + { + "author_name": "Sergio Brandi", + "author_inst": "Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute 2, 80055, Naples, Italy" + }, + { + "author_name": "Biancamaria Pierri", + "author_inst": "Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute 2, 80055, Naples, Italy" + }, + { + "author_name": "Pellegrino Cerino", + "author_inst": "Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute 2, 80055, Naples, Italy" + }, + { + "author_name": "Vittoria Monaco", + "author_inst": "CEINGE Biotecnologie Avanzate, Naples, 80145, Italy" + }, + { + "author_name": "Dong Rac Choi", + "author_inst": "Department of Surgery, Yonsei University College of Medicine, Seoul, Korea" + }, + { + "author_name": "Jae-Ho Cheong", + "author_inst": "Yonsei University College of Medicine" + }, + { + "author_name": "Maria Monti", + "author_inst": "Department of Chemical Sciences, University Federico II, Via Cinthia 4, Naples 80125, Italy." + }, + { + "author_name": "Achille Iolascon", + "author_inst": "Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), Federico II University of Naples, Naples, Italy" + }, + { + "author_name": "Stefano Amente", + "author_inst": "Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), Federico II University of Naples, Naples, Italy" + }, + { + "author_name": "Mario Capasso", + "author_inst": "Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), Federico II University of Naples, Naples, Italy" + }, + { + "author_name": "Hong Yeoul Kim", + "author_inst": "HAIM BIO Co. Ltd, Industrial Park, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, South Korea" + }, + { + "author_name": "Massimo Zollo", + "author_inst": "Dipartimento di Medicina Molecolare e Biotecnologie mediche DMMBM, University of Naples Federico II, Via Pansini 5, 80131, Naples, Italy" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2022.09.05.22278731", "rel_title": "Advanced Care Planning (ACP) in the early phase of COVID-19: A rapid review of the practice and policy lessons learned.", @@ -200209,65 +202353,6 @@ "type": "new results", "category": "neuroscience" }, - { - "rel_doi": "10.1101/2022.09.03.506499", - "rel_title": "Delayed SARS-CoV-2 Spread and Olfactory Cell Lineage Impairment in Close-Contact Infection Syrian Hamster Models", - "rel_date": "2022-09-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.03.506499", - "rel_abs": "ObjectivesClose contact with patients with COVID-19 is speculated to be the most common cause of viral transmission, but the pathogenesis of COVID-19 by close contact remains to be elucidated. In addition, despite olfactory impairment being a unique complication of COVID-19, the impact of SARS-CoV-2 on the olfactory cell lineage has not been fully validated. This study aimed to elucidate close-contact viral transmission to the nose and lungs and to investigate the temporal damage in the olfactory receptor neuron (ORN) lineage caused by SARS-CoV-2.\n\nMethodsSyrian hamsters were orally administered SARS-CoV-2 as direct-infection models. On day 7 after inoculation, infected and uninfected hamsters were housed in the same cage for 30 minutes. These uninfected hamsters were subsequently assigned to a close-contact group. First, viral presence in the nose and lungs was verified in the infection and close-contact groups at several time points. Next, the impacts on the olfactory epithelium, including olfactory progenitors, immature ORNs, and mature ORNs, were examined histologically. Then, the viral transmission status and chronological changes in tissue damage were compared between the direct-infection and close-contact groups.\n\nResultsIn the close-contact group, viral presence could not be detected in both the nose and lungs on day 3, and the virus was identified in both tissues on day 7. In the direct-infection group, the viral load was highest in the nose and lungs on day 3, decreased on day 7, and was no longer detectable on day 14. Histologically, in the direct-infection group, mature ORNs were most depleted on day 3 (p < 0.001) and showed a recovery trend on day 14, with similar trends for olfactory progenitors and immature ORNs. In the close-contact group, there was no obvious tissue damage on day 3, but on day 7, the number of all ORN lineage cells significantly decreased (p < 0.001).\n\nConclusionSARS-CoV-2 was transmitted even after brief contact and subsequent olfactory epithelium and lung damage occurred more than 3 days after the trigger of infection. The present study also indicated that SARS-CoV-2 damages all ORN lineage cells, but this damage can begin to recover approximately 14 days post infection.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Rumi Ueha", - "author_inst": "The University of Tokyo" - }, - { - "author_name": "Toshihiro Ito", - "author_inst": "Nara Medical University" - }, - { - "author_name": "Satoshi Ueha", - "author_inst": "Tokyo University of Science" - }, - { - "author_name": "Ryutaro Furukawa", - "author_inst": "Nara Medical University" - }, - { - "author_name": "Masahiro Kitabatake", - "author_inst": "Nara Medical University" - }, - { - "author_name": "Noriko Ouji-Sageshima", - "author_inst": "Nara Medical University" - }, - { - "author_name": "Tsukasa Uranaka", - "author_inst": "University of Tokyo" - }, - { - "author_name": "Hirotaka Tanaka", - "author_inst": "Jikei University School of Medicine" - }, - { - "author_name": "Hironobu Nishijima", - "author_inst": "the University of Tokyo" - }, - { - "author_name": "Kenji Kondo", - "author_inst": "The University of Tokyo" - }, - { - "author_name": "Tatsuya Yamasoba", - "author_inst": "the University of Tokyo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.09.03.506479", "rel_title": "Combined Molnupiravir and Nirmatrelvir Treatment Improves the Inhibitory Effect on SARS-CoV-2 in Rhesus Macaques", @@ -201000,6 +203085,61 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2022.09.01.22279488", + "rel_title": "Antibiotic Resistance associated with the COVID-19 Pandemic: A Rapid Systematic Review", + "rel_date": "2022-09-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.01.22279488", + "rel_abs": "BackgroundCOVID-19 and antimicrobial resistance (AMR) are two intersecting global public health crises.\n\nObjectiveWe aim to describe the impact of the COVID-19 pandemic on AMR across healthcare settings.\n\nData SourceA search was conducted in December 2021 in World Health Organizations COVID-19 Research Database with forward citation searching up to June 2022.\n\nStudy EligibilityStudies evaluating the impact of COVID-19 on AMR in any population were included and influencing factors were extracted.\n\nMethodsPooling was done separately for Gram-negative and Gram-positive organisms. Random effects meta-analysis was performed.\n\nResultsOf 6036 studies screened, 28 were included and 23 provided sufficient data for meta-analysis. The majority of studies focused on hospital settings (n=25, 89%). The COVID-19 pandemic was not associated with a change in the incidence density (IRR 0.99, 95% CI: 0.67 to 1.47) or proportion (RR 0.91, 95% CI: 0.55 to 1.49) of MRSA or VRE cases. A non-statistically significant increase was noted for resistant Gram-negatives (i.e., ESBL, CRE, MDR or carbapenem-resistant Pseudomonas or Acinetobacter species, IRR 1.64, 95% CI: 0.92 to 2.92; RR 1.08, 95% CI: 0.91 to 1.29). The absence of enhanced IPAC and/or ASP initiatives was associated with an increase in Gram-negative AMR (RR 1.11, 95%CI: 1.03 to 1.20), while studies that did report implementation of these initiatives noted no change in Gram-negative AMR (RR 0.80, 95%CI: 0.38 to 1.70). However, a test for subgroup differences showed no statistically significant difference between these groups (P=0.40)\n\nConclusionThe COVID-19 pandemic could play an important role in the emergence and transmission of AMR, particularly for Gram-negative organisms in hospital settings. There is considerable heterogeneity in both the AMR metrics utilized and the rate of resistance reported across studies. These findings reinforce the need for strengthened infection prevention, antimicrobial stewardship, and AMR surveillance in the context of the COVID-19 pandemic.\n\nPROSPERO registration: CRD42022325831This research was carried out as part of routine work, no funding was received Data collection template, data, and analytic code are available upon request.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Bradley J Langford", + "author_inst": "Public Health Ontario, Dalla Lana School of Public Health" + }, + { + "author_name": "Jean-Paul R. Soucy", + "author_inst": "Dalla Lana School of Public Health, University of Toronto" + }, + { + "author_name": "Valerie Leung", + "author_inst": "Public Health Ontario, Toronto East Health Network" + }, + { + "author_name": "Miranda So", + "author_inst": "University Health Network, University of Toronto" + }, + { + "author_name": "Angela TH Kwan", + "author_inst": "University of Ottawa, Faculty of Medicine, University of Toronto, Department of Chemical & Physical Sciences" + }, + { + "author_name": "Jacob S Portnoff", + "author_inst": "Faculty of Medicine, University of Queensland" + }, + { + "author_name": "Silvia Bertagnolio", + "author_inst": "World Health Organization" + }, + { + "author_name": "Sumit Raybardhan", + "author_inst": "North York General Hospital" + }, + { + "author_name": "Derek MacFadden", + "author_inst": "Ottawa Hospital Research Institute" + }, + { + "author_name": "Nick Daneman", + "author_inst": "Public Health Ontario, Sunnybrook Health Sciences Centre, Institute for Health Policy, Management and Evaluation," + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.09.01.22279517", "rel_title": "Cardiac Magnetic Resonance Findings of COVID-19 Vaccine Associated Myocarditis at Intermediate Follow Up: a Comparison to Classic Myocarditis and MIS-C Related Myocarditis", @@ -201923,61 +204063,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hiv aids" }, - { - "rel_doi": "10.1101/2022.08.30.22279397", - "rel_title": "Heterogeneity in vaccinal immunity to SARS-CoV-2 can be addressed by a personalized booster strategy", - "rel_date": "2022-09-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.30.22279397", - "rel_abs": "The ongoing COVID-19 pandemic has placed an unprecedented burden on global health. Crucial for managing this burden, the existing SARS-CoV-2 vaccines have substantially reduced the risk of severe disease and death up to this point. The induction of neutralizing antibodies (nAbs) by these vaccines leads to protection against both infection and severe disease. However, pharmacokinetic (PK) waning and rapid viral evolution degrade neutralizing antibody binding titers, leading to a rapid loss of vaccinal protection against infection occurring on the order of months after vaccination. Additionally, inter-individual heterogeneity in the strength and durability of the vaccine-induced neutralizing response to SARS-CoV-2 can create a further public-health risk by placing a subset of the population at risk. Here we incorporate the heterogeneity in inter-individual response into a pharmacokinetic/ pharmacodynamic (PK/PD) model to project the degree of heterogeneity in immune protection. We extend our model-based approach to examine the impact of evolutionary immune evasion on vaccinal protection. Our findings suggest that viral evolution can be expected to impact the effectiveness of vaccinal protection against severe disease, particularly for individuals with a shorter duration of immune response. One possible solution to immune heterogeneity may be more frequent boosting for individuals with a weaker immune response. We demonstrate a model-based approach to targeted boosting that involves the use of the ECLIA RBD assay to identify individuals whose immune response is insufficient for protection against severe disease. Our work suggests that vaccinal protection against severe disease is not assured and provides a path forward to reducing the risk to immunologically vulnerable individuals.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Madison Stoddard", - "author_inst": "Fractal Therapeutics, Inc." - }, - { - "author_name": "Lin Yuan", - "author_inst": "Fractal Therapeutics, Inc." - }, - { - "author_name": "Sharanya Sarkar", - "author_inst": "Dartmouth College" - }, - { - "author_name": "Shruthi Mangalaganesh", - "author_inst": "Monash University" - }, - { - "author_name": "Ryan P. Nolan", - "author_inst": "Halozyme Therapeutics" - }, - { - "author_name": "Dean Bottino", - "author_inst": "Millennium Pharmaceuticals, a wholly owned subsidiary of Takeda Pharmaceuticals Inc" - }, - { - "author_name": "Greg Hather", - "author_inst": "Sage Therapeutics" - }, - { - "author_name": "Natasha S. Hochberg", - "author_inst": "Boston University Medical Center" - }, - { - "author_name": "Laura F. White", - "author_inst": "Boston University School of Public Health" - }, - { - "author_name": "Arijit Chakravarty", - "author_inst": "Fractal Therapeutics, Inc." - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.08.30.22279408", "rel_title": "Colorimetric and fluorometric reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for diagnosis of SARS-COV-2", @@ -202650,6 +204735,109 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2022.08.31.505985", + "rel_title": "Neuroinvasion and anosmia are independent phenomena upon infection with SARS-CoV-2 and its variants", + "rel_date": "2022-08-31", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.31.505985", + "rel_abs": "SUMMARYAnosmia was identified as a hallmark of COVID-19 early in the pandemic, however, with the emergence of variants of concern, the clinical profile induced by SARS-CoV-2 infection has changed, with anosmia being less frequent. Here, we assessed the clinical, olfactory and neuroinflammatory conditions of golden hamsters infected with the original Wuhan SARS-CoV-2 strain, its isogenic ORF7-deletion mutant and three variants: Gamma, Delta, and Omicron/BA.1. We show that infected animals developed a variant-dependent clinical disease including anosmia, and that the ORF7 of SARS-CoV-2 contributes to the induction of olfactory dysfunction. Conversely, all SARS- CoV-2 variants were found to be neuroinvasive, regardless of the clinical presentation they induce. Taken together, this confirms that neuroinvasion and anosmia are independent phenomena upon SARS-CoV-2 infection. Using newly generated nanoluciferase-expressing SARS-CoV-2, we validated the olfactory pathway as a major entry point into the brain in vivo and demonstrated in vitro that SARS-CoV-2 travels retrogradely and anterogradely along axons in microfluidic neuron-epithelial networks.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=151 HEIGHT=200 SRC=\"FIGDIR/small/505985v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (58K):\norg.highwire.dtl.DTLVardef@8225ceorg.highwire.dtl.DTLVardef@80342aorg.highwire.dtl.DTLVardef@e0dfd1org.highwire.dtl.DTLVardef@1861e13_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Guilherme Dias de Melo", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Victoire Perraud", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Flavio Alvarez", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Alba Vieites-Prado", + "author_inst": "Institut du Cerveau et de la Moelle Epiniere" + }, + { + "author_name": "Seonhee Kim", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Lauriane Kergoat", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Anthony Coleon", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Bettina S Trueb", + "author_inst": "Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern" + }, + { + "author_name": "Magali Tichit", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Aurele Piazza", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Agnes Thierry", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "David Hardy", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Nicolas Wolff", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Sandie Munier", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Romain Koszul", + "author_inst": "Institut Pasteur / CNRS" + }, + { + "author_name": "Etienne Simon-Loriere", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Volker Thiel", + "author_inst": "Institute for Virology and Immunology" + }, + { + "author_name": "Marc Lecuit", + "author_inst": "Institut Pasteur, Inserm" + }, + { + "author_name": "Pierre-Marie Lledo", + "author_inst": "Institut Pasteur / CNRS" + }, + { + "author_name": "Nicolas Renier", + "author_inst": "Institut du Cerveau et de la Moelle Epiniere" + }, + { + "author_name": "Florence Larrous", + "author_inst": "Pasteur Institute: Institut Pasteur" + }, + { + "author_name": "Herve Bourhy", + "author_inst": "Institut Pasteur" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "neuroscience" + }, { "rel_doi": "10.1101/2022.08.30.505966", "rel_title": "Impact of reinfection with SARS-CoV-2 Omicron variants in previously infected hamsters", @@ -203593,81 +205781,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.08.30.505791", - "rel_title": "Differences in anti-viral immune responses in individuals of Indian and European origin: relevance for the COVID-19 pandemic", - "rel_date": "2022-08-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.30.505791", - "rel_abs": "During the COVID-19 pandemic, large differences in susceptibility and mortality due to SARS-CoV-2 infection have been reported between populations in Europe and South Asia. While both host and environmental factors (including BCG vaccination) have been proposed to explain this, the potential biological substrate of these differences is unknown. We purified peripheral blood mononuclear cells from individuals living in India and the Netherlands at baseline and 10-12 weeks after BCG vaccination. We compared chromatin accessibility between the two populations at baseline, as well as gene transcription profiles and cytokine production capacities upon viral stimulation with influenza and SARS-CoV-2. The chromatin accessibility of genes important for adaptive immunity was higher in Indians compared to Europeans, while the latter had more accessible chromatin regions in genes of the innate immune system. At the transcriptional level, we observed that Indian volunteers displayed a more tolerant immune response to viral stimulation, in contrast to a more exaggerated response in Europeans. BCG vaccination strengthened the tolerance program in Indians, but not in Europeans. These differences may partly explain the different impact of COVID-19 on the two populations.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "B\u00fcsranur Geckin", - "author_inst": "Radboudumc" - }, - { - "author_name": "Martijn Zoodsma", - "author_inst": "Helmholtz Centre for Infection Research: Helmholtz-Zentrum fur Infektionsforschung GmbH" - }, - { - "author_name": "Gizem Kilic", - "author_inst": "Radboudumc" - }, - { - "author_name": "Priya A. Debisarun", - "author_inst": "Radboudumc" - }, - { - "author_name": "Srabanti Rakshit", - "author_inst": "Indian Institute of Science" - }, - { - "author_name": "Vasista Adiga", - "author_inst": "Indian Institute of Science" - }, - { - "author_name": "Asma Ahmed", - "author_inst": "Indian Institute of Science" - }, - { - "author_name": "Chaitra Parthiban", - "author_inst": "Indian Institute of Science" - }, - { - "author_name": "Nirutha Chetan Kumar", - "author_inst": "Indian Institute of Science" - }, - { - "author_name": "George D\u2019Souza", - "author_inst": "Indian Institute of Science" - }, - { - "author_name": "Marijke P Baltissen", - "author_inst": "Radboud University Radboud Institute for Molecular Life Sciences: Radboud Universiteit Radboud Institute for Molecular Life Sciences" - }, - { - "author_name": "Joost H A Martens", - "author_inst": "Radboud University Radboud Institute for Molecular Life Sciences: Radboud Universiteit Radboud Institute for Molecular Life Sciences" - }, - { - "author_name": "Jorge Dominguez Andres", - "author_inst": "Radboudumc" - }, - { - "author_name": "Yang Li", - "author_inst": "Helmholtz Centre for Infection Research: Helmholtz-Zentrum fur Infektionsforschung GmbH" - }, - { - "author_name": "Mihai G Netea", - "author_inst": "Radboudumc" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.08.29.505743", "rel_title": "Molecular fate-mapping of serum antibodies reveals the effects of antigenic imprinting on repeated immunization", @@ -204296,6 +206409,69 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2022.08.27.504955", + "rel_title": "T cell responses induced by SARS-CoV-2 mRNA vaccination are associated with clonal replacement", + "rel_date": "2022-08-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.27.504955", + "rel_abs": "mRNA vaccines against the Spike glycoprotein of severe acute respiratory syndrome type 2 coronavirus (SARS-CoV-2) elicit strong T-cell responses. However, its not known whether T cell clonotypes responding to the first vaccination repeatedly expand with booster vaccinations. Here, we temporally tracked the CD8+ T-cell repertoire in individuals who received three shots of the BNT162b2 mRNA vaccine. By analyzing the kinetic profile of CD8+ T-cell clonotypes responding to the first, second, or third shot, we demonstrated that newly expanded clonotypes elicited by the second shot replaced many of those that responded to the first shot. Although these 2nd responder clonotypes expanded after the third shot, their clonal diversity was skewed, and they were partially replaced by newly elicited the 3rd responders. Furthermore, this replacement of vaccine-responding clonotypes occurred within the same Spike epitope. These results suggest that CD8+ T-cell memory induced by repetitive mRNA vaccination is characterized by the emergence of new dominant clones.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Hiroyasu Aoki", + "author_inst": "Tokyo University of Science" + }, + { + "author_name": "Masahiro Kitabatake", + "author_inst": "Nara Medical University" + }, + { + "author_name": "Haruka Abe", + "author_inst": "Tokyo University of Science" + }, + { + "author_name": "Peng Xu", + "author_inst": "Tokyo University of Science" + }, + { + "author_name": "Mikiya Tsunoda", + "author_inst": "Tokyo University of Science" + }, + { + "author_name": "Shigeyuki Shichino", + "author_inst": "Tokyo University of Science" + }, + { + "author_name": "Atsushi Hara", + "author_inst": "Nara Medical University" + }, + { + "author_name": "Noriko Ouji-Sageshima", + "author_inst": "Nara Medical University" + }, + { + "author_name": "Chihiro Motozono", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Toshihiro Ito", + "author_inst": "Nara Medical University" + }, + { + "author_name": "Kouji Matsushima", + "author_inst": "Tokyo University of Science" + }, + { + "author_name": "Satoshi Ueha", + "author_inst": "Tokyo University of Science" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.08.29.505649", "rel_title": "Validation of saline, PBS and a locally produced VTM at varying storage conditions to detect the SARS-CoV-2 virus by qRT-PCR", @@ -205555,77 +207731,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2022.08.26.505399", - "rel_title": "Niacinamide enhances cathelicidin mediated SARS-CoV-2 membrane disruption", - "rel_date": "2022-08-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.26.505399", - "rel_abs": "The continual emergence of new SARS-CoV-2 variants threatens the effectiveness of worldwide vaccination programs and highlights the need for complementary strategies for a sustainable containment plan. A promising approach is to mobilize the bodys own antimicrobial peptides (AMPs), to combat SARS-CoV-2 infection and propagation. We have found that human cathelicidin (LL37), an AMP found at epithelial barriers as well as in various bodily fluids, has the capacity to neutralise multiple strains of SARS-CoV-2. Biophysical and computational studies indicate that LL37s mechanism of action is through the disruption of the viral membrane. This antiviral activity of LL37 is enhanced by the hydrotropic action of niacinamide, which may increase the bioavailability of the AMP. Interestingly, we observed inverse correlation between LL37 levels and disease severity of COVID-19 positive patients, suggesting enhancement of AMP response would be an effective therapeutic avenue to mitigate disease severity and overcome vaccine escape.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Tanay Bhatt", - "author_inst": "Institute for Stem Cell Science and Regenerative Medicine" - }, - { - "author_name": "Sneha Uday Khedkar", - "author_inst": "Institute for Stem Cell Science and Regenerative Medicine" - }, - { - "author_name": "Binita Dam", - "author_inst": "Institute for Stem Cell Science and Regenerative Medicine" - }, - { - "author_name": "Sahil Lall", - "author_inst": "National Centre for Biological Sciences" - }, - { - "author_name": "Subhashini Pandey", - "author_inst": "Institute for Stem Cell Science and Regenerative Medicine" - }, - { - "author_name": "Sunny Kataria", - "author_inst": "Institute for Stem Cell Science and Regenerative Medicine" - }, - { - "author_name": "Paul M Dias", - "author_inst": "Unilever R&D" - }, - { - "author_name": "Morris Waskar", - "author_inst": "Unilever R&D" - }, - { - "author_name": "Janhavi Raut", - "author_inst": "Unilever R&D" - }, - { - "author_name": "Varadharajan Sundaramurthy", - "author_inst": "National Centre for Biological Sciences" - }, - { - "author_name": "Praveen Kumar Vemula", - "author_inst": "Institute for Stem Cell Science and Regenerative Medicine" - }, - { - "author_name": "Naresh Ghatlia", - "author_inst": "Unilever R&D" - }, - { - "author_name": "Amitabha Majumdar", - "author_inst": "Unilever R&D" - }, - { - "author_name": "Colin Jamora", - "author_inst": "Institute for Stem Cell Science and Regenerative Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "pathology" - }, { "rel_doi": "10.1101/2022.08.23.22279122", "rel_title": "Hospital bed capacity across in Tunisia hospital during the first four waves of the COVID-19 pandemic: A descriptive analysis", @@ -206382,6 +208487,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.08.24.505118", + "rel_title": "The diversity of the glycan shield of sarbecoviruses closely related to SARS-CoV-2", + "rel_date": "2022-08-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.24.505118", + "rel_abs": "The animal reservoirs of sarbecoviruses represent a significant risk of emergent pandemics, as evidenced by the impact of SARS-CoV-2. Vaccines remain successful at limiting severe disease and death, however the continued emergence of SARS-CoV-2 variants, together with the potential for further coronavirus zoonosis, motivates the search for pan-coronavirus vaccines that induce broadly neutralizing antibodies. This necessitates a better understanding of the glycan shields of coronaviruses, which can occlude potential antibody epitopes on spike glycoproteins. Here, we compare the structure of several sarbecovirus glycan shields. Many N-linked glycan attachment sites are shared by all sarbecoviruses, and the processing state of certain sites is highly conserved. However, there are significant differences in the processing state at several glycan sites that surround the receptor binding domain. Our studies reveal similarities and differences in the glycosylation of sarbecoviruses and show how subtle changes in the protein sequence can have pronounced impacts on the glycan shield.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Joel D Allen", + "author_inst": "University Of Southampton" + }, + { + "author_name": "Dylan Ivory", + "author_inst": "University of Southampton" + }, + { + "author_name": "Ge Sophie Song", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Peter Yong", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Tina He", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Raiees Andrabi", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Dennis Burton", + "author_inst": "Scripps Institute" + }, + { + "author_name": "Max Crispin", + "author_inst": "University of Southampton" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2022.08.25.505249", "rel_title": "Modelling SARS-CoV-2 spike-protein mutation effects on ACE2 binding", @@ -207317,29 +209469,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.08.23.504936", - "rel_title": "ENHANCED RECOMBINATION AMONG SARS-COV-2 OMICRON VARIANTS CONTRIBUTES TO VIRAL IMMUNE ESCAPE.", - "rel_date": "2022-08-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.23.504936", - "rel_abs": "SARS-CoV-2 virus evolution occurs as a result of antigenic drift and shift. Although antigenic drift has been extensively studied, antigenic shift, which for SARS-CoV-2 occurs through genetic recombination, has been examined scarcely. To gain a better understanding of the emergence and prevalence of recombinant SARS-CoV-2 lineages through time and space, we analyzed SARS-CoV-2 genome sequences from public databases. Our study revealed an extraordinary increase in the emergence of SARS-CoV-2 recombinant lineages during the Omicron wave, particularly in Northern America and Europe. This phenomenon was independent of sequencing density or genetic diversity of circulating SARS-CoV-2 strains. In SARS-CoV-2 genomes, recombination breakpoints were found to be more concentrated in the 3 UTR followed by ORF1a. Additionally, we noted enrichment of certain amino acids in the spike protein of recombinant lineages, which have been reported to confer immune escape from neutralizing antibodies, increase ACE2 receptor binding, and enhance viral transmission in some cases. Overall, we report an important and timely observation of accelerated recombination in the currently circulating Omicron variants and explore their potential contribution to viral fitness, particularly immune escape.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Rishad Shiraz", - "author_inst": "Indian Institute of Science" - }, - { - "author_name": "Shashank Tripathi", - "author_inst": "Indian Institute of Science" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.08.21.22279036", "rel_title": "RNA polymerase inhibitor enisamium for treatment of moderate COVID-19 patients: a randomized, placebo-controlled, multicenter, double-blind phase 3 clinical trial", @@ -208100,6 +210229,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.08.19.504307", + "rel_title": "The efficiency of Grignard Pure\u2122 to inactivate airborne SARS-CoV-2 surrogate", + "rel_date": "2022-08-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.19.504307", + "rel_abs": "Grignard Pure (GP) is a unique and proprietary blend of Triethylene Glycol (TEG) and inert ingredients designed for continuous antimicrobial treatment of air. GP received approval from the US EPA under its Section 18 Public Health Emergency Exemption program for use in seven states. This study characterizes the efficacy of GP for inactivating MS2 bacteriophage - a non-enveloped virus widely used as a surrogate for SARs-CoV-2. Experiments measured the decrease in the airborne viable MS2 concentration in the presence of different concentrations of GP from 60 to 90 minutes, accounting for both natural die-off and settling of MS2. Experiments were conducted both by introducing GP aerosol into air containing MS2 and by introducing airborne MS2 into air containing GP aerosol. GP is consistently able to rapidly reduce viable MS2 bacteriophage concentration by 2-3 logs at GP concentrations of 0.02 mg/m3 to 0.5 mg/m3 (corresponding to TEG concentrations of 0.012 mg/m3 to 0.287 mg/m3). Related GP efficacy experiments by the US EPA, as well as GP (TEG) safety and toxicology, are also discussed.\n\nSynopsisLimited research on the germicidal properties of triethylene glycol against airborne pathogens was conducted during the 1940s and 50s. This paper investigates the inactivation rate of airborne bacteriophage MS2 by Grignard Pure product, containing a unique and proprietary blend of Triethylene Glycol (TEG) and inert ingredients.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Grishma Desai", + "author_inst": "Grignard Company LLC" + }, + { + "author_name": "Gurumurthy Ramachandran", + "author_inst": "Department of Environmental Health and Engineering, Johns Hopkins Education and Research Center for Occupational Safety and Health, Bloomberg School of Public H" + }, + { + "author_name": "Emanuel Goldman", + "author_inst": "Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School" + }, + { + "author_name": "Antony Galione", + "author_inst": "Department of Pharmacology, University of Oxford" + }, + { + "author_name": "Altaf Lal", + "author_inst": "Former FDA Country Director India" + }, + { + "author_name": "Toni K. Choueiri", + "author_inst": "Dana-Farber Cancer Institute, Harvard Medical School" + }, + { + "author_name": "Andre Fay", + "author_inst": "PUCRS School of Medicine" + }, + { + "author_name": "William Jordan", + "author_inst": "Former Deputy Director, Programs, Office of Pesticide Programs, Environmental Protection Agency" + }, + { + "author_name": "Donald W. Schaffner", + "author_inst": "Department of Food Science, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey" + }, + { + "author_name": "Jack Caravanos", + "author_inst": "Clinical Professor of Environmental Public Health Services, New York University" + }, + { + "author_name": "Etienne Grignard", + "author_inst": "Grignard Pure LLC" + }, + { + "author_name": "Gediminas Mainelis", + "author_inst": "Department of Environmental Sciences, School of Environmental and Biological Sciences, Rutgers, The State University of NJ" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.08.22.504888", "rel_title": "SARS-CoV-2 infects multiple species of North American deer mice and causes clinical disease in the California mouse", @@ -209107,73 +211299,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.08.19.22278985", - "rel_title": "Symptom presentation among SARS-CoV-2 positive cases and the impact of COVID-19 vaccination; three prospective household cohorts", - "rel_date": "2022-08-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.19.22278985", - "rel_abs": "OBJECTIVEUsing data from European prospective household studies, we systematically compared the symptom burden of the wild-type and Alpha variant infected individuals versus the Omicron BA.1 and BA.2 infected individuals across paediatric and adult age-groups. In addition, we measured the impact of COVID-19 vaccination on the Omicron symptom burden.\n\nMETHODSThe household transmission studies were conducted during the wild-type and Alpha period (April 2020 to April 2021) and the early Omicron BA.1 and BA.2 dominant period (January to March 2022). All three studies used similar protocols. Households were prospectively followed from detection of the first SARS-CoV-2 index case until at least day 21 including (repeated) PCR testing, paired serology and daily symptom reporting for all household members. To avoid possible index-case ascertainment bias, we restricted analyses to secondary household cases. Age-stratified SARS-CoV-2 symptom burden was compared for wild-type/Alpha versus Omicron infections and for primary versus primary plus booster series vaccinated adult cases.\n\nFINDINGSIn total 216 secondary cases from wild-type/Alpha, and 130 from the Omicron period were included. Unvaccinated children <12 years experienced more symptoms and higher maximum and cumulative severity scores during the Omicron compared to the wild-type/Alpha period (p=0.004, p=0.011 and p=0.075, respectively). In adults, disease duration and maximum and cumulative severity scores were reduced during the Omicron period. Adjusted for age, gender and prior immunity Omicron was associated with lower odds for loss of smell or taste (Odds Ratio [OR]: 0.14; 95%CI 0.03-0.50), and higher, but non-significant odds for upper respiratory symptoms, fever and fatigue (ORs varying between 1.85-2.23). Comparing primary versus primary plus booster vaccinated adult cases during the Omicron period no differences were observed in disease severity or duration (p[≥]0.12).\n\nINTERPRETATIONIn children, the Omicron variant causes higher symptom burden compared to the wild-type/Alpha. Adults experienced a lower symptom burden possibly due to prior vaccination. A shift in most frequently reported symptoms occurred with a marked reduction in loss of smell or taste during the Omicron period. An additional effect of booster vaccination on symptom severity in infected adults compared to primary series only, could not be demonstrated.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Ilse Westerhof", - "author_inst": "Julius Centre for Health Sciences and Primary Care, Department of Epidemiology, University Medical Centre Utrecht, Utrecht, The Netherlands" - }, - { - "author_name": "Marieke de Hoog", - "author_inst": "Julius Centre for Health Sciences and Primary Care, Department of Epidemiology, University Medical Centre Utrecht, Utrecht, The Netherlands" - }, - { - "author_name": "Margareta Ieven", - "author_inst": "Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium" - }, - { - "author_name": "Christine Lammens", - "author_inst": "Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium" - }, - { - "author_name": "Janko van Beek", - "author_inst": "Department of Viroscience, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands" - }, - { - "author_name": "Ganna Rozhnova", - "author_inst": "Julius Centre for Health Sciences and Primary Care, Department of Epidemiology, University Medical Centre Utrecht, The Netherlands and Biosystems & Integrative " - }, - { - "author_name": "Dirk Eggink", - "author_inst": "Centre for Infectious Disease Control, WHO COVID-19 Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Nether" - }, - { - "author_name": "Sjoerd Euser", - "author_inst": "Streeklaboratorium voor de Volksgezondheid Kennemerland, Department of Epidemiology, Kennemerland, The Netherlands" - }, - { - "author_name": "Joanne Wildenbeest", - "author_inst": "Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Childrens Hospital University Medical Center Utrecht, Utrecht, The Netherlands" - }, - { - "author_name": "Marlies van Houten", - "author_inst": "Spaarne Gasthuis Academy, Spaarne Gasthuis, Hoofddorp, The Netherlands and Spaarne Gasthuis, department of Pediatrics, Haarlem and Hoofddorp, The Netherlands" - }, - { - "author_name": "Herman Goossens", - "author_inst": "Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium" - }, - { - "author_name": "Carlo Giaquinto", - "author_inst": "Department of Women and Child Health, University of Padova, Padova, Italy" - }, - { - "author_name": "Patricia Bruijning Verhagen", - "author_inst": "Julius Centre for Health Sciences and Primary Care, Department of Epidemiology, University Medical Centre Utrecht, Utrecht, The Netherlands" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.08.21.22279047", "rel_title": "Associations of proton pump inhibitors with susceptibility to pneumonia, influenza, and COVID-19: evidence from a large population based cohort study", @@ -209890,6 +212015,41 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2022.08.22.22278860", + "rel_title": "UNDERSTANDING ACTIONS TAKEN BY FEMALE FAMILY CAREGIVERS AND CHALLENGES THEY FACED IN CARING FOR OLDER PEOPLE DURING COVID-19 PANDEMIC IN BELU DISTRICT, INDONESIA: A QUALITATIVE STUDY", + "rel_date": "2022-08-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.22.22278860", + "rel_abs": "COVID-19 has rapidly impacted societies on a global scale, with older people among the most affected. To care for older people living in their own homes, female family caregivers play a pivotal role. The current study aimed to explore the actions of female family caregivers and the challenges they faced in taking care of older people living at homes during the COVID-19 pandemic in Belu district, Indonesia. This qualitative study involved twenty female family caregivers, who were recruited using a combination of purposive and snowball sampling techniques. Findings were grouped into two main categories: (i) actions of female family caregivers in taking care of older adults during the COVID-19 pandemic. These included limiting both visitations of extended family members and older adults activities outside homes; explaining the virus to older adults and controlling their access to news, social media and smartphones; providing nutrition, supplement and maintaining daily diets; and (ii) challenges they faced in taking care of older adults included excessive fear of contracting COVID-19 and possibility of transmitting it to older people; feeling stressed; tired and overburdened. The study highlights the significant role family caregivers played to protect older people living at home. The findings can inform government to develop intervention programs that address and support the needs of both family caregivers and older people living at home.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Gregorius Abanit Asa", + "author_inst": "Sanggar Belajar Alternatif" + }, + { + "author_name": "Nelsensius Klau Fauk", + "author_inst": "Torrens University Australia" + }, + { + "author_name": "Melkianus Ratu", + "author_inst": "Universitas Timor" + }, + { + "author_name": "Elsa Dent", + "author_inst": "Torrens University Australia" + }, + { + "author_name": "Paul Russell Ward", + "author_inst": "Torrens University Australia" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.08.22.22278433", "rel_title": "Knowledge practice gap of nurses towards COVID-19 patients dead body care in a tertiary care hospital.", @@ -210857,61 +213017,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2022.08.19.504551", - "rel_title": "SARS-CoV-2 Airway Infection Results in Time-dependent Sensory Abnormalities in a Hamster Model", - "rel_date": "2022-08-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.19.504551", - "rel_abs": "Despite being largely confined to the airways, SARS-CoV-2 infection has been associated with sensory abnormalities that manifest in both acute and long-lasting phenotypes. To gain insight on the molecular basis of these sensory abnormalities, we used the golden hamster infection model to characterize the effects of SARS-CoV-2 versus Influenza A virus (IAV) infection on the sensory nervous system. Efforts to detect the presence of virus in the cervical/thoracic spinal cord and dorsal root ganglia (DRGs) demonstrated detectable levels of SARS-CoV-2 by quantitative PCR and RNAscope uniquely within the first 24 hours of infection. SARS-CoV-2-infected hamsters demonstrated mechanical hypersensitivity during acute infection; intriguingly, this hypersensitivity was milder, but prolonged when compared to IAV-infected hamsters. RNA sequencing (RNA-seq) of thoracic DRGs from acute infection revealed predominantly neuron-biased signaling perturbations in SARS-CoV-2-infected animals as opposed to type I interferon signaling in tissue derived from IAV-infected animals. RNA-seq of 31dpi thoracic DRGs from SARS-CoV-2-infected animals highlighted a uniquely neuropathic transcriptomic landscape, which was consistent with substantial SARS-CoV-2-specific mechanical hypersensitivity at 28dpi. Ontology analysis of 1, 4, and 30dpi RNA-seq revealed novel targets for pain management, such as ILF3. Meta-analysis of all SARS-CoV-2 RNA-seq timepoints against preclinical pain model datasets highlighted both conserved and unique pro-nociceptive gene expression changes following infection. Overall, this work elucidates novel transcriptomic signatures triggered by SARS-CoV-2 that may underlie both short- and long-term sensory abnormalities while also highlighting several therapeutic targets for alleviation of infection-induced hypersensitivity.\n\nOne Sentence SummarySARS-CoV-2 infection results in an interferon-associated transcriptional response in sensory tissues underlying time-dependent hypersensitivity.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Randal A Serafini", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Justin J Frere", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Jeffrey Zimering", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Ilinca M Giosan", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Kerri D Pryce", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Ilona Golynker", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Mayline Panis", - "author_inst": "NYU Langone" - }, - { - "author_name": "Anne Ruiz", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Benjamin tenOever", - "author_inst": "New York University Langone Medical Center" - }, - { - "author_name": "Venetia Zachariou", - "author_inst": "Icahn School of Medicine at Mount Sinai" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "neuroscience" - }, { "rel_doi": "10.1101/2022.08.17.22278915", "rel_title": "Prevalence and Characterization of Bacteria Present in the Nasopharynx of Outpatients with and without SARS-CoV-2", @@ -211672,6 +213777,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.08.14.22278754", + "rel_title": "Comparative Analysis of Reported Deaths Cases Associated with the New Coronavirus COVID-19 Pandemic in the South Caucasus Countries (Armenia, Azerbaijan, Georgia) from March 2020 to May 2022", + "rel_date": "2022-08-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.14.22278754", + "rel_abs": "The results of a statistical analysis of daily, total by days of the week and monthly data on officially reported deaths cases from the new coronavirus COVID-19 in the countries of the South Caucasus (Armenia, Azerbaijan, Georgia) from March 12, 2020 to May 31, 2022 are presented. All data are normalized per 1 million populations (mortality rate, hereinafter, this normalization is assumed everywhere). In particular, the following results were obtained.\n\nThe daily mortality rate in Armenia averaged 3.591 (range: 0-23.622), in Azerbaijan - 1.184 (range: 0-10.969), in Georgia - 5.596 (range: 0-23.189). The total monthly mortality rate in Armenia averaged 107.9 (variability range: 1.01-415.4), in Azerbaijan - 35.6 (variability range: 0.39-122.9), in Georgia - 168.1 (variability range: 0-547.4).\n\nA direct linear correlation was observed between the indicated countries in cases of daily and total monthly mortality.\n\nAn analysis of the intraweek course of mortality showed that in Armenia, on weekdays, the average daily mortality is 4.319, and on weekends - 3.477 (an increase compared to weekends by about 24%); in Azerbaijan, on weekdays and weekends, the average daily mortality is 1.368 and 1.421, respectively (the difference is insignificant); in Georgia on weekdays, the average daily mortality is 7.558, and on weekends - 6.855 (an increase of about 10% compared to weekends).", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Avtandil G. Amiranashvili", + "author_inst": "Mikheil Nodia Institute of Geophysics of Ivane Javakhishvili Tbilisi State University" + }, + { + "author_name": "Ketevan R. Khazaradze", + "author_inst": "Georgian State Teaching University of Physical Education and Sport, Tbilisi, Georgia; Ministry of Internally Displaced Persons from Occupied Territories, Labour" + }, + { + "author_name": "Nino D. Japaridze", + "author_inst": "Ministry of Internally Displaced Persons from Occupied Territories, Labour, Health and Social Affair of Georgia, Tbilisi, Georgia; Tbilisi State Medical Univers" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.08.16.22278820", "rel_title": "Rapid waning of protection induced by prior BA.1/BA.2 infection against BA.5 infection", @@ -212579,93 +214711,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2022.08.15.22278736", - "rel_title": "Incidence and management of inflammatory arthritis in England before and during the COVID-19 pandemic: a population-level cohort study using OpenSAFELY", - "rel_date": "2022-08-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.15.22278736", - "rel_abs": "ObjectiveTo use the OpenSAFELY platform to replicate key metrics from a national clinical audit, and assess the impact of COVID-19 on disease incidence and care delivery for inflammatory arthritis (IA) in England.\n\nDesignPopulation-based cohort study, with the approval of NHS England.\n\nSettingPrimary care and linked hospital outpatient data for more than 17 million people registered with general practices in England that use TPP electronic health record software.\n\nParticipantsAdults (18-110 years) with new diagnoses of IA (rheumatoid arthritis, psoriatic arthritis, axial spondyloarthritis, undifferentiated IA) between 1 April 2019 and 31 March 2022.\n\nMain outcome measuresThe following outcomes were explored before and after April 2020: 1) incidence of IA diagnoses; 2) time from primary care referral to first rheumatology assessment; 3) time to first prescription of a disease-modifying anti-rheumatic drug (DMARD) in primary care.\n\nResultsFrom a reference population of 17,683,500 adults, there were 31,280 incident IA diagnoses between April 2019 and March 2022. The incidence of IA decreased by 20.3% in the year commencing April 2020, relative to the preceding year (5.1 vs. 6.4 diagnoses per 10,000 adults, respectively). For those who presented with IA, the time to first rheumatology assessment was shorter during the pandemic (median 18 days; interquartile range 8 to 35 days) than before (21 days; 9 to 41 days). Overall, the proportion of patients prescribed DMARDs in primary care was comparable during the pandemic to before; however, the choice of medication changed, with fewer people prescribed methotrexate or leflunomide during the pandemic, and more people prescribed sulfasalazine or hydroxychloroquine.\n\nConclusionsThe incidence of IA diagnoses in England decreased markedly during the early COVID-19 pandemic. However, for people who sought medical attention, the impact of the pandemic on service delivery was less marked than might have been anticipated. This study demonstrates that it is feasible to use routinely captured, near real-time data in the secure OpenSAFELY platform to benchmark care quality for long-term conditions on a national scale, without the need for manual data collection.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Mark D Russell", - "author_inst": "Centre for Rheumatic Diseases, King's College London, SE5 9RJ, UK" - }, - { - "author_name": "James B Galloway", - "author_inst": "Centre for Rheumatic Diseases, King's College London, SE5 9RJ, UK" - }, - { - "author_name": "Colm D Andrews", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, OX2 6GG, UK" - }, - { - "author_name": "Brian MacKenna", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, OX2 6GG, UK" - }, - { - "author_name": "Ben Goldacre", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, OX2 6GG, UK" - }, - { - "author_name": "Amir Mehrkar", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, OX2 6GG, UK" - }, - { - "author_name": "Helen J Curtis", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, OX2 6GG, UK" - }, - { - "author_name": "Benjamin Butler-Cole", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, OX2 6GG, UK" - }, - { - "author_name": "Thomas O'Dwyer", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, OX2 6GG, UK" - }, - { - "author_name": "Sumera Qureshi", - "author_inst": "Centre for Rheumatic Diseases, King's College London, SE5 9RJ, UK" - }, - { - "author_name": "Joanna M Ledingham", - "author_inst": "Rheumatology Department, Portsmouth Hospitals University NHS Trust, Portsmouth, PO6 3LY, UK" - }, - { - "author_name": "Arti Mahto", - "author_inst": "Department of Rheumatology, King's College Hospital NHS Foundation Trust, London, SE5 9RS, UK" - }, - { - "author_name": "Andrew I Rutherford", - "author_inst": "Department of Rheumatology, King's College Hospital NHS Foundation Trust, London, SE5 9RS, UK" - }, - { - "author_name": "Maryam A Adas", - "author_inst": "Centre for Rheumatic Diseases, King's College London, SE5 9RJ, UK" - }, - { - "author_name": "Edward Alveyn", - "author_inst": "Centre for Rheumatic Diseases, King's College London, SE5 9RJ, UK" - }, - { - "author_name": "Sam Norton", - "author_inst": "Centre for Rheumatic Diseases, King's College London, SE5 9RJ, UK" - }, - { - "author_name": "Andrew P Cope", - "author_inst": "Centre for Rheumatic Diseases, King's College London, SE5 9RJ, UK" - }, - { - "author_name": "Katie Bechman", - "author_inst": "Centre for Rheumatic Diseases, King's College London, SE5 9RJ, UK" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "rheumatology" - }, { "rel_doi": "10.1101/2022.08.14.503890", "rel_title": "A pan-cancer analysis of the oncogenic role of COVID-19 risk gene Leucine Zipper Transcription Factor-Like Protein 1 (LZTFL1) in human tumors", @@ -213346,6 +215391,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.08.12.22278705", + "rel_title": "Comparison of antibody responses to SARS-CoV-2 variants in Australian children", + "rel_date": "2022-08-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.12.22278705", + "rel_abs": "There is limited understanding of antibody responses in children across different SARS-CoV-2 variants. As part of an ongoing household cohort study, we assessed the antibody response among unvaccinated children infected with Wuhan, Delta or Omicron variants, as well as vaccinated children with breakthrough Omicron infection, using a SARS-CoV-2 S1-specific IgG assay and surrogate virus neutralisation test (sVNT). Most children infected with Delta (100%, 35/35) or Omicron (81.3%, 13/16) variants seroconverted by one month following infection. In contrast, 37.5% (21/56) children infected with Wuhan seroconverted, as previously reported. However, Omicron-infected children (GMC 46.4 BAU/ml; sVNT % inhibition: 16.3%) mounted a significantly lower antibody response than Delta (435.5 BAU/mL, sVNT=76.9%) or Wuhan (359.0 BAU/mL, sVNT=74.0%). Vaccinated children with breakthrough Omicron infection mounted the highest antibody response (2856 BAU/mL, sVNT=96.5%). Our findings suggest that despite a high seroconversion rate, Omicron infection in children results in lower antibody levels and function compared with Wuhan or Delta infection or with vaccinated children with breakthrough Omicron infection. Our data have important implications for public health measures and vaccination strategies to protect children.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Zheng Quan Toh", + "author_inst": "Murdoch Children's Research Institute" + }, + { + "author_name": "Nadia Mazarakis", + "author_inst": "Murdoch Children's Research Institute" + }, + { + "author_name": "Jill Nguyen", + "author_inst": "Murdoch Children's Research Institute" + }, + { + "author_name": "Rachel A Higgins", + "author_inst": "Murdoch Children's Research Institute" + }, + { + "author_name": "Jeremy Anderson", + "author_inst": "Murdoch Children's Research Institute" + }, + { + "author_name": "Lien Anh Ha Do", + "author_inst": "Murdoch Children's Research Institute" + }, + { + "author_name": "David P Burgner", + "author_inst": "Murdoch Children's Research Institute" + }, + { + "author_name": "Nigel Curtis", + "author_inst": "Murdoch Children's Research Institute" + }, + { + "author_name": "Andrew C Steer", + "author_inst": "Murdoch Children's Research Institute" + }, + { + "author_name": "Kim Mulholland", + "author_inst": "Murdoch Children's Research Institute" + }, + { + "author_name": "Shidan Tosif", + "author_inst": "Murdoch Children's Research Institute" + }, + { + "author_name": "Paul Licciardi", + "author_inst": "Murdoch Children's Research Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.08.11.503574", "rel_title": "SARS-CoV-2 specific plasma cells acquire the phenotype of long-lived plasma cells in the human bone marrow", @@ -214629,73 +216737,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.08.11.503614", - "rel_title": "Interfering with nucleotide excision by the coronavirus 3'-to-5' exoribonuclease", - "rel_date": "2022-08-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.11.503614", - "rel_abs": "Some of the most efficacious antiviral therapeutics are ribonucleos(t)ide analogs. The presence of a 3-to-5 proofreading exoribonuclease (ExoN) in coronaviruses diminishes the potency of many ribonucleotide analogs. The ability to interfere with ExoN activity will create new possibilities for control of SARS-CoV-2 infection. ExoN is formed by a 1:1 complex of nsp14 and nsp10 proteins. We have purified and characterized ExoN using a robust, quantitative system that reveals determinants of specificity and efficiency of hydrolysis. Double-stranded RNA is preferred over single-stranded RNA. Nucleotide excision is distributive, with only one or two nucleotides hydrolyzed in a single binding event. The composition of the terminal basepair modulates excision. A stalled SARS-CoV-2 replicase in complex with either correctly or incorrectly terminated products prevents excision, suggesting that a mispaired end is insufficient to displace the replicase. Finally, we have discovered several modifications to the 3-RNA terminus that interfere with or block ExoN-catalyzed excision. While a 3-OH facilitates hydrolysis of a nucleotide with a normal ribose configuration, this substituent is not required for a nucleotide with a planar ribose configuration such as that present in the antiviral nucleotide produced by viperin. Design of ExoN-resistant, antiviral ribonucleotides should be feasible.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Rukesh Chinthapatla", - "author_inst": "The University of North Carolina at Chapel Hill" - }, - { - "author_name": "Mohamad S. Sotoudegan", - "author_inst": "The University of North Carolina at Chapel Hill" - }, - { - "author_name": "Thomas Anderson", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Ibrahim M. Moustafa", - "author_inst": "The Pennsylvania State University" - }, - { - "author_name": "Kellan T. Passow", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Samantha A. Kennelly", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Ramkumar Moorthy", - "author_inst": "University of Minnesota" - }, - { - "author_name": "David Dulin", - "author_inst": "Vrije Universiteit Amsterdam" - }, - { - "author_name": "Joy Y. Feng", - "author_inst": "Gilead Sciences, Inc" - }, - { - "author_name": "Daniel A. Harki", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Robert Kirchdoerfer", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Craig E. Cameron", - "author_inst": "The University of North Carolina at Chapel Hill" - }, - { - "author_name": "Jamie J. Arnold", - "author_inst": "The University of North Carolina at Chapel Hill" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2022.08.05.22278477", "rel_title": "Anakinra in hospitalized COVID-19 patients guided by baseline soluble urokinase plasminogen receptor plasma levels: a real world, retrospective cohort study", @@ -215756,6 +217797,77 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.08.09.503429", + "rel_title": "Stability of SARS-CoV-2 in cold-chain transportation environments and the efficacy of disinfection measures", + "rel_date": "2022-08-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.09.503429", + "rel_abs": "Cold-chain environment could extend the survival duration of SARS-CoV-2 and increases the risk of transmission. However, the effect of clod-chain environmental factors and packaging materials on SARS-CoV-2 stability and the efficacy of intervention measures to inactivate SARS-CoV-2 under cold-chain environment remains uncertain. This study aimed to unravel cold-chain environmental factors that preserved the stability of SARS-CoV-2 and disinfection measures against SARS-CoV-2 under the cold-chain environment. The spike gene of SARS-CoV-2 isolated from Wuhan hu-1 was used to construct the SARS-CoV-2 pseudovirus and used as model of the SARS-CoV-2 virus. The decay rate of SARS-CoV-2 pseudovirus in the cold-chain environment, various types of packaging material surfaces i.e., PE plastic, stainless steel, Teflon and cardboard, and in frozen seawater was investigated. The influence of LED visible light(wavelength 450 nm-780 nm) and airflow movement on the stability of SARS-CoV-2 pseudovirus at -18{degrees} C were subsequently assessed. The results show that SARS-CoV-2 pseudovirus decayed more rapidly on porous cardboard surface compared with the non-porous surfaces including PE plastic, stainless steel and Teflon. Compared with 25{degrees} C, the decay rate of SARS-CoV-2 pseudovirus was significantly lower at low temperature. Seawater preserved viral stability both at -18{degrees} C and repeated freeze-thawing cycles compared with deionized water. LED visible light illumination and airflow movement environment at -18{degrees} C reduced the SARS-CoV-2 pseudovirus stability. In conclusion, our results indicate cold-chain temperature and seawater as risk factors for SARS-CoV-2 transmission and LED visible light illumination and airflow movement as possible disinfection measures of SARS-CoV-2 under the cold-chain environment.\n\nImportanceIt is widely recognized that low temperature is a condition for maintaining virus vitality, and cold-chain transportation spreads the events of the SARS-CoV-2 were reported. This study provides that the decay rate of the SARS-CoV-2 pseudovirus at low temperatures varies on different packaging materials, and salt ions present in frozen foods such as seafood may protect virus survival. These results provide evidence for the possibility of SARS-CoV-2 transmission through cold-chain transport and also suggest the importance for disinfection of items. However, the commonly used disinfection methods of ultraviolet radiation and chemical reagents are generally not suitable for the disinfection of frozen food. Our study shows LED visible light illumination and airflow movement as possible disinfection measures of SARS-CoV-2 under the cold-chain environment. This has implications for reducing the long-distance transmission of the virus through cold-chain transportation.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Shuyi Peng", + "author_inst": "Guangzhou Medical University" + }, + { + "author_name": "Guojie Li", + "author_inst": "Guangzhou Medical University" + }, + { + "author_name": "Janak L. Pathak", + "author_inst": "Affiliated Stomatology Hospital of Guangzhou Medical University" + }, + { + "author_name": "Xiaolan Guo", + "author_inst": "Guangzhou Medical University" + }, + { + "author_name": "Yuyin Lin", + "author_inst": "Guangzhou Medical University" + }, + { + "author_name": "Hao Xu", + "author_inst": "Guangzhou Medical University" + }, + { + "author_name": "Wenxi Qiu", + "author_inst": "Guangzhou Medical University" + }, + { + "author_name": "Jiaying Zheng", + "author_inst": "Guangzhou Medical University" + }, + { + "author_name": "Wei Sun", + "author_inst": "Guangzhou Institute of Geochemistry" + }, + { + "author_name": "Xiaodong Hu", + "author_inst": "Guangzhou Institute of Geochemistry" + }, + { + "author_name": "Guohua Zhang", + "author_inst": "Guangzhou Institute of Geochemistry" + }, + { + "author_name": "Bing Li", + "author_inst": "The GMJ-GIBH Joint School of Life Science" + }, + { + "author_name": "Xinhui Bi", + "author_inst": "Guangzhou Institute of Geochemistry" + }, + { + "author_name": "Jianwei Dai", + "author_inst": "Guangzhou Medical University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.08.08.22278553", "rel_title": "Early Detection of Emerging SARS-CoV-2 Variants of Interest for Experimental Evaluation", @@ -216835,45 +218947,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.08.07.22278524", - "rel_title": "Utility of IL-6 in the diagnosis, treatment and prognosis of COVID-19 patients: A longitudinal study", - "rel_date": "2022-08-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.07.22278524", - "rel_abs": "IntroductionCovid-19 has caused devastating effects worldwide ever since its origin in December, 2019. Till date, there is no definitive treatment for it. Deaths due to Covid-19 has largely been attributed to cytokine storm and organ dysfunctions, mainly ARDS. Therefore, the focus has been on using inflammatory markers as a marker of severity of the disease. IL-6 is one such marker which has been increasingly used in the management of Covid-19. We conducted a longitudinal study to investigate the role of IL-6 in diagnosis, treatment and prognosis of Covid-19 related cytokine storm.\n\nMethodologyPatients with Covid-19, who were admitted at AIIMS Rishikesh from March to December, 2020 were included in the study. Patients with no baseline IL-6 value at admission and for whom clinical data was not available were excluded. Clinical and laboratory data of these patients were collected from the e-hospital portal and entered in excel sheet. Correlation was seen with other inflammatory markers and outcomes were assessed using MS Excel 2010 and SPSS software.\n\nResultsAt total of 131 patients were included in the study. Majority were males (74.8%), mean age of the subjects being 55.03+13.57 years, with a mean duration from symptom onset being 6.69+6.3 days. Most of them belonged to the WHO severe category (82.4%), with 46.56% having severe hypoxia at presentation and 61.8% of them having some comorbidity-diabetes mellitus being the commonest. Spearman Rank Correlation coefficient of IL-6 with D-dimer was 0.203, with LDH was -0.005, with Ferritin was 0.3, and with Uric acid was 0.123. 11 patients received Tocilizumab at a mean duration from symptom onset of 18.09 days, and 100% mortality was observed. Deaths were reported more in the group with IL-6 more than 40pg/ml (57.1% vs 40.2%,p=0.06). Similarly, ICU admissions and ventilator requirement were reported more in the IL-6 more than 40pg/ml group (95.9% vs 91.4%,p=0.32 and 55.1% vs 37.8%,p=0.05).\n\nConclusionThe study showed that IL-6 can be used as a possible thrombotic cytokine marker. Higher values of IL-6 (>40pg/ml) are associated with more deaths, ICU admissions and ventilator requirement.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Vikram Jain", - "author_inst": "AIIMS Rishikesh" - }, - { - "author_name": "Pratap Kumar", - "author_inst": "AIIMS Rishikesh" - }, - { - "author_name": "Prasan Kumar Panda", - "author_inst": "AIIMS Rishikesh" - }, - { - "author_name": "Karan Kaushal", - "author_inst": "AIIMS Rishikesh" - }, - { - "author_name": "Anissa A Mirza", - "author_inst": "AIIMS Rishikesh" - }, - { - "author_name": "Vivekandan S", - "author_inst": "AIIMS Rishikesh" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.08.08.22278532", "rel_title": "Clinical effectiveness of SARS-CoV-2 booster vaccine against Omicron infection in residents and staff of Long-Term Care Facilities: a prospective cohort study (VIVALDI)", @@ -217654,6 +219727,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.08.09.22278385", + "rel_title": "Impact of Lifting School Masking Requirements on Incidence of COVID-19 among Staff and Students in Greater-Boston Area School Districts: A Difference-in-Differences Analysis", + "rel_date": "2022-08-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.09.22278385", + "rel_abs": "BackgroundIn February 2022, following the rescinding of a Massachusetts statewide school masking mandate, only two cities (Boston and neighboring Chelsea) out of 79 school districts in the greater-Boston area, maintained masking requirements in K-12 schools. This provided an opportunity to examine the impact of removing masking on COVID-19 case rates among students and staff in the public-school setting.\n\nMethodsWe used difference-in-differences for staggered policy adoption to compare incidence of COVID-19 cases among students and staff in greater-Boston area school districts that lifted masking requirements to those that had not yet lifted masking requirements during the 2021-2022 school year.\n\nResultsBefore the statewide school masking policy was lifted, there was no statistically significant difference in case rate trajectories between school districts. However, weekly and cumulative case rates were significantly higher in students and staff in school districts that removed masking requirements, compared to districts that had not yet lifted requirements. We estimate that lifting of school masking requirements was associated with an additional 44.9 (95% CI: 32.6, 57.1) COVID-19 cases per 1,000 students and staff over the 15 weeks since the lifting of the statewide school masking requirement, representing nearly 30% of all cases observed in schools during that time. School districts that sustained masking requirements for longer periods tended to have older school buildings in poorer condition, more crowded classrooms, higher proportion of low income and English learning students and students with disabilities, and a higher proportion of Black and Latinx students and staff.\n\nConclusionsMasking is a relatively low-cost but effective intervention that can protect students and staff from substantial illness and loss of in-person days in school. Despite compelling evidence that masking significantly reduces the spread of SARS-CoV-2, political will and public adherence to masking has waned. Our study confirms that universal masking requirements can benefit all students and staff, and therefore represents an important strategy to mitigate the impacts of structural racism, ensure health equity, and to avoid potential deepening of educational inequities.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Tori L. Cowger", + "author_inst": "FXB Center for Health and Human Rights, Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Jaylen Clarke", + "author_inst": "Boston Public Health Commission" + }, + { + "author_name": "Eleanor J. Murray", + "author_inst": "Boston University" + }, + { + "author_name": "Sarimer M. S\u00e1nchez", + "author_inst": "Boston Public Health Commission" + }, + { + "author_name": "Mary T. Bassett", + "author_inst": "FXB Center for Health and Human Rights, Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Bisola O. Ojikutu", + "author_inst": "Boston Public Health Commission" + }, + { + "author_name": "Natalia Linos", + "author_inst": "FXB Center for Health and Human Rights, Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Kathryn T. Hall", + "author_inst": "Boston Public Health Commission" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.08.04.22278439", "rel_title": "Who is pregnant? defining real-world data-based pregnancy episodes in the National COVID Cohort Collaborative (N3C)", @@ -218845,81 +220965,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.08.04.22278438", - "rel_title": "Optimization of Ventilation Therapy Prioritization Strategies among Patients with COVID-19: Lessons Learned from Real-World Data of nearly 600,000 Hospitalized Patients", - "rel_date": "2022-08-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.04.22278438", - "rel_abs": "ObjectiveTo investigate the benefit of ventilation therapy among various patient groups with COVID-19 admitted to hospitals, based on the real-world data of hospitalized adult patients.\n\nMethodsData used in the longitudinal study included 599,340 records of hospitalized patients. All participants were categorized based on demographics and their date of hospitalization. Two models were used in this study: firstly, participants were assessed by their probability of receiving ventilation therapy during hospitalization using mixed-effects logistic regression. Secondly, the clinical benefit of receiving ventilation therapy among various patient groups was quantified while considering the probability of receiving ventilation therapy during hospital admission, as estimated in the first model.\n\nFindingsAmong participants, 60,113 (10.0%) received ventilation therapy, 85,158 (14.2%) passed away due to COVID-19, and 514,182 (85.8%) recovered. Among all groups with sufficient data for analysis, patients aged 40-64 years who had chronic respiratory diseases (CRD) and malignancy benefitted the most from ventilation therapy; followed by patients aged 65+ years who had malignancy, cardiovascular diseases, and diabetes; and patients aged 18-39 years who had malignancy. Patients aged 65+ who had CRD and cardiovascular disease gained the least benefit from ventilation therapy.\n\nConclusionThis study promotes a new aspect of treating patients for ventilators: it could be suggested that rather than focusing on the scarcity of ventilators, guidelines focus on decision-making algorithms to also take the usefulness of the intervention into account, whose beneficial effect is dependent on the selection of the right time in the right patient.\n\nFundingThis work was supported by the World Health Organization (WHO) Eastern Mediterranean Regional Office (EMRO) (Grant No. 202693061). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.\n\nResearch in contextO_ST_ABSWhat was already knownC_ST_ABSResearch has been ongoing to investigate the main principles for allocating scarce medical resources during pandemics. Medical experts working at the COVID-19 care units interact with patients of different socioeconomic, clinical, paraclinical, and overall health statuses. While physicians should not be faced with situations where they would be obliged to decide which patient to treat due to the risk of human error as well as the double-burden of life-long emotional toll, the pandemic has increased the likelihood of such dilemmas, especially in settings with limited resources. Serious discussions on the ethical considerations of ventilator allocation were also raised during the pandemic. Utility (maximizing benefits) and equity (distributive justice) were two concerns raised in decision making in such dilemma which has also been considered to be \"the toughest triage\".\n\nWhat new knowledge the manuscript contributesThis longitudinal study provides new insights on optimizing the strategies for ventilation therapy prioritization among patients with COVID-19, based on the real-world data of nearly 600,000 hospitalized patients with COVID-19. So far, there has been focus on how to prioritize patients with COVID-19 for ventilation therapy. Nevertheless, there has not been much evidence on how much patients of different age groups with various underlying conditions actually benefitted from ventilation therapy based on real-world data. The results of this study could have a significant message: should the prioritization guidelines for ventilators allocation take no notice of the real-world data, patients might be deprived of ventilation therapy, who could benefit the most from it. This would pave the way to capture clearer picture in the possible future pandemics.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Mohsen Abbasi-Kangevari", - "author_inst": "Non-Communicable Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran" - }, - { - "author_name": "Ali Ghanbari", - "author_inst": "Non-Communicable Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran" - }, - { - "author_name": "Mohammad-Reza Malekpour", - "author_inst": "Non-Communicable Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran" - }, - { - "author_name": "Seyyed-Hadi Ghamari", - "author_inst": "Non-Communicable Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran" - }, - { - "author_name": "Sina Azadnajafabad", - "author_inst": "Non-Communicable Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran" - }, - { - "author_name": "Sahar Saeedi Moghaddam", - "author_inst": "Non-Communicable Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran" - }, - { - "author_name": "Mohammad Keykhaei", - "author_inst": "Feinberg Cardiovascular Research Institute, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611" - }, - { - "author_name": "Rosa Haghshenas", - "author_inst": "Non-Communicable Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran" - }, - { - "author_name": "Ali Golestani", - "author_inst": "Non-Communicable Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran" - }, - { - "author_name": "Mohammad-Mahdi Rashidi", - "author_inst": "Non-Communicable Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran" - }, - { - "author_name": "Erfan Ghasemi", - "author_inst": "Non-Communicable Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran" - }, - { - "author_name": "Nazila Rezaei", - "author_inst": "Non-Communicable Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran" - }, - { - "author_name": "Hamid Reza Jamshidi", - "author_inst": "Department of Pharmacology, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran" - }, - { - "author_name": "Negar Rezaei", - "author_inst": "Non-Communicable Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran" - }, - { - "author_name": "Bagher Larijani", - "author_inst": "Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.08.03.22278351", "rel_title": "A Reagent and Virus Benchmarking Panel for a Uniform Analytical Performance Assessment of N Antigen-Based Diagnostic Tests for COVID-19", @@ -219896,6 +221941,73 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.08.05.502940", + "rel_title": "Human endogenous retrovirus-R envelope is a host restriction factor against severe acute respiratory syndrome-coronavirus-2", + "rel_date": "2022-08-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.05.502940", + "rel_abs": "Coronavirus induced disease-19 (COVID-19), caused by the SARS-CoV-2 remains a major global health challenge. Human endogenous retroviruses (HERVs) represent retroviral elements that got integrated into the ancestral human genome. HERVs are important in development and diseases, including cancer, inflammation and viral infections. Here, we analyzed the expression of several HERVs in SARS-CoV-2 infected cells and observed increased activity of HERV-E, HERV-V, HERV-FRD, HERV-MER34, HERV-W and HERV-KHML2. In contrast, HERV-R-envelope was downregulated in cell-based models and COVID-19 patient PBMCs. HERV-R overexpression inhibited SARS-CoV-2 replication, suggesting its antiviral action. Further studies demonstrated the role of extracellular signal-regulated kinase (ERK) in regulating HERV-R antiviral activity. Cross-talk between the ERK and p38 MAPK controls HERV-R envelope synthesis, which in turn modulates the replication of SARS-CoV-2. These findings establish the importance of HERV-R envelope as a host restriction factor against SARS-CoV-2 and illustrate the advantage of integration and evolutionary maintenance of retroviral-elements in the human genome.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Nidhi Gupta", + "author_inst": "Translational Health Science and Technology Institute" + }, + { + "author_name": "Shabnam Ansari", + "author_inst": "Translational Health Science Technology Institute" + }, + { + "author_name": "Rohit Verma", + "author_inst": "Translational Health Science Technology Institute" + }, + { + "author_name": "Oinam N Singh", + "author_inst": "Translational Health Science Technology Institute" + }, + { + "author_name": "Mukesh Kumar Yadav", + "author_inst": "Translational Health Science Technology Institute" + }, + { + "author_name": "Akshay Binayke", + "author_inst": "Translational Health Science Technology Institute" + }, + { + "author_name": "Kamini Jakhar", + "author_inst": "Transnational Health Science and Technology Institute" + }, + { + "author_name": "Shailendra Mani", + "author_inst": "Transnational Health Science and Technology Institute" + }, + { + "author_name": "Amit Awasti", + "author_inst": "Translational Health Science and Technology Institute" + }, + { + "author_name": "Shalimar", + "author_inst": "All India Institute of Medical Sciences" + }, + { + "author_name": "Baibaswata Nayak", + "author_inst": "All India Institute of Medical Sciences" + }, + { + "author_name": "CT Ranjith-Kumar", + "author_inst": "GGSIPU" + }, + { + "author_name": "Milan Surjit", + "author_inst": "Translational Health Science Technology Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.08.04.22278160", "rel_title": "The effect of Omicron breakthrough infection and extended BNT162b2 booster dosing on neutralization breadth against SARS-CoV-2 variants of concern", @@ -221167,61 +223279,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.08.02.22278311", - "rel_title": "COVID-19 illness, SARS-CoV2 infection, and subsequent suicidal ideation in the French nationwide population-based EpiCov cohort : a propensity score analysis of more than 50,000 individuals.", - "rel_date": "2022-08-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.02.22278311", - "rel_abs": "Symptomatic COVID-19 appears to be associated with suicidal ideation but longitudinal evidence is still scarce. SARS-CoV2-induced neurological damages might underline this association, but findings are inconsistent. We therefore investigated the association between COVID-19 disease and subsequent suicidal ideation in the general population, using both self-reported symptoms and serology as well as inverse probability weighting to draw as near as possible to the direct association.\n\nUsing data from the nationwide French EpiCov cohort, COVID-19 disease was assessed through 1) COVID-19 illness (self-reported symptoms of sudden loss of taste/smell or fever alongside cough, shortness of breath or chest oppression, between February and November 2020), and 2) SARS-CoV2 infection (Spike protein ELISA test screening in dried-blood-spot samples). Suicidal ideation was self-reported between December 2020 and July 2021. Inverse probability weighting with propensity scores was used as an adjustment strategy, leading to balanced sociodemographic and health-related factors between the exposed and non-exposed groups of both COVID-19 disease measures. Then, modified Poisson regression models were used to investigate the association of COVID-19 illness and SARS-CoV2 infection with subsequent suicidal ideation.\n\nAmong 52,050 participants from the EpiCov cohort, 1.68% [1.54% - 1.82%] reported suicidal ideation in the first half of 2021, 9.57% [9.24% - 9.90%] had a SARS-CoV2 infection in 2020 and 13.23% [12.86% - 13.61%] reported COVID-19 symptoms in 2020. COVID-19 illness in 2020 was associated with higher risks of subsequent suicidal ideation in the first half of 2021 (Relative Riskipw [CI95%]= 1.43 [1.20 - 1.69]) while SARS-CoV2 infection in 2020 was not (RRipw = 0.88 [0.69 - 1.12]).\n\nIf COVID-19 illness was associated with subsequent suicidal ideation, the exact role of SARS-CoV2 infection with respect to suicide risk has yet to be clarified. Psychological support should be offered to persons recovering from symptomatic COVID-19 in order to minimize suicidal ideation risk. Moreover, if such psychological support is to be implemented, serology status alone does not seem a relevant criterion to define persons who suffered from COVID-19 to prioritize.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Camille Davisse-Paturet", - "author_inst": "Inserm U1018" - }, - { - "author_name": "Massimiliano Orri", - "author_inst": "McGill University, Department of Psychiatry (Montreal, Quebec, Canada)" - }, - { - "author_name": "Stephane Legleye", - "author_inst": "Paris-Saclay University, UVSQ, Inserm, Center for Epidemiology and Population Health (Paris, France) and ENSAI (Bruz, France)" - }, - { - "author_name": "Aline-Marie Florence", - "author_inst": "Sorbonne University, Inserm, Pierre Louis institute of Epidemiology and Public Health (Paris, France)" - }, - { - "author_name": "Jean-Baptiste Hazo", - "author_inst": "French Ministry of Solidarity and Health, Drees (Paris, France)" - }, - { - "author_name": "Josiane WARSZAWSKI", - "author_inst": "INSERM CESP U1018, Universite Paris-Saclay,Service de sante publique, AP-HP" - }, - { - "author_name": "Bruno Falissard", - "author_inst": "Paris-Saclay University, UVSQ, Inserm, Center for Epidemiology and Population Health (Paris, France)" - }, - { - "author_name": "Marie-Claude Geoffroy", - "author_inst": "McGill University" - }, - { - "author_name": "Maria Melchior", - "author_inst": "INSERM" - }, - { - "author_name": "Alexandra Rouquette", - "author_inst": "Paris-Saclay University, UVSQ, Inserm, Center for Epidemiology and Population Health (Paris, France) and APHP, Paris-Saclay University, Department of Epidemiolo" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.08.02.22278317", "rel_title": "Healthcare workers' worries and Monkeypox vaccine advocacy during the first month of the WHO Monkeypox alert: Cross-sectional survey in Saudi Arabia", @@ -221858,6 +223915,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.08.01.22278235", + "rel_title": "Change in incidence of cardiovascular diseases during the covid-19 pandemic and vaccination campaign: data from the nationwide French hospital discharge database", + "rel_date": "2022-08-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.01.22278235", + "rel_abs": "ImportanceThe covid-19 pandemic induced a severe disruption in hospital activity. Cardiovascular illnesses represent a major health burden in industrialised countries and are second in terms of hospital bed occupancy in France. Considering the resources mobilized and the public health issue involved, it is necessary to study the impact of the pandemic on their incidences.\n\nObjectiveTo monitor changes in the incidence of cardiovascular diseases during years 2020 and 2021 compared to 2019.\n\nDesignNationwide population-based cohort study.\n\nSettingFrench hospital discharge database between January 1 and October 30 in 2019, 2020 and 2021.\n\nParticipantsNew patients hospitalized for vascular disease in Metropolitan France. A patient was considered as incident for a morbidity if not present in the database in the previous two years with the morbidity as the primary reason for admission.\n\nMain outcome measuresStandardized hospitalization incidence difference and relative risk of hospitalization for a series of targeted vascular diseases from January 1 to October 31 for 2021 versus 2019. Demographic data from 2019 were used for the standardization of patient counts by 10-year age strata for each morbidity and year.\n\nResultsWhile the relative risk of hospitalization in 2021 versus 2019 decreased for almost all diseases, an increase in relative risk was observed for myocarditis (28.0%) and pulmonary embolisms (10.0%).\n\nIn 2020, the relative risk of hospitalization versus 2019 also decreased for almost all diseases but remained stable for myocarditis and increased by 4.0% for pulmonary embolisms.\n\nIn 2021, the difference in myocarditis coincided with the vaccination campaign in young individuals. The increase in pulmonary embolism occurred predominantly in older women, with a weak but still noticeable coincidence with the vaccination campaign.\n\nConclusionsThe deficit in care for patients with acute atherothrombotic manifestations in 2021 and 2020 shows a failure by the French healthcare system to rectify the deficiencies of 2020. The risk excess for pulmonary embolism cannot be entirely explained by covid-19 or by vaccine-induced immune thrombotic thrombocytopenia. This warrants investigating the risk/efficacy ratio of a temporary thromboprophylaxis in individuals at risk before vaccine.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Thierry Boudemaghe", + "author_inst": "Centre Hospitalier Universitaire de Nimes, Nimes, France" + }, + { + "author_name": "Lucas Leger", + "author_inst": "Centre Hospitalier Universitaire de Nimes, Nimes, France" + }, + { + "author_name": "Antonia Perez-Martin", + "author_inst": "Centre Hospitalier Universitaire de Nimes, Nimes, France" + }, + { + "author_name": "Carey M Suehs", + "author_inst": "Montpellier University Hospitals" + }, + { + "author_name": "Jean-Christophe Gris", + "author_inst": "Centre Hospitalier Universitaire de Nimes, Nimes, France" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2022.07.31.22278258", "rel_title": "Association of SARS-CoV-2 BA.4/BA.5 Omicron lineages with immune escape and clinical outcome", @@ -222949,65 +225041,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.07.31.502235", - "rel_title": "Antigenic characterization of the SARS-CoV-2 Omicron subvariant BA.2.75", - "rel_date": "2022-08-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.31.502235", - "rel_abs": "The SARS-CoV-2 Omicron subvariant BA.2.75 emerged recently and appears to be spreading rapidly. It has nine mutations in its spike compared to BA.2, raising concerns it may further evade vaccine-elicited and therapeutic antibodies. Here, we found BA.2.75 to be moderately more neutralization resistant to sera from vaccinated/boosted individuals than BA.2 (1.8-fold), similar to BA.2.12.1 (1.1-fold), but more neutralization sensitive than BA.4/5 (0.6-fold). Relative to BA.2, BA.2.75 showed heightened resistance to class 1 and class 3 monoclonal antibodies to the receptor-binding domain, while gaining sensitivity to class 2 antibodies. The resistance was largely conferred by the G446S and R460K mutations. Of note, BA.2.75 was slightly resistant (3.7-fold) to bebtelovimab, the only therapeutic antibody with potent activity against all Omicron subvariants. BA.2.75 also exhibited higher receptor binding affinity than other Omicron subvariants. BA.2.75 provides yet another example of the ongoing evolution of SARS-CoV-2 as it gains transmissibility while incrementally evading antibody neutralization.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Qian Wang", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Sho Iketani", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Zhiteng Li", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Yicheng Guo", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Andre Yanchen Yeh", - "author_inst": "School of Medicine, National Taiwan University, Taipei, Taiwan" - }, - { - "author_name": "Michael Liu", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Jian Yu", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Zizhang Sheng", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Yaoxing Huang", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Lihong Liu", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "David D Ho", - "author_inst": "Columbia University Irving Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.07.30.502143", "rel_title": "Evolution to increased positive charge on the viral spike protein may be part of the adaptation of SARS-CoV-2 to human transmission", @@ -223744,6 +225777,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.07.28.22278155", + "rel_title": "Failure to balance social contact matrices can bias models of infectious disease transmission", + "rel_date": "2022-07-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.28.22278155", + "rel_abs": "Spread of transmissible diseases is dependent on contact patterns in a population (i.e. who contacts whom). Therefore, many epidemic models incorporate contact patterns within a population through contact matrices. Social contact survey data are commonly used to generate contact matrices; however, the resulting matrices are often imbalanced, such that the total number of contacts reported by group A with group B do not match those reported by group B with group A. While the importance of balancing contact matrices has been acknowledged, how these imbalances affect modelled projections (e.g., peak infection incidence, impact of public health measures) has yet to be quantified. Here, we explored how imbalanced contact matrices from age-stratified populations (<15, 15+) may bias transmission dynamics of infectious diseases. First, we compared the basic reproduction number of an infectious disease when using imbalanced versus balanced contact matrices from 177 demographic settings. Then, we constructed a susceptible exposed infected recovered transmission model of SARS-CoV-2 and compared the influence of imbalanced matrices on infection dynamics in three demographic settings. Finally, we compared the impact of age-specific vaccination strategies when modelled with imbalanced versus balanced matrices. Models with imbalanced matrices consistently underestimated the basic reproduction number, had delayed timing of peak infection incidence, and underestimated the magnitude of peak infection incidence. Imbalanced matrices also influenced cumulative infections observed per age group, and the projected impact of age-specific vaccination strategies. For example, when vaccine was prioritized to individuals <15 in a context where individuals 15+ underestimated their contacts with <15, imbalanced models underestimated cumulative infections averted among 15+ by 24.4%. We conclude stratified transmission models that do not consider reciprocity of contacts can generate biased projections of epidemic trajectory and impact of targeted public health interventions. Therefore, modellers should ensure and report on balancing of their contact matrices for stratified transmission models.\n\nAUTHOR SUMMARYTransmissible diseases such as COVID-19 spread according to who contacts whom. Therefore, mathematical transmission models - used to project epidemics of infectious diseases and assess the impact of public health interventions - require estimates of who contacts whom (also referred to as a contact matrix). Contact matrices are commonly generated using contact surveys, but this data is often imbalanced, where the total number of contacts reported by group A with group B does not match those reported by group B with group A. Although these imbalances have been acknowledged as an issue, the influence of imbalanced matrices on modelled projections (e.g. peak incidence, impact of public health interventions) has not been explored. Using a theoretical model of COVID-19 with two age groups (<15 and 15+), we show models with imbalanced matrices had biased epidemic projections. Models with imbalanced matrices underestimated the initial spread of COVID-19 (i.e. the basic reproduction number), had later time to peak COVID-19 incidence and smaller peak COVID-19 incidence. Imbalanced matrices also influenced cumulative infections observed per age group, and the estimated impact of an age-specific vaccination strategy. Given imbalanced contact matrices can reshape transmission dynamics and model projections, modellers should ensure and report on balancing of contact matrices.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Mackenzie A. Hamilton", + "author_inst": "MAP Centre for Urban Health Solutions, St. Michael's Hospital, Unity Health Toronto" + }, + { + "author_name": "Jesse Knight", + "author_inst": "University of Toronto" + }, + { + "author_name": "Sharmistha Mishra", + "author_inst": "University of Toronto" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.07.29.22278190", "rel_title": "SARS-CoV-2 IgG seroprevalence surveys in blood donors before the vaccination campaign, France 2020-2021", @@ -224807,49 +226867,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2022.07.26.22278080", - "rel_title": "The Association of Socioeconomic Status, the Concern for Catching Covid-19, and Anxiety Between Individuals with and without a Cancer History from a Cross-sectional Study", - "rel_date": "2022-07-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.26.22278080", - "rel_abs": "BackgroundCOVID-19 has negative impacts on mental health in all populations. Individuals with a history of cancer have an increased risk of catching and having more severe symptoms of COVID-19 than the general public. The objective of this study was to examine how cancer history and concern for catching COVID-19 relate to anxiety.\n\nMethodsThis cross-sectional study is part of the \"Impact of COVID-19 on Behaviors across the Cancer Control Continuum in Ohio\" project conducted from June to November 2020. The sample consisted of 7012 participants who completed survey online, by phone, or by mail. Self-reported concern for catching COVID-19 and anxiety over the last 7 days were used. Linear and logistic regression models were performed to determine the association between demographics, cancer history, concern for catching COVID-19, and anxiety.\n\nResultsIn our study sample, most participants rated their concern for catching COVID-19 as moderately high or high (56%) and reported anxiety for one day or more (63%). Individuals with a cancer history were more likely to report moderate-high or high concern for catching COVID-19 (59% vs.54%, P<0.001) but less likely to report anxiety (58% vs. 67%, P<0.001) compared to those without a cancer history. Individuals with higher SES were less likely to report anxiety (middle vs. low SES: OR=0.68, 95%CI=0.59-0.79; high vs. low SES: OR=0.70, 95%CI=0.61-0.82). Additionally, increased concern for catching COVID-19 was associated with higher likelihood of reporting anxiety (moderate-low vs. low: OR=1.65, 95%CI=1.42-1.92; moderate-high vs. low: OR=2.98, 95%CI=2.53-3.50; high vs. low: OR=4.35, 95%CI=3.74-5.07).\n\nConclusionsOur findings suggest individuals with a cancer history reported higher concern for catching COVID-19. Higher concern for catching COVID was associated with anxiety. These findings indicate that healthcare providers should pay special attention to the different populations to reduce concerns for catching COVID-19 and provide strategies to improve mental health during a pandemic outbreak.\n\nFundingThis study was supported by a supplement to The Ohio State University Comprehensive Cancer Center (OSUCCC) core support grant (P30 CA016058), and the OSUCCC The Recruitment, Intervention and Survey Shared Resource (RISSR)(P30 CA016058).The Ohio State University Center for Clinical and Translational Science grant support (National Center for Advancing Translational Sciences, Grant UL1TR001070) in publications relating to this project. This work was supported by the National Cancer Institute (F99CA253745 to X.Z.).", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Xiaochen Zhang", - "author_inst": "The Ohio State University" - }, - { - "author_name": "Impact of COVID-19 on Behaviors across the Cancer Control Continuum in Ohio group", - "author_inst": "" - }, - { - "author_name": "Sonya Sasmal", - "author_inst": "The Ohio State University" - }, - { - "author_name": "Mengda Yu", - "author_inst": "The Ohio State University" - }, - { - "author_name": "Brittany Bernardo", - "author_inst": "Denison College" - }, - { - "author_name": "Toyin Adeyanju", - "author_inst": "The Ohio State University" - }, - { - "author_name": "Electra Paskett", - "author_inst": "The Ohio State University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.07.26.22277799", "rel_title": "The COVID-19 pandemic impact on continuity of care provision on rare brain diseases and on Ataxia, Dystonia and PKU. A scoping review protocol", @@ -225550,6 +227567,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.07.27.22278096", + "rel_title": "Assessing COVID-19 pandemic excess deaths in Brazil: years 2020 and 2021", + "rel_date": "2022-07-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.27.22278096", + "rel_abs": "We estimated the impact of the COVID-19 pandemic on mortality in Brazil for 2020 and 2021 years. We used mortality data (2015-2021) from the Health Ministry, the Brazilian government, to fit linear mixed models for forecasting baseline deaths under non-pandemic conditions. An advantage of the linear mixed model is the flexibility to capture year-trend while dealing with the correlations among death counts over time. Following a specified model-building strategy, estimation of all-cause excess deaths at the country level and stratified by sex, age, ethnicity and region of residence, from March 2020 to December 2021. We also considered the estimation of excess deaths due to specific causes. The estimated all-cause excess deaths was 187 842 (95% PI: 164 122; 211 562, P-Score=16.1%) for weeks 10-53, 2020, and 441 048 (95% PI: 411 740; 470 356, P-Score=31.9%) for weeks 1-52, 2021. P-Score values ranged from 1.4% (RS, South) to 38.1% (AM, North) in 2020 and from 21.2% (AL and BA, Northeast) to 66.1% (RO, North) in 2021. Differences among men (18.4%) and women (13.4%) appeared in 2020 only, and the P-Score values were about 30% for both sexes in 2021. Except for youngsters (< 20 years old), all adult age groups were badly hit, especially those from 40 to 79 years old. In 2020, the Indigenous+East Asian population had the highest P-Score (26.2%), and the Black population suffered the greatest impact (34.7%) in 2021. The pandemic impact had enormous regional heterogeneity and substantial differences according to socio-demographic factors, mainly during the first wave, showing that some population strata benefited from the social distancing measures when they could adhere to them. In the second wave, the burden was very high for all but extremely high for some, highlighting that our society must tackle the health inequalities experienced by groups of different socio-demographic status.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Saditt Rocio Robles Colonia", + "author_inst": "UNESP: Universidade Estadual Paulista Julio de Mesquita Filho" + }, + { + "author_name": "Lara Morena Cardeal", + "author_inst": "UNESP: Universidade Estadual Paulista Julio de Mesquita Filho" + }, + { + "author_name": "Rog\u00e9rio Antonio de Oliveira", + "author_inst": "UNESP: Universidade Estadual Paulista Julio de Mesquita Filho" + }, + { + "author_name": "Luzia Aparecida Trinca", + "author_inst": "UNESP: Universidade Estadual Paulista Julio de Mesquita Filho" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.07.26.22278002", "rel_title": "SARS-CoV-2 infection is associated with anti-desmoglein 2 autoantibody detection.", @@ -226729,29 +228777,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.07.27.501717", - "rel_title": "COVID19-vaccination affects breath methane dynamics", - "rel_date": "2022-07-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.27.501717", - "rel_abs": "Methane (CH4) is well known as a component in the exhaled breath of humans. It has been assumed for a long time that formation of CH4 in humans occurs exclusively by anaerobic microbial activity (methanogenesis) in the gastrointestinal tract. A fraction of the produced CH4 is excreted via the lungs and can then be detected in the breath. However, recent studies challenge this view by showing that CH4 might also be produced endogenously in cells by oxidative-reductive stress reactions. Thus, an increased and fluctuating level of breath CH4 compared to the base level of an individual might also indicate enhanced oxidative stress levels. Thus, monitoring breath CH4 levels might have great potential for in vivo diagnostics.\n\nGenerally, vaccines generate a strong immune response including the production of pro-inflammatory cytokines. To evaluate the effect from current vaccines against COVID-19 on breath CH4 dynamics, breath CH4 was monitored from 12 subjects prior and after the injection of several COVID-vaccines. Prior to COVID-19 vaccination the concentration of breath CH4 was frequently measured by gas chromatograph flame ionization detection (GC-FID, with analytical precision better than 10 parts per billion, ppbv) to obtain the individual variation range of breath CH4 for each subject. Following vaccination, CH4 breath samples were collected at high frequency for a period of 14 days.\n\nAll subjects monitored showed a strong response in breath CH4 release within 1 to 72 hours after vaccination including shifts and high fluctuations with maximum peaks showing a factor of up to {+/-}100 compared to base values. Thus, it is highly likely that the observed changes in breath CH4 are coupled to immune responses following Covid-19 vaccination. These preliminary results strongly support the hypothesis that non-microbial methane liberation and utilisation in the human body might be also linked to cellular processes and stress responses independent of classical microbial methanogenesis. Thus, CH4 might be used as a breath biomarker for specific immune responses and individual immune states.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Daniela Polag", - "author_inst": "Institute of Earth Sciences/ Heidelberg University" - }, - { - "author_name": "Frank Keppler", - "author_inst": "Institute of Earth Sciences, Heidelberg University; Heidelberg Center for the Environment (HCE), Heidelberg University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2022.07.26.501658", "rel_title": "Environmental Stability of Enveloped Viruses is Impacted by the Initial Volume and Evaporation Kinetics of Droplets", @@ -227444,6 +229469,33 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2022.07.22.501141", + "rel_title": "SARS-CoV-2 omicron variants succumb in vitro to Artemisia annua hot water extracts", + "rel_date": "2022-07-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.22.501141", + "rel_abs": "The SARS-CoV-2 (COVID-19) global pandemic continuous to infect and kill millions while rapidly evolving new variants that are more transmissible and evading vaccine-elicited antibodies. Artemisia annua L. extracts have shown potency against all previously tested variants. Here we further queried extract efficacy against omicron and its recent subvariants. Using Vero E6 cells, we measured the in vitro efficacy (IC50) of stored (frozen) dried-leaf hot-water A. annua L. extracts of four cultivars (A3, BUR, MED, and SAM) against SARS-CoV-2 variants: original WA1 (WT), BA.1.1.529+R346K (omicron), BA.2, BA.2.12.1, and BA.4. IC50 values normalized to the extract artemisinin (ART) content ranged from 0.5-16.5 {micro}M ART. When normalized to dry mass of the extracted A. annua leaves, values ranged from 20-106 {micro}g. Although IC50 values for these new variants are slightly higher than those reported for previously tested variants, they were within limits of assay variation. There was no measurable loss of cell viability at leaf dry weights [≤]50 {micro}g of any cultivar extract. Results continue to indicate that oral consumption of A. annua hot-water extracts (tea infusions) could potentially provide a cost-effective approach to help stave off this pandemic virus and its rapidly evolving variants.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Manoj S Nair", + "author_inst": "Columbia University" + }, + { + "author_name": "Yaoxing Huang", + "author_inst": "Columbia University" + }, + { + "author_name": "Pamela Weathers", + "author_inst": "Worcester Polytechnic Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2022.07.25.22278017", "rel_title": "Transfer learning for Covid-19 detection in medical images", @@ -228443,165 +230495,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, - { - "rel_doi": "10.1101/2022.07.20.22277797", - "rel_title": "A Randomised -Controlled Phase 2 trial of Molnupiravir in Unvaccinated and Vaccinated Individuals with Early SARS-CoV-2", - "rel_date": "2022-07-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.20.22277797", - "rel_abs": "BackgroundMolnupiravir was licensed for treating high-risk patients with COVID-19 based on data from unvaccinated adults. AGILE CST-2 (NCT04746183) Phase II reports safety and virological efficacy of molnupiravir in vaccinated and unvaccinated individuals.\n\nMethodsAdult out-patients with PCR-confirmed SARS-CoV-2 infection within five days of symptom onset were randomly assigned 1:1 to receive molnupiravir (800mg twice daily for five days) or placebo. The primary outcome was time to swab PCR-negativity, compared using a Bayesian model for estimating the probability of a superior virological response (Hazard Ratio>1) for molnupiravir over placebo. Secondary outcomes included change in viral titre at day 5, safety and tolerability, clinical progression and patient reported outcome measures. We analysed outcomes after the last participant reached day 29.\n\nFindingsOf 180 participants randomised (90 molnupiravir, 90 placebo), 50% were vaccinated. Infections with SARS-CoV-2 variants Delta (40%), Alpha (21%), Omicron (21%) and EU1 (16%) were represented. The median time to negative-PCR was 8 versus 11 days for molnupiravir and placebo (HR=1{middle dot}30, 95% CrI 0{middle dot}92-1{middle dot}71, p=0{middle dot}07 by Logrank and p=0{middle dot}03 by Breslow-Gehan tests). Although small numbers precluded subgroup analysis, no obvious differences were observed between vaccinated and unvaccinated participants. Using a two-point prior the probability of molnupiravir being superior to placebo (HR>1) was 75{middle dot}4%, which was just below our defined threshold of 80% for establishing superiority. Using an uninformative continuous prior, the probability of HR>1 was 94{middle dot}7%. As an exploratory analysis, the change in viral titre on day 5 (end of treatment) was significantly greater with molnupiravir compared with placebo. A total of 4 participants reported severe adverse events (grade 3+), 3 of whom were in the placebo arm.\n\nInterpretationWe found molnupiravir to be well-tolerated, with evidence for high probability of antiviral efficacy in a population of vaccinated and unvaccinated individuals infected with a broad range of viral variants.\n\nFundingFunded by Ridgeback Biotherapeutics and UK National Institute for Health and Care Research infrastructure funding. The AGILE platform infrastructure is supported by the Medical Research Council (grant number MR/V028391/1) and the Wellcome Trust (grant number 221590/Z/20/Z).", - "rel_num_authors": 36, - "rel_authors": [ - { - "author_name": "Saye H Khoo", - "author_inst": "University of Liverpool; Liverpool University Hospital NHS Foundation Trust" - }, - { - "author_name": "Richard FitzGerald", - "author_inst": "University of Liverpool; Liverpool University Hospital NHS Foundation Trust" - }, - { - "author_name": "Geoffrey Saunders", - "author_inst": "Southampton Clinical Trials Unit, University of Southampton" - }, - { - "author_name": "Calley Middleton", - "author_inst": "Southampton Clinical Trials Unit, University of Southampton" - }, - { - "author_name": "Shazaad Ahmad", - "author_inst": "NIHR Manchester Clinical Research Facility" - }, - { - "author_name": "Christopher J Edwards", - "author_inst": "NIHR Southampton Clinical Research Facility; University of Southampton" - }, - { - "author_name": "Dennis Hasdjiyiannaskis", - "author_inst": "NIHR Lancashire Clinical Research Facility" - }, - { - "author_name": "Lauren Walker", - "author_inst": "University of Liverpool; Liverpool University Hospital NHS Foundation Trust" - }, - { - "author_name": "Rebecca Lyon", - "author_inst": "Liverpool University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Victoria Shaw", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Pavel Mozgunov", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Jimstan Periselneris", - "author_inst": "NIHR Kings Clinical Research Facility" - }, - { - "author_name": "Christie Woods", - "author_inst": "Liverpool University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Katie Bullock", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Colin Hale", - "author_inst": "Liverpool University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Helen Reynolds", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Nichola Downs", - "author_inst": "Southampton Clinical Trials Unit, University of Southampton" - }, - { - "author_name": "Sean Ewings", - "author_inst": "Southampton Clinical Trials Unit, University of Southampton" - }, - { - "author_name": "Amanda Buadi", - "author_inst": "NIHR Southampton Clinical Research Facility" - }, - { - "author_name": "David Cameron", - "author_inst": "NIHR Lancashire Clinical Research Facility" - }, - { - "author_name": "Thomas Edwards", - "author_inst": "Liverpool School of Tropical Medicine" - }, - { - "author_name": "Emma Knox", - "author_inst": "Southampton Clinical Trials Unit, University of Southampton" - }, - { - "author_name": "I'ah Donovan-Banfield", - "author_inst": "University of Liverpool" - }, - { - "author_name": "William Greenhalf", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Justin Chiong", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Lara Lavelle-Langham", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Michael Jacobs", - "author_inst": "Royal Free London NHS Foundation Trust" - }, - { - "author_name": "Wendy Painter", - "author_inst": "Ridgeback Biotherapeutics" - }, - { - "author_name": "Wayne Holman", - "author_inst": "Ridgeback Biotherapeutics" - }, - { - "author_name": "David G Lalloo", - "author_inst": "Liverpool School of Tropical Medicine; Liverpool University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Michelle Tetlow", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Julian A Hiscox", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Thomas Jaki", - "author_inst": "University of Cambridge; University of Regensburg" - }, - { - "author_name": "Thomas Fletcher", - "author_inst": "Liverpool School of Tropical Medicine; Liverpool University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Gareth Griffiths", - "author_inst": "Southampton Clinical Trials Unit, University of Southampton" - }, - { - "author_name": "- AGILE CST-2 Study Group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.07.23.22277952", "rel_title": "Vaccination strategies impact the probability of outbreak extinction: a case study of COVID-19 transmission", @@ -229242,6 +231135,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.07.20.22277847", + "rel_title": "Association between pregnancy and severe COVID-19 symptoms in Qatar: a cross-sectional study", + "rel_date": "2022-07-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.20.22277847", + "rel_abs": "BackgroundThere is inconclusive evidence whether pregnancy exacerbates COVID-19 symptoms or not, and scarce data from the Middle East and North Africa region. The aim of this study was to investigate the association between pregnancy and COVID-19 symptoms in Qatar.\n\nMethodsThis cross-sectional study was carried out using data of all women with confirmed COVID-19, comparing pregnant and non-pregnant women of child-bearing age (18-49 years). Data of all COVID-19 cases were collected by the Ministry of Public Health (MoPH) in Qatar, between March and September 2020. Symptoms were compared by pregnancy status and classified into moderate and severe. Multivariable logistic and poisson regression was carried out to investigate the association between pregnancy and severity of COVID-19 symptoms.\n\nResultsDuring the study period, 105744 individuals were diagnosed with COVID-19, 16908 were women of childbearing age. From that sample, 799 women who were pregnant (mean age 29.9 years (SD 5.2)) and 16109 women who were not pregnant (mean age 33.1 years (SD 7.8)). After multivariable logistic regression, pregnancy was associated with a 1.4-fold higher odds of reporting any symptoms of COVID-19 (OR 1.41, 95% CI 1.18-1.68), and 1.3-fold higher odds of reporting shortness of breath (OR 1.29, 95% CI 1.02-1.63). After multivariable poisson regression, pregnancy was also associated with a higher number of symptoms (IRR 1.03, 95%CI 0.98-1.08).\n\nConclusionOur findings suggest that, in this setting, pregnant women are more likely to have symptomatic COVID-19, and shortness of breath, compared to non-pregnant women of childbearing age.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Alla\u2019 K. Al-Qassem", + "author_inst": "Qatar University" + }, + { + "author_name": "Ammar B. Humaidi", + "author_inst": "Qatar University" + }, + { + "author_name": "Amna K. Al-Kuwari", + "author_inst": "Qatar University" + }, + { + "author_name": "Elham M. Hasan", + "author_inst": "Qatar University" + }, + { + "author_name": "Nosaiba H. Yakti", + "author_inst": "Qatar University" + }, + { + "author_name": "Rakan M. Al-Hathal", + "author_inst": "Qatar University" + }, + { + "author_name": "Devendra Bansal", + "author_inst": "MoPH: Ministry of Public Health Qatar" + }, + { + "author_name": "Elmoubashar Abu Baker Abd Farag", + "author_inst": "MoPH: Ministry of Public Health Qatar" + }, + { + "author_name": "Hamad E. Al-Romaihi", + "author_inst": "MoPH: Ministry of Public Health Qatar" + }, + { + "author_name": "Mohammed H. J. Al-Thani", + "author_inst": "MoPH: Ministry of Public Health Qatar" + }, + { + "author_name": "Omran A. H. Musa", + "author_inst": "MoPH: Ministry of Public Health Qatar" + }, + { + "author_name": "Suhail Doi", + "author_inst": "Qatar University" + }, + { + "author_name": "Tawanda Chivese", + "author_inst": "Qatar University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.07.20.22277849", "rel_title": "Changes in mobility patterns during the COVID-19 pandemic in Zambia: implications for the effectiveness of NPIs in Sub-Saharan Africa", @@ -230105,73 +232065,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.07.20.22277866", - "rel_title": "Prevalence and Factors Associated with Mental Illness Symptoms among School Students Post Lockdown of the COVID-19 Pandemic in the United Arab Emirates: A Cross-Sectional National Study", - "rel_date": "2022-07-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.20.22277866", - "rel_abs": "Data from the United Arab Emirates about the mental health status of the younger population is limited. The current study aimed to assess the prevalence of anxiety, depression, and risk for PTSD among school students post lockdown of the current COVID-19 pandemic. A sample of 3745 students and their parents across the country answered a web-based survey. Parents provided bio-demographic data and students answered questions from the Mood and Feeling Questionnaire (MFQ-Child Self-report), Screen for Child Anxiety Related Disorders (SCARED-Child Version), and Childrens Revised Impact of Event Scale (CRIES-8). Findings showed that the risk for PTSD was the most prevalent (40.6%), followed by symptoms of anxiety (23.3%), and depression (17.1%). For gender differences, symptoms of the three conditions were higher in female students by 6.9%. Moreover, symptoms of depression and anxiety were found to be higher among late adolescents. Further analysis revealed that having medical problems ({beta} = 2.0, p < 0.001) and witnessing the death of a close family member due to COVID-19 ({beta} = 1.7, p < 0.001) were positive predictors associated with PTDS, depression, and anxiety. The study concluded that post COVID-19 lockdown, symptoms of anxiety, depression, and risk for PTSD are prevalent among students in the UAE. Researchers recommend the initiation of a national school mental health screening program and the provision of follow-up services for vulnerable students. Another must-have is the integration of a mental health support system in the emergency and disaster preparedness future plans.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Nariman Ghader", - "author_inst": "Emirates Health Services" - }, - { - "author_name": "Noor Al Mheiri", - "author_inst": "Emirates Health Services" - }, - { - "author_name": "Asma Fikri", - "author_inst": "Ministry of Health and Prevention-United Arab Emirates" - }, - { - "author_name": "Hira AbdulRazzak", - "author_inst": "Ministry of Health and Prevention-United Arab Emirates" - }, - { - "author_name": "Hassan Saleheen", - "author_inst": "Abu Dhabi Public Health Center" - }, - { - "author_name": "Basema Saddik", - "author_inst": "University of Sharjah" - }, - { - "author_name": "Yousef Aljawarneh", - "author_inst": "Higher Colleges of Technology, United Arab Emirates" - }, - { - "author_name": "Heyam Dalky", - "author_inst": "Higher Colleges of Technology -United Arab Emirates" - }, - { - "author_name": "Ammar Al Banna", - "author_inst": "Al Jalila Children Hospital-United Arab Emirates" - }, - { - "author_name": "Shamma Al Memari", - "author_inst": "Abu Dhabi Public Health Center" - }, - { - "author_name": "Budoor Al Shehhi", - "author_inst": "Abu Dhabi Public Health Center" - }, - { - "author_name": "Shereena Al Mazrouei", - "author_inst": "Abu Dhabi Public Health Center" - }, - { - "author_name": "Omniyat Al Hajeri", - "author_inst": "Abu Dhabi Public Health Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2022.07.20.22277839", "rel_title": "Risk factors for severe COVID-19 among HIV-infected and-uninfected individuals in South Africa, April 2020- March 2022:data from sentinel surveillance.", @@ -230864,6 +232757,173 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.07.15.22277570", + "rel_title": "Pharmacometric assessment of the in-vivo antiviral activity of ivermectin in early symptomatic COVID-19", + "rel_date": "2022-07-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.15.22277570", + "rel_abs": "BackgroundThere is no generally accepted methodology for in vivo assessment of antiviral activity in SARS-CoV-2 infection. Ivermectin has been recommended widely as a treatment of COVID-19, but whether it has significant antiviral activity in vivo is uncertain.\n\nMethodsIn a multicentre open label, randomized, controlled adaptive platform trial, adult patients with early symptomatic COVID-19 were randomized to one of six treatment arms including high dose ivermectin (600{micro}g/kg daily for seven days), the monoclonal antibodies casirivimab and imdevimab (600mg/600mg), and no study drug. Viral clearance rates were derived from daily duplicate oropharyngeal quantitative PCR measurements. This ongoing trial is registered at ClinicalTrials.gov (NCT05041907).\n\nResultsRandomization to the ivermectin arm was stopped after enrolling 205 patients into all arms, as the prespecified futility threshold was reached. Compared with the no study drug arm, the mean estimated SARS-CoV-2 viral clearance following ivermectin was 9.1% slower [95%CI -27.2% to +11.8%; n=45 versus n=41], whereas in a preliminary analysis of the casirivimab/imdevimab arm it was 52.3% faster [95%CI +7.0% to +115.1%; n=10 (Delta variant) versus n=41].\n\nConclusionsHigh dose ivermectin did not have measurable antiviral activity in early symptomatic COVID-19. Measured in this way viral clearance rate is a valuable pharmacodynamic measure in assessing antiviral COVID-19 therapeutics in vivo.\n\nFunding\"Finding treatments for COVID-19: A phase 2 multi-centre adaptive platform trial to assess antiviral pharmacodynamics in early symptomatic COVID-19 (PLAT-COV)\" is funded by the Wellcome Therapeutics Accelerator (223195/Z/21/Z).\n\nImpactO_LIRate of viral clearance determined from daily duplicate oropharyngeal swabs over one week is an efficient measure of antiviral efficacy in early COVID-19 infection.\nC_LIO_LIHigh dose ivermectin did not demonstrate measurable antiviral activity in early symptomatic COVID-19 infection.\nC_LI", + "rel_num_authors": 38, + "rel_authors": [ + { + "author_name": "William HK Schilling", + "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand; Centre for Tropical Medicine and Global Health, Nuff" + }, + { + "author_name": "Podjanee Jittamala", + "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand; Department of Tropical Hygiene, Faculty of Tropical " + }, + { + "author_name": "James A Watson", + "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand; Centre for Tropical Medicine and Global Health, Nuff" + }, + { + "author_name": "Maneerat Ekkapongpisit", + "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand" + }, + { + "author_name": "Tanaya Siripoon", + "author_inst": "Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Thailand" + }, + { + "author_name": "Thundon Ngamprasertchai", + "author_inst": "Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Thailand" + }, + { + "author_name": "Viravarn Luvira", + "author_inst": "Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Thailand" + }, + { + "author_name": "Sasithon Pongwilai", + "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand" + }, + { + "author_name": "Cintia Cruz", + "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand; Centre for Tropical Medicine and Global Health, Nuff" + }, + { + "author_name": "James J Callery", + "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand; Centre for Tropical Medicine and Global Health, Nuff" + }, + { + "author_name": "Simon Boyd", + "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand; Centre for Tropical Medicine and Global Health, Nuff" + }, + { + "author_name": "Varaporn Kruabkontho", + "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand" + }, + { + "author_name": "Thatsanun Ngernseng", + "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand" + }, + { + "author_name": "Jaruwan Tubprasert", + "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand" + }, + { + "author_name": "Mohammad Yazid Abdad", + "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand; Centre for Tropical Medicine and Global Health, Nuff" + }, + { + "author_name": "Nattaporn Piaraksa", + "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand" + }, + { + "author_name": "Kanokon Suwannasin", + "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand" + }, + { + "author_name": "Pongtorn Hanboonkunupakarn", + "author_inst": "Bangplee Hospital, Ministry of Public Health, Thailand" + }, + { + "author_name": "Borimas Hanboonkunupakarn", + "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand; Department of Clinical Tropical Medicine, Faculty of" + }, + { + "author_name": "Sakol Sookprome", + "author_inst": "Bangplee Hospital, Ministry of Public Health, Thailand" + }, + { + "author_name": "Kittiyod Poovorawan", + "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand; Department of Clinical Tropical Medicine, Faculty of" + }, + { + "author_name": "Janjira Thaipadungpanit", + "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand; Department of Clinical Tropical Medicine, Faculty of" + }, + { + "author_name": "Stuart Blacksell", + "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand; Centre for Tropical Medicine and Global Health, Nuff" + }, + { + "author_name": "Mallika Imwong", + "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand; Department of Molecular Tropical Medicine and Geneti" + }, + { + "author_name": "Joel Tarning", + "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand; Centre for Tropical Medicine and Global Health, Nuff" + }, + { + "author_name": "Walter J Taylor", + "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand; Centre for Tropical Medicine and Global Health, Nuff" + }, + { + "author_name": "Vasin Chotivanich", + "author_inst": "Faculty of Medicine, Navamindradhiraj University, Thailand" + }, + { + "author_name": "Chunlanee Sangketchon", + "author_inst": "Faculty of Science and Health Technology, Navamindradhiraj University, Thailand" + }, + { + "author_name": "Wiroj Ruksakul", + "author_inst": "Faculty of Medicine, Navamindradhiraj University, Thailand" + }, + { + "author_name": "Kesinee Chotivanich", + "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand; Department of Clinical Tropical Medicine, Faculty of" + }, + { + "author_name": "Mauro Martins Teixeira", + "author_inst": "Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Brazil" + }, + { + "author_name": "Sasithon Pukrittayakamee", + "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand; Department of Clinical Tropical Medicine, Faculty of" + }, + { + "author_name": "Arjen M Dondorp", + "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand; Centre for Tropical Medicine and Global Health, Nuff" + }, + { + "author_name": "Nicholas PJ Day", + "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand; Centre for Tropical Medicine and Global Health, Nuff" + }, + { + "author_name": "Watcharapong Piyaphanee", + "author_inst": "Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Thailand" + }, + { + "author_name": "Weerapong Phumratanaprapin", + "author_inst": "Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Thailand" + }, + { + "author_name": "Nicholas J White", + "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand; Centre for Tropical Medicine and Global Health, Nuff" + }, + { + "author_name": "- PLATCOV Collaborative Group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.07.18.22277434", "rel_title": "Adaptive sentinel testing in workplace for COVID-19 pandemic", @@ -231867,53 +233927,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.07.18.22277695", - "rel_title": "Pandemic modelling for regions implementing an elimination strategy", - "rel_date": "2022-07-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.18.22277695", - "rel_abs": "During the COVID-19 pandemic, some countries, such as Australia, China, Iceland, New Zealand, Thailand, and Vietnam successfully implemented an elimination strategy, enacting strict border control and periods of lockdowns to end community transmission. Atlantic Canada and Canadas territories implemented similar policies, and reported long periods with no community cases. In Newfoundland and Labrador (NL), Nova Scotia, and Prince Edward Island a median of 80% or more of daily reported cases were travel-related from July 1, 2020 to May 31, 2021. With increasing vaccination coverage, it may be appropriate to exit an elimination strategy, but most existing epidemiological frameworks are applicable only to situations where most cases occur in the community, and are not appropriate for regions that have implemented an elimination strategy. To inform the pandemic response in regions that are implementing an elimination strategy, we extend importation modelling to consider post-arrival travel restrictions, and pharmaceutical and non-pharmaceutical interventions in the local community. We find that shortly after the Omicron variant had begun spreading in Canada, the expected daily number of spillovers, infections spread to NL community members from travelers and their close contacts, was higher than any time previously in the pandemic. By December 24, 2021, the expected number of spillovers was 44% higher than the previous high, which occurred in late July 2021 shortly after travel restrictions were first relaxed. We develop a method to assess the characteristics of potential future community outbreaks in regions that are implementing an elimination strategy. We apply this method to predict the effect of variant and vaccination coverage on the size of hypothetical community outbreaks in Mount Pearl, a suburb of the St. Johns metropolitan area in NL. Our methodology can be used to evaluate alternative plans to relax public health restrictions when vaccine coverage is high in regions that have implemented an elimination strategy. This manuscript was submitted as part of a theme issue on \"Modelling COVID-19 and Preparedness for Future Pandemics\".", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Amy Hurford", - "author_inst": "Memorial University" - }, - { - "author_name": "Maria M Martignoni", - "author_inst": "Memorial University of Newfoundland" - }, - { - "author_name": "Jesus Concepcion Loredo-Osti", - "author_inst": "Memorial University of Newfoundland and Labrador" - }, - { - "author_name": "Francis Anokye", - "author_inst": "Memorial University of Newfoundland and Labrador" - }, - { - "author_name": "Julien Arino", - "author_inst": "University of Manitoba" - }, - { - "author_name": "Bilal Saleh Husain", - "author_inst": "University of New Brunswick" - }, - { - "author_name": "Brian Gaas", - "author_inst": "Government of Yukon" - }, - { - "author_name": "James Watmough", - "author_inst": "University of New Brunswick" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.07.18.22277757", "rel_title": "COVID-19 Vaccine Booster Dose Willingness Among Patients with Inflammatory Bowel Disease on Infliximab and Vedolizumab: A Cross-Sectional Study", @@ -232642,6 +234655,165 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.07.18.22277743", + "rel_title": "Efficacy of the AZD1222 (ChAdOx1 nCoV-19) COVID-19 Vaccine Against SARS-CoV-2 Variants of Concern", + "rel_date": "2022-07-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.18.22277743", + "rel_abs": "In this South African phase 1/2b study, we demonstrated vaccine efficacy (VE) of two doses of AZD1222 for asymptomatic and symptomatic SARS-CoV-2 infection: 90.6% against wild-type and 77.1% against the Delta variant [≥]9 months after vaccination. VE against infection with the Beta variant, which preceded circulation of Delta, was 6.7%.\n\nClinical trial identifierCT.gov NCT04444674", + "rel_num_authors": 36, + "rel_authors": [ + { + "author_name": "Anthonet L. Koen", + "author_inst": "University of the Witwatersrand" + }, + { + "author_name": "Alane Izu", + "author_inst": "University of the Witwatersrand" + }, + { + "author_name": "Vicky Baillie", + "author_inst": "University of the Witwatersrand" + }, + { + "author_name": "Gaurav Kwatra", + "author_inst": "University of the Witwatersrand" + }, + { + "author_name": "Clare L. Cutland", + "author_inst": "University of the Witwatersrand" + }, + { + "author_name": "Lee Fairlie", + "author_inst": "University of the Witwatersrand" + }, + { + "author_name": "Sherman D. Padayachee", + "author_inst": "Setshaba Research Centre" + }, + { + "author_name": "Keertan Dheda", + "author_inst": "University of Cape Town Lung Institute" + }, + { + "author_name": "Shaun L. Barnabas", + "author_inst": "Family Centre for Research with Ubuntu, Department of Paediatrics, Stellenbosch University" + }, + { + "author_name": "Qasim Ebrahim Bhorat", + "author_inst": "Soweto Clinical Trials Centre, Soweto, South Africa" + }, + { + "author_name": "Carmen Briner", + "author_inst": "University of the Witwatersrand" + }, + { + "author_name": "Katija Ahmed", + "author_inst": "Setshaba Research Centre" + }, + { + "author_name": "Sutika Bhikha", + "author_inst": "University of the Witwatersrand" + }, + { + "author_name": "Jinal N. Bhiman", + "author_inst": "National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa" + }, + { + "author_name": "Jeanine du Plessis", + "author_inst": "University of the Witwatersrand" + }, + { + "author_name": "Aliasgar Esmail", + "author_inst": "Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and University of Cape Town Lung Institute" + }, + { + "author_name": "Elizea Horne", + "author_inst": "University of the Witwatersrand" + }, + { + "author_name": "Shi-Hsia Hwa", + "author_inst": "Africa Health Research Institute" + }, + { + "author_name": "Aylin Oomen-Jose", + "author_inst": "University of the Witwatersrand" + }, + { + "author_name": "Teresa Lambe", + "author_inst": "Oxford Vaccine Group, Department of Paediatrics, University of Oxford" + }, + { + "author_name": "Matt Laubscher", + "author_inst": "University of the Witwatersrand" + }, + { + "author_name": "Mookho Malahleha", + "author_inst": "Setshaba Research Centre" + }, + { + "author_name": "Gabriella Benade", + "author_inst": "University of the Witwatersrand" + }, + { + "author_name": "Shakeel McKenzie", + "author_inst": "University of the Witwatersrand" + }, + { + "author_name": "Suzette Oelofse", + "author_inst": "Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and University of Cape Town Lung Institute" + }, + { + "author_name": "Faeezah Patel", + "author_inst": "University of the Witwatersrand" + }, + { + "author_name": "Sureshnee Pillay", + "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal" + }, + { + "author_name": "Sarah Rhead", + "author_inst": "Oxford Vaccine Group, Department of Paediatrics, University of Oxford" + }, + { + "author_name": "Hylton Rodel", + "author_inst": "Africa Health Research Institute" + }, + { + "author_name": "Carol Taoushanis", + "author_inst": "University of the Witwatersrand" + }, + { + "author_name": "Houriiyah Tegally", + "author_inst": "Stellenbosch University" + }, + { + "author_name": "Asha Thombrayil", + "author_inst": "University of the Witwatersrand" + }, + { + "author_name": "Tonya Villafana", + "author_inst": "AstraZeneca" + }, + { + "author_name": "Sarah Gilbert", + "author_inst": "Nuffield Department of Medicine, University of Oxford" + }, + { + "author_name": "Andrew J. Pollard", + "author_inst": "Oxford Vaccine Group, Department of Paediatrics, University of Oxford" + }, + { + "author_name": "Shabir Madhi", + "author_inst": "University of the Witwatersrand" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.07.18.500430", "rel_title": "Experimental infection of Mexican free-tailed bats (Tadarida brasiliensis) with SARS-CoV-2.", @@ -233701,85 +235873,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.07.15.500232", - "rel_title": "Urban birds' flight responses were unaffected by the COVID-19 shutdowns", - "rel_date": "2022-07-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.15.500232", - "rel_abs": "The coronavirus disease 2019 (COVID-19) pandemic has dramatically altered human activities, potentially relieving human pressures on urban-dwelling animals. Here, we evaluated whether birds from five cities in five countries (Czech Republic - Prague, Finland - Rovaniemi, Hungary - Budapest, Poland - Poznan, and Australia - Melbourne) changed their tolerance towards human presence (measured as flight initiation distance) during the COVID-19 shutdowns. We collected 6369 flight initiation distance estimates for 147 bird species and found that birds tolerated approaching humans to a similar level before and during the COVID-19 shutdowns. Moreover, during the shutdowns, bird escape behaviour did not consistently change with the level of governmental restrictions (measured as the stringency index). Hence, our results indicate that birds do not flexibly and quickly adjust their escape behaviour to the reduced human presence; in other words, the breeding populations of urban birds examined might already be tolerant of human activity and perceive humans as relatively harmless.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Peter Mikula", - "author_inst": "Institute Of Vertebrate Biology, Czech Academy Of Sciences" - }, - { - "author_name": "Martin Bulla", - "author_inst": "Max Planck Institute for Ornithology" - }, - { - "author_name": "Daniel Blumstein", - "author_inst": "Department of Ecology and Evolutionary Biology, University of California" - }, - { - "author_name": "Yanina Benedetti", - "author_inst": "Faculty of Environmental Sciences, Czech University of Life Sciences Prague" - }, - { - "author_name": "Kristina Floigl", - "author_inst": "Faculty of Environmental Sciences, Czech University of Life Sciences Prague" - }, - { - "author_name": "Jukka Jokimaki", - "author_inst": "Arctic Centre, University of Lapland" - }, - { - "author_name": "Marja-Liisa Kaisanlahti-Jokimaki", - "author_inst": "Arctic Centre, University of Lapland" - }, - { - "author_name": "Gabor Marko", - "author_inst": "Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences" - }, - { - "author_name": "Federico Morelli", - "author_inst": "Faculty of Environmental Sciences, Czech University of Life Sciences Prague" - }, - { - "author_name": "Anders Pape Moller", - "author_inst": "Ecologie Systematique Evolution, Universite Paris-Sud, CNRS, AgroParisTech, Universite Paris-Saclay" - }, - { - "author_name": "Anastasiia Siretckaia", - "author_inst": "Faculty of Environmental Sciences, Czech University of Life Sciences Prague" - }, - { - "author_name": "Sara Szakony", - "author_inst": "Department of Ecology, Institute of Biology, University of Veterinary Medicine Budapest" - }, - { - "author_name": "Michael Weston", - "author_inst": "School of Life and Environmental Sciences, Deakin University" - }, - { - "author_name": "Farah Abou Zeid", - "author_inst": "Faculty of Environmental Sciences, Czech University of Life Sciences Prague" - }, - { - "author_name": "Piotr Tryjanowski", - "author_inst": "Institute of Zoology, Poznan University of Life Sciences" - }, - { - "author_name": "Tomas Albrecht", - "author_inst": "Institute of Vertebrate Biology, Czech Academy of Sciences" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "animal behavior and cognition" - }, { "rel_doi": "10.1101/2022.07.13.499991", "rel_title": "SARS-CoV-2 causes brain inflammation via impaired neuro-immune interactions", @@ -234700,6 +236793,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.07.14.22277638", + "rel_title": "Therapeutic potential of IL6R blockade for the treatment of sepsis and sepsis-related death: Findings from a Mendelian randomisation study", + "rel_date": "2022-07-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.14.22277638", + "rel_abs": "IntroductionSepsis is characterised by dysregulated, life-threatening immune responses, which are thought to be driven by cytokines such as interleukin-6 (IL-6). Genetic variants in IL6R known to downregulate IL-6 signalling are associated with improved COVID-19 outcomes, a finding later confirmed in randomised trials of IL-6 receptor antagonists (IL6RA). We hypothesised that blockade of IL6R could also improve outcomes in sepsis.\n\nMethodsWe performed a Mendelian randomisation analysis using single nucleotide polymorphisms (SNPs) in and near IL6R to evaluate the likely causal effects of IL6R blockade on sepsis, sepsis severity, other infections, and COVID-19. We weighted SNPs by their effect on CRP and combined results across them in inverse variance weighted meta-analysis, proxying the effect of IL6RA. Our outcomes were measured in UK Biobank, FinnGen, the COVID-19 Host Genetics Initiative (HGI), and the GenOSept and GainS consortium. We performed several sensitivity analyses to test assumptions of our methods, including utilising variants around CRP in a similar analysis.\n\nResultsIn the UK Biobank cohort (N=485,825, including 11,643 with sepsis), IL6R blockade was associated with a decreased risk of sepsis (OR=0.80; 95% CI 0.66-0.96, per unit of natural log transformed CRP decrease). The size of this effect increased with severity, with larger effects on 28-day sepsis mortality (OR=0.74; 95% CI 0.38-0.70); critical care admission with sepsis (OR=0.48, 95% CI 0.30-0.78) and critical care death with sepsis (OR=0.37, 95% CI 0.14 - 0.98) Similar associations were seen with severe respiratory infection: OR for pneumonia in critical care 0.69 (95% CI 0.49 - 0.97) and for sepsis survival in critical care (OR=0.22; 95% CI 0.04- 1.31) in the GainS and GenOSept consortium. We also confirm the previously reported protective effect of IL6R blockade on severe COVID-19 (OR=0.69, 95% 0.57 - 0.84) in the COVID-19 HGI, which was of similar magnitude to that seen in sepsis. Sensitivity analyses did not alter our primary results.\n\nConclusionsIL6R blockade is causally associated with reduced incidence of sepsis, sepsis related critical care admission, and sepsis related mortality. These effects are comparable in size to the effect seen in severe COVID-19, where IL-6 receptor antagonists were shown to improve survival. This data suggests a randomised trial of IL-6 receptor antagonists in sepsis should be considered.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Fergus W Hamilton", + "author_inst": "University of Bristol" + }, + { + "author_name": "Matt Thomas", + "author_inst": "North Bristol NHS Trust" + }, + { + "author_name": "David T Arnold", + "author_inst": "University of Bristol" + }, + { + "author_name": "Tom M Palmer", + "author_inst": "University of Bristol" + }, + { + "author_name": "Ed Moran", + "author_inst": "North Bristol NHS Trust" + }, + { + "author_name": "Alexander J Mentzer", + "author_inst": "University of Oxford" + }, + { + "author_name": "Nick A Maskell", + "author_inst": "University" + }, + { + "author_name": "J Kenneth Baillie", + "author_inst": "Roslin Institute, University of Edinburgh" + }, + { + "author_name": "Charlotte Summers", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Aroon Dinesh Hingorani", + "author_inst": "University College London" + }, + { + "author_name": "Alasdair P MacGowan", + "author_inst": "North Bristol NHS Trust" + }, + { + "author_name": "Golam M Khandaker", + "author_inst": "University of Bristol" + }, + { + "author_name": "Ruth E Mitchell", + "author_inst": "University of Bristol" + }, + { + "author_name": "George Davey Smith", + "author_inst": "University of Bristol" + }, + { + "author_name": "Peter Ghazal", + "author_inst": "Cardiff University" + }, + { + "author_name": "Nicholas J Timpson", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.07.13.22277113", "rel_title": "SARS-CoV-2 exhibits extreme differences in early viral loads among specimen types suggesting improved detection of pre-infectious and infectious individuals using combination specimen types", @@ -235587,37 +237759,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "otolaryngology" }, - { - "rel_doi": "10.1101/2022.07.14.22277631", - "rel_title": "Practical application of CO2 as an indicator regarding the risk of infection", - "rel_date": "2022-07-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.14.22277631", - "rel_abs": "The air quality of enclosed spaces has attracted great attention due to the ongoing Covid-19 pandemic. The infection risk in these spaces can be estimated for various scenarios with different methods so the important parameters and effective infection prevention measures can be compared. Previous studies showed that indoor CO2 concentration could be considered a surrogate for infection risk. In this regard, a generic relation can be established between the CO2 levels and infection probability. Based on this consideration, some practical evaluations between CO2 concentration and infection risk are conducted in this study. The effect of mask efficiency, viral emission rate, and duration of exposure are also included in the assessments. It is shown that continuous CO2 monitoring can be helpful in the evaluation of possible preventive measures. Findings are expected to contribute to the understanding of the simple parameters related to the infection risk.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Anne Hartmann", - "author_inst": "Technische Universit\u00e4t Berlin" - }, - { - "author_name": "Yunus Emre Cetin", - "author_inst": "TU Berlin: Technische Universitat Berlin" - }, - { - "author_name": "Petra Gastmeier", - "author_inst": "Charite University Hospital Berlin: Charite Universitatsmedizin Berlin" - }, - { - "author_name": "Martin Kriegel", - "author_inst": "Technische Universit\u00e4t Berlin: Technische Universitat Berlin" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.07.14.500042", "rel_title": "Fc effector activity and neutralization against SARS-CoV-2 BA.4 is compromised in convalescent sera, regardless of the infecting variant", @@ -236330,6 +238471,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.07.12.22277554", + "rel_title": "Efficient Tracing of the SARS-CoV-2 Omicron Variants in Santa Barbara County Using a Rapid Quantitative Reverse Transcription PCR Assay", + "rel_date": "2022-07-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.12.22277554", + "rel_abs": "The recent emergence of the SARS-CoV-2 Omicron variant is associated with a dramatic surge of cases around the globe in late 2021 and early 2022. The numerous mutations in this variant, particularly in the Spike protein, enhance its transmission, increase immune evasion, and limit treatment with monoclonal antibodies. Identifying a communitys introduction to a novel SARS-CoV-2 variant with new clinical features related to treatment options and infection control needs is imperative to inform decisions by clinicians and public health officials, and traditional sequencing techniques often take weeks to result. Here, we describe a quantitative reverse transcription PCR assay (RT-qPCR) to accurately and precisely detect the presence of the Omicron sublineages BA.1/BA1.1 and BA.2 viral RNA from patient samples in less than four hours. The assay uses primers targeting the BA.1/BA1.1 unique mutations N211del, L212I, and L214 insertion EPE in the Spike protein gene, and the BA.2 specific mutations T19I and L24/P25/P26 deletion in the Spike protein gene. Using this assay, we detected 169 cases of Omicron, 164 BA.1/BA1.1 and 5 BA.2, from 270 residual SARS-CoV-2 positive samples collected for diagnostic purposes from Santa Barbara County (SBC) between December 2021 to February 2022. The RT-qPCR results show concordance with whole viral genome sequencing. Our observations indicate that Omicron was the dominant variant in SB County and is likely responsible for the surge of cases in the area during the sampling period. Using this inexpensive and accurate test, the rapid detection of Omicron in patient samples allowed clinicians to modify treatment strategies and public health officers to enhance contact tracing strategies. This RT-qPCR assay offers an alternative to current variant-specific detection approaches, provides a template for the fast design of similar assays, and allows the rapid, accurate, and inexpensive detection of Omicron variants in patient samples. It can also be readily adapted to new variants as they emerge in the future.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Zachary Aralis", + "author_inst": "Department of Biomolecular Science and Engineering, University of California, Santa Barbara" + }, + { + "author_name": "Stewart Comer", + "author_inst": "Santa Barbara County, Public Health Department" + }, + { + "author_name": "Henning Ansorg", + "author_inst": "Santa Barbara County, Public Health Department" + }, + { + "author_name": "Carl Palmer", + "author_inst": "LegacyWorks Group, Santa Barbara" + }, + { + "author_name": "Jennifer Smith", + "author_inst": "California NanoSystems Institute, University of California, Santa Barbara" + }, + { + "author_name": "Stu Feinstein", + "author_inst": "Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara" + }, + { + "author_name": "Lynn N Fitzgibbons", + "author_inst": "Department of Medical Education and Division of Infectious Diseases, Santa Barbara Cottage Hospital" + }, + { + "author_name": "Carolina Arias", + "author_inst": "Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.07.12.499813", "rel_title": "Inducible Bronchus-Associated Lymphoid Tissue in SARS-CoV-2 Infected Rhesus Macaques", @@ -237309,61 +239497,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.07.11.22277492", - "rel_title": "Use of illness severity scores to predict mortality in interstitial lung disease patients hospitalised with acute respiratory deterioration", - "rel_date": "2022-07-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.11.22277492", - "rel_abs": "IntroductionHospitalisations relating to acute respiratory deteriorations (ARD) in Interstitial Lung Disease (ILD) have poor outcomes. Factors predicting adverse outcomes are not fully understood and data addressing the use of illness severity scores in prognostication are limited.\n\nObjectiveTo investigate the use of CURB-65 and NEWS-2 severity scores in the prediction of mortality following ARD-ILD hospitalisation, using prospective methodology and to validate previously determined cut-offs, derived from a retrospective study cohort.\n\nMethodsA dual-centre prospective observational cohort study of all adults ([≥]18y) hospitalised with ARD-ILD in Bristol, UK (n=179). Gender-Age-Physiology (GAP), CURB-65 and NEWS-2 scores were calculated for each eligible admission.\n\nReceiver operating characteristics (ROC) curve analysis was used to quantify the strength of discrimination for NEWS-2 and CURB-65 scores. Univariable and multivariable logistic regression analyses were performed to explore the relationship between baseline severity scores and mortality.\n\nResultsGAP showed some merit at predicting 30-day mortality (AUC=0.64, P=0.015); whereas CURB-65 showed modest predictive value for in-hospital (AUC=0.72, P<0.001) and 90-day mortality (AUC=0.67, P<0.001). NEWS-2 showed higher predictive value for in-hospital (AUC=0.80, P<0.001) and 90-day mortality (AUC=0.75, P<0.001), with an optimal derived cut-off [≥]6.5 found to be sensitive and specific for predicting in-hospital (83% and 63%) and 90-day (73% and 72%) mortality. In exploratory analyses, GAP score addition improved the predictive ability of NEWS-2 against 30-day mortality and CURB-65 across all time-periods.\n\nConclusionNEWS-2 has good discriminatory value for predicting in-hospital mortality and moderate discriminatory value for predicting 90-day mortality. The optimal NEWS-2 cut-off value determined was the same as in a previous retrospective cohort, confirming the NEWS-2 score shows promise in predicting mortality following ARD-ILD hospitalisation.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Rachel L Williams", - "author_inst": "Research and Innovation, North Bristol NHS Trust, Southmead, Bristol BS10 5NB" - }, - { - "author_name": "Catherine Hyams", - "author_inst": "Bristol Vaccine Centre and Academic Respiratory Unit, University of Bristol; Bristol Interstitial Lung Disease Service, North Bristol NHS Trust" - }, - { - "author_name": "Joe Robertshaw", - "author_inst": "Bristol Interstitial Lung Disease Service and Academic Research Unit, North Bristol NHS Trust" - }, - { - "author_name": "Maria Garcia Gonzalez", - "author_inst": "Bristol Vaccine Centre, University of Bristol; Vaccine and Testing Team, UHBW NHS Trust" - }, - { - "author_name": "Zsuzsa Szasz-Benczur", - "author_inst": "Bristol Vaccine Centre, University of Bristol" - }, - { - "author_name": "Paul White", - "author_inst": "University of West of England (UWE), Bristol" - }, - { - "author_name": "Nick A Maskell", - "author_inst": "Academic Respiratory Unit, North Bristol NHS Trust" - }, - { - "author_name": "Adam Finn", - "author_inst": "Bristol Vaccine Centre, University of Bristol" - }, - { - "author_name": "Shaney L Barratt", - "author_inst": "Bristol Interstitial Lung Disease Service and Academic Respiratory Unit, North Bristol NHS Trust" - }, - { - "author_name": "- The AvonCAP Research Group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2022.07.11.22277508", "rel_title": "Multi-site disease analytics with applications to estimating COVID-19 undetected cases in Canada", @@ -238260,6 +240393,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2022.07.07.22277365", + "rel_title": "Monkeypox caused less worry than COVID-19 among the general population during the first month of the WHO Monkeypox alert", + "rel_date": "2022-07-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.07.22277365", + "rel_abs": "BackgroundMonkeypox re-emerged in May 2022 as another global health threat. This study assessed the publics perception, worries, and vaccine acceptance for Monkeypox and COVID-19 during the first month of WHO announcement.\n\nMethodsA national cross-sectional survey was conducted between May 27 and June 5, 2022, in Saudi Arabia. Data were collected on sociodemographic characteristics, previous infection with COVID-19, worry levels regarding Monkeypox compared to COVID-19, awareness, and perceptions of Monkeypox, and vaccine acceptance.\n\nResultsAmong the 1546 participants, most respondents (62%) were more worried about COVID-19 than Monkeypox. Respondents aged 45 years and above and those with a university degree or higher had lower odds of agreement with Monkeypox vaccination (OR .871, p-value .006, OR .719, p-value <0.001), respectively. Respondents with moderate to a high level of self and family commitment to infection control precautionary measures and those who expressed self and family worry of Monkeypox infection had significantly higher odds of vaccination agreement (OR 1.089 p-value=0.047, OR1.395 p-value=0.003) respectively. On the other hand, respondents who previously developed COVID-19 were significantly more worried about the Monkeypox disease (1.30 times more, p-value=0.020).\n\nConclusionWorry levels amongst the public are higher from COVID-19 than Monkeypox. Perception of Monkeypox as a dangerous and virulent disease, worry from contracting the disease, and high commitment to infection precautionary measures were predictors of agreement with Monkeypox vaccination. While advanced age and high education level are predictors of low agreement with vaccination.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Mohamad-Hani Temsah", + "author_inst": "King Saud University" + }, + { + "author_name": "Fadi Aljamaan", + "author_inst": "King Saud University" + }, + { + "author_name": "Shuliweeh Alenezi", + "author_inst": "King Saud University" + }, + { + "author_name": "Khalid Alhasan", + "author_inst": "King Saud University" + }, + { + "author_name": "Basema Saddik", + "author_inst": "University of Sharjah" + }, + { + "author_name": "Ahmad Al-Barrag", + "author_inst": "King Saud University" + }, + { + "author_name": "Ali Alhaboob", + "author_inst": "King Saud University" + }, + { + "author_name": "Nizar Bahabri", + "author_inst": "Dr Samir Abbas Hospital" + }, + { + "author_name": "Fatimah Alshahrani", + "author_inst": "King Saud University" + }, + { + "author_name": "Abdulkarim Alrabiaah", + "author_inst": "King Saud University" + }, + { + "author_name": "Ali Alaraj", + "author_inst": "Qassim University" + }, + { + "author_name": "Feras Bahkali", + "author_inst": "King Saud University" + }, + { + "author_name": "Khaled Alkriadees", + "author_inst": "King Saud University" + }, + { + "author_name": "Amr Jamal", + "author_inst": "King Saud University" + }, + { + "author_name": "Rabih Halwani", + "author_inst": "University of Sharjah" + }, + { + "author_name": "Fahad AlZamil", + "author_inst": "King Saud University" + }, + { + "author_name": "Sarah Alsubaie", + "author_inst": "King Saud University" + }, + { + "author_name": "Mazin Barry", + "author_inst": "King Saud University" + }, + { + "author_name": "Ziad A Memish", + "author_inst": "Alfaisal University" + }, + { + "author_name": "Jaffar A Al-Tawfiq", + "author_inst": "Johns Hopkins Aramco Healthcare" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.07.07.22277367", "rel_title": "Non-hospitalised, vaccinated adults with COVID-19 caused by Omicron BA.1 and BA.2 present with changing symptom profiles compared to those with Delta despite similar viral kinetics", @@ -239571,101 +241799,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, - { - "rel_doi": "10.1101/2022.07.07.22277366", - "rel_title": "Diagnostic accuracy of SARS-CoV-2 rapid antigen self-tests in asymptomatic individuals in the Omicron period: cross sectional study", - "rel_date": "2022-07-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.07.22277366", - "rel_abs": "ObjectivesTo assess the performances of three commonly used rapid antigen diagnostic tests (Ag-RDTs) used as self-tests in asymptomatic individuals in the Omicron period.\n\nDesignCross-sectional diagnostic test accuracy study.\n\nSettingThree public health service COVID-19 test sites in the Netherlands.\n\nParticipants3,600 asymptomatic individuals aged [≥]16 years presenting for SARS-CoV-2 testing for any reason except confirmatory testing after a positive self-test.\n\nInterventionsParticipants were sampled for RT-PCR (reference test) and received one self-test (either Acon Flowflex (Flowflex), MP Biomedicals (MPBio), or Siemens-Healthineers Clinitest (Clinitest)) to perform unsupervised at home within three hours and blinded to the RT-PCR result.\n\nMain Outcome(s) and Measures(s)Diagnostic accuracies (sensitivity, specificity, positive and negative predictive values) of each self-test compared to RT-PCR.\n\nResultsOverall sensitivities of the three self-tests were 27.5% (95% CI: 21.3-34.3%) for Flowflex, 20.9% (13.9-29.4%) for MPBio, and 25.6% (19.1-33.1%) for Clinitest. After applying a viral load cut-off ([≥]5.2 log10 SARS-CoV-2 E-gene copies/mL), sensitivities increased to 48.3% (95% CI: 37.6-59.2%), 37.8% (22.5-55.2%), and 40.0% (29.5-51.2%), respectively. No consistent differences were found in sensitivities by COVID-19 vaccination status, having had a prior SARS-CoV-2 infection, gender or age across the three self-tests. Specificities were >99% for all tests in most analyses.\n\nConclusionsThe sensitivities of three commonly used SARS-CoV-2 Ag-RDTs when used as self-tests in asymptomatic individuals in the Omicron period, were very low. Our findings indicate that Ag-RDT self-testing in asymptomatic individuals may only detect the minority of infections at that point in time and may not be sufficient to prevent the spreading of the virus to other (vulnerable) persons. Repeated self-testing in case of a negative self-test is advocated to improve the diagnostic yield of the self-tests, and individuals should certainly be advised to re-test when symptoms develop.\n\nSummary boxO_ST_ABSWhat is already known on this topicC_ST_ABSO_LIIf sufficiently reliable, SARS-CoV-2 self-testing by asymptomatic persons prior to admission in places where groups gather could have a huge public health impact by lowering the reproduction number or keep it below one for longer periods.\nC_LIO_LICurrent evidence suggests that SARS-CoV-2 rapid antigen diagnostic tests (Ag-RDTs) when used as self-tests by asymptomatic individuals perform suboptimal, but sample sizes of the previous studies were too small to draw robust conclusions, and also empirical data on the accuracy of Ag-RDT self-tests in asymptomatic individuals during the Omicron period are scarce.\nC_LI\n\nWhat this study addsO_LICompared to RT-PCR testing, overall sensitivities of three commercially available SARS-CoV-2 Ag-RDTs when used as self-tests by asymptomatic individuals (primary analysis population of non-confirmatory testers; n= 3600, 87% of full analysis population) in the Omicron period, were very low: 27.5% (95% CI: 21.3-34.3%) for the Acon Flowflex test, 20.9% (13.9-29.4%) for the MP Biomedicals test, and 25.6% (19.1-33.1%) for the Siemens Healthineers Clinitest Ag-RDT, which increased to 48.3% (95% CI: 37.6-59.2%), 37.8% (22.5-55.2%), and 40.0% (29.5-51.2%), respectively, when applying a viral load cut-off ([≥]5.2 log10 SARS-CoV-2 E-gene copies/mL).\nC_LIO_LIOur findings indicate that Ag-RDT self-testing in asymptomatic individuals may only detect the minority of infections at that point in time and may not be sufficient to prevent the spreading of the virus to other (vulnerable) persons. Repeated self-testing in case of a negative self-test is advocated to improve the diagnostic yield of the self-tests, and individuals should certainly be advised to re-test when symptoms develop.\nC_LI", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Roderick P Venekamp", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Ewoud Schuit", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Lotty Hooft", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Irene K Veldhuijzen", - "author_inst": "National Institute for Public Health and the Environment (RIVM)" - }, - { - "author_name": "Wouter Bijllaardt", - "author_inst": "Amphia Hospital" - }, - { - "author_name": "Suzan D Pas", - "author_inst": "Bravis Hospital" - }, - { - "author_name": "Vivian F Zwart", - "author_inst": "Amphia Hospital" - }, - { - "author_name": "Esther B Lodder", - "author_inst": "Public Health Service West-Brabant" - }, - { - "author_name": "Marloes Hellwich", - "author_inst": "Public Health Service Hart voor Brabant" - }, - { - "author_name": "Marco Koppelman", - "author_inst": "Sanquin Research" - }, - { - "author_name": "Richard Molenkamp", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Constantijn Wijers", - "author_inst": "Public Health Service Rotterdam-Rijnmond" - }, - { - "author_name": "Irene H Vroom", - "author_inst": "Public Health Service Rotterdam-Rijnmond" - }, - { - "author_name": "Leonard C Smeets", - "author_inst": "Reinier Haga Medical Diagnostic Center" - }, - { - "author_name": "Carla RS Nagel-Imming", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Wanda GH Han", - "author_inst": "National Institute for Public Health and the Environment" - }, - { - "author_name": "Susan van den Hof", - "author_inst": "National Institute for Public Health and the Environment (RIVM)" - }, - { - "author_name": "Jan AJ Kluytmans", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Janneke HHM van de Wijgert", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Karel GM Moons", - "author_inst": "University Medical Center Utrecht" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.07.08.22277413", "rel_title": "Medical complaints after 3 vs 2 doses SARS-CoV-2 mRNA vaccination", @@ -240366,6 +242499,273 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.07.06.22277314", + "rel_title": "Multimodal surveillance of SARS-CoV-2 at a university enables development of a robust outbreak response framework", + "rel_date": "2022-07-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.06.22277314", + "rel_abs": "Universities are particularly vulnerable to infectious disease outbreaks and are also ideal environments to study transmission dynamics and evaluate mitigation and surveillance measures when outbreaks occur. Here, we introduce a SARS-CoV-2 surveillance and response framework based on high-resolution, multimodal data collected during the 2020-2021 academic year at Colorado Mesa University. We analyzed epidemiological and sociobehavioral data (demographics, contact tracing, and wifi-based co-location data) alongside pathogen surveillance data (wastewater, random, and reflexive diagnostic testing; and viral genomic sequencing of wastewater and clinical specimens) to characterize outbreak dynamics and inform policy decisions. We quantified group attributes that increased disease risk, and highlighted parallels between traditional and wifi-based contact tracing. We additionally used clinical and environmental viral sequencing to identify cryptic transmission, cluster overdispersion, and novel lineages or mutations. Ultimately, we used distinct data types to identify information that may help shape institutional policy and to develop a model of pathogen surveillance suitable for the future of outbreak preparedness.", + "rel_num_authors": 63, + "rel_authors": [ + { + "author_name": "Brittany A. Petros", + "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Jillian S. Paull", + "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Christopher H. Tomkins-Tinch", + "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Bryn C. Loftness", + "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Katherine C. DeRuff", + "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Parvathy Nair", + "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Gabrielle L. Gionet", + "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Aaron Benz", + "author_inst": "Degree Analytics, Inc., 1905 Kramer Lane Suite A100, Austin, TX, 78758, USA" + }, + { + "author_name": "Taylor Brock-Fisher", + "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Michael Hughes", + "author_inst": "Colorado Mesa University, Grand Junction, CO, 81501, USA" + }, + { + "author_name": "Leonid Yurkovetskiy", + "author_inst": "Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA" + }, + { + "author_name": "Shandukani Mulaudzi", + "author_inst": "Harvard Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, 02115, USA" + }, + { + "author_name": "Emma Leenerman", + "author_inst": "Colorado Mesa University, Grand Junction, CO, 81501, USA" + }, + { + "author_name": "Thomas Nyalile", + "author_inst": "Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA" + }, + { + "author_name": "Gage K. Moreno", + "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Ivan Specht", + "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Kian Sani", + "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Gordon Adams", + "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Simone V. Babet", + "author_inst": "Department of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, CO, 80309, USA" + }, + { + "author_name": "Emily Baron", + "author_inst": "COVIDCheck Colorado, LLC., Denver, CO, 80202, USA" + }, + { + "author_name": "Jesse T. Blank", + "author_inst": "Colorado Mesa University, Grand Junction, CO, 81501, USA" + }, + { + "author_name": "Chloe Boehm", + "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Yolanda Botti-Lodovico", + "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Jeremy Brown", + "author_inst": "Colorado Mesa University, Grand Junction, CO, 81501, USA" + }, + { + "author_name": "Adam R. Buisker", + "author_inst": "Colorado Mesa University, Grand Junction, CO, 81501, USA" + }, + { + "author_name": "Timothy Burcham", + "author_inst": "Fathom Information Design, Boston, MA, 02114, USA" + }, + { + "author_name": "Lily Chylek", + "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Paul Cronan", + "author_inst": "Fathom Information Design, Boston, MA, 02114, USA" + }, + { + "author_name": "Valentine Desreumaux", + "author_inst": "Department of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, CO, 80309, USA" + }, + { + "author_name": "Megan Doss", + "author_inst": "Warrior Diagnostics, Inc., Loveland, CO, 80538, USA" + }, + { + "author_name": "Belinda Flynn", + "author_inst": "Colorado Mesa University, Grand Junction, CO, 81501, USA" + }, + { + "author_name": "Adrianne Gladden-Young", + "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Olivia Glennon", + "author_inst": "Fathom Information Design, Boston, MA, 02114, USA" + }, + { + "author_name": "Hunter D. Harmon", + "author_inst": "Colorado Mesa University, Grand Junction, CO, 81501, USA" + }, + { + "author_name": "Thomas V. Hook", + "author_inst": "Department of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, CO, 80309, USA" + }, + { + "author_name": "Anton Kary", + "author_inst": "Department of Biological Sciences, Colorado Mesa University, Grand Junction, CO, 81501, USA" + }, + { + "author_name": "Clay King", + "author_inst": "Department of Mathematics and Statistics, Colorado Mesa University, Grand Junction, CO, 81501, USA" + }, + { + "author_name": "Christine Loreth", + "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Libby Marrs", + "author_inst": "Fathom Information Design, Boston, MA, 02114, USA" + }, + { + "author_name": "Kyle J. McQuade", + "author_inst": "Department of Biological Sciences, Colorado Mesa University, Grand Junction, CO, 81501, USA" + }, + { + "author_name": "Thorsen T. Milton", + "author_inst": "Department of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, CO, 80309, USA" + }, + { + "author_name": "Jada M. Mulford", + "author_inst": "Department of Biological Sciences, Colorado Mesa University, Grand Junction, CO, 81501, USA" + }, + { + "author_name": "Kyle Oba", + "author_inst": "Fathom Information Design, Boston, MA, 02114, USA" + }, + { + "author_name": "Leah Pearlman", + "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Mark Schifferli", + "author_inst": "Fathom Information Design, Boston, MA, 02114, USA" + }, + { + "author_name": "Madelyn J. Schmidt", + "author_inst": "Colorado Mesa University, Grand Junction, CO, 81501, USA" + }, + { + "author_name": "Grace M. Tandus", + "author_inst": "Department of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, CO, 80309, USA" + }, + { + "author_name": "Andy Tyler", + "author_inst": "Colorado Mesa University, Grand Junction, CO, 81501, USA" + }, + { + "author_name": "Megan E. Vodzak", + "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Kelly Bevill", + "author_inst": "Department of Computer Science and Engineering, Colorado Mesa University, Grand Junction, CO, 81501, USA" + }, + { + "author_name": "Andres Colubri", + "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Bronwyn L. MacInnis", + "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "A. Zeynep Ozsoy", + "author_inst": "Department of Biological Sciences, Colorado Mesa University, Grand Junction, CO, 81501, USA" + }, + { + "author_name": "Eric Parrie", + "author_inst": "COVIDCheck Colorado, LLC., Denver, CO, 80202, USA" + }, + { + "author_name": "Kari Sholtes", + "author_inst": "Department of Computer Science and Engineering, Colorado Mesa University, Grand Junction, CO, 81501, USA" + }, + { + "author_name": "Katherine J. Siddle", + "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Ben Fry", + "author_inst": "Fathom Information Design, Boston, MA, 02114, USA" + }, + { + "author_name": "Jeremy Luban", + "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Daniel J. Park", + "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "John Marshall", + "author_inst": "Colorado Mesa University, Grand Junction, CO, 81501, USA" + }, + { + "author_name": "Amy Bronson", + "author_inst": "Physician Assistant Program, Department of Kinesiology, Colorado Mesa University, Grand Junction, CO, 81501, USA" + }, + { + "author_name": "Stephen F. Schaffner", + "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Pardis C. Sabeti", + "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.07.06.22277306", "rel_title": "Duration of immune protection of SARS-CoV-2 natural infection against reinfection in Qatar", @@ -241477,25 +243877,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.07.04.22277231", - "rel_title": "Modelling the epidemiological implications for SARS-CoV-2 of Christmas household bubbles in England", - "rel_date": "2022-07-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.04.22277231", - "rel_abs": "The emergence of SARS-CoV-2 saw severe detriments to public health being inflicted by COVID-19 disease throughout 2020. In the lead up to Christmas 2020, the UK Government sought an easement of social restrictions that would permit spending time with others over the Christmas period, whilst limiting the risk of spreading SARS-CoV-2. In November 2020, plans were published to allow individuals to socialise within Christmas bubbles with friends and family. This policy involved a planned easing of restrictions in England between 23-27 December 2020, with Christmas bubbles allowing people from up to three households to meet throughout the holiday period. We estimated the epidemiological impact of both this and alternative bubble strategies that allowed extending contacts beyond the immediate household. We used a stochastic individual-based model for a synthetic population of 100,000 households, with demographic and SARS-CoV-2 epidemiological characteristics comparable to England as of November 2020. We evaluated five Christmas bubble scenarios for the period 23-27 December 2020, assuming our populations of households did not have symptomatic infection present and were not in isolation as the eased social restrictions began. Assessment comprised incidence and cumulative infection metrics. We tested the sensitivity of the results to a situation where it was possible for households to be in isolation at the beginning of the Christmas bubble period and also when there was lower adherence to testing, contact tracing and isolation interventions. We found that visiting family and friends over the holiday period for a shorter duration and in smaller groups was less risky than spending the entire five days together. The increases in infection from greater amounts of social mixing disproportionately impacted the eldest. We provide this account as an illustration of a real-time contribution of modelling insights to a scientific advisory group, the Scientific Pandemic Influenza Group on Modelling, Operational sub-group (SPI-M-O) for the Scientific Advisory Group for Emergencies (SAGE) in the UK, during the COVID-19 pandemic. This manuscript was submitted as part of a theme issue on \"Modelling COVID-19 and Preparedness for Future Pandemics\".", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Edward M Hill", - "author_inst": "University of Warwick" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.07.05.22277273", "rel_title": "Knowledge, attitudes, and practices regarding COVID-19 among university students and employees in Massachusetts, USA: a qualitative study", @@ -242368,6 +244749,57 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2022.07.06.498864", + "rel_title": "A Novel Regioselective Approach to Cyclize Phage-Displayed Peptides in Combination with Epitope-Directed Selection to Identify a Potent Neutralizing Macrocyclic Peptide for SARS-CoV-2", + "rel_date": "2022-07-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.06.498864", + "rel_abs": "Using the regioselective cyanobenzothiazole condensation reaction with the N-terminal cysteine and the chloroacetamide reaction with an internal cysteine, a phage-displayed macrocyclic 12-mer peptide library was constructed and subsequently validated. Using this library in combination with iterative selections against two epitopes from the receptor binding domain (RBD) of the SARS-CoV-2 Spike protein, macrocyclic peptides that strongly inhibit the interaction between the Spike RBD and ACE2, the human host receptor of SARS-CoV-2, were identified. The two epitopes were used instead of the Spike RBD to avoid selection of nonproductive macrocyclic peptides that bind RBD but do not directly inhibit its interactions with ACE2. Antiviral tests against SARS-CoV-2 showed that one macrocyclic peptide is highly potent against viral reproduction in Vero E6 cells with an EC50 value of 3.1 M. The AlphaLISA-detected IC50 value for this macrocyclic peptide was 0.3 M. The current study demonstrates that two kinetically-controlled reactions toward N-terminal and internal cysteines, respectively, are highly effective in the construction of phage-displayed macrocyclic peptides, and the selection based on the SARS-CoV-2 Spike epitopes is a promising methodology in the identification of peptidyl antivirals.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Joshua Trae Hampton", + "author_inst": "Texas A&M University" + }, + { + "author_name": "Tyler J Lalonde", + "author_inst": "Texas A&M University" + }, + { + "author_name": "Jeffery M Tharp", + "author_inst": "Texas A&M University" + }, + { + "author_name": "Yugendar R Alugubelli", + "author_inst": "Texas A&M University" + }, + { + "author_name": "Christopher M Roundy", + "author_inst": "Texas A&M University" + }, + { + "author_name": "Gabriel L Hamer", + "author_inst": "Texas A&M University" + }, + { + "author_name": "Shiqing Xu", + "author_inst": "Texas A&M University" + }, + { + "author_name": "Wenshe R Liu", + "author_inst": "Texas A&M University" + }, + { + "author_name": "Yadagiri Kurra", + "author_inst": "Texas A&M University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2022.07.02.22277178", "rel_title": "CD19+ B cell numbers predict the increase of anti-SARS CoV2 antibodies in fingolimod-treated and COVID-19-vaccinated patients with multiple sclerosis", @@ -244723,57 +247155,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2022.06.28.497919", - "rel_title": "TRIM7 restricts Coxsackievirus and norovirus infection by detecting the C-terminalglutamine generated by 3C protease processing", - "rel_date": "2022-07-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.28.497919", - "rel_abs": "TRIM7 catalyses the ubiquitination of multiple substrates with unrelated biological functions. This cross-reactivity is at odds with the specificity usually displayed by enzymes, including ubiquitin ligases. Here we show that TRIM7s extreme substrate promiscuity is due to a highly unusual binding mechanism, in which the PRYSPRY domain captures any ligand with a C-terminal helix that terminates in a hydrophobic residue followed by a glutamine. Many of the non-structural proteins found in RNA viruses contain C-terminal glutamines as a result of polyprotein cleavage by 3C protease. This viral processing strategy generates novel substrates for TRIM7 and explains its ability to inhibit Coxsackie virus and norovirus replication. In addition to viral proteins, cellular proteins such as glycogenin have evolved C-termini that make them a TRIM7 substrate. The helix-{Phi}Q degron motif recognised by TRIM7 is reminiscent of the N-end degron system and is found in [~] 1% of cellular proteins. These features, together with TRIM7s restricted tissue expression and lack of immune regulation suggest that viral restriction may not be its physiological function.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Jakub Luptak", - "author_inst": "MRC Laboratory of Molecular Biology" - }, - { - "author_name": "Donna Mallery", - "author_inst": "MRC Laboratory of Molecular Biology" - }, - { - "author_name": "Aminu S Jahun", - "author_inst": "Division of Virology, Department of Pathology, University of Cambridge" - }, - { - "author_name": "Anna Albecka", - "author_inst": "MRC Laboratory of Molecular Biology" - }, - { - "author_name": "Dean Clift", - "author_inst": "MRC Laboratory of Molecular Biology" - }, - { - "author_name": "Osaid Ather", - "author_inst": "MRC Laboratory of Molecular Biology" - }, - { - "author_name": "Greg Slodkowicz", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Ian Goodfellow", - "author_inst": "Division of Virology, Department of Pathology, University of Cambridge" - }, - { - "author_name": "Leo James", - "author_inst": "MRC Laboratory of Molecular Biology" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2022.07.03.22277201", "rel_title": "Clinical characteristics and factors associated with COVID-19-related mortality and hospital admission in 5 rural provinces in Indonesia: a retrospective cohort study", @@ -245378,6 +247759,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.07.01.22277132", + "rel_title": "B cell response six months after SARS-CoV-2 mRNA vaccination in people living with HIV under antiretroviral therapy", + "rel_date": "2022-07-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.01.22277132", + "rel_abs": "BackgroundSARS-CoV-2 mRNA vaccines have demonstrated high immunogenicity in healthy subjects and preliminary results for people living with HIV (PLWHIV) are promising too. We have previously reported the persistence of spike-specific circulating IgG and memory B cells in healthy adults up to six months after mRNA SARS-CoV-2 vaccination. Unfortunately, limited longitudinal data are available for PLWHIV and no evidence of persistent spike-specific B cells have been reported yet.\n\nMethodsWe investigated the humoral response and the persistence of spike-specific memory B cells up to six months after vaccination with two doses of mRNA vaccines in 84 PLWHIV under ART and compared them to healthy controls (HCs). Humoral response was analyzed with enzyme-linked immunosorbent assay and with an angiotensin-converting enzyme 2 (ACE2) and receptor binding domain (RBD) inhibition assay. PBMCs were analyzed with a cytofluorimetric approach for B cell phenotyping.\n\nFindingsSpike-specific IgG peaked 1 month after second dose and persisted up to six months after vaccination with no significant differences compared to HCs. The stratification of patients according to CD4+ T cell count showed a significantly lower IgG response in case of CD4<350/{micro}l, remarking the relevance of immune reconstitution. The ability of IgG of blocking the binding between ACE2 and RBD was detected in 58{middle dot}4% of PLWHIV, compared to 86{middle dot}2% in HCs. The amount of circulating spike-specific memory B cells detected in PLWHIV six months after vaccination was not significantly different from HCs, while there was prevalence of antigen-specific double negative (IgD-/CD27-) cells, compared to controls.\n\nInterpretationIn conclusion, the majority of PLWHIV developed spike-specific humoral and B cell responses that persist for at least six months after SARS-CoV-2 mRNA vaccination. However, hints of HIV-dependent immune impairment were revealed by altered spike-specific B cell phenotypes and by reduced spike-specific humoral response in patients with low CD4+ T cell count (<350/{micro}l).", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Jacopo Polvere", + "author_inst": "Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena; Siena, Italy" + }, + { + "author_name": "Massimiliano Fabbiani", + "author_inst": "Department of Medical Sciences, Infectious and Tropical Diseases Unit, University Hospital of Siena; Siena, Italy" + }, + { + "author_name": "Gabiria Pastore", + "author_inst": "Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena; Siena, Italy" + }, + { + "author_name": "Ilaria Rancan", + "author_inst": "Department of Medical Sciences, Infectious and Tropical Diseases Unit, University Hospital of Siena; Siena, Italy" + }, + { + "author_name": "Barbara Rossetti", + "author_inst": "Department of Medical Sciences, Infectious and Tropical Diseases Unit, University Hospital of Siena; Siena, Italy" + }, + { + "author_name": "Miriam Durante", + "author_inst": "Department of Medical Biotechnologies, University of Siena; Siena, Italy" + }, + { + "author_name": "Sara Zirpoli", + "author_inst": "Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena; Siena, Italy" + }, + { + "author_name": "Enrico Morelli", + "author_inst": "Department of Medical Biotechnologies, University of Siena; Siena, Italy" + }, + { + "author_name": "Elena Pettini", + "author_inst": "Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena; Siena, Italy" + }, + { + "author_name": "Simone Lucchesi", + "author_inst": "Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena; Siena, Italy" + }, + { + "author_name": "Fabio Fiorino", + "author_inst": "Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena; Siena, Italy" + }, + { + "author_name": "Mario Tumbarello", + "author_inst": "Department of Medical Sciences, Infectious and Tropical Diseases Unit, University Hospital of Siena; Siena, Italy" + }, + { + "author_name": "Annalisa Ciabattini", + "author_inst": "Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena; Siena, Italy" + }, + { + "author_name": "Francesca Montagnani", + "author_inst": "Department of Medical Sciences, Infectious and Tropical Diseases Unit, University Hospital of Siena; Siena, Italy" + }, + { + "author_name": "Donata Medaglini", + "author_inst": "Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena; Siena, Italy" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "hiv aids" + }, { "rel_doi": "10.1101/2022.06.30.22277105", "rel_title": "Real World Evidence of Effectiveness of COVID-19 Vaccines and Anti SARS-CoV-2 Monoclonal Antibodies Against Post-Acute Sequelae of SARS-CoV-2 Infection", @@ -246313,121 +248769,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.06.29.22277067", - "rel_title": "CASP4/11 contributes to pulmonary inflammation and disease exacerbation in COVID-19", - "rel_date": "2022-06-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.29.22277067", - "rel_abs": "Infection with SARS-CoV-2 induces COVID-19, an inflammatory disease that is usually self-limited, but depending on patient conditions may culminate with critical illness and patient death. The virus triggers activation of intracellular sensors, such as the NLRP3 inflammasome, which promotes inflammation and aggravates the disease. Thus, identification of host components associated with NLRP3 inflammasome is key for understanding the physiopathology of the disease. Here, we reported that SARS-CoV-2 induces upregulation and activation of human Caspase-4/CASP4 (mouse Caspase-11/CASP11) and this process contributes to inflammasome activation in response to SARS-CoV-2. CASP4 was expressed in lung autopsy of lethal cases of COVID-19 and CASP4 expression correlates with expression of inflammasome components and inflammatory mediators such as CASP1, IL1B, IL18 and IL6. In vivo infections performed in transgenic hACE2 humanized mouse, deficient or sufficient for Casp11, indicate that hACE2 Casp11-/- mice were protected from disease development, with reduced body weight loss, reduced temperature variation, increased pulmonary parenchymal area, reduced clinical score of the disease and reduced mortality. Collectively, our data establishes that CASP4/11 contributes to disease pathology and contributes for future immunomodulatory therapeutic interventions to COVID-19.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Tamara Rodrigues", - "author_inst": "USP" - }, - { - "author_name": "Camila Caetano", - "author_inst": "usp" - }, - { - "author_name": "Keyla de Sa", - "author_inst": "USP" - }, - { - "author_name": "Leticia Almeida", - "author_inst": "USP" - }, - { - "author_name": "Amanda Becerra", - "author_inst": "USP" - }, - { - "author_name": "Augusto Goncalves", - "author_inst": "USP" - }, - { - "author_name": "Leticia Lopes", - "author_inst": "USP" - }, - { - "author_name": "Samuel Oliveira", - "author_inst": "USP" - }, - { - "author_name": "Danielle Mascarenhas", - "author_inst": "USP" - }, - { - "author_name": "Sabrina Batah", - "author_inst": "USP" - }, - { - "author_name": "Bruna Silva", - "author_inst": "USP" - }, - { - "author_name": "Giovanni Gomes", - "author_inst": "USP" - }, - { - "author_name": "Ricardo Castro", - "author_inst": "USP" - }, - { - "author_name": "Ronaldo Martins", - "author_inst": "USP" - }, - { - "author_name": "Jonathan Avila", - "author_inst": "Hospital Albert Einstein" - }, - { - "author_name": "Fabiani Frantz", - "author_inst": "USP" - }, - { - "author_name": "Thiago Cunha", - "author_inst": "USP" - }, - { - "author_name": "Eurico Arruda", - "author_inst": "USP" - }, - { - "author_name": "Fernando Cunha", - "author_inst": "USP" - }, - { - "author_name": "Helder Nakaya", - "author_inst": "Hospital Albert Einstein" - }, - { - "author_name": "Larissa Cunha", - "author_inst": "USP" - }, - { - "author_name": "Alexandre Fabro", - "author_inst": "USP" - }, - { - "author_name": "Paulo Louzada-Junior", - "author_inst": "USP" - }, - { - "author_name": "Rene Oliveira", - "author_inst": "USP" - }, - { - "author_name": "Dario S Zamboni", - "author_inst": "Universidade de Sao Paulo, School of Medicine Ribeirao Preto" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.06.30.22277091", "rel_title": "Limitations of models for guiding policy in the COVID-19 pandemic", @@ -246972,6 +249313,73 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2022.06.28.22277016", + "rel_title": "Protection from Omicron infection in residents of nursing and retirement homes in Ontario, Canada", + "rel_date": "2022-06-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.28.22277016", + "rel_abs": "ObjectivesTo identify factors that contribute to protection from infection with the Omicron variant of SARS-CoV-2 in older adults in nursing and retirement homes.\n\nDesignLongitudinal cohort study with retrospective analysis of infection risk.\n\nSetting and Participants997 residents of nursing and retirement homes from Ontario, Canada, in the COVID-in-LTC study.\n\nMethodsResidents with three mRNA dose vaccinations were included in the study. SARS-CoV-2 infection was determined by positive nasopharyngeal PCR test and/or circulating anti-nucleocapsid IgG antibodies. Cumulative probability of Omicron infection after recent COVID-19 was assessed by log-rank test of Kaplan-Meier curves. Cox regression was used to assess risk of Omicron infection by age, sex, mRNA vaccine combination, whether individuals received a fourth dose, as well as recent COVID-19.\n\nResults171 residents (17.2%) had a presumed Omicron variant SARS-CoV-2 infection between December 15, 2021 (local start of the first Omicron wave) and May 3, 2022. Risk of Omicron infection was not different by age [hazard ratio (95% confidence interval): 1.01 (0.99-1.02)], or in women compared to men [0.97 (0.70-1.34)], but infection risk decreased 47% with three vaccine doses of mRNA-1273 (Moderna) compared to BNT162b2 (Pfizer) [0.53 (0.31-0.90)], 81% with any fourth mRNA vaccine dose [0.19 (0.12-0.30)], and 48% with SARS-CoV-2 infection in the 3 months prior to beginning of the Omicron wave [0.52, (0.27-0.99)].\n\nConclusions and ImplicationsVaccine type (i.e., mRNA-1273/Spikevax vs BNT162b2/Cominarty), any fourth vaccine dose, and hybrid immunity from recent COVID-19, were protective against infection with the Omicron variant. These data emphasize the importance of vaccine type, and number of vaccine doses, in maintenance of protective immunity and reduction of risk of Omicron variant breakthrough infection. These findings promote continued public health efforts to support vaccination programs and monitor vaccine immunogenicity in older adults.\n\nBrief summaryRisk of infection with the SARS-CoV-2 Omicron variant in older adults in early 2022 was reduced with triple mRNA-1273 vaccination, any fourth dose vaccine, and within three months of prior COVID-19.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Jessica A. Breznik", + "author_inst": "McMaster University" + }, + { + "author_name": "Ahmad Rahim", + "author_inst": "McMaster University" + }, + { + "author_name": "Tara Kajaks", + "author_inst": "McMaster University" + }, + { + "author_name": "Megan Hagerman", + "author_inst": "McMaster University" + }, + { + "author_name": "Lucas Bilaver", + "author_inst": "McMaster University" + }, + { + "author_name": "Karen Colwill", + "author_inst": "Mount Sinai Hospital Sinai Health" + }, + { + "author_name": "Roaya Dayam", + "author_inst": "Mount Sinai Hospital Sinai Health" + }, + { + "author_name": "Anne-Claude Gingras", + "author_inst": "Mount Sinai Hospital Sinai Health" + }, + { + "author_name": "Chris P. Verschoor", + "author_inst": "Health Sciences North Research Institute" + }, + { + "author_name": "Janet E. McElhaney", + "author_inst": "Health Sciences North Research Institute" + }, + { + "author_name": "Jonathan L. Bramson", + "author_inst": "McMaster University" + }, + { + "author_name": "Dawn M.E. Bowdish", + "author_inst": "McMaster University" + }, + { + "author_name": "Andrew P Costa", + "author_inst": "McMaster University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.06.28.22277015", "rel_title": "Retrospective analysis of SARS-CoV-2 omicron invasion over delta in French regions in 2021-22: a status-based multi-variant model", @@ -248103,49 +250511,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.06.27.22276870", - "rel_title": "Transition to Endemic: Acceptance of Additional COVID-19 Vaccine Doses Among Canadian Adults in A National Cross-Sectional Survey", - "rel_date": "2022-06-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.27.22276870", - "rel_abs": "BackgroundAdditional doses of COVID-19 vaccine have been proposed as solutions to waning immunity and decreased effectiveness of primary doses against infection with new SARS-CoV-2 variants. However, the effectiveness of additional vaccine doses relies on widespread population acceptance. We aimed to assess the acceptance of additional COVID-19 vaccine doses (third and annual doses) among Canadian adults and determine associated factors.\n\nMethodsWe conducted a national, cross-sectional online survey among Canadian adults from October 14 to November 12, 2021. Weighted multinomial logistic regression analyses were used to identify sociodemographic and health-related factors associated with third and annual dose acceptance and indecision, compared to refusal. We also assessed influences on vaccine decision-making, and preferences for future vaccine delivery.\n\nResultsOf 6010 respondents, 70% reported they would accept a third dose, while 15.2% were undecided. For annual doses, 64% reported acceptance, while 17.5% were undecided. Factors associated with third dose acceptance and indecision were similar to those associated with annual dose acceptance and indecision. Previous COVID-19 vaccine receipt, no history of COVID-19 disease, intention to receive an influenza vaccine, and increasing age were strongly associated with both acceptance and indecision. Chronic illness was associated with higher odds of acceptance, while self-reported disability was associated with higher odds of being undecided. Higher education attainment and higher income were associated with higher odds of accepting additional doses. Minority first language was associated with being undecided about additional doses, while visible minority identity was associated with being undecided about a third dose and refusing an annual dose. All respondents reported government recommendations were an important influence on their decision-making and identified pharmacy-based delivery and drop-in appointments as desirable. Co-administration of COVID-19 and influenza vaccines was viewed positively by 75.5% of the dose 3 acceptance group, 12.3% of the undecided group, and 8.4% of the refusal group.\n\nConclusionsTo increase acceptance, targeted interventions among visible minority and minority language populations, and those with a disability, are required. Offering vaccination at pharmacies and through drop-in appointments are important to facilitate uptake, while offering COVID-19/influenza vaccine co-administration may have little benefit among those undecided about additional doses.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Laura Reifferscheid", - "author_inst": "University of Alberta" - }, - { - "author_name": "Janet Sau Wun Lee", - "author_inst": "University of Alberta" - }, - { - "author_name": "Noni E. MacDonald", - "author_inst": "Dalhousie University" - }, - { - "author_name": "Manish Sadarangani", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Ali Assi", - "author_inst": "University of Alberta" - }, - { - "author_name": "Samuel Lemaire-Paquette", - "author_inst": "Centre de Recherche du CHUS" - }, - { - "author_name": "Shannon E MacDonald", - "author_inst": "University of Alberta" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.06.27.22276955", "rel_title": "Impact of COVID-19 on the management and outcomes of ureteric stones in the UK: a multicentre retrospective study", @@ -248966,6 +251331,65 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2022.06.28.497978", + "rel_title": "Naturally occurring mutations of SARS-CoV-2 main protease confer drug resistance to nirmatrelvir", + "rel_date": "2022-06-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.28.497978", + "rel_abs": "The SARS-CoV-2 main protease (Mpro) is the drug target of Pfizers oral drug Paxlovid. The emergence of SARS-CoV-2 variants with mutations in Mpro raised the alarm of potential drug resistance. In this study, we identified 100 naturally occurring Mpro mutations located at the nirmatrelvir binding site, among which 20 mutants, including S144M/F/A/G/Y, M165T, E166G, H172Q/F, and Q192T/S/L/A/I/P/H/V/W/C/F, showed comparable enzymatic activity to the wild-type (kcat/Km <10-fold change) and resistance to nirmatrelvir (Ki >10-fold increase). X-ray crystal structures were determined for seven representative mutants with and/or without GC-376/nirmatrelvir. Viral growth assay showed that Mpro mutants with reduced enzymatic activity led to attenuated viral replication. Overall, our study identified several drug resistant hot spots that warrant close monitoring for possible clinical evidence of Paxlovid resistance.\n\nOne Sentence SummaryPaxlovid resistant SARS-CoV-2 viruses with mutations in the main protease have been identified from clinical isolates.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Yanmei Hu", + "author_inst": "Rutgers, the State University of New Jersey" + }, + { + "author_name": "Eric M Lewandowski", + "author_inst": "University of South Florida" + }, + { + "author_name": "Haozhou Tan", + "author_inst": "Rutgers, the State University of New Jersey" + }, + { + "author_name": "Ryan T Morgan", + "author_inst": "University of South Florida" + }, + { + "author_name": "Xiujun Zhang", + "author_inst": "University of South Florida" + }, + { + "author_name": "Lian M Jacobs", + "author_inst": "University of South Florida" + }, + { + "author_name": "Shane G Butler", + "author_inst": "University of South Florida" + }, + { + "author_name": "Maura V Mongora", + "author_inst": "University of South Florida" + }, + { + "author_name": "John S Choy", + "author_inst": "The Catholic University of America" + }, + { + "author_name": "Yu Chen", + "author_inst": "University of South Florida" + }, + { + "author_name": "Jun Wang", + "author_inst": "Rutgers, the State University of New Jersey" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2022.06.23.22276832", "rel_title": "Patients with affective disorders profit most from telemedical treatment: Evidence from a naturalistic patient cohort during the COVID-19 pandemic", @@ -249829,25 +252253,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.06.24.22276889", - "rel_title": "Modeling the USA Late Winter 2021 and Spring 2022 CoVID-19 Resurgences", - "rel_date": "2022-06-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.24.22276889", - "rel_abs": "Every USA wave, including this latest Spring 2022 Resurgence has been successfully modeled using: O_FD O_INLINEFIG[Formula 1]C_INLINEFIGM_FD(1)C_FD with N (t) being the total number of new CoVID-19 cases above a prior baseline, and tR setting the pandemic wave doubling time tdbl = tR (In 2). The parameters {S ;{delta} o} measure mitigation efforts among the uninfected population. Here, {S > 0} is associated with Social Distancing and vaccinations ; while {{delta}o > 0} is associated with mask-wearing, which results in faster [Formula] post-peak drop-offs. The predicted pandemic wave end is when the calculated N (t) stops increasing.\n\nThe USA Winter 2021 Resurgence resulted in fewer Omicron CoVID-19 cases than calculated in our prior medrxiv.org preprint*, due to an increased{delta} o component, which gives [~]3/11/22 as the predicted wave end. A relatively quiet CoVID-19 period ensued until [~]4/16/22, when a new Omicron variant caused the present Spring 2022 CoVID-19 resurgence.\n\nThe recent CoVID-19 waves have decreasing tR values, with the Spring 2022 tR{approx} 3.55 days (tdbl {approx} 2.46 days) value being the shortest since the initial 2020 pandemic, indicating increasingly infectious variants. The Winter 2021 and the present Spring 2022 CoVID-19 resurgences have identical S {approx} 0.043 / day values, but the{delta} o > 0 mask-wearing parameter decreased from{delta} o {approx} 3. 14 x 10-3/ day to{delta} o {approx} 1. 145 x 10-3/ day, giving the Spring 2022 wave a longer tail, and an expected end date of 8/25/22, with these wave totals: O_FD O_INLINEFIG[Formula 2]C_INLINEFIGM_FD(2)C_FD\n\nWhen all the USA CoVID-19 waves are combined, it gives: O_FD O_INLINEFIG[Formula 3]C_INLINEFIGM_FD(3)C_FD assuming no future CoVID-19 Resurgences (with 5 Figures).\n\n*(10.1101_2022.02.04.22270491)", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Genghmun Eng", - "author_inst": "Retired Scientist" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.06.27.22276377", "rel_title": "Digitalization impacts the COVID-19 pandemic and the stringency of government measures", @@ -250512,6 +252917,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2022.06.26.497634", + "rel_title": "Humanized antibody potently neutralizes all SARS-CoV-2 variants by a novel mechanism", + "rel_date": "2022-06-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.26.497634", + "rel_abs": "SARS-CoV-2 Omicron variants have generated a world-wide health crisis due to resistance to most approved SARS-CoV-2 neutralizing antibodies and evasion of antibodies induced by vaccination. Here, we describe the SARS-CoV-2 neutralizing SP1-77 antibody that was generated from a humanized mouse model with a single human VH1-2 and V{kappa}1-33-associated with immensely diverse complementarity-determining-region-3 (CDR3) sequences. SP1-77 potently and broadly neutralizes SARS-CoV-2 variants of concern and binds the SARS-CoV-2 spike protein receptor-binding-domain (RBD) via a novel-CDR3-based mode. SP1-77 does not block RBD-binding to the ACE2-receptor or endocytosis step of viral entry, but rather blocks membrane fusion. Our findings provide the first mechanistic insight into how a non-ACE2 blocking antibody potently neutralizes SARS-CoV-2, which may inform strategies for designing vaccines that robustly neutralize current and future SARS-CoV-2 variants.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Amanda Eaton", + "author_inst": "Duke University School of Medicine" + }, + { + "author_name": "Robert J. Edwards", + "author_inst": "Duke University School of Medicine" + }, + { + "author_name": "Gregory D. Sempowski", + "author_inst": "Duke University School of Medicine" + }, + { + "author_name": "Kenneth Cronin", + "author_inst": "Duke University School of Medicine" + }, + { + "author_name": "Robert Parks", + "author_inst": "Duke University School of Medicine" + }, + { + "author_name": "Katayoun Mansouri", + "author_inst": "Duke University School of Medicine" + }, + { + "author_name": "Maggie Barr", + "author_inst": "Duke University School of Medicine" + }, + { + "author_name": "Lorenza Bellusci", + "author_inst": "Food and Drug Administration (FDA)" + }, + { + "author_name": "Surender Khurana", + "author_inst": "Food and Drug Administration (FDA)" + }, + { + "author_name": "S. Munir Alam", + "author_inst": "Duke University School of Medicine" + }, + { + "author_name": "David C. Montefiori", + "author_inst": "Duke University School of Medicine" + }, + { + "author_name": "Kevin O. Saunders", + "author_inst": "Duke University School of Medicine" + }, + { + "author_name": "Barton F. Haynes", + "author_inst": "Duke University School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.06.24.22276144", "rel_title": "Humoral Responses in the Omicron Era following Three-Dose SARS-CoV-2 Vaccine Series in Kidney Transplant Recipients", @@ -251523,61 +253995,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2022.06.20.22276672", - "rel_title": "Heterogeneity and district-level factors associated with COVID-19 mortality during three epidemic waves in Indonesia: a nationwide ecological study", - "rel_date": "2022-06-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.20.22276672", - "rel_abs": "IntroductionEnsuring health equity, especially for vulnerable populations in less developed settings with poor health system is essential for the current and future global health threats. This study examined the heterogeneity of COVID-19 mortality and its association with population health characteristics, health care capacity in responding pandemic, and socio-economic characteristics across 514 districts in Indonesia.\n\nMethodsThis nationwide ecological study included aggregated COVID-19 cases data from all 514 districts in Indonesia, recorded in the National COVID-19 Task Force database, during the first two years of the epidemic, from 1 March 2020 to 27 February 2022. We calculated incidence and mortality rate by time, sex, and age. We extracted district-level socio-demographics, population health, and health care capacity data from government official sources. We used multivariable linear regression to examine factors associated with higher mortality rate.\n\nResultsOf total 5,539,333 reported cases, 148,034 (2{middle dot}7%) died, and 5,391,299 (97.4%) were recovered. The national mortality rate was 55 per 100,000 population, ranged from 13 per 100,000 population in Papua to 156 per 100,000 population in East Kalimantan province. At district-level, higher mortality rate was associated with higher COVID-19 incidence (p<0.0001), higher proportion of [≥]60 years old population (p<0.0001), higher prevalence of diabetes mellitus (p<0.0001), lower prevalence of obesity (p=0.019), lower number of doctors per population (p=0.001), higher life expectancy at birth (p=0.035), and lower formal education (p=0.021). There was no association between COVID-19 mortality rate with expenditure, prevalence of hypertension and pneumonia, vaccine coverage for [≥]60 years old population, number of nurses, midwives, and hospitals per population (p>0.05 each).\n\nConclusionCOVID-19 mortality rate in Indonesia was highly heterogeneous and associated with different prevalence of pre-existing comorbidity, healthcare capacity in responding the pandemic, and socio-economic characteristics. This study revealed the need of health capacity strengthening and better resource allocation to ensure optimal health outcomes for vulnerable population.\n\nWhat is already known on this topicO_LIThe severity of COVID-19 illness and clinical outcomes can be affected by the concentration of comorbidities in susceptible groups in communities, and through disparities of access to health care for preventive measures or prompt diagnosis and treatment.\nC_LIO_LIHowever, evidence on the heterogeneity of COVID-19 impact from low- and middle-income country (LMIC) where differences in age distribution, comorbidities, access to quality health services, and other factors, may greatly influence mortality risk, are limited.\nC_LI\n\nWhat this study addsO_LIThis study affirmed that COVID-19 disproportionately affected areas with high proportion of elder population, high prevalence of diabetes mellitus, lower doctor to population ratio, higher life expectancy at birth, and lower level of formal education.\nC_LIO_LIThese findings indicate that vulnerability to death associated with COVID-19 in LMIC includes not only elder and comorbid, but also males and communities living in area with lower health care capacity and with lower level of education.\nC_LI\n\nHow this study might affect research, practice and/or policyO_LIThese findings may inform decisions on health resource allocation against COVID-19 delivering the greatest possible health dividends by prioritising interventions, including even distribution of essential health care need such as doctors, and a tailored risk communication and community engagement for the most vulnerable communities in LMIC, especially with decentralised health systems like in Indonesia.\nC_LI", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Henry Surendra", - "author_inst": "Oxford University Clinical Research Unit, Jakarta, Indonesia" - }, - { - "author_name": "Danarastri Paramita", - "author_inst": "Komite Pengendalian COVID-19 dan Pemulihan Ekonomi Nasional, Jakarta, Indonesia" - }, - { - "author_name": "Nora N Arista", - "author_inst": "United Nations Development Program, Jakarta, Indonesia" - }, - { - "author_name": "Annisa I Putri", - "author_inst": "United States Agency of International Development, Jakarta, Indonesia" - }, - { - "author_name": "Akbar A Siregar", - "author_inst": "United States Agency of International Development, Jakarta, Indonesia" - }, - { - "author_name": "Evelyn Puspaningrum", - "author_inst": "Oxford University Clinical Research Unit, Jakarta, Indonesia" - }, - { - "author_name": "Leni Rosylin", - "author_inst": "Komite Pengendalian COVID-19 dan Pemulihan Ekonomi Nasional, Jakarta, Indonesia" - }, - { - "author_name": "Dida Gardera", - "author_inst": "Komite Pengendalian COVID-19 dan Pemulihan Ekonomi Nasional, Jakarta, Indonesia" - }, - { - "author_name": "Montty Girianna", - "author_inst": "Komite Pengendalian COVID-19 dan Pemulihan Ekonomi Nasional, Jakarta, Indonesia" - }, - { - "author_name": "Iqbal RF Elyazar", - "author_inst": "Oxford University Clinical Research Unit, Jakarta, Indonesia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.06.21.22276659", "rel_title": "Pre-Omicron vaccine breakthrough infection induces superior cross-neutralization against SARS-CoV-2 Omicron BA.1 than primo infection", @@ -252470,6 +254887,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.06.23.22276509", + "rel_title": "In vivo virological efficacy of monoclonal antibodies and direct antiviral agents against the SARS-CoV-2 BA.1 and BA.2 Omicron sublineages", + "rel_date": "2022-06-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.23.22276509", + "rel_abs": "BackgroundOmicron variant questioned the efficacy of the approved therapies for the early COVID-19. I In vitro data show retained neutralizing activity against BA.1 and BA.2 for remdesivir (RDV), molnupiravir (MLN), and nirmatrelvir/ritonavir (NRM/r), while poor efficacy for Sotrovimab (STR) against BA.2. No data about the risk of clinical failure and in vivo antiviral activity are available.\n\nMaterial and methodsSingle-center observational comparison study enrolling all consecutive patients with a confirmed SARS-CoV-2 Omicron (BA.1 or BA.2) diagnosis and who met eligibility criteria for treatment with RDV, MLN, NRM/r, or STR. Treatment allocation was subject to drug availability, time from symptoms onset, and comorbidities. Patients were followed through day 30. Nasopharyngeal swab (NPS) VL was measured on day 1 (D1) and D7 and was expressed by log2 cycle threshold (CT) scale. Comparisons between groups were made by Chi-square and Wilcoxon paired-test. Primary endpoint was D1-D7 VL variation. Potential decrease in VL and average treatment effect (ATE) were calculated from fitting marginal linear regression models weighted for calendar month of infusion, duration of symptoms, and immunodeficiency. Secondary endpoints were the proportion of D7 undetectable VL in NPS and clinical outcomes compared by treatment groups using a Chi-square test.\n\nResultsA total of 521 pts received treatments (STR 202, MLN 117, NRM/r 84, and RDV 118): female 250 (48%), median age 66 yrs (IQR 55-76), 90% vaccinated; 15% with negative baseline serology. At D1, median time from symptoms onset was 3 days (2,4). 378 (73%) pts were infected with BA.1 and 143 (27%) with BA.2. D1 mean viral load was 4.12 log2 (4.16 for BA.1 and 4.01 for BA.2). The adjusted analysis showed that NRM/r significantly reduced VL compared to all the other drugs in pts infected with BA.1 while no evidence for a difference vs. MLP was seen in those infected with BA.2. MLN had comparable activity to STR against BA.1 and to NRM/r against BA.2. There was no significant difference between STR and RDV for BA.2.\n\nAt D7, 35/521 (6.7%) pts had undetectable VL. Of these, 31 were infected with BA.1 [9 (9%) MLN, 7 (14%) NRM/r, 7 (8%) RDV, and 8 (5%) STR)], and only 4 with BA.2, all treated with NRM/r. After 30 days of follow-up, 9/568 pts experienced COVID-19-related clinical failure [7/226 STR (5 BA.1) and 2/87 NRM /r (2 BA.1)].\n\nConclusionsIn this analysis of in vivo early VL reductions, NRM/r appears to be the drug showing the greatest antiviral activity regardless of the VoC, together with MLN, although the latter limited to people with BA.2. In the Omicron era, due to the high prevalence of vaccinated people and the lower probability of hospital admission, VL decrease can be a valuable surrogate of drug activity.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Valentina Mazzotta", + "author_inst": "National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy" + }, + { + "author_name": "alessandro Cozzi Lepri", + "author_inst": "Institute for Global Health, UCL, London, UK" + }, + { + "author_name": "Francesca Colavita", + "author_inst": "National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy" + }, + { + "author_name": "Silvia Rosati", + "author_inst": "National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy;" + }, + { + "author_name": "Eleonora Lalle", + "author_inst": "National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy;" + }, + { + "author_name": "Claudia Cimaglia", + "author_inst": "National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy" + }, + { + "author_name": "Jessica Paulicelli", + "author_inst": "National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy" + }, + { + "author_name": "Ilaria Mastrorosa", + "author_inst": "National Institute for Infectious Diseases: INMI Lazzaro Spallanzani IRCCS" + }, + { + "author_name": "Alessandra Vergori", + "author_inst": "National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy" + }, + { + "author_name": "Enrico Girardi", + "author_inst": "National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy" + }, + { + "author_name": "Anna Rosa Garburglia", + "author_inst": "National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy" + }, + { + "author_name": "Francesco Vaia", + "author_inst": "National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy" + }, + { + "author_name": "Emanuele Nicastri", + "author_inst": "National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy" + }, + { + "author_name": "Andrea Antinori", + "author_inst": "National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.06.23.22276809", "rel_title": "Effectiveness of vaccination against SARS-CoV-2 Omicron variant infection, symptomatic disease, and hospitalisation: a systematic review and meta-analysis.", @@ -253385,69 +255873,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.06.22.497189", - "rel_title": "Increased levels of circulating neurotoxic metabolites in patients with mild Covid19", - "rel_date": "2022-06-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.22.497189", - "rel_abs": "SARS-CoV-2 corona virus causes a multi-faceted and poorly defined clinical and pathological phenotype involving hyperinflammation, cytokine release, and long-term cognitive deficits, with an undefined neuropathological mechanism. Inflammation increases the activity of the kynurenine pathway, which is linked to neurodegenerative and psychiatric disorders. We sought to determine whether the kynurenine pathway is impacted in patients with mild COVID-19, leading to elevated neurotoxic metabolites in blood, and whether such changes are associated with pro-inflammatory cytokines. Serum samples were taken from 150 patients and analyzed by ELISA and ultra-high performance liquid chromatography (UHPLC). The data were analyzed using multiple linear regression models adjusted for age and sex. We found increased levels of kynurenine, quinolinic acid and 3-hydroxykynurenine in serum from patients with mild COVID-19, together with increased levels of IL-6, ICAM-1, VCAM-1 and neopterin. The levels of neurotoxic metabolites were significantly associated with key inflammatory cytokines including IL-6 and TNF. The COVID-19 risk-factor hypertension was associated with the highest levels of neurotoxic metabolites in plasma. These neuroactive metabolites could be part of the pathological mechanisms underlying cognitive impairment during and post-COVID and should be explored as potential biomarkers for long-COVID symptoms.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Estibaliz Santiago-Mujika", - "author_inst": "Van Andel Research Institute" - }, - { - "author_name": "Kevin Heinrich", - "author_inst": "Quire Inc" - }, - { - "author_name": "Sonia George", - "author_inst": "Van Andel Institute" - }, - { - "author_name": "Colt D Capan", - "author_inst": "Van Andel Institute" - }, - { - "author_name": "Cameron Forton", - "author_inst": "Van Andel Institute" - }, - { - "author_name": "Zachary Madaj", - "author_inst": "Van Andel Institute" - }, - { - "author_name": "Amanda R Burmeister", - "author_inst": "Van Andel Institute" - }, - { - "author_name": "Matthew Sims", - "author_inst": "Oakland University William Beaumont School of Medicine" - }, - { - "author_name": "Andrew Pospisilik", - "author_inst": "Van Andel Institute" - }, - { - "author_name": "Patrik Brundin", - "author_inst": "Van Andel Institute" - }, - { - "author_name": "Stewart F Graham", - "author_inst": "Oakland University-William Beaumont School of Medicine" - }, - { - "author_name": "Lena Brundin", - "author_inst": "Van Andel Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "neuroscience" - }, { "rel_doi": "10.1101/2022.06.21.496751", "rel_title": "Fc-modified SARS-CoV-2 neutralizing antibodies with therapeutic effects in two animal models.", @@ -254316,6 +256741,41 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.06.20.496916", + "rel_title": "scPheno: A deep generative model to integrate scRNA-seq with disease phenotypes and its application on prediction of COVID-19 pneumonia and severe assessment", + "rel_date": "2022-06-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.20.496916", + "rel_abs": "Cell-to-cell variability is orchestrated by transcriptional variations participating in different biological processes. However, the dissection of transcriptional variability in specific biological process at single-cell level remains unavailable. Here, we present a deep generative model scPheno to integrate scRNA-seq with disease phenotypes to unravel the invisible phenotype-related transcriptional variations. We applied scPheno on COVID-19 blood scRNA-seq to separate transcriptional variations in regulating COVID-19 host immunity and transcriptional variations in maintaining cell-type identity. In silico, we found CLU+IFI27+S100A9+ monocyte as the efficient cellular marker for the prediction of COVID-19 diagnosis. Inspiringly, using only 4 genes upregulated in CLU+IFI27+S100A9+ monocytes can predict the COVID-19 diagnosis of individuals from different country with an accuracy up to 81.3%. We also found C1+CD163+ monocyte and 8 C1+CD163+ monocyte-upregulated genes as the efficient biomarkers for the prediction of severity assessment. Overall, scPheno is an effective method in dissecting the transcriptional basis of phenotype variations at single-cell level.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Feng Zeng", + "author_inst": "Xiamen University" + }, + { + "author_name": "Xuwen Kong", + "author_inst": "Xiamen University" + }, + { + "author_name": "Fan Yang", + "author_inst": "Xiamen University" + }, + { + "author_name": "Ting Chen", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Jiahuai Han", + "author_inst": "Xiamen University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2022.06.21.496991", "rel_title": "Identification of a guanine-specific pocket in the protein N of SARS-CoV-2", @@ -255307,77 +257767,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.06.19.22276599", - "rel_title": "Temporal trends in COVID-19 outcomes among patients with systemic autoimmune rheumatic diseases: From the first wave to Omicron", - "rel_date": "2022-06-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.19.22276599", - "rel_abs": "ObjectivesTo investigate temporal trends in incidence and severity of COVID-19 among patients with systemic autoimmune rheumatic diseases (SARDs) from the first wave through the Omicron wave.\n\nMethodsWe conducted a retrospective cohort study investigating COVID-19 outcomes among SARD patients systematically identified to have confirmed COVID-19 from March 1, 2020 to January 31, 2022 at a large healthcare system in Massachusetts. We tabulated COVID-19 counts of total and severe cases (hospitalizations or deaths) and compared the proportion with severe COVID-19 by calendar period and by vaccination status. We used logistic regression to estimate the ORs for severe COVID-19 for each period compared to the early COVID-19 period (reference group).\n\nResultsWe identified 1449 SARD patients with COVID-19 (mean age 58.4 years, 75.2% female, 33.9% rheumatoid arthritis). There were 399 (27.5%) cases of severe COVID-19. The proportion of severe COVID-19 outcomes declined over calendar time (p for trend <0.001); 45.6% of cases were severe in the early COVID-19 period (March 1-June 30, 2020) vs. 14.7% in the Omicron wave (December 17, 2021-January 31, 2022; adjusted odds ratio 0.29, 95%CI 0.19-0.43). A higher proportion of those unvaccinated were severe compared to not severe cases (78.4% vs. 59.5%).\n\nConclusionsThe proportion of SARD patients with severe COVID-19 has diminished since early in the pandemic, particularly during the most recent time periods, including the Omicron wave. Advances in prevention, diagnosis, and treatment of COVID-19 may have improved outcomes among SARD patients.\n\nKEY MESSAGESO_ST_ABSWhat is already known about this subject?C_ST_ABSO_LIPatients with systemic autoimmune rheumatic diseases (SARDs) may be at increased risk for severe COVID-19, defined as hospitalization or death.\nC_LIO_LIPrevious studies of SARD patients suggested improving COVID-19 outcomes over calendar time, but most were performed prior to the wide availability of COVID-19 vaccines or the Omicron wave that was characterized by high infectivity.\nC_LI\n\nWhat does this study add?O_LIThe proportion of SARD patients with severe COVID-19 outcomes was lower over calendar time\nC_LIO_LIThe adjusted odds ratio of severe COVID-19 in the Omicron wave was 0.29 (95%CI 0.19-0.43) compared to early COVID-19 period.\nC_LIO_LIThe absolute number of severe COVID-19 cases during the peak of the Omicron variant wave was similar to the peaks of other waves.\nC_LIO_LISARD patients with severe vs. not severe COVID-19 were more likely to be unvaccinated.\nC_LI\n\nHow might this impact on clinical practice or future developments?O_LIThese findings suggest that advances in COVID-19 prevention, diagnosis, and treatment have contributed to improved outcomes among SARD patients over calendar time.\nC_LIO_LIFuture studies should extend findings into future viral variants and consider the roles of waning immunity after vaccination or natural infection among SARD patients who may still be vulnerable to severe COVID-19.\nC_LI", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Yumeko Kawano", - "author_inst": "Brigham and Women's Hospital and Harvard Medical School" - }, - { - "author_name": "Naomi J. Patel", - "author_inst": "Massachusetts General Hospital and Harvard Medical School" - }, - { - "author_name": "Xiaosong Wang", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Claire E. Cook", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Kathleen M.M. Vanni", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Emily N. Kowalski", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Emily P. Banasiak", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Grace Qian", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Michael DiIorio", - "author_inst": "Brigham and Women's Hospital and Harvard Medical School" - }, - { - "author_name": "Tiffany Y.-T. Hsu", - "author_inst": "Brigham and Women's Hospital and Harvard Medical School" - }, - { - "author_name": "Michael E. Weinblatt", - "author_inst": "Brigham and Women's Hospital and Harvard Medical School" - }, - { - "author_name": "Derrick J. Todd", - "author_inst": "Brigham and Women's Hospital and Harvard Medical School" - }, - { - "author_name": "Zachary S. Wallace", - "author_inst": "Massachusetts General Hospital and Harvard Medical School" - }, - { - "author_name": "Jeffrey A. Sparks", - "author_inst": "Brigham and Women's Hospital and Harvard Medical School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "rheumatology" - }, { "rel_doi": "10.1101/2022.06.20.22276205", "rel_title": "Cohort Profile: Longitudinal population-based study of COVID-19 in UK adults (COVIDENCE UK)", @@ -256038,6 +258427,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.06.17.22276575", + "rel_title": "Change in Effectiveness of Sotrovimab for Preventing Hospitalization and Mortality in COVID-19 Outpatients During the Omicron Phase", + "rel_date": "2022-06-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.17.22276575", + "rel_abs": "BackgroundSotrovimab, a neutralizing monoclonal antibody (mAb) treatment authorized for early symptomatic COVID-19 patients, was effective in preventing the progression of severe disease and mortality following SARS-CoV-2 Delta variant infection. It is not known whether sotrovimab is similarly effective for SARS-CoV-2 Omicron variant infection.\n\nMethodsObservational cohort study of non-hospitalized adult patients with SARS-CoV-2 infection from December 26, 2021 to March 10, 2022 (>96% Omicron BA.1 variant), using electronic health records from a statewide health system linked to state-level vaccine and mortality data. We used propensity matching to select up to 3 patients not receiving mAbs or other authorized antivirals for each patient who received outpatient sotrovimab treatment. The primary outcome was 28-day hospitalization; secondary outcomes included mortality. To evaluate change in sotrovimab effectiveness during the Omicron phase, we propensity matched sotrovimab-treated patients from Omicron to Delta (October 1-December 11, 2021) phases to each other and then to untreated controls with a treatment-variant interaction added to the logistic regression model.\n\nResultsOf 30,247 patients with SARS-CoV-2 infection, we matched 1,542 receiving sotrovimab to 3,663 not receiving treatment. Compared to untreated patients, sotrovimab treatment was not associated with reduced odds of all-cause 28-day hospitalization (raw rate 2.5% versus 3.2%; adjusted OR 0.82, 95% CI 0.55, 1.19) or mortality (raw rate 0.1% versus 0.2%; adjusted OR 0.62, 95% CI 0.07, 2.78). In the combined analysis across Omicron and Delta phases, the observed treatment OR was higher during Omicron than during Delta (OR 0.85 vs. 0.39, respectively; interaction p=0.053)\n\nConclusionReal-world evidence demonstrated sotrovimab was not associated with reduced hospitalization and all-cause 28-day mortality among COVID-19 outpatients during the Omicron BA.1 phase and attenuated compared to the Delta phase\n\nSummaryReal-world evidence demonstrates that the neutralizing monoclonal antibody sotrovimab was not associated with lower 28-day hospitalization and mortality rates when administered to high-risk outpatients recently infected with SARS-CoV-2 during the Omicron variant phase, compared to a propensity-matched cohort of untreated outpatients.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Neil Aggarwal", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Laurel E Beaty", + "author_inst": "University of Colorado School of Public Health" + }, + { + "author_name": "Tellen D Bennett", + "author_inst": "University of Colorado School of Medicine" + }, + { + "author_name": "Nichole E Carlson", + "author_inst": "University of Colorado School of Public Health" + }, + { + "author_name": "Adit A Ginde", + "author_inst": "University of Colorado School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.06.17.22276576", "rel_title": "How do Urban Factors Control the Severity of COVID-19?", @@ -257285,61 +259709,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2022.06.15.22276459", - "rel_title": "Comparison of RT-qPCR and Digital PCR Methods for Wastewater-Based Testing of SARS-CoV-2", - "rel_date": "2022-06-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.15.22276459", - "rel_abs": "Wastewater-based epidemiology is an important tool for monitoring SARS-CoV-2 and other molecular targets in populations, using wastewater as a pooled sample. We compared the sensitivity, susceptibility to inhibition, and quantification of reverse transcription quantitative PCR (RT-qPCR), microfluidic well digital RT-PCR (RT-dPCR), and droplet digital RT-PCR (RT-ddPCR) measurements of SARS-CoV-2 (N1 gene target) and Pepper Mild Mottle Virus (PMMoV) RNA in 40 wastewater RNA extracts. All three methods were highly sensitive, but appeared less accurate at very low concentrations. Lower inhibition was observed for RT-ddPCR than RT-qPCR with both SARS-CoV-2 and PMMoV targets, but inhibition appeared to be mitigated by dilution of template RNA. The concentrations of N1 and PMMoV from all three methods were significantly correlated (Pearsons r=0.97-0.98 for N1 and r=0.89-0.93 for PMMoV), although RT-qPCR reported higher concentrations than digital methods. Taken together, this study provides support for the application of all three methods in wastewater-based epidemiology, with additional guidelines for the use of RT-qPCR.\n\nImpact StatementPCR-based assays are the current standard for sensitive, specific, rapid pathogen quantification in environmental samples, including wastewater. The increased availability of multiple digital PCR technologies necessitates side-by-side comparison between platforms, including traditional qPCR, to guide the application of these methods. Specifically, this work can inform interpretation of wastewater SARS-CoV-2 PCR data, as reported to public health agencies for pandemic response.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Adrian Hinkle", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Hannah D Greenwald", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Matthew Metzger", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Melissa Thornton", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Lauren C Kennedy", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Kristin Loomis", - "author_inst": "Bio-Rad Laboratories" - }, - { - "author_name": "Monica Herrera", - "author_inst": "Bio-Rad Laboratories" - }, - { - "author_name": "Raymond-John Abayan", - "author_inst": "Bio-Rad Laboratories" - }, - { - "author_name": "Kara L Nelson", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Rose S Kantor", - "author_inst": "University of California, Berkeley" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.06.15.22276432", "rel_title": "Viral load and timing of infection define neutralization diversity to SARS-CoV-2 infection", @@ -257996,6 +260365,49 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2022.06.13.22276242", + "rel_title": "Managing the evidence infodemic: Automation approaches used for developing NICE COVID-19 living guidelines", + "rel_date": "2022-06-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.13.22276242", + "rel_abs": "Background and ObjectivesThe National Institute for Health and Care Excellence (NICE) produces evidence-based guidance and advice for health, public health and social care practitioners in England and Wales. Between March 2020 and March 2022, NICE produced 24 COVID-19 guidelines to support healthcare workers during the COVID-19 pandemic. This article outlines three automation strategies NICE utilised to facilitate faster processing of evidence on COVID-19 and describes the value of those approaches when there is an increasing volume of evidence and demand on resources.\n\nStudy Design and SettingText classification using machine learning, and regular expression-based pattern matching were used to automate screening of literature search results. Relevant clinical trials were tracked by automated monitoring of clinical trial databases and Pubmed.\n\nResultsThe strategies discussed here brought considerable efficiencies in the processing time without impacting on quality compared to equivalent manual efforts. Additionally, the paper illustrates how to incorporate automation into established processes of the evidence management pipeline.\n\nConclusionsWe have demonstrated through testing and use in live guideline development and surveillance that these are effective and low risk approaches at managing high volumes of evidence.\n\nHighlights- To illustrate how NICE utilised automation to handle the Covid-19 infodemic-managing the infodemic of evidence surveillance is a shared global issue.\n- To outline automation strategies to facilitate faster processing of evidence, especially when there is an increasing volume of evidence and demand on resources.\n- How automation can be included in established processes without disrupting business as usual operations.\n- Automation can take many forms, and depending on risk appetite, can be supplemented with manual checking.\n- Automation can be adopted easily with the right tools and techniques.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Mariam R Sood", + "author_inst": "National Institute of Health and Care Excellence" + }, + { + "author_name": "Steve Sharp", + "author_inst": "National Institute of Health and Care Excellence" + }, + { + "author_name": "Emma McFarlane", + "author_inst": "National Institute of Health and Care Excellence" + }, + { + "author_name": "Robert Willans", + "author_inst": "National Institute of Health and Care Excellence" + }, + { + "author_name": "Kathryn Hopkins", + "author_inst": "National Institute of Health and Care Excellence" + }, + { + "author_name": "Justine Karpusheff", + "author_inst": "National Institute of Health and Care Excellence" + }, + { + "author_name": "Fiona Glen", + "author_inst": "National Institute of Health and Care Excellence" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2022.06.13.22276325", "rel_title": "Sensitivity of rapid antigen tests for COVID-19 during the Omicron variant outbreak", @@ -259191,33 +261603,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.06.16.496383", - "rel_title": "Development and Evaluation of RT-LAMP Assays to Identify Variants of SARS-CoV-2", - "rel_date": "2022-06-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.16.496383", - "rel_abs": "Emergence of new variants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) during current pandemic of Coronavirus Disease 2019 (COVID-19) and several waves of infections by some of variants emphasized the importance of continuous surveillance. While genomic surveillance through whole genome sequencing is performed as a standard method, identification of known variants through mutation-targeting molecular diagnosis such as qRT-PCR is also useful for timely investigation. However, there are limited studies regarding the concurrent detection and identification of SARS-CoV-2 variants through a LAMP-based method. In this study, we developed and evaluated RT-LAMP assays to detect characteristic deletions of SARS-CoV-2 variants. In addition, we evaluated a fluorescent probe mediated method for identification of single nucleotide substitution by RT-LAMP. Finally, we discussed restrictions and perspectives regarding pathogen screening and surveillance of variants by RT-LAMP based on our observations.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Gun-Soo Park", - "author_inst": "CEVI/KFRI" - }, - { - "author_name": "Seong-Jun Kim", - "author_inst": "Korea Research Institute of Chemical Technology" - }, - { - "author_name": "Jin-Soo Maeng", - "author_inst": "CEVI / KFRI" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.06.16.22276024", "rel_title": "Predictive performance of multi-model ensemble forecasts of COVID-19 across European nations", @@ -260406,6 +262791,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "ophthalmology" }, + { + "rel_doi": "10.1101/2022.06.13.22276319", + "rel_title": "Repeated mass testing of staff and residents in prison outbreaks of Covid-19: an enhanced outbreak investigation in two adult prisons in England, 2021", + "rel_date": "2022-06-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.13.22276319", + "rel_abs": "BackgroundThe management of Covid-19 outbreaks presented particular challenges in the prison setting. In this study we describe the results from the implementation of a serial mass testing approach in two adult prisons in northern England. The overall aim was to examine the epidemiology of Covid-19 outbreaks in prisons and help inform public health policy and practice during the pandemic.\n\nMethodsRepeat mass testing was offered to all eligible staff and residents in a womens (nresidents=239; nstaff=246) and a mens (nresidents=703; nstaff=340) prison in February and March 2021 at days 0, 7 and 28 after Covid-19 outbreaks were declared. Positive swab samples were sent for viral whole genome sequencing by COG-UK.\n\nFindingsParticipation in at least one testing round ranged from a low of 67% of staff in the mens prison to a high of 98% of residents in the womens prison. The largest outbreak, in the mens prison (261 cases in residents and 37 cases in staff), continued to see new cases identified at the last testing round on day 28. Test positivity in residents of both prisons was significantly lower (p<0.05) at day 28 than on preceding test days, but no significant difference was observed for staff (p>0.05). Epidemiological data in conjunction with sequencing information provided evidence for multiple introductions of the SARS-CoV-2 virus from the local community into the prisons, with transmission identified both within wings and between wings among residents and staff. Two distinct SARS-CoV-2 lineages were identified in the womens and mens prisons, B.1.177 and B.1.17, respectively.\n\nConclusionsDuring a Covid-19 outbreak, timely implementation of a whole prison testing regime can serve to inform a targeted approach to infection prevention and control by identifying the true extent of disease transmission in all (including asymptomatic) individuals. Staff, in particular, should be tested regularly and testing uptake should be as high as possible to minimise the risk of infection incursion. Ensuring high testing uptake across all testing rounds remains a challenge.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Maciej Czachorowski", + "author_inst": "National Health and Justice, United Kingdom Health Security Agency, London, UK" + }, + { + "author_name": "Matthew Bashton", + "author_inst": "Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK" + }, + { + "author_name": "Nuala McGrath", + "author_inst": "School of Primary Care, Population Sciences and Medical Education, University of Southampton, Southampton, SO17 1BJ, UK; Department of Social Statistics and Dem" + }, + { + "author_name": "Darren Smith", + "author_inst": "Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK." + }, + { + "author_name": "Kerry Gutridge", + "author_inst": "Centre for Women's Mental Health, Division of Psychology and Mental Health, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Ma" + }, + { + "author_name": "Julie Parkes", + "author_inst": "School of Primary Care, Population Sciences and Medical Education, University of Southampton, Southampton, SO17 1BJ, UK" + }, + { + "author_name": "Emma Plugge", + "author_inst": "National Health and Justice, United Kingdom Health Security Agency, London, UK; School of Primary Care, Population Sciences and Medical Education, University of" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.06.08.22275684", "rel_title": "Relation of spice consumption with COVID-19 first wave statistics (infection, recovery and mortality) across India", @@ -261521,57 +263949,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.06.13.22276267", - "rel_title": "Wastewater surveillance in smaller college communities may aid future public health initiatives", - "rel_date": "2022-06-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.13.22276267", - "rel_abs": "Since its declaration, the COVID-19 pandemic has resulted in over 530 million cases and over 6 million deaths worldwide. Predominant clinical testing methods, though invaluable, may create an inaccurate depiction of COVID-19 prevalence due to inadequate access, testing, or most recently under-reporting because of at-home testing. These concerns have created a need for unbiased, community-level surveillance. Wastewater-based epidemiology has been used for previous public health threats, and more recently has been established as a complementary method of SARS-CoV-2 surveillance. Here we describe the application of wastewater surveillance for SARS-CoV-2 in two university campus communities located in rural Lincoln Parish, Louisiana. This cost-effective approach is especially well suited to rural areas where limited access to testing may worsen the spread of COVID-19 and quickly exhaust the capacity of local healthcare systems. Our work demonstrates that local universities can leverage scientific resources to advance public health equity in rural areas and enhance their community involvement.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Laura Lee", - "author_inst": "Louisiana Tech University" - }, - { - "author_name": "Lescia Valmond", - "author_inst": "Grambling State University" - }, - { - "author_name": "John Thomas", - "author_inst": "Grambling State University" - }, - { - "author_name": "Audrey Kim", - "author_inst": "Grambling State University" - }, - { - "author_name": "Paul Austin", - "author_inst": "Louisiana Tech University" - }, - { - "author_name": "Michael Foster", - "author_inst": "Louisiana Tech University" - }, - { - "author_name": "John Matthews", - "author_inst": "Louisiana Tech University" - }, - { - "author_name": "Paul Kim", - "author_inst": "Grambling State University" - }, - { - "author_name": "Jamie J Newman", - "author_inst": "Louisiana Tech University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.06.09.22276129", "rel_title": "Side effects of Covishield vaccine among frontline healthcare workers of a tertiary health care center", @@ -262360,6 +264737,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, + { + "rel_doi": "10.1101/2022.06.10.22276256", + "rel_title": "Baseline Peripheral Blood Counts and Outcomes in Patients Presenting with COVID-19", + "rel_date": "2022-06-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.10.22276256", + "rel_abs": "BackgroundSARS-CoV-2 pandemic has significant impact on hematopoietic system.\n\nObjectiveTo report the incidence and pattern of baseline hematological parameters in patients with COVID-19 and their association with severity of disease and outcome.\n\nMethodsRetrospective observational study.\n\nResultsA total of 440 patients were included in the study. The mean age of the study cohort was 47.5 {+/-}15.8 years. Fifty percent of patients had at least 1 comorbidity. ICU stay was required in 125 (39.6%) patients. Overall mortality in the study cohort was 3.52%. The average age of patients who died was significantly higher than that of patients who were alive (65.1 years vs 46.5 years; p= 0.000). DM, HTN, CAD and CKD were all associated with higher incidence of ICU stay and mortality. Lymphopenia < 1x109/l was observed in 24.3% and eosinopenia was noted in 44.3% patients. Leukocytosis>11x109/l was seen in 8.2 % of patients. The median neutrophil lymphocyte ratio (NLR) of whole cohort was 2.63. NLR, Lymphopenia, eosinopenia, leucocytosis, D dimer, lactate dehydrogenase (LDH), ferritin and IL6 levels all were associated with need for ICU transfer and mortality. Hemoglobin, red cell distribution width (RDW), PT and aPTT correlated with need for ICU transfer but not with mortality. Ferritin cutoff [≥]751 ng/ml and IL6 levels [≥]64pg/ml was able to identify all deaths. Ferritin (0.989) and IL-6 (0.985) had very high negative predictive value.\n\nConclusionsPeripheral blood counts at time of hospitalization is a simple tool to predict outcomes in patients admitted with Covid-19.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Preethi Jeyaraman", + "author_inst": "Max Superspecialty Hospital, Saket, New Delhi" + }, + { + "author_name": "Pronamee Borah", + "author_inst": "Max Superspecialty Hospital, Saket, New Delhi" + }, + { + "author_name": "Omender Singh", + "author_inst": "Max Superspecialty Hospital, Saket, New Delhi" + }, + { + "author_name": "Arun Dewan", + "author_inst": "Max Superspecialty Hospital, Saket, New Delhi" + }, + { + "author_name": "Nitin Dayal", + "author_inst": "Max Superspecialty Hospital, Saket, New Delhi" + }, + { + "author_name": "Rahul Naithani", + "author_inst": "Max Superspecilaity Hospital, Saket" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "hematology" + }, { "rel_doi": "10.1101/2022.06.09.22276142", "rel_title": "Clinical sensitivity and specificity of a high-throughput microfluidic nano-immunoassay combined with capillary blood microsampling for the identification of anti-SARS-CoV-2 Spike IgG serostatus", @@ -263275,25 +265691,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.06.13.22276316", - "rel_title": "Patterns of Reported Infection and Reinfection of SARS-CoV-2 in England", - "rel_date": "2022-06-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.13.22276316", - "rel_abs": "One of the key features of any infectious disease is whether infection generates long-lasting immunity or whether repeated reinfection is common. In the former, the long-term dynamics are driven by the birth of susceptible individuals while in the latter the dynamics are governed by the speed of waning immunity. Between these two extremes a range of scenarios is possible. During the early waves of SARS-CoV-2, the underlying paradigm was for long-lasting immunity, but more recent data and in particular the 2022 Omicron waves have shown that reinfection can be relatively common. Here we investigate reported SARS-CoV-2 cases in England, partitioning the data into four main waves, and consider the temporal distribution of first and second reports of infection. We show that a simple low-dimensional statistical model of random (but scaled) reinfection captures much of the observed dynamics, with the value of this scaling, k, providing information of underlying epidemiological patterns. We conclude that there is considerable heterogeneity in risk of reporting reinfection by wave, age-group and location. The high levels of reinfection in the Omicron wave (we estimate that 18% of all Omicron cases had been previously infected, although not necessarily previously reported infection) point to reinfection events dominating future COVID-19 dynamics.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Matt J Keeling", - "author_inst": "University of Warwick" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.06.12.22276307", "rel_title": "Occupation, Worker Vulnerability, and COVID-19 Vaccination Uptake: Analysis of the Virus Watch prospective cohort study", @@ -263878,6 +266275,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.06.09.495482", + "rel_title": "ARF6 is an important host factor for SARS-CoV-2 infection in vitro", + "rel_date": "2022-06-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.09.495482", + "rel_abs": "SARS-CoV-2 is a newly emerged beta-coronavirus that enter cells via two routes, direct fusion at the plasma membrane or endocytosis followed by fusion with the late endosome/lysosome. While the viral receptor, ACE2, multiple entry factors, and the mechanism of fusion of the virus at the plasma membrane have been extensively investigated, viral entry via the endocytic pathway is less understood. By using a human hepatocarcinoma cell line, Huh-7, which is resistant to the antiviral action of the TMPRSS2 inhibitor camostat, we discovered that SARS-CoV-2 entry is not dependent on dynamin but dependent on cholesterol. ADP-ribosylation factor 6 (ARF6) has been described as a host factor for SARS-CoV-2 replication and it is involved in the entry and infection of several pathogenic viruses. Using CRISPR-Cas9 genetic deletion, we observed that ARF6 is important for SARS-CoV-2 uptake and infection in Huh-7. This finding was corroborated using a pharmacologic inhibitor, whereby the ARF6 inhibitor NAV-2729 showed a dose-dependent inhibition of viral infection. Importantly, NAV-2729 reduced SARS-CoV-2 viral loads also in more physiologic models of infection: Calu-3 and kidney organoids. This highlighted the importance of ARF6 in multiple cell contexts. Together, these experiments points to ARF6 as a putative target to develop antiviral strategies against SARS-CoV-2.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Carmen Mirabelli", + "author_inst": "University of Luebeck" + }, + { + "author_name": "Emily J Sherman", + "author_inst": "Department of Internal Medicine, Division of Hospital Medicine, University of Michigan, Ann Arbor (MI), USA" + }, + { + "author_name": "Juliana Bragazzi Cunha", + "author_inst": "Department of Internal Medicine, Division of Hospital Medicine, University of Michigan, Ann Arbor (MI), USA" + }, + { + "author_name": "Jesse W Wotring", + "author_inst": "Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, Michigan, USA" + }, + { + "author_name": "Jamal El Saghir", + "author_inst": "Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, Michigan, USA" + }, + { + "author_name": "Jennifer Harder", + "author_inst": "Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, Michigan, USA" + }, + { + "author_name": "Jonathan Z Sexton", + "author_inst": "Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, Michigan, USA" + }, + { + "author_name": "Brian T Emmer", + "author_inst": "Department of Internal Medicine, Division of Hospital Medicine, University of Michigan, Ann Arbor (MI), USA" + }, + { + "author_name": "Christiane E Wobus", + "author_inst": "Department of Microbiology and Immunology, University of Michigan medical school, Ann Arbor (MI, USA" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.06.09.495422", "rel_title": "SARS-CoV-2-neutralizing humoral IgA response occurs earlier but modest and diminishes faster compared to IgG response.", @@ -264925,41 +267373,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.05.22.22275423", - "rel_title": "The effect of strict lockdown on Omicron SARS-CoV-2 variant transmission in Shanghai", - "rel_date": "2022-06-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.22.22275423", - "rel_abs": "BackgroundOmicron, the current SARS-CoV-2 variant of concern, is much more contagious than other previous variants. Whether strict lockdown could effectively curb the transmission of Omicron is largely unknown.\n\nMethodsIn this retrospective study, we compared the strictness of government lockdown policies in Shanghai and some countries. Based on the daily Omicron case number from March 1st 2022 to April 30th 2022, the effective reproductive numbers in this Shanghai Omicron wave were calculated to confirm the impact of strict lockdown on Omicron transmission. Pearson correlation was conducted to illustrate the determining factor of strict lockdown outcomes in the 16 different districts of Shanghai.\n\nResultsAfter very strict citywide lockdown since April 1st, the average daily effective reproductive number reduced significantly, indicating that strict lockdown could slow down the spreading of Omicron. Omicron control is more challenging in districts with higher population mobility and lockdown is more likely to decrease the number of asymptomatic carrier than the symptomatic cases.\n\nConclusionsThe strict lockdown could curb the transmission of Omicron effectively, especially for the asymptomatic spread. And urban city with extensive personnel movement is suggested to adopt this lockdown strategy at early stage to maximally control the virus transmission.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Haibo Yang", - "author_inst": "Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China" - }, - { - "author_name": "Hao Nie", - "author_inst": "Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China" - }, - { - "author_name": "Dewei Zhou", - "author_inst": "Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China" - }, - { - "author_name": "Yujia Wang", - "author_inst": "Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China" - }, - { - "author_name": "Wei Zuo", - "author_inst": "Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China; State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory " - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.06.06.22276070", "rel_title": "Hospitalization, death, and probable reinfection in Peruvian healthcare workers infected with SARS-CoV-2: a national retrospective cohort study", @@ -265716,6 +268129,277 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.06.06.22275865", + "rel_title": "Evolution of long-term hybrid immunity in healthcare workers after different COVID-19 vaccination regimens: a longitudinal observational cohort study", + "rel_date": "2022-06-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.06.22275865", + "rel_abs": "Both infection and vaccination, alone or in combination, generate antibody and T cell responses against SARS-CoV-2. However, the maintenance of such responses - and hence protection from disease - requires careful characterisation. In a large prospective study of UK healthcare workers (Protective immunity from T cells in Healthcare workers (PITCH), within the larger SARS-CoV-2 immunity & reinfection evaluation (SIREN) study) we previously observed that prior infection impacted strongly on subsequent cellular and humoral immunity induced after long and short dosing intervals of BNT162b2 (Pfizer/BioNTech) vaccination. Here, we report longer follow up of 684 HCWs in this cohort over 6-9 months following two doses of BNT162b2 or AZD1222 (Oxford/AstraZeneca) vaccination and up to 6 months following a subsequent mRNA booster vaccination. We make three observations: Firstly, the dynamics of humoral and cellular responses differ; binding and neutralising antibodies declined whereas T and memory B cell responses were maintained after the second vaccine dose. Secondly, vaccine boosting restored IgG levels, broadened neutralising activity against variants of concern including omicron BA.1, BA.2 and BA.5, and boosted T cell responses above the 6 month level post dose 2. Thirdly, prior infection maintained its impact driving larger as well as broader T cell responses compared with never-infected people - a feature maintained until 6 months after the third dose. In conclusion, broadly cross-reactive T cell responses are well maintained over time - especially in those with combined vaccine and infection-induced immunity (\"hybrid\" immunity) - and may contribute to continued protection against severe disease.", + "rel_num_authors": 64, + "rel_authors": [ + { + "author_name": "Shona C Moore", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Barbara Kronsteiner", + "author_inst": "University of Oxford" + }, + { + "author_name": "Stephanie Longet", + "author_inst": "University of Oxford" + }, + { + "author_name": "Sandra Adele", + "author_inst": "University of Oxford" + }, + { + "author_name": "Alexandra S Deeks", + "author_inst": "University of Oxford" + }, + { + "author_name": "Chang Liu", + "author_inst": "University of Oxford" + }, + { + "author_name": "Wanwisa Dejnirattisai", + "author_inst": "University of Oxford" + }, + { + "author_name": "Laura Silva Reyes", + "author_inst": "University of Oxford" + }, + { + "author_name": "Naomi Meardon", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Sian Faustini", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Saly Al-Taei", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Tom Tipton", + "author_inst": "University of Oxford" + }, + { + "author_name": "Luisa M Hering", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Adrienn Angyal", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Rebecca Brown", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Alexander R Nicols", + "author_inst": "Newcastle University" + }, + { + "author_name": "Susan L Dobson", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Piyada Supasa", + "author_inst": "University of Oxford" + }, + { + "author_name": "Aekkachai Tuekprakhon", + "author_inst": "University of Oxford" + }, + { + "author_name": "Andrew Cross", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Jessica K Tyerman", + "author_inst": "Newcastle University" + }, + { + "author_name": "Hailey Hornsby", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Irina Grouneva", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Megan Plowright", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Peijun Zhang", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Thomas A.H. Newman", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Jeremy M. Nell", + "author_inst": "Newcastle University" + }, + { + "author_name": "Priyanka Abraham", + "author_inst": "University of Oxford" + }, + { + "author_name": "Mohammad Ali", + "author_inst": "University of Oxford" + }, + { + "author_name": "Tom Malone", + "author_inst": "University of Oxford" + }, + { + "author_name": "Isabel Neale", + "author_inst": "University of Oxford" + }, + { + "author_name": "Eloise Phillips", + "author_inst": "University of Oxford" + }, + { + "author_name": "Joseph D. Wilson", + "author_inst": "University of Oxford" + }, + { + "author_name": "Martha Zewdie", + "author_inst": "Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, UK" + }, + { + "author_name": "Adrian Shields", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Emily C. Horner", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Lucy H. Booth", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Lizzie Stafford", + "author_inst": "University of Oxford" + }, + { + "author_name": "Sagida Bibi", + "author_inst": "University of Oxford" + }, + { + "author_name": "Daniel G. Wootton", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Alexander J. Mentzer", + "author_inst": "University of Oxford" + }, + { + "author_name": "Christopher P. Conlon", + "author_inst": "University of Oxford" + }, + { + "author_name": "Katie Jeffery", + "author_inst": "University of Oxford" + }, + { + "author_name": "Philippa C. Matthews", + "author_inst": "University of Oxford" + }, + { + "author_name": "Andrew J. Pollard", + "author_inst": "University of Oxford" + }, + { + "author_name": "Anthony Brown", + "author_inst": "University of Oxford" + }, + { + "author_name": "Sarah L. Rowland-Jones", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Juthathip Mongkolsapaya", + "author_inst": "University of Oxford" + }, + { + "author_name": "Rebecca P. Payne", + "author_inst": "Newcastle University" + }, + { + "author_name": "Christina Dold", + "author_inst": "University of Oxford" + }, + { + "author_name": "Teresa Lambe", + "author_inst": "University of Oxford" + }, + { + "author_name": "James E.D. Thaventhiran", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Gavin Screaton", + "author_inst": "University of Oxford" + }, + { + "author_name": "Eleanor Barnes", + "author_inst": "University of Oxford" + }, + { + "author_name": "Susan Hopkins", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Victoria Hall", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Christopher JA Duncan", + "author_inst": "Newcastle University" + }, + { + "author_name": "Alex Richter Richter", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Miles Carroll", + "author_inst": "University of Oxford" + }, + { + "author_name": "Thushan I. de Silva", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Paul Klenerman", + "author_inst": "University of Oxford" + }, + { + "author_name": "Susanna Dunachie", + "author_inst": "University of Oxford" + }, + { + "author_name": "Lance Turtle", + "author_inst": "University of Liverpool" + }, + { + "author_name": "- PITCH Consortium", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.06.06.22276060", "rel_title": "COVID-19 and per capita green tea consumption: update", @@ -266767,109 +269451,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.06.03.22275983", - "rel_title": "Heterologous CoronaVac plus Ad5-nCOV versus homologous CoronaVac vaccination among elderly: a phase 4, non-inferiority, randomized study", - "rel_date": "2022-06-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.03.22275983", - "rel_abs": "ImportancePeople over 60 developed less protection after two doses of inactivated COVID-19 vaccine than younger people. Heterologous vaccination might provide greater immunity and protection against variants of concern.\n\nObjectiveTo assess the safety and immunogenicity of a heterologous immunization with an adenovirus type 5-vectored vaccine (Convidecia) among elderly who were primed with an inactivated vaccine (CoronaVac) previously.\n\nDesignAn observer-blind, randomized (1:1) trial, conducted from August 26 to November 13, 2021.\n\nSettingA single center in Jiangsu Province, China.\n\nParticipants299 participants aged 60 years and older, of them 199 primed with two doses of CoronaVac in the past 3-6 months and 100 primed with one dose of CoronaVac in the past 1-2 months.\n\nInterventionConvidecia or CoronaVac as boosting dose\n\nMain Outcomes and MeasuresGeometric mean titers (GMTs) of neutralizing antibodies against wild-type SARS-CoV-2, and Delta and Omicron variants 14 days post boosting, and adverse reactions within 28 days.\n\nResultsIn the three-dose regimen cohort (n=199; mean (SD) age, 66.7 (4.2) years; 74 (37.2%) female), 99 and 100 received a third dose of Convidecia (group A) and CoronaVac (group B), respectively. In the two-dose regimen cohort (n=100; mean (SD) age, 70.5 (6.0) years; 49 (49%) female), 50 and 50 received a second dose of Convidecia (group C) and CoronaVac (group D), respectively. GMTs of neutralizing antibodies against wild-type SARS-CoV-2 at day 14 were 286.4 (95% CI: 244.6, 335.2) in group A and 48.2 (95% CI: 39.5, 58.7) in group B, with GMT ratio of 6.2 (95% CI: 4.7, 8.1), and 70.9 (95% CI: 49.5, 101.7) in group C and 9.3 (95% CI: 6.2, 13.9) in group D, with GMT ratio of 7.6 (95% CI: 4.1, 14.1). There was a 6.3-fold (GMTs, 45.9 vs 7.3) and 7.5-fold (32.9 vs 4.4) increase in neutralizing antibodies against Delta and Omicron variants in group A, respectively, compared with group B. However, there was no significant difference between group C and group D. Both heterologous and homologous booster immunizations were safe and well tolerated.\n\nConclusions and RelevanceHeterologous prime-boost regimens with CoronaVac and Convidecia induced strong neutralizing antibodies in elderly, which was superior to that induced by the homologous boost, without increasing safety concerns.\n\nTrial RegistrationClinicalTrials.gov NCT04952727\n\nKey Points\n\nQuestionDoes a heterologous immunization with recombinant adenovirus type 5-vectored vaccine (Convidecia) produced a non-inferior or superior response of neutralizing antibodies among elderly primed with two doses of inactivated COVID-19 vaccine (CoronaVac), compared to the homologous boosting\n\nFindingsIn this randomized clinical trial, a heterologous third dose of Convidecia resulted in a 6.2-fold (geometric mean titers: 286.4 vs 48.2), 6.3-fold (45.9 vs 7.3) and 7.5-fold (32.9 vs 4.4) increase in neutralizing antibodies against wild-type strain, Delta and Omicron variants 14 days post boosting, respectively, compared to the homologous boost with CoronaVac\n\nMeaningHeterologous prime-boost regimens with CoronaVac and Convidecia induced strong neutralizing antibodies in elderly, which was superior to that induced by the homologous boosting.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Pengfei Jin", - "author_inst": "Jiangsu Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Jingxin Li", - "author_inst": "Jiangsu Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Xiling Guo", - "author_inst": "Jiangsu Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Jinbo Gou", - "author_inst": "CanSino Biologics Inc." - }, - { - "author_name": "Lihua Hou", - "author_inst": "Institute of Biotechnology, Academy of Military Medical Sciences" - }, - { - "author_name": "Zhizhou Song", - "author_inst": "Lianshui County Center for Disease Control and Prevention" - }, - { - "author_name": "Tao Zhu", - "author_inst": "CanSino Biologics Inc., Tianjin, P.R. China." - }, - { - "author_name": "Hongxing Pan", - "author_inst": "Jiangsu Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Jiahong Zhu", - "author_inst": "Lianshui County Center for Disease Control and Prevention" - }, - { - "author_name": "Fengjuan Shi", - "author_inst": "Jiangsu Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Pan Du", - "author_inst": "Vazyme Biotech Co., Ltd." - }, - { - "author_name": "Haitao Huang", - "author_inst": "CanSino Biologics Inc." - }, - { - "author_name": "Jingxian Liu", - "author_inst": "Jiangsu Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Hui Zheng", - "author_inst": "School of Public Health, Southeast University" - }, - { - "author_name": "Xue Wang", - "author_inst": "CanSino Biologics Inc." - }, - { - "author_name": "Yin Chen", - "author_inst": "Jiangsu Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Peng Wan", - "author_inst": "CanSino Biologics Inc." - }, - { - "author_name": "Shipo Wu", - "author_inst": "Institute of Biotechnology, Academy of Military Medical Sceinces" - }, - { - "author_name": "Xuewen Wang", - "author_inst": "Canming Medical Technology Co., Ltd." - }, - { - "author_name": "Xiaoyu Xu", - "author_inst": "Vazyme Biotech Co., Ltd." - }, - { - "author_name": "Wei Chen", - "author_inst": "Institute of Biotechnology, Academy of Military Medical Sciences" - }, - { - "author_name": "Fengcai Zhu", - "author_inst": "Jiangsu Provincial Center for Disease Control and Prevention" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.06.03.494777", "rel_title": "NcPath: A novel tool for visualization and enrichment analysis of human non-coding RNA and KEGG signaling pathways", @@ -267590,6 +270171,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.06.03.22275903", + "rel_title": "An Analysis of PCR Ct Scores and Distributions from the ONS Community Infection Survey during the COVID-19 Second Wave in the UK", + "rel_date": "2022-06-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.03.22275903", + "rel_abs": "This work presents an analysis of PCR cycle threshold (Ct) scores and their distributions, i.e. the probabilities that a test is positive with a score Ct, P(Ct), derived from the survey during the second COVID wave in the UK. Their relation to gene target breakdown is exemplified. Thus a significant parameter for tracking the course of COVID in the second wave is the percentage of positive tests with Ct < 25, %Ct <25, which is obtained by plotting weekly percentiles from the survey against Ct to construct the ogive or cumulative frequency curve (CMF). The biological basis for studying this parameter is the strong correlation between %Ct < 25 and the percentage of positive tests comprising target genes ORF1ab+N and ORF1ab+N+S, or %Inf.\n\nFurthermore, the probability distributions, obtained by differentiating the ogives, were found to be predominantly bimodal with a hot peak at Ct = 20.31+/- 4.65 and a cold peak with Ct = 32.95+/-1.11. These closely match the peaks found for the target genes ORF1ab+N, viz. Ct=18.54+/-2.31 and Ct=32.02+/-0.49 as well as in Walker et al [12]. Similar results were found in [13] and [14]. The cold peak seems likely to be associated with residue from a previous infection. The distributions for gene targets in cfvroc Pillar 2 [15,16] are also bimodal but the peaks occur at lower values of Ct. This suggests the results are machine/sample dependent and emphasises the need for calibration, if quality control in PCR testing is to be improved.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Keith Johnson", + "author_inst": "None" + }, + { + "author_name": "Steven James Hammer", + "author_inst": "None" + }, + { + "author_name": "Tanya Klymenko", + "author_inst": "Sheffield Hallam University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.06.02.22275916", "rel_title": "Long COVID is associated with extensive in-vivo neuroinflammation on DPA-714 PET", @@ -268529,149 +271137,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.06.01.494461", - "rel_title": "A Multitrait Locus Regulates Sarbecovirus Pathogenesis", - "rel_date": "2022-06-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.01.494461", - "rel_abs": "Infectious diseases have shaped the human population genetic structure, and genetic variation influences the susceptibility to many viral diseases. However, a variety of challenges have made the implementation of traditional human Genome-wide Association Studies (GWAS) approaches to study these infectious outcomes challenging. In contrast, mouse models of infectious diseases provide an experimental control and precision, which facilitates analyses and mechanistic studies of the role of genetic variation on infection. Here we use a genetic mapping cross between two distinct Collaborative Cross mouse strains with respect to SARS-CoV disease outcomes. We find several loci control differential disease outcome for a variety of traits in the context of SARS-CoV infection. Importantly, we identify a locus on mouse Chromosome 9 that shows conserved synteny with a human GWAS locus for SARS-CoV-2 severe disease. We follow-up and confirm a role for this locus, and identify two candidate genes, CCR9 and CXCR6 that both play a key role in regulating the severity of SARS-CoV, SARS-CoV-2 and a distantly related bat sarbecovirus disease outcomes. As such we provide a template for using experimental mouse crosses to identify and characterize multitrait loci that regulate pathogenic infectious outcomes across species.", - "rel_num_authors": 32, - "rel_authors": [ - { - "author_name": "Ralph S. Baric", - "author_inst": "University of North Carolina at Chapel Hill Gillings School of Global Public Health" - }, - { - "author_name": "Alexandra Schaefer", - "author_inst": "UNC-CH, School of Public Health" - }, - { - "author_name": "Sarah R. Leist", - "author_inst": "University of North Carolina" - }, - { - "author_name": "Lisa Gralinski", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "David Martinez", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Emma S. Winkler", - "author_inst": "Washington University in Saint Louis" - }, - { - "author_name": "Kenichi Okuda", - "author_inst": "University of North Carolina" - }, - { - "author_name": "Padraig E Hawkins", - "author_inst": "University of North Carolina" - }, - { - "author_name": "Kendra L Gully", - "author_inst": "University of North Carolina" - }, - { - "author_name": "Rachel L Graham", - "author_inst": "University of North Carolina" - }, - { - "author_name": "Trevor D. Scobey", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Timothy A Bell", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Pablo Hock", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Ginger D Shaw", - "author_inst": "University of North Carolina" - }, - { - "author_name": "Jennifer F Loome", - "author_inst": "University of North Carolina" - }, - { - "author_name": "Emily A. Madden", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Elizabeth Anderson", - "author_inst": "University of North Carolina" - }, - { - "author_name": "Victoria Baxter", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Sharon Taft-Benz", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Mark R Zweigart", - "author_inst": "University of North Carolina" - }, - { - "author_name": "Samantha R May", - "author_inst": "University of North Carolina" - }, - { - "author_name": "Stephanie Dong", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Matthew Clark", - "author_inst": "University of North Carolina" - }, - { - "author_name": "Darla R Miller", - "author_inst": "University of North Carolina" - }, - { - "author_name": "Rachel Lynch", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Mark T. Heise", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Roland Tisch", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Richard Boucher", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Fernando Pardo Manuel de Villena", - "author_inst": "University of North Carolina" - }, - { - "author_name": "Stephanie A Montgomery", - "author_inst": "University of North Carolina" - }, - { - "author_name": "Michael S Diamond", - "author_inst": "Washington University" - }, - { - "author_name": "Martin T. Ferris", - "author_inst": "University of North Carolina at Chapel Hill" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.06.01.494373", "rel_title": "Selection for immune evasion in SARS-CoV-2 revealed by high-resolution epitope mapping combined with genome sequence analysis", @@ -269420,6 +271885,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.06.02.22275895", + "rel_title": "Validation of a Deep Learning Model to aid in COVID-19 Detection from Digital Chest Radiographs", + "rel_date": "2022-06-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.02.22275895", + "rel_abs": "IntroductionUsing artificial intelligence in imaging practice helps ensure study list reprioritization, prompt attention to urgent studies, and reduces the reporting turn-around time.\n\nPurposeWe tested a deep learning-based artificial intelligence model that can detect COVID-19 pneumonia patterns from digital chest radiographs.\n\nMaterial and MethodsThe deep learning model was built using the enhanced U-Net architecture with Spatial Attention Gate and Xception Encoder. The model was named DxCOVID and was tested on an external clinical dataset. The dataset included 2247 chest radiographs comprising CXRs from 1046 COVID-19 positive patients (positive on RT-PCR) and 1201 COVID-19 negative patients.\n\nResultsWe compared the performance of the model with three different radiologists by adjusting the models sensitivity as per the individual radiologist. The area under the curve (AUC) on the receiver operating characteristic (ROC) of the model was 0.87 [95% CI: 0.85, 0.89].\n\nConclusionWhen compared to the performance of three expert readers, DxCOVID matched the output of two of the three readers. Disease-specific deep learning models using current technology are mature enough to match radiologists performance and can be a suitable tool to be incorporated into imaging workflows.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Pranav Ajmera", + "author_inst": "Dr DY Patil Medical College, Hospital and Research Center, DY Patil Vidyapeeth, DPU, Pune, India" + }, + { + "author_name": "Amit Kharat", + "author_inst": "Dr DY Patil Medical College, Hospital and Research Center, DY Patil Vidyapeeth, DPU, Pune, India ; DeepTek Medical Imaging Pvt Ltd, Pune, India" + }, + { + "author_name": "Sanjay Khaladkar", + "author_inst": "Dr DY Patil Medical College, Hospital and Research Center, DY Patil Vidyapeeth, DPU, Pune, India" + }, + { + "author_name": "Tanveer Gupte", + "author_inst": "DeepTek Medical Imaging Pvt Ltd, Pune, India" + }, + { + "author_name": "Richa Pant", + "author_inst": "DeepTek Medical Imaging Pvt Ltd" + }, + { + "author_name": "Viraj Kulkarni", + "author_inst": "DeepTeck Medical Imaging Pvt Ltd" + }, + { + "author_name": "Vinay Duddalwar", + "author_inst": "Keck School of Medicine, University of Southern California, Los Angeles, CA , USA" + }, + { + "author_name": "Deepak Patkar", + "author_inst": "Nanavati Super-speciality Hospital, Mumbai, India" + }, + { + "author_name": "Mona Bhatia", + "author_inst": "Fortis Escorts Hospital, New Delhi, India" + }, + { + "author_name": "Purnachandra Lamghare", + "author_inst": "Dr DY Patil Medical College, Hospital and Research Center, DY Patil Vidyapeeth, DPU, Pune, India" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2022.06.02.22275894", "rel_title": "Development and Validation of Multivariable Prediction Models of Serological Response to SARS-CoV-2 Vaccination in Kidney Transplant Recipients", @@ -270331,41 +272851,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.05.30.494036", - "rel_title": "SARS-CoV-2 Helicase might interfere with cellular nonsense-mediated RNA decay, insights from a bioinformatics study", - "rel_date": "2022-05-31", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.30.494036", - "rel_abs": "Unraveling molecular interactions between viral proteins and host cells is key to understanding the pathogenesis of viral diseases. We hypothesized that potential sequence and structural similarities between SARS-CoV2 proteins and proteins of infected cells might influence host cell biology and antiviral defense. Comparing the proteins of SARS-CoV-2 with human and mammalian proteins revealed sequence and structural similarities between viral helicase with human UPF1. The latter is a protein that is involved in nonsense mediated RNA decay (NMD), an mRNA surveillance pathway which also acts as a cellular defense mechanism against viruses. Protein sequence similarities were also observed between viral nsp3 and human Poly ADP-ribose polymerase (PARP) family of proteins. Gene set enrichment analysis on transcriptomic data derived from SARS-CoV-2 positive samples illustrated the enrichment of genes belonging to the NMD pathway compared with control samples. Moreover, comparing transcriptomic data from SARS-CoV2-infected samples with transcriptomic data derived from UPF1 knockout cells demonstrated a significant overlap between datasets. These findings suggest that helicase/UPF1 sequence and structural similarity might have the ability to interfere with the NMD pathway with pathogenic and immunological implications.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Behnia Akbari", - "author_inst": "Tehran University of Medical Sciences" - }, - { - "author_name": "Ehsan Ahmadi", - "author_inst": "Tehran University of Medical Sciences" - }, - { - "author_name": "Mina Roshan Zamir", - "author_inst": "Tehran University of Medical Sciences" - }, - { - "author_name": "Mina Sadeghi Shaker", - "author_inst": "Tehran University of Medical Sciences" - }, - { - "author_name": "Farshid Noorbakhsh", - "author_inst": "Tehran University of Medical Sciences" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2022.05.30.493765", "rel_title": "Potent and pan-neutralization of SARS-CoV-2 variants of concern by DARPins", @@ -271086,6 +273571,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.05.30.22275783", + "rel_title": "Lineage BA.2 dominated the Omicron SARS-CoV-2 epidemic wave in the Philippines", + "rel_date": "2022-05-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.30.22275783", + "rel_abs": "The Omicron SARS-CoV-2 variant led to a dramatic global epidemic wave following detection in South Africa in November, 2021. The Omicron lineage BA.1 was dominant and responsible for most domestic outbreaks during December 2021-January 2022, whilst other Omicron lineages including BA.2 accounted for the minority of global isolates. Here, we describe the Omicron wave in the Philippines by analysing genomic data. Our results identify the presence of both BA.1 and BA.2 lineages in the Philippines in December 2021, before cases surged in January 2022. We infer that only lineage BA.2 underwent sustained transmission in the country, with an estimated emergence around November 18th, 2021 [95% highest posterior density: November 6-28th], whilst despite multiple introductions BA.1 transmission remained limited. These results suggest the Philippines was one of the earliest areas affected by BA.2, and reiterate the importance of whole-genome sequencing for monitoring outbreaks.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Yao-Tsun Li", + "author_inst": "Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow" + }, + { + "author_name": "Francisco Gerardo M. Polotan", + "author_inst": "Research Institute for Tropical Medicine, Muntinlupa City, Philippines" + }, + { + "author_name": "Gerald Ivan S. Sotelo", + "author_inst": "Research Institute for Tropical Medicine, Muntinlupa City, Philippines" + }, + { + "author_name": "Anne Pauline A. Alpino", + "author_inst": "Research Institute for Tropical Medicine, Muntinlupa City, Philippines" + }, + { + "author_name": "Ardiane Ysabelle M. Dolor", + "author_inst": "Research Institute for Tropical Medicine, Muntinlupa City, Philippines" + }, + { + "author_name": "Ma. Angelica A. Tujan", + "author_inst": "Research Institute for Tropical Medicine, Muntinlupa City, Philippines" + }, + { + "author_name": "Ma. Ricci R. Gomez", + "author_inst": "Research Institute for Tropical Medicine, Muntinlupa City, Philippines" + }, + { + "author_name": "Othoniel Jan T. Onza", + "author_inst": "Research Institute for Tropical Medicine, Muntinlupa City, Philippines" + }, + { + "author_name": "Angela Kae T. Chang", + "author_inst": "Research Institute for Tropical Medicine, Muntinlupa City, Philippines" + }, + { + "author_name": "Criselda T. Bautista", + "author_inst": "Research Institute for Tropical Medicine, Muntinlupa City, Philippines" + }, + { + "author_name": "June C. Carandang", + "author_inst": "Research Institute for Tropical Medicine, Muntinlupa City, Philippines" + }, + { + "author_name": "Dodge R. Lim", + "author_inst": "Research Institute for Tropical Medicine, Muntinlupa City, Philippines" + }, + { + "author_name": "Lei Lanna M. Dancel", + "author_inst": "Research Institute for Tropical Medicine, Muntinlupa City, Philippines" + }, + { + "author_name": "Mayan U. Lumandas", + "author_inst": "Research Institute for Tropical Medicine, Muntinlupa City, Philippines" + }, + { + "author_name": "Timothy John R. Dizon", + "author_inst": "Research Institute for Tropical Medicine, Muntinlupa City, Philippines" + }, + { + "author_name": "Katie Hampson", + "author_inst": "Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow" + }, + { + "author_name": "Simon Daldry", + "author_inst": "Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow" + }, + { + "author_name": "Joseph Hughes", + "author_inst": "MRC-University of Glasgow Centre for Virus Research" + }, + { + "author_name": "Kirstyn Brunker", + "author_inst": "Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.05.30.22275753", "rel_title": "Safety and superior immunogenicity of heterologous boosting with an RBD-based SARS-CoV-2 mRNA vaccine in Chinese adults", @@ -271881,121 +274457,6 @@ "type": "new results", "category": "scientific communication and education" }, - { - "rel_doi": "10.1101/2022.05.29.493866", - "rel_title": "Respiratory mucosal vaccination of peptide-poloxamine-DNA nanoparticles provides complete protection against lethal SARS-CoV-2 challenge", - "rel_date": "2022-05-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.29.493866", - "rel_abs": "The ongoing SARS-CoV-2 pandemic represents a brutal reminder of the continual threat of mucosal infectious diseases. Mucosal immunity may provide robust protection at the predominant sites of SARS-CoV-2 infection. However, it remains unclear whether respiratory mucosal administration of DNA vaccines could confer protective immune responses against SARS-CoV-2 challenge due to the insurmountable barriers posed by the airway. Here, we applied self-assembled peptide-poloxamine nanoparticles with mucus-penetrating properties for pulmonary inoculation of a COVID-19 DNA vaccine (pSpike/PP-sNp). Not only displays the pSpike/PP-sNp superior gene-transfection and favorable biocompatibility in the mouse airway, but pSpike/PP-sNp promotes a tripartite immunity consisting of systemic, cellular and mucosal immune responses that are characterized by mucosal IgA secretion, high levels of neutralizing antibodies, and resident memory phenotype T-cell responses in the lungs of mice. Most importantly, pSpike/PP-sNp completely eliminates SARS-CoV-2 infection in both upper and lower respiratory tracts and enables 100% survival rate of mice following lethal SARS-CoV-2 challenge. Our findings indicate PP-sNp might be a promising platform in mediating DNA vaccines to elicit all-around mucosal immunity against SARS-CoV-2.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Si Sun", - "author_inst": "National Engineering Research Center of Immunological Products, Third Military Medical University, Chongqing, China" - }, - { - "author_name": "Entao Li", - "author_inst": "Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changch" - }, - { - "author_name": "Gan Zhao", - "author_inst": "Advaccine (Suzhou) Biopharmaceuticals Co., Ltd, Suzhou, China" - }, - { - "author_name": "Jie Tang", - "author_inst": "Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia" - }, - { - "author_name": "Qianfei Zuo", - "author_inst": "National Engineering Research Center of Immunological Products, Third Military Medical University, Chongqing, China" - }, - { - "author_name": "Larry Cai", - "author_inst": "Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia" - }, - { - "author_name": "Chuanfei Xu", - "author_inst": "National Engineering Research Center of Immunological Products, Third Military Medical University, Chongqing, China" - }, - { - "author_name": "Cheng Sui", - "author_inst": "Advaccine (Suzhou) Biopharmaceuticals Co., Ltd, Suzhou, China" - }, - { - "author_name": "Yangxue Ou", - "author_inst": "National Engineering Research Center of Immunological Products, Third Military Medical University, Chongqing, China" - }, - { - "author_name": "Chang Liu", - "author_inst": "National Engineering Research Center of Immunological Products, Third Military Medical University, Chongqing, China" - }, - { - "author_name": "Haibo Li", - "author_inst": "National Engineering Research Center of Immunological Products, Third Military Medical University, Chongqing, China" - }, - { - "author_name": "Yuan Ding", - "author_inst": "Advaccine (Suzhou) Biopharmaceuticals Co., Ltd, Suzhou, China" - }, - { - "author_name": "Chao Li", - "author_inst": "National Engineering Research Center of Immunological Products, Third Military Medical University, Chongqing, China" - }, - { - "author_name": "Dongshui Lu", - "author_inst": "National Engineering Research Center of Immunological Products, Third Military Medical University, Chongqing, China" - }, - { - "author_name": "Weijun Zhang", - "author_inst": "National Engineering Research Center of Immunological Products, Third Military Medical University, Chongqing, China" - }, - { - "author_name": "Ping Luo", - "author_inst": "National Engineering Research Center of Immunological Products, Third Military Medical University, Chongqing, China" - }, - { - "author_name": "Ping Cheng", - "author_inst": "National Engineering Research Center of Immunological Products, Third Military Medical University, Chongqing, China" - }, - { - "author_name": "Yuwei Gao", - "author_inst": "Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changch" - }, - { - "author_name": "Changchun Tu", - "author_inst": "Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changch" - }, - { - "author_name": "Bruno Pitard", - "author_inst": "Immunology and New Concepts in ImmunoTherapy, INSERM, CNRS, Nantes Universite, Univ Angers, Nantes, France" - }, - { - "author_name": "Joseph Rosenecker", - "author_inst": "Department of Pediatrics, Ludwig-Maximilians University of Munich, Munich, Germany" - }, - { - "author_name": "Bin Wang", - "author_inst": "Advaccine (Suzhou) Biopharmaceuticals Co., Ltd, Suzhou, China; Key Laboratory of Medical Molecular Virology of MOH and MOE and Department of Medical Microbiolog" - }, - { - "author_name": "Yan Liu", - "author_inst": "Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changch" - }, - { - "author_name": "Quanming Zou", - "author_inst": "National Engineering Research Center of Immunological Products, Third Military Medical University, Chongqing, China" - }, - { - "author_name": "Shan Guan", - "author_inst": "National Engineering Research Center of Immunological Products, Third Military Medical University, Chongqing, China" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.05.27.22275037", "rel_title": "Corticosteroids in COVID-19: Optimizing Observational Research through Target Trial Emulations", @@ -272548,6 +275009,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.05.26.22275661", + "rel_title": "A rapid One-Pot RNA-isolation method for simplified clinical detection of SARS-COV-2 infection in India", + "rel_date": "2022-05-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.26.22275661", + "rel_abs": "BackgroundWith the rapid increase in COVID-19 cases and the discovery of new viral variants within India over multiple waves, the expensive reagents and time-consuming sample pretreatment required for qPCR analysis have led to slower detection of the disease. The vast Indian population demands an inexpensive and competent sample preparation strategy for rapid detection of the disease facilitating early and efficient containment of the disease.\n\nMethodsIn this study, we have surveyed the spread of COVID-19 infection over Faridabad, Haryana, India for 6 months. We also devised a simple single-step method for total RNA extraction using a single tube and compared its efficacy with the commercially available kits.\n\nFindingsOur findings suggest that determining Ct values for samples subjected to the One Pot (OP) RNA extraction method was as efficient as the commercially available kits but delivers a subtle advantage in a way, by minimizing the cost, labor, and sample preparation time.\n\nConclusionThis novel crude RNA extraction method is stable and capable of operating in developing countries like India for low resource settings, without the use of expensive reagents and instruments. Additionally, this method can be further adapted to pooling samples strategies owing to its high sensitivity.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Sonia Jain", + "author_inst": "ESIC Medical college and hospital, Faridabad" + }, + { + "author_name": "Arghya Bhowmick", + "author_inst": "Bose Institute" + }, + { + "author_name": "Anil Kumar Pandey", + "author_inst": "ESIC medical college and hospital, Faridabad" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.05.26.22275645", "rel_title": "How is the COVID-19 pandemic impacting our life, mental health, and well-being? Design and preliminary findings of the pan-Canadian longitudinal COHESION Study", @@ -273903,37 +276391,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2022.05.27.22275696", - "rel_title": "Demographic and professional risk factors of COVID-19 infections among physicians in low- and middle-income settings; findings from a representative survey in two Brazilian states.", - "rel_date": "2022-05-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.27.22275696", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSIntroductionC_ST_ABSHealth workers (HWs) are a key resource for health systems worldwide, and have been affected heavily by the COVID-19 pandemic. Evidence is consolidating on incidence and associated drivers of infections, predominantly in high-income settings. It is however still unclear what the risk factors may be for specific health professions, particularly in low- and middle-income countries (LMICs).\n\nMethodsWe conducted a cross-sectional survey in a representative sample of 1,183 medical doctors registered with Brazils Federal Council of Medicine in one developed (Sao Paulo) and one disadvantaged state (Maranhao). Between February-June 2021, we administered a telephone questionnaire to collect data on physicians demographics, deployment to services, vaccination status, and self-reported COVID-19 infections. We performed descriptive, univariate, and multilevel clustered analysis to explore the association between physicians infection rates, and their sociodemographic and employment characteristics. A generalized linear mixed model with a binomial distribution was used to estimate the adjusted odds ratio.\n\nResultsWe found that 35.8% of physicians in our sample were infected with COVID-19 in the first year of the pandemic. The infection rate in Maranhao (49.2%) [95% CI 45.0-53.4] was almost twice that in Sao Paulo (24.1%) [95% CI 20.8-27.5]. Being a physician in Maranhao [95% CI 2.08-3.57], younger than 50 years [95% CI 1.41-2.89], and having worked in a COVID-19 ward [95% CI 1.28-2.27], were positively associated with the probability of infections. Conversely, working with diagnostic services [95% CI 0.53-0.96], in administrative functions [95% CI 0.42-0.80], or in teaching and research [95% CI 0.48-0.91] was negatively associated.\n\nConclusionsBased on data from Brazil, COVID-19 infections in LMICs may be more likely in those health systems with lower physician-to-patient ratios, and younger doctors working in COVID-19 wards may be infected more frequently. Such findings may be used to identify policies to mitigate COVID-19 effects on HWs in LMICs.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Giuliano Russo", - "author_inst": "Queen Mary University of London" - }, - { - "author_name": "Alex Jones Flores Cassenote", - "author_inst": "Universidade de S\u00e3o Paulo: Universidade de Sao Paulo" - }, - { - "author_name": "Bruno Luciano Carneiro Alves de Oliveira", - "author_inst": "Federal University of Maranhao: Universidade Federal do Maranhao" - }, - { - "author_name": "Mario C\u00e9sar Scheffer", - "author_inst": "Universidade de S\u00e3o Paulo Faculdade de Medicina: Universidade de Sao Paulo Faculdade de Medicina" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.05.27.22275672", "rel_title": "Profiling of immune responses to COVID-19 and vaccination uncovers potent adjuvant capacities of SARS CoV-2 infection to vaccination leading to memory T cell responses with a Th17 signature in cancer patients", @@ -275126,6 +277583,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.05.25.493484", + "rel_title": "Molecular Investigations of Selected Spike Protein Mutations in SARS-CoV-2: Delta and Omicron Variants and Omicron BA.2 Sub Variant", + "rel_date": "2022-05-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.25.493484", + "rel_abs": "Among the multiple SARS-CoV-2 variants recently reported, the Delta variant has generated most perilous and widespread effects. Another variant, Omicron, has been identified specifically for its high transmissibility. Omicron contains numerous spike (S) protein mutations and in numbers much larger than those of its predecessor variants. In this report we discuss some essential structural aspects and time-based structure changes of a selected set of spike protein mutations within the Delta and Omicron variants. The expected impact of multiple-point mutations within the spike proteins receptor-binding domain (RBD) and S1 of these variants are examined. Additionally, RBD of the more recently emerged subvariants BA.4, BA.5 and BA.2.12.1 are discussed. Within the latter group, BA.5 represents globally, the most prevalent form of SARS-CoV-2 at the present time. Temporal mutation profile for the subvariant BF.7 and currently circulating variants of interest (VOI) and variants under monitoring (VUMs) including XBB.1.5, BQ.1, BA.2.75, CH.1.1, XBB and XBF are computationally explored here briefly with the expectation that these structural data will be helpful to identify drug targets and to neutralize antibodies for the evolving variants/subvariants of SARS-CoV-2.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Urmi Roy", + "author_inst": "Clarkson University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2022.05.25.22275006", "rel_title": "Overuse in US Medicare during the COVID-19 pandemic", @@ -276197,105 +278673,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.05.23.22275460", - "rel_title": "Humoral Immunity to SARS-CoV-2 and Inferred Protection from Infection in a French Longitudinal Community Cohort", - "rel_date": "2022-05-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.23.22275460", - "rel_abs": "Population-level immunity to SARS-CoV-2 is growing through vaccination as well as ongoing circulation. Given waning immunity and emergence of new variants, it is important to dynamically determine the risk of re-infection in the population. For estimating immune protection, neutralization titers are most informative, but these assays are difficult to conduct at a population level. Measurement of antibody levels can be implemented at high throughput, but has not been robustly validated as a correlate of protection. Here, we have developed a method that predicts neutralization and protection based on variant-specific antibody measurements to SARS-CoV-2 antigens. This approach allowed us to estimate population-immunity in a longitudinal cohort from France followed for up to 2 years. Participants with a single vaccination or immunity caused by infection only are especially vulnerable to COVID-19 or hospitalization due to SARS-CoV-2. While the median reduced risk to COVID-19 in participants with 3 vaccinations was 96%, the median reduced risk among participants with infection-acquired immunity only was 42%. The results presented here are consistent with data from vaccine-effectiveness studies indicating robustness of our approach. Our multiplex serological assay can be readily optimized and employed to study any new variant and provides a framework for development of an assay that would include protection estimates.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Tom Woudenberg", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Laurie Pinaud", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Laura Garcia", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Laura Tondeur", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Stephane Pelleau", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Alix de Thoisy", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Francoise Donnadieu", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Marija Backovic", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Mikael Attia", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Nathanael Hoze", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Cecile Duru", - "author_inst": "Hopital de Crepy-en-Valois" - }, - { - "author_name": "Aymar Davy Koffi", - "author_inst": "Hopital de Crepy-en-Valois" - }, - { - "author_name": "Sandrine Castelain", - "author_inst": "CHU Amiens" - }, - { - "author_name": "Marie-Noelle Ungeheuer", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Sandrine Fernandes Pellerin", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Delphine Planas", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Timothee Bruel", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "SIMON CAUCHEMEZ", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Olivier Schwarz", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Arnaud Fontanet", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Michael White", - "author_inst": "Institut Pasteur" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.05.22.22275323", "rel_title": "Initial protection against Omicron in children and adolescents by BNT162b2", @@ -277056,6 +279433,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.05.24.22275508", + "rel_title": "In the Midst of a Pandemic, Introverts May Have a Mortality Advantage", + "rel_date": "2022-05-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.24.22275508", + "rel_abs": "Extroverts may enjoy lower mortality than introverts under normal circumstances, but the relationship may be different during an airborne pandemic when social contact can be deadly. We used data for midlife Americans surveyed in 1995-96 with mortality follow-up through December 31, 2020 to investigate whether the association between extroversion and mortality changed during the COVID-19 pandemic. We hypothesized that excess mortality during the pandemic will be greater for extroverts than for introverts. Results were based on a Cox model estimating age-specific mortality controlling for sex, race/ethnicity, the period trend in mortality, and an additional indicator for the pandemic period (Mar-Dec 2020). We interacted extroversion with the pandemic indicator to test whether the relationship differed between prepandemic and pandemic periods. Prior to the pandemic, extroversion was associated with somewhat lower mortality (HR=0.93 per SD, 95% CI 0.88-0.97), but the relationship reversed during the pandemic: extroverted individuals appeared to suffer higher mortality than their introverted counterparts, although the effect was not significant (HR=1.20 per SD, 95% CI 0.93-1.54).\n\nExtroversion was associated with greater pandemic-related excess mortality (HR=1.20/0.93=1.29 per SD, 95% CI 1.00-1.67). Compared with someone who scored at the mean level of extroversion, mortality rates prior to the pandemic were 10% lower for a person who was very extroverted (i.e., top 12% of the sample at Wave 1), while they were 12% higher for someone who was very introverted (i.e., 11th percentile). In contrast, mortality rates during the pandemic appeared to be higher for very extroverted individuals (HR=1.15, 95% CI 0.77-1.71) and lower for those who were very introverted (HR=0.70, 95% CI 0.43-1.14) although the difference was not significant because of limited statistical power. In sum, the slight mortality advantage enjoyed by extroverts prior to the pandemic disappeared during the first 10 months of the COVID-19 pandemic. It remains to be seen whether that pattern continued into 2021-22. We suspect that the mortality benefit of introversion during the pandemic is largely a result of reduced exposure to the risk of infection, but it may also derive in part from the ability of introverts to adapt more easily to reduced social interaction without engaging in self-destructive behavior (e.g., drug and alcohol abuse). Introverts have been training for a pandemic their whole lives.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Dana A Glei", + "author_inst": "Georgetown University" + }, + { + "author_name": "Maxine Weinstein", + "author_inst": "Georgetown University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.05.24.22275549", "rel_title": "Population-weighted greenspace exposure tied to lower COVID-19 mortality rates: A nationwide dose-response study", @@ -278183,73 +280583,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.05.17.22275005", - "rel_title": "Safety of the BNT162b2 mRNA COVID-19 Vaccine in Children below 5 Years in Germany (CoVacU5): An Investigator-initiated Retrospective Cohort Study", - "rel_date": "2022-05-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.17.22275005", - "rel_abs": "BackgroundThe safety of SARS-CoV-2 vaccines is unknown in children aged <5 years. Here, we retrospectively evaluated the safety of BNT162b2 vaccine used off-label in children of this age group in Germany.\n\nMethodsAn investigator-initiated retrospective cohort study (CoVacU5) included parents or caregivers having children aged <5 years registered for SARS-CoV-2 vaccination in outpatient care facilities in Germany. Reported short-term safety data of 1-3 doses of 3-10{micro}g BNT162b2 in children aged 0 to <60 months are presented. Co-primary outcomes were the frequencies of 11 categories of symptoms post-vaccination with bivariate analyses and regression models adjusting for age, sex, weight and height. On-label non-SARS-CoV-2 vaccines served as controls in an active-comparator design.\n\nResultsThe study included 7806 of 19,000 registered children representing a 41% response rate. 338 children received the first dose of BNT162b2 at age 0-<12 months, n=1272 at age 12-24 months and n=5629 at age [≥]24 to <60 months. A 10{micro}g dosage was more frequently associated with injection-site symptoms compared to lower dosages. The probability of any symptoms (OR: 1.62 [95% confidence interval (CI): 1.36-1.94]), injection-site, musculoskeletal, dermatological or otolaryngological symptom categories were modestly elevated after BNT12b2 compared to non-SARS-CoV-2 vaccines, whereas the probabilities of general symptoms (OR: 0.74 [95% CI: 0.64-0.85]) and fever (OR: 0.43 [95% CI: 0.35-0.51]) were lower after BNT162b2. Symptoms requiring hospitalization (n=10) were reported only at BNT162b2 dosages higher than 3{micro}g.\n\nConclusionsThe symptoms reported after BNT162b2 administration were overall comparable to on-label non-SARS-CoV-2 vaccines in this cohort of children aged <5 years. (German Clinical Trials Register ID: DRKS00028759).", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Nicole Toepfner", - "author_inst": "Department of Pediatrics, University Hospital Carl Gustav Carus, Technische Universitaet Dresden, Dresden, Germany. Co-first author" - }, - { - "author_name": "Wolfgang C. G. von Meissner", - "author_inst": "Hausaerzte am Spritzenhaus, Family Practice, Baiersbronn, Germany. Co-first author" - }, - { - "author_name": "Christoph Strumann", - "author_inst": "Institute of Family Medicine, University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany" - }, - { - "author_name": "Denisa Drinka", - "author_inst": "Department of Pediatrics, University Hospital Carl Gustav Carus, Technische Universitaet Dresden, Dresden, Germany" - }, - { - "author_name": "David Stuppe", - "author_inst": "University Children's Hospital, University Medical Center Rostock, University of Rostock, Rostock, Germany" - }, - { - "author_name": "Maximilian Jorczyk", - "author_inst": "Department of Pediatrics, University Hospital Carl Gustav Carus, Technische Universitaet Dresden, Dresden, Germany" - }, - { - "author_name": "Jeanne Moor", - "author_inst": "Department of General Internal Medicine, Inselspital University Hospital Bern and Institute of Primary Health Care (BIHAM), University of Bern, Bern Switzerland" - }, - { - "author_name": "Johannes Pueschel", - "author_inst": "Hausarztzentrum Greven, Family Practice, Greven, Germany" - }, - { - "author_name": "Melanie Liss", - "author_inst": "Praxis fuer Kinder- und Jugendmedizin, Duesseldorf, Germany" - }, - { - "author_name": "Emilie von Poblotzki", - "author_inst": "Praxis \"die Kinderaerzte\", Muenchen, Germany" - }, - { - "author_name": "Reinhard Berner", - "author_inst": "Department of Pediatrics, University Hospital Carl Gustav Carus, Technische Universitaet Dresden, Dresden, Germany" - }, - { - "author_name": "Matthias B. Moor", - "author_inst": "Department of Nephrology and Hypertension, Inselspital University Hospital Bern, Bern, Switzerland. Co-senior author" - }, - { - "author_name": "Cho-Ming Chao", - "author_inst": "University Children's Hospital, University Medical Center Rostock, University of Rostock, Rostock, Germany and Cardio-Pulmonary Institute, Universities of Giess" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2022.05.21.22274939", "rel_title": "Patient satisfaction with telemedicine in the Philippines during the COVID-19 pandemic", @@ -279194,6 +281527,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.05.21.22275420", + "rel_title": "Understanding Post-Acute Sequelae of SARS-CoV-2 Infection through Data-Driven Analysis with the Longitudinal Electronic Health Records: Findings from the RECOVER Initiative", + "rel_date": "2022-05-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.21.22275420", + "rel_abs": "Recent studies have investigated post-acute sequelae of SARS-CoV-2 infection (PASC) using real-world patient data such as electronic health records (EHR). Prior studies have typically been conducted on patient cohorts with small sample sizes1 or specific patient populations2,3 limiting generalizability. This study aims to characterize PASC using the EHR data warehouses from two large national patient-centered clinical research networks (PCORnet), INSIGHT and OneFlorida+, which include 11 million patients in New York City (NYC) and 16.8 million patients in Florida respectively. With a high-throughput causal inference pipeline using high-dimensional inverse propensity score adjustment, we identified a broad list of diagnoses and medications with significantly higher incidence 30-180 days after the laboratory-confirmed SARS-CoV-2 infection compared to non-infected patients. We found more PASC diagnoses and a higher risk of PASC in NYC than in Florida, which highlights the heterogeneity of PASC in different populations.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Chengxi Zang", + "author_inst": "Department of Population Health Sciences, Weill Cornell Medicine" + }, + { + "author_name": "Yongkang Zhang", + "author_inst": "Department of Population Health Sciences, Weill Cornell Medicine" + }, + { + "author_name": "Jie Xu", + "author_inst": "Department of Health Outcomes Biomedical Informatics, University of Florida" + }, + { + "author_name": "Jiang Bian", + "author_inst": "Department of Health Outcomes Biomedical Informatics, University of Florida" + }, + { + "author_name": "Dmitry Morozyuk", + "author_inst": "Department of Population Health Sciences, Weill Cornell Medicine" + }, + { + "author_name": "Edward J. Schenck", + "author_inst": "Division of Pulmonary and Critical Care Medicine, Weill Cornell Department of Medicine" + }, + { + "author_name": "Dhruv Khullar", + "author_inst": "Department of Population Health Sciences, Weill Cornell Medicine, New York" + }, + { + "author_name": "Anna S. Nordvig", + "author_inst": "Department of Neurology, Weill Cornell Medicine" + }, + { + "author_name": "Elizabeth A. Shenkman", + "author_inst": "Department of Health Outcomes Biomedical Informatics, University of Florida" + }, + { + "author_name": "Russel L. Rothman", + "author_inst": "Center for Health Services Research, Vanderbilt University Medical Center" + }, + { + "author_name": "Jason P. Block", + "author_inst": "Department of Population Medicine, Harvard Pilgrim Health Care Institute, Harvard Medical School" + }, + { + "author_name": "Kristin Lyman", + "author_inst": "Louisiana Public Health Institute" + }, + { + "author_name": "Mark Weiner", + "author_inst": "Department of Population Health Sciences, Weill Cornell Medicine" + }, + { + "author_name": "Thomas W. Carton", + "author_inst": "Louisiana Public Health Institute" + }, + { + "author_name": "Fei Wang", + "author_inst": "Weill Cornell Medical College" + }, + { + "author_name": "Rainu Kaushal", + "author_inst": "Department of Population Health Sciences, Weill Cornell Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2022.05.19.22275149", "rel_title": "SARS-CoV-2 Variants of Concern (VOC) Alpha, Beta, Gamma, Delta, and Omicron coincident with consecutive pandemic waves in Pakistan", @@ -280169,129 +282581,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2022.05.19.22275026", - "rel_title": "Serial infection with SARS-CoV-2 Omicron BA.1 and BA.2 following three-dose COVID-19 vaccination", - "rel_date": "2022-05-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.19.22275026", - "rel_abs": "SARS-CoV-2 Omicron infections are common among individuals who are vaccinated or have recovered from prior variant infection, but few reports have documented serial Omicron infections. We characterized SARS-CoV-2 humoral responses in a healthy young person who acquired laboratory-confirmed Omicron BA.1.15 ten weeks after a third dose of BNT162b2, and BA.2 thirteen weeks later. Responses were compared to those of 124 COVID-19 naive vaccinees. One month after the second and third vaccine doses, the participants wild-type and BA.1-specific IgG, ACE2 competition and virus neutralization activities were average for a COVID-19 naive triple-vaccinated individual. BA.1 infection boosted the participants responses to the cohort [≥]95th percentile, but even this strong \"hybrid\" immunity failed to protect against BA.2. Moreover, reinfection increased BA.1 and BA.2-specific responses only modestly. Results illustrate the risk of Omicron infection in fully vaccinated individuals and highlight the importance of personal and public health measures as vaccine-induced immune responses wane.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Hope R. Lapointe", - "author_inst": "British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada" - }, - { - "author_name": "Francis Mwimanzi", - "author_inst": "Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada" - }, - { - "author_name": "Peter K. Cheung", - "author_inst": "British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada; Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada" - }, - { - "author_name": "Yurou Sang", - "author_inst": "Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada" - }, - { - "author_name": "Fatima Yaseen", - "author_inst": "Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada" - }, - { - "author_name": "Rebecca Kalikawe", - "author_inst": "Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada" - }, - { - "author_name": "Sneha Datwani", - "author_inst": "Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada" - }, - { - "author_name": "Rachel Waterworth", - "author_inst": "Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada" - }, - { - "author_name": "Gisele Umviligihozo", - "author_inst": "Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada" - }, - { - "author_name": "Siobhan Ennis", - "author_inst": "Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada" - }, - { - "author_name": "Landon Young", - "author_inst": "Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada" - }, - { - "author_name": "Winnie Dong", - "author_inst": "British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada" - }, - { - "author_name": "Don Kirkby", - "author_inst": "British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada" - }, - { - "author_name": "Laura Burns", - "author_inst": "Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada" - }, - { - "author_name": "Victor Leung", - "author_inst": "Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada; Department of Pathology and Laboratory Medicine, Providence Health Care, " - }, - { - "author_name": "Daniel Holmes", - "author_inst": "Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada; Department of Pathology and Laboratory Medicine, University of Briti" - }, - { - "author_name": "Mari L. DeMarco", - "author_inst": "Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada; Department of Pathology and Laboratory Medicine, University of Briti" - }, - { - "author_name": "Janet Simons", - "author_inst": "Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada; Department of Pathology and Laboratory Medicine, University of Briti" - }, - { - "author_name": "Nancy Matic", - "author_inst": "Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada; Department of Pathology and Laboratory Medicine, Providence Health Care, " - }, - { - "author_name": "Julio S.G. Montaner", - "author_inst": "British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada; Department of Medicine, University of British Columbia, Vancouver, Canada;" - }, - { - "author_name": "Chanson J. Brumme", - "author_inst": "British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada; Department of Medicine, University of British Columbia, Vancouver, Canada;" - }, - { - "author_name": "Natalie Prystajecky", - "author_inst": "Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; British Columbia Centre for Disease Control Public Health La" - }, - { - "author_name": "Masahiro Niikura", - "author_inst": "Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada" - }, - { - "author_name": "Christopher F. Lowe", - "author_inst": "Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada; Department of Pathology and Laboratory Medicine, Providence Health Care, " - }, - { - "author_name": "Marc G. Romney", - "author_inst": "Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada; Department of Pathology and Laboratory Medicine, Providence Health Care, " - }, - { - "author_name": "Mark A. Brockman", - "author_inst": "British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada; Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada; Department of Molec" - }, - { - "author_name": "Zabrina L. Brumme", - "author_inst": "British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada; Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada;" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.05.19.492636", "rel_title": "A social media-based framework for quantifying temporal changes to wildlife viewing intensity: Case study of sea turtles before and during COVID-19", @@ -281036,6 +283325,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2022.05.20.22275312", + "rel_title": "Hyperbaric Oxygen for Treatment of Long COVID Syndrome (HOT-LoCO); Protocol for a Randomised, Placebo-Controlled, Double-Blind, Phase II Clinical Trial", + "rel_date": "2022-05-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.20.22275312", + "rel_abs": "IntroductionLong COVID, where symptoms persist 12 weeks after the initial SARS-CoV-2-infection, is a substantial problem for individuals and society in the surge of the pandemic. Common symptoms are fatigue, post-exertional malaise, and cognitive dysfunction. There is currently no effective treatment, and the underlying mechanisms are unknown although several hypotheses exist, with chronic inflammation as a common denominator. In prospective studies, hyperbaric oxygen therapy (HBOT) has been suggested to be effective for the treatment of similar syndromes such as chronic fatigue syndrome and fibromyalgia. A case series has suggested positive effects of HBOT in Long COVID. This randomised placebo-controlled clinical trial will explore HBOT as a potential treatment for Long COVID. The primary objective is to evaluate if HBOT improves health related quality of life (HRQoL) for patients with Long COVID compared to placebo/sham. The main secondary objectives are to evaluate whether HBOT improves endothelial function, objective physical performance, and short term HRQoL.\n\nMethods and AnalysisA randomised, placebo-controlled, double-blind, phase II clinical trial in 80 previously healthy subjects debilitated due to Long COVID, with low HRQoL. Clinical data, HRQoL- questionnaires, blood samples, objective tests and activity meter data will be collected at baseline. Subjects will be randomised to a maximum of 10 treatments with hyperbaric oxygen or sham treatment over six weeks. Assessments for safety and efficacy will be performed at six, 13, 26 and 52 weeks, with the primary endpoint (physical domains in RAND-36) and main secondary endpoints defined at 13 weeks after baseline. Data will be reviewed by an independent Data Safety Monitoring Board.\n\nEthics and DisseminationThe trial is approved by The Swedish National Institutional Review Board (2021-02634) and the Swedish Medical Product Agency (5.1-2020-36673). Positive, negative, and inconclusive results will be published in peer-reviewed scientific journals with open access.\n\nTrial RegistrationNCT04842448. EudraCT: 2021-000764-30\n\nStrengths and limitations of this trialStrengths\n\nO_LIRandomised placebo-controlled, double-blind, parallel groups, clinical trial in compliance with ICH-GCP\nC_LIO_LIEvaluation of safety and efficacy, including objective and explanatory endpoints\nC_LIO_LIIndependent Data Safety Monitoring Board (DSMB)\nC_LI\n\nLimitations\n\nO_LINew syndrome with unknown mechanisms\nC_LIO_LIPower calculation is based on similar syndromes\nC_LIO_LISelection bias as patients are enrolled from the same post-COVID clinic\nC_LI", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Anders Kjellberg", + "author_inst": "Karolinska Institutet, Sweden" + }, + { + "author_name": "Lina Abdel-Halim", + "author_inst": "Karolinska Institutet, Sweden" + }, + { + "author_name": "Adrian Hassler", + "author_inst": "Karolinska Institutet, Sweden" + }, + { + "author_name": "Sara El Gharbi", + "author_inst": "Karolinska University Hospital, Solna, Sweden" + }, + { + "author_name": "Sarah Al-Ezerjawi", + "author_inst": "Karolinska University Hospital, Solna, Sweden" + }, + { + "author_name": "Emil Bostr\u00f6m", + "author_inst": "Karolinska University Hospital, Solna, Sweden" + }, + { + "author_name": "Carl Johan Sundberg", + "author_inst": "Karolinska Institutet, Sweden" + }, + { + "author_name": "John Pernow", + "author_inst": "Karolinska Institutet, Sweden" + }, + { + "author_name": "Koshiar Medson", + "author_inst": "Karolinska Institutet, Sweden" + }, + { + "author_name": "Jan Kowalski", + "author_inst": "JK Biostatistics AB, Stockhholm, Sweden" + }, + { + "author_name": "Kenny A Rodriguez-Wallberg", + "author_inst": "Karolinska Institutet, Sweden" + }, + { + "author_name": "Xiaowei Zheng", + "author_inst": "Karolinska Institutet, Sweden" + }, + { + "author_name": "Sergiu Bogdan Catrina", + "author_inst": "Karolinska Institutet, Sweden" + }, + { + "author_name": "Michael Runold", + "author_inst": "Karolinska Institutet, Sweden" + }, + { + "author_name": "Marcus St\u00e5hlberg", + "author_inst": "Karolinska Institutet, Sweden" + }, + { + "author_name": "Judith Bruchfeld", + "author_inst": "Karolinska Institutet, Sweden" + }, + { + "author_name": "Malin Nygren-Bonnier", + "author_inst": "Karolinska Institutet, Sverige" + }, + { + "author_name": "Peter Lindholm", + "author_inst": "Karolinska Institutet, Sweden" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "pharmacology and therapeutics" + }, { "rel_doi": "10.1101/2022.05.19.22275291", "rel_title": "Real-world effectiveness of molnupiravir and nirmatrelvir/ritonavir among COVID-19 inpatients during Hong Kong's Omicron BA.2 wave: an observational study", @@ -282047,61 +284423,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.05.17.22275210", - "rel_title": "Sequence Proven Reinfections with SARS-CoV-2 at a Large Academic Center", - "rel_date": "2022-05-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.17.22275210", - "rel_abs": "BackgroundIncreased reinfection rates with SARS-CoV-2 have recently been reported, with some locations basing reinfection on a second positive PCR test at least 90 days after initial infection.\n\nMethodsWe identified cases where patients had two positive tests for SARS-CoV-2 and evaluated which of these had been sequenced as part of our surveillance efforts, and evaluated sequencing and clinical data.\n\nResults750 patients (920 samples) had a positive test at least 90 days after the initial test. The median time between tests was 377 days, and 724 (79%) of the post 90-day positives were collected after the emergence of the Omicron variant in November 2021. Sequencing was attempted on 231 samples and successful in 127. Successful sequencing spiked during the Omicron surge and showed higher median days from initial infection compared to failed sequences (median 398 days compared to 276 days, p<0.0005). A total of 122 (98%) patients showed evidence of reinfection, 45 of which had sequence proven reinfection and 77 had inferred reinfections (later sequence showed a clade that was not circulating when the patient was initially infected). Children accounted for only 4% of reinfections. 43 (96%) of 45 infections with sequence proven reinfection were caused by the Omicron variant, 41 (91%) were symptomatic, 32 (71%), were vaccinated prior to the second infection, and 6 (13%) were Immunosuppressed. Only 2 (4%) were hospitalized, and both had underlying conditions.\n\nConclusionSequence proven reinfections increased with the Omicron variant but generally caused mild infections.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "C. Paul Morris", - "author_inst": "Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology; National Institute of Allergy and Infectious Disease, National Inst" - }, - { - "author_name": "Raghda E. Eldesouki", - "author_inst": "Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology; Genetics Unit Histology Department, School of Medicine, Suez Canal" - }, - { - "author_name": "Amary Fall", - "author_inst": "Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology" - }, - { - "author_name": "David C. Gaston", - "author_inst": "Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology" - }, - { - "author_name": "Julie M. Norton", - "author_inst": "Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology" - }, - { - "author_name": "Nicholas Gallagher", - "author_inst": "Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology" - }, - { - "author_name": "Chun Huai Luo", - "author_inst": "Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology" - }, - { - "author_name": "Omar Abdullah", - "author_inst": "Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology" - }, - { - "author_name": "Eili Y. Klein", - "author_inst": "Department of Emergency Medicine, Johns Hopkins School of Medicine," - }, - { - "author_name": "Heba H. Mostafa", - "author_inst": "Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.05.17.22275235", "rel_title": "Reduced Exercise Capacity, Chronotropic Incompetence, Inflammation and Symptoms in Post-Acute COVID-19", @@ -282762,6 +285083,65 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.05.17.492310", + "rel_title": "Adaptation-proof SARS-CoV-2 vaccine design", + "rel_date": "2022-05-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.17.492310", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) surface spike glycoprotein - a major antibody target - is critical for virus entry via engagement of human angiotensin-converting enzyme 2 (ACE2) receptor. Despite successes with existing vaccines and therapies that primarily target the receptor binding domain (RBD) of the spike protein, the susceptibility of RBD to mutations provides escape routes for the SARS-CoV-2 from neutralizing antibodies. On the other hand, structural conservation in the spike protein can be targeted to reduce escape mutations and achieve broad protection. Here, we designed candidate stable immunogens that mimic surface features of selected conserved regions of spike protein through epitope grafting, in which we present the target epitope topology on diverse heterologous scaffolds that can structurally accommodate the spike epitopes. Structural characterization of the epitope-scaffolds showed stark agreement with our computational models and target epitopes. The sera from mice immunized with engineered designs display epitope-scaffolds and spike binding activity. We also demonstrated the utility of the designed epitope-scaffolds in diagnostic applications. Taken all together, our study provides important methodology for targeting the conserved, non-RBD structural motifs of spike protein for SARS-CoV-2 epitope vaccine design and demonstrates the potential utility of epitope grafting in rational vaccine design.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Yashavantha L Vishweshwaraiah", + "author_inst": "Penn State College of Medicine" + }, + { + "author_name": "Brianna Hnath", + "author_inst": "Penn State College of Medicine" + }, + { + "author_name": "Brendan Rackley", + "author_inst": "Penn State College of Medicine" + }, + { + "author_name": "Jian Wang", + "author_inst": "Penn State College of Medicine" + }, + { + "author_name": "Abhinay Gontu", + "author_inst": "Pennsylvania State University" + }, + { + "author_name": "Morgan Chandler", + "author_inst": "University of North Carolina at Charlotte" + }, + { + "author_name": "Kirill A Afonin", + "author_inst": "University of North Carolina at Charlotte" + }, + { + "author_name": "Suresh V Kuchipudi", + "author_inst": "Pennsylvania State University" + }, + { + "author_name": "Neil Christensen", + "author_inst": "Penn State College of Medicine" + }, + { + "author_name": "Neela H Yennawar", + "author_inst": "Pennsylvania State University" + }, + { + "author_name": "Nikolay V Dokholyan", + "author_inst": "Penn State University College of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2022.05.18.492443", "rel_title": "Using unsupervised learning algorithms to identify essential genes associated with SARS-CoV-2 as potential therapeutic targets for COVID-19", @@ -283665,33 +286045,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2022.05.16.22275162", - "rel_title": "United States' political climates and the spread of SARS-2-COVID-19 during 2020", - "rel_date": "2022-05-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.16.22275162", - "rel_abs": "We tested whether the political climate in each U.S. state and Washington, DC determined the nature of the spread of COVID-19 cases and deaths in those polities during 2020. Political climate for each polity was indexed as a weighted average of the proportion of Republicans in legislatures in 2018 and the degree of public trust in both the White House and President Trump to handle COVID-19 in April, 2020. We found that polities higher on the political climate index had faster increases in per capita COVID-19 cases and deaths. Such Republican-trusting polities also had lower access to health care and less public engagement in prevention behavior, both of which mediated the influence of political climate on COVID- 19 cases and deaths. Further, the relationship between incidence of COVID-19 cases and deaths was weaker in more Republican-trusting polities. Political climate can be seen as contributing to more cases and deaths due to lower access to health care and to lower public adherence to public health guidelines in polities led by Republicans and which trusted the Trump White House to handle the pandemic.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Felicia Pratto", - "author_inst": "University of Connecticut" - }, - { - "author_name": "Andrew Cortopassi", - "author_inst": "University of Connecticut" - }, - { - "author_name": "Natasza Marrouch", - "author_inst": "Universidade Nova de Lisboa" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.05.16.492068", "rel_title": "Variation in the ACE2 receptor has limited utility for SARS-CoV-2 host prediction", @@ -284360,6 +286713,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.05.12.22274973", + "rel_title": "Sociodemographic inequalities and excess non-COVID-19 mortality during the COVID-19 pandemic: A data-driven analysis of 1,069,174 death certificates in Mexico", + "rel_date": "2022-05-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.12.22274973", + "rel_abs": "BACKGROUNDIn 2020, Mexico experienced one of the highest rates of excess mortality globally. However, the extent to which non-COVID deaths contributed to excess mortality, its regional characterization, and the association between municipal-and individual-level sociodemographic inequality has not been characterized.\n\nMETHODSWe conducted a retrospective municipal an individual-level study using death certificate data in Mexico from 2016-2020. We analyzed mortality related to COVID-19 and to non-COVID-19 causes using ICD-10 codes to identify cause-specific mortality. Excess mortality was estimated as the increase in deaths in 2020 compared to the average of 2016-2019, disaggregated by primary cause of death, death setting (in-hospital and out-of-hospital) and geographical location. We evaluated correlates of non-COVID-19 mortality at the individual level using mixed effects logistic regression and correlates of non-COVID-19 excess mortality in 2020 at the municipal level using negative binomial regression.\n\nRESULTSWe identified 1,069,174 deaths in 2020 (833.5 per 100,000 inhabitants), which was 49% higher compared to the 2016-2019 average (557.38 per 100,000 inhabitants). Overall excess mortality (276.11 deaths per 100,000 inhabitants) was attributable in 76.1% to COVID-19; however, non-COVID-19 causes comprised one-fifth of excess deaths. COVID-19 deaths occurred primarily in-hospital, while excess non-COVID-19 deaths decreased in this setting and increased out-of-hospital. Excess non-COVID-19 mortality displayed geographical heterogeneity linked to sociodemographic inequalities with clustering in states in southern Mexico. Municipal-level predictors of non-COVID-19 excess mortality included levels of social security coverage, higher rates of COVID-19 hospitalization, and social marginalization. At the individual level, lower educational attainment, blue collar workers, and lack of medical care assistance were associated with non-COVID-19 mortality during 2020.\n\nCONCLUSIONNon-COVID-19 causes of death, largely chronic cardiometabolic conditions, comprised up to one-fifth of excess deaths in Mexico during 2020. Non-COVID-19 excess deaths occurred disproportionately out-of-hospital and were associated with both individual-and municipal-level sociodemographic inequalities. These findings should prompt an urgent call to action to improve healthcare coverage and access to reduce health and sociodemographic inequalities in Mexico to reduce preventable mortality in situations which increase the stress of healthcare systems, including the ongoing COVID-19 pandemic.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Neftali Eduardo Antonio-Villa", + "author_inst": "Instituto Nacional de Geriatria" + }, + { + "author_name": "Carlos A. Ferm\u00edn-Mart\u00ednez", + "author_inst": "Instituto Nacional de Geriatria" + }, + { + "author_name": "Jose Manuel Aburto", + "author_inst": "University of Oxford" + }, + { + "author_name": "Luisa Fern\u00e1ndez-Chirino", + "author_inst": "Instituto Nacional de Geriatria" + }, + { + "author_name": "Daniel Ram\u00edrez-Garc\u00eda", + "author_inst": "Instituto Nacional de Geriatria" + }, + { + "author_name": "Julio Pisanty-Alatorre", + "author_inst": "Instituto Mexicano del Seguro Social" + }, + { + "author_name": "Armando Gonz\u00e1lez-D\u00edaz", + "author_inst": "Universidad Nacional Autonoma de Mexico" + }, + { + "author_name": "Arsenio Vargas-V\u00e1zquez", + "author_inst": "Universidad Nacional Autonoma de Mexico" + }, + { + "author_name": "Jacqueline A. Seiglie", + "author_inst": "Diabetes Unit, Massachusetts General Hospital, Harvard Medical School" + }, + { + "author_name": "Sim\u00f3n Barquera", + "author_inst": "Instituto Nacional de Salud Publica" + }, + { + "author_name": "Luis Miguel Guti\u00e9rrez-Robledo", + "author_inst": "Instituto Nacional de Geriatria" + }, + { + "author_name": "Omar Yaxmehen Bello-Chavolla", + "author_inst": "Instituto Nacional de Geriatria" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.05.15.22273945", "rel_title": "COVID-19 vaccines effectiveness against SARS-CO-V-2 infection among persons attending RT-PCR centre at a medical College Hospital in Telangana: A case control study", @@ -285283,61 +287699,6 @@ "type": "new results", "category": "genetics" }, - { - "rel_doi": "10.1101/2022.05.16.492045", - "rel_title": "Isolation of bat sarbecoviruses of SARS-CoV-2 clade, Japan", - "rel_date": "2022-05-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.16.492045", - "rel_abs": "Betacoronaviruses have caused 3 outbreaks in the past 2 decades. SARS-CoV-2, in particular, has caused a serious pandemic. As the betacoronaviruses are considered to originate from bats, surveillance of bat betacoronaviruses is crucial for understanding the mechanism of cross-species transition and potential for future outbreaks. We previously detected and characterized a SARS-CoV-2-related sarbecovirus, Rc-o319, from Rhinolophus cornutus in Japan. Here, we detected several bat sarbecoviruses of the SARS-CoV-2 clade from R. cornutus in multiple locations in Japan, and successfully isolated them using Vero/TMPRSS2 cells stably expressing R. cornutus ACE2 (Vero-RcACE2). The coding sequences of S1 region varied among isolates, whereas other genetic regions were highly conserved. Isolates were efficiently grown in Vero-RcACE2 cells, but did not replicate in Vero/TMPRSS2 cells stably expressing human ACE2, suggesting a narrow host range. Further long-term epidemiological studies of sarbecoviruses in wildlife are expected to facilitate the assessment of the risk of their spillover potential.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Shin Murakami", - "author_inst": "University of Tokyo: Tokyo Daigaku" - }, - { - "author_name": "Tomoya Kitamura", - "author_inst": "National Agriculture and Food Research Organization (NARO)" - }, - { - "author_name": "Hiromichi Matsugo", - "author_inst": "University of Tokyo" - }, - { - "author_name": "Haruhiko Kamiki", - "author_inst": "University of Tokyo" - }, - { - "author_name": "Ken Oyabu", - "author_inst": "Isumi County-City Nature Preservation Association" - }, - { - "author_name": "Wataru Sekine", - "author_inst": "University of Tokyo: Tokyo Daigaku" - }, - { - "author_name": "Akiko Takenaka-Uema", - "author_inst": "The University of Tokyo: Tokyo Daigaku" - }, - { - "author_name": "Yuko Sakai-Tagawa", - "author_inst": "Institute of Medical Science, The University of Tokyo" - }, - { - "author_name": "Yoshihiro Kawaoka", - "author_inst": "Institute of Medical Science, The University of Tokyo" - }, - { - "author_name": "Taisuke Horimoto", - "author_inst": "University of Tokyo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.05.16.22275120", "rel_title": "Representation of evidence-based clinical practice guideline recommendations on FHIR", @@ -286002,6 +288363,29 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2022.05.12.22275015", + "rel_title": "Optimality of Maximal-Effort Vaccination", + "rel_date": "2022-05-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.12.22275015", + "rel_abs": "It is widely acknowledged that vaccinating at maximal effort in the face of an ongoing epidemic is the best strategy to minimise infections and deaths from the disease. Despite this, no one has proved that this is guaranteed to be true if the disease follows multi-group SIR (Susceptible-Infected-Recovered) dynamics. This paper provides a novel proof of this principle for the existing SIR framework, showing that the total number of deaths or infections from an epidemic is decreasing in vaccination effort. Furthermore, it presents a novel model for vaccination which assumes that vaccines assigned to a subgroup are distributed randomly to the unvaccinated population of that subgroup. It suggests, using COVID-19 data, that this more accurately captures vaccination dynamics than the model commonly found in the literature. However, as the novel model provides a strictly larger set of possible vaccination policies, the results presented in this paper hold for both models.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Matthew J Penn", + "author_inst": "University of Oxford" + }, + { + "author_name": "Christl A. Donnelly", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.05.13.491706", "rel_title": "Three-doses of BNT162b2 COVID-19 mRNA vaccine establishes long-lasting CD8+ T cell immunity in CLL and MDS patients", @@ -286953,109 +289337,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.05.10.491295", - "rel_title": "Biosynthetic proteins targeting the SARS-CoV-2 spike as anti-virals", - "rel_date": "2022-05-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.10.491295", - "rel_abs": "The binding of the SARS-CoV-2 spike to angiotensin-converting enzyme 2 (ACE2) promotes virus entry into the cell. Targeting this interaction represents a promising strategy to generate antivirals. By screening a phage-display library of biosynthetic protein sequences build on a rigid alpha-helicoidal HEAT-like scaffold (named Reps), we selected candidates recognizing the spike receptor binding domain (RBD). Two of them (F9 and C2) bind the RBD with affinities in the nM range, displaying neutralisation activity in vitro and recognizing distinct sites, F9 overlapping the ACE2 binding motif. The F9-C2 fusion protein and a trivalent Rep form (C2-foldon) display 0.1 nM affinities and EC50 of 8-18 nM for neutralization of SARS-CoV-2. In hamsters, F9-C2 instillation in the nasal cavity before or during infections effectively reduced the replication of a SARS-CoV-2 strain harbouring the D614G mutation in the nasal epithelium. Furthermore, F9-C2 and/or C2-foldon effectively neutralized SARS-CoV-2 variants (including delta and omicron variants) with EC50 values ranging from 13 to 32 nM. With their high stability and their high potency against SARS-CoV-2 variants, Reps provide a promising tool for SARS-CoV-2 therapeutics to target the nasal cavity and mitigate virus dissemination in the proximal environment.\n\nAuthor SummaryThe entry of SARS-CoV-2 in permissive cells is mediated by the binding of its spike to angiotensin-converting enzyme 2 (ACE2) on the cell surface. To select ligands able to block this interaction, we screened a library of phages encoding artificial proteins (named Reps) for binding to its receptor binding domain (RBD). Two of them were able to bind the RBD with high affinity and block efficiently the virus entry in cultured cells. Assembled Reps through covalent or non-covalent linkages blocked virus entry at lower concentration than their precursors (with around 20-fold activity increase for a trimeric Rep). These Reps derivates neutralize efficiently SARS-CoV-2 {beta}, {gamma}, {delta} and Omicron virus variants. Instillation of an Rep dimer in the nasal cavity effectively reduced virus replication in the hamster model of SARS-CoV-2 and pathogenicity.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Stephanie Thebault", - "author_inst": "Unite VIM, INRAe" - }, - { - "author_name": "Nathalie Lejal", - "author_inst": "Unite VIM, INRAe" - }, - { - "author_name": "Alexis Dogliani", - "author_inst": "AFMB, CNRS" - }, - { - "author_name": "Amelie Donchet", - "author_inst": "Unite VIM, INRAe" - }, - { - "author_name": "Agathe Urvoas", - "author_inst": "I2BC, Universite Paris-Saclay" - }, - { - "author_name": "Marie Valerio-Lepiniec", - "author_inst": "I2BC, Universite Paris-Saclay" - }, - { - "author_name": "Muriel Lavie", - "author_inst": "Institut Pasteur de Lille" - }, - { - "author_name": "Cecile Baronti", - "author_inst": "Universite Aix-Marseille" - }, - { - "author_name": "Franck Touret", - "author_inst": "Universite Aix-Marseille" - }, - { - "author_name": "Bruno da Costa", - "author_inst": "Unite VIM, INRAe" - }, - { - "author_name": "Clara Bourgon", - "author_inst": "Unite VIM, INRAe" - }, - { - "author_name": "Audrey Fraysse", - "author_inst": "Unite VIM, INRAe" - }, - { - "author_name": "Audrey Saint-Albin-Deliot", - "author_inst": "Unite VIM, INRAe" - }, - { - "author_name": "Jessica Morel", - "author_inst": "Unite VIM, INRAe" - }, - { - "author_name": "Bernard Klonjkowski", - "author_inst": "ENVA" - }, - { - "author_name": "Xavier de Lamballerie", - "author_inst": "Universite Aix-Marseille" - }, - { - "author_name": "Jean Dubuisson", - "author_inst": "Institut Pasteur de Lille" - }, - { - "author_name": "Alain Roussel", - "author_inst": "AFMB, Universite Aix-Marseille" - }, - { - "author_name": "Philippe Minard", - "author_inst": "I2BC, Universite Paris-Saclay" - }, - { - "author_name": "Sophie Le Poder", - "author_inst": "ENVA" - }, - { - "author_name": "Nicolas Meunier", - "author_inst": "Unite VIM, INRAe" - }, - { - "author_name": "Bernard Delmas", - "author_inst": "INRAE" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.05.09.22274623", "rel_title": "COVID-19 Vaccine effectiveness against symptomatic infection and hospitalization in Belgium, July 2021-April 2022", @@ -287836,6 +290117,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.05.08.22274788", + "rel_title": "10.4 Million Children Affected by COVID-19-associated Orphanhood and Caregiver Death: An Imperative for Action", + "rel_date": "2022-05-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.08.22274788", + "rel_abs": "The new WHO estimates for COVID-19 excess deaths allow us to generate updated and more accurate models of COVID-19 associated orphanhood and caregiver loss. Using methodology established in prior studies, we combine age-specific fertility and excess death estimates from January 2020 to May 2022. We find 10.4 million children have lost a parent or caregiver due to COVID-associated excess deaths, and 7.5 million children have experienced COVID-associated orphanhood. Without supportive intervention, caregiver loss can bring severe risks of poverty, school dropout, sexual exploitation, and mental health distress. It is essential that evidence-based care for these children is integrated into all national response plans as a caring action to protect children from immediate and long-term harms of COVID-19.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Susan Hillis", + "author_inst": "University of Oxford" + }, + { + "author_name": "Joel-Pascal Ntwali N'konzi", + "author_inst": "African Institute for Mathematical Sciences" + }, + { + "author_name": "William Msemburi", + "author_inst": "World Health Organisation" + }, + { + "author_name": "Lucie Cluver", + "author_inst": "University of Oxford" + }, + { + "author_name": "Andres Villaveces", + "author_inst": "CDC" + }, + { + "author_name": "Seth Flaxman", + "author_inst": "University of Oxford" + }, + { + "author_name": "H Juliette T Unwin", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.05.08.22274797", "rel_title": "mRNA-based COVID-19 booster vaccination is highly effective and cost-effective in Australia", @@ -289055,77 +291379,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.05.10.22274912", - "rel_title": "Influencing factors of Anti-SARS-CoV-2-Spike IgG antibody titres in healthcare workers - A cross-section study", - "rel_date": "2022-05-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.10.22274912", - "rel_abs": "BackgroundAgainst the background of the current COVID-19 infection dynamics with the rapid spread of SARS-CoV-2 variants of concern (VOC), above all the Omicron VOC, the immunity of healthcare workers (HCWs) against SARS-CoV-2 continues to be of high importance. Vaccination plays a central role in reducing the severity and potentially the spread of the disease. In healthcare, this is important to prevent disease-related staff shortages. However, there is a lack of data on factors influencing the humoral immune response.\n\nAimThe aim of our study was to determine factors influencing the level of Anti-SARS-CoV-2-Spike IgG after SARS-CoV-2 infection or vaccination in healthcare workers.\n\nMethods1,750 study participants were recruited who met the following inclusion criteria: age [≥] 18 years, PCR-confirmed SARS-CoV-2 infection and/or at least one dose of COVID-19 vaccination, working in health care. Anti-SARS-CoV-2-Spike IgG titres were determined by SERION ELISA agile SARS-CoV-2 IgG.\n\nResultsMean Anti-SARS-CoV-2-Spike IgG levels increased significantly with the number of COVID-19 vaccinations (92.2 BAU/ml for single dose, 140.9 BAU/ml for two doses and 1,144.3 BAU/ml after threefold vaccination). Hybrid COVID-19 immunized respondents (after infection and vaccination) had significantly higher antibody titres compared with participants after infection only (525.4 BAU/ml vs. 105.7 BAU/ml). Anti-SARS-CoV-2-Spike IgG titres declined significantly with time after administration of the second vaccine dose. Smoking and high age were associated with lower titres.\n\nConclusionBoth recovered and vaccinated HCWs presented a predominantly good humoral immune response with decreasing antibody levels over the temporal course. Smoking and higher age limited the humoral SARS-CoV-2 immunity. This reduced immune response is an important aspect as people with these risk factors are recognized as people with an increased risk for a severe course of disease.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Julia Reusch", - "author_inst": "Infection Control Unit, University Hospital Wuerzburg, Wuerzburg, Germany; Department of Internal Medicine I, University Hospital Wuerzburg, Germany" - }, - { - "author_name": "Isabell Wagenhaeuser", - "author_inst": "Infection Control Unit, University Hospital Wuerzburg, Wuerzburg, Germany; Department of Internal Medicine I, University Hospital Wuerzburg, Germany" - }, - { - "author_name": "Alexander Gabel", - "author_inst": "Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Annika Eggestein", - "author_inst": "Infection Control Unit, University Hospital Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Anna Hoehn", - "author_inst": "Infection Control Unit, University Hospital Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Thien-Tri Lam", - "author_inst": "Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Anna Frey", - "author_inst": "Department of Internal Medicine I, University Hospital Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Alexandra Schubert-Unkmeir", - "author_inst": "Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Lars Doelken", - "author_inst": "Institute for Virology and Immunobiology, University of Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Stefan Frantz", - "author_inst": "Department of Internal Medicine I, University Hospital Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Oliver Kurzai", - "author_inst": "Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany; Leibniz Institute for Natural Product Research and Infection Biology - Hans" - }, - { - "author_name": "Ulrich Vogel", - "author_inst": "Infection Control Unit, University Hospital Wuerzburg, Wuerzburg, Germany; Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Manuel Krone", - "author_inst": "Infection Control Unit, University Hospital Wuerzburg, Wuerzburg, Germany; Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Nils Petri", - "author_inst": "Department of Internal Medicine I, University Hospital Wuerzburg, Wuerzburg, Germany" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.05.10.22274906", "rel_title": "BA.2 omicron differs immunologically from both BA.1 omicron and pre-omicron variants", @@ -289910,6 +292163,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "endocrinology" }, + { + "rel_doi": "10.1101/2022.05.05.22274434", + "rel_title": "Routine Saliva Testing for SARS-CoV-2 in Children: Partnering with Childcare Centers in the Greater New Haven Community", + "rel_date": "2022-05-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.05.22274434", + "rel_abs": "BackgroundWhile considerable attention was placed on SARS-CoV-2 testing and surveillance programs in the K-12 setting, younger age groups in childcare centers were largely overlooked. Childcare facilities are vital to communities, allowing parents/guardians to remain at work and providing safe environments for both children and staff. Therefore, early in the COVID-19 pandemic, we established a PCR-based COVID-19 surveillance program in childcare facilities, testing children and staff with the goal of collecting actionable public health data and aiding communities in the progressive resumption of standard operations and ways of life. In this study we describe the development of a weekly saliva testing program and provide early results from our experience implementing this in childcare centers.\n\nMethodsWe enrolled children (aged 6 months to 7 years) and staff at 8 childcare facilities and trained participants in saliva collection using video chat technology. Weekly surveys were sent out to assess exposures, symptoms, and vaccination status changes. Participants submitted weekly saliva samples at school. Samples were transported to a partnering clinical laboratory for RT-PCR testing using SalivaDirect and results were uploaded to each participants online patient portal within 24 hours.\n\nResultsThis study fostered a cooperative partnership with participating childcare centers, parents/guardians, and staff with the goal of mitigating COVID-19 transmission in childcare centers. Age-related challenges in saliva collection were overcome by working with parents/guardians to conceptualize new collection strategies and by offering parents/guardians continued virtual guidance and support.\n\nConclusionSARS-CoV-2 screening and routine testing programs have focused less on the childcare population, resulting in knowledge gaps in this critical age group, especially as many are still ineligible for vaccination. SalivaDirect testing for SARS-CoV-2 provides a feasible method of asymptomatic screening and symptomatic testing for children and childcare center staff. Given the relative aversion to nasal swabs in the childcare age group, especially as a routine surveillance tool, an at-home saliva collection method provides an attractive alternative. Results can be shared rapidly electronically through participants private medical chart portals, and video chat technology allows for discussion and instruction between investigators and participants.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Erica Rayack", + "author_inst": "Yale School of Nursing" + }, + { + "author_name": "Hibah Mahwish Askari", + "author_inst": "Yale School of Nursing" + }, + { + "author_name": "Elissa Zirinsky", + "author_inst": "Department of Pediatric Infectious Diseases, Yale School of Medicine" + }, + { + "author_name": "Sarah Lapidus", + "author_inst": "Yale School of Public Health, Department of Epidemiology of Microbial Diseases" + }, + { + "author_name": "Hassan Sheikha", + "author_inst": "Department of Pediatric Infectious Diseases, Yale School of Medicine" + }, + { + "author_name": "Chikondi Peno", + "author_inst": "Yale School of Public Health, Department of Epidemiology of Microbial Diseases" + }, + { + "author_name": "Yasaman Kazemi", + "author_inst": "Yale School of Nursing" + }, + { + "author_name": "Devyn Yolda-Carr", + "author_inst": "Yale School of Public Health, Department of Epidemiology of Microbial Diseases" + }, + { + "author_name": "Chen Liu", + "author_inst": "Department of Pathology, Yale School of Medicine" + }, + { + "author_name": "Nathan D. Grubaugh", + "author_inst": "Yale School of Public Health, Department of Epidemiology of Microbial Diseases" + }, + { + "author_name": "Albert I. Ko", + "author_inst": "Yale School of Public Health, Department of Epidemiology of Microbial Diseases" + }, + { + "author_name": "Anne L. Wyllie", + "author_inst": "Yale School of Public Health, Department of Epidemiology of Microbial Diseases" + }, + { + "author_name": "Erica S. Spatz", + "author_inst": "Department of Cardiology, Yale School of Medicine" + }, + { + "author_name": "Carlos R. Oliveira", + "author_inst": "Department of Pediatric Infectious Diseases, Yale School of Medicine" + }, + { + "author_name": "Amy K. Bei", + "author_inst": "Yale School of Public Health, Department of Epidemiology of Microbial Diseases" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.05.06.490927", "rel_title": "Molecular dynamics of spike variants in the locked conformation: RBD interfaces, fatty acid binding and furin cleavage sites.", @@ -290885,37 +293213,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.05.06.22274771", - "rel_title": "Covid-19 vaccine effectiveness against general SARS-CoV-2 infection from the omicron variant: A retrospective cohort study", - "rel_date": "2022-05-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.06.22274771", - "rel_abs": "ObjectiveTo estimate the effectiveness of 2-dose and 3-dose mRNA vaccination (BNT162b2 and mRNA-1273) against general SARS-CoV-2 infection (asymptomatic or symptomatic) caused by the omicron variant.\n\nDesignPropensity-score matched retrospective Cohort Study.\n\nSettingLarge public university undergoing weekly Covid-19 testing in South Carolina, USA.\n\nParticipantsPopulation consists of 24,145 university students and employees undergoing weekly Covid-19 testing between January 3rd and January 31st, 2022. The analytic sample was constructed via propensity score matching on vaccination status: Unvaccinated, completion of 2-dose mRNA series within previous 5 months, and receipt of mRNA booster dose within previous 5 months. The resulting analytic sample consists of 1,944 university students and 658 university employees.\n\nInterventionVaccination with a two dose or 3 dose regimen of the BNT162b2 or mRNA-1273 vaccine.\n\nResultsBooster protection against any SARS-CoV-2 infection was 66.4% among employees (95% CI: 46.1-79.0%; P<.001) and 45.4% among students (95% CI: 30.0-57.4%; P<.001). Compared to the 2-dose mRNA series, estimated increase in protection from the booster dose was 40.8% among employees (P=.024) and 37.7% among students (P=.001). We did not have enough evidence to conclude a statistically significant protective effect of the 2-dose mRNA vaccination series, nor did we have enough evidence to conclude that protection waned in the 5-month period after receipt of the 2nd or 3rd mRNA dose. Furthermore, we did not find evidence that protection varied by manufacturer.\n\nConclusionsCovid-19 mRNA booster doses offer moderate protection against any SARS-CoV-2 infection caused by the omicron variant and provide a substantial increase in protection relative to the 2-dose mRNA vaccination series.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Lior Rennert", - "author_inst": "Clemson University" - }, - { - "author_name": "Zichen Ma", - "author_inst": "Clemson University" - }, - { - "author_name": "Christopher McMahan", - "author_inst": "Clemson University" - }, - { - "author_name": "Delphine Dean", - "author_inst": "Clemson University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.05.06.22274719", "rel_title": "Antibody responses to known and unknown SARS-CoV-2 infections after mRNA vaccine booster", @@ -291604,6 +293901,29 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.05.06.490915", + "rel_title": "Reaction Conditions Promoting the Specific Detection of SARS-CoV-2 NendoU Enzymatic Activity", + "rel_date": "2022-05-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.06.490915", + "rel_abs": "Methods that enable rapid detection of SARS-CoV-2 provide valuable tools for detecting and controlling Covid-19 outbreaks and also facilitate more effective treatment of infected individuals. The predominant approaches developed use PCR to detect viral nucleic acids or immunoassays to detect viral proteins. Each approach has distinct advantages and disadvantages, but alternatives that do not share the same limitations could enable substantial improvements in outbreak detection and management. For instance, methods that have comparable sensitivity to PCR, but that are not prone to the false-positive results that stem from the tendency of PCR to detect molecular degradation products could improve accurate identification of infected individuals. An alternative approach with potential to achieve this entails harnessing the unique enzymatic properties of SARS-CoV-2 enzymes to generate SARS-Cov-2-specific signals that indicate the presence of the virus. This route benefits from the high sensitivity provided by enzymatic signal amplification and also the fact that signal is generated only by intact viral enzymes, not degradation products. Here, we demonstrate enzymatic reaction conditions that enable the preferential detection of NendoU of SARS-CoV-2, versus several of its orthologues, with a fluorogenic oligonucleotide substrate. These compositions provide a possible technical foundation for a novel approach for detecting SARS-CoV-2 that has distinct advantages from current approaches.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Nodar Makharashvili", + "author_inst": "Nuclease Probe Technologies, Inc." + }, + { + "author_name": "James O. McNamara II", + "author_inst": "Nuclease Probe Technologies, Inc." + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.05.06.490907", "rel_title": "GDF15 and ACE2 stratify COVID19 patients according to severity while ACE2 mutations increase infection susceptibility.", @@ -292767,101 +295087,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2022.05.03.22274594", - "rel_title": "Optimal thromboprophylaxis strategies in non-critically ill patients with COVID-19 pneumonia. The PROTHROMCOVID Randomized Controlled Trial.", - "rel_date": "2022-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.03.22274594", - "rel_abs": "BackgroundHospitalized patients with COVID-19 are at increased risk for thrombosis, acute respiratory distress syndrome and death. The optimal dosage of thromboprophylaxis is unknown.\n\nObjectiveTo evaluate the efficacy and safety of tinzaparin in prophylactic, intermediate, and therapeutic doses in non-critical patients admitted for COVID-19 pneumonia.\n\nDesign, setting, and participantsRandomized controlled, multicenter trial (PROTHROMCOVID) enrolling non-critical, hospitalized adult patients with COVID-19 pneumonia.\n\nInterventionsPatients were randomized to prophylactic (4500 IU), intermediate (100 IU/kg), or therapeutic (175 IU/kg) doses of tinzaparin during hospitalization, followed by 7 days of prophylactic tinzaparin at discharge.\n\nMeasurementsThe primary efficacy outcome was a composite endpoint of symptomatic systemic thrombotic events, need for invasive or non-invasive mechanical ventilation, or death within 30 days. The main safety outcome was major bleeding at 30 days.\n\nResultsOf the 311 subjects randomized, 300 were included in the analysis (mean [SD] age, 56.7 [14.6] years; males, 182 [60.7%]. The composite endpoint at 30 days from randomization occurred in 58 patients (19.3%) of the total population; 19 (17.1 %) in the prophylactic group, 20 (22.1%) in the intermediate group, and 19 (18.5%) in the therapeutic dose group (P= 0.72). No major bleeding event was reported; non-major bleeding was observed in 3.7% of patients, with no intergroup differences.\n\nConclusionsIn non-critically ill COVID-19 patients, intermediate or full-dose tinzaparin compared to standard prophylactic doses did not appear to increase benefit regarding the likelihood of thrombotic event, non-invasive ventilation or high-flow oxygen, or death.\n\nTrial RegistrationClinicalTrials.gov Identifier (NCT04730856).\n\nFundingThis independent research initiative was supported by Leo-Pharma; Tinzaparin was provided by Leo Pharma.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Nuria Mu\u00f1oz-Rivas", - "author_inst": "Hospital Universitario Infanta Leonor: Hospital Infanta Leonor" - }, - { - "author_name": "Jes\u00fas Aibar", - "author_inst": "Hospital Clinic de Barcelona" - }, - { - "author_name": "Cristina Gabara-Xanc\u00f3", - "author_inst": "Hospital Clinic de Barcelona" - }, - { - "author_name": "Angela Trueba-Vicente", - "author_inst": "Hospital de Emergencias Enfermera Isabel Zendal" - }, - { - "author_name": "Ana Urbelz-P\u00e9rez", - "author_inst": "Hospital de Emergencias Enfermera Isabel Zendal" - }, - { - "author_name": "Vicente G\u00f3mez-Del Olmo", - "author_inst": "Hospital Universitario Ramon y Cajal" - }, - { - "author_name": "Pablo Demelo-Rodriguez", - "author_inst": "Hospital General Universitario Gregorio Mara\u00f1\u00f3n: Hospital General Universitario Gregorio Maranon" - }, - { - "author_name": "Alberto Rivera-Gallego", - "author_inst": "Hospital Alvaro Cunqueiro" - }, - { - "author_name": "Pau Bosch-Nicolau", - "author_inst": "Hospital Vall d'Hebron: Vall d'Hebron Hospital Universitari" - }, - { - "author_name": "Montserrat Perez-Pinar", - "author_inst": "Hospital Virgen de la Luz" - }, - { - "author_name": "Monica Rios-Prego", - "author_inst": "Complexo Hospitalario Universitario de Pontevedra" - }, - { - "author_name": "Olga Madridano-Cobo", - "author_inst": "Hospital Universitario Infanta Sofia" - }, - { - "author_name": "Laura Ramos-Alonso", - "author_inst": "Complejo Hospitalario Universitario de La Coru\u00f1a: Complexo Hospitalario Universitario A Coruna" - }, - { - "author_name": "Jesus Alonso-Carrillo", - "author_inst": "Hospital Universitario 12 de Octubre" - }, - { - "author_name": "Iria Francisco-Albelsa", - "author_inst": "Hospital Universitari de Girona Doctor Josep Trueta" - }, - { - "author_name": "Edelmira Mart\u00ed-Saez", - "author_inst": "Hospital Cl\u00ednico de Valencia" - }, - { - "author_name": "Ana Maestre-Peir\u00f3", - "author_inst": "Hospital de Vinalop\u00f3: Hospital Universitario del Vinalopo" - }, - { - "author_name": "Manuel Mendez-Bail\u00f3n", - "author_inst": "Complejo Clinico Universitario San Carlos: Hospital Clinico San Carlos" - }, - { - "author_name": "Jose Angel Hern\u00e1ndez-Rivas", - "author_inst": "Hospital Universitario Infanta Leonor: Hospital Infanta Leonor" - }, - { - "author_name": "Juan Torres-Macho", - "author_inst": "Hospital Universitario Infanta Leonor: Hospital Infanta Leonor" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2022.05.04.22274692", "rel_title": "The spread and burden of the COVID-19 pandemic in sub-Saharan Africa: comparison between predictions and actual data and lessons learned.", @@ -293522,6 +295747,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.05.03.22274608", + "rel_title": "Immunogenicity of BNT162b2 Vaccine Booster Dose in Patients with Inflammatory Bowel Disease Receiving Infliximab Combination Therapy: A Prospective Observational Study", + "rel_date": "2022-05-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.03.22274608", + "rel_abs": "IntroductionFew data exist regarding the immunogenicity of third dose of BNT162b2 relative to second dose in patients with inflammatory bowel disease (IBD) on different immunosuppressive therapies. We investigated the immunogenicity of BNT162b2 vaccine booster dose in patients with IBD on infliximab combination therapy.\n\nMethodsThis is prospective single center observational study conducted between January 1st, 2022 until February 28th, 2022. Patients were recruited at the time of attendance at the infusion center. Eligibility criteria included patients with confirmed diagnosis of IBD who are receiving infliximab with azathioprine or 6-mercaptopurine and have received two or three-dose of BNT162b2 vaccine. Patients were excluded if they were infected or had symptoms of SARS-CoV-2 previously since the start of the pandemic or received other vaccines than the BNT162b2. Our primary outcome was the concentrations of SARS-CoV-2 antibodies Immunoglobulin G (IgG) and neutralizing antibodies 40-45 weeks from the first dose of BNT162b2 in patients with IBD receiving infliximab combination therapy. Medians with interquartile range (IQR) were calculated.\n\nResults162 patients with IBD and receiving infliximab combination therapy were recruited and the number of patients in each group was 81. Median (IQR) SARS-CoV-2 IgG levels were significantly lower after the second dose [125 BAU/mL (43, 192)] compared to patients who received the third booster dose [207 BAU/mL (181, 234)] (p = 0.003). Neutralizing antibody levels were also lower after the second dose [80 BAU/mL (21, 95)] compared to patients who received the third booster dose [96 BAU/mL (93, 99)] (p = <0.001). The percentage of patients who achieved positive SARS-CoV-2 IgG levels in the third (booster) dose group was higher (96.3%) than those in second dose group (90%)(p = 0.026). Percentage of patients who received third (booster) dose and achieved positive SARS-CoV-2-neutralizing antibody level was 100%, whereas it was lower (88.9%) in patients who received second dose only (p=0.009).\n\nConclusionMost patients with IBD on infliximab combination therapy had positive SARS-CoV-2 IgG and neutralizing antibody concentrations 40-45 weeks post BNT162b2 vaccination. However, SARS-CoV-2 IgG and neutralizing antibody concentrations were lower in patients who received 2 doses only compared to patients who received a third dose.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Mohammad Shehab", + "author_inst": "Mubarak Hospital" + }, + { + "author_name": "Fatema Alrashed", + "author_inst": "Kuwait University" + }, + { + "author_name": "Ahmad Alfadhli", + "author_inst": "Mubarak Hospital" + }, + { + "author_name": "Abdulwahab Alsayegh", + "author_inst": "Royal College of Surgeons, Bahrain" + }, + { + "author_name": "Usama Aldallal", + "author_inst": "Royal College of Surgeons, Bahrain" + }, + { + "author_name": "Preethi Cherian", + "author_inst": "Dasman Diabetes Institute" + }, + { + "author_name": "Irina Alkhairi", + "author_inst": "Dasman Diabetes Institute" + }, + { + "author_name": "Thangavel Alphonse Thanaraj", + "author_inst": "Dasman Diabetes Institute" + }, + { + "author_name": "Arshad Channanath", + "author_inst": "Dasman Diabetes Institute" + }, + { + "author_name": "Ali A. Dashti", + "author_inst": "Kuwait University" + }, + { + "author_name": "Anwar Albanaw", + "author_inst": "Kuwait University" + }, + { + "author_name": "Hamad Ali", + "author_inst": "Kuwait University" + }, + { + "author_name": "Mohamed Abu-Farha", + "author_inst": "Dasman Diabetes Institute" + }, + { + "author_name": "Jehad Thanaraj Abubaker", + "author_inst": "Dasman Diabetes Institute" + }, + { + "author_name": "Fahd Al-Mulla", + "author_inst": "Dasman Diabetes Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "gastroenterology" + }, { "rel_doi": "10.1101/2022.05.03.490428", "rel_title": "Protection from Omicron and other VOCs by Bivalent S-Trimer COVID-19 Vaccine", @@ -294981,93 +297281,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.04.28.22274174", - "rel_title": "Promising efficacy of following a third dose of mRNA SARS-CoV-2 vaccination in patients treated with anti-CD20 antibody who failed 2-dose vaccination", - "rel_date": "2022-05-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.28.22274174", - "rel_abs": "Anti-CD20 antibodies react with CD20 expressed not only on malignant B cells but also on normal B cells. It has been reported that patients treated with anti-CD20 antibodies had an insufficient response to two-dose mRNA SARS-CoV-2 vaccination. To investigate the efficacy of a third dose in these patients, we investigated serum IgG antibody titers for S1 protein after third vaccination in 22 patients treated with anti-CD20 antibody who failed two-dose vaccination. Results showed that overall, 50% of patients seroconverted. Although no patient who received the third dose within 1 year of the last anti-CD20 antibody administration showed an increase in S1 antibody titer, 69% of patients who received the third dose more than 1 year after the last anti-CD20 antibody administration seroconverted. Our data show that a third dose of vaccination is effective in improving seroconversion rate in patients treated with anti-CD20 antibody who failed standard two-dose vaccination.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Yohei Funakoshi", - "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine" - }, - { - "author_name": "Kimikazu Yakushijin", - "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine" - }, - { - "author_name": "Goh Ohji", - "author_inst": "Division of Infection Disease Therapeutics, Department of Microbiology and Infectious Diseases, Kobe University Hospital and Graduate School of Medicine" - }, - { - "author_name": "Wataru Hojo", - "author_inst": "R&D, Cellspect Co., Ltd." - }, - { - "author_name": "Hironori Sakai", - "author_inst": "R&D, Cellspect Co., Ltd." - }, - { - "author_name": "Marika Watanabe", - "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine" - }, - { - "author_name": "Akihito Kitao", - "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine" - }, - { - "author_name": "Yoshiharu Miyata", - "author_inst": "BioResource Center, Kobe University Hospital" - }, - { - "author_name": "Yasuyuki Saito", - "author_inst": "Division of Molecular and Cellular Signaling, Kobe University Graduate School of Medicine" - }, - { - "author_name": "Shinichiro Kawamoto", - "author_inst": "Department of Transfusion Medicine and Cell Therapy, Kobe University Hospital" - }, - { - "author_name": "Katsuya Yamamoto", - "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine" - }, - { - "author_name": "Mitsuhiro Ito", - "author_inst": "Division of Medical Biophysics, Kobe University Graduate School of Health Sciences" - }, - { - "author_name": "Taiji Koyama", - "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine" - }, - { - "author_name": "Yoshinori Imamura", - "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine" - }, - { - "author_name": "Naomi Kiyota", - "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine" - }, - { - "author_name": "Hiroshi Matsuoka", - "author_inst": "BioResource Center, Kobe University Hospital" - }, - { - "author_name": "Yasuko Mori", - "author_inst": "Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine" - }, - { - "author_name": "Hironobu Minami", - "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.04.29.22274483", "rel_title": "Effectiveness of ChAdOx1-S COVID-19 Booster Vaccination against the Omicron and Delta variants in England", @@ -295780,6 +297993,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.04.28.22274443", + "rel_title": "Evidence for Aerosol Transfer of SARS-CoV2-specific Humoral Immunity", + "rel_date": "2022-05-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.28.22274443", + "rel_abs": "Despite the obvious knowledge that infectious particles can be shared through respiration, whether other constituents of the nasal/oral fluids can be passed between hosts has surprisingly never even been postulated, let alone investigated. The circumstances of the present pandemic facilitated a unique opportunity to fully examine this provocative idea. The data we show provides evidence for a new mechanism by which herd immunity may be manifested, the aerosol transfer of antibodies between immune and non-immune hosts.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Ross Kedl", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Elena Hsieh", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Thomas E Morrison", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Gabriela Samayoa-Reyes", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Siobhan Flaherty", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Conner Jackson", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Rosemary Rochford", + "author_inst": "University of Colorado Anschutz Medical Campus" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2022.04.28.22274442", "rel_title": "A Solution to the Kermack and McKendrick Integro-Differential Equations", @@ -296631,149 +298887,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.04.26.22274196", - "rel_title": "Multi-omics Characterization of Neutrophil Extracellular Trap Formation in Severe and Mild COVID-19 Infections", - "rel_date": "2022-04-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.26.22274196", - "rel_abs": "The detailed mechanisms of COVID-19 infection pathology remain poorly understood. To improve our understanding of SARS-CoV-2 pathology, we performed a multi-omics analysis of an immunologically naive SARS-CoV-2 clinical cohort from the plasma of uninfected controls, mild, and severe infections. A comparison of healthy controls and patient samples showed activation of neutrophil degranulation pathways and formation of neutrophil extracellular trap (NET) complexes that were activated in a subset of the mild infections and more prevalent in severe infections (containing multiple NET proteins in individual patient samples). As a potential mechanism to suppress NET formation, multiple redox enzymes were elevated in the mild and severe symptom population. Analysis of metabolites from the same cohort showed a 24- and 60-fold elevation in plasma L-cystine, the oxidized form of cysteine, which is a substrate of the powerful antioxidant glutathione, in mild and severe patients, respectively. Unique to patients with mild infections, the carnosine dipeptidase modifying enzyme (CNDP1) was up-regulated. The strong protein and metabolite oxidation signatures suggest multiple compensatory pathways working to suppress oxidation and NET formation in SARS-CoV-2 infections.", - "rel_num_authors": 32, - "rel_authors": [ - { - "author_name": "Lisa Bramer", - "author_inst": "Pacific Northwest National Laboratory" - }, - { - "author_name": "Robert Hontz", - "author_inst": "U.S. Naval Medical Research Unit No. TWO" - }, - { - "author_name": "Amie Eisfeld", - "author_inst": "Department of Pathobiological Sciences, University of Wisconsin" - }, - { - "author_name": "Amy Sims", - "author_inst": "Pacific Northwest National Laboratory" - }, - { - "author_name": "Young-Mo Kim", - "author_inst": "Pacific Northwest National Laboratory" - }, - { - "author_name": "Kelly Stratton", - "author_inst": "Pacific Northwest National Labs" - }, - { - "author_name": "Carrie Nicora", - "author_inst": "Pacific Northwest National Labs" - }, - { - "author_name": "Marina Gritsenko", - "author_inst": "Pacific Northwest National Labs" - }, - { - "author_name": "Athena Schepmoes", - "author_inst": "Pacific Northwest National Labs" - }, - { - "author_name": "Osamu Akasaka", - "author_inst": "Emergency Medical Center, Fujisawa City Hospital" - }, - { - "author_name": "Michiko Koga", - "author_inst": "Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo" - }, - { - "author_name": "Takeya Tsutsumi", - "author_inst": "Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo" - }, - { - "author_name": "Morio Nakamura", - "author_inst": "Department of Pulmonary Medicine, Tokyo Saiseikai Central Hospital" - }, - { - "author_name": "Ichiro Nakachi", - "author_inst": "Pulmonary division, Department of Internal Medicine, Saiseikai Utsunomiya Hospital" - }, - { - "author_name": "Rie Baba", - "author_inst": "Pulmonary division, Department of Internal Medicine, Saiseikai Utsunomiya Hospital" - }, - { - "author_name": "Hiroki Tateno", - "author_inst": "Department of Pulmonary Medicine, Saitama City Hospital" - }, - { - "author_name": "Shoji Suzuki", - "author_inst": "Department of Pulmonary Medicine, Saitama City Hospital" - }, - { - "author_name": "Hideaki Nakajima", - "author_inst": "Department of Hematology and Clinical Immunology, Yokohama City University School of Medicine" - }, - { - "author_name": "Hideaki Kato", - "author_inst": "Department of Hematology and Clinical Immunology, Yokohama City University School of Medicine" - }, - { - "author_name": "Kazunari Ishida", - "author_inst": "Kobe Kaisei Hospital" - }, - { - "author_name": "Makoto Ishii", - "author_inst": "Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine" - }, - { - "author_name": "Yoshifumi Uwamino", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Keiko Mitamura", - "author_inst": "Division of Infection Control, Eiju General Hospital" - }, - { - "author_name": "Venessa Paurus", - "author_inst": "Pacific Northwest National Labs" - }, - { - "author_name": "Ernesto Nakayasu", - "author_inst": "Pacific Northwest National Labs" - }, - { - "author_name": "Isaac Attah", - "author_inst": "Pacific Northwest National Labs" - }, - { - "author_name": "Andrew G Letizia", - "author_inst": "U.S. Naval Medical Research Unit No. TWO" - }, - { - "author_name": "Katrina Waters", - "author_inst": "Pacific Northwest National Labs" - }, - { - "author_name": "Tom Metz", - "author_inst": "Pacific Northwest National Labs" - }, - { - "author_name": "Karen Corson", - "author_inst": "U.S. Naval Medical Research Unit No. TWO" - }, - { - "author_name": "Yoshihiro Kawaoka", - "author_inst": "Department of Microbiology and Immunology and International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, J" - }, - { - "author_name": "Vincent R Gerbasi", - "author_inst": "Pacific Northwest National Labs" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.04.25.22274294", "rel_title": "Effects of boosted mRNA and adenoviral-vectored vaccines on immune responses to omicron BA.1 and BA.2 following the heterologous CoronaVac/AZD1222 vaccination", @@ -297630,6 +299743,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.04.28.22274416", + "rel_title": "The impact of the COVID-19 pandemic on the provision & utilisation of primary health care services in Goma, Democratic Republic of the Congo, Kambia district, Sierra Leone & Masaka district, Uganda", + "rel_date": "2022-04-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.28.22274416", + "rel_abs": "IntroductionThis study aimed to determine whether the COVID-19 pandemic had an impact on the number of people seen at public facilities in Uganda, the Democratic Republic of the Congo (DRC) and Sierra Leone for essential primary healthcare services.\n\nMethodsThe number of weekly consultations for antenatal care (ANC), outpatient (OPD), expanded programme on immunisations (EPI), family planning (FP) services and HIV, for the period of January 2018-December 2020, were collected from 25 primary healthcare facilities in Masaka district, Uganda, 21 health centres in Goma, DRC, and 29 facilities in Kambia district, Sierra Leone. Negative binomial regression models accounting for facility level clustering and season were used to analyse changes in activity levels between 2018, 2019 and 2020.\n\nResultsWe found no evidence that the COVID-19 pandemic affected the number of OPD, EPI or ANC consultations in Goma. Family planning consultations were 17% lower in March-July 2020 compared to 2019, but this recovered by December 2020. New diagnoses of HIV were 34% lower throughout 2020 compared to 2019. Compared to the same periods in 2019, facilities in Sierra Leone had 18-29% fewer OPD consultations throughout 2020, and 27% fewer DTP3 doses in March-July 2020, but this had recovered by Jul-Dec. There was no evidence of differences in other services. In Uganda there were 20-35% fewer under-5 OPD consultations, 21-66% fewer MCV1 doses, and 48-51% fewer new diagnoses of HIV, throughout 2020, compared to 2019. There was no difference in the number of HPV doses delivered in 2020 compared to 2019.\n\nConclusionsThe level of disruption appeared to correlate with the strength of lockdown measures in the different settings and community attitudes towards the risk posed by COVID-19. Mitigation strategies such as health communications campaigns and outreach services proved important to limit the impact of lockdowns on primary healthcare services.\n\nKey messagesO_ST_ABSWhat is already known on this topicC_ST_ABSThe COVID-19 pandemic and the response measures put in place caused disruption to the provision and utilisation of primary healthcare services worldwide.\n\nWhat this study addsWe document that the COVID-19 pandemic had a varied impact on different services in three distinct settings on the African continent. The extent that the pandemic impacted services correlated with the stringency of the lockdowns, community perceptions of the level of danger posed by the pandemic and communities prior exposure to Ebola epidemics and concomitant response measures.\n\nHow this study might affect research, practice, or policystrategies such as communication campaigns and outreach services limited the impact of lockdowns on essential services and would be valuable strategies to implement in future epidemics.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Kambale Kasonia", + "author_inst": "LSHTM-INRB Research Partnership, Goma, Democratic Republic of the Congo" + }, + { + "author_name": "Daniel Tindanbil", + "author_inst": "LSHTM-COMAHS Research Partnership, Kambia, Sierra Leone" + }, + { + "author_name": "Jonathan Kitonsa", + "author_inst": "MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda" + }, + { + "author_name": "Kathy Baisley", + "author_inst": "London School of Hygiene & Tropical Medicine (LSHTM), London, United Kingdom" + }, + { + "author_name": "Flavia Zalwango", + "author_inst": "MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda" + }, + { + "author_name": "Luisa Enria", + "author_inst": "London School of Hygiene & Tropical Medicine (LSHTM), London, United Kingdom" + }, + { + "author_name": "Anthony Mansaray", + "author_inst": "LSHTM-COMAHS Research Partnership, Kambia, Sierra Leone" + }, + { + "author_name": "Myfanwy James", + "author_inst": "LSHTM-INRB Research Partnership, Goma, Democratic Republic of the Congo" + }, + { + "author_name": "Yusupha Njie", + "author_inst": "LSHTM-COMAHS Research Partnership, Kambia, Sierra Leone" + }, + { + "author_name": "Darius Tetsa Tata", + "author_inst": "LSHTM-INRB Research Partnership, Goma, Democratic Republic of the Congo" + }, + { + "author_name": "Bolarinde J Lawal", + "author_inst": "LSHTM-COMAHS Research Partnership, Kambia, Sierra Leone" + }, + { + "author_name": "Abdoulie Drammeh", + "author_inst": "LSHTM-COMAHS Research Partnership, Kambia, Sierra Leone" + }, + { + "author_name": "Brett Lowe", + "author_inst": "London School of Hygiene & Tropical Medicine (LSHTM), London, United Kingdom" + }, + { + "author_name": "Daniel Mukadi-Bamuleka", + "author_inst": "Laboratoire Rodolphe Merieux-Institute National Research biomedical (INRB), Goma, Democratic Republic of the Congo" + }, + { + "author_name": "Sandra Mounier-Jack", + "author_inst": "London School of Hygiene & Tropical Medicine (LSHTM), London, United Kingdom" + }, + { + "author_name": "Faith Nakiyimba", + "author_inst": "Ministry of Health, Masaka District, Uganda" + }, + { + "author_name": "Paul Obady", + "author_inst": "Ministry of Health, Goma, Democratic Republic of Congo" + }, + { + "author_name": "Jeanine Muhavi", + "author_inst": "Ministry of Health, Goma, Democratic Republic of Congo" + }, + { + "author_name": "Joseph Bangura", + "author_inst": "University of Sierra Leone College of Medicine and Allied Health Sciences (COMAHS), Freetown, Sierra Leone & Ministry of Health, Kambia District, Sierra Leone" + }, + { + "author_name": "Brian Greenwood", + "author_inst": "London School of Hygiene & Tropical Medicine (LSHTM), London, United Kingdom" + }, + { + "author_name": "Mohamed Samai", + "author_inst": "University of Sierra Leone College of Medicine and Allied Health Sciences (COMAHS), Freetown, Sierra Leone" + }, + { + "author_name": "Bailah Leigh", + "author_inst": "University of Sierra Leone College of Medicine and Allied Health Sciences (COMAHS), Freetown, Sierra Leone" + }, + { + "author_name": "Deborah Watson-Jones", + "author_inst": "London School of Hygiene & Tropical Medicine (LSHTM), London, United Kingdom & Mwanza Intervention Trials Unit, National Institute for Medical Research, Mwanza," + }, + { + "author_name": "Hugo Kavunga-Membo", + "author_inst": "Laboratoire Rodolphe Merieux-Institute National Research biomedical (INRB), Goma, Democratic Republic of the Congo" + }, + { + "author_name": "Eugene Ruzagira", + "author_inst": "MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda" + }, + { + "author_name": "Katherine E Gallagher", + "author_inst": "London School of Hygiene & Tropical Medicine (LSHTM), London, United Kingdom & KEMRI-Wellcome Trust Research Programme, Kenya" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.04.28.22274370", "rel_title": "Neuropsychological assessments for dementia research in the COVID-19 era: comparing remote and face-to-face testing", @@ -298709,61 +300941,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.04.26.22274332", - "rel_title": "Community factors and excess mortality in the COVID-19 pandemic in England, Italy and Sweden", - "rel_date": "2022-04-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.26.22274332", - "rel_abs": "BackgroundAnalyses of COVID-19 suggest specific risk factors make communities more or less vulnerable to pandemic related deaths within countries. What is unclear is whether the characteristics affecting vulnerability of small communities within countries produce similar patterns of excess mortality across countries with different demographics and public health responses to the pandemic. Our aim is to quantify community-level variations in excess mortality within England, Italy and Sweden and identify how such spatial variability was driven by community-level characteristics.\n\nMethodsWe applied a two-stage Bayesian model to quantify inequalities in excess mortality in people aged 40 years and older at the community level in England, Italy and Sweden during the first year of the pandemic (March 2020-February 2021). We used community characteristics measuring deprivation, air pollution, living conditions, population density and movement of people as covariates to quantify their associations with excess mortality.\n\nResultsWe found just under half of communities in England (48.1%) and Italy (45.8%) had an excess mortality of over 300 per 100,000 males over the age of 40, while for Sweden that covered 23.1% of communities. We showed that deprivation is a strong predictor of excess mortality across the three countries, and communities with high levels of overcrowding were associated with higher excess mortality in England and Sweden.\n\nConclusionThese results highlight some international similarities in factors affecting mortality that will help policy makers target public health measures to increase resilience to the mortality impacts of this and future pandemics.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Brandon Parkes", - "author_inst": "Imperial College London" - }, - { - "author_name": "Massimo Stafoggia", - "author_inst": "Lazio Regional Health Service" - }, - { - "author_name": "Daniela Fecht", - "author_inst": "Imperial College London" - }, - { - "author_name": "Bethan Davies", - "author_inst": "Imperial College London" - }, - { - "author_name": "Carl Bonander", - "author_inst": "University of Gothenburg" - }, - { - "author_name": "Francesca de'Donato", - "author_inst": "Lazio Regional Health Service" - }, - { - "author_name": "Paola Michelozzi", - "author_inst": "Lazio Regional Health Service" - }, - { - "author_name": "Fr\u00e9d\u00e9ric B. Piel", - "author_inst": "Imperial College London" - }, - { - "author_name": "Ulf Str\u00f6mberg", - "author_inst": "University of Gothenburg" - }, - { - "author_name": "Marta Blangiardo", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.04.23.22274112", "rel_title": "Real-world study of the effectiveness of BBIBP-CorV (Sinopharm) COVID-19 vaccine in the Kingdom of Morocco", @@ -299356,6 +301533,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.04.25.22274272", + "rel_title": "Analyses of Omicron genomes from India reveal BA.2 as a more transmissible variant", + "rel_date": "2022-04-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.25.22274272", + "rel_abs": "This is the first study on omicron genomes from India to focus on phylodynamics and phylogenomics trait to provide an insight into the evolution of omicron variants. We analyzed 564 genomes deposited to GISAID database from various states of India. Pangolin COVID-19 Lineage Assigner tool was used to determine lineage assignment of all retrieved genomes. A Maximum likelihood (MLE) tree construction further confirms the separation of genomes into two distinct clades, BA. 1. and BA. 2. A very high reproduction number (R0) of 2.445 was estimated for the lineage BA.2. The highest R0 value in Telangana confirms the prevalence of lineage BA.2 in the state. Construction of the Reduced Median (RM) network shows evolution of some autochthonous haplogroups and haplotypes, which further supports the rapid evolution of omicron as compared to its previous variants. Phylogenomic analyses using maximum likelihood (ML) and RM show the potential for the emergence of sub-sublineages and novel haplogroups respectively. Due to the recombinant property and high transmissibility of omicron virus, we suggest continuous and more widespread genome sequencing in all states of India to track evolution of SARS-CoV-2 in real time.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Ashwin Atkulwar", + "author_inst": "Department of Zoology, Amolakchand Mahavidyalaya, Godhani Road, Yavatmal-445001, India." + }, + { + "author_name": "Akif Rehman", + "author_inst": "Pace Junior Science College, Dadar, Mumbai, India-400028." + }, + { + "author_name": "Y Imaan", + "author_inst": "Mohawk College, 135 Fennell Avenue West Hamilton, ON Canada L9C OE5." + }, + { + "author_name": "Mumtaz Baig", + "author_inst": "Department of Zoology, Laboratory of Molecular and Conservation Genetics, Govt. Vidarbha Institute of Science and Humanities, VMV Road, Amravati-444604-India." + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.04.21.22274152", "rel_title": "Health care use attributable to COVID-19: A propensity matched national electronic health records cohort study of 249,390 people in Wales, UK.", @@ -300395,45 +302603,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.04.21.22273952", - "rel_title": "Seasonal patterns of SARS-CoV-2 transmission in secondary schools: a modelling study", - "rel_date": "2022-04-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.21.22273952", - "rel_abs": "BackgroundThe Omicron variant has caused a new wave of SARS-CoV-2 infections worldwide. We explore crucial epidemiological parameters driving seasonal patterns of SARS-CoV-2 transmission in secondary schools and assess various infection control interventions over a 2.5-year time frame.\n\nMethodsWe developed an agent-based model parameterised with data from secondary schools in the Netherlands. We modelled the circulation of Omicron assuming a stable introduction rate of infections and accounted for uncertainty in epidemiological parameters describing virus transmissibility, susceptibility to reinfection, vaccine immune escape, and waning of sterilising immunity. We quantified the SARS-CoV-2 health burden defined as number of symptomatic student days. We further evaluated the cost-benefit (number of prevented infected students per absent student) for reactive quarantine interventions, regular screening using antigen tests, and annual booster vaccinations.\n\nFindingsDurability of sterilising immunity is a key parameter that governs temporal SARS-CoV-2 transmission patterns in secondary schools. Our model predicts pronounced within-school seasonal patterns with dominant autumn outbreaks and smaller winter outbreaks and a maximum prevalence of 2.9% (95% CI: 0.7%-6.6%) symptomatic students during infection peaks. Regular screening and annual booster vaccination may reduce the health burden up to 15% (95% CI: 1.5%-27.8%) and have a higher cost-benefit ratio than reactive quarantine interventions (reduction: 4.3%; 95% CI: -10.1% to 17.6%).\n\nInterpretationImmunity waning will determine the intensity and pattern of SARS-CoV-2 transmission in secondary schools in the medium-term future. If mitigation strategies are needed, screening and annual booster vaccination have the highest cost-benefit by reducing viral transmission with little educational disruption.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Thi Mui Pham", - "author_inst": "Julius Center for Health Sciences and Primary Care of the UMC Utrecht" - }, - { - "author_name": "Ilse Westerhof", - "author_inst": "Julius Center for Health Sciences and Primary Care, UMC Utrecht" - }, - { - "author_name": "Martin C.J. Bootsma", - "author_inst": "Julius Center for Health Sciences and Primary Care, UMC Utrecht" - }, - { - "author_name": "Mirjam E. Kretzschmar", - "author_inst": "Julius Center for Health Sciences and Primary Care, UMC Utrecht" - }, - { - "author_name": "Ganna Rozhnova", - "author_inst": "Julius Center for Health Sciences and Primary Care, UMC Utrecht" - }, - { - "author_name": "Patricia Bruijning-Verhagen", - "author_inst": "Julius Center for Health Sciences and Primary Care, UMC Utrecht" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.04.20.22270880", "rel_title": "Whole-Genome Sequencing Of Omicron Identified Multiple Outbreaks And Introduction Events In India During November 2021 and January 2022", @@ -301162,6 +303331,45 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2022.04.21.489022", + "rel_title": "SARS-CoV-2 spike variants differ in their allosteric response to linoleic acid", + "rel_date": "2022-04-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.21.489022", + "rel_abs": "The SARS-CoV-2 spike protein contains a fatty acid binding site, also found in some other coronaviruses (e.g. SARS-CoV), which binds linoleic acid and is functionally important. When occupied by linoleic acid, it reduces infectivity, by locking the spike in a less infectious conformation. Here, we use dynamical-nonequilibrium molecular dynamics (D-NEMD) simulations to compare the response of spike variants to linoleic acid removal. These simulations show that the fatty acid site is coupled to functional regions of the protein, some of them far from the site (e.g. in the receptor-binding motif, N-terminal domain, the furin cleavage site located in position 679-685 and the fusion peptide-surrounding regions) and identify the allosteric networks involved in these connections. Comparison of the response of the original ( Wuhan) spike with four variants: Alpha, Delta, Delta plus and Omicron BA.1 show that the variants differ significantly in their response to linoleic acid removal. The allosteric connections to the fatty acid site on Alpha are generally similar to the original protein, except for the receptor-binding motif and S71-R78 region which show a weaker link to the FA site. In contrast, Omicron is the most affected variant exhibiting significant differences in the receptor-binding motif, N-terminal domain, V622-L629 and the furin cleavage site. These differences in allosteric modulation may be of functional relevance, e.g. in differences in transmissibility and virulence. Experimental comparison of the effects of linoleic acid on different variants is warranted.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "A Sofia F Oliveira", + "author_inst": "University of Bristol" + }, + { + "author_name": "Deborah F Shoemark", + "author_inst": "University of Bristol" + }, + { + "author_name": "Andrew D. Davidson", + "author_inst": "University of Bristol" + }, + { + "author_name": "Imre Berger", + "author_inst": "University of Bristol" + }, + { + "author_name": "Christiane Schaffitzel", + "author_inst": "University of Bristol" + }, + { + "author_name": "Adrian J Mulholland", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2022.04.21.22274110", "rel_title": "Prosocial motivation for vaccination", @@ -302049,53 +304257,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.04.20.22274090", - "rel_title": "Monoclonal Antibodies for Treatment of SARS-CoV-2 Infection During Pregnancy", - "rel_date": "2022-04-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.20.22274090", - "rel_abs": "IMPORTANCEMonoclonal antibody (mAb) treatment decreases hospitalization and death in high-risk outpatients with mild to moderate COVID-19. However, no studies have evaluated adverse events and effectiveness of mAbs in pregnant persons compared to no mAb treatment.\n\nOBJECTIVETo determine the frequency of drug-related adverse events and obstetric-associated safety outcomes after treatment with mAb compared to no mAb treatment, and the association between mAb treatment and a composite of 28-day COVID-19-related hospital admission or emergency department visit, COVID-19-associated delivery, or mortality.\n\nDESIGN, SETTING, PARTICIPANTSPropensity-score matched cohort study of persons aged 12 years of age or older with a pregnancy episode and any documented positive SARS-CoV-2 test (polymerase chain reaction or antigen test) in the UPMC health system from April 30, 2021 to January 21, 2022.\n\nEXPOSURESBamalanivmab and etesevimab, casirivimab and imdevimab, or sotrovimab treatment compared to no mAb treatment.\n\nMAIN OUTCOMES AND MEASURESDrug-related adverse events, obstetric-associated safety outcomes among persons who delivered, and a risk-adjusted composite of 28-day COVID-19-related hospital admission or ED visit, COVID-19-associated delivery, or mortality.\n\nRESULTSAmong 944 pregnant persons (median [IQR] age 30 [26, 33] years, White (79.5%, N=750), median [IQR] Charlson Comorbidity Index Score 0 (0,0)), 552 persons received mAb treatment (58%). Median gestational age at COVID-19 diagnosis or treatment was 179 days (IQR: 123, 227), and most persons received sotrovimab (69%, N=382). Of those with known vaccination status, 178 (62%) were fully vaccinated. Drug-related adverse events were uncommon (N=8, 1.4%), and there were no differences in any obstetric-associated outcome among 276 persons who delivered. After propensity score matching, the frequency of the composite 28-day COVID-19-associated outcome was 4.0 per 100 persons (95% CI 1.9, 6.2) in mAb-treated compared to 3.7 per 100 persons (95% CI 1.7, 5.8) in non-treated controls (risk difference = 0.31 per 100 persons [95% CI -2.6, 3.3). There were no deaths among mAb-treated patients compared to 1 death in the non-treated controls (p = 0.24). There were more non-COVID-19-related hospital admissions in the mAb-treated persons (risk difference 2.8 per 100 persons (95% CI 1.1, 4.5)).\n\nCONCLUSIONS AND RELEVANCEIn pregnant persons with mild to moderate COVID-19, adverse events after mAb treatment were mild and rare. There was no difference in obstetric-associated safety outcomes between mAb treatment and no treatment among persons who delivered. MAb treatment was associated with similar 28-day COVID-19-associated outcomes and more non-COVID-19-related hospital admissions compared to no mAb treatment.\n\nKey PointsO_ST_ABSQUESTIONC_ST_ABSAmong pregnant persons with COVID-19, is monoclonal antibody (mAb) treatment associated with drug-related adverse events, similar frequency of obstetric-associated safety outcomes, and improved COVID-19-related clinical outcomes compared to no mAb treatment?\n\nFINDINGSIn 944 pregnant persons with COVID-19, drug-related adverse events were mild and infrequent. Obstetric-associated safety outcomes were similar between mAb treatment and no treatment. There was no evidence of difference in risk of COVID-19-related hospital admission, COVID-19-associated delivery, or mortality between mAb treatment and no mAb treatment.\n\nMEANINGIn pregnant persons with mild to moderate COVID-19, adverse events after mAb treatment were uncommon, and there was no difference in obstetric-associated safety outcomes between mAb treatment and no treatment. MAb treatment was associated with similar 28-day risk of a COVID-19-associated outcome and more non-COVID-19-related hospital admissions compared to no mAb treatment.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Erin K McCreary", - "author_inst": "University of Pittsburgh School of Medicine" - }, - { - "author_name": "Lara Lemon", - "author_inst": "UPMC" - }, - { - "author_name": "Christina Megli", - "author_inst": "UPMC Magee-Womens Research Institute" - }, - { - "author_name": "Amber Oakes", - "author_inst": "UPMC Magee-Womens Hospital" - }, - { - "author_name": "Rachel L Zapf", - "author_inst": "UPMC" - }, - { - "author_name": "Paula L Kip", - "author_inst": "UPMC" - }, - { - "author_name": "Christopher W Seymour", - "author_inst": "University of Pittsburgh School of Medicine" - }, - { - "author_name": "- UPMC Magee Monoclonal Antibody Treatment Group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.04.21.22274025", "rel_title": "Determinants of SARS-CoV-2 anti-spike antibody levels following BNT162b2 vaccination: cross-sectional analysis of 6,000 SIREN study participants", @@ -302916,6 +305077,53 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.04.21.489021", + "rel_title": "Peptide derived nanobody inhibits entry of SARS-CoV-2 variants", + "rel_date": "2022-04-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.21.489021", + "rel_abs": "Emergence of the new escape mutants of the SARS-CoV-2 virus has escalated its penetration among the human population and has reinstated its status as a global pandemic. Therefore, developing effective antiviral therapy against emerging SARS variants and other viruses in a short period of time becomes essential. Blocking the SARS-CoV-2 entry into human host cells by disrupting the spike glycoprotein-ACE2 interaction has been already exploited for vaccine development and monoclonal antibody therapy. Unlike the previous reports, our study used a 9 amino acid peptide from the receptor-binding motif (RBM) of Spike (S) protein as an epitope. We report the identification of an efficacious nanobody N1.2 that blocks the entry of pseudovirus containing SARS-CoV-2 spike as the surface glycoprotein. Moreover, we observe a more potent neutralizing effect against both the hCoV19 (Wuhan/WIV04/2019) and the Omicron (BA.1) pseudotyped spike virus with a bivalent version of the nanobody. In summary, our study presents a faster and efficient methodology to use peptide sequences from a protein-receptor interaction interface as epitopes for screening nanobodies against potential pathogenic targets. This approach can also be widely extended to target other viruses and pathogens in the future.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Nivya Mendon", + "author_inst": "Institute for Stem Cell Science and Regenerative Medicine, GKVK Campus, Bengaluru-560065, India" + }, + { + "author_name": "Rayees Ahmad Ganie", + "author_inst": "Institute for Stem Cell Science and Regenerative Medicine, GKVK Campus, Bengaluru-560065, India" + }, + { + "author_name": "Shubham Kesarwani", + "author_inst": "Institute for Stem Cell Science and Regenerative Medicine, GKVK Campus, Bengaluru-560065, India" + }, + { + "author_name": "Drisya Dileep", + "author_inst": "Institute for Stem Cell Science and Regenerative Medicine, GKVK Campus, Bengaluru-560065, India" + }, + { + "author_name": "Sarika Sasi", + "author_inst": "Institute for Stem Cell Science and Regenerative Medicine, GKVK Campus, Bengaluru-560065, India" + }, + { + "author_name": "Prakash Lama", + "author_inst": "Institute for Stem Cell Science and Regenerative Medicine, GKVK Campus, Bengaluru-560065, India" + }, + { + "author_name": "Anchal Chandra", + "author_inst": "National Center for Biological Sciences, TIFR, GKVK Campus - Bengaluru-560065, India" + }, + { + "author_name": "Minhaj Sirajuddin", + "author_inst": "Institute for Stem Cell Science and Regenerative Medicine, GKVK Campus, Bengaluru-560065, India" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2022.04.18.22273983", "rel_title": "Modeling the initial phase of COVID-19 epidemic: The role of age and disease severity in the Basque Country, Spain", @@ -305591,49 +307799,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.04.15.22273479", - "rel_title": "A retrospective cross-sectional analysis of community perceptions of flu and COVID-19 vaccines at Turtle Creek Primary Care Center", - "rel_date": "2022-04-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.15.22273479", - "rel_abs": "BackgroundInfluenza (flu) and COVID-19 vaccination rates are subpar across the US, especially in racial and/or socioeconomic minority groups who are understudied in public health literature.\n\nObjectiveThe objective of this study was to elucidate the attitudes of Turtle Creek patients towards flu and COVID-19 vaccines, with the goal of establishing targetable vaccine education gaps and ultimately increasing vaccine uptake in the community.\n\nDesign/PatientsThis study was conducted as a retrospective cross-sectional analysis. Authors completed 123 patient phone surveys of patients cared for at the Turtle Creek Primary Care Center inquiring about flu and COVID-19 infection status and vaccination uptake (August 26 - October 10, 2021).\n\nApproach/Key ResultsOur data revealed a significant association between COVID-19 and flu vaccine acceptance. Additionally, we found a strong association between vaccine acceptance and age, with older patients being more likely to be vaccinated against COVID-19. Using multivariable logistic regression models, we assessed how flu and COVID-19 vaccine acceptance was affected by informational sources participants trusted most. In the COVID-19 models, those who cited \"trusting medical professionals\" had higher odds of vaccine acceptance while participants who cited \"trusting social media\" had significantly decreased odds of vaccine acceptance.\n\nConclusionOur study revealed significant trends for flu and COVID-19 vaccine acceptance by sociodemographic factors and trust in the medical system. Using these data, we can create future interventions to overcome vaccine hesitancy.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Anjana Murali", - "author_inst": "University of Pittsburgh School of Medicine" - }, - { - "author_name": "Jorna Sojati", - "author_inst": "University of Pittsburgh School of Medicine" - }, - { - "author_name": "Catherine Pressimone", - "author_inst": "University of Pittsburgh School of Medicine" - }, - { - "author_name": "Marina Levochkina", - "author_inst": "University of Pittsburgh School of Public Health" - }, - { - "author_name": "Kobi Griffith", - "author_inst": "University of Pittsburgh School of Medicine" - }, - { - "author_name": "Erica Fan", - "author_inst": "University of Pittsburgh School of Public Health" - }, - { - "author_name": "Allie Dakroub", - "author_inst": "University of Pittsburgh School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.04.19.22273818", "rel_title": "Predictors of COVID-19 vaccine uptake: An online longitudinal study of US Veterans and non-Veterans", @@ -306286,6 +308451,41 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2022.04.18.488678", + "rel_title": "Read2Tree: scalable and accurate phylogenetic trees from raw reads", + "rel_date": "2022-04-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.18.488678", + "rel_abs": "The inference of phylogenetic trees is foundational to biology. However, state-of-the-art phylogenomics requires running complex pipelines, at significant computational and labour costs, with additional constraints in sequencing coverage, assembly and annotation quality. To overcome these challenges, we present Read2Tree, which directly processes raw sequencing reads into groups of corresponding genes. In a benchmark encompassing a broad variety of datasets, our assembly-free approach was 10-100x faster than conventional approaches, and in most cases more accurate--the exception being when sequencing coverage was high and reference species very distant. To illustrate the broad applicability of the tool, we reconstructed a yeast tree of life of 435 species spanning 590 million years of evolution. Applied to Coronaviridae samples, Read2Tree accurately classified highly diverse animal samples and near-identical SARS-CoV-2 sequences on a single tree--thereby exhibiting remarkable breadth and depth. The speed, accuracy, and versatility of Read2Tree enables comparative genomics at scale.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "David Dylus", + "author_inst": "Department of Computational Biology, University of Lausanne" + }, + { + "author_name": "Adrian M Altenhoff", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Sina Majidian", + "author_inst": "Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland." + }, + { + "author_name": "Fritz J Sedlazeck", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Christophe Dessimoz", + "author_inst": "University of Lausanne" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.04.13.22273788", "rel_title": "The Dawn is Coming -- the Description and Prediction of Omicron SARS-CoV-2 Epidemic Outbreak in Shanghai by Mathematical Modeling", @@ -307249,49 +309449,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.04.15.22273846", - "rel_title": "Effectiveness of a Fourth Dose of COVID-19 Vaccine among Long-Term Care Residents in Ontario, Canada", - "rel_date": "2022-04-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.15.22273846", - "rel_abs": "BackgroundAs of December 30, 2021, Ontario long-term care (LTC) residents who received a third dose of COVID-19 vaccine [≥]84 days previously were offered a fourth dose to prevent a surge in COVID-19-related morbidity and mortality due to the Omicron variant.\n\nMethodsWe used a test-negative design and linked databases to estimate the marginal effectiveness (4 versus 3 doses) and vaccine effectiveness (VE; 2, 3, or 4 doses versus no doses) of mRNA vaccines among Ontario LTC residents aged [≥]60 years who were tested for SARS-CoV-2 between December 30, 2021 and April 27, 2022. Outcome measures included any Omicron infection, symptomatic infection, and severe outcomes (hospitalization or death).\n\nResultsWe included 13,654 Omicron cases and 205,862 test-negative controls. The marginal effectiveness of a fourth dose (with 95% of fourth dose vaccine recipients receiving mRNA-1273) [≥]7 days after vaccination versus a third dose received [≥]84 days prior was 19% (95% Confidence Interval [CI], 12-26%) against infection, 31% (95%CI, 20-41%) against symptomatic infection, and 40% (95%CI, 24-52%) against severe outcomes. VE (compared to an unvaccinated group) increased with each additional dose, and for a fourth dose was 49% (95%CI, 43-54%), 69% (95%CI, 61-76%), and 86% (95%CI, 81-90%), against infection, symptomatic infection, and severe outcomes, respectively.\n\nConclusionsOur findings suggest that compared to a third dose received [≥]84 days ago, a fourth dose improved protection against infection, symptomatic infection, and severe outcomes caused by Omicron among long-term care residents. Compared to unvaccinated individuals, fourth doses provide strong protection against severe outcomes, but the duration of protection remains unknown.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Ramandip Grewal", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Sophie A. Kitchen", - "author_inst": "ICES" - }, - { - "author_name": "Lena Nguyen", - "author_inst": "ICES" - }, - { - "author_name": "Sarah A Buchan", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Sarah E Wilson", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Andrew P Costa", - "author_inst": "McMaster University" - }, - { - "author_name": "Jeff C Kwong", - "author_inst": "ICES" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.04.17.22273949", "rel_title": "Effect of SARS-CoV-2 digital droplet RT-PCR assay sensitivity on COVID-19 wastewater based epidemiology", @@ -308000,6 +310157,73 @@ "type": "new results", "category": "neuroscience" }, + { + "rel_doi": "10.1101/2022.04.17.488095", + "rel_title": "The SARS-CoV-2 Omicron BA.1 spike G446S potentiates HLA-A*24:02-restricted T cell immunity", + "rel_date": "2022-04-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.17.488095", + "rel_abs": "Although the Omicron variant of the SARS-CoV-2 virus is resistant to neutralizing antibodies, it retains susceptibility to cellular immunity. Here, we characterized vaccine-induced T cells specific for various SARS-CoV-2 variants and identified HLA-A*24:02-restricted CD8+ T cells that strongly suppressed Omicron BA.1 replication. Mutagenesis analyses revealed that a G446S mutation, located just outside the N-terminus of the cognate epitope, augmented TCR recognition of this variant. In contrast, no enhanced suppression of replication was observed against cells infected with the prototype, Omicron BA.2, and Delta variants that express G446. The enhancing effect of the G446S mutation was lost when target cells were treated with inhibitors of tripeptidyl peptidase II, a protein that mediates antigen processing. These results demonstrate that the G446S mutation in the Omicron BA.1 variant affects antigen processing/presentation and potentiates antiviral activity by vaccine-induced T cells, leading to enhanced T cell immunity towards emerging variants.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Chihiro Motozono", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Mako Toyoda", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Toong Seng Tan", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Hiroshi Hamana", + "author_inst": "Toyama University" + }, + { + "author_name": "Yoshiki Aritsu", + "author_inst": "Kindai University" + }, + { + "author_name": "Yusuke Miyashita", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Hiroyuki Oshiumi", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Kimitoshi Nakamura", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Seiji Okada", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Keiko Udaka", + "author_inst": "Kochi University" + }, + { + "author_name": "Mizuki Kitamatsu", + "author_inst": "Kindai University" + }, + { + "author_name": "Hiroyuki Kishi", + "author_inst": "Toyama University" + }, + { + "author_name": "Takamasa Ueno", + "author_inst": "Kumamoto University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.04.17.488607", "rel_title": "Ocular tropism of SARS-CoV-2 with retinal inflammation through neuronal invasion in animal models", @@ -309063,53 +311287,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.04.07.22273430", - "rel_title": "Characteristics of Patients with Hematologic Malignancies Without Seroconversion Post-COVID19 Third Vaccine Dosing", - "rel_date": "2022-04-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.07.22273430", - "rel_abs": "Patients with hematologic malignancies (HM) are at greater risk of severe morbidity and mortality caused by COVID19 and show a lower response to a two-dose COVID19 mRNA vaccine series. The primary objective of this retrospective cohort study is to explore the characteristics of the subset of patients with HM who had little to no change in SARS-CoV-2 spike antibody titer levels after a 3rd vaccine dose (3V) (-/-). As a secondary objective, we seek to compare the cohorts of patients who did and did not seroconvert post-3V to get a better understanding of the demographics and potential drivers of serostatus. A total of 625 patients with HM had two titer results at least 21 days apart pre- and post- the 3V dose. Among the participants who were seronegative prior to 3V (268), 149 (55.6%) seroconverted after the 3V dose and 119 (44.4%) did not. HM diagnosis was significantly associated with seroconversion status (P = .0003) with patients non-Hodgkin lymphoma 6 times the odds of not seroconverting compared to multiple myeloma patients (P = .0010). Among the cohort of patients who remained seronegative post-3V, 107 (90.0%) patients showed no reaction to 3V as indicated by pre- and post- 3V index values. This study focuses on an important subset of patients with HM who are not seroconverting after the COVID mRNA 3V, providing much needed data for clinicians to target and counsel this subset of patients.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Sigrun Hallmeyer", - "author_inst": "Advocate Aurora Health" - }, - { - "author_name": "Michael A Thompson", - "author_inst": "Tempus Labs, Chicago, IL" - }, - { - "author_name": "Veronica Fitzpatrick", - "author_inst": "Advocate Aurora Health" - }, - { - "author_name": "Yunqi Liao Liao", - "author_inst": "Advocate Aurora Health" - }, - { - "author_name": "Michael P Mullane", - "author_inst": "Advocate Aurora Health" - }, - { - "author_name": "Stephen C Medlin", - "author_inst": "Advocate Aurora Health" - }, - { - "author_name": "Kenneth Copeland", - "author_inst": "Advocate Aurora Health" - }, - { - "author_name": "James L Weese", - "author_inst": "Advocate Aurora Health" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "oncology" - }, { "rel_doi": "10.1101/2022.04.09.22273653", "rel_title": "Disease profile and plasma neutralizing activity of post-vaccination Omicron BA.1 infection in Tianjin, China: a retrospective study", @@ -309734,6 +311911,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.04.13.22273817", + "rel_title": "Seroprevalence, correlates and kinetics of SARS-CoV-2 Nucleocapsid IgG antibody in healthcare workers at a tertiary hospital: a prevaccine census study", + "rel_date": "2022-04-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.13.22273817", + "rel_abs": "BackgroundHealthcare workers are perceived to be a high-risk group for acquiring SAR-CoV-2 infection, and more so in countries where COVID-19 vaccination uptake is low. Serosurveillance may best determine the true extent of SARS-CoV-2 infection since most infected HCWs may be asymptomatic or present with only mild symptoms. Over time, determining the true extent of SARS-CoV-2 infection could inform hospital management and staff whether the preventive measures instituted are effective and valuable in developing targeted solutions.\n\nMethodsThis was a census survey study conducted at the Aga Khan University Hospital, Nairobi, between November 2020 and February 2021 before the implementation of the COVID-19 vaccination. The SARS-CoV-2 nucleocapsid IgG test was performed using a chemiluminescent assay.\n\nResultsOne thousand six hundred thirty-one (1631) staff enrolled, totalling 60% of the workforce. The overall crude seroprevalence was 18.4% and the adjusted value (for assay sensitivity of 86%) was 21.4% (95% CI; 19.2-23.7). The HCW groups with higher prevalence included pharmacy (25.6%), outreach (24%), hospital-based nursing (22.2%) and catering staff (22.6%). Independent predictors of a positive IgG result included prior COVID-19 like symptoms, odds ratio (OR) 1.9 [95% confidence interval (CI) 1.3-2.9, p=0.002], and a prior positive SARS-CoV-2 PCR result OR 11.0 (CI: 7.2-18.0, p<0.001). Age, sex, comorbidities or working in a COVID-19 designated area were not associated with seropositivity. The odds of testing positive for IgG after a positive PCR test were lowest if the antibody test was performed more than 2 months later; OR 0.7 (CI: 0.48-0.95, p= 0.025).\n\nConclusionsThe prevalence of anti-SARS-CoV-2 nucleocapsid IgG among HCWs was lower than in the general population. Staff working in clinical areas were not at increased risk when compared to staff working in non-clinical areas.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Daniel Maina", + "author_inst": "Aga Khan University - Kenya" + }, + { + "author_name": "Geoffrey Omuse", + "author_inst": "The Aga Khan University Hospital" + }, + { + "author_name": "George Ong'ete", + "author_inst": "Aga Khan University Hospital" + }, + { + "author_name": "Patrick Mugaine", + "author_inst": "Aga Khan University - Kenya" + }, + { + "author_name": "Shahin Sayed", + "author_inst": "Aga Khan University - Kenya" + }, + { + "author_name": "Zahir Moloo", + "author_inst": "Aga Khan Health Services" + }, + { + "author_name": "Reena Shah", + "author_inst": "Aga Khan University - Kenya" + }, + { + "author_name": "Anthony Etyang", + "author_inst": "KEMRI-Wellcome Trust Research Programme: Centre for Geographic Medicine Research Coast" + }, + { + "author_name": "Rodney Adam", + "author_inst": "Aga Khan University - Kenya" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.04.10.22273678", "rel_title": "Dynamics of anti-Spike IgG antibody titer after the third BNT162b2 COVID-19 vaccination in the Japanese health care workers", @@ -310593,33 +312821,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.04.14.488372", - "rel_title": "Hijacking of Cellular Functions by SARS-CoV-2. Permeabilization and Polarization of the Host Lipid Membrane by Viroporins.", - "rel_date": "2022-04-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.14.488372", - "rel_abs": "As all viral infections, SARS-CoV-2 acts at multiple levels hijacking fundamental cellular functions and assuring its replication and immune system evasion. In particular, it has been observed that the viral 3 Open Reading Frame (ORF3a) codes for a hydrophobic protein which embeds in the cellular membrane, where it acts as an ion viroporin and is related to strong inflammatory response. Here we report equilibrium and enhanced sampling molecular dynamic simulation of the SARS-CoV-2 ORF3a in a model lipid bilayer, showing how the protein permeabilizes the lipid membrane, via the formation of a water channel, which in turn assures ion transport. We report the free energy profile for both K+ and Cl- transfer from the cytosol to the extracellular domain. The important role of ORF3a in the viral cycle, and its highly conservation among coronaviruses, may also make it a target of choice for future antiviral development, further justifying the elucidation of its mechanism at the atomistic level.\n\nTOC GRAPHICS O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Emmanuelle Bignon", - "author_inst": "Universite de Lorraine" - }, - { - "author_name": "Marco Marazzi", - "author_inst": "Universidad de Alcala de Henares" - }, - { - "author_name": "Antonio Monari", - "author_inst": "Universite de Paris and CNRS, ITODYS" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2022.04.14.22273759", "rel_title": "Understanding community level influences on COVID-19 prevalence in England: New insights from comparison over time and space", @@ -311252,6 +313453,29 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2022.04.13.488249", + "rel_title": "Whole-body metabolic modelling predicts isoleucine dependency of SARS-CoV-2 replication", + "rel_date": "2022-04-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.13.488249", + "rel_abs": "We aimed at investigating host-virus co-metabolism during SARS-CoV-2 infection. Therefore, we extended comprehensive sex-specific, whole-body organ resolved models of human metabolism with the necessary reactions to replicate SARS-CoV-2 in the lung as well as selected peripheral organs. Using this comprehensive host-virus model, we obtained the following key results: 1. The predicted maximal possible virus shedding rate was limited by isoleucine availability. 2. The supported initial viral load depended on the increase in CD4+ T-cells, consistent with the literature. 3. During viral infection, the whole-body metabolism changed including the blood metabolome, which agreed well with metabolomic studies from COVID-19 patients and healthy controls. 4. The virus shedding rate could be reduced by either inhibition of the guanylate kinase 1 or availability of amino acids, e.g., in the diet. 5. The virus variants achieved differed in their maximal possible virus shedding rates, which could be inversely linked to isoleucine occurrences in the sequences. Taken together, this study presents the metabolic crosstalk between host and virus and emphasis the role of amino acid metabolism during SARS-CoV-2 infection, in particular of isoleucine. As such, it provides an example of how computational modelling can complement more canonical approaches to gain insight into host-virus crosstalk and to identify potential therapeutic strategies.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Ines Thiele", + "author_inst": "National University of Ireland, Galway" + }, + { + "author_name": "Ronan MT Fleming", + "author_inst": "National University of Ireland, Galway" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "systems biology" + }, { "rel_doi": "10.1101/2022.04.13.488264", "rel_title": "Genomic surveillance unfolds the dynamics of SARS-CoV-2 transmission and divergence in Bangladesh over the past two years", @@ -312254,41 +314478,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.04.13.488132", - "rel_title": "The Omicron (B.1.1.529) SARS-CoV-2 variant of concern also affects companion animals", - "rel_date": "2022-04-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.13.488132", - "rel_abs": "The recent emergence of the Omicron variant (B.1.1.529) has brought with it a large increase in the incidence of SARS-CoV-2 disease worldwide. However, there is hardly any data on the incidence of this new variant in companion animals. In this study, we have detected the presence of this new variant in domestic animals such as dogs and cats living with owners with COVID19 in Spain that have been sampled at the most optimal time for the detection of the disease. None of the RT-qPCR positive animals (10.13%) presented any clinical signs and the viral loads detected were very low. In addition, the shedding of viral RNA lasted a short period of time in the positive animals. Infection with the Omicron variant of concern (VOC) was confirmed by a specific RT-qPCR for the detection of this variant and by sequencing. These outcomes suggest a lower virulence of this variant in infected cats and dogs. This study demonstrates the transmission of this new variant from infected humans to domestic animals and highlights the importance of doing active surveillance as well as genomic research to detect the presence of VOCs or mutations associated with animal hosts.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Lidia Sanchez-Morales", - "author_inst": "VISAVET Health Surveillance Centre / Complutense University of Madrid" - }, - { - "author_name": "Jose M. Sanchez-Vizcaino", - "author_inst": "VISAVET Health Surveillance Centre / Complutense University of Madrid" - }, - { - "author_name": "Marta Perez-Sancho", - "author_inst": "VISAVET Health Surveillance Centre / Complutense University of Madrid" - }, - { - "author_name": "Lucas Dominguez", - "author_inst": "VISAVET Health Surveillance Centre / Complutense University of Madrid" - }, - { - "author_name": "Sandra Barroso-Arevalo", - "author_inst": "VISAVET Health Surveillance Centre/Complutense University of Madrid" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2022.04.04.22273376", "rel_title": "From elimination to suppression: genomic epidemiology of a large Delta SARS-CoV-2 outbreak in Aotearoa New Zealand", @@ -313285,6 +315474,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.04.07.22273414", + "rel_title": "COVID-19 vaccine for people who live and work in prisons worldwide: A scoping review.", + "rel_date": "2022-04-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.07.22273414", + "rel_abs": "Overcrowding, poor conditions, and high population turnover make prisons highly susceptible to COVID-19. Vaccination is key to controlling COVID-19, yet there is disagreement regarding whether people who live and work in prisons should be prioritised in national vaccination programmes. To help resolve this, we critically examine the extent, nature, and quality of extant literature regarding prioritisation of COVID-19 vaccinations for people who live and work in prisons.\n\nUsing a scoping review as our methodological framework, we conducted a systematic literature search of 17 databases. From 2,307 potentially eligible articles, we removed duplicates and screened titles and abstracts to retain 45 articles for review and quality appraisal.\n\nFindings indicated that while most countries recognise that prisons are at risk of high levels of COVID-19 transmission, only a minority have explicitly prioritised people who live and work in prisons for COVID-19 vaccination. Even among those that have, prioritisation criteria varies considerably. This is set against a backdrop of political barriers, such as politicians questioning the moral deservingness of people in prison; policy barriers, such as the absence of a unified international framework of how vaccine prioritisation should proceed in prisons; logistical barriers regarding vaccine administration in prisons; and behavioural barriers including vaccine hesitancy.\n\nWe outline five strategies to prioritise people who live and work in prisons in COVID-19 vaccination plans: (1) improving data collection on COVID-19 vaccination, (2) reducing the number of people imprisoned, (3) tackling vaccine populism through advocacy, (4) challenging arbitrary prioritisation processes via legal processes, and (5) conducting more empirical research on COVID-19 vaccination planning, delivery, and acceptability. Implementing these strategies would help to reduce the impact of COVID-19 on the prison population, prevent community transmission, improve vaccine uptake in prisons beyond the current pandemic, foster political accountability, and inform future decision-making.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Nasrul Ismail", + "author_inst": "University of Bristol School for Policy Studies" + }, + { + "author_name": "Lara Tavoschi", + "author_inst": "University of Pisa" + }, + { + "author_name": "Babak Moazen", + "author_inst": "Frankfurt University of Applied Sciences" + }, + { + "author_name": "Alicia Rosell\u00f3", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Emma Plugge", + "author_inst": "University of Southampton" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.04.10.22273663", "rel_title": "The relation between COVID-19 vaccinations and public governance to improve preparedness of next pandemic impacts and crisis management: a global study", @@ -313833,45 +316057,6 @@ "type": "new results", "category": "systems biology" }, - { - "rel_doi": "10.1101/2022.04.11.487836", - "rel_title": "SARS-ANI: A Global Open Access Dataset of Reported SARS-CoV-2 Events in Animals", - "rel_date": "2022-04-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.11.487836", - "rel_abs": "The zoonotic origin of SARS-CoV-2, the etiological agent of COVID-19, is not yet fully resolved. Although natural infections in animals are reported in a wide range of species, large knowledge and data gaps remain regarding SARS-CoV-2 animal hosts. We used two major health databases to extract unstructured data and generated a comprehensive global dataset of thoroughly documented SARS-CoV-2 events in animals. The dataset integrates relevant epidemiological and clinical data on each event and is readily usable for analytical purposes. We also share the code for technical and visual validation of the data and created a user-friendly dashboard for data exploration. Data on SARS-CoV-2 occurrence in animals is critical to adapt monitoring strategy, prevent the formation of animal reservoirs, and tailor future human and animal vaccination programs. The FAIRness and analytical flexibility of the data will support research efforts on SARS-CoV-2 at the human-animal-environment interface. We intend to update this dataset weekly for at least one year and, through collaborative processes, to develop the dataset further and expand its use.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Afra Nerpel", - "author_inst": "Unit of Veterinary Public Health and Epidemiology, University of Veterinary Medicine Vienna, Austria" - }, - { - "author_name": "Liuhuaying Yang", - "author_inst": "Complexity Science Hub Vienna, Austria" - }, - { - "author_name": "Johannes Sorger", - "author_inst": "Complexity Science Hub Vienna, Austria" - }, - { - "author_name": "Annemarie Kaesbohrer", - "author_inst": "Unit of Veterinary Public Health and Epidemiology, University of Veterinary Medicine Vienna, Austria" - }, - { - "author_name": "Chris Walzer", - "author_inst": "Wildlife Conservation Society, NY, United States; Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Austria" - }, - { - "author_name": "Amelie Desvars-Larrive", - "author_inst": "Unit of Veterinary Public Health and Epidemiology, University of Veterinary Medicine Vienna, Austria; Complexity Science Hub Vienna, Austria" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.04.11.487828", "rel_title": "Key mutations on spike protein altering ACE2 receptor utilization and potentially expanding host range of emerging SARS-CoV-2 variants", @@ -314552,6 +316737,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2022.04.06.22273542", + "rel_title": "Effectiveness of convalescent plasma therapy in COVID-19 patients with haematological malignancies", + "rel_date": "2022-04-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.06.22273542", + "rel_abs": "BackgroundImmunocompromised patients, including those with haematological malignancies, are among the high-risk group to develop severe coronavirus disease 2019 (COVID-19) complications. The effectiveness of passive immunotherapy with convalescent plasma (CP) on such patients diagnosed with COVID-19 has not been reviewed. Therefore, the aim of this review was to systematically appraise the current evidence for the efficacy of this therapy in haematological malignancies patients with COVID-19 infection.\n\nMethodsA comprehensive search was conducted up-to October 2021, using four databases: PubMed, Web of Science, Science Direct, and Scopus. Two reviewers independently assessed the quality of the included studies. Data collection analysis were performed using Microsoft Excel 365 and GraphPad Prism software.\n\nResults17 studies met the inclusion criteria; these records included 258 COVID-19 patients with haematological malignancies and treated with CP therapy (CPT). The main findings from the reviewed data suggests CPT may be associated with improved clinical outcomes including (a) higher survival rate, (b) improved SARS-CoV-2 clearance and presence of detectable anti-SARS-CoV-2 antibodies post CP transfusion, (c) improved hospital discharge time, and recovery after 1 month of CP therapy. Furthermore, treatment with convalescent plasma was not associated with development of adverse events.\n\nConclusionOwing to its safety and beneficial effects in improving clinical outcomes, CPT appears to be an effective supportive therapeutic option for haematological malignancy patients infected with COVID-19.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Sapha Shibeeb", + "author_inst": "Qatar University" + }, + { + "author_name": "Ilham Ajaj", + "author_inst": "Qatar University" + }, + { + "author_name": "Hadeel Al-Jighefee", + "author_inst": "Qatar University" + }, + { + "author_name": "Atiyeh Abdallah", + "author_inst": "Qatar university" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "hematology" + }, { "rel_doi": "10.1101/2022.04.07.22273581", "rel_title": "Time series cross-correlation between home range and number of infected people during the medium term of COVID-19 Pandemic in a suburban city", @@ -315675,29 +317891,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.04.06.22273444", - "rel_title": "Does pre-infection stress increase the risk of long COVID? Longitudinal associations between adversity worries and experiences in the month prior to COVID-19 infection and the development of long COVID and specific long COVID symptoms", - "rel_date": "2022-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.06.22273444", - "rel_abs": "BackgroundLong COVID is increasingly recognised as public health burden. Demographic and infection-related characteristics have been identified as risk factors, but less research has focused on psychosocial predictors such as stress immediately preceding the index infection. Research on whether stressors predict the development of specific long COVID symptoms is also lacking.\n\nMethodsData from 1,966 UK adults who had previously been infected with COVID-19 and who took part in the UCL COVID-19 Social Study were analysed. The number of adversity experiences (e.g., job loss) and the number of worries about adversity experiences within the month prior to COVID-19 infection were used to predict the development of self-reported long COVID and the presence of three specific long COVID symptoms (difficulty with mobility, cognition, and self-care). The interaction between a three-level index of socio-economic position (SEP; with higher values indicating lower SEP) and the exposure variables in relation to long COVID status was also examined. Analyses controlled for a range of COVID-19 infection characteristics, socio-demographics, and health-related factors.\n\nFindingsOdds of self-reported long COVID increased by 1.25 (95% confidence interval [CI]: 1.04 to 1.51) for each additional worry about adversity in the month prior to COVID-19 infection. Although there was no evidence for an interaction between SEP and either exposure variable, individuals in the lowest SEP group were nearly twice as likely to have developed long COVID as those in the highest SEP group (OR: 1.95; 95% CI: 1.19 to 3.19) and worries about adversity experiences remained a predictor of long COVID (OR: 1.43; 95% CI: 1.04 to 1.98). The number of worries about adversity experiences also corresponded with increased odds of certain long COVID symptoms such as difficulty with cognition (e.g., difficulty remembering or concentrating) by 1.46 (95% CI: 1.02 to 2.09) but not with mobility (e.g., walking or climbing steps) or self-care (e.g., washing all over or dressing).\n\nInterpretationResults suggest a key role of stress in the time preceding the acute COVID-19 infection for the development of long COVID and for difficulty with cognition specifically. These findings point to the importance of mitigating worries and experiences of adversities during pandemics both to reduce their psychological impact but also help reduce the societal burden of longer-term illness.\n\nFundingThe Nuffield Foundation [WEL/FR-000022583], the MARCH Mental Health Network funded by the Cross-Disciplinary Mental Health Network Plus initiative supported by UK Research and Innovation [ES/S002588/1], and the Wellcome Trust [221400/Z/20/Z and 205407/Z/16/Z].", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Elise Paul", - "author_inst": "University College London" - }, - { - "author_name": "Daisy Fancourt", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.04.03.22273225", "rel_title": "Summaries, Analysis and Simulations of Recent COVID-19 Epidemics in Mainland China", @@ -316514,6 +318707,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.04.05.22273358", + "rel_title": "Built environment's impact on COVID-19 transmission and mental health revealed by COVID-19 Participant Experience data from the All of Us Research Program", + "rel_date": "2022-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.05.22273358", + "rel_abs": "ObjectivesThe coronavirus disease 2019 (COVID-19) pandemic has led to millions of deaths. Effectively cutting the transmission of COVID-19 is essential to reduce the impact. Previous studies have observed the potential relationship between the built environment and COVID-19 transmission; however, to date, stringent studies investigating these relationships at the individual level are still insufficient. Here, we aim to examine the relationship between household types and COVID-19 infection (or mental health) during the early stages of the pandemic by using the All of Us Research Program COVID-19 Participant Experience (COPE) survey data.\n\nDesignBased on 62,664 participants responses to COPE from May to July 2020, we matched the cases of self-reported COVID-19 status, anxiety, or stress, with controls of the same race, sex, age group, and survey version. We conducted multiple logistic regressions between one of the outcomes and household type under the adjustment of other related covariates, such as ethnicity, age, social distancing behavior, and house occupancy.\n\nResultsHousehold type with a shared component was significantly associated with COVID-19 infection (OR=1.19, 95% CI 1.1 to 1.3; p=2x10-4), anxiety (OR=1.26, 95% CI 1.1 to 1.4; p=1.1x10-6), and stress (OR=1.29, 95% CI 1.2 to 1.4, p=4.3x10-10) as compared to free-standing houses after adjusting for the abovementioned confounding factors. Further, frequent nonessential shopping or outings, another indicator of the built environment, was also associated with COVID-19 infection (OR=1.36, 95% CI 1.1 to 1.8; p=0.02), but not associated with elevated mental health conditions.\n\nConclusionOur study demonstrated that the built environment of houses with a shared component tends to increase the risk of COVID-19 transmission, which consequently led to more anxiety and stress for their dwellers. It also suggested the necessity to improve the quality of the built environment through planning, design, and management toward a more resilient society in coping with future pandemics.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Wenting Luo", + "author_inst": "Department of Mathematics, University of Arizona" + }, + { + "author_name": "Edwin Baldwin", + "author_inst": "Department of Biosystems Engineering, University of Arizona" + }, + { + "author_name": "Anna Yi Jiang", + "author_inst": "Department of Biomedical Engineering, University of Arizona" + }, + { + "author_name": "Shujuan Li", + "author_inst": "Sch of Landscape Architecture, University of Arizona" + }, + { + "author_name": "Bo Yang", + "author_inst": "School of Landscape Architecture, University of Arizona" + }, + { + "author_name": "Haiquan Li", + "author_inst": "Department of Biosystems Engineering, University of Arizona" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.04.04.22273418", "rel_title": "Interleukin-6 as a predictor of early weaning from invasive mechanical ventilation in patients with acute respiratory distress syndrome", @@ -317433,73 +319665,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2022.04.06.487257", - "rel_title": "Delineating antibody escape from Omicron variants", - "rel_date": "2022-04-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.06.487257", - "rel_abs": "SARS-CoV-2 neutralizing antibodies play a critical role in prevention and treatment of COVID-19 but are challenged by viral evolution and antibody evasion, exemplified by the highly resistant Omicron BA.1 sublineage.1-12 Importantly, the recently identified Omicron sublineages BA.2.12.1 and BA.4/5 with differing spike mutations are rapidly emerging in various countries. By determining polyclonal serum activity of 50 convalescent or vaccinated individuals against BA.1, BA.1.1, BA.2, BA.2.12.1, and BA.4/5, we reveal a further reduction of BA.4/5 susceptibility to vaccinee sera. Most notably, delineation of the sensitivity to an extended panel of 163 antibodies demonstrates pronounced antigenic differences of individual sublineages with distinct escape patterns and increased antibody resistance of BA.4/5 compared to the most prevalent BA.2 sublineage. These results suggest that the antigenic distance from BA.1 and the increased resistance compared to BA.2 may favor immune escape-mediated expansion of BA.4/5 after the first Omicron wave. Finally, while most monoclonal antibodies in clinical stages are inactive against all Omicron sublineages, we identify promising novel antibodies with high pan-Omicron neutralizing potency. Our study provides a detailed understanding of the antibody escape from the most recently emerging Omicron sublineages that can inform on effective strategies to prevent and treat COVID-19.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Henning Gruell", - "author_inst": "University Hospital Cologne" - }, - { - "author_name": "Kanika Vanshylla", - "author_inst": "University Hospital Cologne" - }, - { - "author_name": "Michael Korenkov", - "author_inst": "University Hospital Cologne" - }, - { - "author_name": "Pinkus Tober-Lau", - "author_inst": "Charite Universitaetsmedizin" - }, - { - "author_name": "Matthias Zehner", - "author_inst": "University Hospital Cologne" - }, - { - "author_name": "Friederike Muenn", - "author_inst": "Charite Universitaetsmedizin" - }, - { - "author_name": "Hanna Janicki", - "author_inst": "University Hospital Cologne" - }, - { - "author_name": "Max Augustin", - "author_inst": "University Hospital Cologne" - }, - { - "author_name": "Philipp Schommers", - "author_inst": "University Hospital Cologne" - }, - { - "author_name": "Leif Erik Sander", - "author_inst": "Charite Universitaetsmedizin" - }, - { - "author_name": "Florian Kurth", - "author_inst": "Charite Universitaetsmedizin" - }, - { - "author_name": "Christoph Kreer", - "author_inst": "University Hospital Cologne" - }, - { - "author_name": "Florian Klein", - "author_inst": "Faculty of Medicine and University Hospital Cologne, University of Cologne" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.04.05.487186", "rel_title": "SARS-CoV-2 Omicron (BA.1 and BA.2) specific novel CD8+ and CD4+ T cell epitopes targeting spike protein.", @@ -318280,6 +320445,37 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.04.04.22271935", + "rel_title": "Workplace ventilation improvement to address coronavirus disease 2019 cluster occurrence in a manufacturing factory", + "rel_date": "2022-04-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.04.22271935", + "rel_abs": "Aim and MethodsA coronavirus disease 2019 (COVID-19) cluster emerged in a manufacturing factory in early August 2021. In November 2021, a ventilation survey using tracer gas and data analysis was performed to reproduce the situation at the time of cluster emergence and verify that ventilation in the office increased the risk of aerosol transmission; verify the effectiveness of measures implemented immediately in August; and verify the effectiveness of additional measures when previously enforced measures proved inadequate.\n\nResultsAt the time of cluster emergence, the average ventilation frequency was 0.73 times/h, less than the 2 times/h recommended by the Ministry of Health, Labour, and Welfare; as such, the factorys situation was deemed to have increased the risk of aerosol transmission. Due to the measures already taken at the time of the survey, the ventilation frequency increased to 3.41 times/h on average. It was confirmed that ventilation frequency increased to 8.33 times/h on average, when additional measures were taken.\n\nConclusionTo prevent the re-emergence of COVID-19 clusters, it is necessary to continue the measures that have already been implemented. Additionally, introduction of real-time monitoring that visualizes CO2 concentrations is recommended. Furthermore, we believe it is helpful that external researchers in multiple fields and internal personnel in charge of health and safety department and occupational health work together to confirm the effectiveness of conducted measures, such as this case.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Hiroko Kitamura", + "author_inst": "University of Occupational and Environmental Health" + }, + { + "author_name": "Yo Ishigaki", + "author_inst": "University of Electro-communications" + }, + { + "author_name": "Hideaki Ohashi", + "author_inst": "University of Occupational and Environmental Health" + }, + { + "author_name": "Shinji Yokogawa", + "author_inst": "University of Electro-communications" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2022.04.05.487103", "rel_title": "Evolution of Delta variant by non-Spike signature co-appearing mutations: trailblazer of COVID-19 disease outcome", @@ -319247,73 +321443,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.04.01.22273117", - "rel_title": "Developing a model for predicting impairing physical symptoms in children 3 months after a SARS-CoV-2 PCR-test: The CLoCk Study", - "rel_date": "2022-04-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.01.22273117", - "rel_abs": "ImportancePredictive models can help identify SARS-CoV-2 patients at greatest risk of post-COVID sequelae and direct them towards appropriate care.\n\nObjectiveTo develop and internally validate a model to predict children and young people most likely to experience at least one impairing physical symptom 3 months after a SARS-CoV-2 PCR-test and to determine whether the impact of these predictors differed by SARS-CoV-2 infection status.\n\nDesignPotential pre-specified predictors included: SARS-CoV-2 status, sex, age, ethnicity, deprivation, quality of life/functioning (5 EQ-5D-Y items), physical and mental health, and loneliness (all prior to SARS-CoV-2 testing), and number of physical symptoms at testing. Logistic regression was used to develop the model. Model performance was assessed using calibration and discrimination measures; internal validation was performed via bootstrapping; the final model was adjusted for overfitting.\n\nSettingNational cohort study of SARS-CoV-2 PCR-positive and PCR-negative participants matched according to age, sex, and geographical area.\n\nParticipantsChildren and young people aged 11-17 years who were tested for SARS-CoV-2 infection in England, January to March 2021.\n\nMain outcome measureone or more physical symptom 3 months after initial PCR-testing which affected physical, mental or social well-being and interfered with daily living.\n\nResultsA total of 50,836 children and young people were approached; 7,096 (3,227 test-positives, 3,869 test-negatives) who completed a questionnaire 3 months after their PCR-test were included. 39.6% (1,279/3,227) of SAR-CoV-2 PCR-positives and 30.6% (1,184/3,869) of SAR-CoV-2 PCR-negatives had at least one impairing physical symptom 3 months post-test. The final model contained predictors: SARS-COV-2 status, number of symptoms at testing, sex, age, ethnicity, self-rated physical and mental health, feelings of loneliness and four EQ-5D-Y items before testing. Internal validation showed minimal overfitting with excellent calibration and discrimination measures (optimism adjusted calibration slope:0.97527; C-statistic:0.83640).\n\nConclusions and relevanceWe developed a risk prediction equation to identify those most at risk of experiencing at least one impairing physical symptom 3 months after a SARS-CoV-2 PCR-test which could serve as a useful triage and management tool for children and young people during the ongoing pandemic. External validation is required before large-scale implementation.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSWhich children have impairing physical symptoms during the COVID-19 pandemic?\n\nFindingsUsing data from a large national matched cohort study in children and young people (CYP) aged 11-17 years (N=7,096), we developed a prediction model for experiencing at least one impairing physical symptom 3 months after testing for SARS-COV-2. Our model had excellent predictive ability, calibration and discrimination; we used it to produce a risk estimation calculator.\n\nMeaningOur developed risk calculator could serve as a useful tool in the early identification and management of CYP at risk of persisting physical symptoms in the context of the COVID-19 pandemic.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Manjula Nugawela", - "author_inst": "UCL Great Ormond Street Institute of Child Health" - }, - { - "author_name": "Terence Stephenson", - "author_inst": "UCL Great Ormond Street Institute of Child Health" - }, - { - "author_name": "Roz Shafran", - "author_inst": "UCL Great Ormond Street Institute of Child Health" - }, - { - "author_name": "Bianca Lucia De Stavola", - "author_inst": "UCL" - }, - { - "author_name": "Shamez Ladhani", - "author_inst": "Public Health England" - }, - { - "author_name": "Ruth Simmons", - "author_inst": "Public Health England" - }, - { - "author_name": "Kelsey McOwatt", - "author_inst": "Public Health England" - }, - { - "author_name": "Natalia Rojas", - "author_inst": "UCL Great Ormond Street Institute of Child Health" - }, - { - "author_name": "Emily Y Cheung", - "author_inst": "UCL Great Ormond Street Institute of Child Health" - }, - { - "author_name": "Tamsin Ford", - "author_inst": "Department of Psychiatry, University of Cambridge" - }, - { - "author_name": "Isobel Heyman", - "author_inst": "UCL Great Ormond Street Institute of Child Health" - }, - { - "author_name": "Esther Crawley", - "author_inst": "Centre for Academic Child Health, Bristol Medical School, University of Bristol" - }, - { - "author_name": "Snehal M Pinto Pereira", - "author_inst": "UCL" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.04.04.22273361", "rel_title": "Long- and short-term effects of cross-immunity in epidemic dynamics", @@ -320042,6 +322171,97 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.03.29.22273042", + "rel_title": "The new normal? Dynamics and scale of the SARS-CoV-2 variant Omicron epidemic in England", + "rel_date": "2022-04-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.29.22273042", + "rel_abs": "The SARS-CoV-2 pandemic has been characterised by the regular emergence of genomic variants which have led to substantial changes in the epidemiology of the virus. With natural and vaccine-induced population immunity at high levels, evolutionary pressure favours variants better able to evade SARS-CoV-2 neutralising antibodies. The Omicron variant was first detected in late November 2021 and exhibited a high degree of immune evasion, leading to increased infection rates in many countries. However, estimates of the magnitude of the Omicron wave have relied mainly on routine testing data, which are prone to several biases. Here we infer the dynamics of the Omicron wave in England using PCR testing and genomic sequencing obtained by the REal-time Assessment of Community Transmission-1 (REACT-1) study, a series of cross-sectional surveys testing random samples of the population of England. We estimate an initial peak in national Omicron prevalence of 6.89% (5.34%, 10.61%) during January 2022, followed by a resurgence in SARS-CoV-2 infections in England during February-March 2022 as the more transmissible Omicron sub-lineage, BA.2 replaced BA.1 and BA.1.1. Assuming the emergence of further distinct genomic variants, intermittent epidemics of similar magnitude as the Omicron wave may become the new normal.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Oliver Eales", + "author_inst": "Imperial College London" + }, + { + "author_name": "Leonardo de Oliveira Martins", + "author_inst": "Quadram Institute, Norwich, UK" + }, + { + "author_name": "Andrew Page", + "author_inst": "Quadram Institute, Norwich, UK" + }, + { + "author_name": "Haowei Wang", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" + }, + { + "author_name": "Barbara Bodinier", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Environment and Health, School of Public Health, Imperial College London, UK" + }, + { + "author_name": "David Tang", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Environment and Health, School of Public Health, Imperial College London, UK" + }, + { + "author_name": "David Haw", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" + }, + { + "author_name": "Jakob Jonnerby", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" + }, + { + "author_name": "Christina Atchison", + "author_inst": "School of Public Health, Imperial College London, UK" + }, + { + "author_name": "Deborah Ashby", + "author_inst": "School of Public Health, Imperial College London, UK" + }, + { + "author_name": "Wendy Barclay", + "author_inst": "Department of Infectious Disease, Imperial College London, UK" + }, + { + "author_name": "Graham Taylor", + "author_inst": "Department of Infectious Disease, Imperial College London, UK" + }, + { + "author_name": "Graham Cooke", + "author_inst": "Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic" + }, + { + "author_name": "Helen Ward", + "author_inst": "School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear" + }, + { + "author_name": "Ara Darzi", + "author_inst": "Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a" + }, + { + "author_name": "Steven Riley", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" + }, + { + "author_name": "Paul Elliott", + "author_inst": "School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear" + }, + { + "author_name": "Christl A Donnelly", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" + }, + { + "author_name": "Marc Chadeau-Hyam", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Environment and Health, School of Public Health, Imperial College London, UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.04.04.487067", "rel_title": "Surface detection of SARS-CoV-2 by lateral flow LAMP", @@ -321189,77 +323409,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.27.22271988", - "rel_title": "Phase 3, multicentre, double-blind, randomised, parallel-group, placebo-controlled study of camostat mesilate (FOY-305) for the treatment of COVID-19 (CANDLE study)", - "rel_date": "2022-04-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.27.22271988", - "rel_abs": "BackgroundIn vitro drug-screening studies have indicated that camostat mesilate (FOY-305) may prevent SARS-CoV-2 infection into human airway epithelial cells. This study was conducted to investigate whether camostat mesilate is an effective treatment for SARS-CoV-2 infection (COVID-19).\n\nMethodsThis was a phase 3, multicentre, double-blind, randomised, parallel-group, placebo-controlled study. Patients were enrolled if they were admitted to a hospital within 5 days of onset of COVID-19 symptoms or within 5 days of a positive test for asymptomatic patients. Severe cases (e.g., those requiring oxygenation/ventilation) were excluded. Patients were administered camostat mesilate (600 mg qid; four to eight times higher than the clinical doses in Japan) or placebo for up to 14 days. The primary efficacy endpoint was the time to the first two consecutive negative tests for SARS-CoV-2.\n\nFindingsOne-hundred and fifty-five patients were randomised to receive camostat mesilate (n=78) or placebo (n=77). The median time to the first test was 11 days in both groups, and conversion to negative status was observed in 60{middle dot}8% and 63{middle dot}5% of patients in the camostat mesilate and placebo groups, respectively. The primary (Bayesian) and secondary (frequentist) analyses found no significant differences in the primary endpoint between the two groups. No additional safety concerns beyond those already known for camostat mesilate were identified.\n\nInterpretationCamostat mesilate is no more effective, based on upper airway viral clearance, than placebo for treating patients with mild to moderate SARS-CoV-2 infection with or without symptoms.\n\nFundingOno Pharmaceutical Co., Ltd.\n\nRESEARCH IN CONTEXT PANELO_ST_ABSEvidence before this studyC_ST_ABSSARS-CoV-2 infection (COVID-19), as a significant global health threat, is characterised by broad symptoms and varying disease severity. At the time of planning this study, there were no specific treatments for COVID-19 beyond the use of antiviral drugs, steroids and, in severe cases, ventilation with oxygen. Pre-clinical screening studies revealed the spike (S) protein of SARS-CoV-2 bind to angiotensin converting enzyme II (ACE2) on the host cell membrane. The S protein is then cleaved by a type II transmembrane serine protease (TMPRSS2) as an essential enzyme for the viral entry into host cells. In vitro drug-screening studies have shown that drugs that block binding of the S protein to ACE2 can prevent viral entry into a cell line derived from human airway epithelium. The studies identified 4-(4-guanidinobenzoyloxy)phenylacetic acid, the active metabolite of a serine protease inhibitor (camostat mesilate, FOY-305), as a candidate inhibitor of SARS-CoV-2 entry into humans. A retrospective study of critically ill COVID-19 patients with organ failure revealed a decline in disease activity within 8 days of admission among patients treated with camostat mesilate. In consideration of the preclinical and early clinical evidence, it was hypothesised that camostat mesilate is an effective treatment for patients with COVID-19. Therefore, we planned and executed a phase 3, randomised, double-blind, placebo-controlled study to investigate the efficacy and safety of camostat mesilate for the treatment of patients with mild to moderate COVID-19 infection with or without symptoms. The primary endpoint was the time to the first two consecutive negative tests for SARS-CoV-2. No controlled clinical studies of camostat mesilate had been conducted at the time of planning this study.\n\nAdded value of this studyThe results of this randomised controlled trial revealed that camostat mesilate, administered at a dose of 600 mg qid for up to 14 days, was no more effective than placebo, based on upper airway viral clearance in patients with mild to moderate SARS-CoV-2 infection with or without symptoms. Furthermore, there were no differences between the study groups in terms of other efficacy endpoints. This study used a dose that was four to eight times higher than the clinical doses of camostat mesilate used in Japan for the acute symptoms of chronic pancreatitis and postoperative reflux oesophagitis. The study identified no additional safety concerns beyond those already known for camostat mesilate.\n\nImplications of all available evidenceAfter starting this study, another randomised, placebo-controlled study reported the efficacy and safety of camostat mesilate for the treatment of patients with COVID-19, albeit at a lower dose of 200 mg three times daily. That study also found no difference between camostat mesilate and placebo for the primary endpoint (the time to discharge or a clinical improvement in clinical severity of at least two points on a seven-point ordinal scale). Along with this evidence, our study did not support the use of camostat mesilate as a treatment option for COVID-19. However, since the administration of camostat mesilate was started after the onset of symptoms and presumably the peak viral load, we cannot exclude the possibility that camostat mesilate may be effective if administration is started earlier in the course of infection, or perhaps as prophylactic use in close contacts.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Taku Kinoshita", - "author_inst": "International University of Health and Welfare Narita Hospital" - }, - { - "author_name": "Masahiro Shinoda", - "author_inst": "Tokyo Shinagawa Hospital" - }, - { - "author_name": "Yasuhiro Nisizaki", - "author_inst": "Tokai University Tokyo Hospital" - }, - { - "author_name": "Katsuya Shiraki", - "author_inst": "Mie Prefectural General Medical Center" - }, - { - "author_name": "Yuji Hirai", - "author_inst": "Tokyo Medical University Hachioji Medical Center" - }, - { - "author_name": "Yoshiko Kichikawa", - "author_inst": "Mishuku Hospital" - }, - { - "author_name": "Kenji Tsushima", - "author_inst": "International University of Health and Welfare Narita Hospital" - }, - { - "author_name": "Masaharu Sinkai", - "author_inst": "Tokyo Shinagawa Hospital" - }, - { - "author_name": "Naoyuki Komura", - "author_inst": "Ono Pharmaceutical Co., Ltd." - }, - { - "author_name": "Kazuo Yoshida", - "author_inst": "Ono Pharmaceutical Co., Ltd." - }, - { - "author_name": "Yasutoshi Kido", - "author_inst": "Osaka City University" - }, - { - "author_name": "Hiroshi Kakeya", - "author_inst": "Osaka City University" - }, - { - "author_name": "Naoto Uemura", - "author_inst": "Oita University" - }, - { - "author_name": "Junichi Kadota", - "author_inst": "Nagasaki Harbor Medical Center" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.30.22273174", "rel_title": "Dupilumab use is associated with protection from COVID-19 mortality: A retrospective analysis.", @@ -322000,6 +324149,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2022.03.28.22273059", + "rel_title": "Engagement of health workers and peer educators from the National Adolescent Health Programme-Rashtriya Kishor Swasthya Karyakram during the COVID-19 pandemic: findings from a situational analysis", + "rel_date": "2022-04-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.28.22273059", + "rel_abs": "BackgroundTo understand the impact of COVID-19 on implementation of the peer education programme of the National Adolescent Health Programme-Rashtriya Kishor Swasthya Karyakram; repurposing of the RKSK health workers and Peer Educators (PE) in COVID-19 response activities and; adolescents' health and development issues.\n\nMethodsVirtual in-depth interviews were conducted with stakeholders (n=31) (aged 15 to 54) engaged in the implementation of the peer education programme at state, district, block, and village levels in Madhya Pradesh and Maharashtra (India). These interviews were thematically coded and analysed to address the research objectives.\n\nResultsDespite most peer education programme activities being stopped, delayed, or disrupted during the pandemic and subsequent lockdown, some communication networks previously established, helped facilitate public health communication regarding COVID-19 and RKSK, between health workers, peer educators, and adolescents. There was significant repurposing of RKSK health workers and Peer Educators role towards COVID-19 response-related activities. Peer educators, with support from health workers, were involved in disseminating COVID-19 information, maintaining migrant and quarantine records, conducting household surveys for finding COVID-19 active cases and providing essential items (grocery, sanitary napkins, etc.) to communities and adolescents.\n\nConclusionPeer Educators with support from community health workers are able to play a crucial role in meeting the needs of the communities during a pandemic. There is a need to further engage, involve and build the skills of Peer Educators to support the health system. PEs can be encouraged by granting more visibility and incorporating their role more formally by paying them within the public health system in India.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Monika Arora", + "author_inst": "Public Health Foundation of India" + }, + { + "author_name": "Stefanie Dringus", + "author_inst": "Independent Consultant" + }, + { + "author_name": "Deepika Bahl", + "author_inst": "Public Health Foundation of India" + }, + { + "author_name": "Zoya Rizvi", + "author_inst": "Ministry of Health and Family Welfare: Government of India" + }, + { + "author_name": "Heeya Maity", + "author_inst": "Public Health Foundation of India" + }, + { + "author_name": "Smritima Lama", + "author_inst": "Public Health Foundation of India" + }, + { + "author_name": "Amanda J. Mason-Jones", + "author_inst": "University of York Department of Health Sciences" + }, + { + "author_name": "Deepak Kumar", + "author_inst": "Ministry of Health and Family Welfare: Government of India" + }, + { + "author_name": "Prairna Koul", + "author_inst": "Ministry of Health and Family Welfare: Government of India" + }, + { + "author_name": "Shalini Bassi", + "author_inst": "Public Health Foundation of India" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.03.31.22273236", "rel_title": "The impact of COVID-19 pandemic on influenza surveillance: a systematic review and meta-analysis", @@ -322883,153 +325087,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.04.01.486719", - "rel_title": "Potent Human Broadly SARS-CoV-2 Neutralizing IgA and IgG Antibodies Effective Against Omicron BA.1 and BA.2", - "rel_date": "2022-04-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.01.486719", - "rel_abs": "Memory B-cell and antibody responses to the SARS-CoV-2 spike protein contribute to long-term immune protection against severe COVID-19, which can also be prevented by antibody-based interventions. Here, wide SARS-CoV-2 immunoprofiling in COVID-19 convalescents combining serological, cellular and monoclonal antibody explorations, revealed humoral immunity coordination. Detailed characterization of a hundred SARS-CoV-2 spike memory B-cell monoclonal antibodies uncovered diversity in their repertoire and antiviral functions. The latter were influenced by the targeted spike region with strong Fc-dependent effectors to the S2 subunit and potent neutralizers to the receptor binding domain. Amongst those, Cv2.1169 and Cv2.3194 antibodies cross-neutralized SARS-CoV-2 variants of concern including Omicron BA.1 and BA.2. Cv2.1169, isolated from a mucosa-derived IgA memory B cell, demonstrated potency boost as IgA dimers and therapeutic efficacy as IgG antibodies in animal models. Structural data provided mechanistic clues to Cv2.1169 potency and breadth. Thus, potent broadly neutralizing IgA antibodies elicited in mucosal tissues can stem SARS-CoV-2 infection, and Cv2.1169 and Cv2.3194 are prime candidates for COVID-19 prevention and treatment.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Cyril Planchais", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Ignacio Fern\u00e1ndez", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Timoth\u00e9e Bruel", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Guilherme Dias de Melo", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Matthieu Prot", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Maxime Beretta", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Pablo Guardado-Calvo", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "J\u00e9r\u00e9my Dufloo", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Luis M. Molinos-Albert", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Marija Backovic", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Jeanne Chiaravalli", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Emilie Giraud", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Benjamin Vesin", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Laurine Conquet", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Ludivine Grzelak", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Delphine Planas", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Isabelle Staropoli", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Florence Guivel-Benhassine", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Mika\u00ebl Boull\u00e9", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Minerva Cervantes-Gonzalez", - "author_inst": "Assistance Publique-H\u00f4pitaux de Paris, Bichat Claude Bernard University Hospital" - }, - { - "author_name": "- French COVID Cohort Study Group", - "author_inst": "-" - }, - { - "author_name": "- CORSER Study Group", - "author_inst": "-" - }, - { - "author_name": "Marie-No\u00eblle Ungeheuer", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Pierre Charneau", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Sylvie van der Werf", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Fabrice Agou", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Jordan D. Dimitrov", - "author_inst": "Centre de Recherche des Cordeliers" - }, - { - "author_name": "Etienne Simon-Lori\u00e8re", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Herv\u00e9 Bourhy", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Xavier Montagutelli", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "F\u00e9lix A. Rey", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Olivier Schwartz", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Hugo Mouquet", - "author_inst": "Institut Pasteur" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.03.31.486561", "rel_title": "Convergence of immune escape strategies highlights plasticity of SARS-CoV-2 spike", @@ -323786,6 +325843,157 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2022.03.31.22273221", + "rel_title": "Immunogenicity and reactogenicity of SARS-CoV-2 vaccines in people living with HIV: a nationwide prospective cohort study in the Netherlands", + "rel_date": "2022-03-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.31.22273221", + "rel_abs": "BackgroundVaccines can be less immunogenic in people living with HIV (PLWH), but for SARS-CoV-2 vaccinations this is unknown.\n\nMethods and FindingsA prospective cohort study to examine the immunogenicity of BNT162b2, mRNA-1273, ChAdOx1-S and Ad26.COV2.S vaccines in adult PLWH, without prior COVID-19, compared to HIV-negative controls. The primary endpoint was the anti-spike SARS-CoV-2 IgG response after mRNA vaccination. Secondary endpoints included the serological response after vector vaccination, anti-SARS-CoV-2 T-cell response and reactogenicity.\n\nBetween February-September 2021, 1154 PLWH (median age 53 [IQR 44-60], 86% male) and 440 controls (median age 43 [IQR 33-53], 29% male) were included. 884 PLWH received BNT162b2, 100 mRNA-1273, 150 ChAdOx1-S, and 20 Ad26.COV2.S. 99% were on antiretroviral therapy, 98% virally suppressed, and the median CD4+T-cell count was 710 cells/{micro}L [IQR 520-913]. 247 controls received mRNA-1273, 94 BNT162b2, 26 ChAdOx1-S and 73 Ad26.COV2.S. After mRNA vaccination, geometric mean concentration was 1418 BAU/mL in PLWH (95%CI 1322-1523), and after adjustment for age, sex, and vaccine type, HIV-status remained associated with a decreased response (0.607, 95%CI 0.508-0.725). In PLWH vaccinated with mRNA-based vaccines, higher antibody responses were predicted by CD4+T-cell counts 250-500 cells/{micro}L (2.845, 95%CI 1.876-4.314) or >500 cells/{micro}L (2.936, 95%CI 1.961-4.394), whilst a viral load >50 copies/mL was associated with a reduced response (0.454, 95%CI 0.286-0.720). Increased IFN-{gamma}, CD4+, and CD8+T-cell responses were observed after stimulation with SARS-CoV-2 spike peptides in ELISpot and activation induced marker assays, comparable to controls. Reactogenicity was generally mild without vaccine-related SAE.\n\nConclusionAfter vaccination with BNT162b2 or mRNA-1273, anti-spike SARS-CoV-2 antibody levels were reduced in PLWH. To reach and maintain the same serological responses and vaccine efficacy as HIV-negative controls, additional vaccinations are probably required.", + "rel_num_authors": 34, + "rel_authors": [ + { + "author_name": "Kathryn Sietske Hensley", + "author_inst": "Erasmus Medical Centre: Erasmus MC" + }, + { + "author_name": "Marlou J. Jongkees", + "author_inst": "Erasmus Medical Centre: Erasmus MC" + }, + { + "author_name": "Daryl Geers", + "author_inst": "Erasmus Medical Centre: Erasmus MC" + }, + { + "author_name": "Corine H. GeurtsvanKessel", + "author_inst": "Erasmus Medical Centre: Erasmus MC" + }, + { + "author_name": "Yvonne M. Mueller", + "author_inst": "Erasmus Medical Centre: Erasmus MC" + }, + { + "author_name": "Virgil A.S.H. Dalm", + "author_inst": "Erasmus Medical Centre: Erasmus MC" + }, + { + "author_name": "Grigorios Papageorgiou", + "author_inst": "Erasmus Medical Centre: Erasmus MC" + }, + { + "author_name": "Hanka Steggink", + "author_inst": "Onze Lieve Vrouwe Hospital: OLVG" + }, + { + "author_name": "Alicja Gorska", + "author_inst": "Erasmus Medical Centre: Erasmus MC" + }, + { + "author_name": "Susanne Bogers", + "author_inst": "Erasmus Medical Centre: Erasmus MC" + }, + { + "author_name": "Jan G. den Hollander", + "author_inst": "Maasstad Hospital: Maasstad Ziekenhuis" + }, + { + "author_name": "Wouter F.W. Bierman", + "author_inst": "University of Groningen: Rijksuniversiteit Groningen" + }, + { + "author_name": "Luc B.S. Gelinck", + "author_inst": "Medical Centre Haaglanden: Medisch Centrum Haaglanden" + }, + { + "author_name": "Emile F. Schippers", + "author_inst": "Haga Hospital: HagaZiekenhuis" + }, + { + "author_name": "Heidi S.M. Ammerlaan", + "author_inst": "Catharina Hospital: Catharina Ziekenhuis" + }, + { + "author_name": "Marc van der Valk", + "author_inst": "Amsterdam UMC -AMC Campus: Amsterdam UMC Locatie AMC" + }, + { + "author_name": "Marit G.A. van Vonderen", + "author_inst": "Medical Centre Leeuwarden: Medisch Centrum Leeuwarden" + }, + { + "author_name": "Corine E. Delsing", + "author_inst": "Medisch Spectrum Twente" + }, + { + "author_name": "Elisabeth H. Gisolf", + "author_inst": "Rijnstate Hospital: Rijnstate" + }, + { + "author_name": "Anke H.W. Bruns", + "author_inst": "UMC Utrecht: Universitair Medisch Centrum Utrecht" + }, + { + "author_name": "Fanny N. Lauw", + "author_inst": "Jan van Goyen Medical Centre" + }, + { + "author_name": "Marvin A.H. Berrevoets", + "author_inst": "Elisabeth-TweeSteden Ziekenhuis" + }, + { + "author_name": "Kim C.E. Sigaloff", + "author_inst": "Amsterdam UMC VUMC Site: Amsterdam UMC Locatie VUmc" + }, + { + "author_name": "Robert Soetekouw", + "author_inst": "Spaarne Hospital: Spaarne Gasthuis Hoofddorp" + }, + { + "author_name": "Judith Branger", + "author_inst": "Flevo Hospital: Flevoziekenhuis" + }, + { + "author_name": "Quirijn de Mast", + "author_inst": "University Medical Center Nijmegen: Radboudumc" + }, + { + "author_name": "Adriana J.J. Lammers", + "author_inst": "Isala Hospital: Isala" + }, + { + "author_name": "Selwyn H. Lowe", + "author_inst": "Maastricht University Hospital: Maastricht Universitair Medisch Centrum+" + }, + { + "author_name": "Rory D. de Vries", + "author_inst": "Erasmus Medical Centre: Erasmus MC" + }, + { + "author_name": "Peter D. Katsikis", + "author_inst": "Erasmus Medical Centre: Erasmus MC" + }, + { + "author_name": "Bart J.A. Rijnders", + "author_inst": "Erasmus Medical Centre: Erasmus MC" + }, + { + "author_name": "Kees Brinkman", + "author_inst": "Onze Lieve Vrouwe Hospital: OLVG" + }, + { + "author_name": "Anna H.E. Roukens", + "author_inst": "Leiden University Medical Center: Leids Universitair Medisch Centrum" + }, + { + "author_name": "Casper Rokx", + "author_inst": "Erasmus Medical Centre: Erasmus MC" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "hiv aids" + }, { "rel_doi": "10.1101/2022.03.28.22273010", "rel_title": "A 21L/BA.2-21K/BA.1 MixOmicron SARS-CoV-2 hybrid undetected by qPCR that screen for variant in routine diagnosis", @@ -325009,57 +327217,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2022.03.29.22273086", - "rel_title": "Age and product dependent vaccine effectiveness against SARS-CoV-2 infection and hospitalisation among adults in Norway: a national cohort study, July - November 2021.", - "rel_date": "2022-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.29.22273086", - "rel_abs": "BackgroundCOVID-19 vaccines have been crucial in the pandemic response and understanding changes in vaccines effectiveness is essential to guide vaccine policies. Though the Delta variant is no longer dominant, understanding vaccines effectiveness properties will provide essential knowledge to comprehend the development of the pandemic and estimate potential changes over time.\n\nMethodsIn this population-based cohort study, we estimated vaccine effectiveness against SARS-CoV-2 infections, hospitalisations, intensive care admissions, and death using Cox proportional hazard models, across different vaccine product regimens and age groups, between 15 July and 31 November 2021 (Delta variant period). Vaccine status is included as a time-varying covariate and all models were adjusted for age, sex, comorbidities, county of residence, country of birth, and living conditions. Data from the entire adult Norwegian population were collated from the National Preparedness Register for COVID-19 (Beredt C19).\n\nResultsThe overall adjusted vaccine effectiveness against infection decreased from 81.3% (confidence interval (CI): 80.7 to 81.9) in the first two to nine weeks after receiving a second dose to 8.6% (CI:4.0 to 13.1) after more than 33 weeks, compared to 98.6% (CI: 97.5 to 99.2) and 66.6% (CI: 57.9 to 73.6) against hospitalisation respectively. After the third dose (booster), the effectiveness was 75.9% (CI: 73.4 to 78.1) against infection and 95.0% (CI: 92.6 to 96.6) against hospitalisation. Spikevax or a combination of mRNA products provided the highest protection, but the vaccine effectiveness decreased with time since vaccination for all vaccine regimens.\n\nConclusionsEven though the vaccine effectiveness against infection wanes over time, all vaccine regimens remained effective against hospitalisation after the second vaccine dose. For all vaccine regimens, a booster facilitated recovery of effectiveness. The results from this support the use of heterologous schedules, increasing flexibility in vaccination policy.\n\nFundingno external funding", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Jostein Starrfelt", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Anders Skyrud Danielsen", - "author_inst": "Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway and Department of Microbiology, Oslo University Hospital" - }, - { - "author_name": "Eirik Alnes Buanes", - "author_inst": "Norwegian Intensive Care and Pandemic Registry (NIPaR), Helse Bergen Health Trust, Bergen, Norway and Department of Anaesthesiology and Intensive Care Haukeland" - }, - { - "author_name": "Lene Kristine Juvet", - "author_inst": "Department of Infection Control and Vaccines, Norwegian Institute of Public Health, Oslo, Norway" - }, - { - "author_name": "Trude Marie Lyngstad", - "author_inst": "Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway" - }, - { - "author_name": "Gunnar Oeyvind Isaksson Roe", - "author_inst": "Department of Development and Analytics, Norwegian Institute of Public Health, Oslo, Norway" - }, - { - "author_name": "Lamprini Veneti", - "author_inst": "Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway" - }, - { - "author_name": "Sara Viksmoen Watle", - "author_inst": "Department of Infection Control and Vaccines, Norwegian Institute of Public Health, Oslo, Norway" - }, - { - "author_name": "Hinta Meijerink", - "author_inst": "Department of Infection Control and Vaccines, Norwegian Institute of Public Health, Oslo, Norway" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.03.25.22272954", "rel_title": "Psychosocial factors affecting COVID-19 vaccine uptake in the UK: a prospective cohort study (CoVAccS - wave 3)", @@ -326452,6 +328609,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.03.29.22273146", + "rel_title": "Endemicity is not a victory: the unmitigated downside risks of widespread SARS-CoV-2 transmission", + "rel_date": "2022-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.29.22273146", + "rel_abs": "We have entered a new phase of the ongoing COVID-19 pandemic, as the strategy of relying solely on the current SARS-CoV-2 vaccines to bring the pandemic to an end has become infeasible. In response, public-health authorities in many countries have advocated for a strategy of using the vaccines to limit morbidity and mortality while permitting unchecked SARS-CoV-2 spread (\"learning to live with the disease\"). The feasibility of this strategy is critically dependent on the infection fatality rate (IFR) of COVID-19. An expectation exists, both in the lay public and in the scientific community, that future waves of the virus will exhibit decreased IFR, either due to viral attenuation or the progressive buildup of immunity. In this work, we examine the basis for that expectation, assessing the impact of virulence on transmission. Our findings suggest that large increases in virulence for SARS-CoV-2 would result in minimal loss of transmission, implying that the IFR may be free to increase or decrease under neutral evolutionary drift. We further examine the effect of changes in the IFR on the steady-state death toll under conditions of endemic COVID-19. Our modeling suggests that endemic SARS-CoV-2 implies vast transmission resulting in yearly US COVID-19 death tolls numbering in the hundreds of thousands under many plausible scenarios, with even modest increases in the IFR leading to an unsustainable mortality burden. Our findings thus highlight the critical importance of enacting a concerted strategy (involving for example global access to vaccines, therapeutics, prophylactics and nonpharmaceutical interventions) to suppress SARS-CoV-2 transmission, thereby reducing the risk of catastrophic outcomes. Our findings also highlight the importance of continued investment in novel biomedical interventions to prevent viral transmission.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Madison Stoddard", + "author_inst": "Fractal Therapeutics" + }, + { + "author_name": "Alexander Novokhodko", + "author_inst": "University of Washington" + }, + { + "author_name": "Sharanya Sarkar", + "author_inst": "Dartmouth College" + }, + { + "author_name": "Debra Van Egeren", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Laura F White", + "author_inst": "Boston University" + }, + { + "author_name": "Natasha S Hochberg", + "author_inst": "Boston University" + }, + { + "author_name": "Michael Rogers", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Bruce Zetter", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Diane Joseph-McCarthy", + "author_inst": "Boston University" + }, + { + "author_name": "Arijit Chakravarty", + "author_inst": "Fractal Therapeutics" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.03.28.22273027", "rel_title": "Unravelling the link between sleep and mental health during the COVID-19 pandemic", @@ -327739,69 +329951,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.03.24.485633", - "rel_title": "Neutralization of Omicron BA.1, BA.2, and BA.3 SARS-CoV-2 by 3 doses of BNT162b2 vaccine", - "rel_date": "2022-03-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.24.485633", - "rel_abs": "The newly emerged Omicron SARS-CoV-2 has 3 distinct sublineages: BA.1, BA.2, and BA.3. BA.1 accounts for the initial surge and is being replaced by BA.2, whereas BA.3 is at a low prevalence at this time. Here we report the neutralization of BNT162b2-vaccinated sera (collected at 1 month after dose 3) against the three Omicron sublineages. To facilitate the neutralization testing, we engineered the complete BA.1, BA.2, or BA.3 spike into an mNeonGreen USA-WA1/2020 SRAS-CoV-2. All BNT162b2-vaccinated sera neutralized USA-WA1/2020, BA.1-, BA.2-, and BA.3-spike SARS-CoV-2s with titers of >20; the neutralization geometric mean titers (GMTs) against the four viruses were 1211, 336, 300, and 190, respectively. Thus, the BA.1-, BA.2-, and BA.3-spike SARS-CoV-2s were 3.6-, 4.0-, and 6.4-fold less efficiently neutralized than the USA-WA1/2020, respectively. Our data have implications in vaccine strategy and understanding the biology of Omicron sublineages.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Chaitanya Kurhade", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "jing Zou", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Hongjing Xia", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Hui Cai", - "author_inst": "Pfizer Vaccines Research & Development" - }, - { - "author_name": "Qi Yang", - "author_inst": "Pfizer Vaccines Research & Development" - }, - { - "author_name": "Mark W Cutler", - "author_inst": "Pfizer Vaccines Research & Development" - }, - { - "author_name": "David Cooper", - "author_inst": "Pfizer Vaccines Research & Development" - }, - { - "author_name": "Alexander Muik", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Kathrin Jansen", - "author_inst": "Pfizer Vaccines Research & Development" - }, - { - "author_name": "Xuping Xie", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Kena Swanson", - "author_inst": "Pfizer Vaccines Research & Development" - }, - { - "author_name": "Pei-Yong Shi", - "author_inst": "University of Texas Medical Branch" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.03.27.485958", "rel_title": "Genetically engineered MRI-trackable extracellular vesicles as SARS-CoV-2 mimetics for mapping ACE2 binding in vivo", @@ -328854,6 +331003,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.26.22272766", + "rel_title": "Analysis of humoral immunity against emerging SARS-CoV-2 variants: a population-based prevalence study in Yokohama, Japan", + "rel_date": "2022-03-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.26.22272766", + "rel_abs": "BackgroundLittle is known about the population prevalence of antibodies against emerging immune escape variants of SARS-CoV-2.\n\nMethodsA population-based prevalence study was conducted in Yokohama City, the most populous municipality of Japan. Quantitative measurements of immunoglobulin G against SARS-CoV-2 spike protein (SP-IgG) and qualitative measurements of neutralization antibodies against the Omicron BA.1 and BA.2 variants were performed.\n\nResultsOf 6,000 randomly selected residents aged 20-74, 1,277 participated in the study during a period from January 30 to February 28, 2022. Of them, 3% had prior diagnosis of COVID-19, 96% received at least two-doses of SARS-CoV-2 vaccines, and 94% were positive for SP-IgG. The positive rates of neutralizing antibodies were 28% to Omicron BA.1 and BA.2 variants in a random sample of 10% of participants (n=123) and 100% to BA.1 and BA.2 among participants who received the third vaccination at least 7 days before (n=66).\n\nConclusionsIn this population-based prevalence study in Japan, most had SP-IgG antibodies but the overall neutralizing antibody positive rate was 28% against the Omicron BA.1 and BA.2 variants. The population-level insufficient humoral immunity against the Omicron variants may explain the outbreak of COVID-19 during this period in Japan.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Atsushi Goto", + "author_inst": "Yokohama City University" + }, + { + "author_name": "Kei Miyakawa", + "author_inst": "Yokohama City University" + }, + { + "author_name": "Izumi Nakayama", + "author_inst": "Yokohama City University" + }, + { + "author_name": "Susumu Yagome", + "author_inst": "Yokohama City University" + }, + { + "author_name": "Juan Xu", + "author_inst": "Yokohama City University" + }, + { + "author_name": "Makoto Kaneko", + "author_inst": "Yokohama City University" + }, + { + "author_name": "Norihisa Ohtake", + "author_inst": "Tosoh Corporation" + }, + { + "author_name": "Hideaki Kato", + "author_inst": "Yokohama City University" + }, + { + "author_name": "Akihide Ryo", + "author_inst": "Yokohama City University School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.26.22272984", "rel_title": "Monitoring of the SARS-CoV-2 Omicron BA.1/BA.2 variant transition in the Swedish population reveals higher viral quantity in BA.2 cases", @@ -329973,49 +332173,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.24.22272919", - "rel_title": "Vaccine Effectiveness Against Hospitalization Among Adolescent and Pediatric SARS-CoV-2 Cases in Ontario, Canada", - "rel_date": "2022-03-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.24.22272919", - "rel_abs": "BackgroundVaccines against SARS-CoV-2 have been shown to reduce risk of infection, as well as severe disease among those with breakthrough infection, in adults. The latter effect is particularly important as Immune evasion by Omicron variants appears to have made vaccines less effective for prevention of infection. There is currently little available information on the protection conferred by vaccination against severe illness due to SARS-CoV-2 in children.\n\nMethodsTo minimize confounding by changing vaccination practices and dominant circulating viral variants, we performed an age- and time-matched nested case-control design. Reported SARS-CoV-2 case records in Ontario children and adolescents aged 4 to 17 were linked to vaccination records. We used multivariable logistic regression to estimate the effectiveness of one and two vaccine doses against hospitalization.\n\nResultsWe identified 130 hospitalized SARS-CoV-2 cases and 1,300 non-hospitalized, age- and time-matched controls, with disease onset between May 28, 2021 and January 9, 2022. One vaccine dose was shown to be 34% effective against hospitalization among SARS-CoV-2 cases (aOR = 0.66 [95% CI: 0.34, 1.21]). In contrast, two doses were 56% (aOR = 0.44 [95% CI: 0.23, 0.83]) effective at preventing hospitalization among SARS-CoV-2 cases. Exploratory instrumental variable analyses, and calculation of E-values, suggested that these effects are unlikely to be explained by unmeasured confounding.\n\nConclusionsEven with immune evasion by SARS-CoV-2 variants, two vaccine doses continue to provide protection against hospitalization among adolescent and pediatric SARS-CoV-2 cases, even when the vaccines do not prevent infection.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Alison E. Simmons", - "author_inst": "University of Toronto" - }, - { - "author_name": "Afia Amoako", - "author_inst": "University of Toronto" - }, - { - "author_name": "Alicia Grima", - "author_inst": "University of Toronto" - }, - { - "author_name": "Kiera Murison", - "author_inst": "University of Toronto" - }, - { - "author_name": "Sarah A Buchan", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Ashleigh Tuite", - "author_inst": "University of Toronto" - }, - { - "author_name": "David Fisman", - "author_inst": "University of Toronto" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.24.22272901", "rel_title": "Impact of Vaccination, Prior Infection, and Therapy on Delta and Omicron Variants", @@ -330492,6 +332649,33 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2022.03.25.485748", + "rel_title": "Changes of urinary proteomic before and after QIV and COVID-19 vaccination", + "rel_date": "2022-03-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.25.485748", + "rel_abs": "We first collected a young peoples urine samples cohort of quadrivalent influenza vaccine. Urine protein at 24 hours after vaccination was enriched in immune-related pathways, though the specific pathways varied. Perhaps because different people may be in a previous life encountered some of the viruses in the vaccine, the second immunization was triggered. Or everyone has a different constitution, exposure to the same virus triggering different immunity. We then collected urine samples from several uninfected SARS-CoV-2 young people before and after the first, second, and third doses of the COVID-19 vaccine. We found that the differential protein compared between after the second dose (24h) and before the second dose enriched pathways were involved in regulated exocytosis and immune-related pathways, indicating not first exposure to antigen. Surprisingly, the urine differential protein-enriched pathways before and after the first dose were similar to those before and after the second dose. We assume that although the volunteers have not been infected with SARS-CoV-2, they might have been exposed to other coimmunogenic coronaviruses. 2~4h after the third vaccination, the differentially expressed protein also enriched regulated exocytosis and immune-related pathways, indicating that the body has triggered the immune response in a very short time after vaccination, and urine proteome is a good window to monitor the changes of human immune function.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Xuanzhen Pan", + "author_inst": "Beijing Normal University" + }, + { + "author_name": "Youhe Gao", + "author_inst": "Beijing Normal University" + }, + { + "author_name": "Yongtao Liu", + "author_inst": "Beijing normal university" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2022.03.24.485649", "rel_title": "B cell receptor repertoire analysis unveils dynamic antibody response and severity markers in COVID-19 patients", @@ -331431,77 +333615,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.03.21.22270828", - "rel_title": "Home Care Follow up determine the point of inversion of IL-6 levels in relation to C-Reactive Protein as the cytokine storm marker in COVID-19", - "rel_date": "2022-03-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.21.22270828", - "rel_abs": "The IL-6 has been used for the characterization of the cytokine storm induced by SARS-CoV-2, but so far, no one has found out when and in whom the cytokine storm develops. Our study demonstrates how early and longitudinal clinical-based monitoring and dosing of five markers (C-reactive protein, IL-6, fibrinogen, ferritin and D-dimer) helped to identify whod developed the cytokine storm. The peak of IL-6 in pg/mL proportionally higher than the peak of CRP in mg/L was sufficient to define the timing of the evolution of cytokine storm syndrome. The administration of antibiotic therapy, anticoagulant therapy and pulse therapy resolved the infection and prevented the progressive deterioration of the lung function of the patients with potential for development of severe COVID-19.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Sergio PM Mendes-Filho Sr.", - "author_inst": "Secretaria Estadual da Saude Estado de Rondonia" - }, - { - "author_name": "Fernanda S Martins", - "author_inst": "Secretaria Estadual da Saude Estado de Rondonia" - }, - { - "author_name": "Paulo J Giroldi", - "author_inst": "Laboratorio Estadual de Patologia e Analises Clinicas (LEPAC)" - }, - { - "author_name": "Raul H Melo", - "author_inst": "Secretaria Estadual da Saude Estado de Rondonia" - }, - { - "author_name": "Edcleia L Oliveira", - "author_inst": "Secretaria Estadual da Saude Estado de Rondonia" - }, - { - "author_name": "Anibal B Santos", - "author_inst": "Secretaria Estadual da Saude Estado de Rondonia" - }, - { - "author_name": "Dayse CO Medeiros", - "author_inst": "Secretaria Estadual da Saude Estado de Rondonia" - }, - { - "author_name": "Sergio A Basano", - "author_inst": "Secretaria Estadual da Saude Estado de Rondonia" - }, - { - "author_name": "Jessica A Lopes", - "author_inst": "FIOCRUZ- Rondonia" - }, - { - "author_name": "Yury O Chaves", - "author_inst": "FIOCRUZ/ILMD" - }, - { - "author_name": "Rebeca S Pinheiro", - "author_inst": "FIOCRUZ/ILMD" - }, - { - "author_name": "Luis MA Camargo", - "author_inst": "ICB5-USP" - }, - { - "author_name": "Juliana P Zuliani", - "author_inst": "FIOCRUZ- Rondonia" - }, - { - "author_name": "Paulo Afonso Nogueira", - "author_inst": "FIOCRUZ/ILMD" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.20.22272651", "rel_title": "Dynamics of anti-SARS-CoV-2 seroconversion in individual patients and at the population level", @@ -332238,6 +334351,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.21.22272669", + "rel_title": "Pre-exposure prophylaxis with Evusheld\u2122 elicits limited neutralizing activity against the omicron variant in kidney transplant patients", + "rel_date": "2022-03-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.21.22272669", + "rel_abs": "The combination of cilgavimab-tixagevimab (Evusheld, Astra Zeneca) became the mainstay for protecting transplant recipients with poor response to vaccination against the omicron variant. Serum neutralizing capacity against SARS-CoV-2 is positively associated with protection against severe forms of Covid-19.\n\nBoth anti-RBD IgG titers and neutralizing antibody titers against the omicron BA.1 variant were measured in serum samples collected from 63 adult kidney transplant recipients who received prophylactic injections of Evusheld. Patients who received prophylactic Ronapreve (casirivimab-imdevimab, n = 39) and those who were infected with SARS-CoV-2 during the fifth wave of the pandemic (n = 14) served as negative and positive controls, respectively.\n\nAfter a median interval from injection of 29 days (interquartile range 29-33 days), only 9.5% of patients who received Evusheld were able to neutralize the omicron variant compared to 71% of patients who were infected with SARS-CoV-2 and 2.6% of those who received Ronapreve. Interestingly, convalescent patients displayed higher levels of neutralizing antibodies than those who received EvusheldTM (median: 2.3 log IC50, IQR: 1.5-2.7 versus 0.00 log IC50, IQR: 0&[ndash] 0.05; p<0.001). A high interindividual variability in anti-RBD IgG titers was observed after Evusheld (range: 262-7032 BAU/mL). This variability was largely explained by the patientsbody mass index, which showed an inverse correlation with anti-RBD IgG titers.\n\nThese findings suggest that Evusheld given at a dose of 300 mg is not sufficient to elicit an anti-RDB titer that confers in vivo neutralizing activity and support recent FDA recommendations, derived from in vitro models, regarding the need to increase the dose of Evusheld", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Ilies Benotmane", + "author_inst": "Hopitaux universitaires de Strasbourg" + }, + { + "author_name": "Aur\u00e9lie Velay", + "author_inst": "Hopitaux Universitaires de Strasbourg" + }, + { + "author_name": "Olivier Thaunant", + "author_inst": "Hospices Civils de Lyon" + }, + { + "author_name": "Gabriela Gautier-Vargas", + "author_inst": "Hopitaux Universitaires de Strasbourg" + }, + { + "author_name": "J\u00e9r\u00f4me Olagne", + "author_inst": "Hopitaux Universitaires de Strasbourg" + }, + { + "author_name": "Samira Fafi-Kremer", + "author_inst": "Hopitaux Universitaires de Strasbourg" + }, + { + "author_name": "Sophie Caillard", + "author_inst": "Hopitaux Universitaires de Strasbourg" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.22.485413", "rel_title": "A CNN model for predicting binding affinity changes between SARS-CoV-2 spike RBD variants and ACE2 homologues", @@ -333533,41 +335689,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.03.21.22272728", - "rel_title": "Where the truth really lies: Listening to voices from African American communities in the Southern States about COVID-19 vaccine information and communication", - "rel_date": "2022-03-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.21.22272728", - "rel_abs": "BackgroundHigh uptake of COVID-19 vaccine is one of the most promising measures to control the pandemic. However, some African American (AA) communities exhibit vaccination hesitancy due to mis-or dis-information. It is important to understand the challenges in accessing reliable COVID-19 vaccine information and to develop feasible health communication interventions based on voices from AA communities.\n\nMethodsWe conducted two focus group discussions (FGDs) among 18 community leaders recruited from three counties in South Carolina on October 8 and October 29, 2021. The FGDs were conducted online via Zoom meetings. The FGD data were managed and thematically analyzed using QSR NVivo 12 software.\n\nResultsParticipants (73% female and 61% between the ages of 18 and 30) worked primarily in colleges (55.5%), churches (39%), and health agencies (5.5%). We found that challenges of accessing reliable COVID-19 vaccine information in AA communities primarily included structural barriers, information barriers, and lack of trust. Community leaders recommended recruiting trusted messengers, using homecoming events, football games, and other social events to reach target populations and conducting health communication campaigns through open dialogue among stakeholders.\n\nConclusionHealth communication interventions on COVID-19 vaccine uptake should be grounded in ongoing community engagement, trust-building activities, and transparent communication about vaccine development. Tailoring health communication interventions to different groups may help reduce misinformation spread and thus promote vaccination in AA communities in the Southern States.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Ran Zhang", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Shan Qiao", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Brooke Mckeever", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Bankole Olatosi", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Xiaoming Li", - "author_inst": "University of South Carolina" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.22.22272769", "rel_title": "Vaccine effectiveness of two and three doses of BNT162b2 and CoronaVac against COVID-19 in Hong Kong", @@ -334380,6 +336501,73 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.03.21.485243", + "rel_title": "A potent SARS-CoV-2 antibody neutralizes Omicron variant by disassembling the spike trimer", + "rel_date": "2022-03-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.21.485243", + "rel_abs": "The continuous emergence of novel SARS-CoV-2 variants poses new challenges to the fight against the COVID-19 pandemic. The newly emerging Omicron strain caused serious immune escape and raised unprecedented concern all over the world. The development of antibody targeting conserved and universal epitope is urgently needed. A subset neutralizing antibody(nAbs) against COVID-19 from convalescent patients were isolated in our previous study. Here in this study, we investigated the accommodation of these nAbs to SARS-CoV-2 variants of concerns (VOCs), revealing that IgG 553-49 neutralizes pseudovirus of SARS-CoV-2 Omicron variant. In addition, we determined the cryo-EM structure of SARS-CoV-2 spike complexed with three antibodies targeting different epitopes, including 553-49, 553-15 and 553-60. Notably, 553-49 targets a novel conserved epitope and neutralizes virus by disassembling spike trimers. 553-15, an antibody that neutralizes all the other VOCs except omicron, cross-links two spike trimers to form trimer dimer, demonstrating that 553-15 neutralizes virus by steric hindrance and virion aggregation. These findings suggest the potential to develop 49 and other antibody targeting this highly conserved epitope as promising cocktail therapeutics reagent for COVID-19.\n\nImportanceThe newly emergence of Omicron strain caused higher immune escape, raising unprecedented concerns about the effectiveness of antibody therapies and vaccines. In this study, we identified a SARS-CoV-2 Omicron neutralizing antibody 553-49, which neutralizes Omicron variant by targeting a completely conserved novel epitope. Besides, we revealed that IgG 553-15 neutralizes SARS-CoV-2 by crosslinking virions and 553-60 functions by blocking receptor binding. Comparison of different RBD epitopes revealed that the epitope of 553-49 is hidden in the S trimer and keeps high conservation during SARS-CoV-2 evolution, making 553-49 a promising therapeutics reagent to fight against the emerging Omicron and future variant of SARS-CoV-2.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Lei Sun", + "author_inst": "Fudan University" + }, + { + "author_name": "Wuqiang Zhan", + "author_inst": "Institutes of Biomedical Sciences, Fudan University" + }, + { + "author_name": "Xiaolong Tian", + "author_inst": "Shanghai Institute of Infectious Disease and Biosecurity, Fudan University" + }, + { + "author_name": "Xiang Zhang", + "author_inst": "Institutes of Biomedical Sciences, Fudan University" + }, + { + "author_name": "Shenghui Xing", + "author_inst": "Shanghai Key Laboratory of Medical Epigenetics and Institutes of Biomedical Sciences, Fudan University" + }, + { + "author_name": "Wenping Song", + "author_inst": "Shanghai Institute of Infectious Disease and Biosecurity, Fudan University" + }, + { + "author_name": "Qianying Liu", + "author_inst": "Institutes of Biomedical Sciences, Fudan University" + }, + { + "author_name": "Aihua Hao", + "author_inst": "Institutes of Biomedical Sciences, Fudan University" + }, + { + "author_name": "Yuxia Hu", + "author_inst": "Institutes of Biomedical Sciences, Fudan University" + }, + { + "author_name": "Meng Zhang", + "author_inst": "Institutes of Biomedical Sciences, Fudan University" + }, + { + "author_name": "Zhenguo Chen", + "author_inst": "Institutes of Biomedical Sciences, Fudan University" + }, + { + "author_name": "Tianlei Ying", + "author_inst": "School of Basic Medical Sciences" + }, + { + "author_name": "Fei Lan", + "author_inst": "Shanghai Key Laboratory of Medical Epigenetics and Institutes of Biomedical Sciences, Fudan University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.03.19.22272419", "rel_title": "Post- intravitreal injection endophthalmitis pattern during the COVID-19 pandemic with implementation of patient masking", @@ -335507,89 +337695,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.19.22272637", - "rel_title": "Evaluation of the Panbio\u2122 COVID-19 Antigen Rapid Diagnostic Test in subjects infected with Omicron using different specimens", - "rel_date": "2022-03-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.19.22272637", - "rel_abs": "Community testing is a crucial tool for the early identification of SARS-CoV-2 infection and transmission control. The emergence of the highly mutated Omicron variant (B.1.1.259) raised concerns about its primary site of replication, impacting sample collection, and its detectability by rapid antigens tests. We tested the Antigen Rapid Diagnostic Test (Ag-RDT) performance using nasal, oral, and saliva specimens for COVID-19 diagnosis in 192 symptomatic individuals, using RT-qPCR from nasopharyngeal samples as control. Variant of Concern (VOC) investigation was determined by the 4Plex SARS-CoV-2 screening kit. SARS-CoV-2 positivity rate was 66.2%, with 99% of the positive samples showing an amplification profile consistent with that of the Omicron variant. Nasal Ag-RDT showed higher sensitivity (89%) than oral (12.6%) and saliva (22.1%) Ag-RDTs. Our data showed the good performance of the Ag-RDT in a pandemic scenario dominated by the Omicron VOC. Furthermore, our data also demonstrated that nasal specimens perform better than oral and saliva ones for Omicron Ag-RDT detection.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Rafael de Mello Galiez", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "Larissa Maciel Bomfim", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "Diana Mariani", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "Isabela de Carvalho Leitao", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "Anna Carla Pinto Castineiras", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "Cassia Cristina Alves Goncalves", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "Bianca Ortiz da Silva", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "Pedro Henrique Cardoso", - "author_inst": "Oswaldo Cruz Foundation" - }, - { - "author_name": "Monica Barcelos Arruda", - "author_inst": "Oswaldo Cruz Foundation" - }, - { - "author_name": "Patricia Alvarez", - "author_inst": "Oswaldo Cruz Foundation" - }, - { - "author_name": "Victor Akira", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "Debora Gomes Marins Rodrigues", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "Luciana Costa", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "Orlando Costa Ferreira Junior", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "Terezinha Marta Pereira Pinto Castineiras", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "Debora Souza Faffe", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "AMILCAR TANURI", - "author_inst": "Federal University of Rio de Janeiro" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.20.22272676", "rel_title": "The outcome of Gynecologic Cancer Patients With The Covid-19 Infection: A Systematic Review And Meta-Analysis", @@ -336354,6 +338459,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, + { + "rel_doi": "10.1101/2022.03.17.22272557", + "rel_title": "Potency and Breadth of Neutralization after 3 doses of mRNA vaccines in COVID-19 Convalescent and Naive individuals", + "rel_date": "2022-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.17.22272557", + "rel_abs": "Third doses of mRNA COVID-19 vaccines induced a significant increase in neutralizing potency and breadth in naive individuals comparable with convalescents who restored levels after the first two doses. These results suggest a limit to elicit neutralization in the number of stimuli by infection or vaccination with ancestral SARS-CoV-2 sequences", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Joanna Luczkowiak", + "author_inst": "Instituto de Investigacion Hospital 12 de Octubre" + }, + { + "author_name": "Gonzalo Rivas", + "author_inst": "Department of Microbiology Hospital Universitario 12 de Octubre" + }, + { + "author_name": "Nuria Labiod", + "author_inst": "Instituto de Investigacion Hospital 12 de Octubre" + }, + { + "author_name": "Fatima Lasala", + "author_inst": "Instituto de Investigacion Hospital 12 de Octubre" + }, + { + "author_name": "Marta Rolo", + "author_inst": "Department of Microbiology Hospital Universitario 12 de Octubre" + }, + { + "author_name": "Jaime Lora-Tamayo", + "author_inst": "Department of Internal Medicine. Hospital Universitario 12 de Octubre" + }, + { + "author_name": "Mikel Mancheno-Losa", + "author_inst": "Department of Internal Medicine. Hospital Universitario 12 de Octubre" + }, + { + "author_name": "David Rial-Crestelo", + "author_inst": "Department of Internal Medicine. Hospital Universitario 12 de Octubre" + }, + { + "author_name": "Maria D Folgueira", + "author_inst": "Department of Microbiology. Hospital Universitario 12 de Octubre" + }, + { + "author_name": "Rafael Delgado", + "author_inst": "Department of Microbiology Hospital Universitario 12 de Octubre" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.20.485024", "rel_title": "A Novel High-Throughput Single B-Cell Cloning Platform for Isolation and Characterization of High-Affinity and potent SARS-CoV-2 Neutralizing Antibodies", @@ -337521,109 +339681,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.03.17.484787", - "rel_title": "Resilience of S309 and AZD7442 monoclonal antibody treatments against infection by SARS-CoV-2 Omicron lineage strains", - "rel_date": "2022-03-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.17.484787", - "rel_abs": "Omicron variant strains encode large numbers of changes in the spike protein compared to historical SARS-CoV-2 isolates. Although in vitro studies have suggested that several monoclonal antibody therapies lose neutralizing activity against Omicron variants1-4, the effects in vivo remain largely unknown. Here, we report on the protective efficacy against three SARS-CoV-2 Omicron lineage strains (BA.1, BA.1.1, and BA.2) of two monoclonal antibody therapeutics (S309 [Vir Biotechnology] monotherapy and AZD7442 [AstraZeneca] combination), which correspond to ones used to treat or prevent SARS-CoV-2 infections in humans. Despite losses in neutralization potency in cell culture, S309 or AZD7442 treatments reduced BA.1, BA.1.1, and BA.2 lung infection in susceptible mice that express human ACE2 (K18-hACE2). Correlation analyses between in vitro neutralizing activity and reductions in viral burden in K18-hACE2 or human Fc{gamma} R transgenic mice suggest that S309 and AZD7442 have different mechanisms of protection against Omicron variants, with S309 utilizing Fc effector function interactions and AZD7442 acting principally by direct neutralization. Our data in mice demonstrate the resilience of S309 and AZD7442 mAbs against emerging SARS-CoV-2 variant strains and provide insight into the relationship between loss of antibody neutralization potency and retained protection in vivo.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "James Brett Case", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Samantha Mackin", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "John Errico", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Zhenlu Chong", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Emily A. Madden", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Barbara Guarino", - "author_inst": "Humabs BioMed SA" - }, - { - "author_name": "Michael A. Schmid", - "author_inst": "Humabs BioMed SA" - }, - { - "author_name": "Kim Rosenthal", - "author_inst": "AstraZeneca" - }, - { - "author_name": "Kuishu Ren", - "author_inst": "AstraZeneca" - }, - { - "author_name": "Ana Jung", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Lindsay Droit", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Scott A. Handley", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Peter J. Halfmann", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Yoshihiro Kawaoka", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "James E. Crowe Jr.", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Daved H. Fremont", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Herbert W. Virgin", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Yueh-Ming Loo", - "author_inst": "AstraZeneca" - }, - { - "author_name": "Mark T. Esser", - "author_inst": "AstraZeneca" - }, - { - "author_name": "Lisa A. Purcell", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Davide Corti", - "author_inst": "Humabs Biomed SA, subsidiary of Vir Biotechnology" - }, - { - "author_name": "Michael S. Diamond", - "author_inst": "Washington University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.03.17.22272516", "rel_title": "SARS-CoV-2 virus dynamics in recently infected people - data from a household transmission study", @@ -338364,6 +340421,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.17.22272414", + "rel_title": "Modelling the impact of non-pharmaceutical interventions on workplace transmission of SARS-CoV-2 in the home-delivery sector", + "rel_date": "2022-03-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.17.22272414", + "rel_abs": "ObjectiveWe aimed to use mathematical models of SARS-COV-2 to assess the potential efficacy of non-pharmaceutical interventions on transmission in the parcel delivery and logistics sector.\n\nMethodsWe developed a network-based model of workplace contacts based on data and consultations from companies in the parcel delivery and logistics sectors. We used these in stochastic simulations of disease transmission to predict the probability of workplace outbreaks in this settings. Individuals in the model have different viral load trajectories based on SARS-CoV-2 in-host dynamics, which couple to their infectiousness and test positive probability over time, in order to determine the impact of testing and isolation measures.\n\nResultsThe baseline model (without any interventions) showed different workplace infection rates for staff in different job roles. Based on our assumptions of contact patterns in the parcel delivery work setting we found that when a delivery driver was the index case, on average they infect only 0.14 other employees, while for warehouse and office workers this went up to 0.65 and 2.24 respectively. In the LIDD setting this was predicted to be 1.40, 0.98, and 1.34 respectively. Nonetheless, the vast majority of simulations resulted in 0 secondary cases among customers (even without contact-free delivery). Our results showed that a combination of social distancing, office staff working from home, and fixed driver pairings (all interventions carried out by the companies we consulted) reduce the risk of workplace outbreaks by 3-4 times.\n\nConclusionThis work suggests that, without interventions, significant transmission could have occured in these workplaces, but that these posed minimal risk to customers. We found that identifying and isolating regular close-contacts of infectious individuals (i.e. house-share, carpools, or delivery pairs) is an efficient measure for stopping workplace outbreaks. Regular testing can make these isolation measures even more effective but also increases the number of staff isolating at one time. It is therefore more efficient to use these isolation measures in addition to social distancing and contact reduction interventions, rather than instead of, as these reduce both transmission and the number of people needing to isolate at one time.\n\nAuthor summaryDuring the COVID-19 pandemic the home-delivery sector was vital to maintaining peoples access to certain goods, and sustaining levels of economic activity for a variety of businesses. However, this important work necessarily involved contact with a large number of customers as well as colleagues. This means that questions have often been raised about whether enough was being done to keep customers and staff safe. Estimating the potential risk to customers and staff is complex, but here we tackle this problem by building a model of workplace and customer contacts, from which we simulate SARS-CoV-2 transmission. By involving industry representatives in the development of this model, we have simulated interventions that have either been applied or considered, and so the findings of this study are relevant to decisions made in that sector. Furthermore, we can learn generic lessons from this specific case study which apply to many types of shared workplace as well as highlighting implications of the highly stochastic nature of disease transmission in small populations.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Carl A Whitfield", + "author_inst": "University of Manchester" + }, + { + "author_name": "Martie Van Tongeren", + "author_inst": "University of Manchester" + }, + { + "author_name": "Yang Han", + "author_inst": "University of Manchester" + }, + { + "author_name": "Hua Wei", + "author_inst": "University of Manchester" + }, + { + "author_name": "Sarah A Daniels", + "author_inst": "University of Manchester" + }, + { + "author_name": "Martyn Regan", + "author_inst": "University of Manchester" + }, + { + "author_name": "David W Denning", + "author_inst": "University of Manchaster" + }, + { + "author_name": "Arpana Verma", + "author_inst": "University of Manchester" + }, + { + "author_name": "Lorenzo Pellis", + "author_inst": "University of Manchester" + }, + { + "author_name": "- University of Manchester COVID-19 Modelling Group", + "author_inst": "" + }, + { + "author_name": "Ian Hall", + "author_inst": "University of Manchester" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.03.16.22272493", "rel_title": "Outdoor long-range transmission of COVID-19 and patient zero", @@ -339371,65 +341487,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.03.14.22272394", - "rel_title": "Detection of bacterial co-infections and prediction of fatal outcomes in COVID-19 patients presenting to the emergency department using a 29 mRNA host response classifier.", - "rel_date": "2022-03-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.14.22272394", - "rel_abs": "ObjectiveClinicians in the emergency department (ED) face challenges in concurrently assessing patients with suspected COVID-19 infection, detecting bacterial co-infection, and determining illness severity since current practices require separate workflows. Here we explore the accuracy of the IMX-BVN-3/IMX-SEV-3 29 mRNA host response classifiers in simultaneously detecting SARS-CoV-2 infection, bacterial co-infections, and predicting clinical severity of COVID-19.\n\nMethods161 patients with PCR-confirmed COVID-19 (52.2% female, median age 50.0 years, 51% hospitalized, 5.6% deaths) were enrolled at the Stanford Hospital ED. RNA was extracted (2.5 mL whole blood in PAXgene Blood RNA) and 29 host mRNAs in response to the infection were quantified using Nanostring nCounter.\n\nResultsThe IMX-BVN-3 classifier identified SARS-CoV-2 infection in 151 patients with a sensitivity of 93.8%. Six of 10 patients undetected by the classifier had positive COVID tests more than 9 days prior to enrolment and the remaining oscillated between positive and negative results in subsequent tests. The classifier also predicted that 6 (3.7%) patients had a bacterial co-infection. Clinical adjudication confirmed that 5/6 (83.3%) of the patients had bacterial infections, i.e. Clostridioides difficile colitis (n=1), urinary tract infection (n=1), and clinically diagnosed bacterial infections (n=3) for a specificity of 99.4%. 2/101 (2.8%) patients in the IMX-SEV-3 Low and 7/60 (11.7%) in the Moderate severity classifications died within thirty days of enrollment.\n\nConclusionsIMX-BVN-3/IMX-SEV-3 classifiers accurately identified patients with COVID-19, bacterial co-infections, and predicted patients risk of death. A point-of-care version of these classifiers, under development, could improve ED patient management including more accurate treatment decisions and optimized resource utilization.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Nikhil Ram-Mohan", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Angela J Rogers", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Catherine A Blish", - "author_inst": "Stanford University" - }, - { - "author_name": "Kari C Nadeau", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Elizabeth J Zudock", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "David Kim", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "James V Quinn", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Lixian Sun", - "author_inst": "Inflammatix Inc." - }, - { - "author_name": "Oliver Liesenfeld", - "author_inst": "Inflammatix Inc." - }, - { - "author_name": "- the Stanford COVID-19 Biobank Study Group", - "author_inst": "" - }, - { - "author_name": "Samuel Yang", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.16.22272465", "rel_title": "No evidence for environmental transmission risk of SARS-CoV-2 in the UK's largest urban river system: London as a case study", @@ -340138,6 +342195,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.03.14.22272316", + "rel_title": "Prevalence, determinants, and impact on general health and working capacity of post-acute sequelae of COVID-19 six to 12 months after infection: a population-based retrospective cohort study from southern Germany", + "rel_date": "2022-03-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.14.22272316", + "rel_abs": "BackgroundPost-acute sequelae of SARS-CoV-2 infection have commonly been described after COVID-19, but few population-based studies have examined symptoms six to 12 months after acute SARS-CoV-2 infection and their associations with general health recovery and working capacity.\n\nMethodsThis population-based retrospective cohort study in four geographically defined regions in southern Germany included persons aged 18-65 years with PCR confirmed SARS-CoV-2 infection between October 2020 and March 2021. Symptom frequencies (six to 12 months after versus before acute infection, expressed as prevalence differences [PD] and prevalence ratios [PR]), symptom severity and clustering, risk factors and associations with general health recovery, and working capacity were analysed.\n\nFindingsAmong a total of 11 710 subjects (mean age 44{middle dot}1 years, 59{middle dot}8% females, 3{middle dot}5% previously admitted with COVID-19, mean follow-up time 8.5 months) the most prevalent symptoms with PDs >20% and PRs >5% were rapid physical exhaustion, shortness of breath, concentration difficulties, chronic fatigue, memory disturbance, and altered sense of smell. Female sex and severity of the initial infection were the main risk factors. Prevalence rates, however, appeared substantial among both men and women who had a mild course of acute infection, and PCS considerably affected also younger subjects. Fatigue (PD 37{middle dot}2%) and neurocognitive impairment (PD 31{middle dot}3%) as symptom clusters contributed most to reduced health recovery and working capacity, but chest symptoms, anxiety/depression, headache/dizziness and pain syndromes were also prevalent and relevant for working capacity, with some differences according to sex and age. When considering new symptoms with at least moderate impairment of daily life and [≤]80% recovered general health or working capacity, the overall estimate for post-COVID syndrome was 28{middle dot}5% (age- and sex-standardised rate 26{middle dot}5%).\n\nInterpretationThe burden of self-reported post-acute symptoms and possible sequelae, notably fatigue and neurocognitive impairment, remains considerable six to 12 months after acute infection even among young and middle-aged adults after mild acute SARS-CoV-2 infection, and impacts general health and working capacity.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSPrevious studies have shown that post-acute sequelae of COVID-19 are common, in particular among patients who had been admitted to hospital for COVID-19. Post-acute self-reported complaints and symptoms often are diverse, nonspecific and sometimes of unknown severity and functional relevance. We searched PubMed and medRxiv for studies published between January 2021 and February 2022, using search terms describing \"long covid, post-acute sequelae of COVID-19, prevalence, and systematic review\", with no language restrictions. Searches with the terms \"long covid\", \"post-acute sequelae of COVID-19\", \"post-covid condition\" and \"post-covid syndrome\" were also done in PROSPERO, and we screened the website of the UK Office for National Statistics (www.ons.gov.uk) for long covid studies. We found more than 20 systematic reviews summarising post-acute symptom patterns among adults and a prevalence of \"any\" or \"defined\" symptoms (such as respiratory symptoms or symptoms related to mental health) or of medically assessed functional impairment (pulmonary or cardiac or neurocognitive function). Two reviews reported of health-related quality of life assessments. The prevalence of post-acute sequelae of COVID-19 or long covid/post-covid syndromes ranged between <10 to >70%, in part due to lack of uniform and clear case definitions, variable follow-up times, and non-inclusion of outpatients with initially mild disease. Most papers reviewed presented high heterogeneity and had a short follow-up, and there were very few papers estimating the prevalence of post-covid syndrome beyond six months after acute infection. The studies with the largest number of subjects were either including only patients after hospital admission, used online surveys of subjects with self-reported suspected and confirmed COVID-19 or electronic medical records only. We found one (small but) comprehensive population-based study from Switzerland assessing post-covid syndrome prevalence and associations with quality of life and health recovery with a follow-up time ranging from six to 10 months. Two further population-based studies from Switzerland and Norway investigated long covid symptoms among subgroups with [≥]6 months (n=498) and 11 to 12 months (n=170) of follow-up after acute infection, respectively.\n\nAdded value of this studyWith this large population-based study, we provide evidence of persistence of new symptom clusters (not present before acute infection) such as fatigue, neurocognitive impairment, chest symptoms, smell or taste disorder, and anxiety/depression beyond six months after acute infection, with a prevalence of >20% for each of these five clusters. We show that the three most frequent clusters (fatigue, neurocognitive impairment, chest symptoms) are often interfering with daily life and activities, often co-occur, and that both fatigue and neurocognitive impairment have the largest impact on working capacity, while long-term smell and taste disorders are reported relatively independent of other complaints. Age in this 18-65-year old adult population was not a major determinant of symptom prevalence, but we confirm severity of the initial infection and female sex as consistent risk factors for various manifestations of medium-term post-COVID syndrome, and age as risk factor for self-reported reduced working capacity, which overall and at population level exceeded 10%.\n\nImplications of all the available evidenceFuture research should include the medical validation of the key symptom clusters of post-COVID syndrome, determine the possible causes, and urgently address prognostic factors and therapeutic options. The described key symptom clusters contributed most to reduced general health status and working capacity in middle-aged adults. The findings of this study may also help develop a more consistent and relevant definition of post-COVID syndrome with major implications for research and medical practice.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Raphael S. Peter", + "author_inst": "Institute for Epidemiology and Medical Biometry, Ulm University, Ulm, Germany" + }, + { + "author_name": "Alexandra Nieters", + "author_inst": "Institute for Immunodeficiency, Medical Centre and Faculty of Medicine, Albert-Ludwigs-University, Freiburg, Germany" + }, + { + "author_name": "Hans-Georg Kraeusslich", + "author_inst": "Institute of Virology, Department of Infectious Diseases, University Hospital Heidelberg, Heidelberg, Germany" + }, + { + "author_name": "Stefan O. Brockmann", + "author_inst": "Department of Health Protection, Infection Control and Epidemiology, Baden-Wuerttemberg Federal State Health Office, Ministry of Social Affairs, Health and Inte" + }, + { + "author_name": "Siri Goepel", + "author_inst": "Division of Infectious Diseases, Department of Internal Medicine I, University Hospital Tuebingen, Tuebingen, Germany" + }, + { + "author_name": "Gerhard Kindle", + "author_inst": "Institute for Immunodeficiency, Medical Centre and Faculty of Medicine, Albert-Ludwigs-University, Freiburg, Germany" + }, + { + "author_name": "Uta Merle", + "author_inst": "Department of Internal Medicine IV, University Hospital Heidelberg, Heidelberg, Germany" + }, + { + "author_name": "Juergen M. Steinacker", + "author_inst": "Division of Sports and Rehabilitation Medicine, Department of Medicine, Ulm University Hospital, Ulm, Germany" + }, + { + "author_name": "Dietrich Rothenbacher", + "author_inst": "Institute for Epidemiology and Medical Biometry, Ulm University, Ulm, Germany" + }, + { + "author_name": "Winfried V. Kern", + "author_inst": "Division of Infectious Diseases, Department of Medicine II, Medical Centre and Faculty of Medicine, Albert-Ludwigs-University, Freiburg, Germany" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.14.22272130", "rel_title": "Mid-term subclinical myocardial injury detection in patients recovered from COVID-19 according pulmonary lesion severity.", @@ -341141,97 +343253,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2022.03.14.22270915", - "rel_title": "Combined administration of inhaled DNase, baricitinib and tocilizumab as rescue treatment in COVID-19 patients with severe respiratory failure", - "rel_date": "2022-03-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.14.22270915", - "rel_abs": "COVID-19-related severe respiratory failure (SRF) leads to mechanical ventilation increasing the in-hospital mortality substantially. Abundancy of lung fibroblasts (LFs) in injured lung tissue has been associated with the progression of respiratory failure in COVID-19. Aiming to reduce mortality in patients with SRF (PaO2/FiO2<100 mmHg) and considering the multi-mechanistic nature of severe COVID-19 pathogenesis, we applied a combined rescue treatment (COMBI) on top of standard-of-care (SOC: dexamethasone and heparin) comprised inhaled DNase to dissolve thrombogenic neutrophil extracellular traps, plus agents against cytokine-mediated hyperinflammation, such as anti-IL-6 receptor tocilizumab and selective JAK1/2 inhibitor baricitinib. COMBI (n=22) was compared with SOC (n= 26), and with two previously and consecutively used therapeutic approaches, including either IL-1 receptor antagonist anakinra (ANA, n=19), or tocilizumab (TOCI, n=11), on top of SOC. In parallel, evaluation of immunothrombosis was assessed in vitro in human LFs, treated with the applied therapeutic agents upon stimulation with COVID-19 plasma. COMBI was associated with lower in-hospital mortality (p=0.014) and intubation rate (p=0.013), shorter duration of hospitalization (p=0.019), and prolonged overall survival after a median follow-up of 110{+/-}4 days (p=0.003). In vitro, COVID-19 plasma markedly induced tissue factor/thrombin pathway in LFs, while this effect was inhibited by the immunomodulatory agents of COMBI providing a mechanistic explanation for the clinical observations. These results suggest the design of randomized trials using combined immunomodulatory therapies in COVID-19-associated SRF targeting multiple interconnected pathways of immunothrombosis.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Efstratios Gavriilidis", - "author_inst": "Democritus University of Thrace" - }, - { - "author_name": "Christina Antoniadou", - "author_inst": "Democritus University of Thrace" - }, - { - "author_name": "Akrivi Chrysanthopoulou", - "author_inst": "Democritus University of Thrace" - }, - { - "author_name": "Maria Ntinopoulou", - "author_inst": "Democritus University of Thrace" - }, - { - "author_name": "Andreas Smyrlis", - "author_inst": "Democritus University of Thrace" - }, - { - "author_name": "Iliana Fotiadou", - "author_inst": "Democritus University of Thrace" - }, - { - "author_name": "Nikoleta Zioga", - "author_inst": "Democritus University of Thrace" - }, - { - "author_name": "Dionysios Kogias", - "author_inst": "Democritus University of Thrace" - }, - { - "author_name": "Anastasia-Maria Natsi", - "author_inst": "Democritus University of Thrace" - }, - { - "author_name": "Christos Pelekoudas", - "author_inst": "Democritus University of Thrace" - }, - { - "author_name": "Evangelia Satiridou", - "author_inst": "Democritus University of Thrace" - }, - { - "author_name": "Stefania-Aspasia Bakola", - "author_inst": "Democritus University of Thrace" - }, - { - "author_name": "Charalampos Papagoras", - "author_inst": "Democritus University of Thrace" - }, - { - "author_name": "Ioannis Mitroulis", - "author_inst": "Democritus University of Thrace" - }, - { - "author_name": "Paschalis Peichamperis", - "author_inst": "Democritus University of Thrace" - }, - { - "author_name": "Dimitrios Mikroulis", - "author_inst": "Democritus University of Thrace" - }, - { - "author_name": "Vasileios Papadopoulos", - "author_inst": "Democritus University of Thrace" - }, - { - "author_name": "Panagiotis Skendros", - "author_inst": "Democritus University of Thrace" - }, - { - "author_name": "Konstantinos Ritis", - "author_inst": "Democritus University of Thrace" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.15.22272192", "rel_title": "Laboratory changes associated with medication non-adherence in patients with hypertension over six months of the COVID-19 pandemic", @@ -341940,6 +343961,89 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.03.14.484208", + "rel_title": "Parsing the role of NSP1 in SARS-CoV-2 infection", + "rel_date": "2022-03-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.14.484208", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the ongoing coronavirus disease 19 (COVID-19) pandemic. Despite its urgency, we still do not fully understand the molecular basis of SARS-CoV-2 pathogenesis and its ability to antagonize innate immune responses. SARS-CoV-2 leads to shutoff of cellular protein synthesis and over-expression of nsp1, a central shutoff factor in coronaviruses, inhibits cellular gene translation. However, the diverse molecular mechanisms nsp1 employs as well as its functional importance in infection are still unresolved. By overexpressing various nsp1 mutants and generating a SARS-CoV-2 mutant in which nsp1 does not bind ribosomes, we untangle the effects of nsp1. We uncover that nsp1, through inhibition of translation and induction of mRNA degradation, is the main driver of host shutoff during SARS-CoV-2 infection. Furthermore, we find the propagation of nsp1 mutant virus is inhibited specifically in cells with intact interferon (IFN) response as well as in-vivo, in infected hamsters, and this attenuation is associated with stronger induction of type I IFN response. This illustrates that nsp1 shutoff activity has an essential role mainly in counteracting the IFN response. Overall, our results reveal the multifaceted approach nsp1 uses to shut off cellular protein synthesis and uncover the central role it plays in SARS-CoV-2 pathogenesis, explicitly through blockage of the IFN response.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Tal Fisher", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Avi Gluck", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Krishna Narayanan", + "author_inst": "Department of Microbiology and Immunology, The University of Texas" + }, + { + "author_name": "Makoto Kuroda", + "author_inst": "School of Veterinary Medicine, University of Wisconsin" + }, + { + "author_name": "Aharon Nachshon", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Jason C Hsu", + "author_inst": "Department of Microbiology and Immunology, The University of Texas" + }, + { + "author_name": "Peter J Halfmann", + "author_inst": "School of Veterinary Medicine, University of Wisconsin" + }, + { + "author_name": "Yfat Yahalom-Ronen", + "author_inst": "Israel Institute for Biological Research" + }, + { + "author_name": "Yaara Finkel", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Michal Schwartz", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Shay Weiss", + "author_inst": "Israel Institute for Biological Research" + }, + { + "author_name": "Chien-Te K Tseng", + "author_inst": "Department of Microbiology and Immunology, The University of Texas" + }, + { + "author_name": "Tomer Israely", + "author_inst": "Israel Institute for Biological Research" + }, + { + "author_name": "Nir Paran", + "author_inst": "Israel Institute for Biological Research" + }, + { + "author_name": "Yoshihiro Kawaoka", + "author_inst": "School of Veterinary Medicine, University of Wisconsin" + }, + { + "author_name": "Shinji Makino", + "author_inst": "Department of Microbiology and Immunology, The University of Texas" + }, + { + "author_name": "Noam Stern-Ginossar", + "author_inst": "Weizmann Institute of Science" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.03.13.484191", "rel_title": "Molecular docking between human TMPRSS2 and the serine protease Kunitz-type inhibitor rBmTI-A", @@ -342867,45 +344971,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.11.22272140", - "rel_title": "High vaccine effectiveness against severe Covid-19 in the elderly in Finland before and after the emergence of Omicron", - "rel_date": "2022-03-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.11.22272140", - "rel_abs": "BackgroundThe elderly are highly vulnerable to severe Covid-19. Waning immunity and emergence of Omicron have caused concerns about reduced effectiveness of Covid-19 vaccines. The objective was to estimate vaccine effectiveness (VE) against severe Covid-19 among the elderly.\n\nMethodsThis nationwide, register-based cohort analysis included all residents aged 70 years and over in Finland. The follow-up started on December 27, 2020, and ended on March 31, 2022. The outcomes of interest were Covid-19-related hospitalization and intensive care unit (ICU) admission timely associated with SARS-CoV-2 infection. VE was estimated as one minus the hazard ratio comparing the vaccinated and unvaccinated and taking into account time since vaccination. Omicron-specific VE was evaluated as the effectiveness observed since January 1, 2022.\n\nResultsThe cohort included 896220 individuals. Comirnaty (BioNTech/Pfizer) VE against Covid-19-related hospitalization was 93% (95% CI 89%-95%) and 85% (95% CI 82%-87%) 14-90 and 91-180 days after the second dose; VE increased to 95% (95% CI 94%-96%) 14-60 days after the third dose. VE of other homologous and heterologous three dose series was similar. Protection against severe Covid-19 requiring ICU treatment was even better. Since January 1, 2022, Comirnaty VE was 98% (95% CI 92%-99%) and 92% (95% CI 87%-95%) 14-90 and 91-180 days after the second and 98% (95% CI 95%-99%) 14-60 days after the third dose.\n\nConclusionsVE against severe Covid-19 is high among the elderly. It waned slightly after two doses, but a third restored the protection. VE against severe Covid-19 remained high even after the emergence of Omicron.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Ulrike Baum", - "author_inst": "Finnish Institute for Health and Welfare" - }, - { - "author_name": "Eero Poukka", - "author_inst": "Finnish institute for Health and Welfare" - }, - { - "author_name": "Tuija Leino", - "author_inst": "Finnish Institute for Health and Welfare" - }, - { - "author_name": "Terhi Kilpi", - "author_inst": "Finnish Institute for Health and Welfare" - }, - { - "author_name": "Hanna Nohynek", - "author_inst": "Finnish Institute for Health and Welfare" - }, - { - "author_name": "Arto A Palmu", - "author_inst": "Finnish Institute for Health and Welfare" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.11.22272269", "rel_title": "Association of frailty, age, and biological sex with SARS-CoV-2 mRNA vaccine-induced immunity in older adults", @@ -343654,6 +345719,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2022.03.13.22271253", + "rel_title": "Detection of COVID-19 dysosmia with paired crushable odorant ampules", + "rel_date": "2022-03-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.13.22271253", + "rel_abs": "BackgroundSigns of anosmia can help detect COVID-19 infection when testing for viral positivity is not available. Inexpensive mass-produced disposable olfactory sensitivity tests suitable for worldwide use might serve not only as a screening tool for potential infection but also to identify cases at elevated risk of severe disease as anosmic COVID-19 patients have a better prognosis.\n\nMethods and FindingsWe adopted paired crushable ampules with two concentrations of a standard test odorant (n-butanol) as standard of care in several clinics as community prevalence of COVID-19 infection waxed and waned. This was not a clinical trial; a chart review was undertaken to evaluate the operating characteristics and potential utility of the test device as RT-PCR testing became routine. The risk of anosmia was greater in COVID-19 patients. Olfactory sensitivity was concentration-dependent, decreased with aging, and was sex-dependent at the highest concentration. Hyposmia was detected across a wider age range than expected from the literature, and tests can be optimized to characterize different age groups.\n\nConclusionsn-Butanol at 0.32 and 3.2% in crushable ampules can be used to characterize olfactory function quickly and inexpensively and thus has potential benefits in pandemic screening, epidemiology, and clinical decision-making.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Ronald W. Wood", + "author_inst": "University of Rochester School of Medicine and Dentistry" + }, + { + "author_name": "Christopher J Stodgell", + "author_inst": "University of Rochester School of Medicine" + }, + { + "author_name": "Mitchell A. Linder", + "author_inst": "University of Rochester School of Medicine" + }, + { + "author_name": "Eva K. Pressman", + "author_inst": "University of Rochester School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "otolaryngology" + }, { "rel_doi": "10.1101/2022.03.13.22272308", "rel_title": "Duration of mRNA vaccine protection against SARS-CoV-2 Omicron BA.1 and BA.2 subvariants in Qatar", @@ -344917,53 +347013,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.09.22270766", - "rel_title": "Rare Variants in Inborn Errors of Immunity Genes Associated with Covid-19 Severity", - "rel_date": "2022-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.09.22270766", - "rel_abs": "Covid-19 is a contagious disease caused by SARS-CoV-2, a novel severe acute respiratory syndrome coronavirus. Common variants and networks underlying host genetic mechanisms have been extensively studied to identify disease-associated genetic factors. However, there are few studies about the rare variants, typically inborn errors of immunity, in understanding the host genetics behind Covid-19 infection, especially in the Chinese population. To fill this gap, we investigate likely-deleterious missense and high-confidence predicted loss-of-function variants by (a) performing gene- and pathway-level association analyses, (b) examining known genes involved in type I interferon signaling and others previously reported in Covid-19 disease, and (c) identifying candidate genes with accumulating mutations and their potential protein-protein interactions with known genes. Based on our analyses, several putative genes and pathways are uncovered and worth further investigation, for example, genes IL12RB1, TBK1, and TLR3, and pathways Tuberculosis (hsa:05152), Primary Immunodeficiency (hsa:05340), and Influenza A (hsa:05164). These regions generally play an essential role in regulating antiviral innate immunity responses to foreign pathogens and in responding to many inflammatory diseases. We believe that to some extent, as an acute inflammatory disease, Covid-19 is also affected by these inborn errors of immunity. We hope that the identification of these rare genetic factors will provide new insights into the genetic architecture of Covid-19.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Panhong Liu Mrs", - "author_inst": "University of Chinese Academy of Sciences" - }, - { - "author_name": "Mingyan Fang Dr", - "author_inst": "BGI-Shenzhen" - }, - { - "author_name": "Yuxue Luo Miss", - "author_inst": "BGI-Shenzhen" - }, - { - "author_name": "Fang Zheng Ms", - "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Yan Jin Ms", - "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Fanjun Cheng Dr", - "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Huanhuan Zhu Dr", - "author_inst": "BGI-Shenzhen" - }, - { - "author_name": "Xin Jin Dr", - "author_inst": "BGI-Shenzhen" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.10.22272024", "rel_title": "Prevalence and Predictors of Depression, Anxiety and Stress among Elderly in the aftermath of COVID-19: A Quantitative Study from Central India", @@ -345908,6 +347957,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.07.483402", + "rel_title": "High-throughput molecular dynamics-based alchemical free energy calculations for predicting the binding free energy change associated with the common mutations in the spike receptor-binding domain of SARS-CoV-2", + "rel_date": "2022-03-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.07.483402", + "rel_abs": "The ongoing pandemic caused by SARS-CoV-2 has gone through various phases. From the initial outbreak the virus has mutated several times, with some lineages showing even stronger infectivity and faster spread than the original virus. Among all the variants, beta, gamma, delta and the latest (omicron) are currently classified as variants of concern (VOC) while the remaining are labelled either as variants of interest (VOI) or variants under monitoring (VUM). In this work, we have focused on the mutations observed in important variants, particularly at the receptor-binding domain (RBD) of the spike protein that is responsible for the interactions with the host ACE2 receptor and binding of antibodies. Studying these mutations is particularly important for understanding the viral infectivity, spread of the disease and for tracking the escape routes of this virus from antibodies. Molecular dynamics (MD) based alchemical free energy calculations have been shown to be very accurate in predicting the free energy change due to a mutation that could have a deleterious or a stabilising effect on the protein itself or its binding affinity to another protein. Here, we investigated the significance of six commonly observed spike RBD mutations on the stability of the spike protein binding to ACE2 by free energy calculations using high throughput MD simulations. For comparison, we also used other (rigorous and non-rigorous) binding free energy prediction methods and compared our results with the experimental data if available. The alchemical free energy-based method consistently predicted the free-energy changes with an accuracy close to {+/-}1.0 kcal/mol when compared with the available experimental values. As per our simulation data the most significant mutations responsible for stabilising the spike RBD interactions with human ACE2 are N501Y and L452R.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Rajendra N Bhadane", + "author_inst": "\u00c5bo Akademi University: Abo Akademi" + }, + { + "author_name": "Outi M. H. Salo-Ahen", + "author_inst": "\u00c5bo Akademi University: Abo Akademi" + } + ], + "version": "1", + "license": "cc_by", + "type": "confirmatory results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2022.03.08.483451", "rel_title": "Reorganization of F-actin nanostructures is required for the late phases of SARS-CoV-2 replication in pulmonary cells.", @@ -346951,185 +349023,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.03.08.22272062", - "rel_title": "Safety and immunogenicity of a hybrid-type vaccine booster in BBIBP-CorV recipients: a randomized controlled phase 2 trial", - "rel_date": "2022-03-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.08.22272062", - "rel_abs": "The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with immune escape ability raises the urgent need for developing cross-neutralizing vaccines against the virus. NVSI-06-08 is a potential broad-spectrum recombinant COVID-19 vaccine that integrates the antigens from multiple SARS-CoV-2 strains into a single immunogen. Here, we evaluated the safety and immunogenicity of NVSI-06-08 as a heterologous booster dose in adults previously vaccinated with the inactivated vaccine BBIBP-CorV in a randomized, double-blind, controlled, phase 2 trial conducted in the United Arab Emirates (NCT05069129). Three groups of healthy adults over 18 years of age (600 participants per group) who had administered two doses of BBIBP-CorV 4-6-month, 7-9-month and >9-month earlier, respectively, were vaccinated with either a homologous booster of BBIBP-CorV or a heterologous booster of NVSI-06-08. The primary outcome was immunogenicity and safety of booster vaccinations. The exploratory outcome was cross-reactive immunogenicity against multiple SARS-CoV-2 variants of concerns (VOCs). The incidence of adverse reactions was low in both booster vaccinations, and the overall safety profile of heterologous boost was quite similar to that of homologous boost. Heterologous NVSI-06-08 booster was immunogenically superior to homologous booster of BBIBP-CorV. Both Neutralizing and IgG antibodies elicited by NVSI-06-08 booster were significantly higher than by the booster of BBIBP-CorV against not only SARS-CoV-2 prototype strain but also multiple VOCs. Especially, the neutralizing activity induced by NVSI-06-08 booster against the immune-evasive Beta variant was no less than that against the prototype strain, and a considerable level of neutralizing antibodies against Omicron (GMT: 367.67; 95%CI, 295.50-457.47) was induced by heterologous booster, which was substantially higher than that boosted by BBIBP-CorV (GMT: 45.03; 95%CI, 36.37-55.74). Our findings showed that NVSI-06-08 was safe and immunogenic as a booster dose following two doses of BBIBP-CorV, which was immunogenically superior to homologous boost with another dose of BBIBP-CorV. Our study also indicated that the design of hybrid antigen may provide an effective strategy for broad-spectrum vaccine developments.", - "rel_num_authors": 41, - "rel_authors": [ - { - "author_name": "Nawal Al Kaabi", - "author_inst": "Sheikh Khalifa Medical City, SEHA, Abu Dhabi, United Arab Emirates" - }, - { - "author_name": "Yun Kai Yang", - "author_inst": "China National Biotec Group Company Limited, Beijing, China" - }, - { - "author_name": "Li Fang Du", - "author_inst": "The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China" - }, - { - "author_name": "Ke Xu", - "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China" - }, - { - "author_name": "Shuai Shao", - "author_inst": "The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China" - }, - { - "author_name": "Yu Liang", - "author_inst": "The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China" - }, - { - "author_name": "Yun Kang", - "author_inst": "Clinical Medicine Office, National Vaccine and Serum Institute (NVSI), Beijing, China" - }, - { - "author_name": "Ji Guo Su", - "author_inst": "The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China" - }, - { - "author_name": "Jing Zhang", - "author_inst": "The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China" - }, - { - "author_name": "Tian Yang", - "author_inst": "China National Biotec Group Company Limited, Beijing, China" - }, - { - "author_name": "Salah Hussein", - "author_inst": "Sheikh Khalifa Medical City, SEHA, Abu Dhabi, United Arab Emirates" - }, - { - "author_name": "Mohamed Saif ElDein", - "author_inst": "Sheikh Khalifa Medical City, SEHA, Abu Dhabi, United Arab Emirates" - }, - { - "author_name": "Sen Sen Yang", - "author_inst": "Clinical Medicine Office, National Vaccine and Serum Institute (NVSI), Beijing, China" - }, - { - "author_name": "Wenwen Lei", - "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China" - }, - { - "author_name": "Xue Jun Gao", - "author_inst": "Lanzhou Institute of Biological Products Company Limited, Lanzhou, China" - }, - { - "author_name": "Zhiwei Jiang", - "author_inst": "Beijing Key Tech Statistical Consulting Co.,Ltd, Beijing, China" - }, - { - "author_name": "Xiangfeng Cong", - "author_inst": "Clinical Medicine Office, National Vaccine and Serum Institute (NVSI), Beijing, China" - }, - { - "author_name": "Yao Tan", - "author_inst": "Clinical Medicine Office, National Vaccine and Serum Institute (NVSI), Beijing, China" - }, - { - "author_name": "Hui Wang", - "author_inst": "Beijing Institute of Biological Products Company Limited, Beijing, China" - }, - { - "author_name": "Meng Li", - "author_inst": "China National Biotec Group Company Limited, Beijing, China" - }, - { - "author_name": "Hanadi Mekki Mekki", - "author_inst": "Union 71, United Arab Emirates" - }, - { - "author_name": "Walid Zaher", - "author_inst": "G42 Healthcare, United Arab Emirates" - }, - { - "author_name": "Sally Mahmoud", - "author_inst": "G42 Healthcare, United Arab Emirates" - }, - { - "author_name": "Xue Zhang", - "author_inst": "China National Biotec Group Company Limited, Beijing, China" - }, - { - "author_name": "Chang Qu", - "author_inst": "China National Biotec Group Company Limited, Beijing, China" - }, - { - "author_name": "Dan Ying Liu", - "author_inst": "China National Biotec Group Company Limited, Beijing, China" - }, - { - "author_name": "Jing Zhang", - "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China" - }, - { - "author_name": "Mengjie Yang", - "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China" - }, - { - "author_name": "Islam Eltantawy", - "author_inst": "G42 Healthcare, United Arab Emirates" - }, - { - "author_name": "Jun Wei Hou", - "author_inst": "The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China" - }, - { - "author_name": "Ze Hua Lei", - "author_inst": "The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China" - }, - { - "author_name": "Peng Xiao", - "author_inst": "G42 Healthcare, United Arab Emirates" - }, - { - "author_name": "Zhao Nian Wang", - "author_inst": "China National Biotec Group Company Limited, Beijing, China" - }, - { - "author_name": "Jin Liang Yin", - "author_inst": "China National Biotec Group Company Limited, Beijing, China" - }, - { - "author_name": "Xiao Yan Mao", - "author_inst": "Lanzhou Institute of Biological Products Company Limited, Lanzhou, China" - }, - { - "author_name": "Jin Zhang", - "author_inst": "Beijing Institute of Biological Products Company Limited, Beijing, China" - }, - { - "author_name": "Liang Qu", - "author_inst": "China National Biotec Group Company Limited, Beijing, China" - }, - { - "author_name": "Yun Tao Zhang", - "author_inst": "China National Biotec Group Company Limited, Beijing, China" - }, - { - "author_name": "Xiao Ming Yang", - "author_inst": "China National Biotec Group Company Limited, Beijing, China" - }, - { - "author_name": "Guizhen Wu", - "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China" - }, - { - "author_name": "Qi Ming Li", - "author_inst": "The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.08.22271905", "rel_title": "Impact of SARS-CoV-2 vaccination of children ages 5-11 years on COVID-19 disease burden and resilience to new variants in the United States, November 2021-March 2022: a multi-model study", @@ -348078,6 +349971,133 @@ "type": "PUBLISHAHEADOFPRINT", "category": "ophthalmology" }, + { + "rel_doi": "10.1101/2022.03.07.22270699", + "rel_title": "Adequacy of Self-Collected Anterior Nares Swabs for SARS-CoV-2 Testing by Grade School Children", + "rel_date": "2022-03-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.07.22270699", + "rel_abs": "BackgroundThe goal of this study was to characterize the ability of school-aged children to self-collect adequate anterior nares (AN) swabs for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing.\n\nMethodsFrom July to August 2021, 287 children, age 4-14 years-old, were prospectively enrolled in the Atlanta area. Symptomatic (n=197) and asymptomatic (n=90) children watched a short instructional video before providing a self-collected AN specimen. Health care workers (HCWs) then collected a second specimen, and useability was assessed by the child and HCW. Swabs were tested side-by-side for SARS-CoV-2. RNase P RNA detection was investigated as a measure of specimen adequacy.\n\nResultsAmong symptomatic children, 87/196 (44.4%) tested positive for SARS-CoV-2 by both self- and HCW-swab. Two children each were positive by self- or HCW-swab; one child had an invalid HCW-swab. Compared to HCW-swabs, self-collected swabs had 97.8% and 98.1% positive and negative percent agreements, respectively, and SARS-CoV-2 Ct values did not differ significantly between groups. Participants [≤]8 years-old were less likely than those >8 to be rated as correctly completing self-collection, but SARS-CoV-2 detection did not differ. Based on RNase P RNA detection, 270/287 children (94.1%) provided adequate self-swabs versus 277/287 (96.5%) HCW-swabs (p=0.24) with no difference when stratified by age.\n\nConclusionsChildren, aged 4-14 years-old, can provide adequate AN specimens for SARS-CoV-2 detection when presented with age-appropriate instructional material, consisting of a video and a handout, at a single timepoint. These data support the use of self-collected AN swabs among school-age children for SARS-CoV-2 testing.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Jesse Waggoner", + "author_inst": "Emory University" + }, + { + "author_name": "Miriam B. Vos", + "author_inst": "Childrens Healthcare of Atlanta" + }, + { + "author_name": "Erika A. Tyburski", + "author_inst": "Georgia Institute of Technology, Atlanta, GA, USA" + }, + { + "author_name": "Phuong-Vi Nguyen", + "author_inst": "Emory University School of Medicine, Atlanta, GA, USA" + }, + { + "author_name": "Jessica M. Ingersoll", + "author_inst": "Emory University School of Medicine, Atlanta, GA, USA" + }, + { + "author_name": "Candace Miller", + "author_inst": "Emory University School of Medicine, Atlanta, GA, USA" + }, + { + "author_name": "Jullie Sullivan", + "author_inst": "Emory University School of Medicine, Atlanta, GA, USA" + }, + { + "author_name": "Mark Griffiths", + "author_inst": "Childrens Healthcare of Atlanta, Atlanta, GA, USA" + }, + { + "author_name": "Cheryl Stone", + "author_inst": "Childrens Healthcare of Atlanta, Atlanta, GA, USA" + }, + { + "author_name": "Macarthur Benoit", + "author_inst": "Childrens Healthcare of Atlanta, Atlanta, GA, USA" + }, + { + "author_name": "Laura Benedit", + "author_inst": "Childrens Healthcare of Atlanta, Atlanta, GA, USA" + }, + { + "author_name": "Brooke Seitter", + "author_inst": "Childrens Healthcare of Atlanta, Atlanta, GA, USA" + }, + { + "author_name": "Robert Jerris", + "author_inst": "Childrens Healthcare of Atlanta, Atlanta, GA, USA" + }, + { + "author_name": "Joshua M. Levy", + "author_inst": "Emory University School of Medicine, Atlanta, GA, USA" + }, + { + "author_name": "Colleen S. Kraft", + "author_inst": "Emory University" + }, + { + "author_name": "Sarah Farmer", + "author_inst": "Georgia Institute of Technology, Atlanta, GA, USA" + }, + { + "author_name": "Amanda Foster", + "author_inst": "Georgia Institute of Technology, Atlanta, GA, USA" + }, + { + "author_name": "Anna Wood", + "author_inst": "Pediatric Biostatistics Core, Department of Pediatrics, Emory University" + }, + { + "author_name": "Adrianna L. Westbrook", + "author_inst": "Pediatric Biostatistics Core, Department of Pediatrics, Emory University" + }, + { + "author_name": "Claudia R. Morris", + "author_inst": "Emory University School of Medicine, Atlanta, GA, USA" + }, + { + "author_name": "Usha N. Sathian", + "author_inst": "Childrens Healthcare of Atlanta, Atlanta, GA, USA" + }, + { + "author_name": "William Heetderks", + "author_inst": "National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, MD" + }, + { + "author_name": "Li Li", + "author_inst": "Center for Devices and Radiological Health, U.S. Food & Drug Administration" + }, + { + "author_name": "Kristian Roth", + "author_inst": "Center for Devices and Radiological Health, U.S. Food & Drug Administration" + }, + { + "author_name": "Mary Barcus", + "author_inst": "Center for Devices and Radiological Health, U.S. Food & Drug Administration" + }, + { + "author_name": "Timothy Stenzel", + "author_inst": "Center for Devices and Radiological Health, U.S. Food & Drug Administration" + }, + { + "author_name": "Greg S. Martin", + "author_inst": "Emory University School of Medicine, Atlanta, GA, USA" + }, + { + "author_name": "Wilbur A. Lam", + "author_inst": "Emory University School of Medicine, Atlanta, GA, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.09.483600", "rel_title": "DiSCERN - Deep Single Cell Expression ReconstructioN for improved cell clustering and cell subtype and state detection", @@ -349129,53 +351149,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.07.22271764", - "rel_title": "Usefulness of real-time RT-PCR to understand the kinetics of SARS-CoV-2 in blood: a prospective study.", - "rel_date": "2022-03-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.07.22271764", - "rel_abs": "BackgroundSARS-CoV-2 viral load and kinetics assessed in serial blood samples from hospitalised COVID-19 patients by RT-PCR are poorly understood.\n\nMethodsWe conducted an observational, prospective case series study in hospitalised COVID-19 patients. Clinical outcome data (Intensive Care Unit admission and mortality) were collected from all patients until discharge. Viremia was determined longitudinally during hospitalisation, in plasma and serum samples using two commercial and standardised RT-PCR techniques approved for use in diagnosis of SARS-CoV-2. Viral load (copies/mL and log10) was determined with quantitative TaqPathCOVID-19 test.\n\nResultsSARS-CoV-2 viremia was studied in 57 hospitalised COVID-19 patients. Persistent viremia (PV) was defined as two or more quantifiable viral loads detected in blood samples (plasma/serum) during hospitalisation. PV was detected in 16 (28%) patients. All of them, except for one who rapidly progressed to death, cleared viremia during hospitalisation. Poor clinical outcome occurred in 62.5% of patients with PV, while none of the negative patients or those with sporadic viremia presented this outcome (p<0.0001). Viral load was significantly higher in patients with PV than in those with Sporadic Viremia (p<0.05). Patients presented PV for a short period of time: median time from admission was 5 days (Range=2-12) and 4.5 days (Range=2-8) for plasma and serum samples, respectively. Similar results were obtained with all RT-PCR assays for both types of samples.\n\nConclusionsDetection of persistent SARS-CoV-2 viremia, by real time RT-PCR, expressed as viral load over time, could allow identifying hospitalised COVID-19 patients at risk of poor clinical outcome.\n\nHighlightsO_LICommercial RT-PCR techniques could be used to monitor SARS-CoV-2 viremia kinetics.\nC_LIO_LISARS-CoV-2 persistent viremia is related with poor outcome in COVID-19 patient.\nC_LIO_LISARS-Cov-2 viremia kinetics could be used as a biomarker of poor prognosis.\nC_LIO_LIPlasma samples are the best choice for analysis of SARS-CoV-2 viremia kinetics.\nC_LI", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Nelly Daniela Zurita Cruz", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Alexandra Martin Ramirez", - "author_inst": "Hospital Universitario de la Princesa" - }, - { - "author_name": "Diego Anibal Rodriguez Serrano", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Isidoro Gonzalez Alvaro", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Emilia Roy Vallejo", - "author_inst": "Hospital Universitario La Princesa" - }, - { - "author_name": "Rafael De la Camar", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Leticia Fontan Garcia-Rodrigo", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Laura Cardenoso Domingo", - "author_inst": "Hospital Universitario de La Princesa" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.07.22271219", "rel_title": "DIAGNOSTIC ACCURACY OF NON-INVASIVE DETECTION OF SARS-COV-2 INFECTION BY CANINE OLFACTION", @@ -349968,6 +351941,89 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2022.03.05.483133", + "rel_title": "Potent universal-coronavirus therapeutic activity mediated by direct respiratory administration of a Spike S2 domain-specific human neutralizing monoclonal antibody", + "rel_date": "2022-03-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.05.483133", + "rel_abs": "Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) marks the third novel {beta}-coronavirus to cause significant human mortality in the last two decades. Although vaccines are available, too few have been administered worldwide to keep the virus in check and to prevent mutations leading to immune escape. To determine if antibodies could be identified with universal coronavirus activity, plasma from convalescent subjects was screened for IgG against a stabilized pre-fusion SARS-CoV-2 spike S2 domain, which is highly conserved between human {beta}-coronavirus. From these subjects, several S2-specific human monoclonal antibodies (hmAbs) were developed that neutralized SARS-CoV-2 with recognition of all variants of concern (VoC) tested (Beta, Gamma, Delta, Epsilon, and Omicron). The hmAb 1249A8 emerged as the most potent and broad hmAb, able to recognize all human {beta}-coronavirus and neutralize SARS-CoV and MERS-CoV. 1249A8 demonstrated significant prophylactic activity in K18 hACE2 mice infected with SARS-CoV-2 lineage A and lineage B Beta, and Omicron VoC. 1249A8 delivered as a single 4 mg/kg intranasal (i.n.) dose to hamsters 12 hours following infection with SARS-CoV-2 Delta protected them from weight loss, with therapeutic activity further enhanced when combined with 1213H7, an S1-specific neutralizing hmAb. As little as 2 mg/kg of 1249A8 i.n. dose 12 hours following infection with SARS-CoV Urbani strain, protected hamsters from weight loss and significantly reduced upper and lower respiratory viral burden. These results indicate in vivo cooperativity between S1 and S2 specific neutralizing hmAbs and that potent universal coronavirus neutralizing mAbs with therapeutic potential can be induced in humans and can guide universal coronavirus vaccine development.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Michael S Piepenbrink", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Jun-Gyu Park", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Ashlesha Deshpande", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Andreas Loos", + "author_inst": "Aridis Pharmaceuticals" + }, + { + "author_name": "Chengjin Ye", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Madhubanti Basu", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Sanghita Sarkar", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "David Chauvin", + "author_inst": "Aridis Pharmaceuticals" + }, + { + "author_name": "Jennifer Woo", + "author_inst": "Aridis Pharmaceuticals" + }, + { + "author_name": "Phillip Lovalenti", + "author_inst": "Aridis Pharmaceuticals" + }, + { + "author_name": "Nathaniel B Erdmann", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Paul A Goepfert", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Vu L Truong", + "author_inst": "Aridis Pharmaceuticals" + }, + { + "author_name": "Richard A Bowen", + "author_inst": "Colorado State University" + }, + { + "author_name": "Mark R Walter", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Luis Martinez-Sobrido", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "James J Kobie", + "author_inst": "University of Alabama at Birmingham" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.03.04.479488", "rel_title": "Broadly neutralizing anti-S2 antibodies protect against all three human betacoronaviruses that cause severe disease", @@ -350971,33 +353027,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2022.03.07.483324", - "rel_title": "In silico screening and testing of FDA approved small molecules to block SARS-CoV-2 entry to the host cell by inhibiting Spike protein cleavage", - "rel_date": "2022-03-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.07.483324", - "rel_abs": "The COVID-19 pandemic began in 2019, but it is still active. The development of an effective vaccine reduced the number of deaths; however, a treatment is still needed. Here, we aimed to inhibit viral entry to the host cell by inhibiting Spike (S) protein cleavage by several proteases. We develop a computational pipeline to repurpose FDA-approved drugs to inhibit protease activity and thus prevent S protein cleavage. We tested some of our drug candidates and demonstrated a decrease in protease activity. We believe our pipeline will be beneficial in identifying a drug regimen for COVID-19 patients.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "E. Sila Ozdemir", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Hillary H. Le", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Adem Yildirim", - "author_inst": "Oregon Health & Science University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2022.03.05.22271084", "rel_title": "Changing dynamics of SARS-CoV2 B.1.617.2 (Delta variant) outbreak in the United Kingdom: Shifting of SARS-CoV2 infections from younger to elderly populations with increasing hospitalizations and mortality among elderly.", @@ -351574,6 +353603,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.03.22271803", + "rel_title": "Testing Frequency Matters | An Evaluation of the Diagnostic Performance of a SARS-CoV-2 Rapid Antigen Test in United States Correctional Facilities", + "rel_date": "2022-03-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.03.22271803", + "rel_abs": "BackgroundThe CDC recommends serial rapid antigen assay collection within congregate facilities for screening and outbreak testing. Though modeling and observational studies from community and long-term care facilities have shown serial collection provides adequate sensitivity and specificity, the diagnostic accuracy of this testing strategy within correctional facilities remains unknown.\n\nMethodsUsing Connecticut Department of Corrections (DOC) data from November 21st 2020 to June 15th 2021, we estimated the accuracy of a rapid assay, BinaxNOW, under three collection strategies, a single test in isolation and two and three serial tests separated by 1-4 day intervals. Diagnostic accuracy metrics were estimated in relation to RT-PCRs collected within one day before the first or after the last included rapid antigen tests in a series.\n\nResultsOf the 17,669 residents who contributed at least one RT-PCR or rapid antigen during the study period, 3,979 contributed [≥]1 paired rapid antigen test series. In relation to RT-PCR, the three-rapid antigen test strategy had a sensitivity of 89.6% (95% confidence intervals: 86.1-92.6%) and specificity of 97.2% (CI: 95.1-98.3%). The sensitivities for two and one-rapid antigen test strategy were 75.2% and 52.8%, respectively, and the specificities were 98.5% and 99.4%, respectively. The sensitivity was higher among symptomatic residents and when the RT-PCR was collected before the rapid antigen tests.\n\nConclusionsWe found the serial collection of an antigen test resulted in high diagnostic accuracy. These findings support serial testing within correctional facilities for outbreak investigation, screening, and when rapid detection is required (such as intakes or transfers).", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Margaret L Lind", + "author_inst": "Yale University School of Public Health" + }, + { + "author_name": "Olivia Schultes", + "author_inst": "University of Washington" + }, + { + "author_name": "Alexander Robertson", + "author_inst": "Yale University School of Public Health" + }, + { + "author_name": "Amy J Houde", + "author_inst": "Connecticut Department of Corrections" + }, + { + "author_name": "Derek A.T. Cummings", + "author_inst": "University of Florida" + }, + { + "author_name": "Albert I Ko", + "author_inst": "Yale University School of Public Health" + }, + { + "author_name": "Byron S Kennedy", + "author_inst": "Connecticut Department of Corrections" + }, + { + "author_name": "Robert P Richenson", + "author_inst": "Connecticut Department of Corrections" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.03.22271601", "rel_title": "Immunogenicity and reactogenicity against the SARS-CoV-2 variants following heterologous primary series involving CoronaVac and ChAdOx1 and BNT162b2 plus heterologous BNT162b2 booster vaccination: An open-label randomized study in healthy Thai adults.", @@ -352709,57 +354785,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.02.22271762", - "rel_title": "Disparities in SARS-CoV-2 case rates by ethnicity, religion, measures of socio-economic position, English proficiency, and self-reported disability: cohort study of 39 million people in England during the Alpha and Delta waves", - "rel_date": "2022-03-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.02.22271762", - "rel_abs": "ObjectiveTo examine socio-demographic disparities in SARS-CoV-2 case rates during the second (Alpha) and third (Delta) waves of the COVID-19 pandemic.\n\nDesignRetrospective, population-based cohort study.\n\nSettingResident population of England.\n\nParticipants39,006,194 people aged 10 years and over who were enumerated at the 2011 Census, registered with the National Health Service (NHS) and alive on 1 September 2020.\n\nMain outcome measuresTesting positive for SARS-CoV-2 during the second wave (1 September 2020 to 22 May 2021) or third wave (23 May to 10 December 2021) of the pandemic. We calculated age-standardised case rates by socio-demographic characteristics and used logistic regression models to estimate adjusted odds ratios (ORs).\n\nResultsDuring the study period, 5,767,584 individuals tested positive for SARS-CoV-2. In the second wave, the fully-adjusted odds of having a positive test, relative to the White British group, were highest for the Bangladeshi (OR: 1.88, 95% CI 1.86 to 1.90) and Pakistani (1.81, 1.79 to 1.82) ethnic groups. Relative to the Christian group, Muslim and Sikh religious groups had fully-adjusted ORs of 1.58 (1.57 to 1.59) and 1.74 (1.72 to 1.76), respectively. Greater area deprivation, disadvantaged socio-economic position, living in a care home and low English language proficiency were also associated with higher odds of having a positive test. However, the disparities between groups varied over time. Being Christian, White British, non-disabled, and from a more advantaged socio-economic position were all associated with increased odds of testing positive during the third wave.\n\nConclusionThere are large socio-demographic disparities on SARS-CoV-2 cases which have varied between different waves of the pandemic. Research is now urgently needed to understand why these disparities exist to inform policy interventions in future waves or pandemics.\n\nWhat is already known on this topicPeople with pre-existing health conditions or disability, ethnic minority groups, the elderly, some religious groups, people with low socio-economic status, and those living in deprived areas have been disproportionately affected by the COVID-19 pandemic in terms of risk of infection and adverse outcomes.\n\nWhat this study addsUsing linked data on 39 million people in England, we found that during the second wave, COVID-19 case rates were highest among the Bangladeshi and Pakistani ethnic groups, the Muslim religious group, individuals from deprived areas and of low socio-economic position; during the third wave, being Christian, White British, non-disabled, and from a more advantaged socio-economic position were all associated with increased odds of receiving a positive test\n\nAdjusting for geographical factors, socio-demographic characteristics, and pre-pandemic health status explained some, but not all, of the excess risk\n\nWhen stratifying the dataset by broad age groups, the odds of receiving a positive test remained higher among the Bangladeshi and Pakistani ethnic groups aged 65 years and over during the third wave, which may partly explain the continued elevated mortality rates in these groups", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Tim Larsen", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Matthew L Bosworth", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Daniel Ayoubkhani", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Ryan Schofield", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Raghib Ali", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Kamlesh Khunti", - "author_inst": "University of Leicester" - }, - { - "author_name": "Ann Sarah Walker", - "author_inst": "University of Oxford" - }, - { - "author_name": "Myer Glickman", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Vahe Nafilyan", - "author_inst": "Office for National Statistics" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.03.02.22271767", "rel_title": "Estimating relative generation times and relative reproduction numbers of Omicron BA.1 and BA.2 with respect to Delta in Denmark", @@ -353348,6 +355373,105 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.03.03.481940", + "rel_title": "Highly Thermotolerant SARS-CoV-2 Vaccine Elicits Neutralising Antibodies Against Delta and Omicron in Mice", + "rel_date": "2022-03-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.03.481940", + "rel_abs": "As existing vaccines fail to completely prevent COVID-19 infections or community transmission, there is an unmet need for vaccines that can better combat SARS-CoV-2 variants of concern (VOC). We have previously developed highly thermo-tolerant monomeric and trimeric receptor binding domain derivatives that can withstand 100{degrees}C for 90 minutes and 37{degrees}C for four weeks, and help eliminate cold chain requirements. We show that mice immunised with these vaccine formulations elicit high titres of antibodies that neutralise SARS-CoV-2 variants VIC31 (with Spike: D614G mutation), Delta and Omicron (BA.1.1) VOC. Compared to VIC31, there was an average 14.4-fold reduction in neutralisation against BA.1.1 for the three monomeric antigen-adjuvant combinations, and 16.5-fold reduction for the three trimeric antigen-adjuvant combinations; the corresponding values against Delta were 2.5 and 3.0. Our findings suggest that monomeric formulations are suitable for the upcoming Phase I human clinical trials, and that there is potential for increasing efficacy with vaccine matching to improve responses against emerging variants. These findings are consistent with in silico modelling and AlphaFold predictions which show that while oligomeric presentation can be generally beneficial, it can make important epitopes inaccessible, and also carries the risk of eliciting unwanted antibodies against the oligomerisation domain.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Petrus Jansen van Vuren", + "author_inst": "Commonwealth Scientific and Industrial Research Organisation" + }, + { + "author_name": "Alexander J McAuley", + "author_inst": "Commonwealth Scientific and Industrial Research Organisation" + }, + { + "author_name": "Michael J Kuiper", + "author_inst": "Commonwealth Scientific and Industrial Research Organisation" + }, + { + "author_name": "Nagendrakumar Balasubramanian Singanallur", + "author_inst": "Commonwealth Scientific and Industrial Research Organisation" + }, + { + "author_name": "Matthew P Bruce", + "author_inst": "Commonwealth Scientific and Industrial Research Organisation" + }, + { + "author_name": "Shane Riddell", + "author_inst": "CSIRO Australian Centre for Disease Preparedness" + }, + { + "author_name": "Sarah Goldie", + "author_inst": "Commonwealth Scientific and Industrial Research Organisation" + }, + { + "author_name": "Shruthi Mangalaganesh", + "author_inst": "Monash University" + }, + { + "author_name": "Simran Chahal", + "author_inst": "Commonwealth Scientific and Industrial Research Organisation" + }, + { + "author_name": "Trevor W Drew", + "author_inst": "Commonwealth Scientific and Industrial Research Organisation" + }, + { + "author_name": "Kim Rebecca Blasdell", + "author_inst": "Commonweath Scientific and Industrial Research Organisation (CSIRO)" + }, + { + "author_name": "Mary Tachedjian", + "author_inst": "Commonwealth Scientific and Industrial Research Organisation" + }, + { + "author_name": "Leon Caly", + "author_inst": "Victorian Infectious Diseases Reference Laboratory" + }, + { + "author_name": "Julian D Druce", + "author_inst": "Victorian Infectious Diseases Reference Laboratory" + }, + { + "author_name": "Shahbaz Ahmed", + "author_inst": "Indian institute of science" + }, + { + "author_name": "Mohammad Suhail Khan", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Sameer Kumar Malladi", + "author_inst": "Indian Institute of Science, Bengaluru" + }, + { + "author_name": "Randhir Singh", + "author_inst": "Mynvax Private Limited" + }, + { + "author_name": "Suman Pandey", + "author_inst": "Mynvax Private Limited" + }, + { + "author_name": "Raghavan Varadarajan", + "author_inst": "Indian Institute of Science, Bengaluru." + }, + { + "author_name": "Seshadri S Vasan", + "author_inst": "Commonwealth Scientific and Industrial Research Organisation" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "confirmatory results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.03.03.482731", "rel_title": "The interaction of calcium ions with specific residues in the SARS-CoV fusion peptide and the regulation of viral infectivity", @@ -354691,53 +356815,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.28.22271671", - "rel_title": "A causal inference approach for estimating effects of non-pharmaceutical interventions during Covid-19 pandemic", - "rel_date": "2022-03-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.28.22271671", - "rel_abs": "In response to the outbreak of the coronavirus disease 2019 (Covid-19), governments worldwide have introduced multiple restriction policies, known as non-pharmaceutical interventions (NPIs). However, the relative impact of control measures and the long-term causal contribution of each NPI are still a topic of debate. We present a method to rigorously study the effectiveness of interventions on the rate of the time-varying reproduction number Rt and on human mobility, considered here as a proxy measure of policy adherence and social distancing. We frame our model using a causal inference approach to quantify the impact of five governmental interventions introduced until June 2020 to control the outbreak in 113 countries: confinement, school closure, mask wearing, cultural closure, and work restrictions. Our results indicate that mobility changes are more accurately predicted when compared to reproduction number. All NPIs, except for mask wearing, significantly affected human mobility trends. From these, schools and cultural closure mandates showed the largest effect on social distancing. We also found that closing schools, issuing face mask usage, and work-from-home mandates also caused a persistent reduction on Rt after their initiation, which was not observed with the other social distancing measures. Our results are robust and consistent across different model specifications and can shed more light on the impact of individual NPIs.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Vesna Barros", - "author_inst": "IBM Haifa Research Labs" - }, - { - "author_name": "Itay Manes", - "author_inst": "IBM Haifa Research Labs" - }, - { - "author_name": "Victor Akinwande", - "author_inst": "IBM Research" - }, - { - "author_name": "Celia Cintas", - "author_inst": "IBM Research" - }, - { - "author_name": "Osnat Bar-Shira", - "author_inst": "IBM Haifa Research Labs" - }, - { - "author_name": "Michal Ozery-Flato", - "author_inst": "IBM Haifa Research Labs" - }, - { - "author_name": "Yishai Shimoni", - "author_inst": "IBM Haifa Research Labs" - }, - { - "author_name": "Michal Rosen-Zvi", - "author_inst": "IBM Haifa Research Labs" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2022.02.28.22271674", "rel_title": "Assessment of Potential Risk Factors for COVID-19 among Health Care Workers in a Health Care Setting in Delhi, India -A Cohort Study", @@ -355498,6 +357575,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.03.01.22270897", + "rel_title": "Descriptive and Narrative Study of Long Covid Cases in General Practice and Diagnostic Value of Single Photon Emission Computed Tomography", + "rel_date": "2022-03-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.01.22270897", + "rel_abs": "Primary care is under great pressure from patients with Covid -19 and those affected by Long Covid. The issue of Long Covid, its diagnosis and therapeutic approach are discussed here in detail. The Long Covid is described on the basis of a review of the literature and also on the basis of clinical experience in general practice. The main characteristics of thirty four cases (twenty five women) of Long Covid encountered in 2021 and early 2022 are outlined. The experience of six of them is reported on the basis of notes from their medical records. These six patients were interviewed and each was asked to reread and correct the texts concerning them. This is therefore a descriptive study based on clinical and narrative experience, verified by the patients.\n\nLong Covid, the first disease in the history of medicine to be described first by patients themselves on social networks, is not yet precisely defined and the multi -systemic symptoms may be non-specific or vary according to the organs affected.\n\nDiagnosis is based on careful listening to the patients history. Previously unknown irrepressible fatigue, brain fog, working memory disorders with possible anomia, anosmia, dysgeusia or other muli-systemic symptoms occurring after an acute Covid are varying characteristics of Long Covid. Biological evidence of Covid is missing in fourteen patients as PCRs may have been not done or came back negative in the acute phase of the disease. Anti-SARS-CoV-2 antibodies are not always present or are indistinguishable from post-vaccine antibodies. In fourteen severe cases presented, Single Photon Emission Computed Tomography (SPECT scan) after intravenous administration of Technetium-99m (Tc-99m HM-PAO) were able to demonstrate a disorder of cerebral perfusion. Two follow -up brain SPECT at three months showed significant improvement. Further genetic and immunologic study is ongoing for all patient with the help of the international consortium COVID Human Genetic Effort. A patient who presents after a Covid with medically unexplained symptoms may well be a Long Covid. Despite some interesting hypothesis, there is no known specific treatment. Neurocognitive revalidation and physiotherapy may help those patients who need long -term empathic support to cope with their condition.\n\nKey messages{square} Long Covid is a recent onset, multi-systemic, long-term condition that can be very debilitating.\n{square}The main symptoms are severe fatigue, exertional exhaustion, and cognitive and memory problems, among others.\n{square}Patients who suffer from it may not realize it, may not talk about it, or may attribute their problem to other causes.\n{square}Single Photon Emission Computed Tomography (SPECT CT) contributes to the hypothesis of a vascular perfusion disorder induced by SARS -coV-2 and should be validated as a diagnostic tool in neurological Long Covid.\n{square}Tissue immunity should be available to prove Long Covid in case of humoral seronegativity\n{square}There is no identified treatment that can be recommended yet. Careful listening, empathic support and cognitive and physical rehabilitation are suggested and should be organised or supported by the Belgian state.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "MARC JAMOULLE", + "author_inst": "University of Liege" + }, + { + "author_name": "Gisele Kazeneza-Mugisha", + "author_inst": "University of Mons" + }, + { + "author_name": "Ayoub zayane", + "author_inst": "Cabinet Medical Janson, Charleroi, Belgium" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "primary care research" + }, { "rel_doi": "10.1101/2022.02.18.22271039", "rel_title": "Severe Neuro-COVID is associated with peripheral immune signatures, autoimmunity and signs of neurodegeneration: a prospective cross-sectional study", @@ -356665,57 +358769,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.26.22271364", - "rel_title": "An Immunobridging study to evaluate the neutralizing antibody titer in adults immunized with two doses of either ChAdOx1-nCov-19 (AstraZeneca) or MVC-COV1901.", - "rel_date": "2022-03-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.26.22271364", - "rel_abs": "BackgroundRapid development and deployment of vaccine is crucial to control the continuously evolving COVID-19 pandemic. Placebo-controlled phase 3 efficacy trial is still standard for authorizing vaccines in majority of the world. However, due to lack of cases or participants in parts of the world, this has not always been feasible. An alternative to efficacy trial is immunobridging, in which the immune response or correlates of protection of a vaccine candidate is compared against an approved vaccine. Here we describe a case study where our candidate vaccine, MVC-COV1901, has been granted for emergency use authorization (EUA) locally based on the non-inferiority immunobridging process.\n\nMethodsThe per protocol immunogenicity (PPI) subset from the MVC-COV1901 phase 2 trial was used for this study and consisted of 903 subjects who have received two doses of MVC-COV1901 as scheduled in the clinical trial. The comparator set of population consisted of 200 subjects of [≥] 20 years of age who were generally healthy and have received two doses of AstraZeneca ChAdOx nCOV-19 (AZD1222) recruited from Taoyuan General Hospital, Ministry of Health and Welfare.\n\nResultsMVC-COV1901 was shown to have a geometric mean titer (GMT) ratio lower bound 95% confidence interval (CI) of 3.4 against the comparator vaccine and a seroconversion rate of 95.5% at the 95% CI lower bound, which both exceeded the criteria set by the Taiwan regulatory authority for EUA approval. These results supported the EUA approval of MVC-COV1901 by the Taiwanese regulatory authority in July 2021. Following the consensus of the International Coalition of Medicines Regulatory Authorities (ICMRA), countries from the Access Consortium has recently adopted the use of immunobridging studies as acceptable for authorizing COVID-19 vaccines in lieu of efficacy data.\n\nConclusionThe data presented in the study showed that it is reasonably likely that the vaccine efficacy of MVC-COV1901 is similar or superior to that of AZ. Data could be used in support of further vaccine development and regulatory approval.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Josue Antonio Garcia Estrada", - "author_inst": "Medigen Vaccine Biologics Corporation" - }, - { - "author_name": "Chien-Yu Cheng", - "author_inst": "Taoyuan General Hospital, Ministry of Health and Welfare and Institute of Public Health, School of Medicine National Yang-Ming Chiao Tung University" - }, - { - "author_name": "Shin-Yen Ku", - "author_inst": "Department of Nursing, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan" - }, - { - "author_name": "Hui-Chun Hu", - "author_inst": "Department of Nursing, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan" - }, - { - "author_name": "Hsiu-Wen Yeh", - "author_inst": "Department of Nursing, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan" - }, - { - "author_name": "Yi-Chun Lin", - "author_inst": "Department of Infectious Diseases, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan" - }, - { - "author_name": "Cheng-Pin Chen", - "author_inst": "Department of Infectious Diseases, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan and School of Clinical Medicine, National Yang-Ming" - }, - { - "author_name": "Shu-Hsing Cheng", - "author_inst": "Department of Infectious Diseases, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan and School of Public Health, Taipei Medical Univers" - }, - { - "author_name": "I-Feng Lin", - "author_inst": "Institute of Public Health, School of Medicine National Yang-Ming Chiao Tung University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.27.22271399", "rel_title": "The Serological Sciences Network (SeroNet) for COVID-19: Depth and Breadth of Serology Assays and Plans for Assay Harmonization", @@ -357484,6 +359537,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2022.02.28.22271636", + "rel_title": "Government restriction efficiency on curbing COVID-19 pandemic transmission in Western Europe", + "rel_date": "2022-03-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.28.22271636", + "rel_abs": "In this article we assess the effectiveness of the restrictions, implemented at government level, to curb the first wave of the COVID-19 outbreak (January-May 2020) in seven European countries. The analysis put in evidence a strong correlation (correlation coefficient greater than 0.85) between one of the statistical parameters of the distribution representing the temporal evolution of the weekly number of patients admitted into the Intensive Cure Unit (ICU), i.e., the skewness, and the Stringency Index, an aggregate synthetic variable that reflects the level of implemented restrictions by a specific country on a scale between 0 (no restrictions) and 100 (full lockdown). Then, to assess if the skewness is consistent in effectively reflecting the applied restrictions, we computed the skewness for non-Covid flu outbreaks during four years from 2014-2015 to 2018-2019 and Covid-19 outbreak, where no restrictions were applied in Italy. The results highlight a significant difference between the values of the skewness for the normal flu with respect to the COVID-19 outbreak. This large difference put in evidence that the implemented restrictions modify the skewness of the ICU hospitalized patient number distribution. The skewness then can be used as a valid indicator to assess if the restriction had any effect on pandemic transmission and can be used as a support for decision makers.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Simone Lolli", + "author_inst": "Italian National Research Council (CNR)" + }, + { + "author_name": "Gemine Vivone", + "author_inst": "IMAA-CNR: Istituto di Metodologie per l'Analisi Ambientale Consiglio Nazionale delle Ricerche" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.02.28.22271624", "rel_title": "A compartmental Mathematical model of COVID-19 intervention scenarios for Mumbai", @@ -358579,85 +360655,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.02.27.22271572", - "rel_title": "OLFACTORY TRAINING EFFICIENCY IN POST-COVID-19 PERSISTENT OLFACTORY DISORDERS", - "rel_date": "2022-02-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.27.22271572", - "rel_abs": "BackgroundPersistent post-viral olfactory disorders (PPVOD) are widely reported after a COVID-19 and estimate to 30% one year after infection. Parosmias are the main qualitative dysosmia associated with olfaction recovery. No treatment is, to date, significantly efficient on PPVOD except olfactory training (OT). The main objective of this work was to evaluate OT efficiency on post-COVID-19 PPVOD.\n\nMethodsConsecutive patients consulting to the ENT department with post-COVID-19 PPVOD were included after mainly clinical examination, the complete Sniffin Stick Test (TDI), the short version of the Questionnaire of olfactory disorders and the SF-36. Patients were trained to practice a self-olfactory training (professional manufactured olfactory training kit) twice a day for 6 months before coming back and undergo the same complete evaluation.\n\nResultsForty-three patients were included and performed 3,5 months of OT in average. There was a significant improvement in the mean TDI score increasing from 24,7 ({+/-}8,9) before the OT to 30,9 ({+/-}9,8) (p<0,001). Parosmias increased significantly from 8 (18,6%) to 27 (62.8%) (p<0,001). Based on normative data divided by sex and age, a significant increase in the number of normosmic participants was only found for the Threshold values (p<0,001). Specific and general olfaction-related quality of life improved after the OT.\n\nConclusionsOT seems to be efficient in post-COVID-19 PPVOD, probably on the peripheral regenerative part of the olfactory recovery. Future therapeutic strategies may focus on the central aspects of the post-COVID-19 PPVOD.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Clair Vandersteen", - "author_inst": "Institut Universitaire de la Face et du Cou, 31 Avenue de Valombrose, 06100, Centre Hospitalier Universitaire, Universite Cote d Azur, Nice, Alpes-Maritimes, Fr" - }, - { - "author_name": "Magali Payne", - "author_inst": "Universite Cote d Azur, laboratoire CoBTeK, Nice, France" - }, - { - "author_name": "Louise-Emilie Dumas", - "author_inst": "Hopitaux Pediatriques de Nice CHU-LENVAL, 57 Avenue de la Californie, 06200, Centre Hospitalier Universitaire, Universite Cote d Azur, Nice, Alpes-Maritimes, Fr" - }, - { - "author_name": "Elisa Cancian", - "author_inst": "Institut Universitaire de la Face et du Cou, 31 Avenue de Valombrose, 06100, Centre Hospitalier Universitaire, Universite Cote d Azur, Nice, Alpes-Maritimes, Fr" - }, - { - "author_name": "Alexandra Plonka", - "author_inst": "Universite Cote d Azur, laboratoire CoBTeK, Nice, France" - }, - { - "author_name": "Gregoire D Andrea", - "author_inst": "Institut Universitaire de la Face et du Cou, 31 Avenue de Valombrose, 06100, Centre Hospitalier Universitaire, Universite Cote d Azur, Nice, Alpes-Maritimes, Fr" - }, - { - "author_name": "David Chirio", - "author_inst": "Departement de medecine infectiologique, hopital de l archet, 151 route de Saint Antoine, 06200, Centre Hospitalier Universitaire, Universite Cote d Azur, Nice," - }, - { - "author_name": "Elisa Demonchy", - "author_inst": "Departement de medecine infectiologique, hopital de l archet, 151 route de Saint-Antoine, 06200, Centre Hospitalier Universitaire, Universite Cote d Azur, Nice," - }, - { - "author_name": "Karine Risso", - "author_inst": "Departement de medecine infectiologique, hopital de l archet, 151 route de Saint-Antoine, 06200, Centre Hospitalier Universitaire, Universite Cote d Azur, Nice," - }, - { - "author_name": "Florence Askenazy-Gittard", - "author_inst": "Hopitaux Pediatriques de Nice CHU-LENVAL, 57 Avenue de la Californie, 06200, Centre Hospitalier Universitaire, Universite Cote d Azur, Nice, Alpes-Maritimes, Fr" - }, - { - "author_name": "Charles Savoldelli", - "author_inst": "Institut Universitaire de la Face et du Cou, 31 Avenue de Valombrose, 06100, Centre Hospitalier Universitaire, Universite Cote d Azur, Nice, Alpes-Maritimes, Fr" - }, - { - "author_name": "Nicolas Guevara", - "author_inst": "Institut Universitaire de la Face et du Cou, 31 Avenue de Valombrose, 06100, Centre Hospitalier Universitaire, Universite Cote d Azur, Nice, Alpes-Maritimes, Fr" - }, - { - "author_name": "Philippe Robert", - "author_inst": "Universite Cote d Azur, laboratoire CoBTeK, Nice, France" - }, - { - "author_name": "Laurent Castillo", - "author_inst": "Institut Universitaire de la Face et du Cou, 31 Avenue de Valombrose, 06100, Centre Hospitalier Universitaire, Universite Cote d Azur, Nice, Alpes-Maritimes, Fr" - }, - { - "author_name": "Valeria Manera", - "author_inst": "Universite Cote d Azur, laboratoire CoBTeK, Nice, France" - }, - { - "author_name": "Auriane Gros", - "author_inst": "Universite Cote d Azur, laboratoire CoBTeK, Nice, France" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "otolaryngology" - }, { "rel_doi": "10.1101/2022.02.28.22271571", "rel_title": "Discriminatory ability of gas chromatography-ion mobility spectrometry to identify patients hospitalised with COVID-19 and predict prognosis", @@ -359390,6 +361387,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "surgery" }, + { + "rel_doi": "10.1101/2022.02.26.22271544", + "rel_title": "Tracing the trajectories of SARS-CoV-2 variants of concern between December 2020 and September 2021 in the Canary Islands (Spain)", + "rel_date": "2022-02-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.26.22271544", + "rel_abs": "Several variants of concern (VOCs) explain most of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) epidemic waves in Europe. We aimed to dissect the spread of the SARS-CoV-2 VOCs in the Canary Islands (Spain) between December 2020 and September 2021 at a micro-geographical level. We sequenced the viral genome of 8,224 respiratory samples collected in the archipelago. We observed that Alpha (B.1.1.7) and Delta (B.1.617.2 and sub-lineages) were ubiquitously present in the islands, while Beta (B.1.351) and Gamma (P.1/P.1.1) had a heterogeneous distribution and were responsible for fewer and more controlled outbreaks. This work represents the largest effort for viral genomic surveillance in the Canary Islands so far, helping the public health bodies in decision-making throughout the pandemic.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Laura Ciuffreda", + "author_inst": "Research Unit, Hospital Universitario N. S. de Candelaria" + }, + { + "author_name": "Rafaela Gonzalez-Montelongo", + "author_inst": "Genomics Division, Instituto Tecnologico y de Energias Renovables" + }, + { + "author_name": "Julia Alcoba-Florez", + "author_inst": "Servicio de Microbiologia, Hospital Universitario N. S. de Candelaria" + }, + { + "author_name": "Diego Garcia-Martinez de Artola", + "author_inst": "Servicio de Microbiologia, Hospital Universitario N. S. de Candelaria" + }, + { + "author_name": "Helena Gil-Campesino", + "author_inst": "Servicio de Microbiologia, Hospital Universitario N. S. de Candelaria" + }, + { + "author_name": "Hector Rodriguez-Perez", + "author_inst": "Research Unit, Hospital Universitario N. S. de Candelaria" + }, + { + "author_name": "Antonio Inigo-Campos", + "author_inst": "Genomics Division, Instituto Tecnologico y de Energias Renovables" + }, + { + "author_name": "Isabel De Miguel-Martinez", + "author_inst": "Servicio de Microbiologia, Hospital Universitario Insular de Gran Canaria" + }, + { + "author_name": "Tomas Tosco-Nunez", + "author_inst": "Servicio de Microbiologia, Hospital Universitario Insular de Gran Canaria" + }, + { + "author_name": "Oscar Diez-Gil", + "author_inst": "Servicio de Microbiologia, Hospital Universitario N. S. de Candelaria" + }, + { + "author_name": "Agustin Valenzuela-Fernandez", + "author_inst": "Laboratorio de Inmunologia Celular y Viral, Unidad de Farmacologia, Facultad de Medicina, Universidad de La Laguna" + }, + { + "author_name": "Jose M. Lorenzo-Salazar", + "author_inst": "Genomics Division, Instituto Tecnologico y de Energias Renovables" + }, + { + "author_name": "Carlos Flores", + "author_inst": "Research Unit, Hospital Universitario N.S. de Candelaria" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.26.22271545", "rel_title": "SARS-CoV-2 Exposures of Healthcare Workers from Primary Care, Long-Term Care Facilities and Hospitals: A Nationwide Matched Case-Control Study", @@ -360253,81 +362317,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.02.24.481899", - "rel_title": "Shifting mutational constraints in the SARS-CoV-2 receptor-binding domain during viral evolution", - "rel_date": "2022-02-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.24.481899", - "rel_abs": "SARS-CoV-2 has evolved variants with substitutions in the spike receptor-binding domain (RBD) that impact its affinity for ACE2 receptor and recognition by antibodies. These substitutions could also shape future evolution by modulating the effects of mutations at other sites--a phenomenon called epistasis. To investigate this possibility, we performed deep mutational scans to measure the effects on ACE2 binding of all single amino-acid mutations in the Wuhan-Hu-1, Alpha, Beta, Delta, and Eta variant RBDs. Some substitutions, most prominently N501Y, cause epistatic shifts in the effects of mutations at other sites, thereby shaping subsequent evolutionary change. These epistatic shifts occur despite high conservation of the overall RBD structure. Our data shed light on RBD sequence-function relationships and facilitate interpretation of ongoing SARS-CoV-2 evolution.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Tyler N Starr", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Allison J Greaney", - "author_inst": "University of Washington" - }, - { - "author_name": "William W Hannon", - "author_inst": "University of Washington" - }, - { - "author_name": "Andrea N Loes", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Kevin Hauser", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Josh R Dillen", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Elena Ferri", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Ariana Ghez Farrell", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Bernadeta Dadonaite", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Matthew McCallum", - "author_inst": "University of Washington" - }, - { - "author_name": "Kenneth A Matreyek", - "author_inst": "Case Western Reserve University School of Medicine" - }, - { - "author_name": "Davide Corti", - "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology" - }, - { - "author_name": "David Veesler", - "author_inst": "University of Washington" - }, - { - "author_name": "Gyorgy Snell", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Jesse D Bloom", - "author_inst": "Fred Hutchinson Cancer Research Center" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.02.25.481978", "rel_title": "Transcriptomic landscapes of SARS-CoV-2-infected and bystander lung cells reveal a selective upregulation of NF-\u03baB-dependent coding and non-coding proviral transcripts", @@ -360988,6 +362977,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.02.16.22271053", + "rel_title": "Detection of SARS-CoV-2 in air and on surfaces in rooms of infected nursing home residents", + "rel_date": "2022-02-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.16.22271053", + "rel_abs": "There is an ongoing debate on airborne transmission of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) as a risk factor for infection. In this study, the level of SARS-CoV-2 in air and on surfaces of SARS-CoV-2 infected nursing home residents was assessed to gain insight in potential transmission routes.\n\nDuring outbreaks, air samples were collected using three different active and one passive air sampling technique in rooms of infected patients. Oropharyngeal swabs (OPS) of the residents and dry surface swabs were collected. Additionally, longitudinal passive air samples were collected during a period of 4 months in common areas of the wards. Presence of SARS-CoV-2 RNA was determined using RT-qPCR, targeting the RdRp- and E-genes. OPS, samples of two active air samplers and surface swabs with Ct value [≤]35 were tested for the presence of infectious virus by cell culture. In total, 360 air and 319 surface samples from patient rooms and common areas were collected. In rooms of 10 residents with detected SARS-CoV-2 RNA in OPS, SARS-CoV-2 RNA was detected in 93 of 184 collected environmental samples (50.5%) (lowest Ct 29,5), substantially more than in the rooms of residents with negative OPS on the day of environmental sampling (n=2) (3.6%). SARS-CoV-2 RNA was most frequently present in the larger particle size fractions (>4 m 60% (6/10); 1-4 m 50% (5/10); <1 m 20% (2/10)) (Fischer exact test p=0.076). The highest proportion of RNA-positive air samples on room level was found with a filtration-based sampler 80% (8/10) and the cyclone-based sampler 70% (7/10), and impingement-based sampler 50% (5/10). SARS-CoV-2 RNA was detected in ten out of twelve (83%) passive air samples in patient rooms. Both high-touch and low-touch surfaces contained SARS-CoV-2 genome in rooms of residents with positive OPS (high 38% (21/55); low 50% (22/44)). In one active air sample, infectious virus in vitro was detected.\n\nIn conclusion, SARS-CoV-2 is frequently detected in air and on surfaces in the immediate surroundings of room-isolated COVID-19 patients, providing evidence of environmental contamination. The environmental contamination of SARS-CoV-2 and infectious aerosols confirm the potential for transmission via air up to several meters.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Kimberly J. Linde", + "author_inst": "Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands" + }, + { + "author_name": "Inge M. Wouters", + "author_inst": "Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands" + }, + { + "author_name": "Jan J.A.J.W. Kluytmans", + "author_inst": "Julius Center for Health Sciences adn Primary Care, University Medical Center Utrecht, University Utrecht, Utrecht, the Netherlands" + }, + { + "author_name": "Marjolein F.Q. Kluytmans", + "author_inst": "Julius Center for Health Sciences adn Primary Care, University Medical Center Utrecht, University Utrecht, Utrecht, the Netherlands and Department of Infection " + }, + { + "author_name": "Suzan D. Pas", + "author_inst": "Microvida location Amphia/Bravis, Breda/Roosendaal, the Netherlands" + }, + { + "author_name": "Corine H. GeurtsvanKessel", + "author_inst": "Department of ViroScience, Erasmus MC, Rotterdam, the Netherlands" + }, + { + "author_name": "Marion P.G. Koopmans", + "author_inst": "Department of Infection Control, Amphia Hospital, Breda, the Netherlands" + }, + { + "author_name": "Melanie Meier", + "author_inst": "Mijzo, Waalwijk, the Netherlands" + }, + { + "author_name": "Patrick Meijer", + "author_inst": "Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands" + }, + { + "author_name": "Ceder R. Raben", + "author_inst": "Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands" + }, + { + "author_name": "Jack Spithoven", + "author_inst": "Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands" + }, + { + "author_name": "Monique H.G. Tersteeg", + "author_inst": "Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands" + }, + { + "author_name": "Dick J.J. Heederik", + "author_inst": "Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands" + }, + { + "author_name": "Wietske Dohmen", + "author_inst": "Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2022.02.23.22271433", "rel_title": "Effectiveness of the third dose of BNT162b2 vaccine on neutralizing Omicron variant in the Japanese population", @@ -362103,49 +364163,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.02.22.481472", - "rel_title": "Ivermectin does not protect against SARS-CoV-2 infection in the Syrian hamster model", - "rel_date": "2022-02-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.22.481472", - "rel_abs": "Ivermectin, an FDA-approved antiparasitic drug, has been reported to have in vitro activity against SARS-CoV-2. An increasing off-label use of Ivermectin for COVID-19 has been reported. We here assessed the effect of Ivermectin in Syrian hamsters infected with the SARS-CoV-2 Beta (B.1.351) variant. Infected animals received a clinically relevant dose of Ivermectin (0.4 mg/kg subcutaneously dosed) once daily for four consecutive days after which the effect was quantified. Ivermectin monotherapy did not reduce lung viral load and even significantly worsened the SARS-CoV-2-induced lung pathology. Additionally, it did not potentiate the activity of Molnupiravir (Lagevrio) when combined with this drug. This study contributes to the growing body of evidence that Ivermectin does not result in a beneficial effect in the treatment of COVID-19. These findings are important given the increasing, dangerous off-label use of Ivermectin for the treatment of COVID-19.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Caroline Shi-Yan Foo", - "author_inst": "Katholieke Universiteit Leuven" - }, - { - "author_name": "Rana Abdelnabi", - "author_inst": "Rega Institute, KU Leuven" - }, - { - "author_name": "Laura Vangeel", - "author_inst": "Rega Institute, KU Leuven" - }, - { - "author_name": "Steven De Jonghe", - "author_inst": "Rega Institute, KU Leuven" - }, - { - "author_name": "Dirk Jochmans", - "author_inst": "REGA Institute - KULeuven" - }, - { - "author_name": "Birgit Weynand", - "author_inst": "UZ leuven" - }, - { - "author_name": "Johan Neyts", - "author_inst": "Rega Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "contradictory results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.02.22.481491", "rel_title": "Molnupiravir (MK-4482) is efficacious against Omicron and other SARS-CoV-2 variants in the Syrian hamster COVID-19 model", @@ -362782,6 +364799,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "otolaryngology" }, + { + "rel_doi": "10.1101/2022.02.23.481492", + "rel_title": "Modeling predicts mechanisms altered by mutations of the SARS-CoV-2 delta and omicron variants", + "rel_date": "2022-02-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.23.481492", + "rel_abs": "We apply our mechanistic, within-host, pre-immunity, respiratory tract infection model for unvaccinated, previously uninfected, and immune-compromised individuals. Starting from published cell infection and viral replication data for the SARS-CoV-2 alpha variant, we explore variability in outcomes of viral load and cell infection due to three plausible mechanisms altered by SARS-CoV-2 mutations of delta and omicron. We seek a mechanistic explanation of clinical test results: delta nasal infections express [~]3 orders-of-magnitude higher viral load than alpha, while omicron infections express an additional 1 to 2 orders-of-magnitude rise over delta. Model simulations reveal shortening of the eclipse phase (the time between cellular uptake of the virus and onset of infectious viral replication and shedding) alone can generate 3-5 orders-of-magnitude higher viral load within 2 days post initial infection. Higher viral replication rates by an infected cell can generate at most one order-of-magnitude rise in viral load, whereas higher cell infectability has minimal impact and lowers the viral load.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Jason Pearson", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Timothy Wessler", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Alex Chen", + "author_inst": "California State University--Dominguez Hills" + }, + { + "author_name": "Richard C. Boucher", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Ronit Freeman", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Samuel K. Lai", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Raymond Pickles", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "M. Gregory Forest", + "author_inst": "University of North Carolina at Chapel Hill" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.02.22.480950", "rel_title": "A high-throughput yeast display approach to profile pathogen proteomes for MHC-II binding", @@ -363625,73 +365689,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.02.22.21268475", - "rel_title": "Clinical severity of COVID-19 patients admitted to hospitals during the Omicron wave in South Africa", - "rel_date": "2022-02-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.22.21268475", - "rel_abs": "BackgroundClinical severity of patients hospitalised with SARS-CoV-2 infection during the Omicron (fourth) wave was assessed and compared to trends in the D614G (first), Beta (second), and Delta (third) waves in South Africa.\n\nMethodsWeekly incidence of 30 laboratory-confirmed SARS-CoV-2 cases/100,000 population defined the start and end of each wave. Hospital admission data were collected through an active national COVID-19-specific surveillance programme. Disease severity was compared across waves by post-imputation random effect multivariable logistic regression models. Severe disease was defined as one or more of acute respiratory distress, supplemental oxygen, mechanical ventilation, intensive-care admission or death.\n\nResults335,219 laboratory-confirmed SARS-CoV-2 admissions were analysed, constituting 10.4% of 3,216,179 cases recorded during the 4 waves. In the Omicron wave, 8.3% of cases were admitted to hospital (52,038/629,617) compared to 12.9% (71,411/553,530) in the D614G, 12.6% (91,843/726,772) in the Beta and 10.0% (131,083/1,306,260) in the Delta waves (p<0.001). During the Omicron wave, 33.6% of admissions experienced severe disease compared to 52.3%, 63.4% and 63.0% in the D614G, Beta and Delta waves (p<0.001). The in-hospital case fatality ratio during the Omicron wave was 10.7%, compared to 21.5%, 28.8% and 26.4% in the D614G, Beta and Delta waves (p<0.001). Compared to the Omicron wave, patients had more severe clinical presentations in the D614G (adjusted odds ratio [aOR] 2.07; 95% confidence interval [CI] 2.01-2.13), Beta (aOR 3.59; CI: 3.49-3.70) and Delta (aOR 3.47: CI: 3.38-3.57) waves.\n\nConclusionThe trend of increasing cases and admissions across South Africas first three waves shifted in Omicron fourth wave, with a higher and quicker peak but fewer admitted patients, who experienced less clinically severe illness and had a lower case-fatality ratio. Omicron marked a change in the SARS-CoV-2 epidemic curve, clinical profile and deaths in South Africa. Extrapolations to other populations should factor in differing vaccination and prior infection levels.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "WAASILA JASSAT", - "author_inst": "National Institute for Communicable Diseases" - }, - { - "author_name": "Salim Abdool Karim", - "author_inst": "Centre for the AIDS Programme of Research in South Africa (CAPRISA)" - }, - { - "author_name": "Caroline Mudara", - "author_inst": "National Institute for Communicable Diseases" - }, - { - "author_name": "Richard Welch", - "author_inst": "National Institute for Communicable Diseases" - }, - { - "author_name": "Lovelyn Ozougwu", - "author_inst": "National Institute for Communicable Diseases" - }, - { - "author_name": "Michelle Groome", - "author_inst": "National Institute for Communicable Diseases" - }, - { - "author_name": "Nevashan Govender", - "author_inst": "National Institute for Communicable Diseases" - }, - { - "author_name": "Anne von Gottberg", - "author_inst": "National Institute for Communicable Diseases" - }, - { - "author_name": "Nicole Wolter", - "author_inst": "National Institute for Communicable Diseases" - }, - { - "author_name": "Milani Wolmarans", - "author_inst": "South Africa Department of Health" - }, - { - "author_name": "Petro Rousseau", - "author_inst": "South Africa Department of Health" - }, - { - "author_name": "Lucille Blumberg", - "author_inst": "National Institute for Communicable Diseases" - }, - { - "author_name": "Cheryl Cohen", - "author_inst": "National Institute for Communicable Diseases" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.22.22271041", "rel_title": "Scottish COVID CAncer iMmunity Prevalence (SCCAMP) - a longitudinal study of patients with cancer receiving active anti-cancer treatment during the COVID-19 pandemic", @@ -364316,6 +366313,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2022.02.21.22270909", + "rel_title": "Persisting pulmonary dysfunction in pediatric post-acute Covid-19", + "rel_date": "2022-02-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.21.22270909", + "rel_abs": "The frequency and extent of persistent sequelae in children and adolescents after infection with SARS-CoV-2 still needs to be comprehensively determined. In this cross-sectional clinical trial, we used non-invasive, label-free morphologic and free-breathing phase-resolved functional low-field magnetic resonance imaging (LF-MRI) to identify pulmonary changes in children and adolescents from 5 to <18 years after previously PCR-confirmed SARS-CoV-2 infection. While morphological pathologies were less frequent in children, functional LF-MRI visualized widespread ventilation, perfusion and combined ventilation/perfusion defects compared to healthy controls. The loss of functional lung parenchyma was more pronounced in long Covid than recovered patients. While pulmonary dysfunction was persistent even month after primary infection, LF-MRI demonstrated high capability to visualize and detect these changes in children and adolescents. (Clinicaltrials.org ID NCT04990531)", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Rafael Heiss", + "author_inst": "Friedrich-Alexander-Universitaet Erlangen-Nuernberg, Universitaetsklinikum Erlangen" + }, + { + "author_name": "Alexandra L Wagner", + "author_inst": "Friedrich-Alexander-Universitaet Erlangen-Nuernberg, Universitaetsklinikum Erlangen" + }, + { + "author_name": "Lina Tan", + "author_inst": "Friedrich-Alexander-Universitaet Erlangen-Nuernberg, Universitaetsklinikum Erlangen" + }, + { + "author_name": "Sandy Schmidt", + "author_inst": "Friedrich-Alexander-Universitaet Erlangen-Nuernberg, Universitaetsklinikum Erlangen" + }, + { + "author_name": "Adrian P. Regensburger", + "author_inst": "Friedrich-Alexander-Universitaet Erlangen-Nuernberg, Universitaetsklinikum Erlangen" + }, + { + "author_name": "Franziska Ewert", + "author_inst": "Friedrich-Alexander-Universitaet Erlangen-Nuernberg, Universitaetsklinikum Erlangen" + }, + { + "author_name": "Dilbar Mammadova", + "author_inst": "Friedrich-Alexander-Universitaet Erlangen-Nuernberg, Universitaetsklinikum Erlangen" + }, + { + "author_name": "Adrian Buehler", + "author_inst": "Friedrich-Alexander-Universitaet Erlangen-Nuernberg, Universitaetsklinikum Erlangen" + }, + { + "author_name": "Jens Vogel-Claussen", + "author_inst": "MH Hannover" + }, + { + "author_name": "Andreas Voskrebenzev", + "author_inst": "MH Hannover" + }, + { + "author_name": "Oliver Rompel", + "author_inst": "Friedrich-Alexander-Universitaet Erlangen-Nuernberg, Universitaetsklinikum Erlangen" + }, + { + "author_name": "Armin M. Nagel", + "author_inst": "Friedrich-Alexander-Universitaet Erlangen-Nuernberg, Universitaetsklinikum Erlangen" + }, + { + "author_name": "Simon Levy", + "author_inst": "Friedrich-Alexander-Universitaet Erlangen-Nuernberg, Universitaetsklinikum Erlangen" + }, + { + "author_name": "Sebastian Bickelhaupt", + "author_inst": "Friedrich-Alexander-Universitaet Erlangen-Nuernberg, Universitaetsklinikum Erlangen" + }, + { + "author_name": "Matthias S. May", + "author_inst": "Friedrich-Alexander-Universitaet Erlangen-Nuernberg, Universitaetsklinikum Erlangen" + }, + { + "author_name": "Michael Uder", + "author_inst": "Friedrich-Alexander-Universitaet Erlangen-Nuernberg, Universitaetsklinikum Erlangen" + }, + { + "author_name": "Markus Metzler", + "author_inst": "Friedrich-Alexander-Universitaet Erlangen-Nuernberg, Universitaetsklinikum Erlangen" + }, + { + "author_name": "Regina Trollmann", + "author_inst": "Friedrich-Alexander-Universitaet Erlangen-Nuernberg, Universitaetsklinikum Erlangen" + }, + { + "author_name": "Joachim Woelfle", + "author_inst": "Friedrich-Alexander-Universitaet Erlangen-Nuernberg, Universitaetsklinikum Erlangen" + }, + { + "author_name": "Ferdinand Knieling", + "author_inst": "Friedrich-Alexander-Universitaet Erlangen-Nuernberg, Universitaetsklinikum Erlangen" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2022.02.20.22270449", "rel_title": "Quantifying the effect of isolation and negative certification on COVID-19 transmission", @@ -365542,73 +367634,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.02.21.22271272", - "rel_title": "Community-based Case Studies of Vaccine Hesitancy and the COVID-19 Response in South Africa; The VaxScenes Study", - "rel_date": "2022-02-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.21.22271272", - "rel_abs": "BackgroundSouth Africa has reported more than half of all COVID-19 cases and deaths in Africa. The South African government has launched a large COVID-19 immunization campaign with the goal of reaching more than 40 million individuals. Nonetheless, certain international, largely internet-based surveys have shown a significant proportion of vaccine hesitancy in South Africa. This study aims to determine and co-create with local stakeholders a comprehensive understanding of vaccine hesitancy and opportunities to support the promotion of other COVID-19 health-promoting behaviours at community level.\n\nMethods and designA mixed-methods, multiple case-study design; informed by the socio-ecological model of behaviour change. Four socio-economically diverse communities across South Africa will be selected and data collection will take place concurrently through three iterative phases. Phase 1 will provide insights into community experiences of COVID-19 (response) through desktop mapping exercises, observations, in-depth interviews, and focus group discussions (FGDs) designed as expression sessions with local stakeholders. Phase 2 will explore the extent and drivers of community acceptance of COVID-19 vaccines. This phase will comprise a quantitative survey based on WHOs Behavioural and Social Drivers of Vaccination tool as well as further FGDs with community members. Phase 3 will involve cross-case study syntheses and presentation of findings to national role-players.\n\nDiscussionThis study will provide ground up, locally responsive, and timeous evidence on the factors influencing COVID-19 health-seeking behaviours to inform ongoing management and mitigation of COVID-19 in South Africa. It will also provide insights into the applicability of a novel vaccine hesitancy model in Africa.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Charles Shey Wiysonge", - "author_inst": "South African Medical Research Council" - }, - { - "author_name": "Nancy Coulson", - "author_inst": "The Sarraounia Public Health Trust" - }, - { - "author_name": "Nirvana Pillay", - "author_inst": "The Sarraounia Public Health Trust" - }, - { - "author_name": "Sara Cooper", - "author_inst": "South African Medical Research Council" - }, - { - "author_name": "Candice Groenewald", - "author_inst": "HSRC: Human Sciences Research Council" - }, - { - "author_name": "Zaynab Essack", - "author_inst": "HSRC: Human Sciences Research Council" - }, - { - "author_name": "Saahier Parker", - "author_inst": "HSRC: Human Sciences Research Council" - }, - { - "author_name": "Gregory Houston", - "author_inst": "HSRC: Human Sciences Research Council" - }, - { - "author_name": "Jane Simmonds", - "author_inst": "South African Medical Research Council" - }, - { - "author_name": "Anelisa Jaca", - "author_inst": "South African Medical Research Council" - }, - { - "author_name": "Muyunda Mutemwa", - "author_inst": "South African Medical Research Council" - }, - { - "author_name": "Patrick DMC Katoto", - "author_inst": "South African Medical Research Council" - }, - { - "author_name": "Heidi van Rooyen", - "author_inst": "HSRC: Human Sciences Research Council" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.02.21.22271306", "rel_title": "Tackling the first COVID-19 wave at the Cape Town Hospital of Hope: Why was it such a positive experience for staff?", @@ -366433,6 +368458,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2022.02.18.22270820", + "rel_title": "Closing the health inequity gap during the pandemic: COVID-19 mortality among racial and ethnic groups in Connecticut, March 2020 to December 2021", + "rel_date": "2022-02-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.18.22270820", + "rel_abs": "COVID-19 has disproportionally burdened racial and ethnic minority groups within the United States. Leveraging statewide data, we examined the evolution of racial and ethnic disparities in COVID-19 related deaths among Connecticut residents residing in non-congregate settings over three periods of the COVID-19 pandemic. Despite observing large disparities in the age-adjusted mortality rates between Hispanics, non-Hispanic Blacks, and non-Hispanic Whites during the initial pandemic period (March to August 2020), we observed meaningful reductions in the disparities during the subsequent periods (August 2020 to July 2021; July to mid December 2021). Further, during the third period, we failed to find a significant difference in age-adjusted mortality between non-Hispanic Blacks and non-Hispanic Whites. These findings provide evidence that attenuation of racial and ethnic disparities in COVID-19 related outcomes are achievable.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Olivia Schultes", + "author_inst": "University of Washington" + }, + { + "author_name": "Margaret L Lind", + "author_inst": "Yale School of Public Health, New Haven" + }, + { + "author_name": "Jessica Brockmeyer", + "author_inst": "Connecticut Department of Health" + }, + { + "author_name": "Peri Sosensky", + "author_inst": "Yale School of Public Health, New Haven" + }, + { + "author_name": "Derek A.T. Cummings", + "author_inst": "Department of Biology, University of Florida" + }, + { + "author_name": "Albert I Ko", + "author_inst": "Yale University School of Public Health" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.02.15.22271018", "rel_title": "COVID-19 Surveillance in the Biobank at the Colorado Center for Personalized Medicine", @@ -367644,45 +369708,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.18.22271179", - "rel_title": "Real-time monitoring of the effectiveness of six COVID-19 vaccines in Hungary in 2021 using the screening method", - "rel_date": "2022-02-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.18.22271179", - "rel_abs": "Several studies have reported a waning of the effectiveness of COVID-19 vaccines. We report real-life vaccine effectiveness in Hungary, estimated with the screening method, in 2021, i.e., covering the dominance of both the Alpha and the Delta variant, and including the booster roll-out. Hungary is in the unique position to use six different vaccines (including the Sputnik V and Sinopharm vaccines, for which limited evidence was available prior to the present study) in the same, relatively homogeneous population. All vaccines provided high level of protection initially which declined over time. While the picture is different in each age group, the waning of immunity is apparent for all vaccines and especially in the younger age groups and the Sinopharm, Sputnik-V and AstraZeneca vaccines, which performed similarly. This is clearly reversed by booster doses, more prominent for those vaccines, where recipients were more likely to take the booster dose (which were the aforementioned three vaccines). Booster doses were almost exclusively mRNA vaccines. Overall, two vaccines, Pfizer/BioNTech and Moderna tend to produce the best results in all age groups, and even with waning taken into account.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Krisztina J. Horvath", - "author_inst": "Epidemiology and Surveillance Centre, Semmelweis University; Mathematical Modelling and Epidemiology Task Force" - }, - { - "author_name": "Tamas Ferenci", - "author_inst": "Mathematical Modelling and Epidemiology Task Force; Physiological Controls Research Center, Obuda University; Department of Statistics, Corvinus University of B" - }, - { - "author_name": "Annamaria Ferenczi", - "author_inst": "Epidemiology and Surveillance Centre, Semmelweis University; Mathematical Modelling and Epidemiology Task Force" - }, - { - "author_name": "Gergo Turi", - "author_inst": "Epidemiology and Surveillance Centre, Semmelweis University; Mathematical Modelling and Epidemiology Task Force" - }, - { - "author_name": "Gergely Rost", - "author_inst": "Mathematical Modelling and Epidemiology Task Force; University of Szeged, Bolyai Institute" - }, - { - "author_name": "Beatrix Oroszi", - "author_inst": "Epidemiology and Surveillance Centre, Semmelweis University; Mathematical Modelling and Epidemiology Task Force" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.02.18.22270995", "rel_title": "Host and microbiome features of secondary infections in lethal covid-19", @@ -368483,6 +370508,29 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2022.02.17.480954", + "rel_title": "Relative positioning of B and T cell epitopes drives immunodominance.", + "rel_date": "2022-02-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.17.480954", + "rel_abs": "Humoral immunity is crucial for protection against invading pathogens. Broadly neutralizing antibodies (bnAbs) provide sterilizing immunity by targeting conserved regions of viral variants and represent the goal of most vaccination approaches. While antibodies can be selected to bind virtually any region of a given antigen, consistent induction of bnAbs in the context of influenza and HIV has been representing a major roadblock. Many possible explanations have been considered, however, none of the arguments proposed so far seems to fully recapitulate the observed counter-selection for broadly protective antibodies.\n\nAntibodies can influence antigen presentation by enhancing the processing of CD4 epitopes adjacent to the binding region while suppressing the overlapping ones. We analyzed the relative positioning of dominant B and T cell epitopes in published antigens that elicit strong and poor humoral responses. In strong immunogenic antigens, regions bound by immunodominant antibodies are frequently adjacent to CD4 epitopes, potentially boosting their presentation. Conversely, poorly immunogenic regions targeted by bnAbs in HIV and influenza overlap with clusters of dominant CD4 epitopes, potentially conferring an intrinsic disadvantage for bnAb-bearing B cells in germinal centers.\n\nHere we propose the theory of immunodominance relativity, according to which relative positioning of immunodominant B and CD4 epitopes within a given antigen drives immunodominance. Thus, we suggest that relative positioning of B-T epitopes may be one additional mechanism that cooperates with other previously described processes to influence immunodominance. If demonstrated, this theory can improve the current understanding of immunodominance, provide a novel explanation on HIV and influenza escape from humoral responses, and pave the way for new rational design of universal vaccines.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Riccardo Biavasco", + "author_inst": "Department of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy" + }, + { + "author_name": "Marco De Giovanni", + "author_inst": "Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.02.17.480940", "rel_title": "Preparing for the next COVID: Deep Reinforcement Learning trained Artificial Intelligence discovery of multi-modal immunomodulatory control of systemic inflammation in the absence of effective anti-microbials", @@ -369562,29 +371610,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.02.10.479891", - "rel_title": "Variational phylodynamic inference using pandemic-scale data", - "rel_date": "2022-02-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.10.479891", - "rel_abs": "The ongoing global pandemic has sharply increased the amount of data available to researchers in epidemiology and public health. Unfortunately, few existing analysis tools are capable of exploiting all of the information contained in a pandemic-scale data set, resulting in missed opportunities for improved surveillance and contact tracing. In this paper, we develop the variational Bayesian skyline (VBSKY), a method for fitting Bayesian phylodynamic models to very large pathogen genetic data sets. By combining recent advances in phylodynamic modeling, scalable Bayesian inference and differentiable programming, along with a few tailored heuristics, VBSKY is capable of analyzing thousands of genomes in a few minutes, providing accurate estimates of epidemiologically relevant quantities such as the effective reproduction number and overall sampling effort through time. We illustrate the utility of our method by performing a rapid analysis of a large number of SARS-CoV-2 genomes, and demonstrate that the resulting estimates closely track those derived from alternative sources of public health data.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Caleb Ki", - "author_inst": "University of Michigan" - }, - { - "author_name": "Jonathan Terhorst", - "author_inst": "University of Michigan" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2022.02.17.22270551", "rel_title": "Natural Trajectory of Recovery of COVID-19 Associated Olfactory Loss", @@ -370397,6 +372422,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.14.22270937", + "rel_title": "Meta-analyses on SARS-CoV-2 Viral Titers in Wastewater and Their Correlations to Epidemiological Indicators", + "rel_date": "2022-02-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.14.22270937", + "rel_abs": "BackgroundRecent applications of wastewater-based epidemiology (WBE) have demonstrated its ability to track the spread and dynamics of COVID-19 at the community level. Despite the growing body of research, quantitative synthesis of SARS-CoV-2 titers in wastewater generated from studies across space and time using diverse methods has not been performed.\n\nObjectiveThe objective of this study is to examine the correlations between SARS-CoV-2 viral titers in wastewater across studies, stratified by key covariates in study methodologies. In addition, we examined the associations of proportions of positive detections (PPD) in wastewater samples and methodological covariates.\n\nMethodsWe systematically searched the Web of Science for studies published by February 16th, 2021, performed a reproducible screen, and employed mixed-effects models to estimate the levels of SARS-CoV-2 viral titers in wastewater samples and their correlations to case prevalence, sampling mode (grab or composite sampling), and the fraction of analysis (FOA, i.e., solids, solid-supernatant mixtures, or supernatants/filtrates)\n\nResultsA hundred and one studies were found; twenty studies (1,877 observations) were retained following a reproducible screen. The mean of PPD across all studies was 0.67 (95%-CI, [0.56, 0.79]). The mean titer was 5,244.37 copies/mL (95%-CI, [0; 16,432.65]). The Pearson Correlation coefficients (PCC) between viral titers and case prevalences were 0.28 (95%-CI, [0.01; 0.51) for daily new cases or 0.29 (95%-CI, [-0.15; 0.73]) for cumulative cases. FOA accounted for 12.4% of the variability in PPD, followed by case prevalence (9.3% by daily new cases and 5.9% by cumulative cases) and sampling mode (0.6%). Among observations with positive detections, FOA accounted for 56.0% of the variability in titers, followed by sampling mode (6.9%) and case prevalence (0.9% by daily new cases and 0.8% by cumulative cases). While sampling mode and FOA both significantly correlated with SARS-CoV-2 titers, the magnitudes of increase in PPD associated with FOA were larger. Mixed-effects model treating studies as random effects and case prevalence as fixed effects accounted for over 90% of the variability in SARS-CoV-2 PPD and titers.\n\nInterpretationsPositive pooled means and confidence intervals in PCC between SARS-CoV-2 titers and case prevalence indicators provide quantitative evidence reinforcing the value of wastewater-based monitoring of COVID-19. Large heterogeneities among studies in proportions of positive detections, titers, and PCC suggest a strong demand in methods to generate data accounting for cross-study heterogeneities and more detailed metadata reporting. Large variance explained by FOA suggesting FOA as a direction that needs to be prioritized in method standardization. Mixed-effects models accounting for study level variations provide a new perspective to synthesize data from multiple studies.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "David Mantilla-Calderon", + "author_inst": "Washington University in St Louis" + }, + { + "author_name": "Kaiyu (Kevin) Huang", + "author_inst": "Washington University in St Louis" + }, + { + "author_name": "Aojie Li", + "author_inst": "Washington University in St Louis" + }, + { + "author_name": "Kaseba Chibwe", + "author_inst": "Washington University in St Louis" + }, + { + "author_name": "Xiaoqian Yu", + "author_inst": "University of Viena" + }, + { + "author_name": "Yinyin Ye", + "author_inst": "University at Buffalo" + }, + { + "author_name": "Lei Liu", + "author_inst": "Washington University in St Louis" + }, + { + "author_name": "Fangqiong Ling", + "author_inst": "Washington University in St Louis" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.02.15.480603", "rel_title": "A possible way to relate the effects of SARS-CoV-2 induced changes in transferrin to severe COVID-19 associated diseases", @@ -371388,41 +373460,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.02.14.22270927", - "rel_title": "Diagnostic Accuracy of Commercially Available Tests for Respiratory Syncytial Virus: A Scoping Literature Review in the COVID-19 Era", - "rel_date": "2022-02-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.14.22270927", - "rel_abs": "BackgroundNon-pharmaceutical interventions to prevent the spread of coronavirus disease 2019 also decreased the spread of respiratory syncytial virus (RSV) and influenza. Viral diagnostic testing in patients with respiratory tract infections (RTI) is a necessary tool for patient management; therefore, sensitive and specific tests are required. This scoping literature review evaluated the analytical validity of commercially available sample-to- answer RSV diagnostic tests in different contexts.\n\nContentPubMed and Embase were queried for studies reporting on the analytical validity of tests for RSV in patients with RTI (published January 2005-January 2021). Sensitivity and specificity of RSV tests and information on study design, patient, and setting characteristics were extracted from 77 studies that met predefined inclusion criteria. A literature gap was identified for studies of RSV tests conducted in adult-only populations (5.3% of total sub- records), and in outpatient (7.5%) or household (0.8%) settings. Overall, RSV tests with analytical time >30 min had higher sensitivity (62.5-100%) versus RSV tests with analytical time [≤] 30 min (25.7-100%), this sensitivity range could be partially attributed to the different modalities (antigen versus molecular) used. Molecular-based rapid RSV tests had higher sensitivity (66.7-100%) and specificity (94.3-100%) than antigen-based RSV tests (25.7- 100%; 80.3-100%).\n\nSummaryMolecular-based RSV tests should be considered for first-line use when possible, given their high sensitivity and specificity and that adults with RTI typically have low viral load, necessitating a highly sensitive test. This review benefits healthcare professionals by summarizing the diagnostic accuracy data available for commercially available RSV tests.\n\nIMPACT STATEMENTViral diagnostic testing in patients with respiratory tract infection is a powerful tool for patient management. This scoping literature review included 77 studies reporting the analytical validity of commercially available respiratory syncytial virus (RSV) diagnostic tests (published January 2005-January 2021) and examined the characteristics of such studies. The data suggest that molecular-based RSV tests have higher sensitivity and specificity than antigen-based tests, thus should be considered for first-line use for timely diagnosis and to detect infections in adults with low level viral load. Future studies should investigate the diagnostic accuracy of RSV tests in adults and in outpatient/household settings.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "David I. Bernstein", - "author_inst": "Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine" - }, - { - "author_name": "Asuncion Mejias", - "author_inst": "Department of Pediatrics, Division of Infectious Diseases, Nationwide Children's Hospital, The Ohio State University" - }, - { - "author_name": "Barbara Rath", - "author_inst": "Vienna Vaccine Safety Initiative" - }, - { - "author_name": "Christopher W. Woods", - "author_inst": "Infectious Diseases Division, Duke University Medical Center" - }, - { - "author_name": "Jamie Philips Deeter", - "author_inst": "ESCMID Study Group for Respiratory Viruses (ESGREV)" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2022.02.14.22268832", "rel_title": "Users' Reactions on Announced Vaccines against COVID-19 Before Marketing in France: Analysis of Twitter posts", @@ -372327,6 +374364,97 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.02.14.480449", + "rel_title": "SARS-CoV-2 Omicron-specific mRNA vaccine induces potent and broad antibody responses in vivo", + "rel_date": "2022-02-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.14.480449", + "rel_abs": "The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has high transmissibility and recently swept the globe. Due to the extensive number of mutations, this variant has high level of immune evasion, which drastically reduced the efficacy of existing antibodies and vaccines. Thus, it is important to test an Omicron-specific vaccine, evaluate its immune response against Omicron and other variants, and compare its immunogenicity as boosters with existing vaccine designed against the reference wildtype virus (WT). Here, we generated an Omicron-specific lipid nanoparticle (LNP) mRNA vaccine candidate, and tested its activity in animals, both alone and as a heterologous booster to existing WT mRNA vaccine. Our Omicron-specific LNP-mRNA vaccine elicited strong and specific antibody response in vaccination-naive mice. Mice that received two-dose WT LNP-mRNA, the one mimicking the commonly used Pfizer/Moderna mRNA vaccine, showed a >40-fold reduction in neutralization potency against Omicron variant than that against WT two weeks post second dose, which further reduced to background level >3 months post second dose. As a booster shot for two-dose WT mRNA vaccinated mice, a single dose of either a homologous booster with WT LNP-mRNA or a heterologous booster with Omicron LNP-mRNA restored the waning antibody response against Omicron, with over 40-fold increase at two weeks post injection as compared to right before booster. Interestingly, the heterologous Omicron LNP-mRNA booster elicited neutralizing titers 10-20 fold higher than the homologous WT booster against the Omicron variant, with comparable titers against the Delta variant. All three types of vaccination, including Omicron mRNA alone, WT mRNA homologous booster, and Omicron heterologous booster, elicited broad binding antibody responses against SARS-CoV-2 WA-1, Beta, and Delta variants, as well as other Betacoronavirus species such as SARS-CoV, but not Middle East respiratory syndrome coronavirus (MERS-CoV). These data provided direct proof-of-concept assessments of an Omicron-specific mRNA vaccination in vivo, both alone and as a heterologous booster to the existing widely-used WT mRNA vaccine form.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Zhenhao Fang", + "author_inst": "Yale University" + }, + { + "author_name": "Lei Peng", + "author_inst": "Yale University" + }, + { + "author_name": "Renata Filler", + "author_inst": "Yale University" + }, + { + "author_name": "Kazushi Suzuki", + "author_inst": "Yale University" + }, + { + "author_name": "Andrew McNamara", + "author_inst": "Yale University" + }, + { + "author_name": "Qianqian Lin", + "author_inst": "Yale University" + }, + { + "author_name": "Paul A Renauer", + "author_inst": "Yale University" + }, + { + "author_name": "Luojia Yang", + "author_inst": "Yale University" + }, + { + "author_name": "Bridget Menasche", + "author_inst": "Yale University" + }, + { + "author_name": "Angie Sanchez", + "author_inst": "Yale University" + }, + { + "author_name": "Ping Ren", + "author_inst": "Yale University" + }, + { + "author_name": "Qiancheng Xiong", + "author_inst": "Yale University" + }, + { + "author_name": "Madison Strine", + "author_inst": "Yale University" + }, + { + "author_name": "Paul Clark", + "author_inst": "Yale University" + }, + { + "author_name": "Chenxiang Lin", + "author_inst": "Yale University" + }, + { + "author_name": "Albert I Ko", + "author_inst": "Yale University" + }, + { + "author_name": "Nathan D Grubaugh", + "author_inst": "Yale University" + }, + { + "author_name": "Craig B Wilen", + "author_inst": "Yale University" + }, + { + "author_name": "Sidi Chen", + "author_inst": "Yale University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.02.14.480353", "rel_title": "The BNT162b2 mRNA SARS-CoV-2 vaccine induces transient afucosylatedIgG1 in naive but not antigen-experienced vaccinees", @@ -373542,49 +375670,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2022.02.13.22270662", - "rel_title": "Brain cortical changes are related to inflammatory biomarkers in hospitalized SARS-CoV-2 patients with neurological symptoms", - "rel_date": "2022-02-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.13.22270662", - "rel_abs": "Increasing evidence shows that the brain is a target of SARS-CoV-2. However, the consequences of the virus on the cortical regions of hospitalized patients are currently unknown. The purpose of this study was to assess brain cortical gray matter volume (GMV), thickness (Th), and surface area (SA) characteristics in SARS-CoV-2 hospitalized patients with a wide range of neurological symptoms and their association with clinical indicators of inflammatory processes. A total of 33 patients were selected from a prospective, multicenter, cross-sectional study during the ongoing pandemic (August 2020-April 2021) at Basel University Hospital. Retrospectively biobank healthy controls with the same image protocol served as controls group. For each anatomical T1w MPRAGE image, the Th and GMV segmentation were performed with the FreeSurfer-5.0. Cortical measures were compared between groups using a linear regression model. The covariates were age, gender, age*gender, MRI magnetic field strength, and total intracranial volume/mean Th/Total SA. The association between cortical features and laboratory variables was assessed using partial correlation adjusting for the same covariates. P-values were adjusted using false discovery rate (FDR). Our findings revealed a lower cortical gray matter volume in orbitofrontal and cingulate regions in patients compared to controls. The orbitofrontal grey matter volume was negatively associated with protein levels, CSF-blood/albumin ratio and CSF EN-RAGE level. CSF EN-RAGE and CSF/Blood-albumin ratio, which are neuroinflammatory biomarkers, were associated with cortical alterations in gray matter volume and thickness in frontal, orbitofrontal, and temporal regions. Our data suggest that viral-triggered inflammation leads to increased neurotoxic damage in some cortical areas.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Gretel Sanabria Diaz", - "author_inst": "Translational Imaging in Neurology (ThINK), Department of Medicine and Biomedical Engineering, University Hospital Basel and University of Basel" - }, - { - "author_name": "Manina Maja Etter", - "author_inst": "Brain Tumor Immunotherapy Lab, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland. Division of Neurosurgery, Unive" - }, - { - "author_name": "Lester Melie Garcia", - "author_inst": "Translational Imaging in Neurology (ThINK), Department of Medicine and Biomedical Engineering, University Hospital Basel and University of Basel, Basel, Switzer" - }, - { - "author_name": "Johanna Maria Lieb", - "author_inst": "Department of Neuroradiology, Clinic of Radiology and Nuclear Medicine, University Hospital Basel, Basel, Switzerland" - }, - { - "author_name": "Marios-Nikos Psychogios", - "author_inst": "Department of Neuroradiology, Clinic of Radiology and Nuclear Medicine, University Hospital Basel, Basel, Switzerland" - }, - { - "author_name": "Gregor Hutter", - "author_inst": "Brain Tumor Immunotherapy Lab, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland. Division of Neurosurgery, Unive" - }, - { - "author_name": "Cristina Granziera", - "author_inst": "Translational Imaging in Neurology (ThINK), Department of Medicine and Biomedical Engineering, University Hospital Basel and University of Basel, Switzerland. D" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2022.02.15.22270974", "rel_title": "A randomized clinical trial of a booster dose with low versus standard dose of AZD1222 in adult after 2 doses of inactivated vaccines", @@ -374445,6 +376530,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.02.09.22270714", + "rel_title": "Quantifying political influence on COVID-19 fatality in Brazil", + "rel_date": "2022-02-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.09.22270714", + "rel_abs": "The COVID-19 pandemic was severely aggravated in Brazil due to its politicization by the countrys central government. However, the impact of diffuse political forces on the fatality of an epidemic is commonly hard to quantify. Here we introduce a method to measure this effect in the Brazilian case, based on the inhomogeneous distribution throughout the national territory of political support to the central government. The correlation between fatality rate and political support grows as the governments misinformation campaign is developed, leading to the dominance of such political factor for the pandemic impact in Brazil in 2021. Once this dominance is established, this correlation allows for an estimation of the total number of deaths due to political influence as 350 {+/-} 70 thousands up to the end of 2021.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Leandro de Almeida", + "author_inst": "Universidade Federal do Rio Grande do Norte" + }, + { + "author_name": "Pedro Carelli", + "author_inst": "Universidade Federal de Pernambuco" + }, + { + "author_name": "Nara Gualberto Cavalcanti", + "author_inst": "Universidade Federal de Pernambuco" + }, + { + "author_name": "Jos\u00e9 Dias do Nascimento Jr.", + "author_inst": "Universidade Federal do Rio Grande do Norte" + }, + { + "author_name": "Daniel Felinto", + "author_inst": "Universidade Federal de Pernambuco" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.02.13.22270898", "rel_title": "Risk of severe COVID-19 in patients with inflammatory rheumatic diseases treated with immunosuppressive therapy in Scotland", @@ -375504,225 +377624,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.10.22270799", - "rel_title": "Evaluating the effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control teams: the COG-UK hospital-onset COVID-19 infection study", - "rel_date": "2022-02-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.10.22270799", - "rel_abs": "IntroductionViral sequencing of SARS-CoV-2 has been used for outbreak investigation, but there is limited evidence supporting routine use for infection prevention and control (IPC) within hospital settings.\n\nMethodsWe conducted a prospective non-randomised trial of sequencing at 14 acute UK hospital trusts. Sites each had a 4-week baseline data-collection period, followed by intervention periods comprising 8 weeks of rapid (<48h) and 4 weeks of longer-turnaround (5-10 day) sequencing using a sequence reporting tool (SRT). Data were collected on all hospital onset COVID-19 infections (HOCIs; detected [≥]48h from admission). The impact of the sequencing intervention on IPC knowledge and actions, and on incidence of probable/definite hospital-acquired infections (HAIs) was evaluated.\n\nResultsA total of 2170 HOCI cases were recorded from October 2020-April 2021, with sequence reports returned for 650/1320 (49.2%) during intervention phases. We did not detect a statistically significant change in weekly incidence of HAIs in longer-turnaround (IRR 1.60, 95%CI 0.85-3.01; P=0.14) or rapid (0.85, 0.48-1.50; P=0.54) intervention phases compared to baseline phase. However, IPC practice was changed in 7.8% and 7.4% of all HOCI cases in rapid and longer-turnaround phases, respectively, and 17.2% and 11.6% of cases where the report was returned. In a per-protocol sensitivity analysis there was an impact on IPC actions in 20.7% of HOCI cases when the SRT report was returned within 5 days.\n\nConclusionWhile we did not demonstrate a direct impact of sequencing on the incidence of nosocomial transmission, our results suggest that sequencing can inform IPC response to HOCIs, particularly when returned within 5 days.", - "rel_num_authors": 51, - "rel_authors": [ - { - "author_name": "Oliver Stirrup", - "author_inst": "Institute for Global Health, UCL, London, UK" - }, - { - "author_name": "James Blackstone", - "author_inst": "Comprehensive Clinical Trials Unit, UCL, London, UK" - }, - { - "author_name": "Fiona Mapp", - "author_inst": "Institute for Global Health, UCL, London, UK" - }, - { - "author_name": "Alyson MacNeil", - "author_inst": "Comprehensive Clinical Trials Unit, UCL, London, UK" - }, - { - "author_name": "Monica Panca", - "author_inst": "Comprehensive Clinical Trials Unit, UCL, London, UK" - }, - { - "author_name": "Alison Holmes", - "author_inst": "Imperial College Healthcare NHS Trust, London, UK" - }, - { - "author_name": "Nicholas Machin", - "author_inst": "Manchester University NHS Foundation Trust, Manchester, UK" - }, - { - "author_name": "Gee Yen Shin", - "author_inst": "University College London Hospitals NHS Foundation Trust, London, UK" - }, - { - "author_name": "Tabitha Mahungu", - "author_inst": "Royal Free NHS Foundation Trust, London, UK" - }, - { - "author_name": "Kordo Saeed", - "author_inst": "University Hospital Southampton NHS Foundation Trust, Southampton, UK" - }, - { - "author_name": "Tranprit Saluja", - "author_inst": "Sandwell and West Birmingham NHS Trust, UK" - }, - { - "author_name": "Yusri Taha", - "author_inst": "Departments of Virology and Infectious Diseases, Newcastle Hospitals NHS Foundation Trust, Newcastle, UK" - }, - { - "author_name": "Nikunj Mahida", - "author_inst": "Nottingham University Hospitals NHS Trust, Nottingham, UK" - }, - { - "author_name": "Cassie Pope", - "author_inst": "St George's University Hospitals NHS Foundation Trust, London, UK" - }, - { - "author_name": "Anu Chawla", - "author_inst": "Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK" - }, - { - "author_name": "Teresa Cutino-Moguel", - "author_inst": "Barts Health NHS Trust, London, UK" - }, - { - "author_name": "Asif Tamuri", - "author_inst": "Research Computing, UCL, London, UK" - }, - { - "author_name": "Rachel Williams", - "author_inst": "Department of Genetics & Genomic Medicine, UCL Great Ormond Street Institute of Child Health, UCL, London, UK" - }, - { - "author_name": "Alistair Darby", - "author_inst": "Centre for Genomic Research, University of Liverpool, Liverpool, UK" - }, - { - "author_name": "David L Robertson", - "author_inst": "MRC-University of Glasgow Centre for Virus Research, Glasgow, UK" - }, - { - "author_name": "Flavia Flaviani", - "author_inst": "Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK" - }, - { - "author_name": "Eleni Nastouli", - "author_inst": "University College London Hospitals NHS Foundation Trust, London, UK" - }, - { - "author_name": "Samuel Robson", - "author_inst": "Centre for Enzyme Innovation, University of Portsmouth, Portsmouth, UK" - }, - { - "author_name": "Darren Smith", - "author_inst": "Department of Applied Sciences, Northumbria University, Newcastle, UK" - }, - { - "author_name": "Matthew Loose", - "author_inst": "School of Life Sciences, University of Nottingham, Nottingham, UK" - }, - { - "author_name": "Kenneth Laing", - "author_inst": "Institute for Infection and Immunity, St George's University of London, London, UK" - }, - { - "author_name": "Irene Monahan", - "author_inst": "Institute for Infection and Immunity, St George's University of London, London, UK" - }, - { - "author_name": "Beatrix Kele", - "author_inst": "Barts Health NHS Trust, London, UK" - }, - { - "author_name": "Sam Haldenby", - "author_inst": "Centre for Genomic Research, University of Liverpool, Liverpool, UK" - }, - { - "author_name": "Ryan George", - "author_inst": "Manchester University NHS Foundation Trust, Manchester, UK" - }, - { - "author_name": "Matthew Bashton", - "author_inst": "The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Northumbria University, Newcastle, UK" - }, - { - "author_name": "Adam Witney", - "author_inst": "Institute for Infection and Immunity, St George's University of London, London, UK" - }, - { - "author_name": "Matthew Byott", - "author_inst": "University College London Hospitals NHS Foundation Trust, London, UK" - }, - { - "author_name": "Francesc Coll", - "author_inst": "Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK" - }, - { - "author_name": "Michael Chapman", - "author_inst": "Health Data Research UK Cambridge Hub, Cambridge UK" - }, - { - "author_name": "Sharon Peacock", - "author_inst": "Department of Medicine, University of Cambridge, Cambridge, UK" - }, - { - "author_name": "- COG-UK HOCI Investigators", - "author_inst": "" - }, - { - "author_name": "- COG-UK Consortium", - "author_inst": "" - }, - { - "author_name": "Joseph Hughes", - "author_inst": "MRC-University of Glasgow Centre for Virus Research, Glasgow, UK" - }, - { - "author_name": "Gaia Nebbia", - "author_inst": "Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK" - }, - { - "author_name": "David G Partridge", - "author_inst": "Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK" - }, - { - "author_name": "Matthew Parker", - "author_inst": "Sheffield Bioinformatics Core, The University of Sheffield, Sheffield, UK" - }, - { - "author_name": "James Richard Price", - "author_inst": "Imperial College Healthcare NHS Trust, London, UK" - }, - { - "author_name": "Christine Peters", - "author_inst": "NHS Greater Glasgow and Clyde, Glasgow, UK" - }, - { - "author_name": "Sunando Roy", - "author_inst": "Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, UCL, London, UK" - }, - { - "author_name": "Luke B Snell", - "author_inst": "Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK" - }, - { - "author_name": "Thushan I de Silva", - "author_inst": "Department of Infection, Immunity and Cardiovascular Disease, Medical School, The University of Sheffield, Sheffield, UK" - }, - { - "author_name": "Emma Thomson", - "author_inst": "MRC-University of Glasgow Centre for Virus Research, Glasgow, UK" - }, - { - "author_name": "Paul Flowers", - "author_inst": "School of Psychological Sciences and Health, University of Strathclyde, Glasgow, UK" - }, - { - "author_name": "Andrew Copas", - "author_inst": "Institute for Global Health, UCL, London, UK" - }, - { - "author_name": "Judith Breuer", - "author_inst": "Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, UCL, London, UK" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.11.22270836", "rel_title": "Persistence, prevalence, and polymorphism of sequelae after COVID-19 in young adults", @@ -376443,6 +378344,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.11.22270785", + "rel_title": "Relation of incident Type 1 diabetes to recent COVID-19 infection: cohort study using e-health record linkage in Scotland", + "rel_date": "2022-02-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.11.22270785", + "rel_abs": "BackgroundStudies using claims databases have reported that SARS-CoV-2 infection >30 days earlier increased the incidence of type 1 diabetes (T1DM). Using exact dates of type 1 diabetes diagnosis from the national register in Scotland linked to virology laboratory data we sought to replicate this finding.\n\nMethodsA cohort of 1849411 individuals aged <35 years without diabetes, including all those in Scotland who subsequently tested positive for SARS-CoV-2, was followed from 1 March 2020 to 22 November 2021. Incident T1DM was identified by linkage to the national registry. Cox regression was used to test the association of time-updated infection with incident T1DM. Trends in incidence of T1DM in the total population from 2015-2021 were estimated in a generalized additive model.\n\nFindingsThere were 365080 in the cohort with at least one detected SARS-CoV-2 infection during follow-up and 1074 who developed T1DM. The rate ratio for incident T1DM associated with first positive test for SARS-CoV-2 (with no previous infection as reference category) was 0.88 (95% CI 0.63 to 1.23) for infection more than 30 days earlier and 2.62 (95% CI 1.81 to 3.79) for infection in the previous 30 days. However negative and positive SARS-CoV-2 tests were more frequent in the days surrounding T1DM presentation. In those aged 0-14 years incidence of T1DM during 2020-2021 was 20% higher than the 7-year average.\n\nInterpretationT1DM incidence in children increased during the pandemic. However the cohort analysis does not support a causal effect of SARS-CoV-2 infection itself on T1DM incidence.\n\nFundingNone", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Paul M McKeigue", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Stuart McGurnaghan", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Luke Blackbourn", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Louise E Bath", + "author_inst": "Royal Infirmary of Edinburgh" + }, + { + "author_name": "David A McAllister", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Thomas M Caparrotta", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Sarah H Wild", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Simon N Wood", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Diane Stockton", + "author_inst": "Public Health Scotland" + }, + { + "author_name": "Helen M Colhoun", + "author_inst": "University of Edinburgh" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.02.10.480009", "rel_title": "Binding Interactions between RBD of Spike-Protein and Human ACE2 in Omicron variant", @@ -377281,49 +379237,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.09.479776", - "rel_title": "Distinct Core Glycan and O-Glycoform Utilization of SARS-CoV-2 Omicron Variant Spike Protein RBD Revealed by Top-Down Mass Spectrometry", - "rel_date": "2022-02-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.09.479776", - "rel_abs": "The SARS-CoV-2 Omicron (B.1.1.529) variant possesses numerous spike (S) mutations particularly in the S receptor-binding domain (S-RBD) that significantly improve transmissibility and evasion of neutralizing antibodies. But exactly how the mutations in the Omicron variant enhance viral escape from immunological protection remains to be understood. The S-RBD remains the principal target for neutralizing antibodies and therapeutics, thus new structural insights into the Omicron S-RBD and characterization of the post-translational glycosylation changes can inform rational design of vaccines and therapeutics. Here we report the molecular variations and O-glycoform changes of the Omicron S-RBD variant as compared to wild-type (WA1/2020) and Delta (B.1.617.2) variants using high-resolution top-down mass spectrometry (MS). A novel O-glycosite (Thr376) unique to the Omicron variant is identified. Moreover, we have directly quantified the Core 1 and Core 2 O-glycan structures and characterized the O-glycoform structural heterogeneity of the three variants. Our findings reveal high resolution detail of Omicron O-glycoforms and their utilization to provide direct molecular evidence of proteoform alterations in the Omicron variant which could shed light on how this variant escapes immunological protection.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "David S. Roberts", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Morgan Mann", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Brad Hualin Li", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Donguk Kim", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Allan R. Brasier", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Song Jin", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Ying Ge", - "author_inst": "University of Wisconsin-Madison" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2022.02.09.479781", "rel_title": "Engineering Defensin \u03b1-helix to produce high-affinity SARS-CoV-2 Spike protein binding ligands.", @@ -378244,6 +380157,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.07.22270646", + "rel_title": "Post-acute sequelae of COVID-19 and adverse psychiatric outcomes: an etiology and risk systematic review protocol", + "rel_date": "2022-02-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.07.22270646", + "rel_abs": "IntroductionThe post-acute sequelae of COVID-19 (PASC) is a syndrome characterized by persistent COVID-19 symptoms or the onset of new symptoms following recovery from the initial or acute phase of the illness. Such symptoms often occur four or more weeks after being diagnosed with COVID-19. Although a lot of work has gone into understanding the long-term mental health effects of PASC, many questions related to the etiology and risk of this condition remain. Thus, this protocol is for a systematic review assessing the association between PASC and adverse psychiatric outcomes and whether people with PASC are at greater risk of developing an adverse psychiatric outcome than those without PASC.\n\nMethods and analysisVarious medical databases (e.g., PubMed and EMBASE) will be searched for eligible articles using predefined search criteria. Gray literature will also be explored. Epidemiological observational studies and secondary analyses of randomized controlled trials that report a quantitative relationship between PASC and at least one adverse psychiatric outcome will be included. The Population, Exposure of interest, Comparator, and Outcome (PECO) framework will be used as a standardized framework for the inclusion criteria. The Joanna Briggs Institute (JBI) critical appraisal tools will be used to assess methodological quality and critically appraise the risk of bias in included studies. A random-effects meta-analysis will be conducted if possible. A formal narrative synthesis will be performed if a meta-analysis is impossible due to substantial heterogeneity across studies. The Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach will be used to rate the cumulative certainty of the evidence for all outcomes.\n\nEthics and DisseminationEthical approval is not required for this study. The study results will be published in a peer-reviewed journal.\n\nProspero registration numberCRD42022308737\n\nStrengths and limitations of this study{blacksquare} This study documents and addresses etiology, risk factors, and long-term symptoms of COVID-19 among people with post-acute sequelae of COVID-19 (PASC).\n{blacksquare}It focuses on a key priority area for new evidence syntheses on the clinical management of COVID-19 and pandemic-related conditions.\n{blacksquare}It will include evidence on non-hospitalized and hospitalized patients with a history of PASC.\n{blacksquare}Substantial heterogeneity across studies may limit the ability to perform a meta-analysis.\n{blacksquare}Findings will inform disease prevention, decision-making, healthcare policy, and clinical research.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Andem Effiong", + "author_inst": "Faculty of Medicine, Memorial University of Newfoundland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.02.08.22270668", "rel_title": "Community vaccination can shorten the COVID-19 isolation period: an individual-based modeling approach", @@ -379259,53 +381191,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2022.02.09.479546", - "rel_title": "Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat", - "rel_date": "2022-02-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.09.479546", - "rel_abs": "The long-term evolution of viruses is ultimately due to viral mutants that arise within infected individuals and transmit to other individuals. Here we use deep sequencing to investigate the transmission of viral genetic variation among individuals during a SARS-CoV-2 outbreak that infected the vast majority of crew members on a fishing boat. We deep-sequenced nasal swabs to characterize the within-host viral population of infected crew members, using experimental duplicates and strict computational filters to ensure accurate variant calling. We find that within-host viral diversity is low in infected crew members. The mutations that did fix in some crew members during the outbreak are not observed at detectable frequencies in any of the sampled crew members in which they are not fixed, suggesting viral evolution involves occasional fixation of low-frequency mutations during transmission rather than persistent maintenance of within-host viral diversity. Overall, our results show that strong transmission bottlenecks dominate viral evolution even during a superspreading event with a very high attack rate.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "William H Hannon", - "author_inst": "University of Washington" - }, - { - "author_name": "Pavitra Roychoudhury", - "author_inst": "University of Washington" - }, - { - "author_name": "Hong Xie", - "author_inst": "University of Washington" - }, - { - "author_name": "Lasata Shrestha", - "author_inst": "University of Washington" - }, - { - "author_name": "Amin Addetia", - "author_inst": "University of Washington" - }, - { - "author_name": "Keith R Jerome", - "author_inst": "Fred Hutch Cancer Center" - }, - { - "author_name": "Alexander L Greninger", - "author_inst": "University of Washington" - }, - { - "author_name": "Jesse D Bloom", - "author_inst": "Fred Hutchinson Cancer Research Center" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2022.02.09.479669", "rel_title": "Auto-Immunoproteomics Analysis of COVID-19 ICU Patients Revealed Increased Levels of Autoantibodies Related to Male Reproductive System", @@ -380310,6 +382195,153 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rheumatology" }, + { + "rel_doi": "10.1101/2022.02.08.22270676", + "rel_title": "Safety and immunogenicity of a live recombinant Newcastle disease virus-based COVID-19 vaccine (Patria) administered via the intramuscular or intranasal route: Interim results of a non-randomized open label phase I trial in Mexico", + "rel_date": "2022-02-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.08.22270676", + "rel_abs": "There is still a need for safe, efficient and low-cost coronavirus disease 2019 (COVID-19) vaccines that can stop transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here we evaluated a vaccine candidate based on a live recombinant Newcastle disease virus (NDV) that expresses a stable version of the spike protein in infected cells as well as on the surface of the viral particle (AVX/COVID-12-HEXAPRO, also known as NDV-HXP-S). This vaccine candidate can be grown in embryonated eggs at low cost similar to influenza virus vaccines and it can also be administered intranasally, potentially to induce mucosal immunity. We evaluated this vaccine candidate in prime-boost regimens via intramuscular, intranasal, or intranasal followed by intramuscular routes in an open label non-randomized non-placebo-controlled phase I clinical trial in Mexico in 91 volunteers. The primary objective of the trial was to assess vaccine safety and the secondary objective was to determine the immunogenicity of the different vaccine regimens. In the interim analysis reported here, the vaccine was found to be safe and the higher doses tested were found to be immunogenic when given intramuscularly or intranasally followed by intramuscular administration, providing the basis for further clinical development of the vaccine candidate. The study is registered under ClinicalTrials.gov identifier NCT04871737. Funding was provided by Avimex and CONACYT.", + "rel_num_authors": 33, + "rel_authors": [ + { + "author_name": "Samuel Ponce-de-Leon", + "author_inst": "Universidad Nacional Autonoma de Mexico" + }, + { + "author_name": "Martha Torres", + "author_inst": "INER" + }, + { + "author_name": "Luis Enrique Soto-Ramirez", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Juan Jose Calva", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Patricio Santillan-Doherty", + "author_inst": "INER" + }, + { + "author_name": "Dora Eugenia Carranza-Salazar", + "author_inst": "ProcliniQ" + }, + { + "author_name": "Juan Manuel Carreno", + "author_inst": "ISMMS" + }, + { + "author_name": "Claudia Carranza", + "author_inst": "INER" + }, + { + "author_name": "Esmeralda Juarez", + "author_inst": "INER" + }, + { + "author_name": "Laura E. Carreto-Binaghi", + "author_inst": "INER" + }, + { + "author_name": "Luis Ramirez-Martinez", + "author_inst": "Avimex" + }, + { + "author_name": "Georgina Paz-De la Rosa", + "author_inst": "Avimex" + }, + { + "author_name": "Rosalia Vigueras-Moreno", + "author_inst": "Avimex" + }, + { + "author_name": "Alejandro Ortiz-Stern", + "author_inst": "iLS Clinical Research" + }, + { + "author_name": "Yolanda Lopez-Vidal", + "author_inst": "UNAM" + }, + { + "author_name": "Alejandro E. Macias", + "author_inst": "Universidad de Guanajuato" + }, + { + "author_name": "Jesus Torres-Flores", + "author_inst": "CONACYT" + }, + { + "author_name": "Oscar Rojas-Martinez", + "author_inst": "Avimex" + }, + { + "author_name": "Alejandro Suarez-Martinez", + "author_inst": "Avimex" + }, + { + "author_name": "Gustavo Peralta-Sanchez", + "author_inst": "Avimex" + }, + { + "author_name": "Hisaaki Kawabata", + "author_inst": "ISMMS" + }, + { + "author_name": "Irene Gonzalez-Dominguez", + "author_inst": "ISMMS" + }, + { + "author_name": "Jose Luis Martinez-Guevara", + "author_inst": "ISMMS" + }, + { + "author_name": "Weina Sun", + "author_inst": "ISMMS" + }, + { + "author_name": "David Sarfati-Mizrahi", + "author_inst": "Avimex" + }, + { + "author_name": "Ernesto Soto-Priante", + "author_inst": "Avimex" + }, + { + "author_name": "Hector Elias Chagoya-Cortes", + "author_inst": "Mextrategy" + }, + { + "author_name": "Constantino Lopez-Macias", + "author_inst": "IMSS" + }, + { + "author_name": "Felipa Castro-Peralta", + "author_inst": "Avimex" + }, + { + "author_name": "Peter Palese", + "author_inst": "ISMMS" + }, + { + "author_name": "Adolfo Garcia-Sastre", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Florian Krammer", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Bernardo Lozano-Dubernard", + "author_inst": "Avimex" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.06.22270346", "rel_title": "Changes in the number of public health nurses employed in local governments in Japan during the Covid-19 pandemic: A cross-sectional study", @@ -381297,141 +383329,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2022.02.07.22270215", - "rel_title": "Safety and efficacy of two immunization schedules with an inactivated SARS-CoV-2 vaccine in adults. A randomized non-inferiority clinical trial.", - "rel_date": "2022-02-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.07.22270215", - "rel_abs": "BackgroundSeveral vaccines have been developed to control the COVID-19 pandemic. CoronaVac(R) (Sinovac Life Sciences), an inactivated SARS-CoV-2 vaccine, has demonstrated safety and immunogenicity in previous studies, preventing severe COVID-19 cases. We further investigated the safety and efficacy of two immunization schedules of CoronaVac(R) in a non-inferiority trial in healthy adults.\n\nMethodsThis is a multi-center and randomized clinical trial. Healthy adults were enrolled at eight centers in Chile. Participants were randomly assigned to two vaccination schedules, receiving two doses with either 14 (0-14) or 28 (0-28) days between each. 2302 participants were vaccinated. The primary safety and efficacy endpoints were solicited adverse events (AE) within 7 days after each dose and compared the number of cases of SARS-CoV-2 infection 14 days after the second dose between schedules, respectively.\n\nFindingsThe most frequent local AE was pain at the injection site, which was less frequent in participants aged [≥]60 years. Other local AEs were reported in less than 5% of participants. The most frequent systemic AEs were headache, fatigue, and myalgia. The remaining AEs were minor allergic reactions and fever. Most AEs were mild and transient. There were no significant differences for local and systemic AE between schedules. No anaphylactic reactions or vaccine-related severe AEs were observed. 58 COVID-19 cases were confirmed, and all but two of them were mild. No differences were observed in protection between schedules.\n\nInterpretationCoronaVac(R) is safe, especially in [≥]60 years-old participants. Both schedules protected against COVID-19 hospitalizations.\n\nFundingMINSAL, Chile, CPC & IMII, Chile.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSCoronaVac(R) (an inactivated SARS-CoV-2 vaccine) was approved on June 1st, 2021, by the WHO for its use in humans. Sinovac Life Sciences generated this vaccine in China and conducted phase 1/2 trials. Good safety, efficacy, and immunogenicity profiles were reported. The results from this study led to the use of CoronaVac(R) in other countries, such as Brazil, Turkey, and Chile, with phase 3 trials being held on them.\n\nAdded-value of this studyThis work compares the safety and efficacy of two immunization schedules with CoronaVac(R), with each dose administrated two or four weeks after the first dose on healthy Chilean adults. To date, no studies showing the safety and efficacy of these two immunization schedules with CoronaVac(R) in healthy adults in a population other than the Chinese have been published. We show that CoronaVac(R) is safe and prevents hospitalization due to COVID-19 in both immunization schedules. No differences were found in the incidence of adverse events between both schedules, and no related severe adverse events were reported. These results give further insight into the immune response induced by CoronaVac(R) and are relevant when deciding on the immunization schedule chosen for vaccination.\n\nImplications of all the available evidenceThe data reported here show that using either immunization schedule with two doses of CoronaVac(R) protects against SARS-CoV-2. The data also indicate that CoronaVac(R) does not induce severe adverse events in either immunization schedule, and the adverse events registered are mild and transient, confirming the safety of this vaccine.", - "rel_num_authors": 30, - "rel_authors": [ - { - "author_name": "Katia Abarca", - "author_inst": "Pontificia Universidad Catolica de Chile Facultad de Medicina" - }, - { - "author_name": "Carolina Iturriaga", - "author_inst": "Pontificia Universidad Catolica de Chile Facultad de Medicina" - }, - { - "author_name": "Marcela Urzua", - "author_inst": "Pontificia Universidad Catolica de Chile Facultad de Medicina" - }, - { - "author_name": "Nicole Le Corre", - "author_inst": "Pontificia Universidad Catolica de Chile Facultad de Medicina" - }, - { - "author_name": "Augusto Pineda", - "author_inst": "Red de Salud UC Christus" - }, - { - "author_name": "Carolina Fernandez", - "author_inst": "Pontificia Universidad Catolica de Chile Facultad de Medicina" - }, - { - "author_name": "Angelica Dominguez", - "author_inst": "Pontificia Universidad Catolica de Chile Facultad de Medicina" - }, - { - "author_name": "Pablo A Gonzalez", - "author_inst": "Pontificia Universidad Catolica de Chile Facultad de Ciencias Biologicas" - }, - { - "author_name": "Susan M Bueno", - "author_inst": "Pontificia Universidad Catolica de Chile Facultad de Ciencias Biologicas" - }, - { - "author_name": "Paulina Donato", - "author_inst": "Complejo Asistencial Dr. Sotero del Rio" - }, - { - "author_name": "Pilar Espinoza", - "author_inst": "Universidad San Sebastian" - }, - { - "author_name": "Daniela Fuentes", - "author_inst": "Universidad de Valparaiso" - }, - { - "author_name": "Marcela Gonzalez", - "author_inst": "Universidad de Valparaiso" - }, - { - "author_name": "Paula Guzman", - "author_inst": "Universidad de Los Andes" - }, - { - "author_name": "Paula Munoz", - "author_inst": "Universidad del Desarrollo" - }, - { - "author_name": "Carlos M Perez", - "author_inst": "Universidad San Sebastian" - }, - { - "author_name": "Marcela Potin", - "author_inst": "Pontificia Universidad Catolica de Chile Facultad de Medicina" - }, - { - "author_name": "Alvaro Rojas", - "author_inst": "Pontificia Universidad Catolica de Chile Facultad de Medicina" - }, - { - "author_name": "Jose V Gonzalez-Aramundiz", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Nicolas M S Galvez", - "author_inst": "Pontificia Universidad Catolica de Chile Facultad de Ciencias Biologicas" - }, - { - "author_name": "Francisca Aguirre-Boza", - "author_inst": "Universidad de Los Andes" - }, - { - "author_name": "Sofia Aljaro", - "author_inst": "Red de Salud UC Christus" - }, - { - "author_name": "Luis F Batiz", - "author_inst": "Universidad de Los Andes" - }, - { - "author_name": "Yessica Campisto", - "author_inst": "Complejo Asistencial Dr. Sotero del Rio" - }, - { - "author_name": "Mariela Cepeda", - "author_inst": "Universidad de Valparaiso" - }, - { - "author_name": "Aaron Cortes", - "author_inst": "Universidad de Los Andes" - }, - { - "author_name": "Sofia Lopez", - "author_inst": "Red de Salud UC Christus" - }, - { - "author_name": "Maria L Perez", - "author_inst": "Universidad San Sebastian" - }, - { - "author_name": "Andrea Schilling", - "author_inst": "Universidad del Desarrollo" - }, - { - "author_name": "Alexis M Kalergis", - "author_inst": "Pontificia Universidad Catolica de Chile Facultad de Ciencias Biologicas" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.07.22270617", "rel_title": "Genetic immune response and antibody repertoire of heterologous ChAdOx1-BNT162b2 vaccination in a Korean cohort", @@ -382272,6 +384169,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.02.07.22270634", + "rel_title": "Deploying wearable sensors for pandemic mitigation", + "rel_date": "2022-02-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.07.22270634", + "rel_abs": "Wearable sensors can continuously and passively detect potential respiratory infections, before or absent symptoms. However, the population-level impact of deploying these devices during pandemics is unclear. We built a compartmental model of Canadas second COVID-19 wave and simulated wearable sensor deployment scenarios, systematically varying detection algorithm accuracy, uptake, and adherence. With current detection algorithms and 4% uptake, we found that deploying wearable sensors could have averted 9% of second wave SARS-CoV-2 infections, though 29% of this reduction is attributed to incorrectly quarantining uninfected device users. Improving detection specificity and offering confirmatory rapid tests each minimized incorrect quarantines and associated costs. With a sufficiently low false positive rate, increasing uptake and adherence became effective strategies for scaling averted infections. We concluded that wearable sensor deployment can meaningfully contribute to pandemic mitigation; in the case of COVID-19, technology improvements or supporting measures are required to reduce social and economic costs to acceptable levels.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Nathan Duarte", + "author_inst": "McGill University" + }, + { + "author_name": "Rahul K Arora", + "author_inst": "Oxford University" + }, + { + "author_name": "Graham Bennett", + "author_inst": "McGill University" + }, + { + "author_name": "Meng Wang", + "author_inst": "Stanford University" + }, + { + "author_name": "Michael P Snyder", + "author_inst": "Stanford University" + }, + { + "author_name": "Jeremy R Cooperstock", + "author_inst": "McGill University" + }, + { + "author_name": "Caroline E Wagner", + "author_inst": "McGill University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.02.07.22270332", "rel_title": "Evaluating Fomite Risk of Brown Paper Bags Storing Personal Protective Equipment Exposed to SARS-CoV-2: A Quasi-Experimental Study", @@ -383479,73 +385419,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.02.06.21266924", - "rel_title": "Single cell sequencing analysis uncovers genetics-influenced CD16+monocytes and memory CD8+T cells involved in severe COVID-19", - "rel_date": "2022-02-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.06.21266924", - "rel_abs": "BackgroundUnderstanding the host genetic architecture and viral immunity contributes to the development of effective vaccines and therapeutics for controlling the COVID-19 pandemic. Alterations of immune responses in peripheral blood mononuclear cells play a crucial role in the detrimental progression of COVID-19. However, the effects of host genetic factors on immune responses for severe COVID-19 remain largely unknown.\n\nMethodsWe constructed a powerful computational framework to characterize the host genetics-influenced immune cell subpopulations for severe COVID-19 by integrating GWAS summary statistics (N = 969,689 samples) with four independent scRNA-seq datasets (N = 606,534 cells).\n\nResultsWe found that 34 risk genes were significantly associated with severe COVID-19, and the number of highly-expressed genetics-risk genes increased with the severity of COVID-19. Three cell-subtypes that are CD16+monocytes, megakaryocytes, and memory CD8+T cells were significantly enriched by COVID-19-related genetic association signals. Notably, three causal risk genes of CCR1, CXCR6, and ABO were specifically expressed in these three cell types, respectively. CCR1+CD16+monocytes and ABO+ megakaryocytes with significant up-regulated genes including S100A12, S100A8, S100A9, and IFITM1 confer higher risk to the cytokine storms among severe patients. CXCR6+ memory CD8+ T cells exhibit a notable polyfunctionality of multiple immunologic features, including elevation of proliferation, migration, and chemotaxis. Moreover, we observed a prominent increase in cell-cell interactions of both CCR1+ CD16+monocytes and CXCR6+ memory CD8+T cells in severe patients compared to normal controls among both PBMCs and lung tissues, and elevated interactions with epithelial cells could contribute to enhance the resident to lung airway for against COVID-19 infection.\n\nConclusionsWe uncover a major genetics-modulated immunological shift between mild and severe infection, including an increase in up-regulated genetic-risk genes, excessive secreted inflammatory cytokines, and functional immune cell subsets contributing high risk to severity, which provides novel insights in parsing the host genetics-influenced immune cells for severe COVID-19.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Yunlong Ma", - "author_inst": "Wenzhou Medical University" - }, - { - "author_name": "Fei Qiu", - "author_inst": "Wenzhou Medical University" - }, - { - "author_name": "Chunyu Deng", - "author_inst": "Wenzhou Medical University" - }, - { - "author_name": "Jingjing Li", - "author_inst": "State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Collaborative Innovation Center for Diagnosis and Treatm" - }, - { - "author_name": "Yukuan Huang", - "author_inst": "Wenzhou Medical University" - }, - { - "author_name": "Zeyi Wu", - "author_inst": "Wenzhou Medical University" - }, - { - "author_name": "Yijun Zhou", - "author_inst": "Wenzhou Medical University" - }, - { - "author_name": "Yaru Zhang", - "author_inst": "Institute of Biomedical Big Data, School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 32" - }, - { - "author_name": "Yichun Xiong", - "author_inst": "Wenzhou Institute, University of Chinese Academy of Sciences" - }, - { - "author_name": "Yinghao Yao", - "author_inst": "Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325011, China" - }, - { - "author_name": "Yigang Zhong", - "author_inst": "Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine" - }, - { - "author_name": "Jia Qu", - "author_inst": "Institute of Biomedical Big Data, School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University" - }, - { - "author_name": "Jianzhong Su", - "author_inst": "Wenzhou Medical University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2022.02.07.22270579", "rel_title": "The use of social media platforms by migrant and ethnic minority populations during the COVID-19 pandemic: a systematic review", @@ -384542,6 +386415,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.02.07.22270394", + "rel_title": "Cross-Sectional Study of University students attitudes to on campus delivery of COVID-19 vaccines and future-proofing MenACWY and MMR vaccination rates by adopting COVID-19 vaccine roll-out strategies", + "rel_date": "2022-02-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.07.22270394", + "rel_abs": "BackgroundUniversity students are a critical group for vaccination programmes against COVID-19, meningococcal disease (MenACWY), and measles, mumps and rubella (MMR). We aimed to evaluate risk factors for vaccine hesitancy (refusal or intention to refuse a vaccine) and views of university students about on-campus vaccine delivery.\n\nMethodsCross-sectional anonymous online questionnaire study of undergraduate students at a British university in June 2021. Chi-squared, Fishers exact, univariate and multivariate tests were applied to detect associations.\n\nResultsComplete data were obtained from 827 participants (7.6% response-rate). Two-thirds (64%; 527/827) reported having been vaccinated against COVID-19 and a further 23% (194/827) agreed to be vaccinated. Other responses were either unclear (66) or indicated an intention to refuse vaccination (40). Hesitancy for COVID-19 vaccines was 5% (40/761). COVID-19 vaccine hesitancy was associated with black ethnicity (aOR, 7.01, 95% CI, 1.8-27.3) and concerns about vaccine side-effects (aOR, 1.72; 95% CI, 1.23-2.39). Lower levels of vaccine hesitancy were detected amongst students living in private accommodation (aOR, 0.13; 95% CI, 0.04-0.38) compared to those living at home. Uncertainty about their personal vaccine status was frequently observed for MMR (11%) and MenACWY (26%) vaccines. Campus-associated COVID-19 vaccine campaigns were definitely (45%) or somewhat (16%) favoured by UK-based students and more so among UK-based international students (62% and 12%, respectively).\n\nConclusionsVaccine hesitancy among students of black ethnicity and those living at home requires further exploration because attitudes in these groups may affect COVID-19 vaccine uptake. High levels of uncertainty among students about their MMR and MenACWY vaccine status are also a concern for the effectiveness of these vaccine programmes. This issue could be tackled by extending the capabilities of digital platforms for accessing vaccine information, such as the NHSapp in the UK. Sector-wide implementation of on-campus vaccine delivery may also improve vaccine uptake, especially for international students.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Adam Webb", + "author_inst": "University of Leicester" + }, + { + "author_name": "Mayuri D Gogoi", + "author_inst": "University of Leicester" + }, + { + "author_name": "Sarah Weidman", + "author_inst": "University of Leicester" + }, + { + "author_name": "Katherine Woolf", + "author_inst": "UCL" + }, + { + "author_name": "Maria Zavala", + "author_inst": "Public Health England" + }, + { + "author_name": "Shamez Ladhani", + "author_inst": "Public Health England" + }, + { + "author_name": "Manish Pareek", + "author_inst": "University of Leicester" + }, + { + "author_name": "Lieve Gies", + "author_inst": "University of Leicester" + }, + { + "author_name": "Christopher D Bayliss", + "author_inst": "University of Leicester" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.02.05.22270453", "rel_title": "Estimating the risk reduction of isolation on COVID-19 non-household transmission and severe/critical illness in non-immune individuals: September to November 2021", @@ -385837,41 +387761,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.02.04.22270483", - "rel_title": "SARS-CoV-2 Testing Strategies for Outbreak Mitigation in Vaccinated Populations", - "rel_date": "2022-02-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.04.22270483", - "rel_abs": "Although COVID-19 vaccines are globally available, waning immunity and emerging vaccine-evasive variants of concern have hindered the international response as COVID-19 cases continue to rise. Mitigating COVID-19 requires testing to identify and isolate infectious individuals. We developed a stochastic compartmentalized model to simulate SARS-CoV-2 spread in the United States and India using Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) assays, rapid antigen tests, and vaccinations. We detail the optimal testing frequency and coverage in the US and India to mitigate an emerging outbreak even in a vaccinated population: overall, maximizing frequency is more important, but high coverage remains necessary when there is sustained transmission. We show that a resource-limited vaccination strategy still requires high-frequency testing and is 16.50% more effective in India than the United States. Tailoring testing strategies to transmission settings can help effectively reduce cases more than if a uniform approach is employed without regard to differences in location.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Chirag K. Kumar", - "author_inst": "Princeton University, Princeton, NJ, USA" - }, - { - "author_name": "Ruchita Balasubramanian", - "author_inst": "Center for Disease Dynamics, Economics, and Policy, New Delhi, India" - }, - { - "author_name": "Stefano Ongarello", - "author_inst": "Foundation for Innovative New Diagnostics, Geneva, Switzerland" - }, - { - "author_name": "Sergio Carmona", - "author_inst": "Foundation for Innovative New Diagnostics, Geneva, Switzerland" - }, - { - "author_name": "Ramanan Laxminarayan", - "author_inst": "Center for Disease Dynamics, Economics, and Policy, New Delhi, India" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.01.31.22270192", "rel_title": "Modinterv COVID-19: An online platform to monitor the evolution of epidemic curves", @@ -386552,6 +388441,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.31.22270036", + "rel_title": "Results From the REsCue Trial: A Randomized Controlled Trial with Extended-Release Calcifediol in Symptomatic Outpatients with COVID-19.", + "rel_date": "2022-02-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.31.22270036", + "rel_abs": "ImportanceThe benefit of vitamin D treatment for coronavirus disease 2019 (COVID-19) remains unclear.\n\nObjectiveTo investigate the effect of raising serum total 25-hydroxyvitamin D (25D) to 50-100 ng/mL with oral extended-release calcifediol (ERC) on time to symptom resolution in mild to moderate COVID-19.\n\nDesign, Setting, and ParticipantsA multicenter, randomized, double-blind, placebo-controlled study evaluated treatment of 160 outpatients with COVID-19 diagnosed between November 2020 and October 2021.\n\nInterventionsPatients were treated for 4 weeks with ERC (30 mcg/capsule; 300 mcg on Days 1-3 and 60 mcg on Days 4-27) or placebo.\n\nOutcome MeasuresPrimary endpoints were raising serum 25D to [≥]50 ng/mL at Day 14 and resolution time for five aggregated symptoms. Secondary endpoints included resolution time for aggregated and individual symptoms as a function of serum 25D and changes in clinical biomarkers.\n\nResults171 subjects randomized, 160 treated and 134 (65 ERC and 69 placebo) retained. Average age was 43 (range: 18-71); 59% female, 92% White, 80% Hispanic, 7% African-American, 1% Other, 76% overweight, 40% obese, 26% comorbidities, mean baseline 25D of 37{+/-}1 (SE) ng/mL. ERC increased mean 25D to 82{+/-}4 ng/mL (p<0.001) by Day 7; 88% of subjects attained a level [≥]50 ng/mL; the placebo group trended lower. Resolution time for five aggregated symptoms was unchanged by ERC given that two composite non-respiratory symptoms responded poorly. Prespecified analyses showed that respiratory symptoms tended to resolve earlier when serum 25D levels reached [≤]50 ng/mL, but statistical significance was limited by small sample size and non-compliance: 25D increased in seven placebo subjects (unauthorized supplementation) and none occurred in five ERC subjects (failure to dose). A post-hoc composite of three respiratory symptoms (trouble breathing, chest congestion and dry or hacking cough) resolved 3.0 days faster when 25D was elevated at Days 7 and 14 (p<0.05); chest congestion resolved 4.0 days faster with 25D increases of [≥]25 ng/mL (p<0.05). Safety concerns including hypercalcemia were absent with ERC treatment.\n\nConclusions and RelevanceERC was effective in increasing serum 25D in outpatients with COVID-19, which may have accelerated resolution of respiratory symptoms suggesting mitigation of COVID-19 pneumonia risk, findings which warrant further study.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Charles W Bishop", + "author_inst": "OPKO Health, MIami, FL" + }, + { + "author_name": "Akhtar Ashfaq", + "author_inst": "OPKO Health, Miami, FL" + }, + { + "author_name": "Joel Z Melnick", + "author_inst": "SCDadvisor, Evanston, IL" + }, + { + "author_name": "Enrique Vazquez-Escarpanter", + "author_inst": "Kendall South Medical Center, Miami , FL" + }, + { + "author_name": "Jonathan A Fialkow", + "author_inst": "Cardiovascular Research Center of South Florida, Miami, FL, USA" + }, + { + "author_name": "Stephen A Strugnell", + "author_inst": "OPKO Health, Miami, FL" + }, + { + "author_name": "John Choe", + "author_inst": "OPKO Health, Miami, FL" + }, + { + "author_name": "Kamyar Kalantar-Zadeh", + "author_inst": "Division of Nephrology, Hypertension and Kidney Transplantation, University of California Irvine, Orange, CA, USA" + }, + { + "author_name": "Noah C Federman", + "author_inst": "Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA," + }, + { + "author_name": "David Ng", + "author_inst": "WuXi Clinical Development, Austin, TX, USA" + }, + { + "author_name": "Johm S Adams", + "author_inst": "Department of Orthopaedic Surgery and Molecular, Cell and Developmental Biology, UCLA, Los Angeles, CA, USA" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.01.22270253", "rel_title": "Safety and Immunogenicity of An Egg-Based Inactivated Newcastle Disease Virus Vaccine Expressing SARS-CoV-2 Spike: Interim Results of a Randomized, Placebo-Controlled, Phase 1/2 Trial in Vietnam", @@ -387867,93 +389815,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.03.22270152", - "rel_title": "Efficacy and safety of nitazoxanide combined with ritonavir-boosted atazanavir for the treatment of mild to moderate COVID-19", - "rel_date": "2022-02-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.03.22270152", - "rel_abs": "BackgroundFinding effective therapeutics for COVID-19 continues to be an urgent need, especially considering use context limitations and high cost of currently approved agents. The NACOVID trial investigated the efficacy and safety of repurposed antiprotozoal and antiretroviral drugs, nitazoxanide and atazanavir/ritonavir, used in combination for COVID-19.\n\nMethodsIn this pilot, randomized, open-label trial conducted in Nigeria, patients diagnosed with mild to moderate COVID-19 were randomly assigned to receive standard of care (SoC) or SoC plus a 14-day course of nitazoxanide (1000 mg b.i.d.) and atazanavir/ritonavir (300/100 mg od) and followed through day 28. Study endpoints included time to clinical improvement, SARS-CoV-2 viral load change, and time to complete symptom resolution. Safety and pharmacokinetics of nitazoxanide active metabolite, tizoxanide, were also evaluated. This trial was registered with ClinicalTrials.gov (NCT04459286).\n\nFindingsThere was no difference in time to clinical improvement between the SoC (n = 26) and SoC plus intervention arms (n = 31; Cox proportional hazards regression analysis adjusted hazard ratio, aHR = 0.898, 95% CI: 0.492-1.638, p = 0.725). No difference was observed in the pattern of saliva SARS-CoV-2 viral load changes from days 2 to 28 in the 35% of patients with detectable virus at baseline (20/57) between the two arms (aHR = 0.948, 95% CI: 0.341-2.636, p = 0.919). There was no significant difference in time from enrolment to complete symptom resolution (aHR = 0.535, 95% CI: 0.251 - 1.140, p = 0.105). Atazanavir/ritonavir increased tizoxanide plasma exposure by 68% and median trough plasma concentration was 1546 ng/ml (95% CI: 797-2557), above its putative EC90 in 54% of patients. Tizoxanide was not detectable in saliva.\n\nInterpretationThese findings should be interpreted in the context of incomplete enrolment (64%) and the limited number of patients with detectable SARS-CoV-2 in saliva at baseline in this trial.\n\nFundingThe University of Liverpool.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSThe potential efficacy of nitazoxanide as a repurposed drug for COVID-19 is being investigated in a number of studies due to confirmed in vitro activity against SARS-CoV-2. Available data from completed randomised controlled trials in which clinical improvement, effect on viral load, and symptom resolution were evaluated as outcomes do not offer conclusive evidence.\n\nAdded value of this studyIn the NACOVID trial, we sought to take advantage of a model-informed strategy and known interaction between nitazoxanide and atazanavir/ritonavir to achieve optimal concentration of tizoxanide in plasma, and possibly in respiratory tracts of patients with mild to moderate COVID-19. While this strategy significantly enhanced tizoxanide exposure in the plasma of patients, our data indicated poor penetration into the respiratory tracts. Specifically, there were no differences in time to clinical improvement, viral load changes, and symptom resolutions between patients who were given standard of care alone and those who combined it with study intervention.\n\nImplications of all the available evidenceThe clinical benefit of nitazoxanide remains uncertain. The present study highlights the need for early insight into target site biodistribution of potential COVID-19 therapeutics to better inform candidate selection for clinical trials.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Adeola Fowotade", - "author_inst": "University of Ibadan, Ibadan" - }, - { - "author_name": "Folasade Bamidele", - "author_inst": "University of Ibadan, Ibadan" - }, - { - "author_name": "Boluwatife Egbetola", - "author_inst": "Olabisis Onabanjo University Teaching Hospital, Sagamu" - }, - { - "author_name": "Bolanle Olufunlola Adefuye", - "author_inst": "Olabisis Onabanjo University Teaching Hospital, Sagamu" - }, - { - "author_name": "Adeniyi Francis Fagbamigbe", - "author_inst": "University of Ibadan, Ibadan" - }, - { - "author_name": "Babatunde Ayodeji Adeagbo", - "author_inst": "Obafemi Awolowo University, Ile-Ife" - }, - { - "author_name": "Ajibola Olagunoye", - "author_inst": "State Specialist Hospital, Osogbo" - }, - { - "author_name": "Temitope Olumuyiwa Ojo", - "author_inst": "Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife" - }, - { - "author_name": "Akindele Olupelumi Adebiyi", - "author_inst": "University of Ibadan, Ibadan" - }, - { - "author_name": "Omobolanle Ibitayo Olagunju", - "author_inst": "Nigeria Centre for Disease Control, Abuja" - }, - { - "author_name": "Olabode Taiwo Ladipo", - "author_inst": "Oyo State Ministry of Health, Ibadan" - }, - { - "author_name": "Abdulafeez Akinloye", - "author_inst": "Obafemi Awolowo University, Ile-Ife" - }, - { - "author_name": "Adedeji Onayade", - "author_inst": "Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife" - }, - { - "author_name": "Oluseye Oladotun Bolaji", - "author_inst": "Obafemi Awolowo University, Ile-Ife" - }, - { - "author_name": "Christian Happi", - "author_inst": "Redeemer's University, Ede" - }, - { - "author_name": "Steve Rannard", - "author_inst": "University of Liverpool, Liverpool" - }, - { - "author_name": "Andrew Owen", - "author_inst": "University of Liverpool, Liverpool" - }, - { - "author_name": "Adeniyi Olagunju", - "author_inst": "University of Liverpool, Liverpool" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.03.22270357", "rel_title": "Transparency and reporting characteristics of COVID-19 randomized controlled trials.", @@ -388730,6 +390591,69 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.01.30.22269685", + "rel_title": "Doxycycline for the prevention of progression of COVID-19 to severe disease requiring intensive care unit (ICU) admission: a randomized, controlled, open-label, parallel group trial (DOXPREVENT.ICU)", + "rel_date": "2022-02-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.30.22269685", + "rel_abs": "BackgroundAfter admission to hospital, COVID-19 progresses in a substantial proportion of patients to critical disease that requires intensive care unit (ICU) admission.\n\nMethodsIn a pragmatic, non-blinded trial, 387 patients aged 40-90 years were randomised to receive treatment with SoC plus doxycycline (n=192) or SoC only (n=195). The primary outcome was the need for ICU admission as judged by the attending physicians. Three types of analyses were carried out for the primary outcome: \"Intention to treat\" (ITT) based on randomisation; \"Per protocol\" (PP), excluding patients not treated according to randomisation; and \"As treated\" (AT), based on actual treatment received. The trial was undertaken in six hospitals in India with high-quality ICU facilities. An online application serving as the electronic case report form was developed to enable screening, randomisation and collection of outcomes data.\n\nResultsAdherence to treatment per protocol was 95.1%. Among all 387 participants, 77 (19.9%) developed critical disease needing ICU admission. In all three primary outcome analyses, doxycycline was associated with a relative risk reduction (RRR) and absolute risk reduction (ARR): ITT 31.6% RRR, 7.4% ARR (P=0.063); PP 40.7% RRR, 9.6% ARR (P=0.017); AT 43.2% RRR, 10.8% ARR (P=0.007), with numbers needed to treat (NTT) of 13.4 (ITT), 10.4 (PP), and 9.3 (AT), respectively. Doxycycline was well tolerated with not a single patient stopping treatment due to adverse events.\n\nConclusionsIn hospitalized COVID-19 patients, doxycycline, a safe, inexpensive, and widely available antibiotic with anti-inflammatory properties, reduces the need for ICU admission when added to SoC.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Raja Dhar", + "author_inst": "Department of Pulmonology, CMRI Hospital, Kolkata, India" + }, + { + "author_name": "John Kirkpatrick", + "author_inst": "Independent researcher, Cambridgeshire, UK" + }, + { + "author_name": "Laura Gilbert", + "author_inst": "Rutherford Research, Hampshire, UK" + }, + { + "author_name": "Arjun Khanna", + "author_inst": "Pulmonary and Critical care medicine, Yashoda Superspeciality Hospital, Kaushambi, Ghaziabad, UP, India" + }, + { + "author_name": "Mahavir Madhavdas Modi", + "author_inst": "Ruby Hall Clinic, Pune, Maharashtra, India" + }, + { + "author_name": "Rakesh K Chawla", + "author_inst": "Saroj Super Speciality Hospital and Jaipur Golden Hospital, Dept of Respiratory Medicine, Critical Care and Sleep Disorders, New Delhi, India" + }, + { + "author_name": "Sonia Dalal", + "author_inst": "Sterling Hospital and Kalyan Hospital, Vadodara, India" + }, + { + "author_name": "Venkata Nagarjuna Maturu", + "author_inst": "Yashoda Hospitals, Hyderabad, India" + }, + { + "author_name": "Marcel Stern", + "author_inst": "Max von Pettenkofer Institute and Gene Center, LMU Munich, Germany" + }, + { + "author_name": "Oliver T Keppler", + "author_inst": "Max von Pettenkofer Institute and Gene Center, LMU Munich, Germany" + }, + { + "author_name": "Ratko Djukanovic", + "author_inst": "University of Southampton and NIHR Southampton Biomedical Research Centre, Southampton, UK" + }, + { + "author_name": "Stephan D Gadola", + "author_inst": "Bethesda Hospital, Switzerland; University of Southampton, UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.02.478719", "rel_title": "COVID-19 infection enhances susceptibility to oxidative-stress induced parkinsonism", @@ -390620,6 +392544,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.02.01.22269999", + "rel_title": "The Investigation of Pulmonary Abnormalities using Hyperpolarised Xenon Magnetic Resonance Imaging in Patients with Long-COVID.", + "rel_date": "2022-02-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.01.22269999", + "rel_abs": "BackgroundLong-COVID is an umbrella term used to describe ongoing symptoms following COVID-19 infection after four weeks. Symptoms are wide-ranging but breathlessness is one of the most common and can persist for months after the initial infection. Investigations including Computed Tomography (CT), and physiological measurements (lung function tests) are usually unremarkable. The mechanisms driving breathlessness remain unclear, and this may be hindering the development of effective treatments.\n\nMethodsEleven non-hospitalised Long-COVID (NHLC, 4 male), 12 post-hospitalised COVID-19 (PHC, 10 male) patients were recruited from a Post-COVID Assessment clinic, and thirteen healthy controls (6 female) were recruited to undergo Hyperpolarized Xenon Magnetic Resonance Imaging (Hp-XeMRI). NHLC and PHC participants underwent contemporaneous CT, Hp-XeMRI, lung function tests, 1-minute sit-to-stand test and breathlessness questionnaires. Statistical analysis included group and pair-wise comparisons between patients and controls, and correlations between patient clinical and imaging data.\n\nResultsNHLC and PHC patients were 287 {+/-} 79 [range 190-437] and 149 {+/-} 68 [range 68-269] days from infection, respectively. All NHLC patients had normal CT scans, and the PHC had normal or near normal CT scans (0.3/25 {+/-} 0.6 [range 0-2] and 7/25 {+/-} 5 [range 4-8], respectively). There was a significant difference in TLco (%) between NHLC and PHC patients (76 {+/-} 8 % vs 86 {+/-} 8%, respectively, p = 0.04) but no differences in other measurements of lung function. There were significant differences in RBC:TP mean between volunteers (0.45 {+/-} 0.07, range [0.33-0.55]) and PHC (0.31 {+/-} 0.11, [range 0.16-0.37]) and NHLC (0.35 {+/-} 0.09, [range 0.26-0.58]) patients, but not between NHLC and PHC (p = 0.26).\n\nConclusionThere are RBC:TP abnormalities in NHLC and PHC patients, with NHLC patients also demonstrating lower TLco than PHC patients despite their having normal CT scans. These abnormalities are present many months after the initial infection.\n\nSummary statementHyperpolarized Xenon MRI and TLco demonstrate significantly impaired gas transfer in non-hospitalised long-COVID patients when all other investigations are normal.\n\nKey resultsO_LIThere are significant differences in RBC:TP mean between healthy controls and PHC/NHLC patients (0.45 {+/-} 0.07, range [0.33-0.55], 0.31 {+/-} 0.11, [range 0.16-0.37], 0.35 {+/-} 0.09, [range 0.26-0.58], respectively, p < 0.05 after correction for multiple comparisons) indicating a change in lung compartment volumes between groups.\nC_LIO_LIThere was a significant difference in TLco (%) between NHLC and PHC patients (76 {+/-} 8 % vs 86 {+/-} 8%, respectively, p = 0.04), despite normal or near normal FEV (%) (100 {+/-} 13% [range 72-123%] and 88 {+/-} 21% [range 62-113%], p>0.05.\nC_LIO_LIThere were significant differences in CT abnormalities between NHLC and PHC patients (0.3/25 {+/-} 0.6 [range 0-2] and 7/25 {+/-} 5 [range 4-8], respectively) despite similarly impaired RBC:TP.\nC_LI", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "James T. Grist", + "author_inst": "University of Oxford" + }, + { + "author_name": "Guilhem J. Collier", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Huw Walters", + "author_inst": "Oxford University Hospitals" + }, + { + "author_name": "Mitchell Chen", + "author_inst": "Oxford University Hospitals" + }, + { + "author_name": "Gabriele Abu Eid", + "author_inst": "Oxford University Hospitals" + }, + { + "author_name": "Aviana Laws", + "author_inst": "Oxford University Hospitals" + }, + { + "author_name": "Violet Matthews", + "author_inst": "Oxford University Hospitals" + }, + { + "author_name": "Kenneth Jacob", + "author_inst": "Oxford University Hospitals" + }, + { + "author_name": "Susan Cross", + "author_inst": "Oxford University Hospitals" + }, + { + "author_name": "Alexandra Eves", + "author_inst": "Oxford University Hospitals" + }, + { + "author_name": "Marianne Durrant", + "author_inst": "Oxford University Hospitals" + }, + { + "author_name": "Anthony Mcintyre", + "author_inst": "Oxford University Hospitals" + }, + { + "author_name": "Roger Thompson", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Rolf F. Schulte", + "author_inst": "GE Healthcare" + }, + { + "author_name": "Betty Raman", + "author_inst": "University of Oxford" + }, + { + "author_name": "Peter A. Robbins", + "author_inst": "University of Oxford" + }, + { + "author_name": "Jim M. Wild", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Emily Fraser", + "author_inst": "Oxford University Hospitals" + }, + { + "author_name": "Fergus Gleeson", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2022.01.31.22270178", "rel_title": "SARS-CoV-2 antibody seroprevalence in cancer patients on systemic antineoplastic treatment in the first wave of the COVID-19 pandemic in Portugal", @@ -391468,57 +393483,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.31.478506", - "rel_title": "Detection and Interspecies Comparison of SARS-CoV-2 Delta Variant (AY.3) in Feces from a Domestic Cat and Human Samples", - "rel_date": "2022-02-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.31.478506", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have spilled over from humans to companion and wild animals since the inception of the global COVID-19 pandemic. However, whole genome sequencing data of the viral genomes that infect non-human animal species has been scant. Here, we detected and sequenced a SARS-CoV-2 delta variant (AY.3) in fecal samples from an 11-year-old domestic house cat previously exposed to an owner who tested positive for SARS-CoV-2. Molecular testing of two fecal samples collected 7 days apart yielded relatively high levels of viral RNA. Sequencing of the feline-derived viral genomes showed the two to be identical, and differing by between 4 and 14 single nucleotide polymorphisms in pairwise comparisons to human-derived lineage AY.3 sequences collected in the same geographic area and time period. However, several mutations unique to the feline samples reveal their divergence from this cohort on phylogenetic analysis. These results demonstrate continued spillover infections of emerging SARS-CoV-2 variants that threaten human and animal health, as well as highlight the importance of collecting fecal samples when testing for SARS-CoV-2 in animals. To the authors knowledge, this is the first published case of a SARS-CoV-2 delta variant in a domestic cat in the United States.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Olivia C Lenz", - "author_inst": "Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania" - }, - { - "author_name": "Andrew D Marques", - "author_inst": "Department of Microbiology, Perelman School of Medicine, University of Pennsylvania" - }, - { - "author_name": "Brendan J Kelly", - "author_inst": "Division of Infectious Diseases; Department of Medicine & Department of Biostatistics, Epidemiology, and Informatics; Perelman School of Medicine, University of" - }, - { - "author_name": "Kyle G Rodino", - "author_inst": "Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania" - }, - { - "author_name": "Stephen D Cole", - "author_inst": "Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania" - }, - { - "author_name": "Ranawaka APM Perera", - "author_inst": "Department of Microbiology, Perelman School of Medicine, University of Pennsylvania" - }, - { - "author_name": "Susan R Weiss", - "author_inst": "Department of Microbiology, Perelman School of Medicine, University of Pennsylvania" - }, - { - "author_name": "Frederic D Bushman", - "author_inst": "Department of Microbiology, Perelman School of Medicine, University of Pennsylvania" - }, - { - "author_name": "Elizabeth M Lennon", - "author_inst": "Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.01.31.478507", "rel_title": "Nanoparticle-delivered TLR4 and RIG-I agonists enhance immune response to SARS-CoV-2 subunit vaccine", @@ -392262,6 +394226,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.31.22270208", + "rel_title": "Prognostic peripheral blood biomarkers at ICU admission predict COVID-19 clinical outcomes", + "rel_date": "2022-02-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.31.22270208", + "rel_abs": "The COVID-19 pandemic continues to challenge the capacities of hospital ICUs which currently lack the ability to identify prospectively those patients who may require extended management. In this study of 90 ICU COVID-19 patients, we evaluated serum levels of four cytokines (IL-1{beta}, IL-6, IL-10 and TNF) as well as standard clinical and laboratory measurements. On 42 of these patients (binned into Initial and Replication Cohorts), we further performed CyTOF-based deep immunophenotyping of peripheral blood mononuclear cells with a panel of 38 antibodies. All measurements and patient samples were taken at time of ICU admission and retrospectively linked to patient clinical outcomes through statistical approaches. These analyses resulted in the definition of a new measure of patient clinical outcome: patients who will recover after short ICU stays (< 6 days) and those who will subsequently die or recover after long ICU stays (> 6 days). Based on these clinical outcome categories, we identified blood prognostic biomarkers that, at time of ICU admission, prospectively distinguish, with 91% sensitivity and 91% specificity (positive likelihood ratio 10.1), patients in the two clinical outcome groups. This is achieved through a tiered evaluation of serum IL-10 and targeted immunophenotyping of monocyte subsets, specifically, CD11clow classical monocytes. Immunophenotyping revealed clear predictors of clinical outcome in COVID-19 providing a highly sensitive and specific prognostic test that could prove useful in guiding clinical resource allocation.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=62 SRC=\"FIGDIR/small/22270208v4_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (15K):\norg.highwire.dtl.DTLVardef@1d4ac2eorg.highwire.dtl.DTLVardef@174167dorg.highwire.dtl.DTLVardef@707492org.highwire.dtl.DTLVardef@f5415f_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Melina Messing", + "author_inst": "The Biomedical Research Centre, Dept of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada" + }, + { + "author_name": "Mypinder S Sekhon", + "author_inst": "UBC Department of Medicine (Division of Respirology), Vancouver, BC, Canada" + }, + { + "author_name": "Michael R Hughes", + "author_inst": "The Biomedical Research Centre, Dept of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada" + }, + { + "author_name": "Sophie Stukas", + "author_inst": "UBC Department of Pathology and Laboratory Medicine, Vancouver, BC, Canada" + }, + { + "author_name": "Ryan L Hoiland", + "author_inst": "UBC Department of Anesthesiology, Pharmacology, and Therapeutics, Vancouver, BC, Canada" + }, + { + "author_name": "Jennifer Cooper", + "author_inst": "UBC Department of Pathology and Laboratory Medicine, Vancouver, BC, Canada" + }, + { + "author_name": "Nyra Ahmed", + "author_inst": "UBC Department of Pathology and Laboratory Medicine, Vancouver, BC, Canada" + }, + { + "author_name": "Mark Hamer", + "author_inst": "The Biomedical Research Centre, Dept of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada" + }, + { + "author_name": "Yicong Li", + "author_inst": "The Biomedical Research Centre, Dept of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada" + }, + { + "author_name": "Samuel B Shin", + "author_inst": "The Biomedical Research Centre, Dept of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada" + }, + { + "author_name": "Lin Wei Tung", + "author_inst": "The Biomedical Research Centre, Dept of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada" + }, + { + "author_name": "Cheryl Wellington", + "author_inst": "UBC Department of Pathology and Laboratory Medicine, Vancouver, BC, Canada" + }, + { + "author_name": "Don D Sin", + "author_inst": "UBC Department of Medicine (Division of Respirology), Vancouver, BC, Canada" + }, + { + "author_name": "Kevin B Leslie", + "author_inst": "The Biomedical Research Centre, Dept of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada" + }, + { + "author_name": "Kelly M McNagny", + "author_inst": "The Biomedical Research Centre, Dept of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.01.22270232", "rel_title": "Protection by 4th dose of BNT162b2 against Omicron in Israel", @@ -393510,65 +395549,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2022.01.29.22270090", - "rel_title": "Doubtful Clinical Benefit of Casirivimab-Imdevimab Treatment for Disease Severity Outcome of High-Risk Patients with SARS-CoV-2 Delta Variant Infection", - "rel_date": "2022-01-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.29.22270090", - "rel_abs": "Casirivimab/Imdevimab therapy reportedly retains neutralization potency against circulating SARS-CoV-2 variants, including Delta (B.1.617.2), but there are sparse data on its clinical benefit against the Delta variant among vaccinated and unvaccinated patients. We explored its therapeutic effect on COVID-19 severity outcome in terms of room air saturation <93% within 14 days of initial presentation and 45-day all-cause mortality among high-risk patients with SARS-CoV-2 Delta variant infection and compared its effect between vaccinated and unvaccinated patients. We conducted a retrospective cohort study at a tertiary care medical center between 6/2021 and 9/2021 and included patients who presented with a positive PCR for SARS-CoV-2 and fulfilled the criteria for Casirivimab/Imdevimab treatment. Of the 359 suitable patients (52% female, median age 63 years), 116 were treated with Casirivimab/Imdevimab and 243 were not. Two-hundred and one (56%) patients had received at least 2 SARS-CoV-2 vaccinations. Casirivimab/Imdevimab treatment was not an independent protective factor of COVID-19 severity outcome (multivariable analysis). Chronic kidney disease (aOR=3.51 [95%CI: 1.34-9.20], P=0.01), lower saturation levels (aOR=0.7 [95%CI: 0.58-0.85], P<0.01), abnormal chest x-ray findings (aOR=2.92, [95%CI: 1.24-6.87, P=0.01), and higher C-reactive protein levels (aOR=1.01 [95%CI: 1.00-1.01], P=0.008) were independent risk factors of COVID-19 severity. Positive immunization status was an independent protective factor (aOR=0.33 [95%CI: 0.14-0.77], P=0.01). A sub analysis of patients treated with Casirivimab/Imdevimab revealed no significant difference in COVID-19 severity between vaccinated and unvaccinated patients. These findings demonstrate no added benefit of Casrivimab/Imdevinab treatment for high-risk patients with the SARS-CoV-2 Delta variant infection, regardless of their vaccination status.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Noah Shopen", - "author_inst": "Tel Aviv Sourasky Medical Center" - }, - { - "author_name": "Michal Dekel", - "author_inst": "Tel Aviv Sourasky Medical Center" - }, - { - "author_name": "Michal Mizrahi", - "author_inst": "Tel Aviv Sourasky Medical Center" - }, - { - "author_name": "Efrat Zandberg", - "author_inst": "Tel Aviv Sourasky Medical Center" - }, - { - "author_name": "Nancy Bishouty", - "author_inst": "Tel Aviv Sourasky Medical Center" - }, - { - "author_name": "Daniel Talmud", - "author_inst": "Tel Aviv Sourasky Medical Center" - }, - { - "author_name": "Ben Vaknin", - "author_inst": "Tel Aviv Sourasky Medical Center" - }, - { - "author_name": "Shira Haberman", - "author_inst": "Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel" - }, - { - "author_name": "Malka Katz Shalhav", - "author_inst": "Tel Aviv Sourasky Medical Center" - }, - { - "author_name": "David Zeltser", - "author_inst": "Tel Aviv Sourasky Medical Center" - }, - { - "author_name": "Neta Cohen", - "author_inst": "Tel Aviv Sourasky Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "emergency medicine" - }, { "rel_doi": "10.1101/2022.01.29.22269933", "rel_title": "Socio-demographic characteristics and their relation to medical service consumption among elderly in Israel during the COVID-19 lockdown in 2020 compared to the corresponding period in 2019", @@ -394172,6 +396152,49 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2022.01.31.478157", + "rel_title": "In silico analysis of predicted differential MHC binding and CD8+ T-cell immune escape of SARS-CoV-2 B.1.1.529 variant mutant epitopes", + "rel_date": "2022-01-31", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.31.478157", + "rel_abs": "IntroductionThe B.1.1.529 (Omicron) SARS-CoV-2 variant has raised global concerns due to its high number of mutations and its rapid spread. It is of major importance to understand the impact of this variant on the acquired and induced immunity. Several preliminary studies have reported the impact of antibody binding and to this date, there are few studies on Omicrons CD8+ T-cell immune escape.\n\nMethodsWe first assessed the impact of Omicron and B.1.617.2 (Delta) variant mutations on the SARS-CoV-2 spike epitopes submitted to the Immune Epitope Database (IEDB) with positive out-come on MHC ligand or T-cell assays (n=411). From those epitopes modified by a mutation, we found the corresponding homologous epitopes in Omicron and Delta. We then ran the netMHCpan computational MHC binding prediction on the pairs of IEDB epitopes and matching homologous epitopes over top 5 MHC I alleles on some selected populations. Lastly, we applied a Fisher test to find mutations enriched for homologous epitopes with decreased predicted binding affinity.\n\nResultsWe found 31 and 78 IEDB epitopes modified by Delta and Omicron mutations, respectively. The IEDB spike protein epitopes redundantly cover the protein sequence. The WT pMHC with a strong predicted binding tend to have homologous mutated pMHC with decreased binding. A similar trend is observed in Delta over all HLA genes, while in Omicron only for HLA-B and HLA-C. Finally, we obtained one and seven mutations enriched for homologous mutated pMHC with decreased MHC binding affinity in Delta and Omicron, respectively. Three of the Omicron mutations, VYY143-145del, K417N and Y505H, are replacing an aromatic or large amino acid, which are reported to be enriched in immunogenic epitopes. K417N is common with Beta variants, while Y505H and VYY143-145del are novel Omicron mutations.\n\nConclusionIn summary, pMHC with Delta and Omicron mutations show decreased MHC binding affinity, which results in a trend specific to SARS-CoV-2 variants. Such epitopes may decrease overall presentation on different HLA alleles suggesting evasion from CD8+ T-cell responses in specific HLA alleles. However, our results show B.1.1.529 (Omicron) will not totally evade the immune system through a CD8+ immune escape mechanism. Yet, we identified mutations in B.1.1.529 (Omicron) introducing amino acids associated with increased immunogenicity.\n\nAvailabilityAll the code and results from this study are available at https://github.com/TRON-bioinformatics/omicron-analysis.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Pablo Riesgo-Ferreiro", + "author_inst": "TRON gGmbH" + }, + { + "author_name": "Gudimella Ranganath", + "author_inst": "TRON gGmbH" + }, + { + "author_name": "Thomas Bukur", + "author_inst": "TRON gGmbH" + }, + { + "author_name": "Patrick Sorn", + "author_inst": "TRON gGmbH" + }, + { + "author_name": "Thomas Rosler", + "author_inst": "TRON gGmbH" + }, + { + "author_name": "Barbara Schrors", + "author_inst": "TRON gGmbH" + }, + { + "author_name": "Martin Lower", + "author_inst": "TRON gGmbH" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.01.26.477819", "rel_title": "Analysis of receptors responsible for the dysfunction of the human immune system by different viral infections", @@ -395140,97 +397163,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.28.22270044", - "rel_title": "Transmission of SARS-CoV-2 Omicron VOC subvariants BA.1 and BA.2: Evidence from Danish Households", - "rel_date": "2022-01-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.28.22270044", - "rel_abs": "1The Omicron SARS-CoV-2 variant of concern (VOC lineage B.1.1.529), which became dominant in many countries during early 2022, includes several subvariants with strikingly different genetic characteristics. Several countries, including Denmark, have observed the two Omicron subvariants: BA.1 and BA.2. In Denmark the latter has rapidly replaced the former as the dominant subvariant.\n\nBased on nationwide Danish data, we estimate the transmission dynamics of BA.1 and BA.2 following the spread of Omicron VOC within Danish households in late December 2021 and early January 2022.\n\nAmong 8,541 primary household cases, of which 2,122 were BA.2, we identified a total of 5,702 secondary infections among 17,945 potential secondary cases during a 1-7 day follow-up period. The secondary attack rate (SAR) was estimated as 29% and 39% in households infected with Omicron BA.1 and BA.2, respectively.\n\nWe found BA.2 to be associated with an increased susceptibility of infection for unvaccinated individuals (Odds Ratio (OR) 2.19; 95%-CI 1.58-3.04), fully vaccinated individuals (OR 2.45; 95%-CI 1.77-3.40) and booster-vaccinated individuals (OR 2.99; 95%-CI 2.11-4.24), compared to BA.1. We also found an increased transmissibility from unvaccinated primary cases in BA.2 households when compared to BA.1 households, with an OR of 2.62 (95%-CI 1.96-3.52). The pattern of increased transmissibility in BA.2 households was not observed for fully vaccinated and booster-vaccinated primary cases, where the OR of transmission was below 1 for BA.2 compared to BA.1.\n\nWe conclude that Omicron BA.2 is inherently substantially more transmissible than BA.1, and that it also possesses immune-evasive properties that further reduce the protective effect of vaccination against infection, but do not increase its transmissibility from vaccinated individuals with breakthrough infections.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Frederik Plesner Lyngse", - "author_inst": "University of Copenhagen" - }, - { - "author_name": "Carsten Thure Kirkeby", - "author_inst": "University of Copenhagen" - }, - { - "author_name": "Matthew Denwood", - "author_inst": "University of Copenhagen" - }, - { - "author_name": "Lasse Engbo Christiansen", - "author_inst": "DTU" - }, - { - "author_name": "K\u00e5re M\u00f8lbak", - "author_inst": "Statens Serum Institut" - }, - { - "author_name": "Camilla Holten M\u00f8ller", - "author_inst": "Statens Serum Institut" - }, - { - "author_name": "Robert Leo Skov", - "author_inst": "Statens Serum Institut" - }, - { - "author_name": "Tyra Grove Krause", - "author_inst": "Statens Serum Institut" - }, - { - "author_name": "Morten Rasmussen", - "author_inst": "Statens Serum Institut" - }, - { - "author_name": "Raphael Niklaus Sieber", - "author_inst": "Statens Serum Institut" - }, - { - "author_name": "Thor Bech Johannesen", - "author_inst": "Statens Serum Institut" - }, - { - "author_name": "Troels Lillebaek", - "author_inst": "Statens Serum Institut" - }, - { - "author_name": "Jannik Fonager", - "author_inst": "Statens Serum Institut" - }, - { - "author_name": "Anders Fomsgaard", - "author_inst": "Statens Serum Institut" - }, - { - "author_name": "Frederik Trier M\u00f8ller", - "author_inst": "Statens Serum Institut" - }, - { - "author_name": "Marc Stegger", - "author_inst": "Statens Serum institut" - }, - { - "author_name": "Maria Overvad", - "author_inst": "Statens Serum Institut" - }, - { - "author_name": "Katja Spiess", - "author_inst": "Statens Serum Institut" - }, - { - "author_name": "Laust Hvas Mortensen", - "author_inst": "Statistics Denmark" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.28.22270033", "rel_title": "User acceptability of saliva and gargle samples for identifying COVID-19 positive high-risk workers", @@ -396058,6 +397990,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2022.01.28.22269756", + "rel_title": "Observed serial intervals of SARS-CoV-2 for the Omicron and Delta varaints in Belgium based on contact tracing data, 19 November to 31 December 2021", + "rel_date": "2022-01-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.28.22269756", + "rel_abs": "The SARS-CoV-2 Omicron BA.1 variant is rapidly spreading worldwide, possibly outcompeting the Delta strain. We investigated the empirical serial interval for both variants using contact tracing data. Overall, we observed a shorter serial interval for Omicron compared to Delta, suggesting faster transmission. Furthermore, results indicate a relation between the empirical serial interval and the vaccination status for both the Omicron and the Delta variant. Consequently, with the progression of the vaccination campaign, the reasons for and extent of dominance of Omicron over Delta may need further assessment.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "C\u00e9cile Kremer", + "author_inst": "Interuniversity Institute for Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, Belgium" + }, + { + "author_name": "Toon Braeye", + "author_inst": "Department of Epidemiology and Public Health, Sciensano, Belgium" + }, + { + "author_name": "Kristiaan Proesmans", + "author_inst": "Department of Epidemiology and Public Health, Sciensano, Belgium" + }, + { + "author_name": "Emmanuel Andr\u00e9", + "author_inst": "Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium" + }, + { + "author_name": "Andrea Torneri", + "author_inst": "Interuniversity Institute for Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, Belgium" + }, + { + "author_name": "Niel Hens", + "author_inst": "Interuniversity Institute for Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, Belgium" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.01.28.22269986", "rel_title": "Neutralizing Activities against the Omicron Variant after a Heterologous Booster in Healthy Adults Receiving Two Doses of CoronaVac Vaccination", @@ -397058,29 +399029,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.25.22269839", - "rel_title": "EPIDEMIOLOGICAL CHARACTERISTICS AND SEVERITY OF OMICRON VARIANT CASES IN THE APHP CRITICAL CARE UNITS; THE APHP REALITY RESEARCH GROUP", - "rel_date": "2022-01-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.25.22269839", - "rel_abs": "ImportanceInformation about the severity of Omicron is scarce.\n\nObjectiveTo report the respective risk of ICU admission in patients hospitalized with Delta and Omicron variants and to compare the characteristics and disease severity of critically ill patients infected with both variants according to vaccination status.\n\nDesignAnalysis from the APHP database, called Reality, prospectively recording the following information in consecutive patients admitted in the ICU for COVID-19: age, sex, immunosuppression, vaccination, pneumonia, need for invasive mechanical ventilation, time between symptom onset and ICU admission, and in-ICU mortality. Retrospective analysis on an administrative database, \"Systeme dInformation pour le Suivi des Victimes\" (SI-VIC), which lists hospitalized COVID-19 patients.\n\nSetting39 hospitals in the Paris area from APHP group.\n\nParticipantsPatients hospitalized from December 1, 2021 to January 18, 2022 for COVID-19.\n\nMain outcomes and measuresRisk of ICU admission was evaluated in 3761 patients and Omicron cases were compared to Delta cases in the ICU in 888 consecutive patients.\n\nResultsOn January 18, 45% of patients in the ICU and 63.8% of patients in conventional hospital units were infected with the Omicron variant (p < 0.001). The risk of ICU admission with Omicron was reduced by 64% than with Delta (9.3% versus 25.8% of cases, respectively, p < 0.001). In critically ill patients, 400 had the Delta variant, 229 the Omicron variant, 98 had an uninformative variant screening test and 161 did not have information on variant screening test. 747 patients (84.1%) were admitted for pneumonia. Compared to patients infected with Delta, Omicron patients were more vaccinated (p<0.001), even with 3 doses, more immunocompromised (p<0.001), less admitted for pneumonia (p<0.001), especially when vaccinated (62.1% in vaccinated versus 80.7% in unvaccinated, p<0.001), and less invasively ventilated (p=0.02). Similar results were found in the subgroup of pneumonia but Omicron cases were older. Unadjusted in-ICU mortality did not differ between Omicron and Delta cases, neither in the overall population (20.0% versus 27.9%, p = 0.08), nor in patients with pneumonia (31.6% versus 29.7%, respectively) where adjusted in-ICU mortality did not differ according to the variant (HR 1.43 95%CI [0.89;2.29], p=0.14).\n\nConclusion and relevanceCompared to the Delta variant, the Omicron variant is less likely to result in ICU admission and less likely to be associated with pneumonia. However, when patients with the Omicron variant are admitted for pneumonia, the severity seems similar to that of patients with the Delta variant, with more immunocompromised and vaccinated patients and no difference in adjusted in-ICU mortality. Further studies are needed to confirm our results.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Antoine Vieillard-Baron Sr.", - "author_inst": "CHU Ambroise Pare, APHP" - }, - { - "author_name": "- APHP Reality research group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2022.01.26.22269868", "rel_title": "Open science policies of medical and health sciences journals before and during the COVID-19 pandemic: a repeat cross-sectional study", @@ -397924,6 +399872,53 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.01.26.22269876", + "rel_title": "SARS-CoV-2 third vaccine immune response in MS patients treated with ocrelizumab", + "rel_date": "2022-01-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.26.22269876", + "rel_abs": "The introduction of a third dose vaccination along with new variants of concerns raises questions regarding serology and T-cell responses in patients with MS (pwMS) treated with B-cell depletion who develop attenuated humoral response to vaccines. The aim of this study is to longitudinally evaluate humoral and cellular response to SARS-CoV-2 mRNA vaccine in ocrelizumab-treated pwMS before and following third vaccine dose. Following the third vaccine dose, patients who are low or non-responders following initial vaccination did not increase antibody titers. In HCs and ocrelizumab-treated pwMS, cellular response decreased 6 months following initial vaccination and increased significantly after the third booster.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Livnat Brill", + "author_inst": "Hadassah medical center" + }, + { + "author_name": "Catarina Raposo", + "author_inst": "Roche" + }, + { + "author_name": "Ariel Rechtman", + "author_inst": "Hadssah medical center" + }, + { + "author_name": "Omri Zveik", + "author_inst": "Hadassah medical center" + }, + { + "author_name": "Netta Levin", + "author_inst": "Hadassah medical center" + }, + { + "author_name": "Esther Djian", + "author_inst": "Hadassah medical center" + }, + { + "author_name": "Dana Wolf", + "author_inst": "Hadassah medical center" + }, + { + "author_name": "Adi Vaknin-Dembinsky", + "author_inst": "Hadassah medical center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2022.01.26.22269910", "rel_title": "Fifteen Days in December: Capture and Analysis of Omicron-Related Travel Restrictions", @@ -399068,137 +401063,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.27.22269922", - "rel_title": "Regional connectivity drove bidirectional transmission of SARS-CoV-2 in the Middle East during travel restrictions", - "rel_date": "2022-01-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.27.22269922", - "rel_abs": "Regional connectivity and land-based travel have been identified as important drivers of SARS-CoV-2 transmission. However, the generalizability of this finding is understudied outside of well-sampled, highly connected regions such as Europe. In this study, we investigated the relative contributions of regional and intercontinental connectivity to the source-sink dynamics of SARS-CoV-2 for Jordan and the wider Middle East. By integrating genomic, epidemiological and travel data we show that the source of introductions into Jordan was dynamic across 2020, shifting from intercontinental seeding from Europe in the early pandemic to more regional seeding for the period travel restrictions were in place. We show that land-based travel, particularly freight transport, drove introduction risk during the period of travel restrictions. Consistently, high regional connectivity and land-based travel also disproportionately drove Jordans export risk to other Middle Eastern countries. Our findings emphasize regional connectedness and land-based travel as drivers of viral transmission in the Middle East. This demonstrates that strategies aiming to stop or slow the spread of viral introductions (including new variants) with travel restrictions need to prioritize risk from land-based travel alongside intercontinental air travel to be effective.\n\nHighlightsO_LIRegional connectivity drove SARS-CoV-2 introduction risk in Jordan during the period travel restrictions were in place in genomic and travel data.\nC_LIO_LILand-based travel rather than air travel disproportionately drove introduction risk during travel restrictions.\nC_LIO_LIHigh regional connectivity disproportionately drove Jordans export risk, with significant contribution from land-based travel.\nC_LIO_LIRegional transmission dynamics were underestimated in genomic data due to unrepresentative sampling.\nC_LI", - "rel_num_authors": 29, - "rel_authors": [ - { - "author_name": "Edyth Parker", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA" - }, - { - "author_name": "Catelyn Anderson", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA" - }, - { - "author_name": "Mark Zeller", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA" - }, - { - "author_name": "Ahmad Tibi", - "author_inst": "Biolab Diagnostic Laboratories, Amman, Jordan" - }, - { - "author_name": "Jennifer L. Havens", - "author_inst": "Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Genevieve Laroche", - "author_inst": "Department of Biochemistry, Microbiology and Immunology, and Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON, Canada" - }, - { - "author_name": "Mehdi Benlarbi", - "author_inst": "Department of Biochemistry, Microbiology and Immunology, and Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON, Canada" - }, - { - "author_name": "Ardeshir Ariana", - "author_inst": "Department of Biochemistry, Microbiology and Immunology, and Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON, Canada" - }, - { - "author_name": "Refugio Robles-Sikisaka", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA" - }, - { - "author_name": "Alaa Latif", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA" - }, - { - "author_name": "Alexander Watts", - "author_inst": "Bluedot, Toronto, Canada" - }, - { - "author_name": "Abdalla Awidi", - "author_inst": "Cell Therapy Center, The University of Jordan, Amman, Jordan; Thrombosis, haemostasis laboratory, School of Medicine, The University of Jordan, Amman, Jordan" - }, - { - "author_name": "Saied A. Jaradat", - "author_inst": "Princess Haya Biotechnology Center, Jordan University of Science and Technology, Irbid, Jordan" - }, - { - "author_name": "Karthik Gangavarapu", - "author_inst": "Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, USA" - }, - { - "author_name": "Ezra Kurzban", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA" - }, - { - "author_name": "Nathaniel L. Matteson", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA" - }, - { - "author_name": "Alvin X. Han", - "author_inst": "Department of Medical Microbiology & Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, th" - }, - { - "author_name": "Laura D. Hughes", - "author_inst": "Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA" - }, - { - "author_name": "Michelle McGraw", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA" - }, - { - "author_name": "Emily Spencer", - "author_inst": "Scripps Research Translational Institute, La Jolla, USA" - }, - { - "author_name": "Laura Nicholson", - "author_inst": "Scripps Research Translational Institute, La Jolla, USA" - }, - { - "author_name": "Kamran Khan", - "author_inst": "Bluedot, Toronto, Canada" - }, - { - "author_name": "Marc A. Suchard", - "author_inst": "Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, USA; Department of Biostatistics, Fielding Sc" - }, - { - "author_name": "Joel O. Wertheim", - "author_inst": "Department of Medicine, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Shirlee Wohl", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA" - }, - { - "author_name": "Marceline Cote", - "author_inst": "Department of Biochemistry, Microbiology and Immunology, and Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON, Canada" - }, - { - "author_name": "Amid Abdelnour", - "author_inst": "Biolab Diagnostic Laboratories, Amman, Jordan" - }, - { - "author_name": "Kristian G. Andersen", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA" - }, - { - "author_name": "Issa Abu-Dayyeh", - "author_inst": "Biolab Diagnostic Laboratories, Amman, Jordan; 6 Cell Therapy Center, The University of Jordan, Amman, Jordan" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.01.18.22269479", "rel_title": "Who was wearing a mask in 2021? Update on gender-, age-, and location-related differences during the COVID-19 pandemic", @@ -399982,6 +401846,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.01.25.476850", + "rel_title": "Impact of various vaccine boosters on neutralization against Omicron following prime vaccinations with inactivated or adenovirus-vectored vaccine", + "rel_date": "2022-01-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.25.476850", + "rel_abs": "Since the first report on November 24, 2021, the Omicron SARS-CoV-2 variant is now overwhelmingly spreading across the world. Two SARS-CoV-2 inactivated vaccines (IAVs), one recombinant protein subunit vaccine (PRV), and one adenovirus-vectored vaccine (AdV) have been widely administrated in many countries including China to pursue herd immunity. Here we investigated cross-neutralizing activities in 341 human serum specimens elicited by full-course vaccinations with IAV, PRV and AdV, and by various vaccine boosters following prime IAV and AdV vaccinations. We found that all types of vaccines induced significantly lower neutralizing antibody titers against the Omicron variant than against the prototype strain. For prime vaccinations with IAV and AdV, heterologous boosters with AdV and PRV, respectively, elevated serum Omicron-neutralizing activities to the highest degrees. In a mouse model, we further demonstrated that among a series of variant-derived RBD-encoding mRNA vaccine boosters, it is only the Omicron booster that significantly enhanced Omicron neutralizing antibody titers compared with the prototype booster following a prime immunization with a prototype S-encoding mRNA vaccine candidate. In summary, our systematical investigations of various vaccine boosters inform potential booster administrations in the future to combat the Omicron variant.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Qingrui Huang", + "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China." + }, + { + "author_name": "Jiawei Zeng", + "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China." + }, + { + "author_name": "Qingyun Lang", + "author_inst": "College of Life Sciences, Anhui Agricultural University, Hefei 230036, China" + }, + { + "author_name": "Feng Gao", + "author_inst": "Health Service Department of the Guard Bureau of the General Office of the Central Committee of the Communist Party of China, Beijing, China" + }, + { + "author_name": "Dejun Liu", + "author_inst": "Health Service Department of the Guard Bureau of the General Office of the Central Committee of the Communist Party of China, Beijing, China" + }, + { + "author_name": "Siyu Tian", + "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China." + }, + { + "author_name": "Rui Shi", + "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China." + }, + { + "author_name": "Ling Luo", + "author_inst": "College of Life Sciences, Anhui Agricultural University, Hefei 230036, China" + }, + { + "author_name": "Hao Wang", + "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China." + }, + { + "author_name": "Liping Hu", + "author_inst": "Institute of Physical Science and Information, Anhui University, Hefei 230039, China" + }, + { + "author_name": "Linrui Jiang", + "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China." + }, + { + "author_name": "Yawei Liu", + "author_inst": "Health Service Department of the Guard Bureau of the General Office of the Central Committee of the Communist Party of China, Beijing, China" + }, + { + "author_name": "Kailiang Li", + "author_inst": "Health Service Department of the Guard Bureau of the General Office of the Central Committee of the Communist Party of China, Beijing, China" + }, + { + "author_name": "Yunbo Wu", + "author_inst": "Health Service Department of the Guard Bureau of the General Office of the Central Committee of the Communist Party of China, Beijing, China" + }, + { + "author_name": "Junjie Xu", + "author_inst": "Health Service Department of the Guard Bureau of the General Office of the Central Committee of the Communist Party of China, Beijing, China" + }, + { + "author_name": "Wenxi Jiang", + "author_inst": "Health Service Department of the Guard Bureau of the General Office of the Central Committee of the Communist Party of China, Beijing, China" + }, + { + "author_name": "Ning Guo", + "author_inst": "College of Life Sciences, Anhui Agricultural University, Hefei 230036, China" + }, + { + "author_name": "Zhihai Chen", + "author_inst": "Beijing Ditan Hospital" + }, + { + "author_name": "Xiaohua Hao", + "author_inst": "National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China" + }, + { + "author_name": "Ronghua Jin", + "author_inst": "National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China" + }, + { + "author_name": "Jinghua Yan", + "author_inst": "Institute of Microbiology, Chinese Academy of Sciences" + }, + { + "author_name": "Yufa Sun", + "author_inst": "Health Service Department of the Guard Bureau of the General Office of the Central Committee of the Communist Party of China, Beijing, China" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.01.25.477757", "rel_title": "Defining the Substrate Envelope of SARS-CoV-2 Main Protease to Predict and Avoid Drug Resistance", @@ -401098,25 +403065,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.01.26.22269347", - "rel_title": "Estimates of the impact on COVID-19 deaths of unequal global allocations of vaccines", - "rel_date": "2022-01-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.26.22269347", - "rel_abs": "During 2021, COVID-19 vaccinations were delivered much more rapidly in some countries than in others. Ethical principles would have suggested allocating available vaccines to people by age, irrespective of where they live, because mortality risks from COVID-19 are much higher for older people. The World Health Organization recommended initial allocations of vaccines to countries based on their total population size, in part due to uncertainty about how COVID-19 would affect different countries.\n\nThis paper estimates how many people would have died from COVID-19 up to 31 October 2021 if either of these allocation rules had been applied, compared to estimates of actual COVID-19 deaths. The estimates suggest that allocating vaccines by age would have resulted in between 500,000 and 1,500,000 fewer deaths globally (with a best estimate of 1,090,000 fewer deaths), while allocating vaccines between countries based on national population sizes would have reduced total deaths globally by between 450,000 and 2,100,000 (with a best estimate of 1,440,000 fewer deaths).\n\nMost low-and middle-income countries would have seen reductions in deaths, with the greatest absolute numbers in large middle-income countries (especially Bangladesh, India and Indonesia). More deaths would have taken place in many high-income countries, with the greatest absolute numbers in the United States and Turkey, and the greatest percentage changes in Arabian Peninsula countries, Israel and some island states. In most European Union countries, deaths would not have differed much if vaccines were allocated by age, because they would have received more vaccine doses during the early months of 2021 but fewer later in the year.\n\nAlthough allocation of vaccines by age should intuitively lead to fewest deaths, the estimated deaths would have been even lower if vaccines were allocated based on population size. Allocation by population would have directed disproportionate numbers of vaccines to a set of countries - especially India, Bangladesh and Indonesia - which experienced large outbreaks due to the Delta variant in 2021 after having previously limited infections through \" flattening the curve\".\n\nSequencing of vaccination by age in national vaccination rollouts is critical to maximizing the numbers of lives saved. The estimated gains from fairer global vaccination allocation would be greater if high-income and upper-middle-income countries did not sequence vaccinations by age cohort, and would be lower if lower-middle-income and low-income countries did not vaccinate most of their elderly before the general population, whether due to policy choices or people not accepting vaccines made available to them or logistical difficulties in vaccine delivery.\n\nThe estimates correspond to a reduction of between 8.5% and 10.7% (with a best estimate of 10.4%) of the total estimated actual deaths from COVID-19 between 1 January and 31 October 2021, if vaccines were allocated by age, and between 7.8% and 15.0% (with a best estimate of 13.6%) of total estimated actual deaths, if vaccines were allocated based on national population sizes. These percentages are small, despite the large differences in vaccine deployment between countries, because the mostly high-income countries which vaccinated their populations faster have disproportionately large numbers of elderly people. If a future SARS-CoV-2 variant, or a future pandemic, were to have fatality rates that are similar across age groups, or that are higher for children and young adults, then unequal global allocation of vaccines would have a much more severe effect on overall global mortality than it has for COVID-19 so far.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "John Paul Callan", - "author_inst": "Personal Capacity" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.01.27.22269602", "rel_title": "Risk factors and survival in patients with COVID-19 in northeastern Brazil.", @@ -402132,6 +404080,113 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.01.25.477770", + "rel_title": "Vaccine-elicited murine antibody WS6 neutralizes diverse beta-coronaviruses by recognizing a helical stem supersite of vulnerability", + "rel_date": "2022-01-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.25.477770", + "rel_abs": "Immunization with SARS-CoV-2 spike elicits diverse antibodies, but can any of these neutralize broadly? Here, we report the isolation and characterization of antibody WS6, from a mouse immunized with mRNA encoding the SARS-CoV-2 spike. WS6 bound diverse beta-coronavirus spikes and neutralized SARS-CoV-2 variants, SARS-CoV, and related sarbecoviruses. Epitope mapping revealed WS6 to target a region in the S2 subunit, which was conserved among SARS-CoV-2, MERS-CoV, and hCoV-OC43. The crystal structure at 2-[A] resolution of WS6 with its S2 epitope revealed recognition to center on a conserved helix, which was occluded in both prefusion and post-fusion spike conformations. Structural and neutralization analyses indicated WS6 to neutralize by inhibiting fusion, post-viral attachment. Comparison of WS6 to other antibodies recently identified from convalescent donors or mice immunized with diverse spikes indicated a stem-helical supersite - centered on hydrophobic residues Phe1148, Leu1152, Tyr1155, and Phe1156 - to be a promising target for vaccine design.\n\nHighlightsO_LISARS-CoV-2 spike mRNA-immunized mouse elicited an antibody, WS6, that cross reacts with spikes of diverse human and bat beta-coronaviruses\nC_LIO_LIWS6 neutralizes SARS-CoV-2 variants, SARS-CoV, and related viruses\nC_LIO_LICrystal structure at 2-[A] resolution of WS6 in complex with a conserved S2 peptide reveals recognition of a helical epitope\nC_LIO_LIWS6 neutralizes by inhibition of fusion, post-viral attachment\nC_LIO_LIWS6 recognizes a supersite of vulnerability also recognized by other recently identified antibodies\nC_LIO_LIHelical supersite of vulnerability comprises a hydrophobic cluster spanning three helical turns, with acid residues framing the center turn\nC_LIO_LIGenetic and structural analysis indicate supersite recognition to be compatible with diverse antibody ontogenies\nC_LI", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Wei Shi", + "author_inst": "Vaccine Research Center, NIAID, NIH" + }, + { + "author_name": "Lingshu Wang", + "author_inst": "VRC/NIAID/NIH" + }, + { + "author_name": "Tongqing Zhou", + "author_inst": "Vaccine Research Center, NIAID, NIH" + }, + { + "author_name": "Mallika Sastry", + "author_inst": "Vaccine Research Center, NIAID, NIH" + }, + { + "author_name": "Eun Sung Yang", + "author_inst": "Vaccine Research Center, NIAID, NIH" + }, + { + "author_name": "Yi Zhang", + "author_inst": "Vaccine Research Center, NIAID, NIH" + }, + { + "author_name": "Man Chen", + "author_inst": "Vaccine Research Center, NIAID, NIH" + }, + { + "author_name": "Xuejun Chen", + "author_inst": "Vaccine Research Center, NIAID, NIH" + }, + { + "author_name": "Misook Choe", + "author_inst": "Vaccine Research Center, NIAID, NIH" + }, + { + "author_name": "Adrian Creanga", + "author_inst": "Vaccine Research Center, NIAID, NIH" + }, + { + "author_name": "Kwan Leung", + "author_inst": "Vaccine Research Center, NIAID, NIH" + }, + { + "author_name": "Adam S. Olia", + "author_inst": "Vaccine Research Center, NIAID, NIH" + }, + { + "author_name": "Amarendra Pegu", + "author_inst": "Vaccine Research Center, NIAID, NIH" + }, + { + "author_name": "Reda Rawi", + "author_inst": "Vaccine Research Center, NIAID, NIH" + }, + { + "author_name": "Chen-Hsiang Shen", + "author_inst": "Vaccine Research Center, NIAID, NIH" + }, + { + "author_name": "Erik-Stephane D. Stancofski", + "author_inst": "Vaccine Research Center, NIAID, NIH" + }, + { + "author_name": "Chloe Adrienna Talana", + "author_inst": "Vaccine Research Center, NIAID, NIH" + }, + { + "author_name": "I-Ting Teng", + "author_inst": "Vaccine Research Center, NIAID, NIH" + }, + { + "author_name": "Shuishu Wang", + "author_inst": "Vaccine Research Center, NIAID, NIH" + }, + { + "author_name": "Kizzmekia S. Corbett", + "author_inst": "Vaccine Research Center, NIAID, NIH" + }, + { + "author_name": "Yaroslav Tsybovsky", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "John R. Mascola", + "author_inst": "Vaccine Research Center, NIAID, NIH" + }, + { + "author_name": "Peter D. Kwong", + "author_inst": "National Institute of Allergy and Infectious Diseases" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.01.25.477789", "rel_title": "Lineage-mosaic and mutation-patched spike proteins for broad-spectrum COVID-19 vaccine", @@ -403172,53 +405227,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "addiction medicine" }, - { - "rel_doi": "10.1101/2022.01.23.22269031", - "rel_title": "Learnings from the Australian First Few X Household Transmission Project for COVID-19", - "rel_date": "2022-01-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.23.22269031", - "rel_abs": "BackgroundFirst Few \"X\" (FFX) studies provide a platform to collect the required epidemiological, clinical and virological data to help address emerging information needs about the COVID-19 pandemic.\n\nMethodsWe adapted the WHO FFX protocol for COVID-19 to understand severity and household transmission dynamics in the early stages of the pandemic in Australia. Implementation strategies were developed for participating sites; all household members provided baseline epidemiological data and were followed for 14 days from case identification. Household contacts completed symptom diaries and had respiratory swabs taken at baseline, day 7 and day 14, and day 28 where applicable. We modelled the spread of COVID-19 within households using a susceptible-exposed-infectious-recovered-type model, and calculated the household secondary attack rate and key epidemiological parameters.\n\nFindings96 households with 101 cases and 286 household contacts were recruited into the study between April-October 2020. Forty household contacts tested positive for SARS-CoV-2 in the study follow-up period. Our model estimated the household secondary attack rate to be 15% (95% CI 8-25%), which scaled up with increasing household size. Children were less infectious than their adult counterparts but were also more susceptible to infection.\n\nInterpretationOur study provides important baseline data characterising the transmission of early SARS-CoV-2 strains from children and adults in Australia, against which properties of variants of concern can be benchmarked. We encountered many challenges with respect to logistics, ethics, governance and data management that may have led to biases in our study. Continued efforts to invest in preparedness research will help to test, refine and further develop Australian FFX study protocols in advance of future outbreaks.\n\nFundingAustralian Government Department of Health\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSThe emergence of SARS-CoV-2 was initially characterised by uncertainty over key epidemiological, clinical and virological characteristics of the pathogen. We conducted a prospective household transmission study of confirmed cases of COVID-19 and their household contacts to collect data to understand severity and household transmission dynamics in Australia and add to the emerging evidence base for decision making. Large systematic reviews and meta-analyses of severity and transmission dynamics of SARS-CoV-2 in households have since been published, although estimates vary by setting.\n\nAdded value of this studyThis is the first multi-jurisdictional prospective household transmission study of its kind for SARS-CoV-2 in Australia. Australia experienced low epidemic activity during the study period in 2020 due to robust public health and social measures including extensive PCR testing of symptomatic persons and isolation of all known contacts of confirmed cases. Hence, we describe the transmission dynamics in our cohort, i.e. in a low incidence setting and provide estimates of the household secondary attack rate, the relative susceptibility of children compared to adults, and transmission from children compared to adults.\n\nImplications of all the available evidenceOur findings describe the epidemiology of COVID-19 in Australian households in 2020, and demonstrate the effectiveness of public health measures to limit transmission in this setting. Comparisons to other household transmission studies must be interpreted in light of the local epidemiology and context including study design, and sampling methods. Additional research is needed to incorporate genomic and serological data to further study transmission dynamics in our cohort. Continued development of the FFX study platform in Australia will enable integration into surveillance systems and help inform targetted public health responses to future infectious disease emergencies.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Adrian John Marcato", - "author_inst": "Department of Infectious Diseases, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia" - }, - { - "author_name": "Andrew J Black", - "author_inst": "School of Mathematical Sciences, The University of Adelaide, Adelaide, Australia" - }, - { - "author_name": "James Walker", - "author_inst": "School of Mathematical Sciences, The University of Adelaide, Adelaide, Australia. School of Mathematics & Statistics, The University of Melbourne, Melbourne, Au" - }, - { - "author_name": "Dylan Morris", - "author_inst": "School of Mathematical Sciences, The University of Adelaide, Adelaide, Australia" - }, - { - "author_name": "Niamh Meagher", - "author_inst": "Department of Infectious Diseases, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia. Centre for Epid" - }, - { - "author_name": "David J Price", - "author_inst": "Department of Infectious Diseases, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia. Centre for Epid" - }, - { - "author_name": "Jodie McVernon", - "author_inst": "The Peter Doherty Institute for Infection and Immunity" - }, - { - "author_name": "- The Australian FFX Household Transmission Project Group", - "author_inst": "-" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.01.22.22269691", "rel_title": "BASELINE METABOLIC PROFILING AND RISK OF DEATH FROM COVID-19", @@ -403822,6 +405830,29 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2022.01.24.477651", + "rel_title": "Structural Ramifications of Spike Protein D614G Mutation in SARS-CoV-2", + "rel_date": "2022-01-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.24.477651", + "rel_abs": "A single mutation from aspartate to glycine at position 614 has dominated all circulating variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). D614G mutation induces structural changes in the Spike (S) protein that strengthen the virus infectivity. Here, we use molecular dynamics simulations to dissect the effects of mutation and 630-loop rigidification on wild-type structure. The introduction of mutation with ordered 630-loop induces structural changes toward S-G614 Cryo-EM structure. An ordered 630-loop weakens the stabilizing interactions of the anionic D614, suggesting its disorder in wild-type. The mutation allosterically alters the receptor binding domain (RBD) forming an asymmetric and mobile Down conformation, which facilitate Up transition. The loss of D614_K854 salt-bridge upon mutation, generally stabilize S-protein protomer, including the fusion peptide proximal region that mediates membrane fusion. Understanding of the molecular basis of D614G is crucial as it dominates in all variants of concern including Delta and Omicron.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Hisham M. Dokainish", + "author_inst": "Riken" + }, + { + "author_name": "Yuji Sugita", + "author_inst": "RIKEN" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2022.01.24.477633", "rel_title": "Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern", @@ -404986,41 +407017,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2022.01.25.22269818", - "rel_title": "Mitigating isolation: further comparing the effect of LFD testing for early release from self-isolation for COVID-19 cases", - "rel_date": "2022-01-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.25.22269818", - "rel_abs": "In a recent paper, we described how lateral flow device (LFD) testing might be used to reduce the amount of excess time individuals spend in isolation following confirmation of a COVID-19 infection. Through the work presented here, we look to expand upon this and explore in more detail the benefit that such an approach might provide. We use our previously described model to study scenarios through the metrics \"proportion released still infectious\", \"excess time spent in isolation\" (time isolated while no longer infectious), and \"time spent infectious after early release\". We also look to consider the effect on these metrics by comparing values obtained when a single negative LFD test is required for early release, versus requiring two and three sequential negative LFD tests. Results show that jointly employing self-isolation and LFD testing may deliver sizeable reductions to the proportion of individuals being release while still infection, the average amount of excess time spent in isolation by those no longer a public health threat, and the average amount of time spent infectious by those released early. These effects considered in conjunction could provide a considerable decrease in the public health risk posed by still infectious individuals being released back into the population by actively monitoring their infection status throughout their isolation period. Such an approach could also help lighten the impact incurred on the individual by reducing the amount of time spent in isolation while posing no further public health risk, in addition to alleviating pressures on the economy and in healthcare settings caused by mass isolation in times of high prevalence.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Declan Bays", - "author_inst": "United Kingdom Health Security Agency" - }, - { - "author_name": "Timothy Whiteley", - "author_inst": "United Kingdom Health Security Agency" - }, - { - "author_name": "Hannah Williams", - "author_inst": "United Kingdom Health Security Agency" - }, - { - "author_name": "Thomas James Ronald Finnie", - "author_inst": "United Kingdom Health Security Agency" - }, - { - "author_name": "Nick Gent", - "author_inst": "United Kingdom Health Security Agency" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.01.24.22269769", "rel_title": "Designing isolation guidelines for COVID-19 patients utilizing rapid antigen tests: a simulation study using viral dynamics models", @@ -405660,6 +407656,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2022.01.24.22269714", + "rel_title": "COVID-19 vaccines effectiveness against symptomatic SARS-CoV-2 Delta variant infection: a population-based case-control study in St. Petersburg, Russia", + "rel_date": "2022-01-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.24.22269714", + "rel_abs": "BackgroundStudies of mRNA and vector-based vaccines used in different countries report acceptable levels of effectiveness against SARS-CoV-2 infection caused by the Delta variants of SARS-CoV-2. No studies estimated vaccine effectiveness (VE) of Gam-COVID-Vac and other vaccines used in Russia against symptomatic infection with Delta variant. In this population-based case-control study, we aimed to estimate the effectiveness of the Russian COVID-19 vaccines against symptomatic SARS-CoV-2 during the recent outbreak caused by the Delta VOC in October 2021 in St. Petersburg, Russia.\n\nMethodsIn a population-based case-control study with density sampling of controls, we acquired information on cases and controls from two independent studies conducted in St. Petersburg. Cases were symptomatic patients with confirmed SARS-CoV-2 (using polymerase chain reaction (PCR) test) referred to low-dose computed tomography (LDCT) triage in two outpatient centres between October 6 and 14, 2021 during the Delta variant outbreak. We recruited the controls during the representative survey of the seroprevalence study conducted during the same period in St. Petersburg using random digit dialling. In the primary analysis, we used logistic regression models to estimate the adjusted (age, gender, and history of confirmed COVID-19) VE against symptomatic SARS-CoV-2 resulted in a referral to triage centre for three vaccines used in Russia: Gam-COVID-Vac, EpiVacCorona, and CoviVac.\n\nFindingsWe included 1,254 cases and 2,747 controls recruited between the 6th and 14th of October in the final analysis. VE was 56% (95% CI: 48 to 63) for Gam-COVID-Vac (Sputnik V), 49% (95% CI: 29 to 63) for 1-dose Gam-COVID-Vac (Sputnik V) or Sputnik Light, -58% (95% CI: -225 to 23) for EpiVacCorona and 40% (95% CI: 3 to 63) for CoviVac. Without adjustment for the history of confirmed COVID-19 VE for all vaccines was lower, except for one-dose Gam-COVID-Vac (Sputnik Light). The adjusted VE was slightly lower in women -- 51% (95% CI: 39 to 60) than men -- 65% (95% CI: 5 to 73). It was also higher in younger age. However, in the analysis restricted to participants without a history of confirmed COVID-19, the differences in VE by age group were smaller.\n\nInterpretationIn contrast to other Russian vaccines, Gam-COVID-Vac is effective against symptomatic SARS-CoV-2 infection caused by Delta VOC. Effectiveness is likely higher than the estimated 56% due to bias arising from high prevalence of the past COVID-19 in St. Petersburg.\n\nFundingPopulation-based survey in St. Petersburg was funded by Polymetal International, plc.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Anton Barchuk", + "author_inst": "The Institute for Interdisciplinary Health Research at the European University at St. Petersburg." + }, + { + "author_name": "Anna Bulina", + "author_inst": "The Institute for Interdisciplinary Health Research at the European University at St. Petersburg." + }, + { + "author_name": "Mikhail Cherkashin", + "author_inst": "Medical Institute named after Berezin Sergey" + }, + { + "author_name": "Natalia Berezina", + "author_inst": "Medical Institute named after Berezin Sergey" + }, + { + "author_name": "Tatyana Rakova", + "author_inst": "Medical Institute named after Berezin Sergey" + }, + { + "author_name": "Darya Kuplevatskaya", + "author_inst": "Medical Institute named after Berezin Sergey" + }, + { + "author_name": "Oksana Stanevich", + "author_inst": "The Institute for Interdisciplinary Health Research at the European University at St. Petersburg." + }, + { + "author_name": "Dmitriy Skougarevskiy", + "author_inst": "European University at St. Petersburg" + }, + { + "author_name": "Artemiy Okhotin", + "author_inst": "Tarusa Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.01.24.22269757", "rel_title": "Modelling preventive measures and their effect on generation times in emerging epidemics", @@ -406552,85 +408599,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.21.22268602", - "rel_title": "B.1.617.2 SARS-CoV-2 (Delta) variant is associated with increased risk of hospitalization and death compared with B.1.1.7 SARS-CoV-2 (Alpha) variant", - "rel_date": "2022-01-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.21.22268602", - "rel_abs": "IntroductionThe B.1.617.2 variant (Delta) was associated with increased transmissibility and lower vaccine effectiveness than the B.1.1.7 variant (Alpha). However, the effect of the B.1.617.2 variant on disease severity remains unclear. This study aims to assess whether infection with the B.1.617.2 variant was associated with a higher risk of serious illness, compared with other co-circulating variants, measured through hospitalization and death by COVID-19 in Portugal.\n\nMethodsWe conducted a matched cohort study in adult individuals diagnosed with SARS-CoV-2/COVID-19 infection between March 29 and August 1, 2021. Cases were individuals with a positive PCR test notified to the surveillance system. SARS-CoV-2 variants were classified first by genomic sequencing (WGS) and, if this information was unavailable, by detecting the S gene target failure.\n\nDelta (B.1.617.2) and Alpha (B.1.1.7) cases were matched on the week of diagnosis at a 1 to k ratio (k being the maximum number of unexposed available in that week) to maximize the inclusion of unexposed, using the nearest-neighbor algorithm. The hazard risk and 95% confidence intervals of hospitalization and death among those infected with the Delta (B.1.617.2) variant vs. Alpha (B.1.1.7) was estimated using a Cox proportional hazards model, adjusting for confounding for sex, age, and vaccination status.\n\nResultsA total of 2,778 cases were included in the study. Of the total, 1 742 (68%) were identified as B.1.617.2 variant cases and 3 629 (32%) as B.1.1.7 variant. Within the B.1.1.7 variant cases 106 (2.9%) were hospitalized, and 110 (6.3%) within the B.1.617.2 variant cases. A total of 29 deaths were reported, 8 (0.2%) in patients infected with B.1.1.7 variant and 21 (1.2%) in patients with the B.1.617.2 variant. The confounding adjusted risk of hospitalization, in persons infected with the B.1.617.2 variant was 2.44 (95%CI 1.85; 3.20) times higher than the risk of hospitalization among B.1.1.7 variant cases, and the confounding-adjusted risk of death for B.1.617.2 variant cases was 5.20 (95%CI 2.20; 12.29) times higher than the risk of death in patients infected by B.1.1.7 variant.\n\nConclusionThe B.1.617.2 variant is associated with an increased risk of hospitalization and death compared with the B.1.1.7 variant.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Eduardo Freire Rodrigues", - "author_inst": "Public Health Unit Amadora, Portugal | Direcao Geral da Saude" - }, - { - "author_name": "Joana Moreno", - "author_inst": "Public Health Unit Gaia, Portugal | Direcao Geral de Saude" - }, - { - "author_name": "Pedro Pinto Leite", - "author_inst": "Direcao Geral da Saude" - }, - { - "author_name": "Baltazar Nunes", - "author_inst": "Department of Epidemiology, National Institute of Health Doutor Ricardo Jorge (INSA), Portugal" - }, - { - "author_name": "Joao Paulo Gomes", - "author_inst": "Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Portugal" - }, - { - "author_name": "Rita Ferreira", - "author_inst": "Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Portugal" - }, - { - "author_name": "Joana Isidro", - "author_inst": "Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Portugal" - }, - { - "author_name": "Vitor Borges", - "author_inst": "Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Portugal" - }, - { - "author_name": "Luis Vieira", - "author_inst": "Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal" - }, - { - "author_name": "Silvia Duarte", - "author_inst": "Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal" - }, - { - "author_name": "Carlos Sousa", - "author_inst": "Unilabs, Porto, Portugal" - }, - { - "author_name": "Jose Pedro Almeida", - "author_inst": "Unilabs, Porto, Portugal" - }, - { - "author_name": "Luis Menezes", - "author_inst": "Unilabs, Porto, Portugal" - }, - { - "author_name": "Dora Vaz", - "author_inst": "Public Health Unit Amadora, Portugal" - }, - { - "author_name": "Andreia Leite", - "author_inst": "NOVA National School of Public Health, Public Health Research Centre, Universidade NOVA de Lisboa | Comprehensive Health Research Centre (CHRC), Universidade NO" - }, - { - "author_name": "ANDRE PERALTA SANTOS", - "author_inst": "Direcao Geral da Saude | NOVA National School of Public Health, Public Health Research Centre, Universidade NOVA de Lisboa | Comprehensive Health Research Centr" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.20.22269406", "rel_title": "Omicron (BA.1) SARS-CoV-2 variant is associated with reduced risk of hospitalization and length of stay compared with Delta (B.1.617.2)", @@ -407542,6 +409510,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.01.22.22269105", + "rel_title": "Risk of COVID-19 Reinfection and Vaccine Breakthrough Infection, Madera County, California, 2021", + "rel_date": "2022-01-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.22.22269105", + "rel_abs": "The probability of either testing COVID-19 positive or dying for three cohorts in Madera County, California in 2021 was compared. These cohorts included 1. those unvaccinated, 2. those vaccinated and 3. persons with a previous COVID-19 infection. The three groups were made generally comparable by matching on age, gender, postal zip code of residence, and the date of either COVID-19 infection or of vaccination.\n\nThe hazard ratio (HR) for death (from all causes) after COVID-19 infection vs. vaccination was 11.7 (95% CI 5.91-23.1, p<0.05). The HR for testing positive for COVID-19 >14 days after initial COVID-19 infection or after completing primary COVID-19 vaccination was 1.98 (95% CI 1.53-2.58 p<0.001). As the majority of positive COVID-19 tests in the post COVID-19 cohort occurred within 90 days of the initial infection, and as these early positives may not represent a new infection, we also compared rates of testing COVID-19 positive [≥] 90 days after initial infection or vaccination. After removing these early positive COVID-19 tests that occurred between days 14-90, the HR ratio for testing COVID-19 positive is now lower for the post COVID-19 cohort compared with the vaccinated cohort. The risk for having a positive COVID-19 test occurring 90 days after an initial COVID-19 infection or after vaccination was 0.54 (95% CI 0.33-0.87, p<0.05) for the post COVID-19 group vs Vaccinated group.\n\nThus the risk for testing COVID-19 positive was higher in the first 90 days after COVID-19 infection compared to those vaccinated. However, from 90 to 300 days after COVID-19 infection, the post COVID-19 infection cohort had a lower risk of testing COVID-19 positive than those fully vaccinated.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Minhphuong Nguyen", + "author_inst": "Madera County Department of Public Health" + }, + { + "author_name": "Eric Paul", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Paul K. Mills", + "author_inst": "University of California, San Francisco-Fresno, Department of Internal Medicine" + }, + { + "author_name": "Simon Paul", + "author_inst": "Madera County Department of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.01.22.22269689", "rel_title": "ESTIMATING THE EFFECT OF VACCINATION ON THE CASE-FATALITY RATE FOR COVID-19", @@ -408726,73 +410725,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.01.19.22269560", - "rel_title": "One vaccine to counter many diseases? Modelling the economics of oral polio vaccine against child mortality and COVID-19", - "rel_date": "2022-01-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.19.22269560", - "rel_abs": "BackgroundRecent reviews summarize evidence that some vaccines have heterologous or non-specific effects (NSE), potentially offering protection against multiple pathogens. Numerous economic evaluations examine vaccines pathogen-specific effects, but we have found only two economic evaluations of NSE. This paper starts to fill this gap by reporting economic evaluations of the NSE of oral polio vaccine (OPV) against under-five mortality and COVID-19.\n\nMethodsWe studied two settings: (1) reducing child mortality in a high-mortality setting (Guinea-Bissau) and (2) preventing COVID-19 in India. In the former, the intervention involves three annual campaigns in which children receive OPV incremental to routine immunization. In the latter, a susceptible-exposed-infectious-recovered model was developed to estimate the population benefits of two scenarios, in which OPV would be co-administered alongside COVID-19 vaccines. Incremental cost-effectiveness and benefit-cost ratios were modelled for ranges of intervention effectiveness estimates to supplement the headline numbers and account for heterogeneity and uncertainty.\n\nResultsFor child mortality, headline cost-effectiveness was $650 per child death averted. For COVID-19, assuming OPV had 20% effectiveness, incremental cost per death averted was $23,000-65,000 if it were administered simultaneously with a COVID-19 vaccine less than 200 days into a wave of the epidemic. If the COVID-19 vaccine availability were delayed, the cost per averted death would decrease to $2600-6100. Estimated benefit-to-cost ratios vary but are consistently high.\n\nConclusionEconomic evaluation suggests the potential of OPV to efficiently reduce child mortality in high mortality environments. Likewise, within a broad range of assumed effect sizes OPV could play an economically attractive role against COVID-19.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Angela Y Chang", - "author_inst": "Danish Institute for Advanced Study" - }, - { - "author_name": "Peter Aaby", - "author_inst": "Bandim Health Project, Bissau, Guinea-Bissau" - }, - { - "author_name": "Michael S Avidan", - "author_inst": "Department of Anesthesiology, Washington University in St. Louis, MO, USA" - }, - { - "author_name": "Christine S Benn", - "author_inst": "Department of Clinical Research, University of Southern Denmark, Odense, Denmark" - }, - { - "author_name": "Stefano M Bertozzi", - "author_inst": "School of Public Health, University of California, Berkeley, CA, USA" - }, - { - "author_name": "Lawrence Blatt", - "author_inst": "Aligos Therapeutics, CA, USA" - }, - { - "author_name": "Konstantin Chumakov", - "author_inst": "Food and Drug Administration Office of Vaccine Research and Review, MD, USA" - }, - { - "author_name": "Shabaana A Khader", - "author_inst": "Department of Molecular Microbiology, Washington University in St. Louis School of Medicine, MO, USA" - }, - { - "author_name": "Shyam Kottilil", - "author_inst": "Institute of Human Virology, University of Maryland School of Medicine, MD, USA" - }, - { - "author_name": "Madhav Nekkar", - "author_inst": "School of Public Health, University of California, Berkeley, CA, USA" - }, - { - "author_name": "Mihai G Netea", - "author_inst": "Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands" - }, - { - "author_name": "Annie Sparrow", - "author_inst": "Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, NY, USA" - }, - { - "author_name": "Dean T Jamison", - "author_inst": "Institute for Global Health Sciences, University of California, San Francisco, CA, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2022.01.20.22269587", "rel_title": "Safety and immunogenicity of Pfizer/BioNTech SARS-CoV-2 mRNA third booster vaccine against SARS-CoV-2 Omicron variant in Japanese healthcare workers", @@ -409500,6 +411432,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.18.22269452", + "rel_title": "Effectiveness of BNT162b2 and mRNA-1273 COVID-19 boosters against SARS-CoV-2 Omicron (B.1.1.529) infection in Qatar", + "rel_date": "2022-01-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.18.22269452", + "rel_abs": "BACKGROUNDWaning of COVID-19 vaccine protection and emergence of SARS-CoV-2 Omicron (B.1.1.529) variant have expedited efforts to scale up booster vaccination. This study compared protection afforded by booster doses of the BNT162b2 (Pfizer-BioNTech) and mRNA-1273 (Moderna) vaccines, compared to the primary series of only two doses in Qatar, during a large, rapidly growing Omicron wave.\n\nMETHODSIn a population of 2,232,224 vaccinated persons with at least two doses, two matched, retrospective cohort studies were implemented to investigate effectiveness of booster vaccination against symptomatic SARS-CoV-2 infection and against COVID-19 hospitalization and death, up to January 9, 2022. Association of booster status with infection was estimated using Cox proportional-hazards regression models.\n\nRESULTSFor BNT162b2, cumulative symptomatic infection incidence was 2.9% (95% CI: 2.8-3.1%) in the booster-dose cohort and 5.5% (95% CI: 5.3-5.7%) in the primary-series cohort, after 49 days of follow-up. Adjusted hazard ratio for symptomatic infection was 0.50 (95% CI: 0.47-0.53). Booster effectiveness relative to primary series was 50.1% (95% CI: 47.3-52.8%). For mRNA-1273, cumulative symptomatic infection incidence was 1.9% (95% CI: 1.7-2.2%) in the booster-dose cohort and 3.5% (95% CI: 3.2-3.9%) in the primary-series cohort, after 35 days of follow-up. The adjusted hazard ratio for symptomatic infection was 0.49 (95% CI: 0.43-0.57). Booster effectiveness relative to primary series was 50.8% (95% CI: 43.4-57.3%). There were fewer cases of severe COVID-19 in booster-dose cohorts than in primary-series cohorts, but cases of severe COVID-19 were rare in all cohorts.\n\nCONCLUSIONSmRNA booster vaccination is associated with modest effectiveness against symptomatic infection with Omicron. The development of a new generation of vaccines targeting a broad range of variants may be warranted.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Laith J Abu-Raddad", + "author_inst": "Weill Cornell Medicine-Qatar" + }, + { + "author_name": "Hiam Chemaitelly", + "author_inst": "Weill Cornell Medicine-Qatar" + }, + { + "author_name": "Houssein H. Ayoub", + "author_inst": "Qatar University" + }, + { + "author_name": "Sawsan AlMukdad", + "author_inst": "Weill Cornell Medicine-Qatar" + }, + { + "author_name": "Patrick J Tang", + "author_inst": "Sidra Medicine" + }, + { + "author_name": "Mohammad Rubayet Hasan", + "author_inst": "Sidra Medicine" + }, + { + "author_name": "Peter Coyle", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "HADI M. YASSINE", + "author_inst": "Qatar University" + }, + { + "author_name": "Hebah A. Al-Khatib", + "author_inst": "Qatar University" + }, + { + "author_name": "Maria K. Smatti", + "author_inst": "Qatar University" + }, + { + "author_name": "Zaina Al-Kanaani", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Einas Al-Kuwari", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Andrew Jeremijenko", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Anvar Hassan Kaleeckal", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Ali Nizar Latif", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Riyazuddin Mohammad Shaik", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Hanan F. Abdul-Rahim", + "author_inst": "Qatar University" + }, + { + "author_name": "Gheyath Nasrallah", + "author_inst": "Qatar University" + }, + { + "author_name": "Mohamed Ghaith Al-Kuwari", + "author_inst": "Primary Health Care Corporation" + }, + { + "author_name": "Adeel A Butt", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Hamad Eid Al-Romaihi", + "author_inst": "Ministry of Public Health" + }, + { + "author_name": "Mohamed H. Al-Thani", + "author_inst": "Ministry of Public Health" + }, + { + "author_name": "Abdullatif Al-Khal", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Roberto Bertollini", + "author_inst": "Ministry of Public Health" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.01.18.22268965", "rel_title": "Safety Profile of Sinopharm COVID-19 Vaccine and Breakthrough Infections in Pakistan", @@ -410400,85 +412443,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.21.22269633", - "rel_title": "A booster dose of mRNA-based COVID-19 vaccines fosters the development of an immune response in immunosuppressed fragile patients.", - "rel_date": "2022-01-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.21.22269633", - "rel_abs": "SARS-CoV-2 vaccination has proven effective in inducing an immune response in healthy individuals and is progressively allowing to overcome the pandemic. Recent evidence has shown that response to vaccination in some vulnerable patients may be diminished, and it has been proposed a booster dose. We tested the kinetic of development of serum antibodies to the SARS-CoV-2 Spike protein, their neutralizing capacity, the CD4 and CD8 IFN-{gamma} T cell response in 328 subjects, including 131 immunocompromised individuals (cancer, rheumatologic, and hemodialysis patients), 160 healthcare workers (HCW) and 37 subjects older than 75 yo, after vaccination with two or three doses of mRNA vaccines. We stratified the patients according to the type of treatment. We found that immunocompromised patients, depending on the type of treatment, poorly respond to SARS-CoV-2 mRNA vaccines. However, an additional booster dose of vaccine induced a good immune response in almost all of the patients except those receiving anti-CD20 antibody. Similarly to HCW, previously infected and vaccinated immunocompromised individuals demonstrate a stronger SARS-CoV-2 specific immune response than those who are vaccinated without prior infection.\n\nSummary blurbImmunocompromised patients poorly respond to two doses of SARS-CoV-2 mRNA vaccines. However, an additional booster dose elicits a strong humoral and cellular immune response in these subjects.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Elena Azzolini", - "author_inst": "IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, MI, Italy." - }, - { - "author_name": "Chiara Pozzi", - "author_inst": "IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, MI, Italy." - }, - { - "author_name": "Luca Germagnoli", - "author_inst": "IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, MI, Italy." - }, - { - "author_name": "Bianca Oresta", - "author_inst": "DiaSorin S.p.A., Via Crescentino, I-13040 Saluggia, VC, Italy" - }, - { - "author_name": "Nicola Carriglio", - "author_inst": "DiaSorin S.p.A., Via Crescentino, I-13040 Saluggia, VC, Italy" - }, - { - "author_name": "Mariella Calleri", - "author_inst": "DiaSorin S.p.A., Via Crescentino, I-13040 Saluggia, VC, Italy" - }, - { - "author_name": "Carlo Selmi", - "author_inst": "Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini, 20072 Pieve Emanuele, MI, Italy" - }, - { - "author_name": "Maria De Santis", - "author_inst": "IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, MI, Italy" - }, - { - "author_name": "Silvia Finazzi", - "author_inst": "IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, MI, Italy" - }, - { - "author_name": "Carmelo Carlo-Stella", - "author_inst": "Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini, 20072 Pieve Emanuele, MI, Italy" - }, - { - "author_name": "Alexia Bertuzzi", - "author_inst": "IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, MI, Italy" - }, - { - "author_name": "Francesca Motta", - "author_inst": "Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini, 20072 Pieve Emanuele, MI, Italy" - }, - { - "author_name": "Angela Ceribelli", - "author_inst": "IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, MI, Italy" - }, - { - "author_name": "Alberto Mantovani", - "author_inst": "IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, MI, Italy" - }, - { - "author_name": "Fabrizio Bonelli", - "author_inst": "DiaSorin S.p.A., Via Crescentino, I-13040 Saluggia, VC, Italy" - }, - { - "author_name": "Maria Rescigno", - "author_inst": "Humanitas University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2022.01.20.22269593", "rel_title": "Causal associations between body fat accumulation and COVID-19 severity: A Mendelian randomization study", @@ -411234,6 +413198,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.01.19.476497", + "rel_title": "T cell response following anti COVID-19 BNT162b2 vaccination is maintained against the SARS-CoV-2 Omicron B.1.1.529 variant of concern", + "rel_date": "2022-01-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.19.476497", + "rel_abs": "The progression of the COVID-19 pandemic leads to the emergence of variants of concern (VOC), which may compromise the efficacy of the currently administered vaccines. Antigenic drift can potentially bring about a reduced protective T cell immunity and consequently to more severe disease manifestations. To assess this possibility, the T cell responses to the wild-type, Wuhan-1 SARS-CoV-2 ancestral spike protein and Omicron B.1.1.529 spike protein were compared. Accordingly, peripheral blood mononuclear cells (PBMC) were collected from 8 healthy volunteers 4-5 months following a third vaccination with BNT162b2, and stimulated with overlapping peptide libraries representing the spike of either the ancestral or Omicron SARS-CoV- 2 virus variants. Quantification of the specific T cells was carried out by a fluorescent ELISPOT assay, monitoring interferon-gamma (IFNg), interleukin-10 (IL-10) and interleukin-4 (IL-4) secreting cells. For all the examined individuals, comparable level of reactivity to both forms of spike protein were determined. In addition, a dominant Th1 response was observed, manifested mainly by IFNg secreting cells and only limited numbers of IL-10 and IL-4 secreting cells. The data demonstrates a stable T cell activity to the emerging Omicron variant in the tested individuals, therefore the protective immunity to the variant following BNT162b2 vaccination is not significantly affected.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Hila Cohen", + "author_inst": "IIBR" + }, + { + "author_name": "Shahar Rotem", + "author_inst": "IIBR" + }, + { + "author_name": "Uri Elia", + "author_inst": "IIBR" + }, + { + "author_name": "Gal Bilinsky", + "author_inst": "IIBR" + }, + { + "author_name": "Itzchak Levy", + "author_inst": "Sheba Medical Center, Israel" + }, + { + "author_name": "Theodor Chitlaru", + "author_inst": "IIBR" + }, + { + "author_name": "Erez Bar-Haim", + "author_inst": "IIBR" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.01.13.22268997", "rel_title": "Detection and upsurge of SARS-CoV-2 Omicron variant in Islamabad Pakistan", @@ -412406,57 +414413,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.01.18.476607", - "rel_title": "Differences in environmental stability among SARS-CoV-2 variants of concern: Omicron has higher stability", - "rel_date": "2022-01-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.18.476607", - "rel_abs": "SARS-CoV-2 variants of concern (VOCs) could cause significant human and economic damage owing to increased infectivity and transmissibility, and understanding their characteristics is crucial for infection control. Here, we analyzed differences in viral stability and disinfection efficacy between the Wuhan strain and all VOCs. On plastic and skin surfaces, Alpha, Beta, Delta, and Omicron variants exhibited more than two-fold longer survival than the Wuhan strain, and the Omicron variant had the longest survival time. Specifically, survival times of the Wuhan strain, Alpha variant, Beta variant, Gamma variant, Delta variant, and Omicron variant on skin surfaces were 8.6 h (95% CI, 6.5-10.9 h), 19.6 h (95% CI, 14.8-25.3 h), 19.1 h (95% CI, 13.9- 25.3 h), 11.0 h (95% CI, 8.1-14.7 h), 16.8 h (95% CI, 13.1-21.1 h), and 21.1 h (95% CI, 15.8- 27.6 h), respectively. In vitro, disinfectant effectiveness evaluations showed that Alpha, Beta, Delta, and Omicron were slightly more resistant to ethanol than the Wuhan strain. However, ex vivo evaluation showed that on human skin, all viruses were completely inactivated by exposure to 35 w/w % ethanol for 15 s. The high environmental stability of these VOCs could increase transmission risk and contribute to spread. Additionally, the Omicron variant might have been replaced by the Delta variant due to its increased environmental stability and rapid spread. To prevent VOC spread, it is highly recommended that current infection control practices use disinfectants with appropriate ethanol concentrations.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Ryohei Hirose", - "author_inst": "Kyoto Prefectural University of Medicine" - }, - { - "author_name": "Yoshito Itoh", - "author_inst": "Kyoto Prefectural University of Medicine" - }, - { - "author_name": "Hiroshi Ikegaya", - "author_inst": "Kyoto Prefectural University of Medicine" - }, - { - "author_name": "Hajime Miyazaki", - "author_inst": "Kyoto Prefectural University of Medicine" - }, - { - "author_name": "Naoto Watanabe", - "author_inst": "Kyoto Prefectural University of Medicine" - }, - { - "author_name": "Takuma Yoshida", - "author_inst": "Kyoto Prefectural University of Medicine" - }, - { - "author_name": "Risa Bandou", - "author_inst": "Kyoto Prefectural University of Medicine" - }, - { - "author_name": "Tomo Daidoji", - "author_inst": "Kyoto Prefectural University of Medicine" - }, - { - "author_name": "Takaaki Nakaya", - "author_inst": "Kyoto Prefectural University of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.01.17.476672", "rel_title": "High activity of an affinity-matured ACE2 decoy against Omicron SARS-CoV-2 and pre-emergent coronaviruses", @@ -413536,6 +415492,20 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.18.22269141", + "rel_title": "Booster vaccination to curtail COVID-19 resurgence - population-level implications of the Israeli campaign", + "rel_date": "2022-01-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.18.22269141", + "rel_abs": "Israel was one of the first countries to administer mass vaccination. Consequently, it was among the first countries to experience significant breakthrough infections due to the waning of vaccine-induced immunity, which led to a resurgence of the epidemic. To mitigate the outbreak, Israel launched a pioneering booster campaign. Israels success in curtailing the Delta resurgence while imposing only mild non-pharmaceutical interventions has been instrumental in influencing the decision of many countries to initiate a booster campaign. By constructing a detailed mathematical model and calibrating it to the Israeli data, we expand our understanding of the impact of the booster campaign from the individual to the population level. We use the calibrated model to explore counterfactual scenarios in which the booster vaccination campaign is altered and to assess the direct and indirect effects in the different scenarios. Our results point to the vast benefits of vaccinating younger age groups that are not at a high risk of developing severe disease but play an important role in transmission. We further show that when the epidemic is exponentially growing the success of the booster campaign is highly sensitive to the timing of its initiation. Hence a rapid response is an important factor in reducing disease burden using booster vaccination.", + "rel_num_authors": 0, + "rel_authors": null, + "version": "1", + "license": "", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.18.21266111", "rel_title": "SARS-CoV-2 induces human endogenous retrovirus type W envelope protein expression in blood lymphocytes and in tissues of COVID-19 patients.", @@ -414280,41 +416250,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.10.475746", - "rel_title": "Tuftsin: a natural molecule against SARS-CoV-2 infection", - "rel_date": "2022-01-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.10.475746", - "rel_abs": "Coronavirus disease 2019 (COVID-19) continuously proceeds despite the application of a variety of vaccines. It is still urgent to find effective ways to treat COVID-19. Recent studies indicate that NRP1, an important receptor of the natural peptide tuftsin, facilitates SARS-CoV-2 infection. Importantly, tuftsin is a natural human molecule released from IgG. Here, we found 91 overlapping genes between tuftsin targets and COVID-19-associated genes. Bioinformatics analyses indicated that tuftsin could also target ACE2 and exert some immune-related functions to treat COVID-19. Using surface plasmon resonance (SPR) analysis, we confirmed that tuftsin can bind ACE2 and NRP1 directly. Moreover, tuftsin effectively impairs the binding of SARS-CoV-2 S1 to ACE2. Thus, tuftsin is an attractive drug against COVID-19. And tuftsin as natural immunostimulating peptide in human, we speculate that tuftsin may has crucial roles in asymptomatic carriers or mild cases of COVID-19.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Jiahao Huang", - "author_inst": "Peking University" - }, - { - "author_name": "Jing Wang", - "author_inst": "Peking University" - }, - { - "author_name": "Ziyuan Wang", - "author_inst": "Peking University" - }, - { - "author_name": "Ming Chu", - "author_inst": "Peking University" - }, - { - "author_name": "Yuedan Wang", - "author_inst": "Peking University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.01.13.22269243", "rel_title": "Limited cross-variant immunity after infection with the SARS-CoV-2 Omicron variant without vaccination", @@ -415138,6 +417073,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.01.12.22269169", + "rel_title": "Background incidence rates of adverse events of special interest related to COVID-19 vaccines in Ontario, Canada, 2015 to 2020, to inform COVID-19 vaccine safety surveillance", + "rel_date": "2022-01-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.12.22269169", + "rel_abs": "BackgroundBackground incidence rates are critical in pharmacovigilance to facilitate identification of vaccine safety signals. We estimated background incidence rates of nine adverse events of special interest related to COVID-19 vaccines in Ontario, Canada.\n\nMethodsWe conducted a population-based retrospective observational study using linked health administrative databases for hospitalizations and emergency department visits among Ontario residents. We estimated incidence rates of Bells palsy, idiopathic thrombocytopenia, febrile convulsions, acute disseminated encephalomyelitis, myocarditis, pericarditis, Kawasaki disease, Guillain-Barre syndrome, and transverse myelitis during five pre-pandemic years (2015- 2019) and 2020.\n\nResultsThe average annual population was 14 million across all age groups with 51% female. The pre-pandemic mean annual rates per 100,000 population during 2015-2019 were 43.9 for idiopathic thrombocytopenia, 27.8 for Bells palsy, 25.0 for febrile convulsions, 22.8 for acute disseminated encephalomyelitis, 11.3 for myocarditis/pericarditis, 8.6 for pericarditis, 2.9 for myocarditis, 1.9 for Guillain-Barre syndrome, 1.7 for transverse myelitis, and 1.6 for Kawasaki disease. Females had higher rates of acute disseminated encephalomyelitis and transverse myelitis while males had higher rates of myocarditis, pericarditis, and Guillain-Barre syndrome. Bells palsy, acute disseminated encephalomyelitis, and Guillain-Barre syndrome increased with age. The mean rates of myocarditis and/or pericarditis increased with age up to 79 years; males had higher rates than females: from 12-59 years for myocarditis and [≥]12 years for pericarditis. Febrile convulsions and Kawasaki disease were predominantly childhood diseases and generally decreased with age.\n\nConclusionsOur estimated background rates will permit estimating numbers of expected events for these conditions and facilitate detection of potential safety signals following COVID-19 vaccination.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Sharifa Nasreen", + "author_inst": "University of Toronto" + }, + { + "author_name": "Andrew Calzavara", + "author_inst": "ICES, Toronto, ON, Canada" + }, + { + "author_name": "Sarah A Buchan", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Nisha Thampi", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Caitlin Johnson", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Sarah E. Wilson", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Jeffrey C. Kwong", + "author_inst": "ICES" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.01.16.22269161", "rel_title": "Forecast of omicron wave time evolution", @@ -415874,29 +417852,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.14.22268980", - "rel_title": "HAT-field: a very cheap, robust and quantitative point-of-care serological test for Covid-19.", - "rel_date": "2022-01-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.14.22268980", - "rel_abs": "We have recently described a very simple and cheap serological test called HAT to detect antibodies directed against the RBD of the SARS-Cov-2 virus. HAT is based on hemagglutination, triggered by a single reagent (IH4-RBD) comprised of the viral RBD domain fused to a nanobody specific for glycophorin, which is expressed at very high levels at the surface of human red blood cells (RBCs).\n\nOne of the main initial goals of this study was to devise a test protocol that would be sensitive and reliable, yet require no specialized laboratory equipment such as adjustable pipets, so that it could be performed in the most remote corners of the world by people with minimal levels of training. Because antibody levels against the viral RBD have been found to correlate closely with sero-neutralisation titers, and thus with protection against reinfection, it has become obvious during the course of this study that making this test reliably quantitative would be a further significant advantage.\n\nUsing IH4-RBD based on the original Wuhan sequence, we have found that, in PBN, a buffer which contains BSA and sodium azide, the reagent is stable for over 6 months at room temperature, and that PBN also improves HAT performance compared to using straight PBS. We also show that performing HAT at either 4{degrees}C, room temperature or 37{degrees}C has minimal influence on the results, and that quantitative evaluation of the levels of antibodies directed against the SARS-CoV-2 RBD can be achieved in a single step using titration of the IH4-RBD reagent.\n\nThe HAT-field protocol described here requires only very simple disposable equipment and a few microliters of whole blood, such as can be obtained by finger prick. Because it is based on a single soluble reagent, the test can be adapted very simply and rapidly to detect antibodies against variants of the SARS-CoV-2, or conceivably against different pathogens. HAT-field appears well suited to provide quantitative assessments of the serological protection of populations as well as individuals, and given its very low cost, the stability of the IH4-RBD reagent in the adapted buffer, and the simplicity of the procedure, could be deployed pretty much anywhere, including in the poorest countries and the most remote corners of the globe.\n\nNote: This manuscript has been refereed by Review Commons, and modified thanks to the comments and suggestions from three referees. Those comments, and our replies, are provided at the end of the manuscripts pdf, and can also be accessed by clicking on the blue tab found to the right of the MedRXiv window.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Etienne Joly", - "author_inst": "Institute of Pharmacology and Structural Biology (IPBS), University of Toulouse, CNRS, Toulouse, 31000, France" - }, - { - "author_name": "Agnes Maurel Ribes", - "author_inst": "Centre Hospitalier Universitaire de Toulouse, 31000, Toulouse, France" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.14.21267633", "rel_title": "National-scale surveillance of emerging SARS-CoV-2 variants in wastewater", @@ -416940,6 +418895,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.01.12.22269179", + "rel_title": "COVID infection severity in children under 5 years old before and after Omicron emergence in the US", + "rel_date": "2022-01-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.12.22269179", + "rel_abs": "ImportancePediatric SARS-CoV-2 infections and hospitalizations are rising in the US and other countries after the emergence of Omicron variant. However data on disease severity from Omicron compared with Delta in children under 5 in the US is lacking.\n\nObjectivesTo compare severity of clinic outcomes in children under 5 who contracted COVID infection for the first time before and after the emergence of Omicron in the US.\n\nDesign, Setting, and ParticipantsThis is a retrospective cohort study of electronic health record (EHR) data of 79,592 children under 5 who contracted SARS-CoV-2 infection for the first time, including 7,201 infected between 12/26/2021-1/6/2022 when the Omicron predominated (Omicron cohort), 63,203 infected between 9/1/2021-11/15/2021 when the Delta predominated (Delta cohort), and another 9,188 infected between 11/16/2021-11/30/2021 when the Delta predominated but immediately before the Omicron variant was detected in the US (Delta-2 cohort).\n\nExposuresFirst time infection of SARS-CoV-2.\n\nMain Outcomes and MeasuresAfter propensity-score matching, severity of COVID infections including emergency department (ED) visits, hospitalizations, intensive care unit (ICU) admissions, and mechanical ventilation use in the 3-day time-window following SARS-CoV-2 infection were compared between Omicron and Delta cohorts, and between Delta-2 and Delta cohorts. Risk ratios, and 95% confidence intervals (CI) were calculated.\n\nResultsAmong 7,201 infected children in the Omicron cohort (average age, 1.49 {+/-} 1.42 years), 47.4% were female, 2.4% Asian, 26.1% Black, 13.7% Hispanic, and 44.0% White. Before propensity score matching, the Omicron cohort were younger than the Delta cohort (average age 1.49 vs 1.73 years), comprised of more Black children, and had fewer comorbidities. After propensity-score matching for demographics, socio-economic determinants of health, comorbidities and medications, risks for severe clinical outcomes in the Omicron cohort were significantly lower than those in the Delta cohort: ED visits: 18.83% vs. 26.67% (risk ratio or RR: 0.71 [0.66-0.75]); hospitalizations: 1.04% vs. 3.14% (RR: 0.33 [0.26-0.43]); ICU admissions: 0.14% vs. 0.43% (RR: 0.32 [0.16-0.66]); mechanical ventilation: 0.33% vs. 1.15% (RR: 0.29 [0.18-0.46]). Control studies comparing Delta-2 to Delta cohorts show no difference.\n\nConclusions and RelevanceFor children under age 5, first time SARS-CoV-2 infections occurring when the Omicron predominated (prevalence >92%) was associated with significantly less severe outcomes than first-time infections in similar children when the Delta variant predominated.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Lindsey Wang", + "author_inst": "Case Western Reserve University" + }, + { + "author_name": "Nathan A Berger", + "author_inst": "Case Western Reserve University" + }, + { + "author_name": "David C Kaelber", + "author_inst": "Metrohealth" + }, + { + "author_name": "Pamela B Davis", + "author_inst": "Case Western Reserve University" + }, + { + "author_name": "Nora D Volkow", + "author_inst": "NIDA" + }, + { + "author_name": "Rong Xu", + "author_inst": "Case Western Reserve University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.12.22269192", "rel_title": "Imprinted SARS-CoV-2-specific memory lymphocytes define hybrid immunity", @@ -418144,113 +420138,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2022.01.12.22269023", - "rel_title": "Extremely potent monoclonal antibodies neutralize Omicron and other SARS-CoV-2 variants", - "rel_date": "2022-01-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.12.22269023", - "rel_abs": "The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has triggered a devastating global health, social and economic crisis. The RNA nature and broad circulation of this virus facilitate the accumulation of mutations, leading to the continuous emergence of variants of concern with increased transmissibility or pathogenicity1. This poses a major challenge to the effectiveness of current vaccines and therapeutic antibodies1, 2. Thus, there is an urgent need for effective therapeutic and preventive measures with a broad spectrum of action, especially against variants with an unparalleled number of mutations such as the recently emerged Omicron variant, which is rapidly spreading across the globe3. Here, we used combinatorial antibody phage-display libraries from convalescent COVID-19 patients to generate monoclonal antibodies against the receptor-binding domain of the SARS-CoV-2 spike protein with ultrapotent neutralizing activity. One such antibody, NE12, neutralizes an early isolate, the WA-1 strain, as well as the Alpha and Delta variants with half-maximal inhibitory concentrations at picomolar level. A second antibody, NA8, has an unusual breadth of neutralization, with picomolar activity against both the Beta and Omicron variants. The prophylactic and therapeutic efficacy of NE12 and NA8 was confirmed in preclinical studies in the golden Syrian hamster model. Analysis by cryo-EM illustrated the structural basis for the neutralization properties of NE12 and NA8. Potent and broadly neutralizing antibodies against conserved regions of the SARS-CoV-2 spike protein may play a key role against future variants of concern that evade immune control.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Zhaochun Chen", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Peng Zhang", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Yumiko Matsuoka", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Yaroslav Tsybovsky", - "author_inst": "Frederick National Laboratory for Cancer Research, Frederick, MD" - }, - { - "author_name": "Kamille West", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Celia Santos", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Lisa F. Boyd", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Hanh Nguyen", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Anna Pomerenke", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Tyler Stephens", - "author_inst": "Frederick National Laboratory for Cancer Research, Frederick, MD" - }, - { - "author_name": "Adam S. Olia", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Valeria De Giorgi", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Michael R. Holbrook", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Robin Gross", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Elena Postnikova", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Nicole L. Garza", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Reed F. Johnson", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "David H. Margulies", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Peter D. Kwong", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Harvey J. Alter", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Ursula J. Buchholz", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Paolo Lusso", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Patrizia Farci", - "author_inst": "National Institutes of Health" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.13.22269213", "rel_title": "Immunity in Omicron SARS-CoV-2 breakthrough COVID-19 in vaccinated adults", @@ -419146,6 +421033,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.01.10.475768", + "rel_title": "SARS-CoV-2 Point Mutation and Deletion Spectra, and Their Association with Different Disease Outcome", + "rel_date": "2022-01-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.10.475768", + "rel_abs": "Mutant spectra of RNA viruses are important to understand viral pathogenesis, and response to selective pressures. There is a need to characterize the complexity of mutant spectra in coronaviruses sampled from infected patients. In particular, the possible relationship between SARS-CoV-2 mutant spectrum complexity and disease associations has not been established. In the present study, we report an ultra-deep sequencing (UDS) analysis of the mutant spectrum of amplicons from the nsp12 (polymerase)- and spike (S)-coding regions of thirty nasopharyngeal isolates (diagnostic samples) of SARS-CoV-2 of the first COVID-19 pandemic wave (Madrid, Spain, April 2020) classified according to the severity of ensuing COVID-19. Low frequency mutations and deletions, counted relative to the consensus sequence of the corresponding isolate, were overwhelmingly abundant. We show that the average number of different point mutations, mutations per haplotype and several diversity indices was significantly higher in SARS-CoV-2 isolated from patients who developed mild disease than in those associated with moderate or severe disease (exitus). No such bias was observed with RNA deletions. Location of amino acid substitutions in the three dimensional structures of nsp12 (polymerase) and S suggest significant structural or functional effects. Thus, patients who develop mild symptoms may be a richer source of genetic variants of SARS-CoV-2 than patients with moderate or severe COVID-19.\n\nIMPORTANCEThe study shows that mutant spectra of SARS-CoV-2 from diagnostic samples differ in point mutation abundance and complexity, and that significantly larger values were observed in virus from patients who developed mild COVID-19 symptoms. Mutant spectrum complexity is not a uniform trait among isolates. The nature and location of low frequency amino acid substitutions present in mutant spectra anticipate great potential for phenotypic diversification of SARS-CoV-2.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Brenda Mart\u00ednez-Gonz\u00e1lez", + "author_inst": "Centro de Biolog\u00eda Molecular Severo Ochoa" + }, + { + "author_name": "Mar\u00eda Eugenia Soria", + "author_inst": "Centro de Biologia Molecular Severo Ochoa" + }, + { + "author_name": "Lucia Vazquez-Sirvent", + "author_inst": "Hospital Universitario Fundaci\u00f3n Jim\u00e9nez D\u00edaz" + }, + { + "author_name": "Cristina Ferrer-Orta", + "author_inst": "Institut de Biologia Molecular de Barcelona (CSIC)" + }, + { + "author_name": "Rebeca Lobo-Vega", + "author_inst": "Hospital Universitario Fundaci\u00f3n Jim\u00e9nez D\u00edaz" + }, + { + "author_name": "Pablo M\u00ednguez", + "author_inst": "Genetics Department, Bioinformatics Unit, IIS-Fundaci\u00f3n Jim\u00e9nez D\u00edaz" + }, + { + "author_name": "Lorena De la Fuente", + "author_inst": "Genetics Department, Bioinformatics Unit, IIS-Fundaci\u00f3n Jim\u00e9nez D\u00edaz" + }, + { + "author_name": "Carlos Llorens", + "author_inst": "Biotechvana, Parc Cientific, Universitat de Valencia" + }, + { + "author_name": "Beatriz Soriano", + "author_inst": "Biotechvana, Parc Cientific, Universitat de Valencia" + }, + { + "author_name": "Ricardo Ramos-Ruiz", + "author_inst": "parque cient\u00edfico de madrid" + }, + { + "author_name": "Marta Cort\u00f3n", + "author_inst": "Genetics Department, Bioinformatics Unit, IIS-Fundaci\u00f3n Jim\u00e9nez D\u00edaz" + }, + { + "author_name": "Rosario L\u00f3pez-Rodr\u00edguez", + "author_inst": "Genetics Department, Bioinformatics Unit, IIS-Fundaci\u00f3n Jim\u00e9nez D\u00edaz" + }, + { + "author_name": "Carlos Garc\u00eda-Crespo", + "author_inst": "Centro de Biologia Molecular Severo Ochoa" + }, + { + "author_name": "Isabel Gallego", + "author_inst": "Centro de Biolog\u00eda Molecular" + }, + { + "author_name": "Ana Isabel de \u00c1vila", + "author_inst": "CBMSO (CSIC-UAM)" + }, + { + "author_name": "Jordi Gomez", + "author_inst": "CSIC.Inst Parasitologia y Biomed Lopez Neyra. Ciberehd" + }, + { + "author_name": "Luis Enjuanes", + "author_inst": "Centro Nacional de Biotecnologia, CNB-CSIC" + }, + { + "author_name": "Llanos Salar-Vidal", + "author_inst": "IIS-Fundaci\u00f3n Jim\u00e9nez D\u00edaz" + }, + { + "author_name": "Jaime Esteban", + "author_inst": "IIS-Fundaci\u00f3n Jim\u00e9nez D\u00edaz" + }, + { + "author_name": "Ricardo Fern\u00e1ndez Roblas", + "author_inst": "IIS-Fundaci\u00f3n Jim\u00e9nez D\u00edaz" + }, + { + "author_name": "Ignacio Gadea Giron\u00e9s", + "author_inst": "IIS-Fundaci\u00f3n Jim\u00e9nez D\u00edaz" + }, + { + "author_name": "Carmen Ayuso", + "author_inst": "Genetics Department, Bioinformatics Unit, IIS-Fundaci\u00f3n Jim\u00e9nez D\u00edaz" + }, + { + "author_name": "Javier Ru\u00edz-Hornillos", + "author_inst": "Allergy Unit, Hospital Infanta Elena, Valdemoro" + }, + { + "author_name": "Nuria Verdaguer", + "author_inst": "Institut de Biologia Molecular de Barcelona (CSIC)" + }, + { + "author_name": "Esteban Domingo", + "author_inst": "Severo Ochoa" + }, + { + "author_name": "Celia Perales", + "author_inst": "Hospital Universitario Fundaci\u00f3n Jim\u00e9nez D\u00edaz" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.01.11.22269101", "rel_title": "Racial/ethnic disparities in exposure to COVID-19, susceptibility to COVID-19 and access to health care - findings from a U.S. national cohort", @@ -420210,29 +422216,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.11.22269046", - "rel_title": "Two viruses competition in the SIR model of epidemic spread: application to COVID-19", - "rel_date": "2022-01-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.11.22269046", - "rel_abs": "The SIR model of the epidemic spread is used for consideration the problem of the competition of two viruses having different contagiousness. It is shown how the more contagious strain replaces over time the less contagious one. In particular the results can be applied to the current situation when the omicron strain appeared in population affected by the delta strain.\n\nPACS number(s)02.50.-r, 05.60.-k, 82.39.-k, 87.19.Xx", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Sergey A Trigger", - "author_inst": "Joint Institute for High Temperatures Russian Academy of Sciences" - }, - { - "author_name": "Alexander M. Ignatov", - "author_inst": "General Physics Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.01.11.22269045", "rel_title": "Clinical outcomes among patients infected with Omicron (B.1.1.529) SARS-CoV-2 variant in southern California", @@ -421088,6 +423071,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.11.22269049", + "rel_title": "Systematic review and meta-analysis of COVID-19 vaccines safety, tolerability, and efficacy among HIV-infected patients", + "rel_date": "2022-01-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.11.22269049", + "rel_abs": "ObjectiveTo conduct a comprehensive systematic review and meta-analysis of all recommended SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) vaccines in people living with HIV (PLWH), as well as an overview of the safety, tolerability, and efficacy of the vaccines in PLWH.\n\nMethodsWe searched six databases, Cochrane Central Register of Controlled Trials (CENTRAL), PubMed, Medline, Medrxiv, Global research on COVID-19 database, and Google Scholar for studies investigating the effects of SARS-CoV-2 vaccines on PLWH. Results of the association were summarised by SARS-CoV IgG seroconversion and level, vaccines efficacy and tolerability. A meta-analysis was performed for studies, using random-effects model and a pooled RR with 95% CI was reported.\n\nResultsTwenty-three of the 1052 studies screened met the inclusion criteria. The review included 28, 246 participants among whom 79.55% (22,469/28, 246) were PLWH with median CD4 [≥] 200 cells/{micro}L. The pooled estimate of SARS-CoV-2 IgG seroconversion and positive neutralizing antibodies after the second vaccination dose between PLWH vs HIV negative were RR 0.95 (95%CI: 0.92 - 0.99, P = 0.006) and 0.88 (95%CI: 0.82- 0.95, P = 0.0007), respectively. The mean difference of IgG antibodies level (BAU/ml) was found higher in mRNA vaccines MD -1444.97 (95%CI: -1871.39, -1018.55). PLWH with CD4 less than 500 cells/ {micro}l had 15% risk reduction of neutralizing antibodies response compared to those with CD4 [≥] 500 cells/{micro}l (P = 0.003). The SARS-CoV-2 vaccine effectiveness was 65% (95%CI: 56%-72%, P <0.001) among vaccinated compared to unvaccinated PLWH. PLWH with CD4 count <350 cells/{micro}l had lower vaccine effectiveness compared to CD4 count [≥] 350 cells/{micro}l with 59% vs 72%, respectively. Vaccine tolerability was the same between PLWH and HIV negatives.\n\nConclusionAccording to our findings, PLWH with CD4 [≥] 200 cells/{micro}L had lower immunogenicity and antigenicity in COVID-19 vaccines than HIV negatives. Additional doses of SARS-CoV- 2 vaccination are needful in PLWH.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Jacques JL Tamuzi", + "author_inst": "Stellenbosch University" + }, + { + "author_name": "Ley M Muyaya", + "author_inst": "Stellenobosch University" + }, + { + "author_name": "Amal Mitra", + "author_inst": "Jackson State University" + }, + { + "author_name": "Peter Nyasulu", + "author_inst": "Stellenbosch University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "hiv aids" + }, { "rel_doi": "10.1101/2022.01.11.22268736", "rel_title": "COVID-19 vaccination breakthrough infections in a real-world setting: Using community reporters to evaluate vaccine effectiveness", @@ -422060,73 +424074,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.07.22268874", - "rel_title": "Clinical Performance of the cobas Liat SARS-CoV-2 & Influenza AB for the Detection of SARS-CoV-2 in Nasal Samples", - "rel_date": "2022-01-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.07.22268874", - "rel_abs": "Background and ObjectivePoint-of-care type molecular diagnostic tests have been used for detecting SARS-CoV-2, although their clinical utility with nasal samples has yet to be established. This study evaluated the clinical performance of the cobas Liat SARS-CoV-2 & Influenza AB (Liat) in nasal samples.\n\nMethodsNasal and nasopharyngeal samples were collected and were tested using the Liat, the cobas 6800 system and the cobas SARS-CoV-2 & Influenza AB (cobas), and a method developed by National Institute of Infectious Diseases, Japan (NIID).\n\nResultsA total of 814 nasal samples were collected. The Liat assay was positive for SARS-CoV-2 in 113 (13.9%). The total, positive, and negative concordance rate between the Liat and cobas/NIID assays were 99.3%/98.4%, 99.1%/100%, and 99.3%/98.2%, respectively. Five samples were positive only using the Liat assay. Their Ct values ranged from 31.9 to 37.2. The Ct values of the Liat assay were significantly lower (p < 0.001) but were correlated (p < 0.001) with those of other molecular assays. In the participants who tested positive for SARS-CoV-2 on the Liat assay using nasopharyngeal samples, 88.2% of their nasal samples also tested positive using the Liat assay.\n\nConclusionThe Liat assay showed high concordance with other molecular assays in nasal samples. Some discordance occurred in samples with Ct values > 30 on the Liat assay.\n\nKey PointsO_LIThe cobas Liat SARS-CoV-2 & Influenza AB assay showed high concordance with other molecular assays in nasal and nasopharyngeal samples, providing results within 20 minutes.\nC_LIO_LISome discordance occurred in samples with Ct values > 30 on the Liat assay.\nC_LIO_LIThe Liat assay may be suitable for use in a variety of clinical situations, primarily where accurate detection of SARS-CoV-2 is necessary.\nC_LI", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Yusaku Akashi", - "author_inst": "Department of Infectious Diseases, Faculty of Medicine, University of Tsukuba" - }, - { - "author_name": "Michiko Horie", - "author_inst": "Roche Diagnostics K.K., Medical, Quality & Regulatory" - }, - { - "author_name": "Junichi Kiyotaki", - "author_inst": "Miroku Medical Laboratory Inc" - }, - { - "author_name": "Yuto Takeuchi", - "author_inst": "Department of Infectious Diseases, University of Tsukuba Hospital" - }, - { - "author_name": "Kenichi Togashi", - "author_inst": "Roche Diagnostics K.K., Medical, Quality & Regulatory" - }, - { - "author_name": "Yuki Adachi", - "author_inst": "Roche Diagnostics K.K., Technical Support, Customer Solution" - }, - { - "author_name": "Atsuo Ueda", - "author_inst": "Department of Clinical Laboratory, Tsukuba Medical Center Hospital" - }, - { - "author_name": "Shigeyuki Notake", - "author_inst": "Department of Clinical Laboratory, Tsukuba Medical Center Hospital" - }, - { - "author_name": "Koji Nakamura", - "author_inst": "Department of Clinical Laboratory, Tsukuba Medical Center Hospital" - }, - { - "author_name": "Norihiko Terada", - "author_inst": "Department of Infectious Diseases, University of Tsukuba Hospital" - }, - { - "author_name": "Yoko Kurihara", - "author_inst": "Department of Infectious Diseases, University of Tsukuba Hospital" - }, - { - "author_name": "Yoshihiko Kiyasu", - "author_inst": "Department of Infectious Diseases, University of Tsukuba Hospital" - }, - { - "author_name": "Hiromichi Suzuki", - "author_inst": "Department of Infectious Diseases, Faculty of Medicine, University of Tsukuba" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.08.22268944", "rel_title": "The Dynamics of SARS-CoV-2 Infectivity with Changes in Aerosol Microenvironment", @@ -422950,6 +424897,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2022.01.09.22268975", + "rel_title": "A Novel Scoring System for Early Assessment of the Risk of the COVID-19-associated Mortality in Hospitalized Patients: COVID-19 BURDEN", + "rel_date": "2022-01-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.09.22268975", + "rel_abs": "BackgroundCorona Virus Disease 2019 (COVID-19) presentation resembles common flu or can be more severe; it can result in hospitalization with significant morbidity and/or mortality. We made an attempt to develop a predictive model and a scoring system to improve the diagnostic efficiency for COVID-19 mortality via analysis of clinical features and laboratory data on admission.\n\nMethodsWe retrospectively enrolled 480 consecutive adult patients, aged 21-95, who were admitted to Faghihi Teaching Hospital. Clinical and laboratory features were extracted from the medical records and analyzed using multiple logistic regression analysis.\n\nResultsA novel mortality risk score (COVID-19 BURDEN) was calculated, incorporating risk factors from this cohort. CRP (> 73.1 mg/L), O2 saturation variation (greater than 90%, 84-90%, and less than 84%), increased PT (>16.2s), diastolic blood pressure ([≤]75 mmHg), BUN (>23 mg/dL), and raised LDH (>731 U/L) are the features comprising the scoring system. The patients are triaged to the groups of low- (score <4) and high-risk (score [≥] 4) groups. The area under the curve, sensitivity, and specificity for predicting non-response to medical therapy with scores of [≥] 4 were 0.831, 78.12%, and 70.95%, respectively.\n\nConclusionUsing this scoring system in COVID-19 patients, the severity of the disease will be determined in the early stages of the disease, which will help to reduce hospital care costs and improve its quality and outcome.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Fatemeh Amirzadehfard", + "author_inst": "Shiraz University of Medical Sciences" + }, + { + "author_name": "Mohammad Hossein Imanieh", + "author_inst": "Shiraz University of Medical Sciences" + }, + { + "author_name": "Sina Zoghi", + "author_inst": "Shiraz University of Medical Sciences" + }, + { + "author_name": "Faezeh sehatpour", + "author_inst": "Shiraz University of Medical Sciences" + }, + { + "author_name": "Peyman Jafari", + "author_inst": "Shiraz University of Medical Sciences" + }, + { + "author_name": "Hamidreza hassanipour", + "author_inst": "Shiraz University of Medical Sciences" + }, + { + "author_name": "Maryam Feili", + "author_inst": "Shiraz University of Medical Sciences" + }, + { + "author_name": "Maryam Mollaie", + "author_inst": "Shiraz University of Medical Sciences" + }, + { + "author_name": "Pardis Bostanian", + "author_inst": "Shiraz University of Medical Sciences" + }, + { + "author_name": "Samrad Mehrabi", + "author_inst": "Shiraz University of Medical Sciences" + }, + { + "author_name": "Reyhaneh Dashtianeh", + "author_inst": "Shiraz University of Medical Sciences" + }, + { + "author_name": "Afrooz Feili", + "author_inst": "Shiraz University of Medical Sciences" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.09.22268991", "rel_title": "COVID-19 impact on Socio-economic and Health Interventions: A Gaps and Peaks analysis using Clustering Approach", @@ -423885,165 +425895,6 @@ "type": "new results", "category": "zoology" }, - { - "rel_doi": "10.1101/2022.01.06.22268792", - "rel_title": "Consensus on COVID-19 vaccination in pediatric oncohematological patients, on behalf of infectious working group of Italian Association of Pediatric Hematology Oncology", - "rel_date": "2022-01-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.06.22268792", - "rel_abs": "Vaccines represent the best tool to prevent the severity course and fatal consequences of pandemic by new Coronavirus 2019 infection (SARS-CoV-2). Considering the limited data on vaccination of pediatric oncohematological patients, we develop a Consensus document to support the Italian pediatric hematological oncological (AIEOP) centers in a scientifically correct communication with families and patients and to promote vaccination. The topics of the Consensus were: SARS-CoV-2 infection and disease (COVID-19) in the pediatric subjects; COVID-19 vaccines (type, schedule); which and when to vaccinate; contraindications and risk of serious adverse events; rare adverse events; third dose and vaccination after COVID-19; and other general prevention measures. Using the Delphi methodology for Consensus, 21 statements and their corresponding rationale were elaborated and discussed with the representatives of 31 centers, followed by voting. AIEOP Centers showed an overall agreement on all the statements that were therefore approved.\n\nThis consensus document highlights that children and adolescents affected by hematological and oncological diseases are a fragile category. Vaccination plays an important role to prevent COVID-19, to permit the regular administration of chemotherapy or other treatments, to perform control visits and hospital admissions, and to prevent treatment delays.", - "rel_num_authors": 36, - "rel_authors": [ - { - "author_name": "Simone Cesaro", - "author_inst": "Pediatric Hematology Oncology, Department of Mother and Child, Azienda Ospedaliera Universitaria Integrata Verona, Italy" - }, - { - "author_name": "Paola Muggeo", - "author_inst": "Pediatric Onco-Hematology, Department of Pediatrics, AOU Policlinico, Bari" - }, - { - "author_name": "Daniele Zama", - "author_inst": "Pediatric Oncology and Hematology Unit, Pediatric Unit, Azienda Ospedaliero-Universitaria di Bologna, Bologna" - }, - { - "author_name": "Monica Cellini", - "author_inst": "Pediatric Oncology-Hematology Unit, Modena University Hospital, Modena" - }, - { - "author_name": "Katia Perruccio", - "author_inst": "Pediatric Oncology-Hematology, Santa Maria della Misericordia Hospital, Perugia" - }, - { - "author_name": "Antonella Colombini", - "author_inst": "University of Milano-Bicocca, Department of Pediatrics, Fondazione MBBM/Ospedale San Gerardo, Monza" - }, - { - "author_name": "Francesca Carraro", - "author_inst": "Department of Public Health and Pediatrics, University of Torino, Turin, Italy, Division of Paediatric Onco-Haematology, Stem Cell Transplantation and Cellular " - }, - { - "author_name": "Mariagrazia Petris", - "author_inst": "Hematology Oncology Division, Department of Women's and Children's Health, University of Padova, Padova" - }, - { - "author_name": "Valeria Petroni", - "author_inst": "Division of Pediatric Hematology and Oncology, Ospedale G. Salesi, Ancona" - }, - { - "author_name": "Maurizio Mascarin", - "author_inst": "AYA Oncology and Pediatric Radiotherapy Unit, CRO - Centro di Riferimento Oncologico di Aviano, IRCCS, Aviano" - }, - { - "author_name": "Francesco Baccelli", - "author_inst": "Pediatric Oncology and Hematology Unit, Pediatric Unit, Azienda Ospedaliero-Universitaria di Bologna, Bologna" - }, - { - "author_name": "Elena Soncini", - "author_inst": "Pediatric Oncohematology and Bone Marrow Transplant Unit, Children's Hospital, Spedali Civili, Brescia" - }, - { - "author_name": "Rosamaria Mura", - "author_inst": "Pediatric Oncology Unit, AO Brotzu, Cagliari" - }, - { - "author_name": "Milena Laspina", - "author_inst": "Pediatric Hematology and Oncology Unit - AOU Policlinico \"Rodolico-San Marco\", University of Catania, Catania" - }, - { - "author_name": "Nunzia Decembrino", - "author_inst": "Pediatric Hematology and Oncology Unit - AOU Policlinico \"Rodolico-San Marco\", University of Catania, Catania" - }, - { - "author_name": "Roberta Burnelli", - "author_inst": "Pediatric Onco-Hematology Unit, Sant'Anna Hospital, Ferrara" - }, - { - "author_name": "Stefano Frenos", - "author_inst": "Division of Pediatric Oncology/Hematology, Meyer University Children's Hospital, Florence" - }, - { - "author_name": "Elio Castagnola", - "author_inst": "IRCCS Istituto Giannina Gaslini, Istituto di Ricovero e Cura a Carattere Scientifico, Genova" - }, - { - "author_name": "Maura Faraci", - "author_inst": "IRCCS Istituto Giannina Gaslini, Istituto di Ricovero e Cura a Carattere Scientifico, Genova" - }, - { - "author_name": "Cristina Meazza", - "author_inst": "Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan" - }, - { - "author_name": "Federica Barzaghi", - "author_inst": "Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan" - }, - { - "author_name": "Maria Rosaria D'Amico", - "author_inst": "Department of Pediatric Hemato-Oncology, AORN Santobono-Pausilipon, Naples" - }, - { - "author_name": "Maria Capasso", - "author_inst": "Department of Pediatric Hemato-Oncology, AORN Santobono-Pausilipon, Naples" - }, - { - "author_name": "Elisabetta Calore", - "author_inst": "Hematology Oncology Division, Department of Women's and Children's Health, University of Padova, Padova" - }, - { - "author_name": "Ottavio Ziino", - "author_inst": "Department of Pediatric Hemato-Oncology, ARNAS Ospedali Civico, G. Di Cristina, Palermo" - }, - { - "author_name": "Angelica Barone", - "author_inst": "Pediatric Onco-Hematology Unit, Pediatric Clinic, Pietro Barilla Children's Hospital, University of Parma, Parma" - }, - { - "author_name": "Francesca Compagno", - "author_inst": "Pediatric Hematology/Oncology, Fondazione IRCCS Policlinico San Matteo, Pavia" - }, - { - "author_name": "Laura Luti", - "author_inst": "Pediatric Onco-haematology Unit, Pisa University Hospital, Pisa" - }, - { - "author_name": "Federica Galaverna", - "author_inst": "Department of Pediatric Hematology and Oncology, Bambino Gesu Children's Hospital, Rome" - }, - { - "author_name": "Raffaella De Santis", - "author_inst": "Department of Pediatrics, Hemato-Oncology Unit, 'Casa Sollievo della Sofferenza' Hospital, San Giovanni Rotondo" - }, - { - "author_name": "Letizia Brescia", - "author_inst": "Hemato-Oncology Unit, SS. Annunziata Hospital, Taranto" - }, - { - "author_name": "Linda Meneghello", - "author_inst": "U.O.M. Pediatria Ospedale S. Chiara, Trento" - }, - { - "author_name": "Angelamaria Petrone", - "author_inst": "U.O.M. Pediatria Ospedale S. Chiara, Trento" - }, - { - "author_name": "Nagua Giurici", - "author_inst": "Pediatric Hematology-Oncology, Institute for Maternal and Child Health IRCCS \"Burlo Garofolo,\", Trieste" - }, - { - "author_name": "Fabian Schumacher", - "author_inst": "Pediatric Oncohematology and Bone Marrow Transplant Unit, Children's Hospital, Spedali Civili, Brescia" - }, - { - "author_name": "Federico Mercolini", - "author_inst": "Hematology Oncology Unit, Department of Pediatrics, Hospital of Bolzano" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "oncology" - }, { "rel_doi": "10.1101/2022.01.07.22268806", "rel_title": "Innate and adaptive immune defects associated with lower SARS-CoV-2 BNT162b2 mRNA vaccine response in elderly people", @@ -424955,6 +426806,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.01.06.22268855", + "rel_title": "Persistence of endogenous SARS-CoV-2 and pepper mild mottle virus RNA in wastewater settled solids", + "rel_date": "2022-01-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.06.22268855", + "rel_abs": "Limited information is available on the decay rate of endogenous SARS-CoV-2 and pepper mild mottle virus (PMMoV) RNA in wastewater and primary settled solids, potentially limiting an understanding of how transit or holding times within wastewater infrastructure might impact RNA measurements and their relationship to community COVID-19 infections. In this study, primary settled solids samples were collected from two wastewater treatment plants in the San Francisco Bay Area. Samples were thoroughly mixed, aliquoted into subsamples, and stored at 4{degrees}C, 22{degrees}C, and 37 {degrees}C for 10 days. The concentration of SARS-CoV-2 (N1 and N2 targets) and PMMoV RNA was measured using an RT-ddPCR. Limited decay (< 1 log10 reduction) was observed in the detection of viral RNA targets at all temperature conditions, suggesting that SARS-CoV-2 and PMMoV RNA can be highly persistent in solids. First-order decay rate constants ranged from 0.011 - 0.098 day-1 for SARS-CoV-2 RNA and 0.010 - 0.091 day-1 for PMMoV RNA, depending on temperature conditions. Slower decay was observed for SARS-CoV-2 RNA in primary settled solids compared to previously reported decay in wastewater influent. Further research is needed to understand if solid content and wastewater characteristics might influence the persistence of viral RNA targets.\n\nSynopsisSARS-CoV-2 and PMMoV genomic RNA is highly stable in wastewater settled solids over 10 days at several environmentally relevant temperatures.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=72 SRC=\"FIGDIR/small/22268855v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (15K):\norg.highwire.dtl.DTLVardef@1a508forg.highwire.dtl.DTLVardef@19efc23org.highwire.dtl.DTLVardef@bb7748org.highwire.dtl.DTLVardef@194371e_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Laura Roldan-Hernandez", + "author_inst": "Stanford University" + }, + { + "author_name": "Katherine Graham", + "author_inst": "Stanford University" + }, + { + "author_name": "Dorothea Duong", + "author_inst": "Verily Life Sciences" + }, + { + "author_name": "Alexandria Boehm", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.06.475303", "rel_title": "Engineering SARS-CoV-2 neutralizing antibodies for increased potency and reduced viral escape", @@ -425931,29 +427813,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.01.05.22268787", - "rel_title": "The impact of demographic factors on numbers of COVID-19 cases and deaths in Europe and the regions of Ukraine", - "rel_date": "2022-01-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.05.22268787", - "rel_abs": "The accumulated numbers of COVID-19 cases and deaths per capita are important characteristics of the pandemic dynamics that may also indicate the effectiveness of quarantine, testing, vaccination, and treatment. The statistical analysis based on the number of cases per capita accumulated to the end of June 2021 showed no correlations with the volume of population, its density, and the urbanization level both in European countries and regions of Ukraine. The same result was obtained with the use of fresher datasets (as of December 23, 2021). The number of deaths per capita and per case may depend on the urbanization level. For European countries these relative characteristics decrease with the increase of the urbanization level. Opposite trend was revealed for the number of deaths per capita in Ukrainian regions.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Igor Nesteruk", - "author_inst": "Institute of Hydromechanics National Academy of sciences of Ukraine" - }, - { - "author_name": "Oleksii Rodionov", - "author_inst": "Private consulting office, Kyiv, Ukraine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.01.05.22268800", "rel_title": "Association between vaccination status and reported incidence of post-acute COVID-19 symptoms in Israel: a cross-sectional study of patients infected between March 2020 and November 2021", @@ -426740,6 +428599,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.04.22268770", + "rel_title": "Discordant SARS-CoV-2 PCR and Rapid Antigen Test Results When Infectious: A December 2021 Occupational Case Series", + "rel_date": "2022-01-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.04.22268770", + "rel_abs": "The performance of Covid-19 diagnostic tests must continue to be reassessed with new variants of concern. The objective of this study was to describe the discordance in saliva SARS-CoV-2 PCR and nasal rapid antigen test results during the early infectious period. We identified a high-risk occupational case cohort of 30 individuals with daily testing during an Omicron outbreak in December 2021. Based on viral load and transmissions confirmed through epidemiological investigation, most Omicron cases were infectious for several days before being detectable by rapid antigen tests.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Blythe J Adamson", + "author_inst": "Infectious Economics" + }, + { + "author_name": "Robby Sikka", + "author_inst": "COVID-19 Sports and Society Working Group" + }, + { + "author_name": "Anne L Wyllie", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Prem K Premsrirut", + "author_inst": "Mirimus Inc" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.01.21268271", "rel_title": "Safety and immunogenicity of anti-SARS CoV-2 conjugate vaccine SOBERANA 02 in a two-dose or three-dose heterologous scheme in adults: Phase IIb Clinical Trial", @@ -427672,61 +429562,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2022.01.05.474231", - "rel_title": "Genomic perspectives on the emerging SARS-CoV-2 Omicron variant", - "rel_date": "2022-01-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.05.474231", - "rel_abs": "A new variant of concern for SARS-CoV-2, Omicron (B.1.1.529), was designated by the World Health Organization on November 26, 2021. This study analyzed the viral genome sequencing data of 108 samples collected from patients infected with Omicron. First, we found that the enrichment efficiency of viral nucleic acids was reduced due to mutations in the region where the primers anneal to. Second, the Omicron variant possesses an excessive number of mutations compared to other variants circulating at the same time (62 vs. 45), especially in the Spike gene. Mutations in the Spike gene confer alterations in 32 amino acid residues, which was more than those observed in other SARS-CoV-2 variants. Moreover, a large number of nonsynonymous mutations occur in the codons for the amino acid residues located on the surface of the Spike protein, which could potentially affect the replication, infectivity, and antigenicity of SARS-CoV-2. Third, there are 53 mutations between the Omicron variant and its closest sequences available in public databases. Many of those mutations were rarely observed in the public database and had a low mutation rate. In addition, the linkage disequilibrium between these mutations were low, with a limited number of mutations (6) concurrently observed in the same genome, suggesting that the Omicron variant would be in a different evolutionary branch from the currently prevalent variants. To improve our ability to detect and track the source of new variants rapidly, it is imperative to further strengthen genomic surveillance and data sharing globally in a timely manner.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Wentai Ma", - "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences" - }, - { - "author_name": "Jing Yang", - "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences" - }, - { - "author_name": "Haoyi Fu", - "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences" - }, - { - "author_name": "Chao Su", - "author_inst": "Institute of Microbiology, Chinese Academy of Sciences" - }, - { - "author_name": "Caixia Yu", - "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences" - }, - { - "author_name": "Qihui Wang", - "author_inst": "Institute of Microbiology, Chinese Academy of Sciences" - }, - { - "author_name": "Ana Tereza Ribeiro de Vasconcelos", - "author_inst": "Laboratorio de Bioinformatica, Laboratorio Nacional de Computacao Cientifica" - }, - { - "author_name": "Georgii Bazykin", - "author_inst": "Skolkovo Institute of Science and Technology" - }, - { - "author_name": "Yiming Bao", - "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences" - }, - { - "author_name": "Mingkun Li", - "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2022.01.04.475011", "rel_title": "Computational study of the furin cleavage domain of SARS-CoV-2: delta binds strongest of extant variants", @@ -428450,6 +430285,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.01.04.22268766", + "rel_title": "Effects of Varying Approaches to Lifting COVID-19 Pandemic Restrictions in the United States", + "rel_date": "2022-01-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.04.22268766", + "rel_abs": "BackgroundPolicy approaches to lifting COVID-19 restrictions have varied significantly across the United States. An evaluation of the effects of state reopening policies on population health outcomes can inform ongoing and future pandemic responses. This study evaluates the approaches to lifting social distancing restrictions based on adherence to the Centers for Disease Control and Prevention (CDC) guidance established during the first wave of the COVID-19 pandemic.\n\nMethodsWe performed a retrospective study using difference-in-differences analyses to examine the effects of reopening policies on COVID-19 outcomes with risk-adjustment for population density, temporal changes, and concurrent mask policy implementation. We examined the effects of reopening policies on per capita case rates and rates of severe COVID-19 outcomes, including hospitalizations and deaths.\n\nResultsAdherence to the CDCs reopening gating metrics and phased social distancing guidelines resulted in fewer COVID-19 cases, hospitalizations, and deaths. Phase one adherent states exhibited a 50-fold reduction in daily new cases and a 3-fold reduction in daily new deaths after reopening. Phase two adherent states experienced improvements in COVID-19 outcomes after reopening, while non-adherent states had a resurgence of worsening outcomes after lifting restrictions.\n\nConclusionsOur study findings indicate that adherence to the CDCs reopening guidance after implementing social distancing restrictions during the COVID-19 pandemic substantially prevents new cases, hospitalizations, and deaths. Following a stepwise reopening strategy and ensuring a sustained decline in case rates and test positivity rates before lifting restrictions can mitigate on a large scale the negative effects of a pandemic on population health outcomes.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Jessica E Galarraga", + "author_inst": "MedStar Health Research Institute, Georgetown University School of Medicine" + }, + { + "author_name": "Daniel Popovsky", + "author_inst": "Georgetown University School of Medicine" + }, + { + "author_name": "Kevin Delijani", + "author_inst": "Georgetown University School of Medicine" + }, + { + "author_name": "Hannah Hanson", + "author_inst": "Georgetown University" + }, + { + "author_name": "Mark Hanlon", + "author_inst": "Georgetown University School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2022.01.04.22268771", "rel_title": "Detection of fecal coliforms and SARS-CoV-2 RNA in sewage and recreational waters in the Ecuadorian Coast: a call for improving water quality regulation", @@ -429446,173 +431316,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.29.21268499", - "rel_title": "Safety and immunogenicity of a heterologous boost with a recombinant vaccine, NVSI-06-07, in the inactivated vaccine recipients from UAE: a phase 2 randomised, double-blinded, controlled clinical trial", - "rel_date": "2022-01-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.29.21268499", - "rel_abs": "BackgroundThe increased coronavirus disease 2019 (COVID-19) breakthrough cases pose the need of booster vaccinations. In this study, we reported the safety and immunogenicity of a heterologous boost with a recombinant COVID-19 vaccine (CHO cells), named NVSI-06-07, as a third dose in participants who have previously received two doses of the inactivated vaccine (BBIBP-CorV) at pre-specified time intervals. Using homologous boost with BBIBP-CorV as control, the safety and immunogenicity of the heterologous boost with NVSI-06-07 against various SARS-CoV-2 strains, including Omicron, were characterized.\n\nMethodsThis study is a single-center, randomised, double-blinded, controlled phase 2 trial for heterologous boost of NVSI-06-07 in BBIBP-CorV recipients from the United Arab Emirates (UAE). Healthy adults (aged [≥]18 years) were enrolled and grouped by the specified prior vaccination interval of BBIBP-CorV, i.e., 1-3 months, 4-6 months or [≥]6 months, respectively, with 600 individuals per group. For each group, participants were randomly assigned at 1:1 ratio to receive either a heterologous boost of NVSI-06-07 or a homologous booster dose of BBIBP-CorV. The primary outcome was to comparatively assess the immunogenicity between heterologous and homologous boosts at 14 and 28 days post-boosting immunization, by evaluation of the geometric mean titers (GMTs) of IgG and neutralizing antibodies as well as the corresponding seroconversion rate ([≥]4-fold rise in antibody titers). The secondary outcomes were the safety profile of the boosting strategies within 30 days post vaccination. The exploratory outcome was the immune efficacy against Omicron and other variants of concern (VOCs) of SARS-CoV-2. This trial is registered with ClinicalTrials.gov, NCT05033847.\n\nFindingsA total of 1800 individuals who have received two doses of BBIBP-CorV were enrolled, of which 899 participants received a heterologous boost of NVSI-06-07 and 901 received a homologous boost for comparison. No vaccine-related serious adverse event (SAE) and no adverse events of special interest (AESI) were reported. 184 (20{middle dot}47%) participants in the heterologous boost groups and 177 (19{middle dot}64%) in the homologous boost groups reported at least one adverse reaction within 30 days. Most of the local and systemic adverse reactions reported were grades 1 (mild) or 2 (moderate), and there was no significant difference in the overall safety between heterologous and homologous boosts. Immunogenicity assays showed that the seroconversion rates in neutralizing antibodies against prototype SARS-CoV-2 elicited by heterologous boost were 89{middle dot}96% - 97{middle dot}52% on day 28 post-boosting vaccination, which was much higher than what was induced by homologous boost (36{middle dot}80% - 81{middle dot}75%). Similarly, in heterologous NVSI-06-07 booster groups, the neutralizing geometric mean titers (GMTs) against the prototype strain increased by 21{middle dot}01 - 63{middle dot}85 folds from baseline to 28 days post-boosting vaccination, whereas only 4{middle dot}20 - 16{middle dot}78 folds of increases were observed in homologous BBIBP-CorV booster group. For Omicron variant, the neutralizing antibody GMT elicited by the homologous boost of BBIBP-CorV was 37{middle dot}91 (95%CI, 30{middle dot}35-47{middle dot}35), however, a significantly higher level of neutralizing antibodies with GMT 292{middle dot}53 (95%CI, 222{middle dot}81-384{middle dot}07) was induced by the heterologous boost of NVSI-06-07, suggesting that it may serve as an effective boosting strategy combating the pandemic of Omicron. The similar results were obtained for other VOCs, including Alpha, Beta and Delta, in which the neutralizing response elicited by the heterologous boost was also significantly greater than that of the homologous boost. In the participants primed with BBIBP-CorV over 6 months, the largest increase in the neutralizing GMTs was obtained both in the heterologous and homologous boost groups, and thus the booster vaccination with over 6 months intervals was optimal.\n\nInterpretationOur findings indicated that the heterologous boost with NVSI-06-07 was safe, well-tolerated and immunogenic in adults primed with a full regimen of BBIBP-CorV. Compared to homologous boost with a third dose of BBIBP-CorV, incremental increases in immune responses were achieved by the heterologous boost with NVSI-06-07 against SARS-CoV-2 prototype strain, Omicron variant, and other VOCs. The heterologous BBIBP-CorV/NVSI-06-07 prime-boosting vaccination may be valuable in preventing the pandemic of Omicron. The optimal booster strategy was the heterologous boost with NVSI-06-07 over 6 months after a priming with two doses of BBIBP-CorV.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed for clinical trials or prospective/cohort studies involving heterologous booster vaccination in non-immunocompromised population published up to Dec 25, 2021, using the term \"(COVID) AND (vaccin*) AND (clinical trial OR cohort OR prospective) AND (heterologous) AND (booster OR prime-boost OR third dose)\" with no language restrictions. Nine studies of heterologous prime-boost vaccinations with adenovirus-vector vaccines (ChAdOx1 nCov-19, Oxford-AstraZeneca, Ad26.COV2.S, Janssen) and mRNA vaccines (BNT162b2, Pfizer-BioNtech; mRNA1273, Moderna) were identified. The adenovirus-vector and mRNA heterologous prime-boost vaccination was found to be well tolerated and immunogenic. In individuals primed with adenovirus-vector vaccine, mRNA booster vaccination led to greater immune response than homologous boost. However, varied results were obtained on whether heterologous boost was immunogenically superior to the homologous mRNA prime-boost vaccination. Besides that, A preprint trial in population previously immunized with inactivated vaccines (CoronaVac, Sinovac Biotech) showed that the heterologous boost with adenovirus-vector vaccine (Convidecia, CanSino Biologicals) was safe and induced higher level of live-virus neutralizing antibodies than by the homogeneous boost. A pilot study reported that boosting with BNT162b2 in individuals primed with two doses of inactivated vaccines (BBIBP-CorV) was significantly more immunogenic than homologous vaccination with two-dose of BNT162b2. In addition, a preprint paper demonstrated that heterologous boost of ZF2001, a recombinant protein subunit vaccine, after CoronaVac or BBIBP-CorV vaccination potently improved the immunogenicity. But only a small size of samples was tested in this study and the live-virus neutralization was not detected. Till now, it is still lacking a formal clinical trial to evaluate the immunogenicity and safety of the heterologous prime-boost vaccination with an inactivated vaccine followed by a recombinant protein subunit-based vaccine.\n\nAdded value of this studyTo our knowledge, this is the first reported result of a large-scale randomised, controlled clinical trial of heterologous prime-boost vaccination with an inactivated vaccine followed by a recombinant protein subunit vaccine. This trial demonstrated that the heterologous prime-booster vaccination with BBIBP-CorV/NVSI-06-07 is safe and immunogenic. Its immunoreactivity is similar to that of homologous vaccination with BBIBP-CorV. Compared to homologous boost, heterologous boost with NVSI-06-07 in BBIBP-CorV recipients elicited significantly higher immunogenicity not only against the SARS-CoV-2 prototype strain but also against Omicron and other variants of concern (VOCs).\n\nImplications of all the available evidenceBooster vaccination is considered an effective strategy to improve the protection efficacy of COVID-19 vaccines and control the epidemic waves of SARS-CoV-2. Data from our trial suggested that the booster vaccination of NVSI-06-07 in BBIBP-CorV recipients significantly improved the immune responses against various SARS-CoV-2 strains, including Omicron. Due to no Omicron-specific vaccine available currently, the BBIBP-CorV/NVSI-06-07 heterologous prime-boost might serve as an effective strategy combating Omicron variant. Besides that, BBIBP-CorV has been widely inoculated in population, and thus further boosting vaccination with NVSI-06-07 is valuable in preventing the COVID-19 pandemic. But further studies are needed to assess the long-term protection of BBIBP-CorV/NVSI-06-07 prime-booster vaccination.", - "rel_num_authors": 38, - "rel_authors": [ - { - "author_name": "Nawal AlKaabi", - "author_inst": "Sheikh Khalifa Medical City, SEHA, Abu Dhabi, United Arab Emirates; College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates" - }, - { - "author_name": "Yun Kai Yang", - "author_inst": "China National Biotec Group Company Limited, Beijing, China" - }, - { - "author_name": "Jing Zhang", - "author_inst": "The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China; National Engineering Center for New Vaccine Research, Beijing, China" - }, - { - "author_name": "Ke Xu", - "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China" - }, - { - "author_name": "Yu Liang", - "author_inst": "The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China; National Engineering Center for New Vaccine Research, Beijing, China" - }, - { - "author_name": "Yun Kang", - "author_inst": "National Vaccine and Serum Institute (NVSI), Beijing, China; National Engineering Center for New Vaccine Research, Beijing, China" - }, - { - "author_name": "Ji Guo Su", - "author_inst": "The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China; National Engineering Center for New Vaccine Research, Beijing, China" - }, - { - "author_name": "Tian Yang", - "author_inst": "China National Biotec Group Company Limited, Beijing, China" - }, - { - "author_name": "Salah Hussein", - "author_inst": "Sheikh Khalifa Medical City, SEHA, Abu Dhabi, United Arab Emirates" - }, - { - "author_name": "Mohamed Saif ElDein", - "author_inst": "Sheikh Khalifa Medical City, SEHA, Abu Dhabi, United Arab Emirates" - }, - { - "author_name": "Shuai Shao", - "author_inst": "The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China; National Engineering Center for New Vaccine Research, Beijing, China" - }, - { - "author_name": "Sen Sen Yang", - "author_inst": "National Vaccine and Serum Institute (NVSI), Beijing, China; National Engineering Center for New Vaccine Research, Beijing, China" - }, - { - "author_name": "Wenwen Lei", - "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China" - }, - { - "author_name": "Xue Jun Gao", - "author_inst": "Lanzhou Institute of Biological Products Company Limited, Lanzhou, China" - }, - { - "author_name": "Zhiwei Jiang", - "author_inst": "Beijing KeyTech Statistical Consulting Co.,Ltd, Beijing, China" - }, - { - "author_name": "Hui Wang", - "author_inst": "Beijing Institute of Biological Products Company Limited, Beijing, China" - }, - { - "author_name": "Meng Li", - "author_inst": "China National Biotec Group Company Limited, Beijing, China" - }, - { - "author_name": "Hanadi Mekki Mekki", - "author_inst": "Union 71, United Arab Emirates" - }, - { - "author_name": "Walid Zaher", - "author_inst": "G42 Healthcare, IROS (Insights Research Organization & Solutions), United Arab Emirates" - }, - { - "author_name": "Sally Mahmoud", - "author_inst": "G42 Healthcare, IROS (Insights Research Organization & Solutions), United Arab Emirates" - }, - { - "author_name": "Xue Zhang", - "author_inst": "China National Biotec Group Company Limited, Beijing, China" - }, - { - "author_name": "Chang Qu", - "author_inst": "China National Biotec Group Company Limited, Beijing, China" - }, - { - "author_name": "Dan Ying Liu", - "author_inst": "China National Biotec Group Company Limited, Beijing, China" - }, - { - "author_name": "Jing Zhang", - "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China" - }, - { - "author_name": "Mengjie Yang", - "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China" - }, - { - "author_name": "Islam ElTantawy", - "author_inst": "G42 Healthcare, IROS (Insights Research Organization & Solutions), United Arab Emirates" - }, - { - "author_name": "Peng Xiao", - "author_inst": "G42 Healthcare, IROS (Insights Research Organization & Solutions), United Arab Emirates" - }, - { - "author_name": "Zhao Nian Wang", - "author_inst": "China National Biotec Group Company Limited, Beijing, China" - }, - { - "author_name": "Jin Liang Yin", - "author_inst": "China National Biotec Group Company Limited, Beijing, China" - }, - { - "author_name": "Xiao Yan Mao", - "author_inst": "Lanzhou Institute of Biological Products Company Limited, Lanzhou, China" - }, - { - "author_name": "Jin Zhang", - "author_inst": "Beijing Institute of Biological Products Company Limited, Beijing, China" - }, - { - "author_name": "Ning Liu", - "author_inst": "The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China; National Engineering Center for New Vaccine Research, Beijing, China" - }, - { - "author_name": "Fu Jie Shen", - "author_inst": "The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China; National Engineering Center for New Vaccine Research, Beijing, China" - }, - { - "author_name": "Liang Qu", - "author_inst": "China National Biotec Group Company Limited, Beijing, China" - }, - { - "author_name": "Yun Tao Zhang", - "author_inst": "China National Biotec Group Company Limited, Beijing, China" - }, - { - "author_name": "Xiao Ming Yang", - "author_inst": "China National Biotec Group Company Limited, Beijing, China" - }, - { - "author_name": "Guizhen Wu", - "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China" - }, - { - "author_name": "Qi Ming Li", - "author_inst": "The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China; National Engineering Center for New Vaccine Research, Beijing, China" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.01.474713", "rel_title": "The SARS-CoV-2 infection in Thailand: analysis of spike variants complemented by protein structure insights", @@ -430404,6 +432107,101 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.12.31.474653", + "rel_title": "The SARS-CoV-2 variant, Omicron, shows rapid replication in human primary nasal epithelial cultures and efficiently uses the endosomal route of entry.", + "rel_date": "2022-01-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.31.474653", + "rel_abs": "The SARS-CoV-2 Omicron/BA.1 lineage emerged in late 2021 and rapidly displaced the Delta variant before being overtaken itself globally by, the Omicron/BA.2 lineage in early 2022. Here, we describe how Omicron BA.1 and BA.2 show a lower severity phenotype in a hamster model of pathogenicity which maps specifically to the spike gene. We further show that Omicron is attenuated in a lung cell line but replicates more rapidly, albeit to lower peak titres, in human primary nasal cells. This replication phenotype also maps to the spike gene. Omicron spike (including the emerging Omicron lineage BA.4) shows attenuated fusogenicity and a preference for cell entry via the endosomal route. We map the altered Omicron spike entry route and partially map the lower fusogenicity to the S2 domain, particularly the substitution N969K. Finally, we show that pseudovirus with Omicron spike, engineered in the S2 domain to confer a more Delta-like cell entry route retains the antigenic properties of Omicron. This shows a distinct separation between the genetic determinants of these two key Omicron phenotypes, raising the concerning possibility that future variants with large antigenic distance from currently circulating and vaccine strains will not necessarily display the lower intrinsic severity seen during Omicron infection.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Thomas P. Peacock", + "author_inst": "Imperial College London" + }, + { + "author_name": "Jonathan C Brown", + "author_inst": "Imperial College London" + }, + { + "author_name": "Jie Zhou", + "author_inst": "Imperial College London" + }, + { + "author_name": "Nazia Thakur", + "author_inst": "The Pirbright Institute" + }, + { + "author_name": "Ksenia Sukhova", + "author_inst": "Imperial College London" + }, + { + "author_name": "Joseph Newman", + "author_inst": "The Pirbright Institute" + }, + { + "author_name": "Ruthiran Kugathasan", + "author_inst": "Imperial College London" + }, + { + "author_name": "Ada W. C. Yan", + "author_inst": "Imperial College London" + }, + { + "author_name": "Wilhelm Furnon", + "author_inst": "MRC-University of Glasgow Centre for Virus Research, Glasgow, UK" + }, + { + "author_name": "Giuditta De Lorenzo", + "author_inst": "MRC-University of Glasgow Centre for Virus Research, Glasgow, UK" + }, + { + "author_name": "Vanessa M. Cowton", + "author_inst": "MRC-University of Glasgow Centre for Virus Research, Glasgow, UK" + }, + { + "author_name": "Dorothee Reuss", + "author_inst": "Department of Infectious Diseases, Imperial College London, UK, W2 1PG" + }, + { + "author_name": "Maya Moshe", + "author_inst": "Department of Infectious Diseases, Imperial College London, UK, W2 1PG" + }, + { + "author_name": "Olivia K. Platt", + "author_inst": "Department of Infectious Diseases, Imperial College London, UK, W2 1PG" + }, + { + "author_name": "Jessica L. Quantrill", + "author_inst": "Department of Infectious Disease, Imperial College London, UK, W2 1PG" + }, + { + "author_name": "Myrsini Kaforou", + "author_inst": "Imperial College London" + }, + { + "author_name": "Arvind H. Patel", + "author_inst": "MRC-University of Glasgow Centre for Virus Research, Glasgow, UK" + }, + { + "author_name": "Massimo Palmarini", + "author_inst": "MRC-University of Glasgow Centre for Virus Research, Glasgow, UK" + }, + { + "author_name": "Dalan Bailey", + "author_inst": "The Pirbright Institute" + }, + { + "author_name": "Wendy S Barclay", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.01.02.474028", "rel_title": "A dual-receptor mechanism between integrins and ACE2 widens SARS-CoV-2 tissue tropism", @@ -431512,53 +433310,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.01.22268609", - "rel_title": "The efficacy of Andrographis paniculata (Burm.f.) Wall. ex Nees crude extract in hospitalised mild COVID-19 patients: a retrospective cohort study", - "rel_date": "2022-01-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.01.22268609", - "rel_abs": "BackgroundAndrographis paniculata (Burm.f.) Wall. ex Nees (AP) has been widely used in Thailand to treat mild COVID-19 infections since early 2020; however, supporting evidence is scarce and ambiguous. Thus, this study aimed to examine whether the use of AP is associated with a decreased risk of pneumonia in hospitalised mild COVID-19 patients.\n\nMethodsWe collected data between March 2020 and August 2021 from COVID-19 patients admitted to one hospital in Thailand. Patients whose infection was confirmed by real-time polymerase chain reaction, had normal chest radiography and did not receive favipiravir at admission were included and categorised as either AP (deriving from a dried and ground aerial part of the plant), given as capsules with a total daily dose of 180 mg of andrographolide for five days or standard of care. They were followed for pneumonia confirmed by chest radiography. Multiple logistic regression was used for the analysis controlling for age, sex, diabetes, hypertension, statin use, and antihypertensive drug use.\n\nResultsA total of 605 out of 1,054 patients (mostly unvaccinated) were included in the analysis. Of these, 59 patients (9.8%) developed pneumonia during the median follow-up of 7 days. The incidence rates of pneumonia were 13.93 (95% CI 10.09, 19.23) and 12.47 (95% CI 8.21, 18.94) per 1,000 person-days in the AP and standard of care groups, respectively. Compared to the standard of care group, the odds ratios of having pneumonia in the AP group were 1.24 (95% CI 0.71, 2.16; unadjusted model) and 1.42 (95% CI 0.79, 2.55; fully adjusted model). All sensitivity analyses were consistent with the main results.\n\nConclusionsThe use of AP was not significantly associated with a decreased risk of pneumonia in mild COVID-19 patients. While waiting for insights from ongoing trials, APs use in COVID-19 should be done with caution.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Jeeranan Tanwettiyanont", - "author_inst": "Division of Clinical Pharmacy, Department of Pharmaceutical Care, School of Pharmaceutical Sciences, University of Phayao, Phayao, 56000 Thailand" - }, - { - "author_name": "Napacha Piriyachananusorn", - "author_inst": "Division of Pharmaceutical care, Department of Pharmacy, Phrae Hospital, Phrae, 54000 Thailand" - }, - { - "author_name": "Lilit Sangsoi", - "author_inst": "Division of Pharmaceutical care, Department of Pharmacy, Phrae Hospital, Phrae, 54000 Thailand" - }, - { - "author_name": "Benjawan Boonsong", - "author_inst": "Division of Pharmaceutical care, Department of Pharmacy, Phrae Hospital, Phrae, 54000 Thailand" - }, - { - "author_name": "Chamlong Sunpapoa", - "author_inst": "Division of Internal Medicine, Department of Nurse, Phrae Hospital, Phrae, 54000 Thailand" - }, - { - "author_name": "Patcharawan Tanamatayarat", - "author_inst": "Division of Pharmacy and Technology, Department of Pharmaceutical Care, School of Pharmaceutical Sciences, University of Phayao, Phayao, 56000 Thailand" - }, - { - "author_name": "Sukrit Kanchanasurakit", - "author_inst": "Division of Clinical Pharmacy, Department of Pharmaceutical Care, School of Pharmaceutical Sciences, University of Phayao, Phayao, 56000 Thailand" - }, - { - "author_name": "Nat Na-Ek", - "author_inst": "Division of Social and Administration Pharmacy, Department of Pharmaceutical Care, School of Pharmaceutical Sciences, University of Phayao, Phayao, 56000 Thaila" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.31.474032", "rel_title": "Analysis of SARS-CoV-2 Omicron Neutralization Data up to 2021-12-22", @@ -432314,6 +434065,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, + { + "rel_doi": "10.1101/2021.12.29.21268527", + "rel_title": "COVIDFast: A high-throughput and RNA extraction-free method for SARS-CoV-2 detection in swab (SwabFAST) or saliva (SalivaFAST)", + "rel_date": "2022-01-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.29.21268527", + "rel_abs": "There is an urgent need of having a rapid, high throughput, yet accurate SARS-COV-2 PCR testing to control the COVID19 pandemic. However, the RNA extraction step in conventional PCR creates a major bottle neck in the diagnostic process. In this paper we modified the CDC COVID-19 assay and developed an RNA-extraction free RT-qPCR assay for SARS-CoV-2, i.e. COVIDFast. Depending on sample types, the assay is further divided into SwabFAST, which uses anterior nares nasal swab, and SalivaFAST, which uses saliva. By utilizing the proprietary buffer for either swab or saliva samples, the performance of SwabFAST or SalivaFAST is equivalent to RNA-extraction SARS-CoV-2 RT-qPCR in both contrived and clinical samples. The limit of detection of either assay is 4 copies/L. We further developed a semi-automatic system, which is easy to adapt by clinical lab for implementation of a high-throughput SARS-CoV-2 test. Working together with the COVIDCheck Colorado, we have tested over 400,000 samples using COVIDFast (83.62% SwabFAST and 16.38% SalivaFAST) in less than a year, resulting in significant clinical contribution in the battle against COVID-19 during the pandemic.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Yue Qiu", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Ling Lu", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Amanda Halven", + "author_inst": "Summit Biolabs" + }, + { + "author_name": "Rachel Terrio", + "author_inst": "Summit Biolabs" + }, + { + "author_name": "Sydney Yuldelson", + "author_inst": "Summit Biolabs" + }, + { + "author_name": "Natalie Dougal", + "author_inst": "Summit Biolabs" + }, + { + "author_name": "Filippo Galbo", + "author_inst": "Summit Biolabs" + }, + { + "author_name": "Andrew Lu", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Dexiang Gao", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Bob Blomquist", + "author_inst": "Summit Biolabs" + }, + { + "author_name": "Jose Zevallos", + "author_inst": "Washington University" + }, + { + "author_name": "Brian Harry", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Xin Yao", + "author_inst": "Summit Biolabs" + }, + { + "author_name": "Shi-Long Lu", + "author_inst": "University of Colorado Denver - Anschutz Medical Campus" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.30.21268558", "rel_title": "Point-of-care lung ultrasound predicts severe disease and death due to COVID-19: a prospective cohort study.", @@ -433486,117 +435308,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.30.21268554", - "rel_title": "Preferential expansion of cross-reactive pre-existing switched memory B cells that recognize the SARS-CoV-2 Omicron variant Spike protein", - "rel_date": "2022-01-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.30.21268554", - "rel_abs": "In previously unvaccinated and uninfected individuals, non-RBD SARS-CoV-2 spike-specific B cells were prominent in two distinct, durable, resting, cross-reactive, \"pre-existing\" switched memory B cell compartments. While pre-existing RBD-specific B cells were extremely rare in uninfected and unvaccinated individuals, these two pre-existing switched memory B cell compartments were molded by vaccination and infection to become the primary source of RBD-specific B cells that are triggered by vaccine boosting. The frequency of wild-type RBD-binding memory B cells that cross-react with the Omicron variant RBD did not alter with boosting. In contrast, after a boost, B cells recognizing the full-length Omicron variant spike protein expanded, with pre-existing resting memory B cells differentiating almost quantitatively into effector B cell populations. B cells derived from \"ancient\" pre-existing memory cells and that recognize the full-length wild-type spike with the highest avidity after boosting are the B cells that also bind the Omicron variant spike protein.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC=\"FIGDIR/small/21268554v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (32K):\norg.highwire.dtl.DTLVardef@1de97acorg.highwire.dtl.DTLVardef@b7ab7forg.highwire.dtl.DTLVardef@5c38dcorg.highwire.dtl.DTLVardef@99106c_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Cory A Perugino", - "author_inst": "Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital" - }, - { - "author_name": "Hang Liu", - "author_inst": "Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "Jared Feldman", - "author_inst": "Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "Blake M Hauser", - "author_inst": "Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "Catherine Jacob-Dolan", - "author_inst": "Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "Anusha Nathan", - "author_inst": "Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "Zezhou Zhou", - "author_inst": "Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "Clarety Kaseke", - "author_inst": "Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "Rhoda Tano-Menka", - "author_inst": "Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "Matthew A Getz", - "author_inst": "Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "Fernando Sanjobe", - "author_inst": "Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "Cristhian Berrios", - "author_inst": "Department of Pathology, Massachusetts General Hospital" - }, - { - "author_name": "Onosereme Ofoman", - "author_inst": "Department of Pathology, Massachusetts General Hospital" - }, - { - "author_name": "Jacob Lemieux", - "author_inst": "Infectious Diseases Division, Massachusetts General Hospital" - }, - { - "author_name": "Marcia B. A Goldberg", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Kerstin Nundel", - "author_inst": "University of Massachusetts Medical School" - }, - { - "author_name": "Ann Marshak-Rothstein", - "author_inst": "University of Massachusetts Medical School" - }, - { - "author_name": "John Iafrate", - "author_inst": "Department of Pathology, Massachusetts General Hospital" - }, - { - "author_name": "Gaurav Gaiha", - "author_inst": "Gastrointestinal Unit, Massachusetts General Hospital" - }, - { - "author_name": "Richelle Charles", - "author_inst": "Infectious Diseases Division, Massachusetts General Hospital" - }, - { - "author_name": "Alejandro B Balazs", - "author_inst": "Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "Vivek Naranbhai", - "author_inst": "Massachusetts General Hospital/ Dana Farber Cancer Institute" - }, - { - "author_name": "Aaron G Schmidt", - "author_inst": "Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "Shiv Pillai", - "author_inst": "Ragon Institute, Massachusetts General Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2021.12.30.21267928", "rel_title": "Vaccine Effectiveness against COVID-19 among Symptomatic Persons Aged >=12 Years with Reported Contact with COVID-19 Cases, February - September 2021", @@ -434560,6 +436271,25 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.12.28.21268496", + "rel_title": "The Effect of Weather Pattern on the Second Wave of Coronavirus: A cross study between cold and tropical climates of France, Italy, Colombia, and Brazil", + "rel_date": "2021-12-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.28.21268496", + "rel_abs": "This study aims to explore and understand the common belief that COVID infection rate is highly dependent on either the outside temperature and/or the humidity. Thirty-six regions/states from two humid-tropical countries, namely Brazil and Colombia and two countries with temperate climate, France and Italy, are studied over the period of October to December. Daily outside temperature, relative humidity and hospitalization/cases are analyzed using Spearmans correlation. The eighteen cold regions of France and Italy has seen an average drop in temperature from 10{degrees}C to 6{degrees}C and 17{degrees}C to 7{degrees}C, respectively, and France recorded an addition of 2.3 million cases, while Italy recorded an addition of 1.8 million cases. Outside temperature did not fluctuate much in tropical countries, but Brazil and Colombia added 4.17 million and 1.1 million cases, respectively. Koppen-Geiger classification showed the differences in weather pattern between the four countries, and the analysis showed that there is very weak correlation between either outside weather and/or relative humidity alone to the COVID-19 pandemic.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Ahmed Islam", + "author_inst": "University of Louisville" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2021.12.29.21268501", "rel_title": "A cohort study of the effect of SARS-CoV-2 point of care rapid RT-PCR at the Emergency Department on targeted admission", @@ -435696,37 +437426,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.12.29.474353", - "rel_title": "Pipeline for retrieval of COVID-19 immune signatures", - "rel_date": "2021-12-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.29.474353", - "rel_abs": "ObjectiveThe accelerating pace of biomedical publication has made retrieving papers and extracting specific comprehensive scientific information a key challenge. A timely example of such a challenge is to retrieve the subset of papers that report on immune signatures (coherent sets of biomarkers) to understand the immune response mechanisms which drive differential SARS-CoV-2 infection outcomes. A systematic and scalable approach is needed to identify and extract COVID-19 immune signatures in a structured and machine-readable format.\n\nMaterials and MethodsWe used SPECTER embeddings with SVM classifiers to automatically identify papers containing immune signatures. A generic web platform was used to manually screen papers and allow anonymous submission.\n\nResultsWe demonstrate a classifier that retrieves papers with human COVID-19 immune signatures with a positive predictive value of 86%. Semi-automated queries to the corresponding authors of these publications requesting signature information achieved a 31% response rate. This demonstrates the efficacy of using a SVM classifier with document embeddings of the abstract and title, to retrieve papers with scientifically salient information, even when that information is rarely present in the abstract. Additionally, classification based on the embeddings identified the type of immune signature (e.g., gene expression vs. other types of profiling) with a positive predictive value of 74%.\n\nConclusionCoupling a classifier based on document embeddings with direct author engagement offers a promising pathway to build a semistructured representation of scientifically relevant information. Through this approach, partially automated literature mining can help rapidly create semistructured knowledge repositories for automatic analysis of emerging health threats.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Adam J H Newton", - "author_inst": "SUNY Downstate Health Sciences University" - }, - { - "author_name": "David Chartash", - "author_inst": "University College Dublin" - }, - { - "author_name": "Steven H Kleinstein", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Robert A McDougal", - "author_inst": "Yale School of Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.12.28.474369", "rel_title": "Increased resistance of SARS-CoV-2 Omicron Variant to Neutralization by Vaccine-Elicited and Therapeutic Antibodies", @@ -436566,6 +438265,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.21.21268190", + "rel_title": "Evaluation of the Cepheid Xpert Xpress SARS-CoV-2 test for bronchoalveolar lavage", + "rel_date": "2021-12-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.21.21268190", + "rel_abs": "Accurate and rapid laboratory tests are essential for the prompt diagnosis of COVID-19, which is important to patients and infection control. The Xpert Xpress SARS-CoV-2 test is a real-time RT-PCR intended for the qualitative detection of nucleic acid from SARS-CoV-2 in upper respiratory specimens. In this study, we assessed the analytical and clinical performance characteristics of this rapid test for SARS-CoV-2 in 60 bronchoalveolar lavage (BAL) specimens. BAL is a specimen type that is not authorized under EUA for the Xpert Xpress SARS-CoV-2 test. The limit of detection of the Xpert Xpress SARS-CoV-2 test was 500 copies/ml. The overall agreement of the Xpert Xpress SARS-CoV-2 test was 100%. The Xpert Xpress SARS-CoV-2 test is sensitive and specific to aid in diagnosis of COVID-19 using bronchoalveolar lavage.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Tung Phan", + "author_inst": "University of Pittsburgh Medical Center" + }, + { + "author_name": "Ashley Mays", + "author_inst": "UPMC Hospital System" + }, + { + "author_name": "Melissa McCullough", + "author_inst": "UPMC Hospital System" + }, + { + "author_name": "Alan Wells", + "author_inst": "University of Pittsburgh" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.27.21268429", "rel_title": "Detection of the omicron variant in international travellers and their family contacts in India", @@ -437842,49 +439572,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.28.21268183", - "rel_title": "A novel assessment method for COVID-19 humoral immunity duration using serial measurements in naturally-infected and vaccinated subjects.", - "rel_date": "2021-12-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.28.21268183", - "rel_abs": "BackgroundIt is crucial for medical decision-making and vaccination strategies to collect information on sustainability of immune responses after infection or vaccination, and how long-lasting antibodies against SARS-COV-2 could provide a humoral and protective immunity, preventing reinfection with SARS-CoV-2 or its variants. The aim of this study is to present a novel method to quantitatively measure and monitor the diversity of SARS-CoV-2 specific antibody profiles over time.\n\nMethodsTwo collections of serum samples were used in this study: A collection from 20 naturally infected subjects (follow-ups to 1 year) and a collection from 83 subjects vaccinated with one or two doses of Pfizer BioNtech vaccine (BNT162b2/BNT162b2) (follow-ups to 6 months). The Multi-SARS-CoV-2 assay, a multiparameter serology test, developed for the serological confirmation of past-infections was used to determine the reactivity of six different SARS-CoV-2 antigens. For each patient sample, 3 dilutions (1/50, 1/400 and 1/3200) were defined as an optimal set over the six antigens and their respective linear ranges, allowing accurate quantitation of the corresponding six specific antibodies. Nonlinear mixed-effects modelling was applied to convert intensity readings from 3 determined dilutions to a single quantification value for each antibody.\n\nResultsMedian half-life for the 20 naturally infected vs 74 vaccinated subjects (two doses) was respectively 120 vs 50 days for RBD, 127 vs 53 days for S1 and 187 vs 86 days for S2 antibodies. Respectively, 90% of the antibody concentration wanes after 398 vs 158 days for RBD, 420 vs 171 days for S1, and 620 vs 225 days for S2 after the second vaccine shot.\n\nConclusionThe newly proposed method, based on a series of a limited number of dilutions, can convert a conventional qualitative assay into a quantitative assay. This conversion helps define the sustainability of specific immune responses against each relevant viral antigen and can help in defining the protection characteristics after an infection or a vaccination.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Jasper de Boer", - "author_inst": "Department of Public Health and Primary Care, KU Leuven Campus Kulak Kortrijk, Kortrijk, Belgium" - }, - { - "author_name": "Ursula Saade", - "author_inst": "InfYnity Biomarkers, Lyon, France" - }, - { - "author_name": "Elodie Granjon", - "author_inst": "InfYnity Biomarkers, Lyon, France" - }, - { - "author_name": "Sophie Trouillet-Assant", - "author_inst": "Hospices Civils de Lyon" - }, - { - "author_name": "Carla Saade", - "author_inst": "Centre international de recherche en infectiologie" - }, - { - "author_name": "Hans Pottel", - "author_inst": "Department of Public Health and Primary Care, KU Leuven Campus Kulak Kortrijk, Kortrijk, Belgium" - }, - { - "author_name": "Maan Zrein", - "author_inst": "InfYnity Biomarkers, Lyon, France" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.26.21268419", "rel_title": "Predicting the course of Covid-19 and other epidemic and endemic disease", @@ -438620,6 +440307,173 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2021.12.27.21268448", + "rel_title": "Risk of Cardiovascular Events after Covid-19: a double-cohort study", + "rel_date": "2021-12-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.27.21268448", + "rel_abs": "ObjectiveTo determine absolute and relative risks of either symptomatic or asymptomatic SARS-CoV-2 infection for late cardiovascular events and all-cause mortality.\n\nMethodsWe conducted a retrospective double-cohort study of patients with either symptomatic or asymptomatic SARS-CoV-2 infection [COVID-19(+) cohort] and its documented absence [COVID-19(-) cohort]. The study investigators drew a simple random sample of records from all Oregon Health & Science University (OHSU) Healthcare patients (N=65,585) with available COVID-19 test results, performed 03.01.2020 - 09.13.2020. Exclusion criteria were age < 18y and no established OHSU care. The primary outcome was a composite of cardiovascular morbidity and mortality. All-cause mortality was the secondary outcome.\n\nResultsThe study population included 1355 patients (mean age 48.7{+/-}20.5 y; 770(57%) female, 977(72%) white non-Hispanic; 1072(79%) insured; 563(42%) with cardiovascular disease (CVD) history). During a median 6 months at risk, the primary composite outcome was observed in 38/319 (12%) COVID-19(+) and 65/1036 (6%) COVID-19(-) patients (p=0.001). In Cox regression adjusted for demographics, health insurance, and reason for COVID-19 testing, SARS-CoV-2 infection was associated with the risk of the primary composite outcome (HR 1.71; 95%CI 1.06-2.78; p=0.029). Inverse-probability-weighted estimation, conditioned for 31 covariates, showed that for every COVID-19(+) patient, the average time to all-cause death was 65.5 days less than when all these patients were COVID-19(-): average treatment effect on the treated -65.5 (95%CI -125.4 to -5.61) days; p=0.032.\n\nConclusionsEither symptomatic or asymptomatic SARS-CoV-2 infection is associated with increased risk of late cardiovascular outcomes and has causal effect on all-cause mortality in a late post-COVID-19 period.\n\nClinicalTrials.gov Identifier: NCT04555187\n\nKey messagesO_ST_ABSWhat is already known about this subjectC_ST_ABSO_LIAcute, symptomatic COVID-19 can cause acute cardiovascular manifestations.\nC_LIO_LIPost-acute or \"long\" COVID-19 can be a debilitating disease following acute infection with a heterogenous presentation.\nC_LI\n\nWhat might this study add?O_LIEither symptomatic or asymptomatic SARS-CoV-2 infection is associated with increased risk of late cardiovascular outcomes.\nC_LIO_LIEither symptomatic or asymptomatic SARS-CoV-2 infection has causal effect on all-cause mortality in a late post-COVID-19 period.\nC_LI\n\nHow might this impact on clinical practice?O_LIAs we begin to care for more survivors of COVID-19, we will need to better understand not only how to care for their acute symptoms and complications following infection, but also recognize future cardiovascular risk and mitigate such risk with appropriate screening and preventative measures.\nC_LI", + "rel_num_authors": 38, + "rel_authors": [ + { + "author_name": "Larisa G Tereshchenko", + "author_inst": "Cleveland Clinic Lerner Research Institute" + }, + { + "author_name": "Adam Bishop", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Nora Fisher-Campbell", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Jacqueline Levene", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Craig Morris", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Hetal Patel", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Erynn Beeson", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Jessica Blank", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "J.G. Bradner", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Michelle Coblens", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Jacob Corpron", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Jenna Davison", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Kathleen Denny", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Mary Earp", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Simeon Florea", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Howard Freeman", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Olivia Fuson", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Florian Guillot", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Kazi Haq", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Jessica Hyde", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Ayesha Khader", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Clinton Kolseth", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Morris Kim", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Olivia Krol", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Lisa Lin", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Liat Litwin", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Aneeq Malik", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Evan Mitchell", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Aman Mohapatra", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Cassandra Mullen", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Chad Nix", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Ayodele Oyeyemi", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Christine Rutlen", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Lisa Corley-Stampke", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Ashley Tam", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Inga Van Buren", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Jessica Wallace", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Akram Khan", + "author_inst": "Oregon Health & Science University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2021.12.27.21268464", "rel_title": "Control Strategies for the Third wave of COVID-19 infection in India: A Mathematical Model Incorporating Vaccine Effectiveness", @@ -439796,69 +441650,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.12.26.474192", - "rel_title": "Super-immunity by broadly protective nanobodies to sarbecoviruses", - "rel_date": "2021-12-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.26.474192", - "rel_abs": "Vaccine boosters and infection can facilitate the development of SARS-CoV-2 antibodies with improved potency and breadth. Here, we observed super-immunity in a camelid extensively immunized with the SARS-CoV-2 receptor-binding domain (RBD). We rapidly isolated a large repertoire of specific ultrahigh-affinity nanobodies that bind strongly to all known sarbecovirus clades using integrative proteomics. These pan-sarbecovirus nanobodies (psNbs) are highly effective against SARS-CoV and SARS-CoV-2 variants including the Omicron, with the best median neutralization potency at single-digit ng/ml. Structural determinations of 13 psNbs with the SARS-CoV-2 spike or RBD revealed five epitope classes, providing insights into the mechanisms and evolution of their broad activities. The highly evolved psNbs target small, flat, and flexible epitopes that contain over 75% of conserved RBD surface residues. Their potencies are strongly and negatively correlated with the distance of the epitopes to the receptor binding sites. A highly potent, inhalable and bispecific psNb (PiN-31) was developed. Our findings inform on the development of broadly protective vaccines and therapeutics.\n\nOne sentence summarySuccessive immunization of SARS-CoV-2 RBD in a camelid enhanced the development of super-immunity and isolation and systematic characterization of a large repertoire of ultrahigh-affinity pan-sarbecovirus single-chain VHH antibodies to understand the evolution of this potent and broad immune response.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Yufei Xiang", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Wei Huang", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "Hejun Liu", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Zhe Sang", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Sham Nambulli", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Jerome Tubiana", - "author_inst": "The Hebrew University of Jerusalem" - }, - { - "author_name": "Kevin L Williams", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Paul Duprex", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Dian Schneidman-Duhovny", - "author_inst": "The Hebrew University of Jerusalem" - }, - { - "author_name": "Ian A Wilson", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Derek J Taylor", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "Yi Shi", - "author_inst": "University of Pittsburgh" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.12.27.474275", "rel_title": "Remdesivir, Molnupiravir and Nirmatrelvir remain active against SARS-CoV-2 Omicron and other variants of concern.", @@ -440846,6 +442637,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.12.22.21268195", + "rel_title": "Utilization of a SARS-CoV-2 Variant Assay for the Rapid Differentiation of Omicron and Delta", + "rel_date": "2021-12-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.22.21268195", + "rel_abs": "The emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant (B.1.1.529), creates a diagnostic vacuum, since differentiation of Omicron from Delta relies on relatively slow next generation sequencing (NGS) technology delaying epidemiologic understanding and therapeutic intervention. The RUO SARS-CoV-2 Variant Set 1 Test (RSCov2V1) RT-PCR for detection of spike gene N501Y, E484K and del69-70 was designed to differentiate Alpha from Beta and Gamma variants. While Delta lacks these three variants, Omicron has the N501Y and del69-70 mutation. We submitted 88 samples for RSCov2V1 identifying 9 samples with the N501Y and del69-70 mutations while all other samples (79) were negative for all three variants. 9/9 samples with the del69-70 and N501Y were identified by NGS to be Omicron while 47/47 other samples assessed by NGS were confirmed to be Delta family variants. We demonstrate here that an immediately available RT-PCR assay for detection of spike gene N501Y and del69-70 can be utilized to rapidly differentiate Omicron from Delta variants in the proper epidemiologic context", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Nicholas Jacob Barasch", + "author_inst": "James J. Peters Veterans Affairs Medical Center, Bronx, NY" + }, + { + "author_name": "James Iqbal", + "author_inst": "DaVita Labs, DeLand, FL" + }, + { + "author_name": "Marvin Coombs", + "author_inst": "James J. Peters Veterans Affairs Medical Center, Bronx, NY" + }, + { + "author_name": "Sofia Kazi", + "author_inst": "James J. Peters Veterans Affairs Medical Center, Bronx, NY" + }, + { + "author_name": "Jessica Wang-Rodriguez", + "author_inst": "National Pathology and Laboratory Medicine, Veterans Health Administration, Washington, DC" + }, + { + "author_name": "Mark Holodniy", + "author_inst": "Office of Public Health, Veterans Health Administration, Washington, DC" + }, + { + "author_name": "Michael Gelman", + "author_inst": "James J. Peters Veterans Affairs Medical Center, Bronx, NY" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "pathology" + }, { "rel_doi": "10.1101/2021.12.21.21268075", "rel_title": "Assessing Immunity by Quantitative Measurement of SARS-CoV-2 IgG Antibodies in Fingerstick Samples", @@ -442406,41 +444240,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, - { - "rel_doi": "10.1101/2021.12.21.21268166", - "rel_title": "SARS-CoV-2 seroprevalence in Kaduna State, Nigeria during October/November 2021, following three waves of infection and immediately prior to detection of the Omicron variant", - "rel_date": "2021-12-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.21.21268166", - "rel_abs": "Nigeria is the most populated country in Africa with an estimated [~]213 million inhabitants. As of November 2021 there have been three waves of SARS-CoV-2 infection in Nigeria but there has been only one seroprevalence survey conducted to assess the proportion of a population that have been infected, which was performed in December 2020 after the first wave of infection. To provide an update on seroprevalence in Nigeria, we conducted survey at one urban site (n=400) and one rural site (n=402) in Kaduna State, Nigeria during October and November 2021 following the third wave of infection. Seroprevalence for the urban and rural sites was 42.5% and 53.5% respectively (mean 48.0%). Symptoms associated with seropositivity were identified for each site. The overall seroprevalence among unvaccinated individuals was 45.4%. The data indicates an infection rate in Kaduna State at least 387 times greater than that derived from cases confirmed by PCR. Extrapolating to the whole of Nigeria, it would suggest there has been at least 96.7 million infections (compared to 206,138 confirmed cases at the time of surveillance). The work presented here will inform public health policy and deployment strategies for testing, treatment, and vaccination in Nigeria, and provide a baseline for SARS-CoV-2 seroprevalence in Nigeria immediately prior to the spread of the Omicron variant.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Gloria Dada Chechet", - "author_inst": "Ahmadu Bello University" - }, - { - "author_name": "Jacob KP Kwaga", - "author_inst": "Ahmadu Bello University" - }, - { - "author_name": "Joseph Yahaya", - "author_inst": "Ahmadu Bello University" - }, - { - "author_name": "Annette MacLeod", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Walt E Adamson", - "author_inst": "University of Glasgow" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.20.21268053", "rel_title": "A simple and quick PCR based method for detection of Omicron variant of SARS-CoV-2", @@ -443236,6 +445035,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.22.21268201", + "rel_title": "Reliably Assessing Duration of Protection for COVID-19 Vaccines", + "rel_date": "2021-12-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.22.21268201", + "rel_abs": "Decision-making about booster dosing for COVID-19 vaccine recipients hinges on reliable methods for evaluating the longevity of vaccine protection. We show that modeling of protection as a piecewise linear function of time since vaccination for the log hazard ratio of the vaccine effect provides more reliable estimates of vaccine effectiveness at the end of an observation period and also more reliably detects plateaus in protective effectiveness as compared with the traditional method of estimating a constant vaccine effect over each time period. This approach will be useful for analyzing data pertaining to COVID-19 vaccines and other vaccines where rapid and reliable understanding of vaccine effectiveness over time is desired.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Danyu Lin", + "author_inst": "University of North Carolina" + }, + { + "author_name": "Donglin Zeng", + "author_inst": "University of North Carolina" + }, + { + "author_name": "Yu Gu", + "author_inst": "University of North Carolina" + }, + { + "author_name": "Thomas Fleming", + "author_inst": "University of Washington" + }, + { + "author_name": "Phillip Krause", + "author_inst": "US Food and Drug Administration" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.20.21267877", "rel_title": "Immunosequencing and epitope mapping reveal substantial preservation of the T cell immune response to Omicron generated by SARS-CoV-2 vaccines", @@ -444268,77 +446102,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.12.24.21268371", - "rel_title": "Relative Importance of Various Inflammatory Markers and Their Critical Thresholds for COVID-19 Mortality", - "rel_date": "2021-12-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.24.21268371", - "rel_abs": "BackgroundVarious inflammatory markers are commonly assessed in many patients to help in the management of COVID-19 patients. It is not clear, though, how much risk of mortality their different levels of elevations entail, and which marker signifies more risk than others and how much. This study was undertaken to describe their levels and to answer these questions regarding eight inflammatory markers, namely, CRP, D-dimer, ferritin, IL-6, LDH, CPK, troponin-I.\n\nMethodsThe data were retrieved from the electronic records of 19852 CoViD-19 patients admitted to a chain of hospitals in north India from March 2020 to July 2021. Levels for most markers were available for more than 10,000 patients. In view of widely different ranges of values of different markers, we divided their values into quintiles (Qs) and studied the pattern of mortality and for running the logistic regression. In addition, logarithm transformation was also tried. The statistical distribution of the values was compared by Mann-Whitney test. Relative importance was judged by the mortality rates, area under the ROC curves (AUROCs), and the odds ratios.\n\nResultsAlthough the mortality increased with decreasing ALC and increasing level of all the other markers, more than 70% survived even with levels in the extreme quintile. The adjusted odds ratio was the highest (7.62) for the Q5 levels of IL-6, closely followed by D-dimer (OR = 6.04). The AUROC was the highest (0.817) for LDH and the least (0.612) for CPK. However, the optimal cut-off for any marker could correctly classify not more than 80% deaths and the multivariable logistic regression could correctly classify patients with mortality in less than 24% cases.\n\nConclusionAlthough elevated levels of all the markers and low values of ALC were significant risk factor but no firm evidence was available for any of the eight markers to be a major indicator of the mortality in COVID-19 unless they reach to a critical threshold. Among those studied, D-Dimer (>192 ng/mL) followed by IL-6 (>4.5 pg/mL) had stronger association with mortality even with moderate and higher end of the normal levels and LDH (>433 U/L) and troponin-I (>0.002ng/mL) with only steeply increased levels. Ferritin had modest association, and CPK, CRP and ALC were a relatively poor risk of mortality.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "sandeep budhiraja", - "author_inst": "Clinical Directorate and Dept of Internal Medicine, Max Healthcare" - }, - { - "author_name": "Abhaya Indrayan", - "author_inst": "Max Healthcare" - }, - { - "author_name": "poonam das", - "author_inst": "max healthcare" - }, - { - "author_name": "arun dewan", - "author_inst": "max healthcare" - }, - { - "author_name": "omender singh", - "author_inst": "max healthcare" - }, - { - "author_name": "vivek nangia", - "author_inst": "max healthcare" - }, - { - "author_name": "yogendra pal singh", - "author_inst": "max healthcare" - }, - { - "author_name": "rajesh pandey", - "author_inst": "max healthcare" - }, - { - "author_name": "ajay kumar gupta", - "author_inst": "max healthcare" - }, - { - "author_name": "manish gupta", - "author_inst": "max healthcare" - }, - { - "author_name": "deepak bhasin", - "author_inst": "max healthcare" - }, - { - "author_name": "bhupesh uniyal", - "author_inst": "max healthcare" - }, - { - "author_name": "mohit mathur", - "author_inst": "max healthcare" - }, - { - "author_name": "mayur pawar", - "author_inst": "Clinical directorate, max healthcare" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.23.21268321", "rel_title": "Influenza A H1N1 mediated pre-existing immunity to SARS-CoV-2 predicts COVID-19 outbreak dynamics", @@ -445066,6 +446829,37 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.12.23.473991", + "rel_title": "Analyzing the interaction of human ACE2 and RBD of spike protein of SARS-CoV-2 in perspective of Omicron variant", + "rel_date": "2021-12-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.23.473991", + "rel_abs": "The newly identified Omicron (B.1.1.529) variant of Severe Acute Respiratory Syndrome Voronavirus 2 (SARS-CoV-2) has steered concerns across the world due to the possession of large number of mutations leading to high infectivity and vaccine escape potential. The Omicron variant houses 32 mutations in S protein alone. The viral infectivity is determined mainly by the ability of spike (S) protein receptor binding domain (RBD) to bind to the human Angiotensin I Converting Enzyme 2 (hACE2) receptor. In this paper, the interaction of the RBDs of SARS-CoV-2 variants with hACE2 was analyzed by using protein-protein docking and compared with the novel Omicron variant. Our findings reveal that the Omicron RBD interacts strongly with hACE2 receptor via unique amino acid residues as compared to the Wuhan and many other variants. However, the interacting residues of RBD are found to be the same in Lamda (C.37) variant. These unique binding of Omicron RBD with hACE2 suggests an increased potential of infectivity and vaccine evasion potential of the new variant. The evolutionary drive of the SARS-CoV-2 may not be exclusively driven by RBD variants but surely provides for the platform for emergence of new variants.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Arijit Samanta", + "author_inst": "Aliah University" + }, + { + "author_name": "Syed Sahajada Mahafujul Alam", + "author_inst": "Aliah University" + }, + { + "author_name": "Safdar Ali", + "author_inst": "Aliah University" + }, + { + "author_name": "Mehboob Hoque", + "author_inst": "Aliah University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.12.23.21268347", "rel_title": "Ex-vivo mucolytic and anti-inflammatory activity of BromAc in tracheal aspirates from COVID-19", @@ -446162,53 +447956,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.12.23.21268272", - "rel_title": "Population immunity to SARS-CoV-2 in US states and counties due to infection and vaccination, January 2020-November 2021", - "rel_date": "2021-12-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.23.21268272", - "rel_abs": "Prior infection and vaccination both contribute to population-level SARS-CoV-2 immunity. We used a Bayesian model to synthesize evidence and estimate population immunity to prevalent SARS-CoV-2 variants in the United States over the course of the epidemic until December 1, 2021, and how this changed with the introduction of the Omicron variant. We used daily SARS-CoV-2 infection estimates and vaccination coverage data for each US state and county. We estimated relative rates of vaccination conditional on previous infection status using the Census Bureaus Household Pulse Survey. We used published evidence on natural and vaccine-induced immunity, including waning and immune escape. The estimated percentage of the US population with a history of SARS-CoV-2 infection or vaccination as of December 1, 2021, was 88.2% (95%CrI: 83.6%-93.5%), compared to 24.9% (95%CrI: 18.5%-34.1%) on January 1, 2021. State-level estimates for December 1, 2021, ranged between 76.9% (95%CrI: 67.6%-87.6%, West Virginia) and 94.4% (95%CrI: 91.2%-97.3%, New Mexico). Accounting for waning and immune escape, the effective protection against the Omicron variant on December 1, 2021, was 21.8% (95%CrI: 20.7%-23.4%) nationally and ranged between 14.4% (95%CrI: 13.2%-15.8%, West Virginia), to 26.4% (95%CrI: 25.3%-27.8%, Colorado). Effective protection against severe disease from Omicron was 61.2% (95%CrI: 59.1%-64.0%) nationally and ranged between 53.0% (95%CrI: 47.3%-60.0%, Vermont) and 65.8% (95%CrI: 64.9%-66.7%, Colorado). While over three-quarters of the US population had prior immunological exposure to SARS-CoV-2 via vaccination or infection on December 1, 2021, only a fifth of the population was estimated to have effective protection to infection with the immune-evading Omicron variant.\n\nSignificanceBoth SARS-CoV-2 infection and COVID-19 vaccination contribute to population-level immunity against SARS-CoV-2. This study estimates the immunity and effective protection against future SARS-CoV-2 infection in each US state and county over 2020-2021. The estimated percentage of the US population with a history of SARS-CoV-2 infection or vaccination as of December 1, 2021, was 88.2% (95%CrI: 83.6%-93.5%). Accounting for waning and immune escape, protection against the Omicron variant was 21.8% (95%CrI: 20.7%-23.4%). Protection against infection with the Omicron variant ranged between 14.4% (95%CrI: 13.2%-15.8%%, West Virginia) and 26.4% (95%CrI: 25.3%-27.8%, Colorado) across US states. The introduction of the immune-evading Omicron variant resulted in an effective absolute increase of approximately 30 percentage points in the fraction of the population susceptible to infection.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Fayette Klaassen", - "author_inst": "Harvard" - }, - { - "author_name": "Melanie H Chitwood", - "author_inst": "Department of Epidemiology of Microbial Diseases and Public Health Modeling Unit, Yale School of Public Health, New Haven CT" - }, - { - "author_name": "Ted Cohen", - "author_inst": "Department of Epidemiology of Microbial Diseases and Public Health Modeling Unit, Yale School of Public Health, New Haven CT" - }, - { - "author_name": "Virginia E Pitzer", - "author_inst": "Department of Epidemiology of Microbial Diseases and Public Health Modeling Unit, Yale School of Public Health, New Haven CT" - }, - { - "author_name": "Marcus Russi", - "author_inst": "Department of Epidemiology of Microbial Diseases and Public Health Modeling Unit, Yale School of Public Health, New Haven CT" - }, - { - "author_name": "Nicole A Swartwood", - "author_inst": "Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston MA" - }, - { - "author_name": "Joshua A Salomon", - "author_inst": "Department of Health Policy, Stanford University School of Medicine, Stanford CA." - }, - { - "author_name": "Nicolas A Menzies", - "author_inst": "Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston MA" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.12.23.21268335", "rel_title": "Change in COVID-19 risk over time following vaccination with CoronaVac: A test-negative case-control study", @@ -447128,6 +448875,137 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.12.22.473880", + "rel_title": "SARS-CoV-2 Omicron neutralization by therapeutic antibodies, convalescent sera, and post-mRNA vaccine booster", + "rel_date": "2021-12-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.22.473880", + "rel_abs": "The rapid spread of the highly contagious Omicron variant of SARS-CoV-2 along with its high number of mutations in the spike gene has raised alarm about the effectiveness of current medical countermeasures. To address this concern, we measured neutralizing antibodies against Omicron in three important settings: (1) post-vaccination sera after two and three immunizations with the Pfizer/BNT162b2 vaccine, (2) convalescent sera from unvaccinated individuals infected by different variants, and (3) clinical-stage therapeutic antibodies. Using a pseudovirus neutralization assay, we found that titers against Omicron were low or undetectable after two immunizations and in most convalescent sera. A booster vaccination significantly increased titers against Omicron to levels comparable to those seen against the ancestral (D614G) variant after two immunizations. Neither age nor sex were associated with differences in post-vaccination antibody responses. Only three of 24 therapeutic antibodies tested retained their full potency against Omicron and high-level resistance was seen against fifteen. These findings underscore the potential benefit of booster mRNA vaccines for protection against Omicron and the need for additional therapeutic antibodies that are more robust to highly mutated variants.\n\nOne Sentence SummaryThird dose of Pfizer/BioNTech COVID-19 vaccine significantly boosts neutralizing antibodies to the Omicron variant compared to a second dose, while neutralization of Omicron by convalescent sera, two-dose vaccine-elicited sera, or therapeutic antibodies is variable and often low.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Sabrina Lusvarghi", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Simon D. Pollett", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Sabari Nath Neerukonda", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Wei Wang", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Richard Wang", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Russell Vassell", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Nusrat J. Epsi", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Anthony C. Fries", + "author_inst": "U.S. Air Force School of Aerospace Medicine" + }, + { + "author_name": "Brian K Agan", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "David A. Lindholm", + "author_inst": "Brooke Army Medical Center, Joint Base San Antonio-Fort Sam Houston" + }, + { + "author_name": "Christopher J Colombo", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Rupal Mody", + "author_inst": "William Beaumont Army Medical Center" + }, + { + "author_name": "Evan C. Ewers", + "author_inst": "Fort Belvoir Community Hospital" + }, + { + "author_name": "Tahaniyat Lalani", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Anuradha Ganesan", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Emilie Goguet", + "author_inst": "Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc." + }, + { + "author_name": "Monique Hollis-Perry", + "author_inst": "Naval Medical Research Center" + }, + { + "author_name": "Mark P. Simons", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Leah C. Katzelnick", + "author_inst": "National Institute of Allergy and Infectious Diseases, National Institutes of Health" + }, + { + "author_name": "Gregory Wang", + "author_inst": "Naval Medical Research Center" + }, + { + "author_name": "Christopher C. Broder", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "David R. Tribble", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Lisa Marie Bentley", + "author_inst": "Office of the Assistance Secretary for Preparedness and Response, U.S. Department of Human Health and Services" + }, + { + "author_name": "Ann E. Eakin", + "author_inst": "National Institute of Allergy and Infectious Disease, National Institutes of Health" + }, + { + "author_name": "Karl J. Erlandson", + "author_inst": "Biomedical Advanced Research and Development Authority, U.S. Department of Health and Human Services" + }, + { + "author_name": "Eric D. Laing", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Timothy H. Burgess", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Edward Mitre", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Carol D. Weiss", + "author_inst": "US Food and Drug Administration" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.12.21.473679", "rel_title": "SARS-CoV-2 Omicron Spike recognition by plasma from individuals receiving BNT162b2 mRNA vaccination with a 16-weeks interval between doses", @@ -448071,85 +449949,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2021.12.22.21268103", - "rel_title": "Neutralization of SARS-CoV-2 Omicron pseudovirus by BNT162b2 vaccine-elicited human sera", - "rel_date": "2021-12-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.22.21268103", - "rel_abs": "A new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage, B.1.1.529, was recently detected in Botswana and South Africa and is now circulating globally. Just two days after it was first reported to the World Health Organization (WHO), this strain was classified as a variant of concern (VOC) and named Omicron. Omicron has an unusually large number of mutations, including up to 39 amino acid modifications in the spike (S) protein, raising concerns that its recognition by neutralizing antibodies from convalescent and vaccinated individuals may be severely compromised. In this study, we tested pseudoviruses carrying the SARS-CoV-2 spike glycoproteins of either the Wuhan reference strain, the Beta, the Delta or the Omicron variants of concern with sera of 51 participants that received two doses or a third dose ([≥]6 months after dose 2) of the mRNA-based COVID-19 vaccine BNT162b2. Immune sera from individuals who received two doses of BNT162b2 had more than 22-fold reduced neutralizing titers against the Omicron as compared to the Wuhan pseudovirus. One month after a third dose of BNT162b2, the neutralization titer against Omicron was increased 23-fold compared to two doses and antibody titers were similar to those observed against the Wuhan pseudovirus after two doses of BNT162b2. These data suggest that a third dose of BNT162b2 may protect against Omicron-mediated COVID-19, but further analyses of longer-term antibody persistence and real-world effectiveness data are needed.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Alexander Muik", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Bonny Gaby Lui", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Ann-Kathrin Wallisch", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Maren Bacher", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Julia Muehl", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Jonas Reinholz", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Orkun Ozhelvaci", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Nina Beckmann", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Ramon de la Caridad Guimil Garcia", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Asaf Poran", - "author_inst": "BioNTech US" - }, - { - "author_name": "Svetlana Shpyro", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Hui Cai", - "author_inst": "Pfizer" - }, - { - "author_name": "Qi Yang", - "author_inst": "Pfizer" - }, - { - "author_name": "Kena Anne Swanson", - "author_inst": "Pfizer" - }, - { - "author_name": "Oezlem Tuereci", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Ugur Sahin", - "author_inst": "BioNTech SE" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.21.473620", "rel_title": "Structural basis for antibody resistance to SARS-CoV-2 omicron variant", @@ -449037,6 +450836,125 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2021.12.21.473774", + "rel_title": "Longitudinal characterisation of phagocytic and neutralisation functions of anti-Spike antibodies in plasma of patients after SARS-CoV-2 infection.", + "rel_date": "2021-12-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.21.473774", + "rel_abs": "Phagocytic responses by effector cells to antibody or complement-opsonised viruses have been recognized to play a key role in anti-viral immunity. These include antibody dependent cellular phagocytosis mediated via Fc-receptors, phagocytosis mediated by classically activated complement-fixing IgM or IgG1 antibodies and antibody independent phagocytosis mediated via direct opsonisation of viruses by complement products activated via the mannose-binding lectin pathway. Limited data suggest these phagocytic responses by effector cells may contribute to the immunological and inflammatory responses in SARS-CoV-2 infection, however, their development and clinical significance remain to be fully elucidated. In this cohort of 62 patients, acutely ill individuals were shown to mount phagocytic responses to autologous plasma-opsonised SARS-CoV-2 Spike protein-coated microbeads as early as 10 days post symptom onset. Heat inactivation of the plasma prior to use as an opsonin caused 77-95% abrogation of the phagocytic response, and pre-blocking of Fc-receptors on the effector cells showed only 18-60% inhibition. These results suggest that SARS-CoV-2 can provoke early phagocytosis, which is primarily driven by heat labile components, likely activated complements, with variable contribution from anti-Spike antibodies. During convalescence, phagocytic responses correlated significantly with anti-Spike IgG titers. Older patients and patients with severe disease had significantly higher phagocytosis and neutralisation functions when compared to younger patients or patients with asymptomatic, mild, or moderate disease. A longitudinal study of a subset of these patients over 12 months showed preservation of phagocytic and neutralisation functions in all patients, despite a drop in the endpoint antibody titers by more than 90%. Interestingly, surface plasmon resonance showed a significant increase in the affinity of the anti-Spike antibodies over time correlating with the maintenance of both the phagocytic and neutralisation functions suggesting that improvement in the antibody quality over the 12 months contributed to the retention of effector functions.\n\nAuthor SummaryLimited data suggest antibody dependent effector functions including phagocytosis may contribute to the immunological and inflammatory responses in SARS CoV-2 infection, however, their development, maintenance, and clinical significance remain unknown. In this study we show: O_LIPatients with acute SARS CoV-2 infection can mount phagocytic responses as early as 10 days post symptom onset and these responses were primarily driven by heat labile components of the autologous plasma. These results indicate that the current approach of studying phagocytosis using purified or monoclonal antibodies does not recapitulate contribution by all components in the plasma.\nC_LIO_LIIn convalescent patients, high phagocytic responses significantly correlated with increasing age, increasing disease severity, high neutralisation functions and high anti-Spike antibody titers, particularly IgG1.\nC_LIO_LILongitudinal study of convalescent patients over a 12-month period showed maintenance of phagocytic and neutralisation functions, despite a drop in the anti-Spike endpoint antibody titers by more than 90%. However, we found significant increase in the affinity of the anti-Spike antibodies over the 12-month period and these correlated with the maintenance of functions suggesting that improvement in the antibody quality over time contributed to the retention of effector functions. Clinically, measuring antibody titers in sera but not the quality of antibodies is considered a gold standard indicator of immune protection following SARS-CoV 2 infection or vaccination. Our results challenge this notion and recommends change in the current clinical practice.\nC_LI", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Anurag Adhikari", + "author_inst": "UNSW: University of New South Wales" + }, + { + "author_name": "Arunasingam Abayasingam", + "author_inst": "University of New South Wales - Kensington Campus: University of New South Wales" + }, + { + "author_name": "Chaturaka Rodrigo", + "author_inst": "UNSW: University of New South Wales" + }, + { + "author_name": "David Agapiou", + "author_inst": "UNSW: University of New South Wales" + }, + { + "author_name": "Elvis Pandzic", + "author_inst": "UNSW: University of New South Wales" + }, + { + "author_name": "Nicholas A Brasher", + "author_inst": "UNSW: University of New South Wales" + }, + { + "author_name": "Bentotage Samitha Madushan Fernando", + "author_inst": "UNSW: University of New South Wales" + }, + { + "author_name": "Elizabeth Keoshkerian", + "author_inst": "UNSW: University of New South Wales" + }, + { + "author_name": "Hui Li", + "author_inst": "UNSW: University of New South Wales" + }, + { + "author_name": "Ha Na Kim", + "author_inst": "UNSW: University of New South Wales" + }, + { + "author_name": "Megan Lord", + "author_inst": "UNSW: University of New South Wales" + }, + { + "author_name": "Gordona Popovic", + "author_inst": "UNSW: University of New South Wales" + }, + { + "author_name": "William Rawlinson", + "author_inst": "UNSW: University of New South Wales" + }, + { + "author_name": "Michael Mina", + "author_inst": "Northern Beaches Hospital" + }, + { + "author_name": "Jeffrey J Post", + "author_inst": "Prince of Wales Hospital" + }, + { + "author_name": "Bernard Hudson", + "author_inst": "Royal North Shore Hospital" + }, + { + "author_name": "Nicole Gilroy", + "author_inst": "Westmead Hospital" + }, + { + "author_name": "Adam W. Bartlett", + "author_inst": "UNSW Medicne Kirby Institute: The Kirby Institute" + }, + { + "author_name": "Golo Ahlenstiel", + "author_inst": "Blacktown & Mount Druitt Hospital" + }, + { + "author_name": "Branka Grubor-Bauk", + "author_inst": "University of Adelaide School of Medical Sciences: The University of Adelaide Adelaide Medical School" + }, + { + "author_name": "Dominic Dwyer", + "author_inst": "Westmead Hospital" + }, + { + "author_name": "Pamela Konecny", + "author_inst": "UNSW: University of New South Wales" + }, + { + "author_name": "Andrew R Lloyd", + "author_inst": "UNSW Medicne Kirby Institute: The Kirby Institute" + }, + { + "author_name": "Marianne Martinello", + "author_inst": "UNSW: University of New South Wales" + }, + { + "author_name": "Rowena A Bull", + "author_inst": "UNSW: University of New South Wales" + }, + { + "author_name": "Nicodemus Tedla", + "author_inst": "The University of New South Wales" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.12.20.473557", "rel_title": "mRNA-1273 and BNT162b2 mRNA vaccines have reduced neutralizing activity against the SARS-CoV-2 Omicron variant", @@ -450349,61 +452267,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.12.20.21268034", - "rel_title": "Binding and Neutralizing Antibody Responses to SARS-CoV-2 in Infants and Young Children Exceed Those in Adults", - "rel_date": "2021-12-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.20.21268034", - "rel_abs": "SARS-CoV-2 infections are frequently milder in children than adults, suggesting that immune responses may vary with age. However, information is limited regarding SARS-CoV-2 immune responses in young children. We compared Receptor Binding Domain binding antibody (RBDAb) and SARS-CoV-2 neutralizing antibody (neutAb) in children aged 0-4 years, 5-17 years, and in adults aged 18-62 years in a SARS-CoV-2 household study. Among 55 participants seropositive at enrollment, children aged 0-4 years had >10-fold higher RBDAb titers than adults (373 vs.35, P<0.0001), and the highest RBDAb titers in 11/12 households with seropositive children and adults. Children aged 0-4 years had 2-fold higher neutAb than adults, resulting in higher binding to neutralizing (B/N)Ab ratios compared to adults (1.9 vs. 0.4 for ID50, P=0.0002). Findings suggest that young children mount robust antibody responses to SARS-CoV-2 following community infections. Additionally, these results support using neutAb to measure the immunogenicity of COVID-19 vaccines in children aged 0-4 years.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Ruth A. Karron", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Maria Garcia Quesada", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Elizabeth A. Schappell", - "author_inst": "JohnsHopkins Bloomberg School of Public Health" - }, - { - "author_name": "Stephen D. Schmidt", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD" - }, - { - "author_name": "Maria Deloria Knoll", - "author_inst": "Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD" - }, - { - "author_name": "Marissa K. Hetrich", - "author_inst": "Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD" - }, - { - "author_name": "Vic Veguilla", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Nicole Doria-Rose", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health" - }, - { - "author_name": "Fatimah S. Dawood", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "- SEARCh Study Team", - "author_inst": "-" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.10.21267485", "rel_title": "Randomized Controlled Trial of Early Outpatient COVID-19 Treatment with High-Titer Convalescent Plasma", @@ -451535,6 +453398,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2021.12.19.21268073", + "rel_title": "SARS-CoV-2 transmission dynamics in South Africa and epidemiological characteristics of the Omicron variant", + "rel_date": "2021-12-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.19.21268073", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) have been key drivers of new coronavirus disease 2019 (COVID-19) pandemic waves. To better understand variant epidemiologic characteristics, here we apply a model-inference system to reconstruct SARS-CoV-2 transmission dynamics in South Africa, a country that has experienced three VOC pandemic waves (i.e. Beta, Delta, and Omicron). We estimate key epidemiologic quantities in each of the nine South African provinces during March 2020 - Feb 2022, while accounting for changing detection rates, infection seasonality, nonpharmaceutical interventions, and vaccination. Model validation shows that estimated underlying infection rates and key parameters (e.g., infection-detection rate and infection-fatality risk) are in line with independent epidemiological data and investigations. In addition, retrospective predictions capture pandemic trajectories beyond the model training period. These detailed, validated model-inference estimates thus enable quantification of both the immune erosion potential and transmissibility of three major SARS-CoV-2 VOCs, i.e., Beta, Delta, and Omicron. These findings help elucidate changing COVID-19 dynamics and inform future public health planning.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Wan Yang", + "author_inst": "Columbia University" + }, + { + "author_name": "Jeffrey Shaman", + "author_inst": "Columbia University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.12.21.21268077", "rel_title": "Quantitative detection of SARS-CoV-2 Omicron variant in wastewater through allele-specific RT-qPCR", @@ -452586,193 +454472,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hiv aids" }, - { - "rel_doi": "10.1101/2021.12.20.21268098", - "rel_title": "Therapies for Long COVID in non-hospitalised individuals - from symptoms, patient-reported outcomes, and immunology to targeted therapies (The TLC Study): Study protocol", - "rel_date": "2021-12-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.20.21268098", - "rel_abs": "IntroductionIndividuals with COVID-19 frequently experience symptoms and impaired quality of life beyond 4-12 weeks, commonly referred to as Long COVID. Whether Long COVID is one or several distinct syndromes is unknown. Establishing the evidence base for appropriate therapies is needed. We aim to evaluate the symptom burden and underlying pathophysiology of Long COVID syndromes in non-hospitalised individuals and evaluate potential therapies.\n\nMethods and analysisA cohort of 4000 non-hospitalised individuals with a past COVID-19 diagnosis and 1000 matched controls will be selected from anonymised primary care records from the Clinical Practice Research Datalink (CPRD) and invited by their general practitioners to participate on a digital platform (Atom5). Individuals will report symptoms, quality of life, work capability, and patient reported outcome measures. Data will be collected monthly for one year.\n\nStatistical clustering methods will be used to identify distinct Long COVID symptom clusters. Individuals from the four most prevalent clusters and two control groups will be invited to participate in the BioWear sub-study which will further phenotype Long COVID symptom clusters by measurement of immunological parameters and actigraphy.\n\nWe will review existing evidence on interventions for post-viral syndromes and Long COVID to map and prioritise interventions for each newly characterised Long COVID syndrome. Recommendations will be made using the cumulated evidence in an expert consensus workshop. A virtual supportive intervention will be coproduced with patients and health service providers for future evaluation.\n\nIndividuals with lived experience of Long COVID will be involved throughout this programme through a patient and public involvement group.\n\nEthics and disseminationEthical approval was obtained from the Solihull Research Ethics Committee, West Midlands (21/WM/0203). The study is registered on the ISRCTN Registry (1567490). Research findings will be presented at international conferences, in peer-reviewed journals, to Long COVID patient support groups and to policymakers.\n\nArticle SummaryO_ST_ABSStrengths and limitations of the studyC_ST_ABSO_LIThe study will generate a nationally representative cohort of individuals with Long COVID recruited from primary care.\nC_LIO_LIWe will recruit controls matched on a wide range of demographic and clinical factors to assess differences in symptoms between people with Long COVID and similar individuals without a history of COVID-19.\nC_LIO_LIWe will use a newly developed electronic patient reported outcome measure (Symptom Burden Questionnaire) for Long COVID to comprehensively assess a wide range of symptoms highlighted by existing literature, patients, and clinicians.\nC_LIO_LIImmunological, proteomic, genetic, and wearable data captured in the study will allow deep phenotyping of Long COVID syndromes to help better target therapies.\nC_LIO_LIA limitation is that a significant proportion of non-hospitalised individuals affected by COVID-19 in the first wave of the pandemic will lack confirmatory testing and will be excluded from recruitment to the study.\nC_LI", - "rel_num_authors": 43, - "rel_authors": [ - { - "author_name": "Shamil Haroon", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Krishnarajah Nirantharakumar", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Sarah Hughes", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Anuradhaa Subramanian", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Olalekan Lee Aiyegbusi", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Elin Haf Davies", - "author_inst": "Aparito" - }, - { - "author_name": "Puja Myles", - "author_inst": "Medicines and Healthcare Products Regulatory Agency" - }, - { - "author_name": "Tim Williams", - "author_inst": "Medicines and Healthcare Products Regulatory Agency" - }, - { - "author_name": "Grace Turner", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Joht Singh Chandan", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Christel McMullan", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Janet Lord", - "author_inst": "University of Birmingham" - }, - { - "author_name": "David Wraith", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Kirsty McGee", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Alastair Denniston", - "author_inst": "University Hospitals Birmingham NHS Foundation Trust" - }, - { - "author_name": "Tom Taverner", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Louise Jackson", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Elizabeth Sapey", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Georgios Gkoutos", - "author_inst": "University ofBirmingham" - }, - { - "author_name": "Krishna Gokhale", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Edward Leggett", - "author_inst": "Medicines and Healthcare Products Regulatory Agency" - }, - { - "author_name": "Clare Iles", - "author_inst": "Medicines and Healthcare Products Regulatory Agency" - }, - { - "author_name": "Christopher Frost", - "author_inst": "Aparito" - }, - { - "author_name": "Gary McNamara", - "author_inst": "Aparito" - }, - { - "author_name": "Amy Bamford", - "author_inst": "University Hospitals Birmingham NHS Foundation Trust" - }, - { - "author_name": "Tom Marshall", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Dawit Zemedikun", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Gary Price", - "author_inst": "N/A" - }, - { - "author_name": "Steven Marwaha", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Nikita Simms-Williams", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Kirsty Brown", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Anita Walker", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Karen Jones", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Karen Matthews", - "author_inst": "Not applicable" - }, - { - "author_name": "Jennifer Camaradou", - "author_inst": "Not applicable" - }, - { - "author_name": "Michael Saint-Cricq", - "author_inst": "Not applicable" - }, - { - "author_name": "Sumita Kumar", - "author_inst": "Not applicable" - }, - { - "author_name": "Yvonne Alder", - "author_inst": "Not applicable" - }, - { - "author_name": "David Stanton", - "author_inst": "Not applicable" - }, - { - "author_name": "Lisa Agyen", - "author_inst": "Not applicable" - }, - { - "author_name": "Megan Baber", - "author_inst": "Not applicable" - }, - { - "author_name": "Hannah Blaize", - "author_inst": "Not applicable" - }, - { - "author_name": "Melanie Calvert", - "author_inst": "University ofBirmingham" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.19.21268078", "rel_title": "Real-world clinical outcomes of treatment with casirivimab-imdevimab among patients with mild-to-moderate coronavirus disease 2019 during the Delta variant pandemic", @@ -453504,6 +455203,129 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.12.20.21267967", + "rel_title": "Safety of the single-dose Ad26.CoV2.S vaccine among healthcare workers in the phase 3b Sisonke study in South Africa", + "rel_date": "2021-12-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.20.21267967", + "rel_abs": "BackgroundThe Sisonke open-label phase 3b implementation study aimed to assess the safety and effectiveness of the Janssen Ad26.CoV2.S vaccine among health care workers (HCWs) in South Africa. Here, we present the safety data.\n\nMethodsWe monitored adverse events (AEs) at vaccination sites, through self-reporting triggered by text messages after vaccination, health care provider reports and by active case finding. The frequency and incidence rate of non-serious and serious AEs were evaluated from day of first vaccination (17 February 2021) until 28 days after the final vaccination (15 June 2021). COVID-19 breakthrough infections, hospitalisations and deaths were ascertained via linkage of the electronic vaccination register with existing national databases.\n\nFindingsOf 477,234 participants, 10,279 (2.2%) reported AEs, of which 139 (1.4%) were serious. Women reported more AEs than men (2.3% vs. 1.6%). AE reports decreased with increasing age (3.2% for 18-30, 2.1% for 31-45, 1.8% for 46-55 and 1.5% in >55-year-olds). Participants with previous COVID-19 infection reported slightly more AEs (2.6% vs. 2.1%). The commonest reactogenicity events were headache and body aches, followed by injection site pain and fever, and most occurred within 48 hours of vaccination. Two cases of Thrombosis with Thrombocytopenia Syndrome and four cases of Guillain-Barre Syndrome were reported post-vaccination. Serious AEs and AEs of special interest including vascular and nervous system events, immune system disorders and deaths occurred at lower than the expected population rates.\n\nInterpretationThe single-dose Ad26.CoV2.S vaccine had an acceptable safety profile supporting the continued use of this vaccine in our setting.\n\nFundingFunding was provided by the National Treasury of South Africa, the National Department of Health, Solidarity Response Fund NPC, The Michael & Susan Dell Foundation, The Elma Vaccines and Immunization Foundation - Grant number 21-V0001, and the Bill & Melinda Gates Foundation - grant number INV-030342.", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Simbarashe Takuva", + "author_inst": "School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa" + }, + { + "author_name": "Azwidhwi Takalani", + "author_inst": "Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America" + }, + { + "author_name": "Ishen Seocharan", + "author_inst": "Medical Research Council, Durban, South Africa" + }, + { + "author_name": "Nonhlanhla Yende-Zuma", + "author_inst": "Centre for the AIDS Programme of Research in South Africa, Durban, South Africa" + }, + { + "author_name": "Tarylee Reddy", + "author_inst": "Medical Research Council, Durban, South Africa" + }, + { + "author_name": "Imke Engelbrecht", + "author_inst": "Right to Care, Johannesburg, Gauteng South Africa" + }, + { + "author_name": "Mark Faesen", + "author_inst": "Right to Care, Johannesburg, Gauteng South Africa" + }, + { + "author_name": "Kentse Khuto", + "author_inst": "Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America" + }, + { + "author_name": "Carmen Whyte", + "author_inst": "Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America" + }, + { + "author_name": "Veronique Bailey", + "author_inst": "Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America" + }, + { + "author_name": "Valentina Trivella", + "author_inst": "Right to Care, Johannesburg, Gauteng South Africa" + }, + { + "author_name": "Jonathan Peter", + "author_inst": "Division of Allergy and Clinical Immunology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa" + }, + { + "author_name": "Jessica Opie", + "author_inst": "Division of Haematology, Department of Pathology, Faculty of Health Sciences, University of Cape Town and National Health Laboratory Service, Groote Schuur Hosp" + }, + { + "author_name": "Vernon Louw", + "author_inst": "Division of Clinical Haematology, Department of Medicine, Faculty of Health Sciences, University of Cape Town and Groote Schuur Hospital, Cape Town, South Afric" + }, + { + "author_name": "Pradeep Rowji", + "author_inst": "Milpark Hospital, Johannesburg, South Africa" + }, + { + "author_name": "Barry Jacobson", + "author_inst": "Department of Molecular Medicine and Haematology, Charlotte Maxeke Johannesburg Academic Hospital National Health Laboratory System Complex, University of Witwa" + }, + { + "author_name": "Pamela Groenewald", + "author_inst": "Burden of Disease Research Unit, Medical Research Council of South Africa, South Africa" + }, + { + "author_name": "Rob E. Dorrington", + "author_inst": "Centre for Actuarial Research, Faculty of Commerce, University of Cape Town, South Africa" + }, + { + "author_name": "Ria Laubscher", + "author_inst": "Medical Research Council, Durban, South Africa" + }, + { + "author_name": "Debbie Bradshaw", + "author_inst": "Burden of Disease Research Unit, Medical Research Council of South Africa, South Africa" + }, + { + "author_name": "Harry Moultrie", + "author_inst": "National Institutes for Communicable Diseases, National Health Laboratory Service, Sandringham, South Africa" + }, + { + "author_name": "Lara Fairall", + "author_inst": "Knowledge Translation Unit, University of Cape Town Lung Institute, Department of Medicine, University of Cape Town, Cape Town" + }, + { + "author_name": "Ian Sanne", + "author_inst": "Right to Care, Johannesburg, Gauteng South Africa" + }, + { + "author_name": "Linda Gail-Bekker", + "author_inst": "Desmond Tutu HIV Centre, University of Cape Town, Cape Town, South Africa" + }, + { + "author_name": "Glenda Gray", + "author_inst": "South African Medical Research Council, Cape Town, South Africa" + }, + { + "author_name": "Ameena Goga", + "author_inst": "HIV Prevention Research Unit, South African Medical Research Council, Tygerberg, South Africa" + }, + { + "author_name": "Nigel Garrett", + "author_inst": "Centre for the AIDS Programme of Research in South Africa, Durban, South Africa" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.12.20.21267832", "rel_title": "PREVALENCE AND PREDICTORS OF STRESS AMONG COVID 19 HEALTH WORKERS IN KABWE DISTRICT: A CROSS SECTIONAL STUDY", @@ -454652,81 +456474,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.12.16.472982", - "rel_title": "Changes of small non-coding RNAs by severe acute respiratory syndrome coronavirus 2 infection", - "rel_date": "2021-12-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.16.472982", - "rel_abs": "The ongoing pandemic of coronavirus disease 2019 (COVID-19), which results from the rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a significant global public health threat, with molecular mechanisms underlying its pathogenesis largely unknown. Small non-coding RNAs (sncRNAs) are known to play important roles in almost all biological processes. In the context of viral infections, sncRNAs have been shown to regulate the host responses, viral replication, and host-virus interaction. Compared with other subfamilies of sncRNAs, including microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), tRNA-derived RNA fragments (tRFs) are relatively new and emerge as a significant regulator of host-virus interactions. Using T4 PNK-RNA-seq, a modified next-generation sequencing (NGS), we recently found that nasopharyngeal swabs (NPS) samples from SARS-CoV-2 positive and negative subjects show a significant difference in sncRNA profiles. There are about 166 SARS-CoV-2-impacted sncRNAs. Among them, tRFs are the most significantly affected and almost all impacted tRFs are derived from the 5-end of tRNAs (tRF5). Using a modified qRT-PCR, which was recently developed to specifically quantify tRF5s by isolating the tRF signals from its corresponding parent tRNA signals, we validated that tRF5s derived from tRNA GluCTC (tRF5-GluCTC), LysCTT (tRF5-LysCTT), ValCAC (tRF5-ValCAC), CysGCA (tRF5-CysGCA) and GlnCTG (tRF5-GlnCTG) are enhanced in NPS samples of SARS-CoV2 patients and SARS-CoV2-infected airway epithelial cells. In addition to host-derived ncRNAs, we also identified several sncRNAs derived from the virus (svRNAs), among which a svRNA derived from CoV2 genomic site 346 to 382 (sv-CoV2-346) has the highest expression. The induction of both tRFs and sv-CoV2-346 has not been reported previously, as the lack of the 3-OH ends of these sncRNAs prevents them to be detected by routine NGS. In summary, our studies demonstrated the involvement of tRFs in COVID-19 and revealed new CoV2 svRNAs.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Wenzhe Wu", - "author_inst": "The University of Texas Medical Branch" - }, - { - "author_name": "Eun-Jin Choi", - "author_inst": "The University of Texas Medical Branch" - }, - { - "author_name": "Binbin Wang", - "author_inst": "The University of Texas Medical Branch" - }, - { - "author_name": "Ke Zhang", - "author_inst": "The University of Texas Medical Branch" - }, - { - "author_name": "Awadalkareem Adam", - "author_inst": "The University of Texas Medical Branch" - }, - { - "author_name": "Gengming Huang", - "author_inst": "The University of Texas Medical Branch" - }, - { - "author_name": "Leo Tunkle", - "author_inst": "University of Michigan" - }, - { - "author_name": "Philip Huang", - "author_inst": "University of Michigan" - }, - { - "author_name": "Rohit Goru", - "author_inst": "University of Michigan" - }, - { - "author_name": "Isabella Imirowicz", - "author_inst": "University of Michigan" - }, - { - "author_name": "Leanne Henry", - "author_inst": "University of Michigan" - }, - { - "author_name": "Inhan Lee", - "author_inst": "miRcore , Ann Arbor, MI, 48105, USA" - }, - { - "author_name": "Jianli Dong", - "author_inst": "The University of Texas Medical Branch" - }, - { - "author_name": "Tian Wang", - "author_inst": "The University of Texas Medical Branch" - }, - { - "author_name": "Xiaoyong Bao", - "author_inst": "The University of Texas Medical Branch" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.12.16.472934", "rel_title": "Neutralization and Stability of SARS-CoV-2 Omicron Variant", @@ -455518,6 +457265,109 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.12.16.472155", + "rel_title": "Vandetanib Reduces Inflammatory Cytokines and Ameliorates COVID-19 in Infected Mice", + "rel_date": "2021-12-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.16.472155", + "rel_abs": "The portfolio of SARS-CoV-2 small molecule drugs is currently limited to a handful that are either approved (remdesivir), emergency approved (dexamethasone, baricitinib) or in advanced clinical trials. We have tested 45 FDA-approved kinase inhibitors in vitro against murine hepatitis virus (MHV) as a model of SARS-CoV-2 replication and identified 12 showing inhibition in the delayed brain tumor (DBT) cell line. Vandetanib, which targets the vascular endothelial growth factor receptor (VEGFR), the epidermal growth factor receptor (EGFR), and the RET-tyrosine kinase showed the most promising results on inhibition versus toxic effect on SARS-CoV-2-infected Caco-2 and A549-hACE2 cells (IC50 0.79 M) while also showing a reduction of > 3 log TCID50/mL for HCoV-229E. The in vivo efficacy of vandetanib was assessed in a mouse model of SARS-CoV-2 infection and statistically significantly reduced the levels of IL-6, IL-10, TNF-, and mitigated inflammatory cell infiltrates in the lungs of infected animals but did not reduce viral load.\n\nVandetanib rescued the decreased IFN-1{beta} caused by SARS-CoV-2 infection in mice to levels similar to that in uninfected animals. Our results indicate that the FDA-approved vandetanib is a potential therapeutic candidate for COVID-19 positioned for follow up in clinical trials either alone or in combination with other drugs to address the cytokine storm associated with this viral infection.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Ana C. Puhl", + "author_inst": "Collaborations Pharmaceuticals" + }, + { + "author_name": "Giovanni F. Gomes", + "author_inst": "Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo, Brazil." + }, + { + "author_name": "Samara Damasceno", + "author_inst": "Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo Preto, Brazil." + }, + { + "author_name": "Ethan J. Fritch", + "author_inst": "Department of Microbiology and Immunology, University of North Carolina School of Medicine" + }, + { + "author_name": "James A. Levi", + "author_inst": "Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA." + }, + { + "author_name": "Nicole J. Johnson", + "author_inst": "Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA." + }, + { + "author_name": "Frank Scholle", + "author_inst": "Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA." + }, + { + "author_name": "Lakshmanane Premkumar", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Brett L. Hurst", + "author_inst": "Institute for Antiviral Research, Utah State University, Logan, UT, USA" + }, + { + "author_name": "Felipe LeeMontiel", + "author_inst": "PhenoVista Biosciences, 6195 Cornerstone Ct E. #114 San Diego CA 92121" + }, + { + "author_name": "Flavio P. Veras", + "author_inst": "Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo, Brazil." + }, + { + "author_name": "Sabrina S. Batah", + "author_inst": "Department of Pathology and Legal Medicine, Ribeirao Preto Medical School, University of Sao Paulo, Brazil." + }, + { + "author_name": "Alexandre T. Fabro", + "author_inst": "Department of Pathology and Legal Medicine, Ribeirao Preto Medical School, University of Sao Paulo, Brazil." + }, + { + "author_name": "Nathaniel J. Moorman", + "author_inst": "Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA." + }, + { + "author_name": "Boyd Yount", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Rebekah Dickmander", + "author_inst": "University of North Carolina School of Medicine, Chapel Hill." + }, + { + "author_name": "Ralph S. Baric", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Kenneth H. Pearce", + "author_inst": "University of North Carolina, Chapel Hill, North Carolina, USA" + }, + { + "author_name": "Fernando Cunha", + "author_inst": "Universidade de Sao Paulo Campus de Ribeirao Preto" + }, + { + "author_name": "Jose C. Alves-Filho", + "author_inst": "Ribeirao Preto Medical School, University of Sao Paulo, Brazil." + }, + { + "author_name": "Thiago Cunha", + "author_inst": "Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo, Brazil." + }, + { + "author_name": "Sean Ekins", + "author_inst": "Collaborations Pharmaceuticals, Inc." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.12.16.472880", "rel_title": "Unraveling the antiviral activity of plitidepsin by subcellular and morphological analysis", @@ -456326,77 +458176,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, - { - "rel_doi": "10.1101/2021.12.17.21267942", - "rel_title": "Resource Profile: The Regenstrief Institute COVID-19 Research Data Commons (CoRDaCo)", - "rel_date": "2021-12-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.17.21267942", - "rel_abs": "The primary objective of the COVID-19 Research Data Commons (CoRDaCo) is to provide broad and efficient access to a large corpus of clinical data related to COVID-19 in Indiana, facilitating research and discovery. This curated collection of data elements provides information on a significant portion of COVID-19 positive patients in the State from the beginning of the pandemic, as well as two years of health information prior its onset. CoRDaCo combines data from multiple sources, including clinical data from a large, regional health information exchange, clinical data repositories of two health systems, and state laboratory reporting and vital records, as well as geographic-based social variables. Clinical data cover information such as healthcare encounters, vital measurements, laboratory orders and results, medications, diagnoses, the Charlson Comorbidity Index and Pediatric Early Warning Score, COVID-19 vaccinations, mechanical ventilation, restraint use, intensive care unit and ICU and hospital lengths of stay, and mortality. Interested researchers can visit ridata.org or email askrds@regenstrief.org to discuss access to CoRDaCo.\n\nKey FeaturesO_LICoRDaCo includes patient-level data on diagnosis and treatment, healthcare utilization, outcomes, and demographics. The level of detail available for each patient varies depending on the source of the clinical data.\nC_LIO_LICoRDaCo uses geographic identifiers to link patient-specific data to area-level social factors, such as census variables and social deprivation indices.\nC_LIO_LIAs of 4/30/21, the CoRDaCo cohort consists of over 776,000 cases, including granular data on over 15,000 patients who were admitted to an intensive care unit, and over 1,362,000 COVID-19-negative controls. Data is currently refreshed two times per month.\nC_LIO_LIThe most prevalent comorbidities in the data set include hypertension, diabetes, chronic pulmonary disease, renal disease, cancer, and congestive heart failure.\nC_LI", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Katie S. Allen", - "author_inst": "Regenstrief Institute" - }, - { - "author_name": "Nader Zidan", - "author_inst": "Ohio State University" - }, - { - "author_name": "Vishal Dey", - "author_inst": "Ohio State University" - }, - { - "author_name": "Eneida Mendonca", - "author_inst": "Regenstrief Institute" - }, - { - "author_name": "Shaun Grannis", - "author_inst": "Regenstrief Institute" - }, - { - "author_name": "Suranga Kasturi", - "author_inst": "Regenstrief Institute" - }, - { - "author_name": "Babar Khan", - "author_inst": "Regenstrief Institute" - }, - { - "author_name": "Sarah R. Zappone", - "author_inst": "Regenstrief Institute" - }, - { - "author_name": "David Haggstrom", - "author_inst": "Regenstrief Institute" - }, - { - "author_name": "Laura Ruppert", - "author_inst": "Regenstrief Institute" - }, - { - "author_name": "Titus Schleyer", - "author_inst": "Regenstrief Institute" - }, - { - "author_name": "Xia Ning", - "author_inst": "Ohio State University" - }, - { - "author_name": "Peter Embi", - "author_inst": "Vanderbilt University" - }, - { - "author_name": "Umberto Tachinardi", - "author_inst": "Regenstrief Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2021.12.18.21268024", "rel_title": "Vaccine efficacy for COVID-19 outbreak in New York City", @@ -457124,6 +458903,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.15.21267799", + "rel_title": "Vaccines provide disproportional protection to the increased hospitalisation risk posed by the Delta variant of SARS-CoV2: a meta-analysis", + "rel_date": "2021-12-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.15.21267799", + "rel_abs": "Variants of SARS-CoV2 that achieved global dominance (Alpha and Delta) have been associated with increased hospitalisation risk. A quantification of this risk across studies is currently lacking for Delta. Furthermore, how risk for severe disease changes in both vaccinated and unvaccinated individuals is important as the underlying risks determine public health impact. The surplus risk of Delta versus Alpha on hospitalisation was determined using random-effects meta-analysis. Infection with the Delta compared to the Alpha variant increased hospitalisation risk (unvaccinated: log HR 0.62, CI: 0.41 - 0.84, P < 0.0001; linear HR 1.87). This finding should inform our response to future variants of concern, currently Omicron. SARS-CoV2 variants that achieve dominance, have achieved this through a higher rate of infection and this evolutionary trajectory has also come with a correlated higher risk of severe disease. The surplus risk posed by Delta was significantly lower however in the vaccinated (model estimate -0.40, CI: -0.73 - -0.07, P = 0.017). Vaccination thus provided a disproportionate level of protection to hospitalisation with the Delta variant and provides further rationale for vaccination for SARS-CoV2 as a durable public health measure.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Mirre J P Simons", + "author_inst": "University of Sheffield" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.12.17.21267980", "rel_title": "How effective is vaccination protection?", @@ -458504,85 +460302,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.12.17.21267993", - "rel_title": "Predictive value of isolated symptoms for diagnosis of SARS-CoV-2 infection in children tested during peak circulation of the delta variant", - "rel_date": "2021-12-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.17.21267993", - "rel_abs": "BackgroundCOVID-19 testing policies for symptomatic children attending U.S. schools or daycare vary, and whether isolated symptoms should prompt testing is unclear. We evaluated children presenting for SARS-CoV-2 testing to determine if the likelihood of having a positive SARS-CoV-2 test differed between participants with one versus [≥]2 symptoms, and to examine the predictive capability of isolated symptoms.\n\nMethodsParticipants [≤] 18 years presenting for clinical SARS-CoV-2 molecular testing in six sites in urban/suburban/rural Georgia (July-October, 2021; delta variant predominant) were queried about individual symptoms. Participants were classified into three groups: asymptomatic, one symptom only, or [≥]2 symptoms. SARS-CoV-2 test results and clinical characteristics of the three groups were compared. Sensitivity, specificity, and positive/negative predictive values (PPV/NPV) for isolated symptoms were calculated by fitting a saturated Poisson model.\n\nResultsOf 602 participants, 21.8% tested positive and 48.7% had a known or suspected close contact. Children reporting one symptom (n=82; OR=6.00, 95% CI: 2.70-13.33) and children reporting [≥]2 symptoms (n=365; OR=5.25: 2.66-10.38) were significantly more likely to have a positive COVID-19 test than asymptomatic children (n=155), but they were not significantly different from each other (OR=0.88: 0.52-1.49). Sensitivity/PPV were highest for isolated fever (33%/57%), cough (25%/32%), and sore throat (21%/45%); headache had low sensitivity (8%) but higher PPV (33%). Sensitivity/PPV of isolated congestion/rhinorrhea were 8%/9%.\n\nConclusionsWith high delta variant prevalence, children with isolated symptoms were as likely as those with multiple symptoms to test positive for COVID-19. Isolated fever, cough, sore throat, or headache, but not congestion/rhinorrhea, offered highest predictive value.\n\nKey pointsIn an area with high community prevalence of the delta variant, children presenting with one symptom were as likely as those with two or more symptoms to test positive for SARS-CoV-2 infection. Isolated symptoms should be considered in testing decisions.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Adrianna L. Westbrook", - "author_inst": "Pediatric Biostatistics Core, Department of Pediatrics, Emory University, Atlanta, GA USA" - }, - { - "author_name": "Laura C. Benedit", - "author_inst": "Department of Clinical Research, Children's Healthcare of Atlanta, Atlanta, GA USA" - }, - { - "author_name": "Jennifer K. Frediani", - "author_inst": "Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA USA" - }, - { - "author_name": "Mark A. Griffiths", - "author_inst": "Children's Healthcare of Atlanta, Atlanta, GA USA; Department of Pediatrics, Emory University School of Medicine, Atlanta, GA USA" - }, - { - "author_name": "Nabeel Y. Khan", - "author_inst": "Department of Pediatrics, Emory University School of Medicine, Atlanta, GA USA" - }, - { - "author_name": "Joshua M. Levy", - "author_inst": "Department of Otolaryngology-HNS, Emory University School of Medicine, Atlanta, GA USA" - }, - { - "author_name": "Claudia R. Morris", - "author_inst": "Department of Pediatrics, Emory University School of Medicine, Atlanta, GA USA; Division of Pediatric Emergency Medicine, Children's Healthcare of Atlanta, Atla" - }, - { - "author_name": "Christina A. Rostad", - "author_inst": "Children's Healthcare of Atlanta, Atlanta, GA USA; Department of Pediatrics, Emory University School of Medicine, Atlanta, GA USA" - }, - { - "author_name": "Cheryl L. Stone", - "author_inst": "Department of Clinical Research, Children's Healthcare of Atlanta, Atlanta, GA USA" - }, - { - "author_name": "Julie Sullivan", - "author_inst": "Department of Pediatrics, Emory University School of Medicine, Atlanta, GA USA" - }, - { - "author_name": "Miriam B. Vos", - "author_inst": "Children's Healthcare of Atlanta, Atlanta, GA USA; Department of Pediatrics, Emory University School of Medicine, Atlanta, GA USA" - }, - { - "author_name": "Jean Welsh", - "author_inst": "Children's Healthcare of Atlanta, Atlanta, GA USA; Department of Pediatrics, Emory University School of Medicine, Atlanta, GA USA" - }, - { - "author_name": "Anna Wood", - "author_inst": "Pediatric Biostatistics Core, Department of Pediatrics, Emory University, Atlanta, GA USA" - }, - { - "author_name": "Greg S. Martin", - "author_inst": "Department of Medicine, Emory University School of Medicine, Atlanta, GA USA" - }, - { - "author_name": "Wilbur Lam", - "author_inst": "Department of Pediatrics, Emory University School of Medicine; Aflac Cancer and Blood Disorders Center of Children's Healthcare of Atlanta; Wallace H. Coulter D" - }, - { - "author_name": "Nira R. Pollock", - "author_inst": "Department of Laboratory Medicine, Boston Children's Hospital, Boston, MA USA" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.17.21267350", "rel_title": "Risk of SARS-CoV-2 testing, PCR-confirmed infections and COVID-19-related hospital admissions in children and young people: birth cohort study", @@ -459318,6 +461037,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.12.15.21267858", + "rel_title": "Projected epidemiological consequences of the Omicron SARS-CoV-2 variant in England, December 2021 to April 2022", + "rel_date": "2021-12-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.15.21267858", + "rel_abs": "The Omicron B.1.1.529 SARS-CoV-2 variant was first detected in late November 2021 and has since spread to multiple countries worldwide. We model the potential consequences of the Omicron variant on SARS-CoV-2 transmission and health outcomes in England between December 2021 and April 2022, using a deterministic compartmental model fitted to epidemiological data from March 2020 onwards. Because of uncertainty around the characteristics of Omicron, we explore scenarios varying the extent of Omicrons immune escape and the effectiveness of COVID-19 booster vaccinations against Omicron, assuming the level of Omicrons transmissibility relative to Delta to match the growth in observed S gene target failure data in England. We consider strategies for the re-introduction of control measures in response to projected surges in transmission, as well as scenarios varying the uptake and speed of COVID-19 booster vaccinations and the rate of Omicrons introduction into the population. These results suggest that Omicron has the potential to cause substantial surges in cases, hospital admissions and deaths in populations with high levels of immunity, including England. The reintroduction of additional non-pharmaceutical interventions may be required to prevent hospital admissions exceeding the levels seen in England during the previous peak in winter 2020-2021.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Rosanna C Barnard", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Nicholas G Davies", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Carl A B Pearson", + "author_inst": "London School of Hygiene & Tropical Medicine; Stellenbosch University" + }, + { + "author_name": "Mark Jit", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "W John Edmunds", + "author_inst": "London School of Hygiene & Tropical Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.12.15.21267860", "rel_title": "The impact of COVID-19 restrictions on older adults' loneliness: Evidence from high-frequency panel data", @@ -460194,33 +461948,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.12.15.472466", - "rel_title": "Enrichment analysis on regulatory subspaces: a novel direction for the superior description of cellular responses to SARS-CoV-2", - "rel_date": "2021-12-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.15.472466", - "rel_abs": "StatementThe enrichment analysis of discriminative cell transcriptional responses to SARS-CoV-2 infection using biclustering produces a broader set of superiorly enriched GO terms and KEGG pathways against alternative state-of-the-art machine learning approaches, unraveling novel knowledge.\n\nMotivation and methodsThe comprehensive understanding of the impacts of the SARS-CoV-2 virus on infected cells is still incomplete. This work identifies and analyses the main cell regulatory processes affected and induced by SARS-CoV-2, using transcriptomic data from several infectable cell lines available in public databases and in vivo samples. We propose a new class of statistical models to handle three major challenges, namely the scarcity of observations, the high dimensionality of the data, and the complexity of the interactions between genes. Additionally, we analyse the function of these genes and their interactions within cells to compare them to ones affected by IAV (H1N1), RSV and HPIV3 in the target cell lines.\n\nResultsGathered results show that, although clustering and predictive algorithms aid classic functional enrichment analysis, recent pattern-based biclustering algorithms significantly improve the number and quality of the detected biological processes. Additionally, a comparative analysis of these processes is performed to identify potential pathophysiological characteristics of COVID-19. These are further compared to those identified by other authors for the same virus as well as related ones such as SARS-CoV-1. This approach is particularly relevant due to a lack of other works utilizing more complex machine learning tools within this context.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Pedro P. Rodrigues", - "author_inst": "IDMEC and INESC-ID, Instituto Superior Tecnico, Universidade de Lisboa" - }, - { - "author_name": "Rafael S. Costa", - "author_inst": "LAQV-REQUIMTE, DQ, NOVA School of Science and Technology" - }, - { - "author_name": "Rui Henriques", - "author_inst": "INESC-ID and Instituto Superior Tecnico, Universidade de Lisboa" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.12.15.472619", "rel_title": "Transcriptomic responses of the human kidney to acute injury at single cell resolution", @@ -461388,6 +463115,69 @@ "type": "confirmatory results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2021.12.14.472725", + "rel_title": "Long-read RNA sequencing identifies polyadenylation elongation and differential transcript usage of host transcripts during SARS-CoV-2 in vitro infection", + "rel_date": "2021-12-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.14.472725", + "rel_abs": "Better methods to interrogate host-pathogen interactions during Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infections are imperative to help understand and prevent this disease. Here we implemented RNA-sequencing (RNA-seq) combined with the Oxford Nanopore Technologies (ONT) long-reads to measure differential host gene expression, transcript polyadenylation and isoform usage within various epithelial cell lines permissive and non-permissive for SARS-CoV-2 infection. SARS-CoV-2-infected and mock-infected Vero (African green monkey kidney epithelial cells), Calu-3 (human lung adenocarcinoma epithelial cells), Caco-2 (human colorectal adenocarcinoma epithelial cells) and A549 (human lung carcinoma epithelial cells) were analysed over time (0, 2, 24, 48 hours). Differential polyadenylation was found to occur in both infected Calu-3 and Vero cells during a late time point (48 hpi), with Gene Ontology (GO) terms such as viral transcription and translation shown to be significantly enriched in Calu-3 data. Poly(A) tails showed increased lengths in the majority of the differentially polyadenylated transcripts in Calu-3 and Vero cell lines (up to ~136 nt in mean poly(A) length, padj = 0.029). Of these genes, ribosomal protein genes such as RPS4X and RPS6 also showed downregulation in expression levels, suggesting the importance of ribosomal protein genes during infection. Furthermore, differential transcript usage was identified in Caco-2, Calu-3 and Vero cells, including transcripts of genes such as GSDMB and KPNA2, which have previously been implicated in SARS-CoV-2 infections. Overall, these results highlight the potential role of differential polyadenylation and transcript usage in host immune response or viral manipulation of host mechanisms during infection, and therefore, showcase the value of long-read sequencing in identifying less-explored host responses to disease.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Jessie J-Y Chang", + "author_inst": "The University of Melbourne at The Peter Doherty Institute for Infection and Immunity" + }, + { + "author_name": "Josie Gleeson", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Daniel Rawlinson", + "author_inst": "The University of Melbourne at The Peter Doherty Institute for Infection and Immunity" + }, + { + "author_name": "Miranda E Pitt", + "author_inst": "The University of Melbourne at The Peter Doherty Institute for Infection and Immunity" + }, + { + "author_name": "Ricardo De Paoli-Iseppi", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Chenxi Zhou", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Francesca L Mordant", + "author_inst": "The University of Melbourne at The Peter Doherty Institute for Infection and Immunity" + }, + { + "author_name": "Sarah L Londrigan", + "author_inst": "The University of Melbourne at The Peter Doherty Institute for Infection and Immunity" + }, + { + "author_name": "Michael B Clark", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Kanta Subbarao", + "author_inst": "The University of Melbourne at The Peter Doherty Institute for Infection and Immunity" + }, + { + "author_name": "Timothy P Stinear", + "author_inst": "University of Melbourne at The Peter Doherty Institute for Infection and Immunity" + }, + { + "author_name": "Lachlan J M Coin", + "author_inst": "The University of Melbourne at The Peter Doherty Institute for Infection and Immunity" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.12.14.472614", "rel_title": "Viral infection engenders bona fide and bystander lung memory B cell subsets through permissive selection", @@ -462515,65 +464305,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.14.21267696", - "rel_title": "Impact Of an Immune Modulator Mycobacterium-w On Adaptive Natural Killer Cells and Protection Against COVID-19", - "rel_date": "2021-12-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.14.21267696", - "rel_abs": "The kinetics of NKG2C+ adaptive natural killer (ANK) cells and NKG2A+inhibitory NK (iNK) cells with respect to the incidence of SARS-CoV-2 infection were studied for 6 months in a cohort of health-care workers following administration of heat killed Mycobacterium w (Mw group) in comparison to a control group. In both groups, COVID-19 correlated with a lower NKG2C+ANK cells at baseline. There was a significant upregulation of NKG2C expression and IFN-{gamma} release in Mw group (p=0.0009), particularly in those with lower baseline NKG2C expression, along with downregulation of iNK cells (p<0.0001). This translated to a significant reduction in incidence and severity of COVID-19 in the Mw group (IRR-0.15, p=0.0004). RNA-seq analysis at 6 months showed an upregulation of ANK pathway genes and an enhanced ANK mediated ADCC signature. Thus, Mw was observed to have a salutary impact on the ANK cell profile and a long-term upregulation of ANK-ADCC pathways, which could have provided protection against COVID-19 in a non-immune high-risk population.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Sarita Rani Jaiswal", - "author_inst": "Manashi Chakrabarti Foundation, New Delhi and Dharamshila Narayana Superspeciality Hospital Research and Development, New Delhi." - }, - { - "author_name": "Jaganath Arunachalam", - "author_inst": "Manashi Chakrabarti Foundation, New Delhi" - }, - { - "author_name": "Ashraf Saifullah", - "author_inst": "Dharamshila Narayana Superspeciality Hospital Research and Development, New Delhi" - }, - { - "author_name": "Dhanir Tailor", - "author_inst": "Development & Cancer Biology and Center for Experimental Therapeutics, Knight Cancer Institute, Oregon Health & Science University, Portland, USA" - }, - { - "author_name": "Rohit Lakhchaura", - "author_inst": "Dharamshila Narayana Superspeciality Hospital Research and Development, New Delhi" - }, - { - "author_name": "Anupama Mehta", - "author_inst": "Dharamshila Narayana Superspeciality Hospital Research and Development." - }, - { - "author_name": "Gitali Bhagawati", - "author_inst": "Dharamshila Narayana Superspeciality Hospital Research and Development." - }, - { - "author_name": "Hemamalini Aiyer", - "author_inst": "Dharamshila Narayana Superspeciality Hospital Research and Development, New Delhi" - }, - { - "author_name": "Bakulesh M Khamar", - "author_inst": "Cadila Pharmaceuticals Limited" - }, - { - "author_name": "Sanjay Malhotra", - "author_inst": "Development & Cancer Biology and Center for Experimental Therapeutics, Knight Cancer Institute, Oregon Health & Science University, Portland, USA" - }, - { - "author_name": "Suparno Chakrabarti", - "author_inst": "Manashi Chakrabarti Foundation" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.15.21267816", "rel_title": "COVID-19 and Indian population: a comparative genetic analysis", @@ -463729,6 +465460,129 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.12.14.21267615", + "rel_title": "Effectiveness of COVID-19 vaccines against the Omicron (B.1.1.529) variant of concern", + "rel_date": "2021-12-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.14.21267615", + "rel_abs": "BackgroundA rapid increase in cases due to the SARS-CoV-2 Omicron (B.1.1.529) variant in highly vaccinated populations has raised concerns about the effectiveness of current vaccines.\n\nMethodsWe used a test-negative case-control design to estimate vaccine effectiveness (VE) against symptomatic disease caused by the Omicron and Delta variants in England. VE was calculated after primary immunisation with two BNT162b2 or ChAdOx1 doses, and at 2+ weeks following a BNT162b2 booster.\n\nResultsBetween 27 November and 06 December 2021, 581 and 56,439 eligible Omicron and Delta cases respectively were identified. There were 130,867 eligible test-negative controls. There was no effect against Omicron from 15 weeks after two ChAdOx1 doses, while VE after two BNT162b2 doses was 88.0% (95%CI: 65.9 to 95.8%) 2-9 weeks after dose 2, dropping to between 34 and 37% from 15 weeks post dose 2.From two weeks after a BNT162b2 booster, VE increased to 71.4% (95%CI: 41.8 to 86.0%) for ChAdOx1 primary course recipients and 75.5% (95%CI: 56.1 to 86.3%) for BNT162b2 primary course recipients.\n\nFor cases with Delta, VE was 41.8% (95%CI: 39.4-44.1%) at 25+ weeks after two ChAdOx1 doses, increasing to 93.8% (95%CI: 93.2-94.3%) after a BNT162b2 booster. With a BNT162b2 primary course, VE was 63.5% (95%CI: 61.4 to 65.5%) 25+ weeks after dose 2, increasing to 92.6% (95%CI: 92.0-93.1%) two weeks after the booster.\n\nConclusionsPrimary immunisation with two BNT162b2 or ChAdOx1 doses provided no or limited protection against symptomatic disease with the Omicron variant. Boosting with BNT162b2 following either primary course significantly increased protection.", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Nick Andrews", + "author_inst": "UK Health Security Agency, London, United Kingdom & NIHR Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Med" + }, + { + "author_name": "Julia Stowe", + "author_inst": "UK Health Security Agency, London, United Kingdom" + }, + { + "author_name": "Freja Kirsebom", + "author_inst": "UK Health Security Agency, London, United Kingdom" + }, + { + "author_name": "Samuel Toffa", + "author_inst": "UK Health Security Agency, London, United Kingdom" + }, + { + "author_name": "Tim Rickeard", + "author_inst": "UK Health Security Agency, London, United Kingdom" + }, + { + "author_name": "Eileen Gallagher", + "author_inst": "UK Health Security Agency, London, United Kingdom" + }, + { + "author_name": "Charlotte Gower", + "author_inst": "UK Health Security Agency, London, United Kingdom" + }, + { + "author_name": "Meaghan Kall", + "author_inst": "UK Health Security Agency, London, United Kingdom" + }, + { + "author_name": "Natalie Groves", + "author_inst": "UK Health Security Agency, London, United Kingdom" + }, + { + "author_name": "Anne-Marie O'Connell", + "author_inst": "UK Health Security Agency, London, United Kingdom" + }, + { + "author_name": "David Simons", + "author_inst": "UK Health Security Agency, London, United Kingdom" + }, + { + "author_name": "Paula B Blomquist", + "author_inst": "UK Health Security Agency, London, United Kingdom" + }, + { + "author_name": "Gavin Dabrera", + "author_inst": "UK Health Security Agency, London, United Kingdom" + }, + { + "author_name": "Richard Myers", + "author_inst": "UK Health Security Agency, London, United Kingdom" + }, + { + "author_name": "Shamez N Ladhani", + "author_inst": "UK Health Security Agency, London, United Kingdom &Paediatric Infectious Diseases Research Group (PIDRG), St George's University of London, London, United Kingd" + }, + { + "author_name": "Gayatri Amirthalingam", + "author_inst": "UK Health Security Agency, London, United Kingdom & NIHR Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Med" + }, + { + "author_name": "Saheer Gharbia", + "author_inst": "UK Health Security Agency, London, United Kingdom" + }, + { + "author_name": "Jeffrey C Barrett", + "author_inst": "Wellcome Sanger Institute, Hinxton, UK" + }, + { + "author_name": "Richard Elson", + "author_inst": "UK Health Security Agency, London, United Kingdom" + }, + { + "author_name": "Neil Ferguson", + "author_inst": "MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK &NIHR Health Protection Research Unit in Respiratory Infections, Imperial" + }, + { + "author_name": "Maria Zambon", + "author_inst": "UK Health Security Agency, London, United Kingdom &NIHR Health Protection Research Unit in Respiratory Infections, Imperial College London, United Kingdom" + }, + { + "author_name": "Colin NJ Campbell", + "author_inst": "UK Health Security Agency, London, United Kingdom & NIHR Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Med" + }, + { + "author_name": "Kevin Brown", + "author_inst": "UK Health Security Agency, London, United Kingdom & NIHR Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Med" + }, + { + "author_name": "Susan Hopkins", + "author_inst": "UK Health Security Agency, London, United Kingdom & Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK" + }, + { + "author_name": "Meera Chand", + "author_inst": "UK Health Security Agency, London, United Kingdom & Guys and St Thomas's Hospital NHS Trust, London, UK" + }, + { + "author_name": "Mary Ramsay", + "author_inst": "UK Health Security Agency, London, United Kingdom & NIHR Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Med" + }, + { + "author_name": "Jamie Lopez Bernal", + "author_inst": "UK Health Security Agency, London, United Kingdom & NIHR Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Med" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.12.13.472433", "rel_title": "Production and secretion of functional full-length SARS-CoV-2 spike protein in Chlamydomonas reinhardtii", @@ -464669,57 +466523,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.12.13.21267711", - "rel_title": "Relationship Between Alcohol Consumption and Telecommuting Preference-Practice Mismatch During the COVID-19 Pandemic.", - "rel_date": "2021-12-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.13.21267711", - "rel_abs": "IntroductionThis study examined the association between increased alcohol consumption and telecommuting, comparing employees who expressed a preference for telecommuting and those who did not.\n\nMethodsWe conducted an internet monitor survey. Responses from 20,395 of the 33,302 participants were included in the final sample. Participants were asked about their desire for and frequency of telecommuting, and about changes in alcohol consumption under the COVID-19 pandemic. Data were analyzed by logistic regression analysis.\n\nResultsParticipants who telecommuted despite preferring not to do so reported significantly increased alcohol consumption, as revealed by a multivariate analysis (OR=1.62, 95% CI 1.25-2.12). Participants who expressed a preference for telecommuting showed no such increase.\n\nConclusionsUnder the COVID-19 pandemic, telecommuting that involves a mismatch with employee preference for way of working may be a new risk factor for problematic drinking.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Chihiro Watanabe", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Yusuke Konno", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Masako Nagata", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Ayako Hino", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Seiichiro Tateishi", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Keiji Muramatsu", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Mayumi Tsuji", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Akira Ogami", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Yoshihisa Fujino", - "author_inst": "University of Occupational and Environmental Health, Japan" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2021.12.12.21267695", "rel_title": "Immunogenicity and reactogenicity after booster dose with AZD1222 via intradermal route among adult who had received CoronaVac", @@ -465563,6 +467366,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.13.21267603", + "rel_title": "Humoral and cellular immune responses and their kinetics vary in dependence of diagnosis and treatment in immunocompromised patients upon COVID-19 mRNA vaccination.", + "rel_date": "2021-12-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.13.21267603", + "rel_abs": "BackgroundKnowledge about humoral and cellular immunogenicity and their kinetics following SARS-CoV-2 mRNA vaccinations in immunosuppressed patients is limited.\n\nMethodsAntibody and cytokine responses were assessed in 263 patients with either solid tumors (SOT, n=63), multiple myeloma (MM, n=70) or inflammatory bowel diseases (IBD, n=130) undergoing various immunosuppressive regimens and from 66 healthy controls before the first and the second, as well as four weeks and 5-6 months after the second mRNA vaccine dose with either BNT162b2 or mRNA-1273.\n\nFindingsFour weeks after the second dose, seroconversion was lower in cancer than in IBD patients and controls, with the highest non-responder rate in MM patients (17.1%). S1-specific IgG levels correlated with neutralizing antibody titers. While antibody responses correlated with cellular responses in controls and IBD patients, IFN-{gamma} and antibody responses did not in SOT and MM patients. At six months, 19.6% of patients with MM and 7.3% with SOT had become seronegative, while IBD patients and controls remained seropositive in 96.3% and 100%, respectively. Vaccinees receiving mRNA-1273 presented higher antibody levels than those vaccinated with BNT162b2.\n\nInterpretationCancer patients may launch an inadequate seroresponse in the immediate time range following vaccination and up to six months, correlating with vaccine-specific cellular responses. These findings propose antibody testing in immunosuppressed - along with cellular testing - provides guidance for administration of additional vaccine doses, or may indicate the necessity for antibody treatment. IBD patients respond well to the vaccine, but treatment such as with TNF- inhibitors may reduce persistence of immune responses.\n\nFundingThe study was sponsored and financed by the Medical University of Vienna - third party funding by the Institute of Specific Prophylaxis and Tropical Medicine. AOR. and HS acknowledge funding by the Austrian Science Fund (FWF, P 34253-B).", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Angelika Wagner", + "author_inst": "Institute of Specific Prophylaxis and Tropical Medicine, Center of Pathophysiology, Infectiology and Immunology, Medical University Vienna, Vienna, Austria" + }, + { + "author_name": "Erika Garner-Spitzer", + "author_inst": "Institute of Specific Prophylaxis and Tropical Medicine, Center of Pathophysiology, Infectiology and Immunology, Medical University Vienna, Vienna, Austria" + }, + { + "author_name": "Anna Margarita Schoetta", + "author_inst": "Institute for Hygiene and Applied Immunology, Center of Pathophysiology, Infectiology and Immunology, Medical University Vienna, Vienna, Austria" + }, + { + "author_name": "Maria Orola", + "author_inst": "Institute of Specific Prophylaxis and Tropical Medicine, Center of Pathophysiology, Infectiology and Immunology, Medical University Vienna, Vienna, Austria" + }, + { + "author_name": "Andrea Wessely", + "author_inst": "Institute of Specific Prophylaxis and Tropical Medicine, Center of Pathophysiology, Infectiology and Immunology, Medical University Vienna, Vienna, Austria" + }, + { + "author_name": "Ines Zwazl", + "author_inst": "Institute of Specific Prophylaxis and Tropical Medicine, Center of Pathophysiology, Infectiology and Immunology, Medical University Vienna, Vienna, Austria" + }, + { + "author_name": "Ana Ohradanova-Repic", + "author_inst": "Institute for Hygiene and Applied Immunology, Center of Pathophysiology, Infectiology and Immunology, Medical University Vienna, Vienna, Austria" + }, + { + "author_name": "Gabor Tajti", + "author_inst": "Institute for Hygiene and Applied Immunology, Center of Pathophysiology, Infectiology and Immunology, Medical University Vienna, Vienna, Austria" + }, + { + "author_name": "Laura Gebetsberger", + "author_inst": "Institute for Hygiene and Applied Immunology, Center of Pathophysiology, Infectiology and Immunology, Medical University Vienna, Vienna, Austria" + }, + { + "author_name": "Bernhard Kratzer", + "author_inst": "Institute of Immunology, Center of Pathophysiology, Infectiology and Immunology, Medical University Vienna, Vienna, Austria" + }, + { + "author_name": "Elena Tomosel", + "author_inst": "Institute of Specific Prophylaxis and Tropical Medicine, Center of Pathophysiology, Infectiology and Immunology, Medical University Vienna, Vienna, Austria" + }, + { + "author_name": "Maximilian Kutschera", + "author_inst": "Department of Internal Medicine III, Division of Gastroenterology and Hepatology, Medical University Vienna, Vienna, Austria" + }, + { + "author_name": "Selma Tobudic", + "author_inst": "Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria" + }, + { + "author_name": "Winfried W Pickl", + "author_inst": "Institute of Immunology, Center of Pathophysiology, Infectiology and Immunology, Medical University Vienna, Vienna, Austria" + }, + { + "author_name": "Michael Kundi", + "author_inst": "Center for Public Health, Medical University Vienna, Vienna, Austria" + }, + { + "author_name": "Hannes Stockinger", + "author_inst": "Institute for Hygiene and Applied Immunology, Center of Pathophysiology, Infectiology and Immunology, Medical University Vienna, Vienna, Austria" + }, + { + "author_name": "Gottfried Novacek", + "author_inst": "Department of Internal Medicine III, Division of Gastroenterology and Hepatology, Medical University Vienna, Vienna, Austria" + }, + { + "author_name": "Walter Reinisch", + "author_inst": "Department of Internal Medicine III, Division of Gastroenterology and Hepatology, Medical University Vienna, Vienna, Austria" + }, + { + "author_name": "Christoph Zielinski", + "author_inst": "Central European Cancer Center, Wiener Privatklinik, Vienna, Austria, and Central European Cooperative Oncology Group, HQ: Vienna, Austria" + }, + { + "author_name": "Ursula Wiedermann", + "author_inst": "Institute of Specific Prophylaxis and Tropical Medicine, Center of Pathophysiology, Infectiology and Immunology, Medical University Vienna, Vienna, Austria" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2021.12.13.21267723", "rel_title": "Differential impact of Covid-19 on incidence of diabetes mellitus and cardiovascular diseases in acute, post-acute and long Covid-19: population-based cohort study in the United Kingdom", @@ -466531,41 +468429,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.12.12.21267673", - "rel_title": "Assessing impact of Omicron on SARS-CoV-2 dynamics and public health burden", - "rel_date": "2021-12-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.12.21267673", - "rel_abs": "SARS-CoV-2 variant Omicron (B.1.1.529) was classified as a variant of concern (VOC) on November 26, 2021. (1, 2) The infectivity, severity, and immune evasion properties of Omicron relative to the Delta variant would determine 1) the probability of dominant future transmission, and 2) the impact on disease burden. (3, 4) Here we apply individual-based transmission model OpenCOVID to identify thresholds for Omicrons or any VOCs potential future dominance, impact on health, and risk to health systems; and identify for which combinations of viral properties, current interventions would be sufficient to control transmission. We show that, with first-generation SARS-CoV-2 vaccines (5) and limited physical distancing in place, the threshold for Omicrons future dominance was primarily be driven by its degree of infectivity. However, we identified that a VOCs potential dominance will not necessarily lead to increased public health burden. Expanded vaccination, that includes a third-dose for adults and child vaccination strategies, was projected to have the biggest public health benefit for a highly infective, highly severe VOC with low immune evasion capacity. However, a highly immune evading variant that becomes dominant would likely require alternative measures for control, such as strengthened physical distancing measures, novel treatments, and second-generation vaccines. These findings provide quantitative guidance to decision-makers at a critical time while Omicrons properties are being assessed and preparedness for new VOCs is eminent. (6) We emphasize the importance of both genomic and population epidemiological surveillance.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Epke A. Le Rutte", - "author_inst": "Swiss Tropical and Public Health Institute" - }, - { - "author_name": "Andrew J. Shattock", - "author_inst": "Swiss Tropical and Public Health Institute" - }, - { - "author_name": "Nakul Chitnis", - "author_inst": "Swiss Tropical and Public Health Institute" - }, - { - "author_name": "Sherrie L. Kelly", - "author_inst": "Swiss Tropical and Public Health Institute" - }, - { - "author_name": "Melissa A Penny", - "author_inst": "Swiss Tropical and Public Health Institute" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.12.10.21267568", "rel_title": "Resources Required for Implementation of SARS-CoV-2 Screening in Massachusetts K-12 Public Schools in Winter/Spring 2021", @@ -467357,6 +469220,49 @@ "type": "new results", "category": "ecology" }, + { + "rel_doi": "10.1101/2021.12.12.472313", + "rel_title": "Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces", + "rel_date": "2021-12-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.12.472313", + "rel_abs": "There is enormous ongoing interest in characterizing the binding properties of the SARS-CoV-2 Omicron Variant of Concern (VOC) (B.1.1.529), which continues to spread towards potential dominance worldwide. To aid these studies, based on the wealth of available structural information about several SARS-CoV-2 variants in the Protein Data Bank (PDB) and a modeling pipeline we have previously developed for tracking the ongoing global evolution of SARS-CoV-2 proteins, we provide a set of computed structural models (henceforth models) of the Omicron VOC receptor-binding domain (omRBD) bound to its corresponding receptor Angiotensin-Converting Enzyme (ACE2) and a variety of therapeutic entities, including neutralizing and therapeutic antibodies targeting previously-detected viral strains. We generated bound omRBD models using both experimentally-determined structures in the PDB as well as machine learningbased structure predictions as starting points. Examination of ACE2-bound omRBD models reveals an interdigitated multi-residue interaction network formed by omRBD-specific substituted residues (R493, S496, Y501, R498) and ACE2 residues at the interface, which was not present in the original Wuhan-Hu-1 RBD-ACE2 complex. Emergence of this interaction network suggests optimization of a key region of the binding interface, and positive cooperativity among various sites of residue substitutions in omRBD mediating ACE2 binding. Examination of neutralizing antibody complexes for Barnes Class 1 and Class 2 antibodies modeled with omRBD highlights an overall loss of interfacial interactions (with gain of new interactions in rare cases) mediated by substituted residues. Many of these substitutions have previously been found to independently dampen or even ablate antibody binding, and perhaps mediate antibody-mediated neutralization escape (e.g., K417N). We observe little compensation of corresponding interaction loss at interfaces when potential escape substitutions occur in combination. A few selected antibodies (e.g., Barnes Class 3 S309), however, feature largely unaltered or modestly affected protein-protein interfaces. While we stress that only qualitative insights can be obtained directly from our models at this time, we anticipate that they can provide starting points for more detailed and quantitative computational characterization, and, if needed, redesign of monoclonal antibodies for targeting the Omicron VOC Spike protein. In the broader context, the computational pipeline we developed provides a framework for rapidly and efficiently generating retrospective and prospective models for other novel variants of SARS-CoV-2 bound to entities of virological and therapeutic interest, in the setting of a global pandemic.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Joseph H. Lubin", + "author_inst": "Rutgers University" + }, + { + "author_name": "Christopher Markosian", + "author_inst": "Rutgers University" + }, + { + "author_name": "D. Balamurugan", + "author_inst": "Rutgers University" + }, + { + "author_name": "Renata Pasqualini", + "author_inst": "Rutgers University" + }, + { + "author_name": "Wadih Arap", + "author_inst": "Rutgers University" + }, + { + "author_name": "Stephen K. Burley", + "author_inst": "Rutgers University" + }, + { + "author_name": "Sagar D. Khare", + "author_inst": "Rutgers University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.12.10.472066", "rel_title": "Structure of the 5' untranslated region in SARS-CoV-2 genome and its specific recognition by innate immune system via the human oligoadenylate synthase 1", @@ -468185,153 +470091,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.09.21266492", - "rel_title": "Severe COVID-19 infection is associated with aberrant cytokine production by infected lung epithelial cells rather than by systemic immune dysfunction", - "rel_date": "2021-12-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.09.21266492", - "rel_abs": "The mechanisms explaining progression to severe COVID-19 remain poorly understood. It has been proposed that immune system dysregulation/over-stimulation may be implicated, but it is not clear how such processes would lead to respiratory failure. We performed comprehensive multiparameter immune monitoring in a tightly controlled cohort of 128 COVID-19 patients, and used the ratio of oxygen saturation to fraction of inspired oxygen (SpO2 / FiO2) as a physiologic measure of disease severity. Machine learning algorithms integrating 139 parameters identified IL-6 and CCL2 as two factors predictive of severe disease, consistent with the therapeutic benefit observed with anti-IL6-R antibody treatment. However, transcripts encoding these cytokines were not detected among circulating immune cells. Rather, in situ analysis of lung specimens using RNAscope and immunofluorescent staining revealed that elevated IL-6 and CCL2 were dominantly produced by infected lung type II pneumocytes. Severe disease was not associated with higher viral load, deficient antibody responses, or dysfunctional T cell responses. These results refine our understanding of severe COVID-19 pathophysiology, indicating that aberrant cytokine production by infected lung epithelial cells is a major driver of immunopathology. We propose that these factors cause local immune regulation towards the benefit of the virus.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Sherin J Rouhani", - "author_inst": "University of Chicago Medicine, Section of Hematology/Oncology" - }, - { - "author_name": "Jonathan A Trujillo", - "author_inst": "University of Chicago Medicine, Section of Hematology/Oncology" - }, - { - "author_name": "Athalia Rachel Pyzer", - "author_inst": "University of Chicago Medicine" - }, - { - "author_name": "Jovian Yu", - "author_inst": "University of Chicago Medicine, Section of Hematology/Oncology" - }, - { - "author_name": "Jessica L Fessler", - "author_inst": "Department of Pathology, University of Chicago, 5841 S. Maryland Ave, MC2115, Chicago, IL" - }, - { - "author_name": "Alexandra Cabanov", - "author_inst": "Department of Pathology, University of Chicago, 5841 S. Maryland Ave, MC2115, Chicago, IL" - }, - { - "author_name": "Emily F Higgs", - "author_inst": "Department of Pathology, University of Chicago, 5841 S. Maryland Ave, MC2115, Chicago, IL" - }, - { - "author_name": "Kyle R Cron", - "author_inst": "Department of Pathology, University of Chicago, 5841 S. Maryland Ave, MC2115, Chicago, IL" - }, - { - "author_name": "Yuanyuan Zha", - "author_inst": "The Human Immunological Monitoring Facility, University of Chicago, Chicago, IL 60637" - }, - { - "author_name": "Yihao Lu", - "author_inst": "Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637" - }, - { - "author_name": "Jeffrey C Bloodworth", - "author_inst": "Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, IL" - }, - { - "author_name": "Mustafa Fatih Abasiyanik", - "author_inst": "Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA" - }, - { - "author_name": "Susan Okrah", - "author_inst": "Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA" - }, - { - "author_name": "Blake A Flood", - "author_inst": "Department of Pathology, University of Chicago, 5841 S. Maryland Ave, MC2115, Chicago, IL" - }, - { - "author_name": "Ken Hatogai", - "author_inst": "Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, IL" - }, - { - "author_name": "Michael YK Leung", - "author_inst": "Department of Pathology, University of Chicago, 5841 S. Maryland Ave, MC2115, Chicago, IL" - }, - { - "author_name": "Apameh Pezeshk", - "author_inst": "Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, IL" - }, - { - "author_name": "Lara Kozloff", - "author_inst": "Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, IL" - }, - { - "author_name": "Robin Reschke", - "author_inst": "Department of Pathology, University of Chicago, 5841 S. Maryland Ave, MC2115, Chicago, IL" - }, - { - "author_name": "Garth W Strohbehn", - "author_inst": "Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, IL" - }, - { - "author_name": "Carolina Soto Chervin", - "author_inst": "Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, IL" - }, - { - "author_name": "Madan Kumar", - "author_inst": "Department of Pediatrics, Section of Infectious Diseases, University of Chicago" - }, - { - "author_name": "Stephen Schrantz", - "author_inst": "Department of Medicine, Section of Infectious Diseases, University of Chicago" - }, - { - "author_name": "Maria Lucia Madariaga", - "author_inst": "Department of Surgery, University of Chicago" - }, - { - "author_name": "Kathleen G Beavis", - "author_inst": "Department of Pathology, University of Chicago, 5841 S. Maryland Ave, MC2115, Chicago, IL" - }, - { - "author_name": "Kiang-Teck J Yeo", - "author_inst": "Department of Pathology, University of Chicago, 5841 S. Maryland Ave, MC2115, Chicago, IL" - }, - { - "author_name": "Randy Sweis", - "author_inst": "University of Chicago" - }, - { - "author_name": "Jeremy Segal", - "author_inst": "Department of Pathology, University of Chicago, 5841 S. Maryland Ave, MC2115, Chicago, IL" - }, - { - "author_name": "Sava\u015f Tay", - "author_inst": "Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA" - }, - { - "author_name": "Evgeny Izumchenko", - "author_inst": "Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, IL" - }, - { - "author_name": "Jeffrey Mueller", - "author_inst": "Department of Pathology, University of Chicago, 5841 S. Maryland Ave, MC2115, Chicago, IL" - }, - { - "author_name": "Lin S Chen", - "author_inst": "Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637" - }, - { - "author_name": "Thomas F Gajewski", - "author_inst": "Department of Pathology, University of Chicago, 5841 S. Maryland Ave, MC2115, Chicago, IL" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.10.21267583", "rel_title": "Emergence of the Delta Variant and risk of SARS-CoV-2 infection in secondary school students and staff: prospective surveillance in 18 schools, England", @@ -469291,6 +471050,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.12.09.21267531", + "rel_title": "Patients with benign breast disease and breast cancer need more COVID-19 vaccines", + "rel_date": "2021-12-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.09.21267531", + "rel_abs": "Albeit the efficacy of COVID-19 vaccines in immunocompromised patients is undermined, it is still found beneficial. Patients with cancer have a much lower COVID-19 vaccination rate globally, and the vaccination coverage in breast cancer patients in China remains elusive. A total of 23029 patients with benign breast diseases and breast cancers were included in the study, and the vaccination rates of patients with benign breast tumors and other benign breast diseases, nonmetastatic and metastatic breast cancer were 44.0%, 54.7%, 19.2% and 9.6%, respectively. Breast cancer in situ patients had a similar vaccination rate with patients with benign breast tumors (45.9% vs 44.0%) while those with invasive breast cancer had much lower vaccination rates. The overall vaccination rate remains meager in breast cancer patients, and gap was found in patients with lower clinical stage. Hence vaccination should be further promoted among patients with benign breast diseases and breast cancer.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Huailiang Wu", + "author_inst": "Fudan University" + }, + { + "author_name": "Zonglin He", + "author_inst": "Jinan University" + }, + { + "author_name": "Yue Gong", + "author_inst": "Fudan University" + }, + { + "author_name": "Miao Mo", + "author_inst": "Fudan University" + }, + { + "author_name": "Guang-yu Liu", + "author_inst": "Fudan University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.12.09.21267565", "rel_title": "CalScope: Monitoring SARS-CoV-2 Seroprevalence from Vaccination and Prior Infection in Adults and Children in California May 2021 to July 2021", @@ -470591,69 +472385,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2021.12.07.21267409", - "rel_title": "Serum levels of specialised pro-resolving molecule pathways are greatly increased in SARS-CoV-2 patients and correlate with markers of the adaptive immune response.", - "rel_date": "2021-12-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.07.21267409", - "rel_abs": "BackgroundSpecialised pro-resolution molecules (SPMs) halt the transition to chronic pathogenic inflammation. We aimed to quantify serum levels of pro- and anti-inflammatory bioactive lipids in SARS-CoV-2 patients, and to identify potential relationships with innate responses and clinical outcome.\n\nMethodsSerum from 50 hospital admitted inpatients (22 female, 28 male) with confirmed symptomatic SARS-CoV-2 infection and 94 age and sex matched cohort collected prior to the pandemic, were processed for quantification of bioactive lipids. Anti-nucleocapsid and anti-spike quantitative binding assays were performed.\n\nResultsSARS-CoV-2 serum had significantly higher concentrations of omega-6 derived pro-inflammatory lipids and omega-6 and omega-3 derived SPMs, compared to age and sex matched controls. Levels of SPMs were not markedly altered by age. There were significant positive correlations between SPMs and other bioactive lipids and anti-spike antibody binding. Levels of some SPMs were significantly higher in patients with an anti-spike antibody value >0.5. Levels of linoleic acid (LA) and 5,6-dihydroxy-8Z,11Z,14Z-eicosatrienoic acid (5,6-DHET) were significantly lower in SARS-COV-2 patients who died.\n\nDiscussionSARS-COV-2 infection was associated with a robust activation of the pathways that generate the specialised pro-resolution molecules and other anti-inflammatory bioactive lipids, supporting the future investigation of these pathways which may inform the development of novel treatments.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "James Turnbull", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Rakesh Jha", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Catherine A. Ortori", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Eleanor Lunt", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Patrick J. Tighe", - "author_inst": "University of Nottingham" - }, - { - "author_name": "William L. Irving", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Sameer A. Gohir", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Dong-Hyun Kim", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Ana M. Valdes", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Alexander W. Tarr", - "author_inst": "University of Nottingham" - }, - { - "author_name": "David A. Barrett", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Victoria Chapman", - "author_inst": "University of Nottingham" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.09.21267476", "rel_title": "Emotional Distress, Stress, Anxiety and the Impact of the COVID-19 Pandemic on Early Career Women in Healthcare Sciences Research", @@ -471373,6 +473104,141 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.12.07.470392", + "rel_title": "B.1.1.529 escapes the majority of SARS-CoV-2 neutralizing antibodies of diverse epitopes", + "rel_date": "2021-12-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.07.470392", + "rel_abs": "The SARS-CoV-2 B.1.1.529 variant (Omicron) contains 15 mutations on the receptor-binding domain (RBD). How Omicron would evade RBD neutralizing antibodies (NAbs) requires immediate investigation. Here, we used high-throughput yeast display screening1,2 to determine the RBD escaping mutation profiles for 247 human anti-RBD NAbs and showed that the NAbs could be unsupervised clustered into six epitope groups (A-F), which is highly concordant with knowledge-based structural classifications3-5. Strikingly, various single mutations of Omicron could impair NAbs of different epitope groups. Specifically, NAbs in Group A-D, whose epitope overlap with ACE2-binding motif, are largely escaped by K417N, G446S, E484A, and Q493R. Group E (S309 site)6 and F (CR3022 site)7 NAbs, which often exhibit broad sarbecovirus neutralizing activity, are less affected by Omicron, but still, a subset of NAbs are escaped by G339D, N440K, and S371L. Furthermore, Omicron pseudovirus neutralization showed that single mutation tolerating NAbs could also be escaped due to multiple synergetic mutations on their epitopes. In total, over 85% of the tested NAbs are escaped by Omicron. Regarding NAb drugs, the neutralization potency of LY-CoV016/LY-CoV555, REGN10933/REGN10987, AZD1061/AZD8895, and BRII-196 were greatly reduced by Omicron, while VIR-7831 and DXP-604 still function at reduced efficacy. Together, data suggest Omicron would cause significant humoral immune evasion, while NAbs targeting the sarbecovirus conserved region remain most effective. Our results offer instructions for developing NAb drugs and vaccines against Omicron and future variants.", + "rel_num_authors": 30, + "rel_authors": [ + { + "author_name": "Yunlong Richard Cao", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China." + }, + { + "author_name": "Jing Wang", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China." + }, + { + "author_name": "Fanchong Jian", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China." + }, + { + "author_name": "Tianhe Xiao", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China." + }, + { + "author_name": "Weiliang Song", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China." + }, + { + "author_name": "Ayijiang Yisimayi", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China." + }, + { + "author_name": "Weijin Huang", + "author_inst": "Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijin" + }, + { + "author_name": "Qianqian Li", + "author_inst": "Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijin" + }, + { + "author_name": "Peng Wang", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China." + }, + { + "author_name": "Ran An", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China." + }, + { + "author_name": "Jing Wang", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China." + }, + { + "author_name": "Yao Wang", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China." + }, + { + "author_name": "Xiao Niu", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China." + }, + { + "author_name": "Sijie Yang", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China." + }, + { + "author_name": "Hui Liang", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China." + }, + { + "author_name": "Haiyan Sun", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China." + }, + { + "author_name": "Tao Li", + "author_inst": "Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijin" + }, + { + "author_name": "Yuanling Yu", + "author_inst": "Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijin" + }, + { + "author_name": "Qianqian Cui", + "author_inst": "Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), and WH" + }, + { + "author_name": "Shuo Liu", + "author_inst": "Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijin" + }, + { + "author_name": "Xiaodong Yang", + "author_inst": "Beijing YouAn Hospital, Capital Medical University, Beijing, P.R. China." + }, + { + "author_name": "Shuo Du", + "author_inst": "School of Life Sciences, Peking University, Beijing, P.R. China." + }, + { + "author_name": "Zhiying Zhang", + "author_inst": "School of Life Sciences, Peking University, Beijing, P.R. China." + }, + { + "author_name": "Xiaohua Hao", + "author_inst": "Beijing Ditan Hospital, Capital Medical University, Beijing, P.R. China." + }, + { + "author_name": "Fei Shao", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China." + }, + { + "author_name": "Ronghua Jin", + "author_inst": "Beijing Ditan Hospital, Capital Medical University, Beijing, P.R. China." + }, + { + "author_name": "Xiangxi Wang", + "author_inst": "CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China." + }, + { + "author_name": "Junyu Xiao", + "author_inst": "Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, P.R. China." + }, + { + "author_name": "Youchun Wang", + "author_inst": "Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijin" + }, + { + "author_name": "Xiaoliang Sunney Xie", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China." + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.12.08.471664", "rel_title": "Combinatorial mRNA vaccination enhances protection against SARS-CoV-2 delta variant", @@ -472413,37 +474279,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.08.21267499", - "rel_title": "Modeling COVID-19 Aerosol Transmission in Primary Schools", - "rel_date": "2021-12-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.08.21267499", - "rel_abs": "Schools must balance public health, education, and social risks associated with returning to in-person learning. These risks are compounded by the ongoing uncertainty about vaccine availability and uptake for children under 12 years of age. In this paper, we show how the risk of infections that result directly from in-class aerosol transmission within an elementary school population can be estimated in order to compare the effects of different countermeasures. We compare the effectiveness of these countermeasures in reducing transmission including required masking at three levels of mask effectiveness, improving room airflow exchange rates, weekly testing of the students, and lunch partitioning. Our results show that multiple layers of interventions are necessary to keep in-class infections relatively low. These results can inform school administrators about how these interventions can help manage COVID-19 spread within their own elementary school populations.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Tessa Swanson", - "author_inst": "University of Michigan" - }, - { - "author_name": "Seth D. Guikema", - "author_inst": "University of Michigan" - }, - { - "author_name": "James Bagian", - "author_inst": "University of Michigan" - }, - { - "author_name": "Claire Payne", - "author_inst": "University of Michigan" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.09.471885", "rel_title": "SARS-CoV-2 Omicron Spike Glycoprotein Receptor Binding Domain Exhibits Super-Binder Ability with ACE2 but not Convalescent Monoclonal Antibody", @@ -472947,6 +474782,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.03.21267237", + "rel_title": "COVID-19 Vaccine Hesitancy Among Patients with Inflammatory Bowel Disease on Biologic Therapies; A cross-sectional study.", + "rel_date": "2021-12-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.03.21267237", + "rel_abs": "BackgroundCOVID-19 Vaccinations have been shown to be effective in reducing risk of severe infection, hospitalization, and death. They also have been shown to be safe and effective in patients with inflammatory bowel disease (IBD) on biologic therapies. In this study, we aimed to evaluate the prevalence of vaccination among patients with IBD on biologic therapies.\n\nMethodsA single-center prospective cross-sectional study conducted at a tertiary care inflammatory bowel disease center. Data from patients with inflammatory bowel disease (IBD) who attended the gastroenterology infusion clinic from June 1st, 2021 until October 31st, 2021 were retrieved. Patients received infliximab or vedolizumab at least 6 weeks before recruitment were included. The primary outcome was prevalence of COVID-19 vaccination. The secondary outcome was to assess whether prevalence of COVID-19 vaccination differed based sex, age, type of biologic therapy and citizenship status.\n\nResultsThe total number of inflammatory bowel disease (IBD) patients enrolled in the study was 280 (56.0% male and 44.0% female). The median age was 33.2 years and BMI was 24.8 kg/m2. 112 patients with ulcerative colitis (40.0%) and 168 (60.0%) with Crohns disease. 117 (41.8%) were vaccinated with either BNT162b2 or ChAdOx1 nCoV-19 and 163 (58.2%) were not vaccinated. Female patients were more likely to receive the vaccine compared to male patients (83.0% vs. 63.8%, p < 0.001). In addition, older patients (above the age 50) were also more likely to receive the vaccine than younger patients, below the age of 50 (95.6% vs 31.2% p< 0.001). Expatriates were more likely to receive the vaccine than citizens (84.8% vs 25.0%, p < 0.001). There was no statistical difference between patients on Infliximab and vedolizumab in terms of prevalence of vaccination (40.0% vs 48.0%, p= 0.34).\n\nConclusionThe overall prevalence of COVID-19 vaccination among patients with inflammatory bowel disease (IBD) on biologic therapies was lower than the general population and world health organization (WHO) recommendation. Female patients, patients above the age of 50, and expatriates were more likely to be vaccinated. On the other hand, male patients, patients below the age of 50, and citizens were less likely to be vaccinated.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Mohammad Shehab", + "author_inst": "Mubarak Al-Kaber Hospital" + }, + { + "author_name": "Yasmin Zurba", + "author_inst": "Mubarak Al-kaber Hospital" + }, + { + "author_name": "Ali Al Abdulsalam", + "author_inst": "Mubarak Al-Kaber Hospital" + }, + { + "author_name": "Ahmad Alfadhli", + "author_inst": "Mubarak Al-Kaber Hospital" + }, + { + "author_name": "Sara Elouali", + "author_inst": "Cleveland Clinic, Abu Dhabi, UAE" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "gastroenterology" + }, { "rel_doi": "10.1101/2021.12.07.21267287", "rel_title": "PROBABILITY OF HOSPITALIZATION AND DEATH AMONG COVID-19 PATIENTS WITH COMORBIDITY DURING OUTBREAKS OCCURRING IN MEXICO CITY.", @@ -473775,33 +475645,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.12.07.21267277", - "rel_title": "A Quantitative Systems Pharmacology Model of the Pathophysiology and Treatment of COVID-19 Predicts Optimal Timing of Pharmacological Interventions", - "rel_date": "2021-12-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.07.21267277", - "rel_abs": "A quantitative systems pharmacology (QSP) model of the pathogenesis and treatment of SARS-CoV-2 infection can streamline and accelerate the development of novel medicines to treat COVID-19. Simulation of clinical trials allows in silico exploration of the uncertainties of clinical trial design and can rapidly inform their protocols. We previously published a preliminary model of the immune response to SARS-CoV-2 infection. To further our understanding of COVID-19 and treatment we significantly updated the model by matching a curated dataset spanning viral load and immune responses in plasma and lung. We identified a population of parameter sets to generate heterogeneity in pathophysiology and treatment and tested this model against published reports from interventional SARS-CoV-2 targeting Ab and anti-viral trials. Upon generation and selection of a virtual population, we match both the placebo and treated responses in viral load in these trials. We extended the model to predict the rate of hospitalization or death within a population. Via comparison of the in silico predictions with clinical data, we hypothesize that the immune response to virus is log-linear over a wide range of viral load. To validate this approach, we show the model matches a published subgroup analysis, sorted by baseline viral load, of patients treated with neutralizing Abs. By simulating intervention at different timepoints post infection, the model predicts efficacy is not sensitive to interventions within five days of symptom onset, but efficacy is dramatically reduced if more than five days pass post-symptom onset prior to treatment.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Rohit Rao", - "author_inst": "Pfizer Inc" - }, - { - "author_name": "Cynthia J Musante", - "author_inst": "Pfizer Inc" - }, - { - "author_name": "Richard Allen", - "author_inst": "Pfizer Inc" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pharmacology and therapeutics" - }, { "rel_doi": "10.1101/2021.12.08.21267181", "rel_title": "Long COVID Citizen Scientists - Developing a needs-based research agenda by persons affected by Long COVID", @@ -474821,6 +476664,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.12.08.21267444", + "rel_title": "The T-cell clonal response to SARS-CoV-2 vaccination in inflammatory bowel disease patients is augmented by anti-TNF therapy and often deficient in antibody-responders", + "rel_date": "2021-12-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.08.21267444", + "rel_abs": "BackgroundVaccination against SARS-CoV-2 is a highly effective strategy to protect against infection, which is predominantly mediated by vaccine-induced antibodies. Postvaccination antibodies are robustly produced by those with inflammatory bowel disease (IBD) even on immune-modifying therapies but are blunted by anti-TNF therapy. In contrast, T-cell response which primarily determines long-term efficacy against disease progression,, is less well understood. We aimed to assess the post-vaccination T-cell response and its relationship to antibody responses in patients with inflammatory bowel disease (IBD) on immune-modifying therapies.\n\nMethodsWe evaluated IBD patients who completed SARS-CoV-2 vaccination using samples collected at four time points (dose 1, dose 2, 2 weeks after dose 2, 8 weeks after dose 2). T-cell clonal analysis was performed by T-cell Receptor (TCR) immunosequencing. The breadth (number of unique sequences to a given protein) and depth (relative abundance of all the unique sequences to a given protein) of the T-cell clonal response were quantified using reference datasets and were compared to antibody responses.\n\nResultsOverall, 303 subjects were included (55% female; 5% with prior COVID) (Table). 53% received BNT262b (Pfizer), 42% mRNA-1273 (Moderna) and 5% Ad26CoV2 (J&J). The Spike-specific clonal response peaked 2 weeks after completion of the vaccine regimen (3- and 5-fold for breadth and depth, respectively); no changes were seen for non-Spike clones, suggesting vaccine specificity. Reduced T-cell clonal depth was associated with chronologic age, male sex, and immunomodulator treatment. It was preserved by non-anti-TNF biologic therapies, and augmented clonal depth was associated with anti-TNF treatment. TCR depth and breadth were associated with vaccine type; after adjusting for age and gender, Ad26CoV2 (J&J) exhibited weaker metrics than mRNA-1273 (Moderna) (p=0.01 for each) or BNT262b (Pfizer) (p=0.056 for depth). Antibody and T-cell responses were only modestly correlated. While those with robust humoral responses also had robust TCR clonal expansion, a substantial fraction of patients with high antibody levels had only a minimal T-cell clonal response.\n\nConclusionAge, sex and select immunotherapies are associated with the T-cell clonal response to SARS-CoV-2 vaccines, and T-cell responses are low in many patients despite high antibody levels. These factors, as well as differences seen by vaccine type may help guide reimmunization vaccine strategy in immune-impaired populations. Further study of the effects of anti-TNF therapy on vaccine responses are warranted.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Dalin Li", + "author_inst": "F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA" + }, + { + "author_name": "Alexander Xu", + "author_inst": "Cedars-Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA" + }, + { + "author_name": "Emebet Mengesha", + "author_inst": "F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA" + }, + { + "author_name": "Rebecca Elyanow", + "author_inst": "Adaptive Biotechnologies, Seattle, WA, USA" + }, + { + "author_name": "Rachel M. Gittelman", + "author_inst": "Adaptive Biotechnologies, Seattle, WA, USA" + }, + { + "author_name": "Heidi Chapman", + "author_inst": "Adaptive Biotechnologies, Seattle, WA, USA" + }, + { + "author_name": "John C. Prostko", + "author_inst": "Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL" + }, + { + "author_name": "Edwin C. Frias", + "author_inst": "Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL" + }, + { + "author_name": "James L. Stewart", + "author_inst": "Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL" + }, + { + "author_name": "Valeriya Pozdnyakova", + "author_inst": "F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA" + }, + { + "author_name": "Philip Debbas", + "author_inst": "F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA" + }, + { + "author_name": "Angela Muzukian", + "author_inst": "F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA" + }, + { + "author_name": "Arash. A. Horizon", + "author_inst": "Center for Rheumatology Medical Group, Los Angeles, CA, USA" + }, + { + "author_name": "Noah Merin", + "author_inst": "Cedars-Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA" + }, + { + "author_name": "Sandy Joung", + "author_inst": "Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA" + }, + { + "author_name": "Gregory J. Botwin", + "author_inst": "F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA" + }, + { + "author_name": "Kimia Sobhani", + "author_inst": "Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA" + }, + { + "author_name": "Jane C. Figueiredo", + "author_inst": "Cedars-Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA" + }, + { + "author_name": "Susan Cheng", + "author_inst": "Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA" + }, + { + "author_name": "Ian M. Kaplan", + "author_inst": "Adaptive Biotechnologies, Seattle, WA, USA" + }, + { + "author_name": "Dermot P.B. McGovern", + "author_inst": "F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA" + }, + { + "author_name": "Akil Merchant", + "author_inst": "Cedars-Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA" + }, + { + "author_name": "Gil Y. Melmed", + "author_inst": "F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA" + }, + { + "author_name": "Jonathan Braun", + "author_inst": "F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "gastroenterology" + }, { "rel_doi": "10.1101/2021.12.07.21267429", "rel_title": "Clinical characteristics of Chilean patients with rheumatic diseases and COVID-19: data from the Covid-19 Global Rheumatology Alliance physician-reported registry", @@ -475957,33 +477911,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.12.06.471415", - "rel_title": "Decoupling SARS-CoV-2 ORF6 localization and interferon antagonism", - "rel_date": "2021-12-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.06.471415", - "rel_abs": "Like many pathogenic viruses, SARS-CoV-2 must overcome interferon (IFN)-mediated host defenses for infection establishment. To achieve this, SARS-CoV-2 deploys overlapping mechanisms to antagonize IFN production and signaling. The strongest IFN antagonist is the accessory protein ORF6, which localizes to multiple membranous compartments, including the nuclear envelope, where it directly binds the nuclear pore components Nup98-Rae1 to inhibit nuclear translocation of activated STAT1/IRF3 transcription factors. However, a direct cause-and-effect relationship between ORF6 localization and IFN antagonism has yet to be explored experimentally. Here, we use extensive mutagenesis studies to define the structural determinants required for steady-state localization and demonstrate that mis-localized ORF6 variants can still potently inhibit nuclear trafficking and IFN signaling. Additionally, expression of a peptide that mimics the ORF6/Nup98 interaction domain robustly inhibited nuclear trafficking. Furthermore, pharmacologic and mutational approaches combined to suggest that ORF6 is likely a peripheral-membrane protein, opposed to being a transmembrane protein as previously speculated. Thus, ORF6 localization and IFN antagonism are independent activities, which raises the possibility that ORF6 may have additional functions within membrane networks to enhance virus replication.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Hoi Tong Wong", - "author_inst": "Stony Brook University" - }, - { - "author_name": "Victoria Cheung", - "author_inst": "Stony Brook University" - }, - { - "author_name": "Daniel J Salamango", - "author_inst": "Stony Brook University" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2021.12.05.21267330", "rel_title": "Waning antibody levels after vaccination with mRNA BNT162b2 and inactivated CoronaVac COVID-19 vaccines in Hong Kong blood donors", @@ -476603,6 +478530,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hiv aids" }, + { + "rel_doi": "10.1101/2021.12.06.21267328", + "rel_title": "Comprehensive Serological Profile and Specificity of Maternal and Neonatal Cord Blood SARS CoV-2 Antibodies", + "rel_date": "2021-12-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.06.21267328", + "rel_abs": "ObjectiveTo describe the profile and specificity of maternal and neonatal cord-blood antibody profile in response SARS-CoV-2 virus exposure\n\nMethodsThis is a Prospective cohort study of delivering patients at Thomas Jefferson University Hospital from April 2020-February 2021. Primary objective was to describe unique maternal and fetal antibody epitope titers and specificity in those patients with COVID-19 history. Serologic profile assessed with a multiplex platform. Antigens used were: HA-trimer Influenza A (Hong Kong H3), spike trimers for SARS-CoV-2, SARS-CoV-1, MERS-CoV, and betacoronaviruses HKU-1 and OC43, as well as the spike N-terminal domain (NTD), spike receptor binding domain (RBD), and nucleocapsid protein (N; full length) for SARS-CoV-2.\n\nResults112 maternal samples and 101 maternal and cord blood pairs were analyzed. Thirty-seven had a known history of COVID-19 (positive PCR test) in the pregnancy and of those, 17 (47%) were diagnosed with COVID-19 within 30 days of delivery. Fifteen of remaining seventy-six (20%) without a known diagnosis had positive maternal serology. For those with history of COVID-19 we identified robust IgG response in maternal blood to CoV2 nucleocapsid (N), spike (S) full-length and S (RBD) antigens with more modest responses to the S (NTD) antigen. By contrast, the maternal blood IgM response appeared more specific to S (full-length), than N, S (RBD) or S (NTD) epitopes. There were significantly higher maternal and cord blood IgG response not just to CoV2 spike (p < 10-18), but also CoV1 spike (p < 10-9) and MERS spike (p < 10-8). By contrast, maternal IgM responses were more specific to CoV2 (p < 10-19), but to a lesser degree for CoV1 (p < 10-5), and no significant differences for MERS. Maternal and cord-blood IgG were highly correlated for both S and N (R2 = 0.96 and 0.94).\n\nConclusionsPlacental transfer is efficient, with robust N and S responses. Both nucleocapsid and spike antibody responses should be studied for a better understanding of COVID-19 immunity. IgG antibodies are cross reactive with related CoV-1 and MERS spike epitopes while IgM, which cannot cross placenta to provide neonatal passive immunity, is more SARS CoV-2 specific. Neonatal cord blood may have significantly different fine-specificity than maternal blood, despite the high efficiency of IgG transfer.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Rupsa C Boelig", + "author_inst": "Thomas Jefferson University" + }, + { + "author_name": "Sidhartha Chaudhury", + "author_inst": "Center for Enabling Capabilities, Walter Reed Army Institute of Research" + }, + { + "author_name": "Zubair Aghai", + "author_inst": "Division of Neonatology, Department of Pediatrics Nemours" + }, + { + "author_name": "Emily Oliver", + "author_inst": "Thomas Jefferson University" + }, + { + "author_name": "Francesca Mancuso", + "author_inst": "Sidney Kimmel Medical College, Thomas Jefferson University" + }, + { + "author_name": "Vincenzo Berghella", + "author_inst": "Thomas Jefferson University" + }, + { + "author_name": "Elke C Bergmann-Leitner", + "author_inst": "WRAIR" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.04.21267265", "rel_title": "RT-PCR/MALDI-TOF diagnostic target performance reflects circulating SARS-CoV-2 variant diversity in New York City", @@ -477679,101 +479649,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.30.21267102", - "rel_title": "Individual vaccine efficacy variation with time since mRNA BNT162b2 vaccination estimated by rapid, quantitative antibody measurements from a finger-prick sample.", - "rel_date": "2021-12-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.30.21267102", - "rel_abs": "We show that an individuals immune status to Covid-19 can be monitored through quantitative antibody measurements using a method based on centrifugal microfluidics, specifically designed for speed to result (20 min), high throughput (8 samples simultaneously) and accuracy from a finger-prick blood sample. Anti-Receptor Binding Domain (RBD) IgG concentration showed a log-normal distribution with mean decreasing with time following the second vaccination with mRNA BNT162b2 (Pfizer). Using a model for an individuals antibody concentration-dependent vaccine efficacy allowed comparison with literature data on changing vaccine efficacy against symptomatic disease across a population. Even though the trial was small (n = 100) the computed population vaccine efficacy was in reasonable agreement with that obtained from a large population survey. The derived parameters for the vaccine efficacy model were in good agreement with those expected from previous studies and from a simple theoretical model. The results and modelling show that the major proportion of breakthrough infections are for people whose antibody concentration is in the tail of the distribution. The results provide strong support for personalized booster programmes that, by targeting people in the tail of the distribution, should be more effective at diminishing breakthrough infection and optimising booster dose supply than a program that simply mandates a booster at a specific post-vaccination time point.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Matheus J,T Vargas", - "author_inst": "Orbis Diagnostics Ltd" - }, - { - "author_name": "Mithileshwari Chandrasekhar", - "author_inst": "Orbis Diagnostics Ltd" - }, - { - "author_name": "Yong Je Kwon", - "author_inst": "Orbis Diagnostics Ltd" - }, - { - "author_name": "Gerrit Sjoerd Deijs", - "author_inst": "Orbis Diagnostics Ltd" - }, - { - "author_name": "Carsten Ma On Wong Corazza", - "author_inst": "Orbis Diagnostics Ltd" - }, - { - "author_name": "Angela (Wai Yin) Chai", - "author_inst": "Orbis Diagnostics Ltd" - }, - { - "author_name": "Rebecca L Binedell", - "author_inst": "Orbis Diagnostics Ltd" - }, - { - "author_name": "Ellen Jose", - "author_inst": "Orbis Diagnostics Ltd" - }, - { - "author_name": "Bhavesh Govind", - "author_inst": "OrbisDiagnostics Ltd" - }, - { - "author_name": "Laura Huyet", - "author_inst": "Orbis Diagnostics Ltd" - }, - { - "author_name": "Pooja K Patel", - "author_inst": "Orbis Diagnostics Ltd" - }, - { - "author_name": "Gabrielle Reshef", - "author_inst": "Orbis Diagnostics Ltd" - }, - { - "author_name": "Vijaya Kumar", - "author_inst": "Orbis Diagnostics Ltd" - }, - { - "author_name": "Tiffany Lowe", - "author_inst": "Orbis Diagnostics Ltd" - }, - { - "author_name": "Robert J Powell", - "author_inst": "Pacific Channel Ltd" - }, - { - "author_name": "Kieran C Jina", - "author_inst": "Orbis Diagnostics Ltd" - }, - { - "author_name": "Flynn C.W. Walker", - "author_inst": "Orbis Diagnostics Ltd" - }, - { - "author_name": "Apisalome Talemaitoga", - "author_inst": "Cavendish Clinic" - }, - { - "author_name": "M. Cather Simpson", - "author_inst": "University of Auckland" - }, - { - "author_name": "David Edward Williams", - "author_inst": "University of Auckland" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.02.21267170", "rel_title": "Facilitating safe discharge through predicting disease progression in moderate COVID-19: a prospective cohort study to develop and validate a clinical prediction model in resource-limited settings", @@ -478465,6 +480340,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.04.471198", + "rel_title": "Modeling the trajectory of SARS-CoV-2 spike protein evolution in continuous latent space using a neural network and Gaussian process", + "rel_date": "2021-12-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.04.471198", + "rel_abs": "Viral vaccines can lose their efficacy as the genomes of targeted viruses rapidly evolve, resulting in new variants that may evade vaccine-induced immunity. This process is apparent in the emergence of new SARS-CoV-2 variants which have the potential to undermine vaccination efforts and cause further outbreaks. Predictive vaccinology points to a future of pandemic preparedness in which vaccines can be developed preemptively based in part on predictive models of viral evolution. Thus, modeling the trajectory of SARS-CoV-2 spike protein evolution could have value for mRNA vaccine development. Traditionally, in silico sequence evolution has been modeled discretely, while there has been limited investigation into continuous models. Here we present the Viral Predictor for mRNA Evolution (VPRE), an open-source software tool which learns from mutational patterns in viral proteins and models their most statistically likely evolutionary trajectories. We trained a variational autoencoder with real-time and simulated SARS-CoV-2 genome data from Australia to encode discrete spike protein sequences into continuous numerical variables. To simulate evolution along a phylogenetic path, we trained a Gaussian process model with the numerical variables to project spike protein evolution up to five months in advance. Our predictions mapped primarily to a sequence that differed by a single amino acid from the most reported spike protein in Australia within the prediction timeframe, indicating the utility of deep learning and continuous latent spaces for modeling viral protein evolution. VPRE can be readily adapted to investigate and predict the evolution of viruses other than SARS-CoV-2 in temporal, geographic, and lineage-specific pathways.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Samuel King", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Xinyi E. Chen", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Sarah W.S. Ng", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Kimia Rostin", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Tylo Roberts", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Samuel V. Hahn", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Janella C. Schwab", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Parneet Sekhon", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Madina Kagieva", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Taylor Reilly", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Ruo Chen Qi", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Paarsa Salman", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Ryan J. Hong", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Eric J. Ma", + "author_inst": "Independent Researcher" + }, + { + "author_name": "Steven J. Hallam", + "author_inst": "University of British Columbia" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.12.03.470766", "rel_title": "Pandemic-scale phylogenetics", @@ -479453,57 +481403,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.12.02.21267211", - "rel_title": "Fusion of Imaging and Non-Imaging Data for Disease Trajectory Prediction for COVID-19 Patients", - "rel_date": "2021-12-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.02.21267211", - "rel_abs": "ABSTRCATO_ST_ABSPurposeC_ST_ABSThis study investigates whether graph-based fusion of imaging data with non-imaging EHR data can improve the prediction of disease trajectory for COVID-19 patients, beyond the prediction performance of only imaging or non-imaging EHR data.\n\nMaterials and MethodsWe present a novel graph-based framework for fine-grained clinical outcome prediction (discharge, ICU admission, or death) that fuses imaging and non-imaging information using a similarity-based graph structure. Node features are represented by image embedding and edges are encoded with clinical or demographic similarity.\n\nResultsOur experiments on data collected from Emory Healthcare network indicate that our fusion modeling scheme performs consistently better than predictive models using only imaging or non-imaging features, with f1-scores of 0.73, 0.77, and 0.66 for discharge from hospital, mortality, and ICU admission, respectively. External validation was performed on data collected from Mayo Clinic. Our scheme highlights known biases in the model prediction such as bias against patients with alcohol abuse history and bias based on insurance status.\n\nConclusionThe study signifies the importance of fusion of multiple data modalities for accurate prediction of clinical trajectory. Proposed graph structure can model relationships between patients based on non-imaging EHR data and graph convolutional networks can fuse this relationship information with imaging data to effectively predict future disease trajectory more effectively than models employing only imaging or non-imaging data. Forecasting clinical events can enable intelligent resource allocation in hospitals. Our graph-based fusion modeling frameworks can be easily extended to other prediction tasks to efficiently combine imaging data with non-imaging clinical data.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Amara Tariq", - "author_inst": "Mayo Clinic, AZ" - }, - { - "author_name": "Siyi Tang", - "author_inst": "Stanford University" - }, - { - "author_name": "Hifza Sakhi", - "author_inst": "Philadelphia College of Osteopathic Medicine - Georgia Campus, Swanee, GA, USA" - }, - { - "author_name": "Leo Anthony Celi", - "author_inst": "Massachusetts Institute of Technology, Boston, MA, USA." - }, - { - "author_name": "Janice Newsome", - "author_inst": "Emory University, GA" - }, - { - "author_name": "Daniel Rubin", - "author_inst": "Stanford University" - }, - { - "author_name": "Hari Trivedi", - "author_inst": "Emory University, GA" - }, - { - "author_name": "Judy Wawira Gichoya", - "author_inst": "Emory University, GA" - }, - { - "author_name": "Imon Banerjee", - "author_inst": "Mayo Clinic, AZ" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2021.12.03.21267253", "rel_title": "A multiplex protein panel assay determines disease severity and is prognostic about outcome in COVID-19 patients", @@ -480463,6 +482362,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "geriatric medicine" }, + { + "rel_doi": "10.1101/2021.12.03.21266946", + "rel_title": "A randomized clinical trial to stimulate the cholinergic anti-inflammatory pathway in patients with moderate COVID-19-pneumonia using a slow-paced breathing technique", + "rel_date": "2021-12-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.03.21266946", + "rel_abs": "ImportanceVagus nerve stimulation via slow-paced breathing could serve as an adjuvant therapeutic approach to reduce excessive inflammation in coronavirus disease 2019 (COVID-19) pneumonia.\n\nObjectiveDoes a slow-paced breathing technique increasing vagal activity reduce Interleukin-6 (IL-6) in patients hospitalized with moderate COVID-19 pneumonia compared to standard care?\n\nDesignSingle-center randomized controlled clinical trial with enrolment from February 23rd 2021 through June 17th 2021 and follow-up until July 22nd 2021.\n\nSettingWard for infectious diseases and temporary COVID-19 ward, Ulm University Hospital, Germany\n\nParticipantsConsecutive sample of patients hospitalized with confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and moderate COVID-19 pneumonia (primary diagnosis). Of 131 patients screened, 48 patients were randomized and 46 patients analyzed (N=23 per group).\n\nInterventionsSlow-paced 20-minute breathing exercise three times a day with six breaths per minute (inhalation-to-exhalation ratio 4:6).\n\nMain outcomes and measuresDifferences between intervention and control group in IL-6 calculated using multilevel mixed-effect linear regression models with random slope including the covariates relevant comorbidities, COVID-19 medication, and age.\n\nResultsMean age 57 years{+/-}13 years, N= 28 (60%) male, N=30 (65%) with relevant comorbidities.\n\nThe model including group by time interaction revealed a significantly lower trajectory of IL-6 in the intervention group compared to the control group (effect size Cohens f2=0.11, LR-test p=.040) in the intention-to-treat sample, confirmed by treatment-per-protocol analysis (f2=0.15, LR-test p=.022). Exploratory analysis using the median split of practice time to predict IL-6 of the next morning indicated a dose-response relationship with beneficial effects of practice time above 45 minutes a day.\n\nThree patients in each group were admitted to ICU, one died. Oxygen saturation increased during slow-paced breathing (from 95.1%{+/-}2.1% to 95.4%{+/-}1.6%, p=0.006).\n\nConclusion and relevancePatients practicing slow-paced breathing had significantly lower IL-6 values than controls with a small to medium effect size and without relevant side effects. Further trials should evaluate clinical outcomes as well as an earlier start of the intervention, i.e., at symptom onset. This would offer an access to a therapy option not only for high-income, but also for low- and middle-income countries.\n\nTrial registrationGerman register of clinical trials (ID: DRKS00023971) https://www.drks.de, Universal Trial Number (UTN) U1111-1263-8658;", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Elisabeth M Balint", + "author_inst": "Clinic for Psychosomatic Medicine and Psychotherapy, University Hospital Ulm, Germany" + }, + { + "author_name": "Beate Gruener", + "author_inst": "Clinic for Internal Medicine III, Division of Infectious Diseases, University Hospital Ulm, Germany" + }, + { + "author_name": "Sophia Haase", + "author_inst": "Clinic for Psychosomatic Medicine and Psychotherapy, University Hospital Ulm, Germany" + }, + { + "author_name": "Mandakini Kaw-Geppert", + "author_inst": "Clinic for Psychosomatic Medicine and Psychotherapy, University Hospital Ulm, Germany" + }, + { + "author_name": "Julian F Thayer", + "author_inst": "Department of Psychological Science, University of California, 4201 Social & Behavioral Sciences Gateway, Irvine, CA 92697-7085, USA" + }, + { + "author_name": "Harald O Guendel", + "author_inst": "Clinic for Psychosomatic Medicine and Psychotherapy, University Hospital Ulm, Germany" + }, + { + "author_name": "Marc N. Jarczok", + "author_inst": "Clinic for Psychosomatic Medicine and Psychotherapy, University Hospital Ulm, Germany" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.01.21266680", "rel_title": "A kinetic model considering the decline of antibody level and vaccination of COVID-19", @@ -481259,29 +483201,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.12.01.470796", - "rel_title": "Thermal Analysis of Protein Stability and Ligand Binding in Complex Media", - "rel_date": "2021-12-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.01.470796", - "rel_abs": "Screening of ligands that can bind to biologic products of in vitro expression systems typically requires some purification of the expressed biologic target. Such purification is often laborious and time consuming and a limiting challenge. What is required, that could represent an enormous advantage, is the ability to screen expressed proteins in the crude lysate stage without purification. For that purpose, we explore here the utility of differential scanning calorimetry (DSC) measurements for detecting the presence of specific proteins and their interactions with ligands in the complex media where they were prepared, i.e. crude lysates. Model systems were designed to mimic analogous conditions comparable to those that might be encountered in actual in vitro expression systems. Results are reported for several examples where DSC measurements distinctly showed differences in the thermal denaturation behaviors of the crude lysate alone, proteins and proteins plus binding ligands added to the crude lysate. Results were obtained for Streptavidin/Biotin binding in E. coli lysate, and binding of Angiotensin Converting Enzyme 2 (ACE2) by captopril or lisinopril in the lysate supernatant derived from cultured Human Kidney cells (HEK293). ACE2 binding by the reactive binding domain (RBC) of SARS-CoV-2 was also examined. Binding of ACE2 by RBC and lisinopril were similar and consistent with the reported ACE2 inhibitory activity of lisinopril.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Matthew W Eskew", - "author_inst": "ThermoCap Laboratories, Portland State University" - }, - { - "author_name": "Albert S Benight", - "author_inst": "ThermoCap Laboratories, Portland State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.12.01.470748", "rel_title": "Investigating the mutational landscape of the SARS-CoV-2 Omicron variant via ab initio quantum mechanical modeling", @@ -482065,6 +483984,37 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.12.02.470917", + "rel_title": "PEPPI: Whole-proteome protein-protein interaction prediction through structure and sequence similarity, functional association, and machine learning", + "rel_date": "2021-12-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.02.470917", + "rel_abs": "Proteome-wide identification of protein-protein interactions is a formidable task which has yet to be sufficiently addressed by experimental methodologies. Many computational methods have been developed to predict proteome-wide interaction networks, but few leverage both the sensitivity of structural information and the wide availability of sequence data. We present PEPPI, a pipeline which integrates structural similarity, sequence similarity, functional association data, and machine learning-based classification through a naive Bayesian classifier model to accurately predict protein-protein interactions at a proteomic scale. Through benchmarking against a set of 798 ground truth interactions and an equal number of noninteractions, we have found that PEPPI attains 4.5% higher AUROC than the best of other state-of-the-art methods. As a proteomic-scale application, PEPPI was applied to model the interactions which occur between SARS-CoV-2 and human host cells during coronavirus infection, where 403 high-confidence interactions were identified with predictions covering 73% of a gold standard dataset from PSICQUIC and demonstrating significant complementarity with the most recent high-throughput experiments. PEPPI is available both as a webserver and in a standalone version and should be a powerful and generally applicable tool for computational screening of protein-protein interactions.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Eric W Bell", + "author_inst": "University of Michigan" + }, + { + "author_name": "Jacob H Schwartz", + "author_inst": "University of Michigan" + }, + { + "author_name": "Peter L. Freddolino", + "author_inst": "University of Michigan" + }, + { + "author_name": "Yang Zhang", + "author_inst": "University of Michigan" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "systems biology" + }, { "rel_doi": "10.1101/2021.12.02.470987", "rel_title": "Single immunization with recombinant ACAM2000 vaccinia viruses expressing the spike and the nucleocapsid proteins protect hamsters against SARS-CoV-2 caused clinical disease", @@ -483025,37 +484975,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2021.11.30.470640", - "rel_title": "T cell receptor repertoire signatures associated with COVID-19 severity", - "rel_date": "2021-12-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.30.470640", - "rel_abs": "T cell receptor (TCR) repertoires are critical for antiviral immunity. Determining the TCR repertoires composition, diversity, and dynamics and how they change during viral infection can inform the molecular specificity of viral infection such as SARS-CoV-2. To determine signatures associated with COVID-19 disease severity, here we performed a large-scale analysis of over 4.7 billion sequences across 2,130 TCR repertoires from COVID-19 patients and healthy donors. TCR repertoire analyses from these data identified and characterized convergent COVID-19 associated CDR3 gene usages, specificity groups, and sequence patterns. T cell clonal expansion was found to be associated with upregulation of T cell effector function, TCR signaling, NF-kB signaling, and Interferon-gamma signaling pathways. Machine learning approaches accurately predicted disease severity for patients based on TCR sequence features, with certain high-power models reaching near-perfect AUROC scores across various predictor permutations. These analyses provided an integrative, systems immunology view of T cell adaptive immune responses to COVID-19.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Jonathan Park", - "author_inst": "Yale University" - }, - { - "author_name": "Kyoung Lee", - "author_inst": "Yale University" - }, - { - "author_name": "Stanley Lam", - "author_inst": "Yale University" - }, - { - "author_name": "Sidi Chen", - "author_inst": "Yale University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.12.01.21267122", "rel_title": "Evaluating COVID-19 booster vaccination strategies in a partially vaccinated population: a modeling study.", @@ -483659,6 +485578,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.11.29.21267019", + "rel_title": "Lifestyle behaviours of children and adolescents during the first two waves of the COVID-19 pandemic in Switzerland and their relation to well-being: a population-based study", + "rel_date": "2021-12-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.29.21267019", + "rel_abs": "BackgroundPrevious studies assessing the impact of the COVID-19 pandemic on childrens and adolescents lifestyle focused mainly on the first wave in early 2020. We aimed to describe changes in adherence to recommendations for physical activity (PA), screen time (ST), and sleep duration over the first two waves of the pandemic (March-May 2020 and October 2020-January 2021) in Switzerland, and to assess the associations of these lifestyle behaviours with life satisfaction and overall health, as indicators of well-being.\n\nMethodsWe included 3168 participants aged 5 to 18 years from four Swiss cantons. Participants or their parents completed repeated questionnaires and reported on their (childs) PA, ST, sleep, life satisfaction, and overall health. We analysed lifestyle behaviours in terms of adherence to international recommendations. We used linear and logistic regression models to assess the associations of number of recommendations met and adherence patterns with well-being indicators.\n\nFindingsCompared to the pre-pandemic period, the percentage of participants meeting the recommendations for PA and ST decreased strikingly during March-May 2020, while there was a slight increase in those meeting recommendations for sleep. During October 2020-January 2021, the percentage of compliant children for PA and ST increased but remained lower than before the pandemic. Participants meeting all three recommendations were more likely to report excellent health (OR: 1{middle dot}87 [1{middle dot}15-3{middle dot}08]) and a higher life satisfaction score ({beta}: 0{middle dot}59 [0{middle dot}30-0{middle dot}88]) than participants not meeting any recommendation. Adherence to recommendations for PA and sleep, PA and ST, and sleep and ST was similarly associated with both well-being indicators.\n\nInterpretationWe show a substantial impact of the COVID-19 pandemic on childrens and adolescents lifestyle behaviours with a partial recovery over time, and an association between lifestyle and well-being. Public health policies to promote childrens and adolescents well-being should target PA, ST, and sleep simultaneously.\n\nFundingCorona Immunitas.\n\nRESEARCH IN CONTEXTO_ST_ABSEvidence before the studyC_ST_ABSWe searched PubMed for studies assessing the effects of the COVID-19 pandemic on childrens and adolescents lifestyle behaviours, published up to September 6, 2021, with no language restrictions. Of the studies found, nearly all compared lifestyle behaviours before and during the strict confinement in the first wave of the pandemic, and very few studies extended their assessment beyond June 2020. The only longitudinal study assessing lifestyle changes up to 2021 included a sample of nineteen boys. Some studies assessed the association between lifestyle behaviours and well-being after the outbreak of the pandemic, but all used a single-behaviour approach (i.e., evaluated only one lifestyle behaviour) and no study considered the combined contribution of physical activity (PA), screen time (ST), and sleep. In addition, most studies were cross-sectional and did not consider pre-pandemic lifestyle behaviours.\n\nAdded value of this studyThis is the first study assessing changes in adherence to international recommendations regarding PA, ST, and sleep duration in children and adolescents during the first two waves of the COVID-19 pandemic and the joint associations of these lifestyle behaviours with well-being. We used data from 3168 children and adolescents from four different Swiss cantons. We included measurements of PA, ST, and sleep before the pandemic, during the first wave between March and May 2020, and during the second wave between October 2020 and January 2021. We also assessed life satisfaction and overall health as indicators of well-being, between January and April 2021. We showed that, compared to the pre-pandemic period, the proportion of children and adolescents following the recommendations for PA and ST decreased during the first wave (lockdown period), while there was a slight increase in those meeting recommendations for sleep. During the second wave, the prevalence of compliant children and adolescents for PA and ST recovered but remained below pre-pandemic levels. Furthermore, we found an association between the number of recommendations met for lifestyle behaviours during the second wave and well-being assessed between January and April 2021. In contrast, there was no such association for the periods before the pandemic or during the lockdown. Participants following the recommendations for all three lifestyle behaviours or for combinations of two of them in the second wave were more likely to report excellent health and had a higher life satisfaction score, than those not meeting any recommendation.\n\nImplications of all the available evidenceOur findings demonstrate that the COVID-19 pandemic has had a strong negative effect on childrens and adolescents lifestyle behaviours, but some recovery has taken place within the first year since the outbreak. Policymakers should imperatively consider the balance of disease prevention and promotion of a healthy lifestyle when (re-)activating restrictive measures. Given the already high prevalence of children and adolescents not meeting lifestyle recommendations in the pre-pandemic period, our findings highlight the urgent need for public health policies aiming to avoid permanent negative changes on childrens and adolescents lifestyle and to mitigate the health risks associated with adverse changes during the pandemic. In addition, our study indicates that lifestyle is an important predictor of childrens and adolescents well-being, and it further suggests that future public health strategies aiming to promote well-being should target sufficient time for PA and sleep as well as reduce ST.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Gabriela P Peralta", + "author_inst": "University of Zurich" + }, + { + "author_name": "Anne-Linda Camerini", + "author_inst": "Universit\u00e0 della Svizzera italiana" + }, + { + "author_name": "Sarah R Haile", + "author_inst": "University of Zurich" + }, + { + "author_name": "Christian R Kahlert", + "author_inst": "Children's Hospital of Eastern Switzerland; Cantonal Hospital St. Gallen" + }, + { + "author_name": "Elsa Lorthe", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Laura Marciano", + "author_inst": "Universit\u00e0 della Svizzera italiana" + }, + { + "author_name": "Andres Nussbaumer", + "author_inst": "Cantonal Hospital St. Gallen" + }, + { + "author_name": "Thomas Radtke", + "author_inst": "University of Zurich" + }, + { + "author_name": "Agne Ulyte", + "author_inst": "University of Zurich" + }, + { + "author_name": "Milo A Puhan", + "author_inst": "University of Zurich" + }, + { + "author_name": "Susi Kriemler", + "author_inst": "University of Zurich" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.11.29.21267009", "rel_title": "Evaluation of Vaccination Strategies for the metropolitan area of Madrid", @@ -484847,61 +486825,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.11.28.470269", - "rel_title": "COVID-19 lung disease shares driver AT2 cytopathic features with Idiopathic pulmonary fibrosis", - "rel_date": "2021-11-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.28.470269", - "rel_abs": "BackgroundIn the aftermath of Covid-19, some patients develop a fibrotic lung disease, i.e., post-COVID-19 lung disease (PCLD), for which we currently lack insights into pathogenesis, disease models, or treatment options.\n\nMethodUsing an AI-guided approach, we analyzed > 1000 human lung transcriptomic datasets associated with various lung conditions using two viral pandemic signatures (ViP and sViP) and one covid lung-derived signature. Upon identifying similarities between COVID-19 and idiopathic pulmonary fibrosis (IPF), we subsequently dissected the basis for such similarity from molecular, cytopathic, and immunologic perspectives using a panel of IPF-specific gene signatures, alongside signatures of alveolar type II (AT2) cytopathies and of prognostic monocyte-driven processes that are known drivers of IPF. Transcriptome-derived findings were used to construct protein-protein interaction (PPI) network to identify the major triggers of AT2 dysfunction. Key findings were validated in hamster and human adult lung organoid (ALO) pre-clinical models of COVID-19 using immunohistochemistry and qPCR.\n\nFindingsCOVID-19 resembles IPF at a fundamental level; it recapitulates the gene expression patterns (ViP and IPF signatures), cytokine storm (IL15-centric), and the AT2 cytopathic changes, e.g., injury, DNA damage, arrest in a transient, damage-induced progenitor state, and senescence-associated secretory phenotype (SASP). These immunocytopathic features were induced in pre-clinical COVID models (ALO and hamster) and reversed with effective anti-CoV-2 therapeutics in hamsters. PPI-network analyses pinpointed ER stress as one of the shared early triggers of both diseases, and IHC studies validated the same in the lungs of deceased subjects with COVID-19 and SARS-CoV-2-challenged hamster lungs. Lungs from tg-mice, in which ER stress is induced specifically in the AT2 cells, faithfully recapitulate the host immune response and alveolar cytopathic changes that are induced by SARS-CoV-2.\n\nInterpretationLike IPF, COVID-19 may be driven by injury-induced ER stress that culminates into progenitor state arrest and SASP in AT2 cells. The ViP signatures in monocytes may be key determinants of prognosis. The insights, signatures, disease models identified here are likely to spur the development of therapies for patients with IPF and other fibrotic interstitial lung diseases.\n\nFundingThis work was supported by the National Institutes for Health grants R01-GM138385 and AI155696 and funding from the Tobacco-Related disease Research Program (R01RG3780).\n\nOne Sentence SummarySevere COVID-19 triggers cellular processes seen in fibrosing Interstitial Lung Disease\n\nRESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSIn its aftermath, the COVID-19 pandemic has left many survivors, almost a third of those who recovered, with a mysterious long-haul form of the disease which culminates in a fibrotic form of interstitial lung disease (post-COVID-19 ILD). Post-COVID-19 ILD remains a largely unknown entity. Currently, we lack insights into the core cytopathic features that drive this condition.\n\nAdded value of this studyUsing an AI-guided approach, which involves the use of sets of gene signatures, protein-protein network analysis, and a hamster model of COVID-19, we have revealed here that COVID-19 -lung fibrosis resembles IPF, the most common form of ILD, at a fundamental level--showing similar gene expression patterns in the lungs and blood, and dysfunctional AT2 processes (ER stress, telomere instability, progenitor cell arrest, and senescence). These findings are insightful because AT2 cells are known to contain an elegant quality control network to respond to intrinsic or extrinsic stress; a failure of such quality control results in diverse cellular phenotypes, of which ER stress appears to be a point of convergence, which appears to be sufficient to drive downstream fibrotic remodeling in the lung.\n\nImplications of all the available evidenceBecause unbiased computational methods identified the shared fundamental aspects of gene expression and cellular processes between COVID-19 and IPF, the impact of our findings is likely to go beyond COVID-19 or any viral pandemic. The insights, tools (disease models, gene signatures, and biomarkers), and mechanisms identified here are likely to spur the development of therapies for patients with IPF and, other fibrotic interstitial lung diseases, all of whom have limited or no treatment options. To dissect the validated prognostic biomarkers to assess and track the risk of pulmonary fibrosis and develop therapeutics to halt fibrogenic progression.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Saptarshi Sinha", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Vanessa Castillo", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Celia R. Espinoza", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Courtney Tindle", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Ayden G. Fonseca", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Jennifer M Dan", - "author_inst": "La Jolla Institute for Allergy and Immunology" - }, - { - "author_name": "Gajanan D. Katkar", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Soumita Das", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Debashis Sahoo", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Pradipta Ghosh", - "author_inst": "University of California, San Diego" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.11.26.470043", "rel_title": "A recombinant SARS-CoV-2 RBD antigen expressed in insect cells elicits immunogenicity and confirms safety in animal models", @@ -485961,6 +487884,41 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.11.29.470414", + "rel_title": "Th1, Th2 and Th17 inflammatory pathways synergistically correlate with cardiometabolic processes. A case study in COVID-19.", + "rel_date": "2021-11-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.29.470414", + "rel_abs": "A predominant source of complication in SARS-CoV-2 patients arises from the cytokine storm, an elevated expression of inflammatory helper T-cell associated cytokines that can lead to tissue damage and organ failure. The high inflammatory burden of this viral infection often results in cardiovascular comorbidities. A better understanding of the interaction between the cytokine storm and cardiovascular proteins might inform medical decisions and therapeutic approaches. We hypothesized that all major helper T-cell inflammatory pathways (Th1, Th2 and Th17) synergistically contribute to cardiometabolic modifications in serum of COVID-19 patients. We proved our hypothesis by integrating Th1, Th2 and Th17 cytokines to predict expression of cardiometabolic proteins profiled by OLINK proteomics.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "James R Michels", + "author_inst": "University of Mississippi" + }, + { + "author_name": "Mohammad Shaheed Nazrul", + "author_inst": "University of Mississippi" + }, + { + "author_name": "Sudeep Adhikari", + "author_inst": "University of Mississippi" + }, + { + "author_name": "Dawn Wilkins", + "author_inst": "University of Mississippi" + }, + { + "author_name": "Ana B Pavel", + "author_inst": "University of Mississippi" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.11.29.21267032", "rel_title": "Use of heat-not-burn tobacco products, moderate alcohol drinking, and anti-SARS-CoV-2 IgG antibody titers after BNT162b2 vaccination among Japanese healthcare workers", @@ -486813,61 +488771,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.11.29.21266617", - "rel_title": "Unequal impact of the COVID-19 pandemic on excess deaths, life expectancy, and premature mortality across Spanish regions in 2020 and 2021", - "rel_date": "2021-11-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.29.21266617", - "rel_abs": "Spain is one of the most heavily affected countries by the Covid-19 pandemic. In this study, we estimated the regional inequalities in excess deaths and premature mortality in Spain. Between January 2020 and June 2021, an estimated 89,200 (men: 48,000; women: 41,200) excess deaths occurred in the 17 Spanish regions with a substantial variability (highest in Madrid: 22,000, lowest in Canary Islands: -210). Highest reductions in life expectancy at birth (e0) in 2020 were observed in Madrid (men: -3.48 years, women: -2.15), Castile La Mancha (men: -2.67, women: -2.30), and Castile and Leon (men: -2.00, women: -1.32). In the first six months of 2021, the highest reduction in e0 was observed in Valencian Community (men: -2.04, women: -1.63), Madrid (men: - 2.37), and Andalusia (men: -1.75; women: -1.43). In some Spanish regions, life expectancy at age 65 during the Covid-19 pandemic in 2020 was comparable to that observed as far back as 20 years ago.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Nazrul Islam", - "author_inst": "University of Oxford" - }, - { - "author_name": "Fernando J. Garcia Lopez", - "author_inst": "Instituto de Salud Carlos III" - }, - { - "author_name": "Dmitri A. Jdanov", - "author_inst": "Max Planck Institute for Demographic Research" - }, - { - "author_name": "Miguel Angel Royo-Bordonada", - "author_inst": "Spanish National School of Public Health" - }, - { - "author_name": "Kamlesh Khunti", - "author_inst": "University of Leicester" - }, - { - "author_name": "Sarah Lewington", - "author_inst": "University of Oxford" - }, - { - "author_name": "Ben Lacey", - "author_inst": "University of Oxford" - }, - { - "author_name": "Martin White", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Eva JA Morris", - "author_inst": "University of Oxford" - }, - { - "author_name": "Maria Victoria Zunzunegui", - "author_inst": "Universite de Montreal" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.11.25.21266848", "rel_title": "Evaluating the impact of a pulse oximetry remote monitoring programme on mortality and healthcare utilisation in patients with covid-19 assessed in Accident and Emergency departments in England: a retrospective matched cohort study", @@ -487571,6 +489474,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.11.25.21266704", + "rel_title": "A fourth dose of the mRNA-1273 SARS-CoV-2 vaccine improves serum neutralization against the delta variant in kidney transplant recipients", + "rel_date": "2021-11-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.25.21266704", + "rel_abs": "In immunocompetent subjects, the effectiveness of SARS-CoV-2 vaccines against the delta variant appears three- to five-fold lower than that observed against the alpha variant. Additionally, three doses of SARS-CoV-2 mRNA-based vaccines might be unable to elicit a sufficient immune response against any variant in immunocompromised kidney transplant recipients. This study describes the kinetics of the neutralizing antibody (NAbs) response against the delta strain before and after a fourth dose of a mRNA vaccine in 67 kidney transplant recipients who had experienced a weak antibody response after three doses. While only 16% of patients harbored NAbs against the delta strain prior to the fourth injection - this percentage raised to 66% afterwards. We also found that, after the fourth dose, the NAbs titer increased significantly (p=0.0001) from <7.5 (IQR : <7.5-15.1) to 47.1 (IQR <7.5-284.2). Collectively, our data indicate that a fourth dose of the mRNA-1273 vaccine in kidney transplant recipients with a weak antibody response after three previous doses improves serum neutralization against the delta variant.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Ilies Benotmane", + "author_inst": "Hopitaux universitaires de Strasbourg" + }, + { + "author_name": "Timoth\u00e9e Bruel", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Delphine Planas", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Samira Fafi-Kremer", + "author_inst": "Hopitaux universitaires de Strasbourg" + }, + { + "author_name": "Olivier Schwartz", + "author_inst": "Institut Psateur" + }, + { + "author_name": "Sophie Caillard", + "author_inst": "Hopitaux Universitaires de Strasbourg" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "transplantation" + }, { "rel_doi": "10.1101/2021.11.26.21266650", "rel_title": "Community healthcare workers' experiences during and after COVID-19 lockdown: a qualitative study from Aotearoa New Zealand", @@ -488643,37 +490585,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.11.24.21266757", - "rel_title": "Exploring the Temporal Dynamics of County-Level Vulnerability Factors on COVID-19 Outcomes", - "rel_date": "2021-11-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.24.21266757", - "rel_abs": "As the outbreak of COVID-19 has become a severe worldwide pandemic, every country fights against the spread of this deadly disease with incredible efforts. There are numerous researches along with every conceivable dimension for COVID-19. Among these researches, different demographic and contextual factors of populations and communities also play an essential role in providing more information for decision-makers. This paper mainly utilizes existing data on county contextual factors at the United States county-level to develop a model that can capture the dynamic trajectory of COVID-19 (i.e., cases) and its impacts across the United States. Moreover, our methods applied to contextual data achieves better results compared with existing measures of vulnerability.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Jing Zhang", - "author_inst": "Emory University" - }, - { - "author_name": "Daesung Choi", - "author_inst": "Emory University" - }, - { - "author_name": "Shivani A. Patel", - "author_inst": "Emory University" - }, - { - "author_name": "Joyce C. Ho", - "author_inst": "Emory University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.11.24.21266396", "rel_title": "High Burden of COVID-19 among Unvaccinated Law Enforcement Officers and Firefighters", @@ -489457,6 +491368,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.11.21.21264092", + "rel_title": "Distribution of confirmed with COVID-19 by age and gender in Mexico", + "rel_date": "2021-11-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.21.21264092", + "rel_abs": "Social, economic, and cultural factors can influence the likelihood of exposure to the virus of each person in sanitary emergencies like those of COVID-19. In this sense, parallel to the biological vulnerability to infection with SARS-CoV-2, said factors determine a complementary vulnerability to infection. Hence, they can influence in gender and age distributions of those confirmed, which is not entirely comprehended yet. The effect that age and gender can have on total vulnerability in Mexico thus far is not understood. A better understanding of such dependence can help policy optimization and decision-making to future similar emergencies. We aim to study the age and gender distributions of those confirmed with COVID-19 in Mexico. We also investigate the vulnerability to the infection with SARS-CoV-2 depending on such features. Two different samples of the Mexican population are analyzed in this non-experimental study to compare each other and evaluate the association of the result of the COVID-19 test with gender and age. Data up until the beginning of the vaccination are considered. The percentage of confirmed males is higher than females in both samples, and most tested and confirmed are working-age. Age distributions are positively skewed, with the peak in [30,39] years, which disagrees with the distribution of the Mexican population. The data suggest that the vulnerability to infection weakly depends on gender and age. Males were identified as the most vulnerable gender, and the age group [70,79] showed a higher vulnerability to infection.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Adalberto Maldonado", + "author_inst": "BMSA Group" + }, + { + "author_name": "Marco Antonio Reyes", + "author_inst": "BMSA Group" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.11.23.21266785", "rel_title": "A RANDOMIZED CLINICAL TRIAL OF 2-WEEK METHOTREXATE DISCONTINUATION IN RHEUMATOID ARTHRITIS PATIENTS VACCINATED WITH INACTIVATED SARS-COV-2 VACCINE", @@ -490505,25 +492439,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.11.22.21266669", - "rel_title": "The Failures of an Ideal COVID-19 Vaccine: A Simulation Study", - "rel_date": "2021-11-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.22.21266669", - "rel_abs": "This paper simulates an ideal COVID-19 vaccine that confers immediate sterilizing immunity against all SARS-CoV-2 variants. The purpose was to explore how well this ideal vaccine could protect a population against common conditions (such as vaccine hesitancy) that might impair vaccine effectiveness. Simulations were done with an SEIRS spreadsheet model that ran two parallel subpopulations: one that accepted vaccination, and another that refused it. The two subpopulations could transmit infections to one another. Success was judged by the rate of new cases in the period from 1-5 years after the introduction of the vaccine.\n\nUnder good conditions, including a small subpopulation that refused vaccination, rapid distribution of the vaccine, duration of vaccinal immunity longer than 12 months, good retention of interest in getting vaccinated after the first year, strict maintenance of nonpharmaceutical interventions (NPIs) such as masking, and new variants with R0s less than 4.0, the vaccine was able to end the epidemic. With violation of these conditions, the post-vaccine era futures ranged from endemic COVID at a low or medium level to rates of COVID cases worse than anything seen in the US up to late 2021. The most important conditions for keeping case rates low were a fast speed of vaccine distribution, a low percentage of the population that refuses vaccination, a long duration of vaccinal immunity, and continuing maintenance of NPIs after vaccination began. On the other hand, a short duration of vaccinal immunity, abandonment of NPIs, and new variants with a high R0 were powerful barriers to disease control. New variants with high R0s were particularly damaging, producing high case rates except when vaccination speed was unrealistically rapid. A recurring finding was that most disease afflicting the vaccinated population in these simulations originated in the unvaccinated population, and cutting off interaction with the unvaccinated population caused a sharp drop in the case rate of the vaccinated population.\n\nIn conclusion, multiple common conditions can compromise the effectiveness of even an \"ideal\" vaccine.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Robert Joseph Kosinski", - "author_inst": "retired from Clemson University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.11.22.21266719", "rel_title": "Development and Performance verification of colloidal gold labeled SARS-CoV-2 antigen detection method for routine popular screening of COVID-19 with clinical samples in Poland and China", @@ -491415,6 +493330,57 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.11.23.469714", + "rel_title": "LRRC15 is an inhibitory receptor blocking SARS-CoV-2 spike-mediated entry in trans", + "rel_date": "2021-11-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.23.469714", + "rel_abs": "SARS-CoV-2 infection is mediated by the entry receptor ACE2. Although attachment factors and co-receptors facilitating entry are extensively studied, cellular entry factors inhibiting viral entry are largely unknown. Using a surfaceome CRISPR activation screen, we identified human LRRC15 as an inhibitory receptor for SARS-CoV-2 entry. LRRC15 directly binds to the receptor-binding domain (RBD) of spike protein with a moderate affinity and inhibits spike-mediated entry. Analysis of human lung single cell RNA sequencing dataset reveals that expression of LRRC15 is primarily detected in fibroblasts and particularly enriched in pathological fibroblasts in COVID-19 patients. ACE2 and LRRC15 are not co-expressed in the same cell types in the lung. Strikingly, expression of LRRC15 in ACE2-negative cells blocks spike-mediated viral entry in ACE2+ cell in trans, suggesting a protective role of LRRC15 in a physiological context. Therefore, LRRC15 represents an inhibitory receptor for SARS-CoV-2 regulating viral entry in trans.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Jaewon Song", + "author_inst": "Brown University" + }, + { + "author_name": "Ryan D Chow", + "author_inst": "Yale University" + }, + { + "author_name": "Mario Pena-Hernandez", + "author_inst": "Yale University" + }, + { + "author_name": "Li Zhang", + "author_inst": "Brown University" + }, + { + "author_name": "Skylar A Loeb", + "author_inst": "Brown University" + }, + { + "author_name": "Eui-Young So", + "author_inst": "Brown University" + }, + { + "author_name": "Olin D Liang", + "author_inst": "Brown University" + }, + { + "author_name": "Craig B Wilen", + "author_inst": "Yale University" + }, + { + "author_name": "Sanghyun Lee", + "author_inst": "Brown University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.11.23.469695", "rel_title": "Antiviral activity of molnupiravir precursor NHC against Variants of Concern (VOCs) and its therapeutic window in a human lung cell model", @@ -492247,69 +494213,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2021.11.22.469576", - "rel_title": "A modified porous silicon microparticle promotes mucosal delivery of SARS-CoV-2 antigen and induction of potent and durable systemic and mucosal T helper 1 skewed protective immunity", - "rel_date": "2021-11-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.22.469576", - "rel_abs": "Development of optimal SARS-CoV-2 vaccines to induce potent, long-lasting immunity and provide cross-reactive protection against emerging variants remains a high priority. Here, we report that a modified porous silicon microparticle (mPSM)-adjuvanted SARS-CoV-2 receptor-binding domain (RBD) vaccine activated dendritic cells and generated more potent and durable SARS-CoV-2-specific systemic humoral and type 1 helper T (Th) cell-mediated immune responses than alum-formulated RBD following parenteral vaccination, and protected mice from SARS-CoV-2 and Beta variant infection. mPSM facilitated the uptake of SARS-CoV-2 RBD antigens by nasal and airway epithelial cells. Parenteral and intranasal prime and boost vaccinations with mPSM-RBD elicited potent systemic and lung resident memory T and B cells and SARS-CoV-2 specific IgA responses, and markedly diminished viral loads and inflammation in the lung following SARS-CoV-2 Delta variant infection. Our results suggest that mPSM can serve as potent adjuvant for SARS-CoV-2 subunit vaccine which is effective for systemic and mucosal vaccination.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Qing Shi", - "author_inst": "Department of Nanomedicine, Houston Methodist Academic Institute, Houston, TX 77030" - }, - { - "author_name": "Binbin Wang", - "author_inst": "Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA" - }, - { - "author_name": "Jing Zou", - "author_inst": "Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA" - }, - { - "author_name": "Junhua Mai", - "author_inst": "Department of Nanomedicine, Houston Methodist Academic Institute, Houston, TX 77030" - }, - { - "author_name": "Samantha R Osman", - "author_inst": "Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA" - }, - { - "author_name": "Wenzhe Wu", - "author_inst": "Department of Pediatrics, The University of Texas Medical Branch, Galveston, TX 77555, USA" - }, - { - "author_name": "Xuping Xie", - "author_inst": "Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA" - }, - { - "author_name": "Patricia V Aguilar", - "author_inst": "Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA." - }, - { - "author_name": "Xiaoyong Bao", - "author_inst": "Department of Pediatrics, The University of Texas Medical Branch, Galveston, TX 77555, USA" - }, - { - "author_name": "Pei-Yong Shi", - "author_inst": "Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA" - }, - { - "author_name": "Haifa Shen", - "author_inst": "Department of Nanomedicine, Houston Methodist Academic Institute, Houston, TX 77030" - }, - { - "author_name": "Tian Wang", - "author_inst": "Department of Microbiology & Immunology, The University of Texas Medical Branch, Galveston, TX, 77555, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.11.23.469663", "rel_title": "SARS-CoV-2 variants of concern Alpha, Beta, Gamma and Delta have extended ACE2 receptor host-ranges", @@ -493165,6 +495068,209 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2021.11.17.468943", + "rel_title": "SARS-CoV-2 papain-like protease PLpro in complex with natural compounds reveal allosteric sites for antiviral drug design", + "rel_date": "2021-11-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.17.468943", + "rel_abs": "SARS-CoV-2 papain-like protease (PLpro) covers multiple functions. Beside the cysteine-protease activity, PLpro has the additional and vital function of removing ubiquitin and ISG15 (Interferon-stimulated gene 15) from host-cell proteins to aid coronaviruses in evading the hosts innate immune responses. We established a high-throughput X-ray screening to identify inhibitors by elucidating the native PLpro structure refined to 1.42 [A] and performing co-crystallization utilizing a diverse library of selected natural compounds. We identified three phenolic compounds as potential inhibitors. Crystal structures of PLpro inhibitor complexes, obtained to resolutions between 1.7-1.9 [A], show that all three compounds bind at the ISG15/Ub-S2 allosteric binding site, preventing the essential ISG15-PLpro molecular interactions. All compounds demonstrate clear inhibition in a deISGylation assay, two exhibit distinct antiviral activity and one inhibited a cytopathic effect in a non-cytotoxic concentration range. These results highlight the druggability of the rarely explored ISG15/Ub-S2 PLpro allosteric binding site to identify new and effective antiviral compounds. Importantly, in the context of increasing PLpro mutations in the evolving new variants of SARS-CoV-2, the natural compounds we identified may also reinstate the antiviral immune response processes of the host that are down-regulated in COVID-19 infections.", + "rel_num_authors": 47, + "rel_authors": [ + { + "author_name": "Vasundara Srinivasan", + "author_inst": "University of Hamburg" + }, + { + "author_name": "Hevila Brognaro", + "author_inst": "Universitaet Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation," + }, + { + "author_name": "Prince Rajaiah Prabhu", + "author_inst": "Universitaet Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation," + }, + { + "author_name": "Edmarci Elisa de Souza", + "author_inst": "Department of Parasitology,Institute of Biomedical Sciences, University of Sao Paulo" + }, + { + "author_name": "Sebastian Guenther", + "author_inst": "Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY" + }, + { + "author_name": "Patrick Y. A. Reinke", + "author_inst": "Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY" + }, + { + "author_name": "Thomas J. Lane", + "author_inst": "Universitaet Hamburg, Hamburg Centre for Ultrafast Imaging (CUI), Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY" + }, + { + "author_name": "Helen Ginn", + "author_inst": "Diamond Light Source Ltd. Diamond House, Harwell Science and Innovation Campus" + }, + { + "author_name": "Huijong Han", + "author_inst": "European XFEL GmbH" + }, + { + "author_name": "Wiebke Ewert", + "author_inst": "Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY" + }, + { + "author_name": "Janina Sprenger", + "author_inst": "Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY" + }, + { + "author_name": "Faisal H. M. Koua", + "author_inst": "Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY" + }, + { + "author_name": "Sven Falke", + "author_inst": "Universitaet Hamburg, Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY" + }, + { + "author_name": "Nadine Werner", + "author_inst": "Universitaet Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation," + }, + { + "author_name": "Hina Andaleeb", + "author_inst": "Universitaet Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation," + }, + { + "author_name": "Najeeb Ullah", + "author_inst": "Universitaet Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation," + }, + { + "author_name": "Bruno Alves Franca", + "author_inst": "Universitaet Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation," + }, + { + "author_name": "Mengying Wang", + "author_inst": "Universitaet Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation," + }, + { + "author_name": "Angelica Luana C Barra", + "author_inst": "Universitaet Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation," + }, + { + "author_name": "Markus Perbandt", + "author_inst": "Universitaet Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation," + }, + { + "author_name": "Martin Schwinzer", + "author_inst": "Universitaet Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation," + }, + { + "author_name": "Christina Schmidt", + "author_inst": "European XFEL GmbH" + }, + { + "author_name": "Lea Brings", + "author_inst": "European XFEL GmbH" + }, + { + "author_name": "Kristina Lorenzen", + "author_inst": "European XFEL GmbH" + }, + { + "author_name": "Robin Schubert", + "author_inst": "European XFEL GmbH" + }, + { + "author_name": "Rafael Rahal Guaragna Machado", + "author_inst": "Department of Microbiology, Institute of Biomedical Sciences,University of Sao Paulo" + }, + { + "author_name": "Erika Donizette Candido", + "author_inst": "Department of Microbiology, Institute of Biomedical Sciences,University of Sao Paulo" + }, + { + "author_name": "Danielle Bruna Leal Oliveira", + "author_inst": "Department of Microbiology, Institute of Biomedical Sciences,University of Sao Paulo;Clinical Laboratory, Hospital Israelita Albert Einstein" + }, + { + "author_name": "Edison Luiz Durigon", + "author_inst": "Department of Microbiology, Institute of Biomedical Sciences,University of Sao Paulo;Scientific Platform Pasteur USP" + }, + { + "author_name": "Oleksandr Yefanov", + "author_inst": "Hamburg Centre for Ultrafast Imaging (CUI), Universitaet Hamburg" + }, + { + "author_name": "Julia Lieske", + "author_inst": "Hamburg Centre for Ultrafast Imaging (CUI), Universitaet Hamburg" + }, + { + "author_name": "Luca Gelisio", + "author_inst": "Hamburg Centre for Ultrafast Imaging (CUI), Universitaet Hamburg" + }, + { + "author_name": "Martin Domaracky", + "author_inst": "Hamburg Centre for Ultrafast Imaging (CUI), Universitaet Hamburg" + }, + { + "author_name": "Philipp Middendorf", + "author_inst": "Hamburg Centre for Ultrafast Imaging (CUI), Universitaet Hamburg" + }, + { + "author_name": "Michael Groessler", + "author_inst": "Hamburg Centre for Ultrafast Imaging (CUI), Universitaet Hamburg" + }, + { + "author_name": "Fabian Trost", + "author_inst": "Hamburg Centre for Ultrafast Imaging (CUI), Universitaet Hamburg" + }, + { + "author_name": "Marina Galchenkova", + "author_inst": "Hamburg Centre for Ultrafast Imaging (CUI), Universitaet Hamburg" + }, + { + "author_name": "Sofiane Saouane", + "author_inst": "Photon Science, Deutsches Elektronen Synchrotron (DESY)" + }, + { + "author_name": "Johanna Hakanpaeae", + "author_inst": "Photon Science, Deutsches Elektronen Synchrotron (DESY)" + }, + { + "author_name": "Markus Wolf", + "author_inst": "Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP)" + }, + { + "author_name": "Dusan Turk", + "author_inst": "Department of Biochemistry & Molecular & Structural Biology, Jozef Stefan Institute;Centre of excellence for Integrated Approaches in Chemistry and Biology of P" + }, + { + "author_name": "Arwen R. Pearson", + "author_inst": "Hamburg Centre for Ultrafast Imaging (CUI), Universitaet Hamburg,Universitaet Hamburg, Institut fuer Nanostruktur- und Festkoerperphysik" + }, + { + "author_name": "Henry N. Chapman", + "author_inst": "Hamburg Centre for Ultrafast Imaging (CUI), Universitaet Hamburg,Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY,Department " + }, + { + "author_name": "Winfried Hinrichs", + "author_inst": "Universitaet Greifswald, Institute of Biochemistry" + }, + { + "author_name": "Carsten Wrenger", + "author_inst": "Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo" + }, + { + "author_name": "Alke Meents", + "author_inst": "Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY" + }, + { + "author_name": "Christian Betzel", + "author_inst": "Universitaet Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation," + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2021.11.19.469183", "rel_title": "Self-assembling short immunostimulatory duplex RNAs with broad spectrum antiviral activity", @@ -494013,113 +496119,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.18.21266502", - "rel_title": "Limited immune responses after three months of BNT162b2 vaccine in SARS-CoV-2 uninfected elders living in long-term care facilities", - "rel_date": "2021-11-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.18.21266502", - "rel_abs": "BackgroundSARS-CoV-2 vaccination is the most effective strategy to protect elders living in long-term care facilities (LTCF) against severe COVID-19, but primary vaccine responses are less effective in older adults. Here, we characterized the humoral responses following 3 months after mRNA/BNT162b2 vaccine in institutionalized elders.\n\nMethodsPlasma levels of specific SARS-CoV-2 total IgG, IgM and IgA antibodies were measured before and 3 months after vaccination in elders living in LTCF. Neutralization capacity was assessed in a pseudovirus neutralization assay against WH1 (original) and B.1.617.2/Delta variants. A group of younger adults was used as reference group.\n\nResultsThree months after vaccination, uninfected-elders presented reduced specific SARS-CoV-2 IgG levels and significantly lower neutralization capacity against the WH1 and Delta virus compared to vaccinated uninfected younger individuals. In contrast, COVID-19 recovered elders showed significantly higher specific SARS-CoV-2 IgG levels after vaccination than younger counterparts, while showing similar neutralization activity against WH1 virus and increased neutralization capacity against Delta variant. Despite previously infected elders elicit potent cross-reactive immune responses similarly to younger individuals, higher quantities of specific SARS-CoV-2 IgG antibodies are required to reach the same neutralization levels.\n\nConclusionsWhile hybrid immunity seems to be active in previously infected elders after three months from mRNA/BNT162b2 vaccination, humoral immune responses are diminished in COVID-19 uninfected vaccinated residents living in LTCF. These results suggests that a vaccine booster dose should be prioritized for this particularly vulnerable population.\n\nWord summaryWhile previously infected and vaccinated elders living in LTCF had comparable neutralizing antibody levels to younger individuals, vaccinated uninfected-residents showed limited neutralization capacity against both original and delta variants. Hybrid immunity seems to be active in elders and can be relevant to design vaccine boosting campaigns.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Macedonia Trigueros", - "author_inst": "IrsiCaixa AIDS Research Institute" - }, - { - "author_name": "Edwards Pradenas", - "author_inst": "IrsiCaixa AIDS Research Institute" - }, - { - "author_name": "Dolors Palacin", - "author_inst": "Direccio d'Atencio Primaria Metropolitana Nord" - }, - { - "author_name": "Carlos Avila-Nieto", - "author_inst": "IrsiCaixa AIDS Research Institute" - }, - { - "author_name": "Benjamin Trinite", - "author_inst": "IrsiCaixa AIDS Research Institute" - }, - { - "author_name": "Josep Maria Bonet-Simo", - "author_inst": "Direccio d'Atencio Primaria Metropolitana Nord" - }, - { - "author_name": "Mar Isnard", - "author_inst": "Direccio d'Atencio Primaria Metropolitana Nord" - }, - { - "author_name": "Nemesio Moreno", - "author_inst": "Direccio d'Atencio Primaria Metropolitana Nord" - }, - { - "author_name": "Silvia Marfil", - "author_inst": "IrsiCaixa AIDS Research Institute" - }, - { - "author_name": "Carla Rovirosa", - "author_inst": "IrsiCaixa AIDS Research Institute" - }, - { - "author_name": "Teresa Puig", - "author_inst": "IrsiCaixa AIDS Research Institute" - }, - { - "author_name": "Eulalia Grau", - "author_inst": "IrsiCaixa AIDS Research Institute" - }, - { - "author_name": "Anna Chamorro", - "author_inst": "Fight against AIDS Foundation" - }, - { - "author_name": "Ana Martinez", - "author_inst": "Fight against AIDS Foundation" - }, - { - "author_name": "Ruth Toledo", - "author_inst": "Fight against AIDS Foundation" - }, - { - "author_name": "Marta Font", - "author_inst": "Fight against AIDS Foundation" - }, - { - "author_name": "Jordi Ara", - "author_inst": "Germans Trias i Pujol Hospital and Universitat Autonoma de Barcelona" - }, - { - "author_name": "Jorge Carrillo", - "author_inst": "IrsiCaixa AIDS Research Institute" - }, - { - "author_name": "Lourdes Mateu", - "author_inst": "Hospital Germans Trias i Pujol" - }, - { - "author_name": "Julia Blanco", - "author_inst": "IrsiCaixa AIDS Reseach Institute" - }, - { - "author_name": "Bonaventura Clotet", - "author_inst": "AIDS Research Institute IrsiCaixa" - }, - { - "author_name": "Nuria Prat", - "author_inst": "Direccio d'Atencio Primaria Metropolitana Nord" - }, - { - "author_name": "Marta Massanella", - "author_inst": "AIDS Research Institute IrsiCaixa" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.17.21266463", "rel_title": "How many relevant SARS-CoV-2 variants might we expect in the future?", @@ -494771,6 +496770,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.11.19.21266612", + "rel_title": "Race-Specific, U.S. State-Specific COVID-19 Vaccination Rates Adjusted for Age", + "rel_date": "2021-11-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.19.21266612", + "rel_abs": "We provide the first age-standardized race/ethnicity-specific, state-specific vaccination rates for the United States, encompassing all states reporting race/ethnicity-specific vaccinations. The data reflect vaccinations through mid-October 2021. We use indirect age standardization to compare racial/ethnic state vaccination rates to national age-specific vaccination patterns. Results show that white and Black state median vaccination rates are, respectively, 89% and 76% of what would be predicted based on age; Hispanic and Native rates are almost identical to what would be predicted; and Asian-American/Pacific Islander rates are 110% of what would be predicted. We also find that racial/ethnic group vaccination rates are associated with state politics, as proxied by 2020 Trump vote share: for each percentage point increase in 2020 Trump vote share, vaccination rates decline by 1.08 percent of what would be predicted based on age. This decline is sharpest for Native American populations, although Native vaccinations are reported for relatively few states.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Elizabeth Wrigley-Field", + "author_inst": "University of Minnesota, Twin Cities" + }, + { + "author_name": "Kaitlyn M. Berry", + "author_inst": "University of Minnesota School of Public Health" + }, + { + "author_name": "Govind Persad", + "author_inst": "Sturm College of Law, University of Denver" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.11.20.21266640", "rel_title": "Patient experience with healthcare: Feedback for a Post COVID-19 clinic at a tertiary care center in rural area", @@ -495711,77 +497737,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.15.21266284", - "rel_title": "Symptomatic and asymptomatic transmission of SARS-CoV-2 in K-12 schools, British Columbia, April to June 2021", - "rel_date": "2021-11-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.15.21266284", - "rel_abs": "We prospectively studied SARS-CoV-2 transmission at schools in an era of Variants of Concern (VoCs), offering all close contacts serial viral asymptomatic testing up to 14 days. Of 229 school close contacts, 3 tested positive (1.3%), of which 2 were detected through asymptomatic testing. Most secondary transmission (90%) occurred in households. Routine asymptomatic testing of close contacts should be examined in the context of local testing rates, preventive measures, programmatic costs, and health impacts of asymptomatic transmission.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Alex Choi", - "author_inst": "Vancouver Coastal Health, Vancouver, BC, Canada" - }, - { - "author_name": "Louise Masse", - "author_inst": "BC Childrens Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada" - }, - { - "author_name": "Samantha Bardwell", - "author_inst": "University of British Columbia, Vancouver, BC, Canada" - }, - { - "author_name": "Yanjie Zhao", - "author_inst": "Vancouver Coastal Health, Vancouver, BC, Canada" - }, - { - "author_name": "Yang Xin Zi Xu", - "author_inst": "Vancouver Coastal Health, Vancouver, BC, Canada" - }, - { - "author_name": "Ani Markarian", - "author_inst": "Vancouver Coastal Health, Vancouver, BC, Canada" - }, - { - "author_name": "Daniel Coombs", - "author_inst": "University of British Columbia, Vancouver, BC, Canada" - }, - { - "author_name": "Allison Watts", - "author_inst": "Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada" - }, - { - "author_name": "Adrienne Macdonald", - "author_inst": "Vancouver Coastal Health, Vancouver, BC, Canada" - }, - { - "author_name": "Nalin Dhillon", - "author_inst": "Vancouver Coastal Health, Vancouver, BC, Canada" - }, - { - "author_name": "Michael Irvine", - "author_inst": "British Columbia Centre for Disease Control, Vancouver, BC, Canada" - }, - { - "author_name": "Collette O'Reilly", - "author_inst": "Vancouver School District, Vancouver, BC, Canada" - }, - { - "author_name": "Pascal M. Lavoie", - "author_inst": "BC Childrens Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada" - }, - { - "author_name": "David M. Goldfarb", - "author_inst": "BC Childrens Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.11.17.21266415", "rel_title": "Durability of anti-Spike antibodies in the infant after maternal COVID-19 vaccination", @@ -496469,6 +498424,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.11.17.468980", + "rel_title": "Nanoviricides platform technology based NV-CoV-2 polymer increases the half-life of Remdesivir in vivo", + "rel_date": "2021-11-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.17.468980", + "rel_abs": "So far, there are seven coronaviruses identified that infect humans and only 4 of them belong to the beta family of coronavirus (HCoV-HKU1, SARS-CoV-2, MERS-CoV and SARS-CoV). SARS family are known to cause severe respiratory disease in humans. In fact, SARS-CoV-2 infection caused a pandemic COVID-19 disease with high morbidity and mortality. Remdesivir (RDV) is the only antiviral drug so far approved for COVID-19 therapy by the FDA. However, the efficacy of RDV in vivo is limited due to its low stability in presence of plasma. This is the report of analysis of the non-clinical pharmacology study of NV-CoV-2 (Polymer) and NV-CoV-2-R (Polymer encapsulated Remdesivir) in both infected and uninfected rats with SARS-CoV-2.\n\nDetection and quantification of NV-CoV-2-R in plasma samples was done by MS-HPLC chromatography analyses of precipitated plasma samples from rat subjects.\n\nO_LINV-CoV-2-R show RDV peak in MS-HPLC chromatography, whereas only NV-CoV-2 does not show any RDV-Peak, as expected.\nC_LIO_LINV-CoV-2 polymer encapsulation protects RDV in vivo from plasma-mediated catabolism.\nC_LIO_LIBody weight measurements of the normal (uninfected) rats after administration of the test materials (NV-CoV-2, and NV-CoV-2-R) show no toxic effects on them.\nC_LI\n\nOur platform technology based NV-387-encapsulated-RDV (NV-CoV-2-R) drug has a dual effect on coronaviruses. First, NV-CoV-2 itself as an antiviral regimen. Secondly, RDV is protected from plasma-mediated degradation in transit, rendering altogether the safest and an efficient regimen against COVID-19.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Ashok Chakraborty", + "author_inst": "Allexcel" + }, + { + "author_name": "Anil Diwan", + "author_inst": "Nanoviricides, inc" + }, + { + "author_name": "Vinod Arora", + "author_inst": "Allexcel, Inc." + }, + { + "author_name": "Yogesh Thakur", + "author_inst": "Allexcel, Inc." + }, + { + "author_name": "Vijetha Chiniga", + "author_inst": "Allexcel, Inc." + }, + { + "author_name": "Jayant Tatake", + "author_inst": "Allexcel, Inc" + }, + { + "author_name": "Preetam Holkar", + "author_inst": "Allexcel, Inc" + }, + { + "author_name": "Neelam Holkar", + "author_inst": "Allexcel, Inc" + }, + { + "author_name": "Bethany Pond", + "author_inst": "Allexcel, Inc" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2021.11.19.21266529", "rel_title": "Impact of the COVID-19 pandemic on community antibiotic prescribing and stewardship: a qualitative interview study with general practitioners in England", @@ -497337,41 +499343,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.11.15.468633", - "rel_title": "Tunneling nanotubes provide a novel route for SARS-CoV-2 spreading between permissive cells and to non-permissive neuronal cells.", - "rel_date": "2021-11-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.15.468633", - "rel_abs": "SARS-CoV-2 entry into host cells is mediated by the binding of its spike glycoprotein to the angiotensin-converting enzyme 2 (ACE2) receptor, highly expressed in several organs, but very low in the brain. The mechanism through which SARS-CoV-2 infects neurons is not understood. Tunneling nanotubes (TNTs), actin-based intercellular conduits that connect distant cells, allow the transfer of cargos, including viruses. Here, we explored the neuroinvasive potential of SARS-CoV-2 and whether TNTs are involved in its spreading between cells in vitro. We report that neuronal cells, not permissive to SARS-CoV-2 through an exocytosis/endocytosis dependent pathway, can be infected when co-cultured with permissive infected epithelial cells. SARS-CoV-2 induces TNTs formation between permissive cells and exploits this route to spread to uninfected permissive cells in co-culture. Correlative Cryo-electron tomography reveals that SARS-CoV-2 is associated with the plasma membrane of TNTs formed between permissive cells and virus-like vesicular structures are inside TNTs established both between permissive cells and between permissive and non-permissive cells. Our data highlight a potential novel mechanism of SARS-CoV-2 spreading which could serve as route to invade non-permissive cells and potentiate infection in permissive cells.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Anna Pepe", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Stefano Pietropaoli", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Matthijn Vos", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Giovanna Barba-Spaeth", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Chiara Zurzolo", - "author_inst": "Institut Pasteur" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2021.11.15.468709", "rel_title": "Recent zoonotic spillover and tropism shift of a Canine Coronavirus is associated with relaxed selection and putative loss of function in NTD subdomain of spike protein.", @@ -498235,6 +500206,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.11.15.21266315", + "rel_title": "Precise blood proteome profiling in an undiagnosed population with COVID-19.", + "rel_date": "2021-11-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.15.21266315", + "rel_abs": "Self-sampled blood provided valuable information about the COVID-19 seroprevalence in the general population. To enable an even deeper understanding of pathophysiological processes following SARS-CoV-2 infections, 276 circulating proteins were quantified by proximity extension assays in dried blood spots (DBS). Samples from undiagnosed individuals collected during the first wave of the pandemic were selected based on their serological immune response and matched on self-reported symptoms. We stratified these as seropositive (IgM+IgG+; N = 41) or seronegative (IgM-IgG-; N = 37), and to represent the acute (IgM+IgG-; N = 26) and convalescent phases (IgM-IgG+; N = 40). This revealed proteins from a variety of clinical processes including inflammation and immune response (MBL2, MMP3, IL2RA, FCGR2A, CCL5), haemostasis (GP1BA, VWF), stress response (ANG), virus entry (SDC4) or nerve regeneration (CHL1). The presented approach complements clinical surveys and enables a deep molecular and population-wide analysis of COVID-19 from blood specimens collected outside a hospital setting.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Claudia Fredolini", + "author_inst": "KTH Royal Institute of Technology" + }, + { + "author_name": "Tea Dodig-Crnkovic", + "author_inst": "KTH Royal Institute of Technology" + }, + { + "author_name": "Annika Bendes", + "author_inst": "KTH Royal Institute of Technology" + }, + { + "author_name": "Leo Dahl", + "author_inst": "KTH Royal Institute of Technology" + }, + { + "author_name": "Matilda Dale", + "author_inst": "KTH Royal Institute of Technology" + }, + { + "author_name": "Cecilia Mattsson", + "author_inst": "KTH Royal Institute of Technology" + }, + { + "author_name": "Cecilia Engel Thomas", + "author_inst": "KTH Royal Institute of Technology" + }, + { + "author_name": "Olof Beck", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Niclas Roxhed", + "author_inst": "KTH Royal Institute of Technology" + }, + { + "author_name": "Jochen M Schwenk", + "author_inst": "KTH Royal Institute of Technology" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.15.21266157", "rel_title": "Positive end expiratory pressure in invasive and non-invasive ventilation of COVID-19 acute respiratory distress syndrome: computational modeling illuminates the data", @@ -498931,101 +500957,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.14.21265758", - "rel_title": "Seroprevalence in Tamil Nadu through India's two COVID waves: Evidence on antibody decline following infection and vaccination", - "rel_date": "2021-11-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.14.21265758", - "rel_abs": "Four rounds of serological surveys were conducted, spanning two COVID waves (October 2020 and April-May 2021), in Tamil Nadu (population 72 million) state in India. Each round included representative populations in each district of the state, totaling [≥]20,000 persons per round. State-level seroprevalence was 31.5% in round 1 (October-November 2020), after Indias first COVID wave. Seroprevalence fell to 22.9% in 2 (April 2021), consistent with waning of antibodies from natural infection. Seroprevalence rose to 67.1% by round 3 (June-July 2021), reflecting infections from the Delta-variant induced second COVID wave. Seroprevalence rose to 93.1% by round 4 (December 2021-January 2022), reflecting higher vaccination rates. Antibodies also appear to wane after vaccination. Seroprevalence in urban areas was higher than in rural areas, but the gap shrunk over time (35.7 v. 25.7% in round 1, 89.8% v. 91.4% in round 4) as the epidemic spread even in low-density rural areas.\n\nArticle Summary LineAntibodies waned after Indias first COVID wave and both vaccination and infection contributed its roughly 90% seroprevalence after its second wave.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "T. S. Selvavinayagam", - "author_inst": "Directorate of Public Health & Preventative Medicine, Government of Tamil Nadu" - }, - { - "author_name": "Anavarathan Somasundaram", - "author_inst": "Directorate of Public Health & Preventative Medicine, Government of Tamil Nadu" - }, - { - "author_name": "Jerard Maria Selvam", - "author_inst": "Directorate of Public Health & Preventative Medicine, Government of Tamil Nadu" - }, - { - "author_name": "Sabareesh Ramachandran", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Sampath P.", - "author_inst": "Directorate of Public Health & Preventative Medicine, Government of Tamil Nadu" - }, - { - "author_name": "Vijayalakshmi V.", - "author_inst": "Directorate of Public Health & Preventative Medicine, Government of Tamil Nadu" - }, - { - "author_name": "Ajith Brabhu Kumar C.", - "author_inst": "Directorate of Public Health & Preventative Medicine, Government of Tamil Nadu" - }, - { - "author_name": "Sudharshini Subramanian", - "author_inst": "Directorate of Public Health & Preventative Medicine, Government of Tamil Nadu" - }, - { - "author_name": "S. Raju", - "author_inst": "Directorate of Public Health & Preventative Medicine, Government of Tamil Nadu" - }, - { - "author_name": "Avudaiselvi R.", - "author_inst": "Directorate of Public Health & Preventative Medicine, Government of Tamil Nadu, Chennai, Tamil Nadu, India" - }, - { - "author_name": "Prakash V.", - "author_inst": "Directorate of Public Health & Preventative Medicine, Government of Tamil Nadu" - }, - { - "author_name": "Yogananth N.", - "author_inst": "Directorate of Public Health & Preventative Medicine, Government of Tamil Nadu" - }, - { - "author_name": "Gurunathan Subramanian", - "author_inst": "Directorate of Public Health and Preventive Medicine, Government of Tamil Nadu" - }, - { - "author_name": "Roshini A.", - "author_inst": "Directorate of Public Health and Preventive Medicine, Government of Tamil Nadu" - }, - { - "author_name": "Dhiliban D.N.", - "author_inst": "Directorate of Public Health and Preventive Medicine, Government of Tamil Nadu" - }, - { - "author_name": "Sofia Imad", - "author_inst": "IDFC Institute" - }, - { - "author_name": "Vaidehi Tandel", - "author_inst": "Independent" - }, - { - "author_name": "Rajeswari Parasa", - "author_inst": "IDFC Institute" - }, - { - "author_name": "Stuti Sachdeva", - "author_inst": "Independent" - }, - { - "author_name": "Anup Malani", - "author_inst": "University of Chicago" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.12.21266249", "rel_title": "Early and rapid identification of COVID-19 patients with neutralizing type I-interferon auto-antibodies by an easily implementable algorithm", @@ -500237,6 +502168,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.11.14.21266322", + "rel_title": "Should We Mitigate or Suppress the Next Pandemic? Time-Horizons and Costs Shape Optimal Social Distancing Strategies", + "rel_date": "2021-11-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.14.21266322", + "rel_abs": "The COVID-19 pandemic has called for swift action from local governments, which have instated Nonpharmaceutical Interventions (NPIs) to curb the spread of SARS-Cov-2. The quick and decisive decision to save lives through blunt instruments has raised questions about the conditions under which decision-makers should employ mitigation or suppression strategies to tackle the COVID-19 pandemic. More broadly, there are still debates over which set of strategies should be adopted to control different pandemics, and the lessons learned for SARS-Cov-2 may not apply to a new pathogen. While curbing SARS-Cov-2 required blunt instruments, it is unclear whether a less-transmissible and less-deadly emerging pathogen would justify the same response. This paper illuminates this question using a parsimonious transmission model by formulating the social distancing lives vs. livelihoods dilemma as a boundary value problem. In this setup, society balances the costs and benefits of social distancing contingent on the costs of reducing transmission relative to the burden imposed by the disease. To the best of our knowledge, our approach is distinct in the sense that strategies emerge from the problem structure rather than being imposed a priori. We find that the relative time-horizon of the pandemic (i.e., the time it takes to develop effective vaccines and treatments) and the relative cost of social distancing influence the choice of the optimal policy. Unsurprisingly, we find that the appropriate policy response depends on these two factors. We discuss the conditions under which each policy archetype (suppression vs. mitigation) appears to be the most appropriate.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Sarah A Nowak", + "author_inst": "Larner College of Medicine at the University of Vermont" + }, + { + "author_name": "Pedro Nascimento de Lima", + "author_inst": "Pardee RAND Graduate School" + }, + { + "author_name": "Raffaele Vardavas", + "author_inst": "RAND Corporation" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.11.15.21266187", "rel_title": "Controlling SARS-CoV-2 in schools using repetitive testing strategies", @@ -501277,109 +503235,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.11.12.21266273", - "rel_title": "Maternal immune response and placental antibody transfer after COVID-19 vaccination across trimester and platforms", - "rel_date": "2021-11-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.12.21266273", - "rel_abs": "The availability of three COVID-19 vaccines in the United States provides an unprecedented opportunity to examine how vaccine platforms and timing of vaccination in pregnancy impact maternal and neonatal immunity. Here, we characterized the antibody profile after Ad26.COV2.S, mRNA-1273 or BNT162b2 vaccination in 158 pregnant individuals, and evaluated transplacental antibody transfer by profiling maternal and umbilical cord blood in 175 maternal-neonatal dyads. These analyses revealed lower vaccine-induced functions and Fc-receptor binding after Ad26.COV2.S compared to mRNA vaccination, and subtle advantages in titer and function with mRNA-1273 versus BN162b2. mRNA vaccinees had higher titers and functions against SARS-CoV-2 variants of concern. First and third trimester vaccination resulted in enhanced maternal immune responses relative to second trimester. Higher cord:maternal transfer ratios following first and second trimester vaccination reflect placental compensation for waning maternal titers. These results support vaccination early in pregnancy to maximize maternal protection throughout gestation, without compromising neonatal antibody protection.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Caroline G. Atyeo", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard" - }, - { - "author_name": "Lydia L. Shook", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Sarah Brigida", - "author_inst": "Department of Obstetrics & Gynecology, Massachusetts General Hospital, Harvard Medical School" - }, - { - "author_name": "Rose M. De Guzman", - "author_inst": "Department of Obstetrics & Gynecology, Massachusetts General Hospital, Harvard Medical School" - }, - { - "author_name": "Stepan Demidkin", - "author_inst": "Department of Obstetrics & Gynecology, Massachusetts General Hospital, Harvard Medical School" - }, - { - "author_name": "Cordelia Muir", - "author_inst": "Department of Obstetrics & Gynecology, Massachusetts General Hospital, Harvard Medical School" - }, - { - "author_name": "Babatunde Akinwunmi", - "author_inst": "Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Harvard Medical School" - }, - { - "author_name": "Arantxa Medina Baez", - "author_inst": "Department of Obstetrics & Gynecology, Massachusetts General Hospital, Harvard Medical School" - }, - { - "author_name": "Erin McSweeney", - "author_inst": "Department of Obstetrics & Gynecology, Massachusetts General Hospital, Harvard Medical School" - }, - { - "author_name": "Madeleine Burns", - "author_inst": "Mucosal Immunology and Biology Research Center, Massachusetts General Hospital" - }, - { - "author_name": "Ruhi Nayak", - "author_inst": "Department of Obstetrics & Gynecology, Massachusetts General Hospital, Harvard Medical School" - }, - { - "author_name": "Maya K. Kumar", - "author_inst": "Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Harvard Medical School" - }, - { - "author_name": "Chinmay D. Patel", - "author_inst": "Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Harvard Medical School" - }, - { - "author_name": "Allison Fialkowski", - "author_inst": "Mucosal Immunology and Biology Research Center, Massachusetts General Hospital" - }, - { - "author_name": "Dana Cvrk", - "author_inst": "Department of Obstetrics & Gynecology, Massachusetts General Hospital, Harvard Medical School" - }, - { - "author_name": "Ilona T. Goldfarb", - "author_inst": "Department of Obstetrics & Gynecology, Massachusetts General Hospital, Harvard Medical School" - }, - { - "author_name": "Lael M. Yonker", - "author_inst": "Mucosal Immunology and Biology Research Center, Massachusetts General Hospital" - }, - { - "author_name": "Alessio Fasano", - "author_inst": "Mucosal Immunology and Biology Research Center, Massachusetts General Hospital" - }, - { - "author_name": "Michal A. Elovitz", - "author_inst": "Maternal and Child Health Research Program, Department of Obstetrics and Gynecology, University of Pennsylvania" - }, - { - "author_name": "Kathryn J. Gray", - "author_inst": "Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Harvard Medical School" - }, - { - "author_name": "Galit Alter", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard" - }, - { - "author_name": "Andrea G. Edlow", - "author_inst": "Department of Obstetrics & Gynecology, Massachusetts General Hospital, Harvard Medical School" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "obstetrics and gynecology" - }, { "rel_doi": "10.1101/2021.11.12.21266254", "rel_title": "Revisiting the estimation of Covid-19 prevalence: Implications for rapid testing", @@ -502135,6 +503990,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.11.11.21265536", + "rel_title": "Myocarditis After mRNA-1273 Vaccination: A Population-Based Analysis of 151 Million Vaccine Recipients Worldwide", + "rel_date": "2021-11-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.11.21265536", + "rel_abs": "BackgroundGrowing evidence indicates a causal relationship between SARS-CoV-2 infection and myocarditis. Post-authorization safety data have also identified myocarditis as a rare safety event following mRNA COVID-19 vaccination, most notably among younger adult males and after dose 2. To further evaluate the potential risk after vaccination, we queried the Moderna global safety database to assess the occurrence of myocarditis/myopericarditis among mRNA-1273 vaccine recipients worldwide since first international Emergency Use Authorization issuance.\n\nMethodsReports of myocarditis/myopericarditis entered into the Moderna global safety database from December 18, 2020 to September 30, 2021 were reviewed and classified based on the Brighton Collaboration case definition. The cumulative observed occurrence of myocarditis/myopericarditis was assessed by calculating the reported rate after any known dose of mRNA-1273 according to age and sex. This reporting rate was compared to a population-based incidence rate (US military) to calculate observed-to-expected rate ratios (RR).\n\nResultsThrough September 30, 2021, a total of 1,439 cases of myocarditis/myopericarditis among approximately 151.1 million mRNA-1273 vaccine recipients were reported to the Moderna global safety database. The overall reporting rate among all vaccine recipients was 0.95 cases per 100,000 vaccine recipients, which was lower than the expected rate from the reference population (2.12 cases per 100,000 vaccine recipients; RR [95% CI]: 0.45 [0.42-0.48]). When stratified by sex and age, observed rates were highest for males aged [≤]39 years, particularly those aged 18-24 years (7.40 cases per 100,000 vaccine recipients), which was higher than expected (RR [95% CI]: 3.49 [2.88-4.22]). For males and females aged <18 years, the rate ratio for myocarditis was 1.05 (95% CI, 0.52-2.13) and 0.21 (95% CI, 0.04-0.94), respectively. When considering only cases occurring within 7 days after vaccination, the observed rate was highest for males aged 18-24 years after dose 2 (4.9 cases per 100,000 doses administered).\n\nConclusionMyocarditis/myopericarditis accounted for 0.4% of adverse events reported to the Moderna global safety database after mRNA-1273 vaccination; rates were higher than expected in males aged 18-24 years, with most occurring by 7 days after dose 2, but were not higher than expected for the overall population of vaccine recipients and were lower than that observed in individuals infected with SARS-CoV-2.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Walter Straus", + "author_inst": "Moderna, Inc., 200 Technology Square, Cambridge, Massachusetts, 02139, USA" + }, + { + "author_name": "Veronica Urdaneta", + "author_inst": "Moderna, Inc., 200 Technology Square, Cambridge, Massachusetts, 02139, USA" + }, + { + "author_name": "Daina B. Esposito", + "author_inst": "Moderna, Inc., 200 Technology Square, Cambridge, Massachusetts, 02139, USA" + }, + { + "author_name": "James A. Mansi", + "author_inst": "Moderna, Inc., 200 Technology Square, Cambridge, Massachusetts, 02139, USA" + }, + { + "author_name": "Cesar Sanz Rodriguez", + "author_inst": "Moderna, Inc., 200 Technology Square, Cambridge, Massachusetts, 02139, USA" + }, + { + "author_name": "Paul Burton", + "author_inst": "Moderna, Inc., 200 Technology Square, Cambridge, Massachusetts, 02139, USA" + }, + { + "author_name": "Jose M. Vega", + "author_inst": "Moderna, Inc., 200 Technology Square, Cambridge, Massachusetts, 02139, USA" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.11.21266119", "rel_title": "Quantification and progress over time of specific antibodies against SARS-CoV-2 in breast milk of lactating women vaccinated with BNT162b2 Pfizer-BioNTech COVID-19 vaccine (LacCOVID)", @@ -503007,49 +504905,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2021.11.11.21266223", - "rel_title": "The \u03b2-NGF/TrkA signalling pathway is associated with the production of anti- nucleoprotein IgG in convalescent COVID-19", - "rel_date": "2021-11-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.11.21266223", - "rel_abs": "BackgroundThe presentation of SARS-CoV-2 infection varies from asymptomatic to severe COVID. Similarly, high variability in the presence, titre and duration of specific antibodies has been reported. While some host factors determining these differences, such as age and ethnicity have been identified, the underlying molecular mechanisms underpinning these differences remain poorly defined.\n\nMethodsWe analysed serum and PBMC from 17 subjects with a previous PCR confirmed SARS-CoV-2 infection and 10 unexposed volunteers following the first wave of the pandemic, in the UK. Anti-NP IgG and neutralising antibodies were measured, as well as a panel of infection and inflammation related cytokines. The virus-specific T cell response was determined by IFN-{gamma} ELISPOT and flow cytometry after over-night incubation of PBMCs with pools of selected SARS-CoV-2 specific peptides.\n\nResultsSeven of 17 convalescent subjects had undetectable levels of anti-NP IgG, and a positive correlation was shown between anti-NP IgG levels and the titre of neutralising antibodies (IC50). In contrast, a discrepancy was noted between antibody levels and T cell IFN-{gamma} production by ELISpot following stimulation with specific peptides. Among the analysed cytokines, {beta}-NGF and IL-1 levels were significantly different between anti-NP positive and negative subjects, and only {beta}-NGF significantly correlated with anti-NP positivity. Interestingly, CD4+ T cells of anti-NP negative subjects expressed lower amounts of the {beta}-NGF-specific receptor TrkA.\n\nConclusionsOur results suggest that the {beta}-NGF/TrkA signalling pathway is associated with the production of anti-NP specific antibody in mild SARS-CoV-2 infection and the mechanistic regulation of this pathway in COVID-19 requires further investigation.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Carla Usai", - "author_inst": "Centre for Immunobiology, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom." - }, - { - "author_name": "Joseph M Gibbons", - "author_inst": "Centre for Immunobiology, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom." - }, - { - "author_name": "Corinna Pade", - "author_inst": "Centre for Immunobiology, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom." - }, - { - "author_name": "Wenhao Li", - "author_inst": "Centre for Immunobiology, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom ; Ba" - }, - { - "author_name": "Aine McKnight", - "author_inst": "Centre for Immunobiology, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom." - }, - { - "author_name": "Patrick T F Kennedy", - "author_inst": "Centre for Immunobiology, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom ; Ba" - }, - { - "author_name": "Upkar S Gill", - "author_inst": "Centre for Immunobiology, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom ; Ba" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.08.21266035", "rel_title": "COVID-19 convalescents exhibit deficient humoral and T cell responses to variant of concern Spike antigens at 12 month post-infection", @@ -504085,6 +505940,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.11.01.21260020", + "rel_title": "A Flexible Data-Driven Framework for COVID-19 Case Forecasting Deployed in a Developing-world Public Health Setting", + "rel_date": "2021-11-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.01.21260020", + "rel_abs": "Forecasting infection case counts and estimating accurate epidemiological parameters are critical components of managing the response to a pandemic. This paper describes a modular, extensible framework for a COVID-19 forecasting system, primarily deployed during the first Covid wave in Mumbai and Jharkhand, India. We employ a variant of the SEIR compartmental model motivated by the nature of the available data and operational constraints. We estimate best fit parameters using Sequential Model-Based Optimization (SMBO), and describe the use of a novel, fast and approximate Bayesian model averaging method (ABMA) for parameter uncertainty estimation that compares well with a more rigorous Markov Chain Monte Carlo (MCMC) approach in practice. We address on-the-ground deployment challenges such as spikes in the reported input data using a novel weighted smoothing method. We describe extensive empirical analyses to evaluate the accuracy of our method on ground truth as well as against other state-of-the-art approaches. Finally, we outline deployment lessons and describe how inferred model parameters were used by government partners to interpret the state of the epidemic and how model forecasts were used to estimate staffing and planning needs essential for addressing COVID-19 hospital burden.\n\nCCS CONCEPTSO_LIApplied computing [->] Health care information systems; Forecasting;\nC_LIO_LIComputing methodologies [->] Modeling methodologies.\nC_LI", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Sansiddh Jain", + "author_inst": "Wadhwani AI" + }, + { + "author_name": "Avtansh Tiwari", + "author_inst": "Wadhwani AI" + }, + { + "author_name": "Nayana Bannur", + "author_inst": "Wadhwani AI" + }, + { + "author_name": "Ayush Deva", + "author_inst": "Wadhwani AI" + }, + { + "author_name": "Siddhant Shingi", + "author_inst": "Wadhwani AI" + }, + { + "author_name": "Vishwa Shah", + "author_inst": "Wadhwani AI" + }, + { + "author_name": "Mihir Kulkarni", + "author_inst": "Wadhwani AI" + }, + { + "author_name": "Namrata Deka", + "author_inst": "Wadhwani AI" + }, + { + "author_name": "Keshav Ramaswami", + "author_inst": "Wadhwani AI" + }, + { + "author_name": "Vasudha Khare", + "author_inst": "Wadhwani AI" + }, + { + "author_name": "Harsh Maheshwari", + "author_inst": "Flipkart" + }, + { + "author_name": "Soma Dhavala", + "author_inst": "Wadhwani AI" + }, + { + "author_name": "Jithin Sreedharan", + "author_inst": "Wadhwani AI" + }, + { + "author_name": "Jerome White", + "author_inst": "Wadhwani AI" + }, + { + "author_name": "Srujana Merugu", + "author_inst": "Wadhwani AI" + }, + { + "author_name": "Alpan Raval", + "author_inst": "Wadhwani AI" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.11.05.467537", "rel_title": "Transcriptome analysis of SARS-CoV-2 naive and recovered individuals vaccinated with inactivated vaccine", @@ -505000,45 +506934,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, - { - "rel_doi": "10.1101/2021.11.09.21266060", - "rel_title": "Vaccine effectiveness against COVID-19 related hospital admission in the Netherlands: a test-negative case-control study", - "rel_date": "2021-11-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.09.21266060", - "rel_abs": "IntroductionReal-world vaccine effectiveness (VE) estimates are essential to identify potential groups at higher risk of break-through infections and to guide policy. We assessed the VE of COVID-19 vaccination against COVID-19 hospitalization, while adjusting and stratifying for patient characteristics.\n\nMethodsWe performed a test-negative case-control study in six Dutch hospitals. The study population consisted of adults eligible for COVID-19 vaccination hospitalized between May 1 and June 28 2021 with respiratory symptoms. Cases were defined as patients who tested positive for SARS-CoV-2 by PCR during the first 48 hours of admission or within 14 days prior to hospital admission. Controls were patients tested negative at admission and did not have a positive test during the 2 weeks prior to hospitalization. VE was calculated using multivariable logistic regression, adjusting for calendar week, sex, age, comorbidity and nursing home residency. Subgroup analysis was performed for age, sex and different comorbidities. Secondary endpoints were ICU-admission and mortality.\n\nResults379 cases and 255 controls were included of whom 157 (18%) were vaccinated prior to admission. Five cases (1%) and 40 controls (16%) were fully vaccinated (VE: 93%; 95% CI: 81 - 98), and 40 cases (11%) and 70 controls (27%) were partially vaccinated (VE: 70%; 95% CI: 50-82). A strongly protective effect of vaccination was found in all comorbidity subgroups. No ICU-admission or mortality were reported among fully vaccinated cases. Of unvaccinated cases, mortality was 10% and 19% was admitted at the ICU\n\nConclusionCOVID-19 vaccination provides a strong protective effect against COVID-19 related hospital admission, in patients with and without comorbidity.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Annabel FA Niessen", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven" - }, - { - "author_name": "Mirjam J Knol", - "author_inst": "National Institute of Public Health and the Environment, the Netherlands (RIVM)" - }, - { - "author_name": "Susan JM Hahne", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven" - }, - { - "author_name": "- VECTOR study group", - "author_inst": "" - }, - { - "author_name": "Marc JM Bonten", - "author_inst": "Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands" - }, - { - "author_name": "Patricia PCJL Bruijning-Verhagen", - "author_inst": "Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.10.21266147", "rel_title": "Nanopore 16S rRNA sequencing reveals alterations in nasopharyngeal microbiome and enrichment of Mycobacterium and Mycoplasma in patients with COVID 19", @@ -505834,6 +507729,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.11.06.21266007", + "rel_title": "Forecasting the COVID-19 Pandemic: Lessons learned and future directions", + "rel_date": "2021-11-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.06.21266007", + "rel_abs": "I.AO_SCPLOWBSTRACTC_SCPLOWThe Coronavirus Disease 2019 (COVID-19) has demonstrated that accurate forecasts of infection and mortality rates are essential for informing healthcare resource allocation, designing countermeasures, implementing public health policies, and increasing public awareness. However, there exist a multitude of modeling methodologies, and their relative performances in accurately forecasting pandemic dynamics are not currently comprehensively understood.\n\nIn this paper, we introduce the non-mechanistic MIT-LCP forecasting model, and assess and compare its performance to various mechanistic and non-mechanistic models that have been proposed for forecasting COVID-19 dynamics. We performed a comprehensive experimental evaluation which covered the time period of November 2020 to April 2021, in order to determine the relative performances of MIT-LCP and seven other forecasting models from the United States Centers for Disease Control and Prevention (CDC) Forecast Hub.\n\nOur results show that there exist forecasting scenarios well-suited to both mechanistic and non-mechanistic models, with mechanistic models being particularly performant for forecasts that are further in the future when recent data may not be as informative, and non-mechanistic models being more effective with shorter prediction horizons when recent representative data is available. Improving our understanding of which forecasting approaches are more reliable, and in which forecasting scenarios, can assist effective pandemic preparation and management.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Saketh Sundar", + "author_inst": "MIT Critical Data, Cambridge, MA; River Hill High School, Clarksville, MD" + }, + { + "author_name": "Patrick Schwab", + "author_inst": "GlaxoSmithKline, Artificial Intelligence & Machine Learning, Zug, Switzerland" + }, + { + "author_name": "Jade Z.H. Tan", + "author_inst": "U.S. Department of Health and Human Services (HHS)" + }, + { + "author_name": "Santiago Romero-Brufau", + "author_inst": "Department of Medicine, Mayo Clinic, Rochester, MN; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA" + }, + { + "author_name": "Leo Anthony Celi", + "author_inst": "MIT Critical Data, Massachusetts Institute of Technology; Institute for Medical Engineering and Science, Massachusetts Institute of Technology; Department of Me" + }, + { + "author_name": "Dechen Wangmo", + "author_inst": "Ministry of Health, Royal Government of Bhutan" + }, + { + "author_name": "Nicolas Della Penna", + "author_inst": "Amurado Research" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.11.05.21265900", "rel_title": "Parents intention to vaccinate their 5-11 years old children with the COVID-19: vaccine rates, predictors and the role of incentives", @@ -506666,49 +508604,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.08.21265966", - "rel_title": "Cumulative incidence of SARS-CoV-2 and associated risk factors among healthcare workers in the Eastern Cape, South Africa", - "rel_date": "2021-11-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.08.21265966", - "rel_abs": "ObjectivesThis study assesses the cumulative incidence of SARS-CoV-2 infection among healthcare workers (HCWs) during South Africas first wave and examines the associated demographic, health-related, and occupational risk factors for infection.\n\nMethodsMulti-stage cluster sampling was used in a cross-sectional study to recruit 1,309 HCWs from two academic hospitals in the Eastern Cape, South Africa over six weeks in November and December 2020. Prior test results for SARS-CoV-2 polymerase chain reaction (PCR) and participants characteristics were recorded while a blood sample was drawn for detection of IgG antibodies against SARS-CoV-2 nucleocapsid protein. The primary outcome measure was the SARS-CoV-2 cumulative incidence rate, defined as the combined total of positive results for either PCR or IgG antibodies, divided by the total sample. The secondary outcome was significant risk factors associated with infection.\n\nResultsOf the total participants included in the analysis (N=1295), the majority were female (81.5%), of black race (78.7%) and nurses (44.8%). A total of 390 (30.1%) HCWs had a positive SARS-CoV-2 PCR result and SARS-CoV-2 antibodies were detected in 488 (37.7%), yielding a cumulative incidence of 47.2% (n = 611). In the adjusted logistic regression model, being overweight (Adjusted odds ratio (AOR) = 2.15, 95% CI 1.44-3.20), obese (AOR = 1.37, 95% CI 1.02-1.85) and living with HIV (AOR = 1.78, 95% CI 1.38-were independently associated with SARS-CoV-2 infection. There was no significant difference in infection rates between high, medium and low COVID-19 exposure working environments.\n\nConclusionsThe high SARS-CoV-2 cumulative incidence in the cohort was surprising this early in the epidemic and probably related to exposure both in and outside the hospitals. To mitigate the impact of SARS-CoV-2 among HCWs, infection prevention and control (IPC) strategies should target community transmission in addition to screening for HIV and metabolic conditions.\n\nStrengths and limitations of this studyO_LIThis is a large representative sample of the total workforce of the two hospitals, with a good spectrum of staff category.\nC_LIO_LICombining the historical SARS-CoV-2 PCR results with the Nucleocapsid IgG enabled capturing of some of the asymptomatic and missed SARS-CoV-2 infections.\nC_LIO_LIThis is one of the first studies to look at SARS-CoV-2 infection risk factors in a high exposure environment in Africa.\nC_LIO_LIA limitation is that HIV ELISA and CD4 counts were not tested, but relied on self-report, which may likely underestimate the burden of HIV in the cohort.\nC_LI", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "David F. Stead", - "author_inst": "Frere Hospital; Walter Sisulu University" - }, - { - "author_name": "Oladele Vincent Adeniyi", - "author_inst": "Cecilia Makiwane hospital; Walter Sisulu University" - }, - { - "author_name": "Mandisa Singata-Madliki", - "author_inst": "University of Fort Hare" - }, - { - "author_name": "Shareef Abrahams", - "author_inst": "National Health Laboratory Service" - }, - { - "author_name": "Joanne Batting", - "author_inst": "University of Fort Hare" - }, - { - "author_name": "Eloise Jelliman", - "author_inst": "Frere Hospital" - }, - { - "author_name": "Andrew G. Parrish", - "author_inst": "Frere Hospital; Walter Sisulu University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.08.21266091", "rel_title": "Data-driven prognosis for COVID-19 patients based on symptoms and age", @@ -507308,6 +509203,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2021.11.08.21266058", + "rel_title": "Defining the determinants of under-vaccination in migrant populations in Europe to improve routine and COVID-19 vaccine uptake: a systematic review", + "rel_date": "2021-11-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.08.21266058", + "rel_abs": "Diverse migrant populations in Europe are at risk of under-immunisation and have recently shown lower levels of COVID-19 vaccination intent and uptake. Understanding the determinants of vaccine uptake in migrants is critical to address immediate COVID-19 vaccination inequities, and longer-term will help improve coverage for routine vaccinations, aligning with the goals of the new Immunisation Agenda 2030. We did a systematic review following PRISMA guidelines and using a PICOS framework (PROSPERO CRD42020219214; MEDLINE, CINAHL, PsycINFO databases, 1 January 2000 - 14 September 2021) exploring barriers and facilitators to vaccine uptake and determinants of under-vaccination in migrants in the EU/EEA, UK, and Switzerland. We categorised barriers/facilitators using the 5As Determinants of Vaccine Uptake Taxonomy. 5259 data sources were screened, with 67 studies included from 16 countries, representing 366,529 migrants. Access barriers were most commonly reported (language, literacy and communication barriers; practical and legal barriers to accessing/delivering vaccination services; service barriers, including lack of specific guidelines and knowledge of healthcare professionals) for key vaccines including MMR, DTP, HPV, influenza, polio, COVID-19 vaccines. Acceptance barriers were mostly reported in Eastern European and Muslim communities for HPV, measles, and influenza vaccines. We identified 23 determinants of under-vaccination in migrants, including geographical origin (where 25/26 (96%) studies showed significance) - particularly African/Eastern European origin; recent migration; being a refugee/asylum seeker; higher income; parental education level; no healthcare contact in the past year; and lower language skills. Facilitators of migrants vaccine uptake included tailored vaccination messaging, community outreach and nudging interventions. Migrants barriers to accessing healthcare are already well documented, and this review confirms their role in limiting vaccine uptake. These data hold immediate relevance to strengthening vaccination programmes in high-income countries, including for COVID-19. Our findings suggested that targeted, evidence-informed strategies are needed to address access and acceptance barriers to vaccination in migrants, including the development of migrant-sensitive and adaptable vaccination services and systems, unambiguous public health messaging, and coproduction of tailored interventions.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Alison F Crawshaw", + "author_inst": "St George's, University of London" + }, + { + "author_name": "Yasmin Farah", + "author_inst": "St George's, University of London" + }, + { + "author_name": "Anna Deal", + "author_inst": "St George's, UOL" + }, + { + "author_name": "Kieran Rustage", + "author_inst": "St George's, University of London" + }, + { + "author_name": "Sally E Hayward", + "author_inst": "St George's, University of London" + }, + { + "author_name": "Jessica Carter", + "author_inst": "St George's, University of London" + }, + { + "author_name": "Felicity Knights", + "author_inst": "St George's, University of London" + }, + { + "author_name": "Lucy P Goldsmith", + "author_inst": "St George's, University of London" + }, + { + "author_name": "Ines Campos-Matos", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Fatima Wurie", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Azeem Majeed", + "author_inst": "Department of Primary Care and Public Health, Imperial College London" + }, + { + "author_name": "Helen Bedford", + "author_inst": "UCL Great Ormond Street Institute of Child Health" + }, + { + "author_name": "Alice S Forster", + "author_inst": "Our Future Health" + }, + { + "author_name": "Sally Hargreaves", + "author_inst": "Institute for Infection and Immunity, St George's University of London" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.11.07.21266036", "rel_title": "Association between long working hours and psychological distress: The effect of sick leave criteria in the workplace during the COVID-19 pandemic", @@ -508572,97 +510538,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.11.08.467705", - "rel_title": "Molecular signature of postmortem lung tissue from COVID-19 patients suggests distinct trajectories driving mortality", - "rel_date": "2021-11-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.08.467705", - "rel_abs": "The precise molecular mechanisms behind life-threatening lung abnormalities during severe SARS-CoV-2 infections are still unclear. To address this challenge, we performed whole transcriptome sequencing of lung autopsies from 31 patients suffering from severe COVID-19 related complications and 10 uninfected controls. Using a metatranscriptome analysis of lung tissue samples we identified the existence of two distinct molecular signatures of lethal COVID-19. The dominant \"classical\" signature (n=23) showed upregulation of unfolded protein response, steroid biosynthesis and complement activation supported by massive metabolic reprogramming leading to characteristic lung damage. The rarer signature (n=8) potentially representing \"Cytokine Release Syndrome\" (CRS) showed upregulation of cytokines such IL1 and CCL19 but absence of complement activation and muted inflammation. Further, dissecting expression of individual genes within enriched pathways for patient signature suggests heterogeneity in host response to the primary infection. We found that the majority of patients cleared the SARS-CoV-2 infection, but all suffered from acute dysbiosis with characteristic enrichment of opportunistic pathogens such as Staphylococcus cohnii in \"classical\" patients and Pasteurella multocida in CRS patients. Our results suggest two distinct models of lung pathology in severe COVID-19 patients that can be identified through the status of the complement activation, presence of specific cytokines and characteristic microbiome. This information can be used to design personalized therapy to treat COVID-19 related complications corresponding to patient signature such as using the identified drug molecules or mitigating specific secondary infections.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Anshul Budhraja", - "author_inst": "Indian Institute of Technology, Delhi" - }, - { - "author_name": "Anubhav Basu", - "author_inst": "Indian Institute of Technology, Delhi" - }, - { - "author_name": "Atish Gheware", - "author_inst": "All India Institute of Medical Sciences" - }, - { - "author_name": "Dasari Abhilash", - "author_inst": "Indian Institute of Technology, Delhi" - }, - { - "author_name": "Seesandra Rajagopala", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Suman Pakala", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Madhuresh Sumit", - "author_inst": "Indian Institute of Technology, Delhi" - }, - { - "author_name": "Animesh Ray", - "author_inst": "All India Institute of Medical Sciences" - }, - { - "author_name": "S Arulselvi", - "author_inst": "All India Institute of Medical Sciences" - }, - { - "author_name": "Purva Mathur", - "author_inst": "All India Institute of Medical Sciences" - }, - { - "author_name": "Aruna Nambirajan", - "author_inst": "All India Institute of Medical Sciences" - }, - { - "author_name": "Sachin Kumar", - "author_inst": "All India Institute of Medical Sciences" - }, - { - "author_name": "Ritu Gupa", - "author_inst": "Dr. B. R. Ambedkar Institute Rotary Cancer Hospital (IRCH), All India Institute of Medical Sciences" - }, - { - "author_name": "Naveet Wig", - "author_inst": "All India Institute of Medical Sciences" - }, - { - "author_name": "Anjan Trikha", - "author_inst": "All India Institute of Medical Sciences" - }, - { - "author_name": "Randeep Guleria", - "author_inst": "All India Institute of Medical Sciences" - }, - { - "author_name": "Chitra Sarkar", - "author_inst": "All India Institute of Medical Sciences" - }, - { - "author_name": "Ishaan Gupta", - "author_inst": "Indian Institute of Technology, Delhi" - }, - { - "author_name": "Deepali Jain", - "author_inst": "All India Institute of Medical Sciences" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2021.11.07.467640", "rel_title": "An interactome landscape of SARS-CoV-2 virus-human protein-protein interactions by protein sequence-based multi-label classifiers", @@ -509382,6 +511257,89 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.11.04.467077", + "rel_title": "The oral protease inhibitor (PF-07321332) protects Syrian hamsters against infection with SARS-CoV-2 variants of concern", + "rel_date": "2021-11-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.04.467077", + "rel_abs": "There is an urgent need for potent and selective antivirals against SARS-CoV-2. Pfizer developed PF-07321332 (PF-332), a potent inhibitor of the viral main protease (Mpro, 3CLpro) that can be dosed orally and that is in clinical development. We here report that PF-332 exerts equipotent in vitro activity against the four SARS-CoV-2 variants of concerns (VoC) and that it can completely arrest replication of the alpha variant in primary human airway epithelial cells grown at the air-liquid interface. Treatment of Syrian Golden hamsters with PF-332 (250 mg/kg, twice daily) completely protected the animals against intranasal infection with the beta (B.1.351) and delta (B.1.617.2) SARS-CoV-2 variants. Moreover, treatment of SARS-CoV-2 (B.1.617.2) infected animals with PF-332 completely prevented transmission to untreated co-housed sentinels.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Rana Abdelnabi", + "author_inst": "Rega Institute, KU Leuven" + }, + { + "author_name": "Caroline Shi-Yan Foo", + "author_inst": "Katholieke Universiteit Leuven" + }, + { + "author_name": "Dirk Jochmans", + "author_inst": "REGA Institute - KULeuven" + }, + { + "author_name": "Laura Vangeel", + "author_inst": "Rega Institute, KU Leuven" + }, + { + "author_name": "Steven De Jonghe", + "author_inst": "Rega Institute, KU Leuven" + }, + { + "author_name": "Patrick Augustijns", + "author_inst": "KU Leuven" + }, + { + "author_name": "Raf Mols", + "author_inst": "KU Leuven" + }, + { + "author_name": "Birgit Weynand", + "author_inst": "KU Leuven" + }, + { + "author_name": "Thanaporn Wattanakul", + "author_inst": "Faculty of Tropical Medicine, Mahidol University" + }, + { + "author_name": "Richard Hoglund", + "author_inst": "Faculty of Tropical Medicine, Mahidol University" + }, + { + "author_name": "Joel Tarning", + "author_inst": "Mahidol-Oxford Tropical Medicine Research Unit" + }, + { + "author_name": "Charles Mowbray", + "author_inst": "Drugs for Neglected Diseases initiative" + }, + { + "author_name": "Peter Sjo", + "author_inst": "Drugs for Neglected Diseases initiative" + }, + { + "author_name": "Fanny Escudie", + "author_inst": "Drugs for Neglected Diseases initiative" + }, + { + "author_name": "Ivan Scandale", + "author_inst": "Drugs for Neglected Diseases initiative" + }, + { + "author_name": "Eric Chatelain", + "author_inst": "Drugs for Neglected Diseases initiative" + }, + { + "author_name": "Johan Neyts", + "author_inst": "Rega Institute KU Leuven" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.11.04.467274", "rel_title": "Prolonged and extended impacts of SARS-CoV-2 on the olfactory neurocircuit", @@ -510438,29 +512396,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.11.03.21265897", - "rel_title": "Influence of heterogeneous age-group contact patterns on critical vaccination rates for herd immunity to SARS-CoV-2", - "rel_date": "2021-11-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.03.21265897", - "rel_abs": "Currently, several western countries have more than half of their population fully vaccinated against COVID-19. At the same time, some of them are experiencing a fourth or even a fifth wave of cases, most of them concentrated in sectors of the populations whose vaccination coverage is lower than the average. So, the initial scenario of vaccine prioritization has given way to a new one where achieving herd immunity is the primary concern. Using an age-structured vaccination model with waning immunity, we show that, under a limited supply of vaccines, a vaccination strategy based on minimizing the basic reproduction number allows for the deployment of a number of vaccine doses lower than the one required for maximizing the vaccination coverage. Such minimization is achieved by giving greater protection to those age groups that, for a given social contact pattern, have smaller fractions of susceptible individuals at the endemic equilibrium without vaccination, that is, to those groups that are more vulnerable to infection.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Joan Saldana", - "author_inst": "Universitat de Girona" - }, - { - "author_name": "Caterina M Scoglio", - "author_inst": "Kansas State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.11.03.21265902", "rel_title": "Primary Care Diagnosis and Treatment of Attention-Deficit/Hyperactivity Disorder in School-aged Children: Trends and Disparities During the COVID-19 Pandemic", @@ -511100,6 +513035,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2021.11.02.21265843", + "rel_title": "A RCT of a third dose CoronaVac or BNT162b2 vaccine in adults with two doses of CoronaVac", + "rel_date": "2021-11-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.02.21265843", + "rel_abs": "BackgroundPoor immunogenicity and antibody waning were found in vaccinees of CoronaVac. There is lack of randomized controlled trial (RCT) data to compare the immunogenicity and safety of schedules using homologous and heterologous vaccine as a booster dose.\n\nMethodsWe randomly assigned adults who had received 2 doses of CoronaVac with low antibody response to receive an additional booster dose of either BNT162b2 or CoronaVac. The local and systemic adverse reactions were recorded. Levels of SARS-CoV-2 neutralizing and spike binding antibody in plasma were measured.\n\nFindingsAt one month after the third dose of vaccine, BNT162b2 vaccines elicited significantly higher surrogate virus neutralizing test (sVNT), spike receptor binding, spike N terminal domain binding, spike S2 domain binding levels than CoronaVac. More participants from the BNT162b2 group reported injection site pain and swelling as well as fatigue and muscle pain than those who received CoronaVac as the third dose. The mean results of the sVNT against the wild type, beta, gamma and delta variants in the BNT162b2 boosted group was 96.83%, 92.29%, 92.51% and 95.33% respectively which were significantly higher than the CoronaVac boosted group (Wild type: 57.75%; Beta: 38.79 %; Gamma: 32.22%; Delta: 48.87%)\n\nConclusionOur RCT study shows that BNT162b2 booster dose for those people who poorly responded to the previous vaccination of CoronaVac is significantly more immunogenic than a CoronaVac booster. BNT162b2 also elicits higher levels of SARS-CoV-2 specific neutralizing antibodies to different variants of concern. The adverse reactions were only mild and short-lived.\n\nAt a Glance CommentaryO_ST_ABSScientific Knowledge on the SubjectC_ST_ABSPoor immunogenicity and antibody waning were found in vaccinees of CoronaVac. There is lack of randomized controlled trial (RCT) data to compare the immunogenicity and safety of schedules using homologous and heterologous vaccine as a booster dose.\n\nWhat This Study Adds to the FieldOur RCT study shows that BNT162b2 booster dose for those people who poorly responded to the previous vaccination of CoronaVac is significantly more immunogenic than a CoronaVac booster. The adverse reactions were only mild and short-lived.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Chris Ka Pun Mok", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Samuel M.S. Cheng", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Chunke Chen", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Karen Yiu", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Tat-On Chan", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Kiu Cheung Lai", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Kwun Cheung Ling", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Lun Lai Ho", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Malik Peiris", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "David S Hui", + "author_inst": "The Chinese University of Hong Kong" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.02.21265668", "rel_title": "Black and Native Overdose Mortality Overtook that of White Individuals During the COVID-19 Pandemic", @@ -512220,97 +514210,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.28.21265593", - "rel_title": "The UK COVID-19 furlough scheme and associations with smoking, alcohol consumption and vaping: evidence from 8 UK longitudinal population surveys.", - "rel_date": "2021-11-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.28.21265593", - "rel_abs": "BackgroundDisruptions to employment status can impact smoking and alcohol consumption. During the COVID-19 pandemic, the UK implemented a furlough scheme to prevent job loss. We examine how furlough was associated with participants smoking, vaping and alcohol consumption behaviours in the early stages of the pandemic.\n\nMethodsData were from 27,841 participants in eight UK adult longitudinal surveys. Participants self-reported employment status and current smoking, current vaping and drinking alcohol (>4 days/week or 5+ drinks per typical occasion) both before and during the pandemic (April-July 2020). Risk ratios were estimated within each study using modified Poisson regression, adjusting for a range of potential confounders, including pre-pandemic behaviour. Findings were synthesised using random effects meta-analysis. Sub-group analyses were used to identify whether associations differed by gender, age or education.\n\nResultsCompared to stable employment, neither furlough, no longer being employed, nor stable unemployment were associated with smoking, vaping or drinking, following adjustment for pre-pandemic characteristics. However, some sex differences in these associations were observed, with stable unemployment associated with smoking for women (ARR=1.35; 95% CI: 1.00-1.82; I2: 47%) but not men (0.84; 95% CI: 0.67-1.05; I2: 0%). No longer being employed was associated with vaping among women (ARR=2.74; 95% CI: 1.59-4.72; I2: 0%) but not men (ARR=1.25; 95% CI: 0.83-1.87; I2: 0%). There was little indication of associations with drinking differing by age, gender or education.\n\nConclusionsWe found no clear evidence of furlough or unemployment having adverse impacts on smoking, vaping or drinking behaviours during the early stages of the COVID-19 pandemic in the UK, with differences in risk compared to those who remained employed largely explained by pre-pandemic characteristics.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Michael J Green PhD", - "author_inst": "MRC/CSO Social & Public Health Sciences Unit, University of Glasgow" - }, - { - "author_name": "Jane Maddock PhD", - "author_inst": "MRC Unit for Lifelong Health and Ageing, University College London" - }, - { - "author_name": "Giorgio Di Gessa PhD", - "author_inst": "Institute of Epidemiology and Health Care, University College London" - }, - { - "author_name": "Bo\u017cena Wielgoszewska PhD", - "author_inst": "Centre for Longitudinal Studies, UCL Social Research Institute, University College London" - }, - { - "author_name": "Sam Parsons PhD", - "author_inst": "Centre for Longitudinal Studies, UCL Social Research Institute, University College London" - }, - { - "author_name": "Gareth J Griffith PhD", - "author_inst": "MRC Integrative Epidemiology Unit, University of Bristol" - }, - { - "author_name": "Jazz Croft PhD", - "author_inst": "MRC Integrative Epidemiology Unit, University of Bristol" - }, - { - "author_name": "Anna J Stevenson PhD", - "author_inst": "Centre for Genomic and Experimental Medicine, University of Edinburgh" - }, - { - "author_name": "Charlotte F Huggins PhD", - "author_inst": "Centre for Genomic and Experimental Medicine, University of Edinburgh" - }, - { - "author_name": "Charlotte Booth PhD", - "author_inst": "Centre for Longitudinal Studies, UCL Social Research Institute, University College London" - }, - { - "author_name": "Jacques Wels", - "author_inst": "MRC Unit for Lifelong Health and Ageing, University College London" - }, - { - "author_name": "Richard J Silverwood PhD", - "author_inst": "Centre for Longitudinal Studies, UCL Social Research Institute, University College" - }, - { - "author_name": "Praveetha Patalay PhD", - "author_inst": "MRC Unit for Lifelong Health and Ageing, University College London; Centre for Longitudinal Studies, UCL Social Research Institute, University College London" - }, - { - "author_name": "Alun D Hughes PhD", - "author_inst": "MRC Unit for Lifelong Health and Ageing, University College London" - }, - { - "author_name": "Nishi Chaturvedi MD", - "author_inst": "MRC Unit for Lifelong Health and Ageing, University College London" - }, - { - "author_name": "Laura D Howe PhD", - "author_inst": "MRC Integrative Epidemiology Unit, University of Bristol" - }, - { - "author_name": "Emla Fitzsimons PhD", - "author_inst": "Centre for Longitudinal Studies, UCL Social Research Institute, University College London" - }, - { - "author_name": "Srinivasa Vittal Katikireddi PhD", - "author_inst": "MRC/CSO Social & Public Health Sciences Unit, University of Glasgow" - }, - { - "author_name": "George B Ploubidis PhD", - "author_inst": "Centre for Longitudinal Studies, UCL Social Research Institute, University College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.11.01.21265731", "rel_title": "Factors driving extensive spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals", @@ -513602,6 +515501,41 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.11.01.466834", + "rel_title": "Glycan-masking spike antigen in NTD and RBD elicits broadly neutralizing antibodies against SARS-CoV-2 variants", + "rel_date": "2021-11-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.01.466834", + "rel_abs": "Glycan-masking the vaccine antigen by mutating the undesired antigenic sites with an additional N-linked glycosylation motif can refocus B-cell responses to desired/undesired epitopes, without affecting the antigens overall-folded structure. This study examine the impact of glycan-masking mutants of the N-terminal domain (NTD) and receptor-binding domain (RBD) of SARS-CoV-2, and found that the antigenic design of the S protein increases the neutralizing antibody titers against the Wuhan-Hu-1 ancestral strain and the recently emerged SARS-CoV-2 variants Alpha (B.1.1.7), Beta (B.1.351), and Delta (B.1.617.2). Our results demonstrated that the use of glycan-masking Ad-S-R158N/Y160T in the NTD elicited a 2.8-fold, 6.5-fold, and 4.6-fold increase in the IC-50 NT titer against the Alpha (B.1.1.7), Beta (B.1.351) and Delta (B.1.617.2) variants, respectively. Glycan-masking of Ad-S-D428N in the RBD resulted in a 3.0-fold and 2.0-fold increase in the IC50 neutralization titer against the Alpha (B.1.1.7) and Beta (B.1.351) variants, respectively. The use of glycan-masking in Ad-S-R158N/Y160T and Ad-S-D428N antigen design may help develop universal COVID-19 vaccines against current and future emerging SARS-CoV-2 variants.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Wei-Shuo Lin", + "author_inst": "Institute of Biotechnology, National Tsing Hua University" + }, + { + "author_name": "I-Chen Chen", + "author_inst": "Institute of Biotechnology, National Tsing Hua University" + }, + { + "author_name": "Hui-Chen Chen", + "author_inst": "Institute of Biotechnology, National Tsing Hua University" + }, + { + "author_name": "Yi-Chien Lee", + "author_inst": "Department of Infectious Diseases, Fu Jen Catholic University Hospital, New Taipei City, Taiwan" + }, + { + "author_name": "Suh-Chin Wu", + "author_inst": "Institute of Biotechnology and Department of Medical Science, National Tsing Hua University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.11.01.466695", "rel_title": "Antiviral activity of Pacific oyster (Crassostrea gigas) hemolymph against a human coronavirus.", @@ -514562,53 +516496,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.11.01.21265737", - "rel_title": "Anti-SARS-CoV-2 vaccination does not induce the formation of autoantibodies but provides humoral immunity following heterologous and homologous vaccination regimens: Results from a clinical and prospective study within professionals of a German University Hospital", - "rel_date": "2021-11-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.01.21265737", - "rel_abs": "By the end of 2019 a global pandemic by the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV2) causing the coronavirus disease-19 (COVID-19) has emerged. Yet, COVID-19 represents a significant economic burden to healthcare systems, destabilizes global financial markets and has caused the death of almost 5 million people worldwide. In order to prevent severe disease courses of COVID-19 especially in elderly and to establish collective immunity on the long run, different vaccines have been developed, tested and were approved within a very short time period. In Germany, the first vaccines that have been approved by local authorities were AstraZenecas vector virus-based vaccine Vaxzevria and the mRNA vaccines Comirnaty and Spikevax, developed by BioNTech and Moderna, respectively. As it was reported that the novel coronavirus SARS-CoV2 can trigger autoimmunity, it is of significant interest to investigate whether anti-SARS-CoV2 vaccines evoke the formation of autoantibodies and subsequent autoimmunity. Here, we did set out to systematically analyze immune responses after homologous vaccinations with mRNA or vector virus-based vaccines or after heterologous Vector/mRNA vaccinations with respect to anti-COVID-19 immune responses and, in parallel, the development of autoantibodies. In our study, we obtained serum samples one day before and 14 as well as 28 days following booster vaccination and tested them for anti-SARS-CoV2 antibodies and for autoantibodies against Cardiolipin, Prothrombin, {beta}2-Glycoprotein, cyclic citrullinated peptides (CCP), tissue-transglutaminase (TTG) and anti-nuclear antibodies (ANA). We find that compared to homologous mRNA and heterologous Vector/mRNA vaccination, anti-SARS-CoV2 antibody levels were 90% lower after homologous vector vaccination. Of note, heterologous Vector/mRNA vaccination was found to be more effective than homologous mRNA vaccination in terms of IgM and IgA responses against SARS-CoV2. However, in terms of autoantibody generation, we only detected increases after booster vaccination in participants with already pre-existing autoantibodies. In contrast, vaccinees showing no autoantibody formation before vaccination, did not respond with sustained autoantibody production upon vaccination. Taken together, our study suggests that all used SARS-CoV2 vaccines do not significantly foster autoantibody production over time but provide humoral immunity to SARS-CoV2.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Christoph Thurm", - "author_inst": "Institute of Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke-University, Magdeburg, Germany" - }, - { - "author_name": "Annegret Reinhold", - "author_inst": "Institute of Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke-University, Magdeburg, Germany" - }, - { - "author_name": "Katrin Borucki", - "author_inst": "Institute of Clinical Chemistry and Pathobiochemistry, Medical Faculty, Otto-von-Guericke-University, Magdeburg, Germany" - }, - { - "author_name": "Sascha Kahlfuss", - "author_inst": "Institute of Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke-University, Magdeburg, Germany" - }, - { - "author_name": "Eugen Feist", - "author_inst": "Department of Rheumatology, Helios Specialist Hospital Vogelsang, Gommern, Germany" - }, - { - "author_name": "Jens Schreiber", - "author_inst": "Department of Pneumology, University Hospital, Otto-von-Guericke-University, Magdeburg, Germany" - }, - { - "author_name": "Dirk Reinhold", - "author_inst": "Institute of Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke-University, Magdeburg, Germany" - }, - { - "author_name": "Burkhart Schraven", - "author_inst": "Institute of Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke-University, Magdeburg, Germany" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.30.21265694", "rel_title": "Comparative genomics and characterization of SARS-CoV-2 P.1 (Gamma) Variant of Concern (VOC) from Amazonas, Brazil", @@ -515400,6 +517287,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.10.30.21265693", + "rel_title": "Vaccine-induced humoral and cellular immunity against SARS-CoV-2 at 6 months post BNT162b2 vaccination", + "rel_date": "2021-10-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.30.21265693", + "rel_abs": "To evaluate vaccine-induced humoral and cell-mediated immunity at 6 months post BNT162b2 vaccination, immunoglobulin G against SARS-CoV-2 spike protein (SP IgG), 50% neutralizing antibody (NT50), and spot-forming cell (SFC) counts were evaluated by interferon-{gamma} releasing ELISpot assay of 98 healthy subjects (median age, 43 years). The geometric mean titers of SP IgG and NT50 decreased from 95.2 (95% confidence interval (CI) 79.8-113.4) to 5.7 (95% CI 4.9-6.7) and from 680.4 (588.0-787.2) to 130.4 (95% CI 104.2-163.1), respectively, at 3 weeks and 6 months after the vaccination. SP IgG titer was negatively correlated with age and alcohol consumption. Spot-forming cell counts at 6 months did not correlate with age, gender, and other parameters of the patients. SP IgG, NT50, and SFC titers were elevated in the breakthrough infected subjects. Although the levels of vaccine-induced antibodies dramatically declined at 6 months after vaccination, a certain degree of cellular immunity was observed irrespective of the age.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Hideaki Kato", + "author_inst": "Infection Prevention and Control Department, Yokohama City University Hospital, Yokohama, Japan" + }, + { + "author_name": "Kei Miyakawa", + "author_inst": "Department of Microbiology, Yokohama City University School of Medicine, Yokohama, Japan" + }, + { + "author_name": "Norihisa Ohtake", + "author_inst": "Bioscience Division, Research and Development Department, Tosoh Corporation, Tokyo Research Center, Kanagawa, Japan" + }, + { + "author_name": "Yutaro Yamaoka", + "author_inst": "Life Science Laboratory, Technology and Development Division, Kanto Chemical Co, Inc., Isehara, Japan" + }, + { + "author_name": "Satoshi Yajima", + "author_inst": "Clinical Laboratory Department, Yokohama City University Hospital, Yokohama, Japan" + }, + { + "author_name": "Etsuko Yamazaki", + "author_inst": "Clinical Laboratory Department, Yokohama City University Hospital, Yokohama, Japan" + }, + { + "author_name": "Tomoko Shimada", + "author_inst": "Nursing Department, Yokohama City University Hospital, Yokohama, Japan" + }, + { + "author_name": "Atsushi Goto", + "author_inst": "Department of Health Data Science, Yokohama City University Graduate School of Data Science, Yokohama, Japan" + }, + { + "author_name": "Hideaki Nakajima", + "author_inst": "Department of Hematology and Clinical Immunology, Yokohama City University School of Medicine, Yokohama, Japan" + }, + { + "author_name": "Akihide Ryo", + "author_inst": "Department of Microbiology, Yokohama City University School of Medicine, Yokohama, Japan" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.14.21264837", "rel_title": "COVID-19 vaccine brand hesitancy and other challenges to vaccination in the Philippines", @@ -516152,45 +518094,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.10.28.21265608", - "rel_title": "Social discrimination and stigma on the community of health professionals during the Covid-19 pandemic. An ethnographic approach", - "rel_date": "2021-10-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.28.21265608", - "rel_abs": "Severe Acute Respiratory Syndrome Coronavirus Type 2 (SARS-CoV-2) that caused the pandemic since March 2020, has affected among others, health professionals who work in covid-19 units by facing social discrimination. The aim of this study was to record the experiences of health professionals working in the first line of treatment of the pandemic, to analyse the effects of the pandemic on the interpersonal relationships of health professionals, and to ask about the stigma they faced during their work with people with covid-19.\n\nThis is a qualitative study with an ethnographic approach based on 160 semi-structured interviews with health professionals living and working in the Epirus Region, Greece. For the data collection we used semi-structured interviews, discussions and participatory observation. Specifically, the interviews were conducted on health professionals and more specifically doctors, nurses, rescuers, physiotherapists and administrative staff, working in covid-19 units at the University General Hospital of Ioannina (Reference hospital for Ioannina, in Epirus), which assists in the treatment of patients with covid-19, and in the branch of the rescue department of Ioannina.\n\nThe data were analysed in four thematic units based on their common characteristics: a) emotions and experiences of health professionals, b) interpersonal relations of health professionals, c) social exclusion and discrimination, and d) health professionals as patients. The results showed that the main emotions that health professionals experienced when they were moved to covid-19 clinics were fear, anxiety, distress, anger and insecurity. These feelings worsened when their family environment treated them with fear and hesitancy. Their social environment tended to avoid them, leading to a state of self-isolation. To conclude, health professionals faced discriminating behaviors and stigma both from their families and social environment, and from other health professionals. The government struggled to handle the situation in keeping a balance between both the security and well-being of health professionals as it was not prepared for a pandemic like this.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Alexandros Argyriadis", - "author_inst": "Frederick University" - }, - { - "author_name": "Athina Patelarou", - "author_inst": "Hellenic Mediterranean University" - }, - { - "author_name": "Vasiliki Kitsona", - "author_inst": "General Hospital of Ioannina, Greece" - }, - { - "author_name": "Alexandra Trivli", - "author_inst": "Ophthalmology Department of Agios Nikolaos General Hospital, Crete, Greece" - }, - { - "author_name": "Evridiki Patelarou", - "author_inst": "Hellenic Mediterranean University" - }, - { - "author_name": "Agathi Argyriadi", - "author_inst": "Frederick University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "nursing" - }, { "rel_doi": "10.1101/2021.10.28.21265615", "rel_title": "Transmission dynamics of SARS-CoV-2 in a strictly-Orthodox Jewish community in the UK", @@ -517190,6 +519093,57 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.10.29.466401", + "rel_title": "SARS-CoV-2 spike protein as a bacterial lipopolysaccharide delivery system in an overzealous inflammatory cascade", + "rel_date": "2021-10-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.29.466401", + "rel_abs": "Accumulating evidence indicates a potential role for bacterial lipopolysaccharide (LPS) in the overactivation of the immune response during SARS-CoV-2 infection. LPS is recognised by Toll-like receptor 4 (TLR4) in innate immunity. Here, we showed that LPS binds to multiple hydrophobic pockets spanning both the S1 and S2 subunits of the SARS-CoV-2 spike (S) protein. LPS binds to the S2 pocket with a lower affinity compared to S1, suggesting its possible role as an intermediate in the TLR4 cascade. Congruently, nuclear factor-kappa B (NF-{kappa}B) activation in vitro is strongly boosted by S2. In vivo, however, a boosting effect is observed for both S1 and S2, with the former potentially facilitated by proteolysis. Collectively, our study suggests the S protein may act as a delivery system for LPS in host innate immune pathways. The LPS binding pockets are highly conserved across different SARS-CoV-2 variants and therefore represent potential therapeutic targets.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Firdaus Samsudin", + "author_inst": "Bioinformatics Institute, A*STAR" + }, + { + "author_name": "Palur Raghuvamsi", + "author_inst": "Bioinformatics Institute, A*STAR" + }, + { + "author_name": "Ganna Petruk", + "author_inst": "Lund University" + }, + { + "author_name": "Manoj Puthia", + "author_inst": "Lund University" + }, + { + "author_name": "Jitka Petrlova", + "author_inst": "Lund University" + }, + { + "author_name": "Paul MacAry", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Ganesh S Anand", + "author_inst": "The Pennsylvania State University" + }, + { + "author_name": "Artur Schmidtchen", + "author_inst": "Lund University" + }, + { + "author_name": "Peter J Bond", + "author_inst": "Bioinformatics Institute, A*STAR" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.10.27.466067", "rel_title": "Novel pectin from crude polysaccharide of Syzygium aromaticum against SARS-CoV-2 activities by targeting 3CLpro", @@ -518118,61 +520072,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.10.26.21265512", - "rel_title": "Dampening of the respiratory cytokine storm is promoted by inhaled budesonide in patients with early COVID-19", - "rel_date": "2021-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.26.21265512", - "rel_abs": "Vaccinations against SARS-CoV-2 are effective in COVID-19. However, with limited vaccine access, vaccine hesitancy and variant breakthroughs, there is still a need for effective and safe early treatments. Two community-based clinical trials of the inhaled corticosteroid, budesonide, have recently been published showing and improvement in patients with COVID-19 treated early with budesonide1,2. To understand mechanistically how budesonide was beneficial, inflammatory mediators were assessed in the nasal mucosa of patients recruited to the Steroids in COVID (STOIC1) trial and a cohort of SARS-CoV-2 negative individuals. Here we show that in early COVID-19, elevation in viral response proteins and Th1 and Th2 inflammation occurs. Longitudinal sampling in the natural course of COVID-19 showed persistently high interferon levels and elevated concentrations of the eosinophil chemokine, CCL11. In patients who deteriorate, the initial nasal mucosal signal is characterised by a marked suppression of the early inflammatory response, with reduced concentrations of interferon and inflammatory cytokines, but elevated eosinophil chemokines. Systemic inflammation remained altered in COVID-19 patients, implying that even after symptom resolution, changes in immunological mediators do not resolve. Budesonide treatment decreased IL-33 and IFN-{gamma}, implying a reduction in epithelial damage and dampening of the interferon response. Budesonide treatment also increased CCL17 concentrations, suggesting an improved T-cell response; and significantly alters inflammatory pathways giving further insight into how this treatment can accelerate patient recovery.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=92 SRC=\"FIGDIR/small/21265512v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (27K):\norg.highwire.dtl.DTLVardef@849719org.highwire.dtl.DTLVardef@dc1087org.highwire.dtl.DTLVardef@1c13369org.highwire.dtl.DTLVardef@1163fb4_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Jonathan R Baker", - "author_inst": "National Heart and Lung Institute, Imperial College London, London, United Kingdom" - }, - { - "author_name": "Mahdi Mahdi", - "author_inst": "National Institute of Health Research (NIHR) Oxford Biomedical Research Centre (BRC), University of Oxford, United Kingdom" - }, - { - "author_name": "Dan V Nicolau Jr.", - "author_inst": "Nuffield Department of Medicine, University of Oxford, United Kingdom" - }, - { - "author_name": "Sanjay Ramakrishnan", - "author_inst": "National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC), University of Oxford, United Kingdom" - }, - { - "author_name": "Peter J Barnes", - "author_inst": "National Heart and Lung Institute, Imperial College London, London, United Kingdom" - }, - { - "author_name": "Jodie L Simpson", - "author_inst": "School of Medicine and Public Health, Priority Centre for Healthy Lungs, University of Newcastle, Australia" - }, - { - "author_name": "Steven Cass", - "author_inst": "National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC), University of Oxford, United Kingdom" - }, - { - "author_name": "Richard E K Russell", - "author_inst": "National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC), University of Oxford, United Kingdom" - }, - { - "author_name": "Louise E Donnelly", - "author_inst": "National Heart and Lung Institute, Imperial College London, London, United Kingdom" - }, - { - "author_name": "Mona Bafadhel", - "author_inst": "National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC), University of Oxford, United Kingdom" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.26.21265501", "rel_title": "The Persistence of Neutralising Antibodies up to 11 months after SARS-CoV-2 Infection in the Southern Region of New Zealand", @@ -518980,6 +520879,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.10.25.21265462", + "rel_title": "REcovery and SURvival of patients with moderate to severe acute REspiratory distress syndrome (ARDS) due to COVID-19: a multicentre, single-arm, Phase IV Itolizumab Trial: RESURRECT", + "rel_date": "2021-10-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.25.21265462", + "rel_abs": "ObjectiveTo evaluate safety and efficacy of Itolizumab in hospitalized COVID-19 patients with PaO2/FiO2 ratio (PFR) [≤]200 requiring oxygen therapy.\n\nDesignA multicentre, single-arm, Phase-4 study with a treatment period of 30-Days and an extended follow-up period of 90-Days.\n\nMethodsHospitalized adult patients (n=300) with SARS-CoV-2 infection, with PFR [≤]200; oxygen saturation [≤]94% and [≥]1 elevated inflammatory markers were included from 17 COVID-19-specific tertiary hospitals in India. Patients received Itolizumab infusion 1.6 mg/kg and were assessed for 1-month and then followed up to Day-90.\n\nResultsDay-30 post-treatment safety/efficacy results and Day-90 mortality results are presented. Primary outcome measures: incidence of severe acute infusion-related reactions (IRRs) ([≥]Grade-3) was 1.3% and mortality rate at 1-month was 6.7% (n=20/300). Key secondary analyses: Mortality rate at Day-90 was 8.0% (24/300). 91.7% patients came off the oxygen therapy within Day-30 of treatment. By Day-7, most patients had stable/improved SpO2 without increasing FiO2. Mean PFR improved by 50% by Day-7 (p<0.001) and the trend remained consistent till Day-30. Median time of recovery was 8 days. Cumulatively, at Day-30, 260(86.7%), 256(85.3%), 132(44.0%), 113(37.6%) and 32(10.7%) patients showed >1-point, >2-point, >3-point, >4-point and 5-point improvement on the modified COVID-19 8-point ordinal scale and worsening of symptoms by >1 point, >2 points and 3-points was seen in 26(8.7%), 20(6.7%) and 6(2.0%) patients, respectively. CRP, D-dimer, LDH, and serum ferritin levels significantly decreased (p[≤]0.01) compared with baseline. IL-6 and TNF levels also decreased 48-hours post-infusion. Overall, 123 treatment-emergent adverse events (TEAEs) were reported in 63 patients, most being Grades 1-3. Most common TEAEs were IRRs and lymphopenia; most common serious TEAEs were septic shock, worsening of ARDS, and respiratory failure. No deaths were attributable to Itolizumab.\n\nConclusionItolizumab shows no new safety concerns and suggests a mortality and recovery benefit at 1-month in hospitalized COVID-19 patients requiring oxygen therapy.\n\nTrial registry numberCTRI/2020/09/027941", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Raveendra KR", + "author_inst": "Victoria Hospital, Bangalore Medical College and Research Institute, Bangalore, Karnataka, India" + }, + { + "author_name": "Chirag Rathod", + "author_inst": "GMERS Medical College & Hospital, Old TB Hospital Campus, Vadodara, Gujarat, India" + }, + { + "author_name": "Rahul Darnule", + "author_inst": "Saint Georges Hospital, Mumbai, Maharashtra, India" + }, + { + "author_name": "Subramanian Loganathan", + "author_inst": "Biocon Biologics India Limited" + }, + { + "author_name": "Sarika Deodhar", + "author_inst": "Clinical Development and Medical Affairs, Biocon Biologics Ltd, Bengaluru, Karnataka, India" + }, + { + "author_name": "Radhika A", + "author_inst": "Clinical Development and Medical Affairs, Biocon Biologics Ltd, Bengaluru, Karnataka, India" + }, + { + "author_name": "Ashwani Marwah", + "author_inst": "Clinical Development and Medical Affairs, Biocon Biologics Ltd, Bengaluru, Karnataka, India" + }, + { + "author_name": "Nitin M Chaudhari", + "author_inst": "Clinical Development and Medical Affairs, Biocon Biologics Ltd, Bengaluru, Karnataka, India" + }, + { + "author_name": "Binay K Thakur", + "author_inst": "Clinical Development and Medical Affairs, Biocon Biologics Ltd, Bengaluru, Karnataka, India" + }, + { + "author_name": "Sivakumar Vaidyanathan", + "author_inst": "Clinical Development and Medical Affairs, Biocon Biologics Ltd, Bengaluru, Karnataka, India" + }, + { + "author_name": "Sandeep Nilkanth Athalye", + "author_inst": "Clinical Development and Medical Affairs, Biocon Biologics Ltd, Bengaluru, Karnataka, India" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "emergency medicine" + }, { "rel_doi": "10.1101/2021.10.26.21265363", "rel_title": "Network analysis of England single parent household COVID-19 control policy impact; a proof-of-concept study", @@ -519904,33 +521862,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2021.10.26.21265508", - "rel_title": "Six-month sequelae of post-vaccination SARS-CoV-2 infection: a retrospective cohort study of 10,024 breakthrough infections", - "rel_date": "2021-10-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.26.21265508", - "rel_abs": "Vaccination has proven effective against infection with SARS-CoV-2, as well as death and hospitalisation following COVID-19 illness. However, little is known about the effect of vaccination on other acute and post-acute outcomes of COVID-19. Data were obtained from the TriNetX electronic health records network (over 81 million patients mostly in the USA). Using a retrospective cohort study and time-to-event analysis, we compared the incidences of COVID-19 outcomes between individuals who received a COVID-19 vaccine (approved for use in the USA) at least 2 weeks before SARS-CoV-2 infection and propensity score-matched individuals unvaccinated for COVID-19 but who had received an influenza vaccine. Outcomes were ICD-10 codes representing documented COVID-19 sequelae in the 6 months after a confirmed SARS-CoV-2 infection (recorded between January 1 and August 31, 2021). Associations with the number of vaccine doses (1 vs. 2) and age (< 60 vs. [≥] 60 years-old) were assessed. Among 10,024 vaccinated individuals with SARS-CoV-2 infection, 9479 were matched to unvaccinated controls. Receiving at least one COVID-19 vaccine dose was associated with a significantly lower risk of respiratory failure, ICU admission, intubation/ventilation, hypoxaemia, oxygen requirement, hypercoagulopathy/venous thromboembolism, seizures, psychotic disorder, and hair loss (each as composite endpoints with death to account for competing risks; HR 0.70-0.83, Bonferroni-corrected p<.05), but not other outcomes, including long-COVID features, renal disease, mood, anxiety, and sleep disorders. Receiving 2 vaccine doses was associated with lower risks for most outcomes. Associations between prior vaccination and outcomes of SARS-CoV-2 infection were marked in those < 60 years-old, whereas no robust associations were observed in those [≥] 60 years-old. In summary, COVID-19 vaccination is associated with lower risk of several, but not all, COVID-19 sequelae in those with breakthrough SARS-CoV-2 infection. These benefits of vaccination were clear in younger people but not in the over-60s. The findings may inform service planning, contribute to forecasting public health impacts of vaccination programmes, and highlight the need to identify additional interventions for COVID-19 sequelae.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Maxime Taquet", - "author_inst": "University of Oxford" - }, - { - "author_name": "Quentin Dercon", - "author_inst": "University of Oxford" - }, - { - "author_name": "Paul J Harrison", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.25.21265408", "rel_title": "Immunoprecipitation-targeted proteomics assays facilitate rational development of SARS-CoV-2 serological diagnostics", @@ -520790,6 +522721,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.10.26.21265509", + "rel_title": "Epidemiological, virological and serological investigation into a SARS-CoV-2 outbreak (Alpha variant) in a primary school in Geneva, Switzerland: a prospective longitudinal study", + "rel_date": "2021-10-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.26.21265509", + "rel_abs": "We report a prospective epidemiological, virological and serological investigation of a SARS-CoV-2 outbreak in a primary school, as part of a longitudinal, prospective, primary school-based surveillance study. It involved repeated testing of pupils and teachers and household members of participants who tested positive, with rapid antigen tests and/or RT-PCR (Day 0-2 and Day 5-7), serologies on dried capillary blood samples (Day 0-2 and Day 30), contact tracing interviews and SARS-CoV-2 whole genome sequencing. This SARS-CoV-2 outbreak caused by the Alpha variant involved 20 children aged 4 to 6 years from 4 classes, 2 teachers and a total of 4 household members. Infection attack rates were between 11.8 and 62.0% among pupils from the 4 classes, 22.2% among teachers and 0% among non-teaching staff. Secondary attack rate among household members was 15.4%. Symptoms were reported by 63% of infected children, 100% of teachers and 50% of household members. All analysed sequences but one showed 100% identity. Serological tests detected 8 seroconversions unidentified by SARS-CoV-2 virological tests. This study confirmed child-to-child and child-to-adult transmission of the infection. Effective measures to limit transmission in schools have the potential to reduce the overall community circulation.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Elsa Lorthe", + "author_inst": "HUG" + }, + { + "author_name": "Mathilde Bellon", + "author_inst": "HUG" + }, + { + "author_name": "Gregoire Michielin", + "author_inst": "EPFL" + }, + { + "author_name": "Julie Berthelot", + "author_inst": "HUG" + }, + { + "author_name": "Maria-Eugenia Zaballa", + "author_inst": "HUG" + }, + { + "author_name": "Francesco Pennacchio", + "author_inst": "HUG" + }, + { + "author_name": "Meriem Bekliz", + "author_inst": "UNIGE" + }, + { + "author_name": "Florian Laubscher", + "author_inst": "HUG" + }, + { + "author_name": "Fatemeh Arefi", + "author_inst": "EPFL" + }, + { + "author_name": "Javier Perez-Saez", + "author_inst": "HUG" + }, + { + "author_name": "Andrew S Azman", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Arnaud G L'Huillier", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Klara M Posfay-Barbe", + "author_inst": "HUG" + }, + { + "author_name": "Laurent Kaiser", + "author_inst": "University of Geneva Hospitals" + }, + { + "author_name": "Idris Guessous", + "author_inst": "HUG" + }, + { + "author_name": "Sebastian J Maerkl", + "author_inst": "Ecole Polytechnique Federale de Lausanne" + }, + { + "author_name": "Isabella Eckerle", + "author_inst": "HUG" + }, + { + "author_name": "Silvia Stringhini", + "author_inst": "HUG" + }, + { + "author_name": "- SEROCoV-Schools Study Group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.10.25.21265500", "rel_title": "Third doses of COVID-19 vaccines reduce infection and transmission of SARS-CoV-2 and could prevent future surges in some populations", @@ -521930,57 +523952,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.10.21.21265302", - "rel_title": "COVID-19 Prevention Facilitators and Barriers among Specific Ethnic Minority Communities in Rural Ohio", - "rel_date": "2021-10-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.21.21265302", - "rel_abs": "ObjectiveTo assess knowledge, beliefs, and behaviors concerning COVID-19 among Guatemalan, Marshallese, and Amish populations in rural Ohio; identify individual, interpersonal, community, and structural level challenges within each community; and provide population-specific recommendations to prevent and mitigate further SARS-CoV-2 transmission among these rural communities.\n\nMethodsWe conducted 30 key informant interviews in four rural counties in Ohio, in May 2020. Three teams of two investigators conducted interviews with local health department staff, community members, meat packing plant management, and community leaders from three communities disproportionately affected by the COVID-19 pandemic [Guatemalan (N=12), Marshallese (N=7), Amish (N=11)]. We used the Social Ecological Model to identify and categorize themes.\n\nResultsEmerging and overall themes were identified and defined. Investigators identified COVID-19 knowledge gaps, myths, and misinformation, food insecurity, community cohesion, stigma, community culture and norms, lack of workplace safety policies, and access to testing as key themes to COVID-19 prevention.\n\nConclusionsUnderstanding specific barriers and identifying facilitators that most effectively provide resources, healthcare services, education, and social support tailored to specific communities would help deter SARS-CoV-2 transmission.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Paran Pordell", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Hammad Ali", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Gisela Medina Martinez", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Brandi Taylor", - "author_inst": "Ohio Department of Health" - }, - { - "author_name": "Karthik Kondapally", - "author_inst": "Ohio Department of Health" - }, - { - "author_name": "Ellen Salehi", - "author_inst": "Ohio Department of Health" - }, - { - "author_name": "Sietske de Fijter", - "author_inst": "Ohio Department of Health" - }, - { - "author_name": "Nikki Hayes", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Spencer Lloyd", - "author_inst": "Centers for Disease Control and Prevention" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.10.21.21265355", "rel_title": "COVID-19 Vaccination Mandates and Vaccine Uptake", @@ -522748,6 +524719,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2021.10.17.21265058", + "rel_title": "A randomized, controlled, feasibility study of RD-X19 in patients with mild-to-moderate COVID-19 in the outpatient setting", + "rel_date": "2021-10-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.17.21265058", + "rel_abs": "These studies aimed to further understand the antiviral effects of safe, visible light and demonstrate a therapeutic effect of an investigational treatment device for outpatients with mild to moderate COVID-19. RD-X19 is a handheld medical device precisely engineered to emit blue light through the oral cavity to target the oropharynx and surrounding tissues. At doses that are well-tolerated in an in vitro human epithelial tissue model, the monochromatic visible light delivered by RD-X19 results in light-initiated expression of IL-1 and IL-1{beta} cytokines with corresponding inhibition of SARS-CoV-2 replication. A randomized, double-blind, sham-controlled early feasibility study using the investigational device enrolled 31 subjects with a positive SARS-CoV-2 antigen test and possessing at least two moderate COVID-19 signs and symptoms. Subjects were randomized 2:1 (RD-X19 to sham), treated twice daily for four days, and evaluated over one week. Prespecified outcome measures included assessments of SARS-CoV-2 viral load and clinical assessments of COVID-19. There were no local application site reactions and no device-related adverse events. The time-weighted average change in log viral load throughout the study demonstrated a favorable reduction for RD-X19 compared to sham and at the end of study the mean change in log10 viral load was -3.29 for RD-X19 and -1.81 for sham at Day 8, demonstrating a treatment benefit of -1.48 [95% confidence internal (CI), -2.88 to -0.071]. Among the clinical outcome measures, differences between RD-X19 and sham were also observed, with a 57-hour reduction of median time to sustained resolution of COVID-19 signs and symptoms.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Nathan Stasko", + "author_inst": "EmitBio, Inc." + }, + { + "author_name": "Adam S Cockrell", + "author_inst": "EmitBio, Inc." + }, + { + "author_name": "Jacob F Kocher", + "author_inst": "EmitBio, Inc." + }, + { + "author_name": "Ibrahim Henson", + "author_inst": "EmitBio, Inc." + }, + { + "author_name": "David Emerson", + "author_inst": "EmitBio, Inc." + }, + { + "author_name": "Ye Wang", + "author_inst": "Symbio, LLC" + }, + { + "author_name": "Jonathan R Smith", + "author_inst": "Adaptive Plus, LLC" + }, + { + "author_name": "Nathan H Henderson", + "author_inst": "MRI Global" + }, + { + "author_name": "Hillary Wood", + "author_inst": "MRI Global" + }, + { + "author_name": "Shelton S Bradrick", + "author_inst": "MRI Global" + }, + { + "author_name": "Terry Jones", + "author_inst": "J&S Studies, Inc." + }, + { + "author_name": "Jorge Santander", + "author_inst": "APF Research, LLC" + }, + { + "author_name": "John G McNeil", + "author_inst": "EmitBio, Inc." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.21.21265322", "rel_title": "Seroconversion rate and socioeconomic and ethnic risk factors for SARS-CoV-2 infection in children in a population-based cohort", @@ -524156,53 +526194,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.10.20.21265293", - "rel_title": "In-person schooling and associated COVID-19 risk in the United States over Spring Semester 2021", - "rel_date": "2021-10-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.20.21265293", - "rel_abs": "Because of the importance of schools to childhood development, the relationship between in-person schooling and COVID-19 risk has been one of the most important questions of the COVID-19 pandemic. Previous work using data from the United States in winter 2020-21 showed that in-person schooling carried some risk for household members, and that mitigation measures reduced this risk. However, in-person schooling behavior and the COVID-19 landscape changed radically over the 2021 spring semester. Here we use data from a massive online survey to characterize changes in in-person schooling behavior and associated risks over that period. We find a significant increase in the frequency of in-person schooling and a reduction in mitigation, and that in-person schooling is associated with increased reporting of COVID-19 outcomes, even among vaccinated individuals (though the absolute risk among the vaccinated is greatly reduced). Moreover, vaccinated teachers working outside the home were less likely to report COVID-19-related outcomes than unvaccinated teachers reporting no work outside the home. Adequate mitigation measures appear to eliminate the excess risk associated with in person schooling.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Kirsten E. Wiens", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Claire P. Smith", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Elena Badillo-Goicoechea", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Kyra H. Grantz", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "M. Kate Grabowski", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Andrew S. Azman", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Elizabeth A. Stuart", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Justin Lessler", - "author_inst": "University of North Carolina at Chapel Hill" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.10.19.21265107", "rel_title": "Epidemic Surveillance Models for Containing the Spread of SARS-CoV-2 Variants: Taiwan Experience", @@ -525002,6 +526993,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.10.18.21264979", + "rel_title": "Immunogenicity and reactogenicity of booster vaccinations after Ad26.COV2.S priming", + "rel_date": "2021-10-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.18.21264979", + "rel_abs": "BackgroundIn face of the developing COVID-19 pandemic with a need for rapid and practical vaccination strategies, Ad26.COV2.S was approved as single shot immunization regimen. While effective against severe COVID-19, Ad26.COV2.S vaccination induces lower SARS-CoV-2-specific antibody levels compared to its mRNA-based counterparts. To support decision making on the need for booster vaccinations in Ad26.COV2.S-primed individuals, we assessed the immunogenicity and reactogenicity of homologous and heterologous booster vaccinations in Ad26.COV2.S-primed health care workers (HCWs).\n\nMethodsThe SWITCH trial is a single-(participant)-blinded, multi-center, randomized controlled trial among 434 HCWs who received a single Ad26.COV2.S vaccination. HCWs were randomized to no boost, Ad26.COV2.S boost, mRNA-1273 boost, or BNT162b2 boost. We assessed the level of SARS-CoV-2-specific binding antibodies, neutralizing antibodies against infectious virus, SARS-CoV-2-specific T-cell responses, and reactogenicity.\n\nResultsHomologous and heterologous booster vaccinations resulted in an increase in SARS-CoV-2-specific binding antibodies, neutralizing antibodies and T-cell responses when compared to single Ad26.COV.2.S vaccination. In comparison with the homologous boost, the increase was significantly larger in heterologous regimens with the mRNA-based vaccines. mRNA-1273 boosting was most immunogenic, associated with higher reactogenicity. Only mild to moderate local and systemic reactions were observed on the first two days following booster.\n\nConclusionsBoosting of Ad26.COV2.S-primed HCWs was well-tolerated and immunogenic. Strongest responses were detected after boosting with mRNA-based vaccines. Based on our data, efficacy on infection and transmission of boosters is expected. In addition to efficacy, decision making on boost vaccinations should include timing, target population, level of SARS CoV-2 circulation, and the global inequity in vaccine access.\n\nTrial registrationFunded by ZonMW (10430072110001); ClinicalTrials.gov number, NCT04927936.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Roos Sablerolles", + "author_inst": "Erasmus MC, Rotterdam" + }, + { + "author_name": "Wim Rietdijk", + "author_inst": "Erasmus MC, Rotterdam" + }, + { + "author_name": "Bram Goorhuis", + "author_inst": "Amsterdam UMC, Amsterdam" + }, + { + "author_name": "Douwe Postma", + "author_inst": "UMCG, Groningen" + }, + { + "author_name": "Leo Visser", + "author_inst": "LUMC, Leiden" + }, + { + "author_name": "Daryl Geers", + "author_inst": "Erasmus MC, Rotterdam" + }, + { + "author_name": "Katharina Schmitz", + "author_inst": "Erasmus MC, Rotterdam" + }, + { + "author_name": "Hannah Garcia Garrido", + "author_inst": "Amsterdam UMC, Amsterdam" + }, + { + "author_name": "Marion Koopmans", + "author_inst": "Erasmus Medical Center" + }, + { + "author_name": "Virgil Dalm", + "author_inst": "Erasmus MC, Rotterdam" + }, + { + "author_name": "Neeltje A. Kootstra", + "author_inst": "Amsterdam UMC, Amsterdam" + }, + { + "author_name": "Anke Huckriede", + "author_inst": "UMCG, Groningen" + }, + { + "author_name": "Melvin Lafeber", + "author_inst": "Erasmus MC, Rotterdam" + }, + { + "author_name": "Debbie van Baarle", + "author_inst": "UMCG, Groningen" + }, + { + "author_name": "Corine GeurtsvanKessel", + "author_inst": "Erasmus MC, Rotterdam" + }, + { + "author_name": "Rory D. de Vries", + "author_inst": "Erasmus MC, Rotterdam" + }, + { + "author_name": "Hugo van der Kuy", + "author_inst": "Erasmus MC, Rotterdam" + }, + { + "author_name": "- SWITCH research group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pharmacology and therapeutics" + }, { "rel_doi": "10.1101/2021.10.19.21265194", "rel_title": "General Practitioner perspectives and wellbeing during the COVID-19 Pandemic: a mixed method social media analysis", @@ -525925,49 +528003,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.10.20.464686", - "rel_title": "S100A8 and S100A9, biomarkers of SARS-Cov-2-infected patients, suppress HIV replication in primary macrophages", - "rel_date": "2021-10-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.20.464686", - "rel_abs": "S100A8 and S100A9 are members of the Alarmin family; these proteins are abundantly expressed in neutrophils and form a heterodimer complex. Recently, both proteins were identified as novel biomarkers of SARS-CoV-2 infection and were shown to play key roles in inducing an aggressive inflammatory response by mediating the release of large amounts of pro-inflammatory cytokines, called the \"cytokine storm.\" Although co-infection with SARS-CoV-2 in people living with HIV-1 may result in an immunocompromised status, the role of the S100A8/A9 complex in HIV-1 replication in primary T cells and macrophages is still unclear. Here, we evaluated the roles of the proteins in HIV replication to elucidate their functions. We found that the complex had no impact on virus replication in both cell types; however, the subunits of S100A8 and S100A9 inhibits HIV in macrophages. These findings provide important insights into the regulation of HIV viral loads in SARS-CoV2 co-infection.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Raphael M. Oguariri", - "author_inst": "FNLCR" - }, - { - "author_name": "Terrence W. Brann", - "author_inst": "FNLCR" - }, - { - "author_name": "Joseph W. Adelsberger", - "author_inst": "FNLCR" - }, - { - "author_name": "Qian Chen", - "author_inst": "FNLCR" - }, - { - "author_name": "Suranjana Goswami", - "author_inst": "FNLCR" - }, - { - "author_name": "Anthony R. Mele", - "author_inst": "FNLCR" - }, - { - "author_name": "Tomozumi Imamichi", - "author_inst": "FNLCR" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.10.20.21265273", "rel_title": "Impaired Neutralizing Antibody Response to COVID-19 mRNA Vaccines in Cancer Patients", @@ -527067,6 +529102,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.10.18.464926", + "rel_title": "Intensive Single Cell Analysis Reveals Immune Cell Diversity among Healthy Individuals", + "rel_date": "2021-10-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.18.464926", + "rel_abs": "It is believed that immune responses are different between individuals and at different times. In addition, personal health histories and unique environmental conditions should collectively determine the present state of immune cells. However, the cellular and molecular system mechanisms underlying such heterogeneity remain largely elusive. In this study, we conducted a systematic time-lapse single-cell analysis, using 171 single-cell libraries and 30 mass cytometry datasets intensively for seven healthy individuals. We found substantial diversity in immune cell populations and their gene expression patterns between different individuals. These patterns showed daily fluctuations even within the same individual spending a usual life. Similar diversities were also observed for the T cell receptor and B cell receptor repertoires. Detailed immune cell profiles at healthy statuses should give an essential background information to understand their immune responses, when the individual is exposed to various environmental conditions. To demonstrate this idea, we conducted the similar analysis for the same individuals on the vaccination of Influenza and SARS-CoV-2, since the date and the dose of the antigens are well-defined in these cases. In fact, we found that the distinct responses to vaccines between individuals, althougth key responses are common. Single cell immune cell profile data should make fundamental data resource to understand variable immune responses, which are unique to each individual.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Yukie Kashima", + "author_inst": "University of Tokyo" + }, + { + "author_name": "Keiya Kaneko", + "author_inst": "University of Tokyo" + }, + { + "author_name": "Patrick Reteng", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Nina Yoshitake", + "author_inst": "University of Tokyo" + }, + { + "author_name": "Lucky Ronald Runtuwene", + "author_inst": "National Institute of Infectious Disease" + }, + { + "author_name": "Satoi Nagasawa", + "author_inst": "University of Tokyo" + }, + { + "author_name": "Masaya Onishi", + "author_inst": "University of Tokyo" + }, + { + "author_name": "Masahide Seki", + "author_inst": "University of Tokyo" + }, + { + "author_name": "Ayako Suzuki", + "author_inst": "University of Tokyo" + }, + { + "author_name": "Sumio Sugano", + "author_inst": "Institute of Kashiwa-no-ha Omics Gate" + }, + { + "author_name": "Mamiko Sakata-Yanagimoto", + "author_inst": "University of Tsukuba" + }, + { + "author_name": "Yumiko Imai", + "author_inst": "National Institutes of Biomedical Innovation, Health and Nutrition" + }, + { + "author_name": "Kaori Nakayama-Hosoya", + "author_inst": "National Institute of Infectious Disease" + }, + { + "author_name": "Ai Kawana-Tachikawa", + "author_inst": "National Institute of Infectious Disease" + }, + { + "author_name": "Taketoshi Mizutani", + "author_inst": "University of Tokyo" + }, + { + "author_name": "Yutaka Suzuki", + "author_inst": "The University of Tokyo" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2021.10.19.464931", "rel_title": "Repurposed nystatin to inhibit SARS-CoV-2 and mutants in the GI tract", @@ -528059,45 +530173,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.10.18.21265130", - "rel_title": "Survey of Direct and Indirect Effects of COVID-19 on Eyes and the Common Ocular Manifestations", - "rel_date": "2021-10-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.18.21265130", - "rel_abs": "PurposeOcular manifestations were reported in many recent observations that studied either the effect of COVID-19 directly on eyes or of face mask use. Hence, this study aimed to investigate the effect of COVID-19 on the eyes and make a clear comparison of its direct and indirect effect from face mask-wearing.\n\nMethodsThis was a cross-sectional study of both written and web-based questionnaires, distributed among a group of COVID-19 patients and a matched control group, the questionnaire consisted of common demographic data, COVID-19 infection history and its symptoms, focusing on ocular symptoms and the presence of conditions related to or cause eye symptoms. As well as the use of face masks that were assessed in terms of the complained ocular manifestation\n\nResultsOf 618 participants, 252 had COVID-19 and 366 never had COVID-19. Ocular manifestation among COVID-19 incidence was 44%, significantly higher than non-infected participants incidence (35.8%), adjusted odds ratio, 95% confidence interval (AOR, 95%CI); 1.45 (1.02-2.06)). Eye discharges (p-value = 0.033) and photosensitivity (p-value = 0.003) were noted more commonly among COVID-19 participants compared to healthy control. When comparing long periods of face mask use with each ocular symptom; dry eye based on OSDI, forging body sensation, eye pain and eye discharges, were found significantly common among extended periods of face mask use.\n\nConclusionCOVID-19 pandemic affected eyes, both directly from the virus or from its preventive measure of face mask use.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Dianeh Rabi", - "author_inst": "An-najah national university" - }, - { - "author_name": "razan Rabi", - "author_inst": "Ministry of health, Palestine" - }, - { - "author_name": "Arkan Jarrar", - "author_inst": "Ministry of health" - }, - { - "author_name": "Sarah Maharma", - "author_inst": "An-najah national university" - }, - { - "author_name": "Aya Jaradat", - "author_inst": "An-najah national university" - }, - { - "author_name": "shatha Bzoor", - "author_inst": "An-najah national university" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.16.21265095", "rel_title": "One-dose ChAdOx1 nCoV-19 Vaccine Effectiveness Against Symptomatic COVID-19 in a vulnerable community in Rio de Janeiro, Brazil: test-negative design study", @@ -528781,6 +530856,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2021.10.18.21265135", + "rel_title": "Conflicts of interest and physicians' attitudes towards hydroxychloroquine as a treatment against COVID-19: A replication and extension of Roussel & Raoult (2020)", + "rel_date": "2021-10-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.18.21265135", + "rel_abs": "Hydroxychloroquine (HCQ) and its use as a treatment against COVID-19 have been at the center of heated debates. Some claim that physicians hostility towards HCQ was partly orchestrated by rival pharmaceutical companies seeking to promote their own treatment. In favor of this hypothesis, Roussel and Raoult (2020) have presented the results of a study in which they find a perfect positive correlation ({rho} = 1.00) between French physicians attitudes towards HCQ and their conflict of interest with Gilead Sciences - the company that has promoted Remdesivir (REM) as a treatment against COVID-19. However, Roussel and Raoults study suffers from serious methodological shortcomings, among which is the fact that the statistical methods they employed might tend to artificially inflate correlations. In this study, we use a similar method and sample, but correct for their studys original shortcomings: we provide a detailed, pre-registered method for collecting and coding data, computer inter-rater agreement and use a wide array of appropriate statistical methods to achieve a more reliable estimate the association between conflicts of interest and physicians attitudes towards HCQ. We conclude that Roussel and Raoults conclusion was misguided and that financial conflicts of interest were not the main predictors of the attitudes of physicians when compared to other factors, such as academic affiliation. Moreover, compared to other pharmaceutical companies, there was no specific link between attitudes towards HCQ and conflicts of interest with Gilead Sciences.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Louis Freget", + "author_inst": "University of Copenhagen" + }, + { + "author_name": "Matthieu Mulot", + "author_inst": "University of Neuchatel, Laboratory of Soil Biodiversity, 2000 Neuchatel Switzerland." + }, + { + "author_name": "Michael Rochoy", + "author_inst": "Univ. Lille, CHU Lille, ULR 2694 - METRICS, CERIM, Liberal practice F-62230 O, F-59000 Lille, France" + }, + { + "author_name": "Valentin RUGGERI", + "author_inst": "Nuclear Medicine Department, Grenoble-Alpes University Hospital, 38000 Grenoble, France." + }, + { + "author_name": "Celine SCHOPFER", + "author_inst": "University of Geneva, Department of Philosophy" + }, + { + "author_name": "Florian Cova", + "author_inst": "University of Geneva, Department of Philosophy" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2021.10.16.21264948", "rel_title": "Impact of SARS-CoV-2 infection on longitudinal vaccine immune responses", @@ -529812,49 +531926,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.10.14.21264978", - "rel_title": "The SARS-CoV-2 infection among students in the University of Porto: a cross-sectional study", - "rel_date": "2021-10-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.14.21264978", - "rel_abs": "IntroductionIncidence based on notified cases of SARS-CoV-2 infection underestimates the real extension of the infection. We aimed to quantify SARS-CoV-2 specific antibodies seroprevalence among University students in Porto.\n\nMethodsA rapid point of care testing for SARS-CoV-2 specific immunoglobulin (Ig) M and IgG antibodies was performed, and a questionnaire was applied to the 6512 voluntary students from September to December 2020. We computed the apparent IgM, IgG and IgM or IgG prevalence, and the true prevalence and 95% credible intervals (95% CI) using Bayesian inference.\n\nResultsWe found an apparent prevalence (IgM or IgG) of 9.7%, the true prevalence being 7.9% (95% CI 4.9-11.1). Prevalence was significantly higher among males (10.9% vs 9.2%), international students (18.1% vs 10.4% local vs 8.8% nationally displaced) and increased with age. Those with a known risk contact, that experienced quarantine, had symptoms, or a previous negative molecular test had a higher seroprevalence. Of the 91 (1.4%) students who reported a molecular diagnosis, 86.7% were reactive for IgM or IgG.\n\nConclusionBased on immunological evidence infection was 5.6 times more frequent than if based on a molecular diagnosis. The higher seroprevalence among male, older, and international students emphasizes the importance of identifying particular groups.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Paula Meireles", - "author_inst": "EPIUnit - Instituto de Saude Publica, Universidade do Porto" - }, - { - "author_name": "Joana Pinto Costa", - "author_inst": "EPIUnit - Instituto de Saude Publica, Universidade do Porto" - }, - { - "author_name": "Maria Novais", - "author_inst": "EPIUnit - Instituto de Saude Publica, Universidade do Porto" - }, - { - "author_name": "Daniela Miranda", - "author_inst": "EPIUnit - Instituto de Saude Publica, Universidade do Porto" - }, - { - "author_name": "Mariana Mendes Lopes", - "author_inst": "EPIUnit - Instituto de Saude Publica, Universidade do Porto" - }, - { - "author_name": "Milton Severo", - "author_inst": "EPIUnit - Instituto de Saude Publica, Universidade do Porto" - }, - { - "author_name": "Henrique Barros", - "author_inst": "EPIUnit - Instituto de Saude Publica, Universidade do Porto" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.10.14.21264847", "rel_title": "Variation at Spike position 142 in SARS-CoV-2 Delta genomes is a technical artifact caused by dropout of a sequencing amplicon", @@ -530354,6 +532425,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.10.14.21265031", + "rel_title": "Evaluation of viral loads in patients with SARS-CoV-2 Delta variant infection: Higher loads do not translate into different testing scenarios", + "rel_date": "2021-10-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.14.21265031", + "rel_abs": "The Delta SARS-CoV-2 variant is very infectious, and it is spreading quickly during this pandemic. In the study, we compared viral loads in surging cases infected with the SARS-CoV-2 Delta variant in the fourth wave of COVID-19 with the three prior waves. The data comprised viral loads from positive cases detected within the UPMC health care system in Allegheny County, Pennsylvania. A total of 2,059 upper airway samples were collected and tested for SARS-CoV-2 positive by RT-PCR during March 2020-September 2021. We did not observe significant difference in viral load difference between the third (December 2020 - January 2021) and fourth (June 2021 - September 2021) waves; however, they had the higher viral load than the first (March 2020 - June 2020) and second waves (June 2020 - August 2020). We did find an age-related effect with the elderly presenting with lower viral loads, which was also seen in the earlier waves. However, the level of viral load in the fourth wave was not sufficient higher to qualitatively change our expected detected rates using various testing modalities.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Juan Luis Gomez Marti", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Ashley Mays", + "author_inst": "UPMC Hospital System" + }, + { + "author_name": "Melissa McCullough", + "author_inst": "UPMC Hospital System" + }, + { + "author_name": "Alan Wells", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Tung Phan", + "author_inst": "University of Pittsburgh Medical Center" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pathology" + }, { "rel_doi": "10.1101/2021.10.17.21265111", "rel_title": "SARS-CoV-2 Pandemic Preventive Methods Efficacy - A Simulation Case Study", @@ -531426,57 +533532,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.10.18.464814", - "rel_title": "Bees can be trained to identify SARS-CoV-2 infected samples.", - "rel_date": "2021-10-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.18.464814", - "rel_abs": "The COVID-19 pandemic has illustrated the need for the development of fast and reliable testing methods for novel, zoonotic, viral diseases in both humans and animals. Pathologies lead to detectable changes in the Volatile Organic Compound (VOC) profile of animals, which can be monitored, thus allowing the development of a rapid VOC-based test. In the current study, we successfully trained honeybees (Apis mellifera) to identify SARS-CoV-2 infected minks (Neovison vison) thanks to Pavlovian conditioning protocols. The bees can be quickly conditioned to respond specifically to infected minks odours and could therefore be part of a wider SARS-CoV-2 diagnostic system. We tested two different training protocols to evaluate their performance in terms of learning rate, accuracy and memory retention. We designed a non-invasive rapid test in which multiple bees are tested in parallel on the same samples. This provided reliable results regarding a subjects health status. Using the data from the training experiments, we simulated a diagnostic evaluation trial to predict the potential efficacy of our diagnostic test, which yielded a diagnostic sensitivity of 92% and specificity of 86%. We suggest that a honeybee-based diagnostics can offer a reliable and rapid test that provides a readily available, low-input addition to the currently available testing methods. A honeybee-based diagnostic test might be particularly relevant for remote and developing communities that lack the resources and infrastructure required for mainstream testing methods.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Evangelos Kontos", - "author_inst": "Insectsense" - }, - { - "author_name": "Aria Samimi", - "author_inst": "Insectsense" - }, - { - "author_name": "Renate W Hakze-van der Honing", - "author_inst": "Wageningen University and Research" - }, - { - "author_name": "Jan Priem", - "author_inst": "Wageningen University and Research" - }, - { - "author_name": "Aurore Avargues-Weber", - "author_inst": "University Toulouse III - Paul Sabatier" - }, - { - "author_name": "Alexander Haverkamp", - "author_inst": "Wageningen University" - }, - { - "author_name": "Marcel Dicke", - "author_inst": "Wageningen University and Research" - }, - { - "author_name": "Jose Gonzales", - "author_inst": "Wageningen University and Research" - }, - { - "author_name": "Wim H van der Poel", - "author_inst": "Wageningen University and Research" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.10.17.464700", "rel_title": "Plant-based production of SARS-CoV-2 antigens for use in a subunit vaccine", @@ -532163,6 +534218,53 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.10.14.464416", + "rel_title": "Efficient incorporation and template-dependent polymerase inhibition are major determinants for the broad-spectrum antiviral activity of remdesivir", + "rel_date": "2021-10-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.14.464416", + "rel_abs": "Remdesivir (RDV) is a direct antiviral agent that is approved in several countries for the treatment of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). RDV exhibits broad-spectrum antiviral activity against positive-sense RNA viruses, e.g., SARS-CoV-2 and hepatitis C virus (HCV) and non-segmented negative-sense RNA viruses, e.g., Nipah virus (NiV), while several segmented negative-sense RNA viruses such as influenza (Flu) virus or Crimean-Congo hemorrhagic fever virus (CCHFV) are not sensitive to the drug. The reasons for this apparent pattern are unknown. Here, we expressed and purified representative RNA-dependent RNA polymerases (RdRp) and studied three biochemical parameters that have been associated with the inhibitory effects of RDV-triphosphate (TP): (i) selective incorporation of the nucleotide substrate RDV-TP, (ii) the effect of the incorporated RDV-monophosphate (MP) on primer extension, and (iii) the effect of RDV-MP in the template during incorporation of the complementary UTP. The results of this study revealed a strong correlation between antiviral effects and efficient incorporation of RDV-TP. Delayed chain-termination is heterogeneous and usually inefficient at higher NTP concentrations. In contrast, template-dependent inhibition of UTP incorporation opposite the embedded RDV-MP is seen with all polymerases. Molecular modeling suggests a steric conflict between the 1-cyano group of RDV-MP and conserved residues of RdRp motif F. We conclude that future efforts in the development of nucleotide analogues with a broader spectrum of antiviral activities should focus on improving rates of incorporation while capitalizing on the inhibitory effects of a bulky 1-modification.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Matthias G\u00f6tte", + "author_inst": "University of Alberta" + }, + { + "author_name": "Calvin J. Gordon", + "author_inst": "University of Alberta" + }, + { + "author_name": "Hery W. Lee", + "author_inst": "University of Alberta" + }, + { + "author_name": "Egor P. Tchesnokov", + "author_inst": "University of Alberta" + }, + { + "author_name": "Jason K. Perry", + "author_inst": "Gilead Sciences" + }, + { + "author_name": "Joy Y. Feng", + "author_inst": "Gilead Sciences" + }, + { + "author_name": "John P. Bilello", + "author_inst": "Gilead Sciences" + }, + { + "author_name": "Danielle P. Porter", + "author_inst": "Gilead Sciences" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2021.10.14.464320", "rel_title": "Enhanced metanephric specification to functional proximal tubule enables toxicity screening and infectious disease modelling in kidney organoids", @@ -533483,73 +535585,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2021.10.14.21264981", - "rel_title": "Differential immunogenicity of homologous versus heterologous boost in Ad26.COV2.S vaccine recipients.", - "rel_date": "2021-10-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.14.21264981", - "rel_abs": "Protection offered by COVID-19 vaccines wanes over time, requiring an evaluation of different boosting strategies to revert such a trend and enhance the quantity and quality of Spike-specific humoral and cellular immune responses. These immunological parameters in homologous or heterologous vaccination boosts have thus far been studied for mRNA and ChAdOx1 nCoV-19 vaccines, but knowledge on individuals who received a single dose of Ad26.COV2.S is lacking.\n\nWe studied Spike-specific humoral and cellular immunity in Ad26.COV2.S vaccinated individuals (n=55) who were either primed with Ad26.COV2.S only (n=13), or boosted with a homologous (Ad26.COV2.S, n=28) or heterologous (BNT162b2, n=14) second dose. We compared our findings with the results found in individuals vaccinated with a single (n=16) or double (n=44) dose of BNT162b2. We observed that a strategy of heterologous vaccination enhanced the quantity and breadth of both, Spike-specific humoral and cellular immunity in Ad26.COV2.S vaccinated. In contrast, the impact of homologous boost was quantitatively minimal in Ad26.COV2.S vaccinated and Spike-specific antibodies and T cells were narrowly focused to the S1 region. Although a direct association between quantity and quality of immunological parameters and in vivo protection has not been demonstrated, the immunological features of Spike-specific humoral and cellular immune responses support the utilization of a heterologous strategy of vaccine boost in individuals who received Ad26.COV2.S vaccination.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Nicholas Kim Huat Khoo", - "author_inst": "Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore" - }, - { - "author_name": "Joey Ming Er Lim", - "author_inst": "Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore" - }, - { - "author_name": "Upkar Singh Gill", - "author_inst": "Barts Liver Centre, Barts and The London School of Medicine & Dentistry, Queen Mary University of London, London, UK" - }, - { - "author_name": "Ruklanthi de Alwis", - "author_inst": "Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore" - }, - { - "author_name": "Nicole Tan", - "author_inst": "Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore" - }, - { - "author_name": "Justin Zhen Nan Toh", - "author_inst": "Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore" - }, - { - "author_name": "Jane E Abbott", - "author_inst": "Barts Liver Centre, Barts and The London School of Medicine & Dentistry, Queen Mary University of London, London, UK" - }, - { - "author_name": "Carla Usai", - "author_inst": "Barts Liver Centre, Barts and The London School of Medicine & Dentistry, Queen Mary University of London, London, UK" - }, - { - "author_name": "Eng Eong Ooi", - "author_inst": "Duke-NUS Medical School" - }, - { - "author_name": "Jenny Guek Hong Low", - "author_inst": "Department of Infectious Diseases, Singapore General Hospital, Singapore" - }, - { - "author_name": "Nina Le Bert", - "author_inst": "Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore" - }, - { - "author_name": "Patrick TF Kennedy", - "author_inst": "Barts Liver Centre, Barts and The London School of Medicine & Dentistry, Queen Mary University of London, London, UK" - }, - { - "author_name": "Antonio Bertoletti", - "author_inst": "Duke-Nus Medical School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.11.21264606", "rel_title": "Genome Recombination between Delta and Alpha Variants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)", @@ -534485,6 +536520,49 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2021.10.12.21264883", + "rel_title": "Public acceptability of non-pharmaceutical interventions to control a pandemic in the United Kingdom: a discrete choice experiment", + "rel_date": "2021-10-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.12.21264883", + "rel_abs": "ObjectiveTo understand how individuals make trade-offs between features of lockdown interventions to control a pandemic across the four nations of the United Kingdom.\n\nDesignSurvey that included a Discrete Choice Experiment (DCE). The survey design was informed using policy documents, social media analysis and with input from remote think aloud interviews with members of the public (n=23).\n\nSettingNation-wide survey across the four nations of the United Kingdom. Representative sample in terms of age and sex for each of the nations recruited using an online panel between 29th October and 12th December 2020.\n\nParticipantsIndividuals who are over 18 years old. A total of 4120 adults completed the survey (1112 in England, 848 in Northern Ireland, 1143 in Scotland and 1098 in Wales).\n\nPrimary outcome measureAdults preferences for, and trade-offs between, type of lockdown restrictions, length of lockdown, postponement of routine healthcare, excess deaths, impact on ability to buy things and unemployment.\n\nResultsIn all four countries, one out of five respondents were willing to reduce excess deaths at all costs. The majority of adults are willing to accept higher excess deaths if this means lockdowns that are less strict, shorter and do not postpone routine healthcare. On average, respondents in England were willing to accept a higher increase in excess deaths to have less strict lockdown restrictions introduced compared to Scotland, Northern Ireland, and Wales, respectively.\n\nConclusionsThe majority of the UK population is willing to accept the increase in excess deaths associated with introducing less strict lockdown restrictions. The acceptability of different restriction scenarios varies according to the features of the lockdown and across countries. Authorities can use information about trade-off preferences to inform the introduction of different lockdown restriction levels, and design compensation policies that maximise societal welfare.\n\nStrengths and limitations of this studyO_LIThis study offers empirical evidence that, unlike existing data from opinion polls and citizens panels, offers a clear understanding of the trade-offs between restrictions and impacts of lockdown on society.\nC_LIO_LIEstimating preferences for each nation, and quantifying them in terms of a common denominator, allows a comparison that takes into account the heterogeneity of UK nations and can be used to inform the introduction of different levels of lockdown restrictions in each.\nC_LIO_LIA limitation of our study is that we are not able to estimate the effect of on-going lockdowns in preferences. Furthermore, our results are not necessarily transferable to other nations.\nC_LI", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Luis Enrique Loria-Rebolledo", + "author_inst": "Health Economics Research Unit, University of Aberdeen" + }, + { + "author_name": "Mandy Ryan", + "author_inst": "Health Economics Research Unit, University of Aberdeen" + }, + { + "author_name": "Verity Watson", + "author_inst": "Health Economics Research Unit, University of Aberdeen" + }, + { + "author_name": "Mesfin G Genie", + "author_inst": "Health Economics Research Unit, University of Aberdeen" + }, + { + "author_name": "Ruben Andreas Sakowsky", + "author_inst": "Department of Medical Ethics and History of Medicine, University Medical Center Gottingen" + }, + { + "author_name": "Daniel Powell", + "author_inst": "Health Data Science Research Centre, University of Aberdeen" + }, + { + "author_name": "Shantini Paranjothy", + "author_inst": "Health Psychology, University of Aberdeen" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2021.10.12.21264898", "rel_title": "Why one size fits all is not enough when designing immunity certificates for domestic use: a UK wide cross-sectional online survey", @@ -535297,113 +537375,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.10.21264812", - "rel_title": "Breakthrough SARS-CoV-2 Infections after Vaccination in North Carolina", - "rel_date": "2021-10-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.10.21264812", - "rel_abs": "ImportanceReal-world data are needed to assess incidence and factors associated with breakthrough SARS-CoV-2 infections following vaccination.\n\nObjectiveEstimate incidence of breakthrough infections and assess associations with risk factors using self-reported data from a large NC population sample.\n\nDesignProspective observational cohort study utilizing daily online survey data to capture information about COVID-19 symptoms, testing, and vaccination status.\n\nSettingSix health care systems in North Carolina with data collected between January 15, 2021 and September 24, 2021.\n\nParticipantsAdult study participants who reported full vaccination with a COVID-19 mRNA or J&J non-replicating viral vector vaccine (n =16,020).\n\nExposuresPotential community exposure to SARS-CoV-2.\n\nMain Outcome and MeasuresSelf-reported breakthrough infection.\n\nResultsSARS-CoV-2 infection after vaccination was self-reported in 1.9% of participants, with an incidence rate of 7.3 per 100,000 person-years. Younger age (45-64 vs. 18-44: HR (95% CI) = 0.65 (0.51 - 0.82); 65+ vs. 18-44: HR (95% CI) = 0.59 (0.39 - 0.90)), and vaccination with J&J Ad26.COV2.S were associated with a higher risk of breakthrough infection compared to vaccination with Pfizer BNT162b2 (Ad26.COV2.S vs. BNT162b2: HR (95% CI) = 2.23 (1.40 - 3.56)), while participants vaccinated with mRNA-1273 (mRNA-1273 vs. BNT162b2: HR (95% CI) = 0.69 (0.50 - 0.96) and those residing in urban counties experienced a lower rate of SARS-CoV-2 breakthrough infection compared with those from suburban (HR (95% CI) = 1.39 (1.01 - 1.90) or rural (HR (95% CI) = 1.57 (1.16 - 2.11) counties. There was no significant association between breakthrough infection and participant sex, race, healthcare worker status, prior COVID-19 infection, routine mask use, or overall vaccination rate in the county of residence.\n\nConclusions and RelevanceThis NC community-based observational study showed that the proportion of the cohort who self-report breakthrough SARS-CoV-2 infections was 7.3 events per 100,000 person-years. Younger adults, those vaccinated with J&J Ad26.COV2.S, and those residing in suburban or rural counties were at higher risk of breakthrough infections and should be targeted for additional risk mitigation strategies to decrease community transmission.\n\nTrial RegistrationThe COVID-19 Community Research Partnership is listed in clinicaltrials.gov (NCT04342884).\n\nKey PointsO_ST_ABSQuestionC_ST_ABSWhat are the characteristics of those with breakthrough infections after SARS-CoV-2 vaccination in North Carolinaa\n\nFindingsIn this NC-based observational study of 16,020 participants, 1.9% self-reported a positive SARS-CoV-2 viral test at least 2 weeks following full vaccination, reflecting an event rate of 7.3 infections per 100,000 person years. Rates were higher among younger participants, participants from more rural areas in North Carolina, and those vaccinated with J&J Ad26.COV2.S.\n\nMeaningOur results show a relatively low rate of COVID-19 infection following full vaccination. Younger adults and those vaccinated with J&J Ad26.COV2.S should be targeted for additional risk mitigation strategies.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Diane Uschner", - "author_inst": "The George Washington University Biostatistics Center" - }, - { - "author_name": "Matthew Bott", - "author_inst": "The George Washington University Biostatistics Center" - }, - { - "author_name": "Michele Santacatterina", - "author_inst": "The George Washington University Biostatistics Center" - }, - { - "author_name": "Mihili P Gunaratne", - "author_inst": "The George Washington University Biostatistics Center" - }, - { - "author_name": "Lida Fette", - "author_inst": "The George Washington University Biostatistics Center" - }, - { - "author_name": "Brian K Burke", - "author_inst": "The George Washington University Biostatistics Center" - }, - { - "author_name": "Greg Strylewicz", - "author_inst": "The George Washington University Biostatistics Center" - }, - { - "author_name": "Sharon L Edelstein", - "author_inst": "The George Washington University Biostatistics Center" - }, - { - "author_name": "William H Lagarde", - "author_inst": "WakeMed Health and Hospitals" - }, - { - "author_name": "Kristen E Miller", - "author_inst": "MedStar Health Research Institute" - }, - { - "author_name": "William S Weintraub", - "author_inst": "MedStar Health Research Institute and Georgetown University" - }, - { - "author_name": "Joshua Yukich", - "author_inst": "Tulane University" - }, - { - "author_name": "Hazel Tapp", - "author_inst": "Atrium Health" - }, - { - "author_name": "John Schieffelin", - "author_inst": "Tulane University" - }, - { - "author_name": "Amina Ahmed", - "author_inst": "Atrium Health" - }, - { - "author_name": "Andrea A Berry", - "author_inst": "University of Maryland School of Medicine" - }, - { - "author_name": "Iqra Munawar", - "author_inst": "Wake Forest School of Medicine" - }, - { - "author_name": "Austin L Seals", - "author_inst": "Wake Forest School of Medicine" - }, - { - "author_name": "John Williamson", - "author_inst": "Wake Forest School of Medicine" - }, - { - "author_name": "David Herrington", - "author_inst": "Wake Forest School of Medicine" - }, - { - "author_name": "John W Sanders", - "author_inst": "Wake Forest School of Medicine" - }, - { - "author_name": "Michael Runyon", - "author_inst": "Atrium Health" - }, - { - "author_name": "- COVID-19 Community Research Partnership", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.08.21264472", "rel_title": "Highly sensitive and specific detection of the SARS-CoV-2 Delta variant by double-mismatch allele-specific PCR", @@ -536251,6 +538222,85 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.10.08.21264776", + "rel_title": "A molecular surveillance-guided vector control response to concurrent dengue and West Nile virus outbreaks in a COVID-19 hotspot of Florida", + "rel_date": "2021-10-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.08.21264776", + "rel_abs": "Simultaneous dengue virus (DENV) and West Nile virus (WNV) outbreaks in Florida, USA, in 2020 resulted in 71 dengue virus serotype 1 and 86 WNV human cases. Our outbreak response leveraged a molecular diagnostic screen of mosquito populations for DENV and WNV in Miami-Dade County to quickly employ targeted mosquito abatement efforts. We detected DENV serotypes 2 and 4 in mosquito pools, highlighting the silent circulation of diverse dengue serotypes in mosquitoes. Additionally, we found WNV-positive mosquito pools in areas with no historical reports of WNV transmission. These findings demonstrate the importance of proactive, strategic arbovirus surveillance in mosquito populations to prevent and control outbreaks, particularly when other illnesses (e.g., COVID-19), which present with similar symptoms are circulating concurrently. Growing evidence for substantial infection prevalence of dengue in competent mosquito vectors in the absence of local index cases suggests a higher level of dengue endemicity in Florida than previously thought.\n\nArticle Summary LineEvidence of increasing dengue endemicity in Florida: Vector surveillance during dengue and West Nile virus outbreaks revealed widespread presence of other dengue virus serotypes in the absence of local index cases.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Heather Coatsworth", + "author_inst": "University of Florida" + }, + { + "author_name": "Cat Lippi", + "author_inst": "University of Florida" + }, + { + "author_name": "Chalmers Vasquez", + "author_inst": "Miami-Dade Mosquito Control District" + }, + { + "author_name": "Jasmine B Ayers", + "author_inst": "University of Florida" + }, + { + "author_name": "Caroline J. Stephenson", + "author_inst": "University of Florida" + }, + { + "author_name": "Christy Waits", + "author_inst": "University of Florida" + }, + { + "author_name": "Mary Florez", + "author_inst": "University of Florida" + }, + { + "author_name": "Andre B. B. Wilke", + "author_inst": "University of Miami" + }, + { + "author_name": "Isik Unlu", + "author_inst": "Miami-Dade County" + }, + { + "author_name": "Johana Medina", + "author_inst": "Miami-Dade Mosquito Control District" + }, + { + "author_name": "Maria L. Alcaide", + "author_inst": "University of Miami" + }, + { + "author_name": "Sadie J. Ryan", + "author_inst": "University of Florida" + }, + { + "author_name": "John A Lednicky", + "author_inst": "University of Florida" + }, + { + "author_name": "John C Beier", + "author_inst": "University of Miami School of Medicine" + }, + { + "author_name": "William Petrie", + "author_inst": "Miami-Dade Mosquito Control District" + }, + { + "author_name": "Rhoel R. Dinglasan", + "author_inst": "University of Florida" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.10.05.21264578", "rel_title": "Ondansetron use is associated with lower COVID-19 mortality in a Real-World Data network-based analysis", @@ -537095,37 +539145,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2021.10.09.21264799", - "rel_title": "Diagnostic accuracy of point-of-care lung ultrasound for COVID-19: A systematic review and meta-analysis", - "rel_date": "2021-10-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.09.21264799", - "rel_abs": "BackgroundPoint-of-care (POC) lung ultrasound (LUS) is widely used in the emergency setting and there is an established evidence base across a range of respiratory diseases, including previous viral epidemics. The necessity for rapid testing combined with the limitations of other diagnostic tests has led to the proposal of various potential roles for LUS during the COVID-19 pandemic. This systematic review and meta-analysis focused specifically on the diagnostic accuracy of LUS in adult patients presenting with suspected COVID-19.\n\nMethodsTraditional and grey-literature searches were performed on June 1st 2021. Two authors independently carried out the searches, selected studies and completed the Quality Assessment Tool for Diagnostic Test Accuracy Studies (QUADAS-2). Meta-analysis was carried out using established open-source packages in R. We report overall sensitivity, specificity, positive and negative predictive values and the hierarchical summary receiver operating characteristic curve for LUS. Heterogeneity was determined using the I2 statistic.\n\nResultsTwenty studies were included, providing data from a total of 4,314 patients. The prevalence and admission rates were generally high across all studies. Overall LUS was found to be 87.2% sensitive (95% CI 83.6-90.2) and 69.5% specific (95% CI 62.2-72.5) and demonstrated overall positive and negative predictive values of 3.0 (95% 2.3-4.1) and 0.16 (95% 0.12-0.22) respectively. Separate analyses for each reference standard revealed similar sensitivities and specificities for LUS. Heterogeneity between studies was found to be high, and QUADAS-2 assessment identified risks of bias in many studies.\n\nConclusionDuring a period of high prevalence, LUS is a highly sensitive diagnostic test for COVID-19. However, more research is required to confirm these results in more generalisable populations, including those less likely to be admitted to hospital.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Ashley Matthies", - "author_inst": "Homerton University Hospital Foundation Trust" - }, - { - "author_name": "Michael Trauer", - "author_inst": "Guy's and St Thomas' NHS Foundation Trust" - }, - { - "author_name": "Karl Chopra", - "author_inst": "Homerton University Hospital Foundation Trust" - }, - { - "author_name": "Robert Jarman", - "author_inst": "Royal Victoria Infirmary, The Newcastle upon Tyne Hospitals NHS Foundation Trust" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "emergency medicine" - }, { "rel_doi": "10.1101/2021.10.07.21264549", "rel_title": "Impact of the COVID-19 pandemic on mental healthcare consultations among children and adolescents in Norway: a nationwide registry study", @@ -537632,6 +539651,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "sexual and reproductive health" }, + { + "rel_doi": "10.1101/2021.10.09.21264695", + "rel_title": "Defining the analytical and clinical sensitivity of the ARTIC method for the detection of SARS-CoV-2", + "rel_date": "2021-10-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.09.21264695", + "rel_abs": "The SARS-CoV-2 ARTIC amplicon protocol is the most widely used genome sequencing method for SARS-CoV-2, accounting for over 43% of publicly-available genome sequences. The protocol utilises 98 primers to amplify [~]400bp fragments of the SARS-CoV-2 genome covering all 30,000 bases. Understanding the analytical performance metrics of this protocol will improve how the data is used and interpreted. Different concentrations of SARS-CoV-2 control material were used to establish the limit of detection (LoD) of the ARTIC protocol. Results demonstrated the LoD was a minimum of 25-50 virus particles per mL. The sensitivity of ARTIC was comparable to the published sensitivities of commercial diagnostics assays and could therefore be used to confirm diagnostic testing results. A set of over 3,600 clinical samples from three UK regions were then evaluated to compare the protocols performance to clinical diagnostic assays (Roche Lightcycler 480 II, AusDiagnostics, Roche Cobas, Hologic Panther, Corman RdRp, Roche Flow, ABI QuantStudio 5, Seegene Nimbus, Qiagen Rotorgene, Abbott M2000, Thermo TaqPath, Xpert). We developed a Python tool, RonaLDO, to perform this validation (available under the GNU GPL3 open-source licence from https://github.com/quadram-institute-bioscience/ronaldo). Positives detected by diagnostic platforms were generally supported by sequencing data; platforms that used RT-qPCR were the best predictors of whether the sample would subsequently sequence successfully. To maximise success of sample sequencing for phylogenetic analysis, samples with Ct <31 should be chosen. For diagnostic tests that do not provide a quantifiable Ct value, adding a quantification step is recommended. The ARTIC SARS-CoV-2 sequencing protocol is highly sensitive, capable of detecting SARS-CoV-2 in samples with Cts in the high 30s. However, to routinely obtain whole genome coverage, samples with Ct <31 are recommended. Comparing different virus detection methods close to their LoD was challenging and significant discordance was observed.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Nabil-Fareed Alikhan", + "author_inst": "Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK" + }, + { + "author_name": "Joshua Quick", + "author_inst": "Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK" + }, + { + "author_name": "Alexander J. Trotter", + "author_inst": "Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK" + }, + { + "author_name": "Samuel C. Robson", + "author_inst": "Centre for Enzyme Innovation, University of Portsmouth, Portsmouth, PO1 2DT, UK, School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmout" + }, + { + "author_name": "Matthew Bashton", + "author_inst": "Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne" + }, + { + "author_name": "Gemma L. Kay_", + "author_inst": "Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK" + }, + { + "author_name": "Matt Loose", + "author_inst": "School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK" + }, + { + "author_name": "Stefan Rooke", + "author_inst": "Usher Institute, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh EH9 3JT, UK" + }, + { + "author_name": "Martin McHugh", + "author_inst": "Viral Sequencing Service, Royal Infirmary of Edinburgh, Edinburgh, UK, School of Medicine, University of St Andrews, St Andrews, UK." + }, + { + "author_name": "Alistair C. Darby", + "author_inst": "Centre for Genomics Research,University of Liverpool, Liverpool, L69 7ZB, UK" + }, + { + "author_name": "Samuel M. Nicholls", + "author_inst": "Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK." + }, + { + "author_name": "Nicholas J. Loman", + "author_inst": "Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK." + }, + { + "author_name": "- The COVID-19 Genomics UK (COG-UK) consortium", + "author_inst": "https://www.cogconsortium.uk" + }, + { + "author_name": "Samir Dervisevic", + "author_inst": "Norfolk and Norwich University Hospital, Colney Lane, Norwich, NR4 7UY, UK." + }, + { + "author_name": "Andrew J. Page", + "author_inst": "Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK." + }, + { + "author_name": "Justin O'Grady", + "author_inst": "Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK. University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK." + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.08.21264760", "rel_title": "Decline in prenatal buprenorphine/naloxone fills during the COVID-19 pandemic in the United States", @@ -538968,53 +541066,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.08.21264785", - "rel_title": "COVIDNearTerm: A Simple Method to Forecast COVID-19 Hospitalizations", - "rel_date": "2021-10-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.08.21264785", - "rel_abs": "1COVID-19 has caused tremendous death and suffering since it first emerged in 2019. In response, models were developed to help predict the course of various disease metrics, and these models have been relied upon to help guide public health policy. Here we present a method called COVIDNearTerm to \"forecast\" hospitalizations in the short term, two to four weeks from the time of prediction. COVIDNearTerm is based on an autoregressive model and utilizes a parametric bootstrap approach to make predictions. We evaluated COVIDNearTerm on San Francisco Bay Area hospitalizations and compared it to models from the California COVID Assessment Tool (CalCAT). We found that that COVIDNearTerm pre-dictions were more accurate than the CalCAT ensemble predictions for all comparisons and any CalCAT component for a majority of comparisons. For instance, at the county level our 14-day hospitalization median absolute percentage errors ranged from 16% to 36%. For those same comparisons the CalCAT ensemble errors were between 30% and 59%. COVIDNearT-erm is also easier to use than some other methods. It requires only previous hospitalization data and there is an open source R package that implements the algorithm.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Adam B. Olshen", - "author_inst": "UCSF" - }, - { - "author_name": "Ariadna Garcia", - "author_inst": "Stanford University" - }, - { - "author_name": "Kristopher I. Kapphahn", - "author_inst": "Stanford University" - }, - { - "author_name": "Yingjie Weng", - "author_inst": "Stanford University" - }, - { - "author_name": "Paul D. Wesson", - "author_inst": "UCSF" - }, - { - "author_name": "George W. Rutherford", - "author_inst": "UCSF" - }, - { - "author_name": "Mithat Gonen", - "author_inst": "Memorial Sloan-Kettering Cancer Center" - }, - { - "author_name": "Manisha Desai", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.07.21264491", "rel_title": "Plant Formulation ATRICOV 452 in Improving the Level of COVID-19 Specific Inflammatory Markers in Patients", @@ -539622,6 +541673,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2021.10.06.21264664", + "rel_title": "Covid-19 vaccine perceptions in Senegal and in Mali: a mixed approach", + "rel_date": "2021-10-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.06.21264664", + "rel_abs": "This paper presents the results of two qualitative surveys in Senegal and in Mali, which include questions about hesitancy to the COVID-19 vaccine between April and June 2021. It took place within a larger 2-year research project involving researchers in Senegal, Mali and Canada which examines the uses of artificial intelligence technologies in the fight against COVID-19. The study involved 1000 respondents in Senegal and 555 in Mali. The researchers found that overall, 55% of respondents in Senegal and 52% of respondents in Mali did not plan to be vaccinated. Hesitancy was much higher in youth aged 15-35 in both cases, with 70% of youth in Senegal and 57% of youth in Mali not planning to be vaccinated, compared to only 42% of elderly in Senegal and 37% of elderly in Mali. The researchers did not find disparities between male and female respondents in Senegal but found some in Mali. They also found that those who had a member of the family with chronic disease (diabetes or hypertension) were slightly more likely to want to be vaccinated. Reasons for vaccine hesitancy fell in several categories, including fear of vaccine side-effects, disbelief in vaccine efficacy or usefulness, and general distrust in the public health system.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Eleonore Fournier-Tombs", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Massamba Diouf", + "author_inst": "University Cheikh Anta Diop" + }, + { + "author_name": "Abdine Maiga", + "author_inst": "CERCAD Mali" + }, + { + "author_name": "Sylvain Faye", + "author_inst": "University Cheikh Anta Diop" + }, + { + "author_name": "Tidiane Ndoye", + "author_inst": "University Cheikh Anta Diop" + }, + { + "author_name": "Lalla Haidara", + "author_inst": "CERCAD Mali" + }, + { + "author_name": "Moussa Batchily", + "author_inst": "CERCAD Mali" + }, + { + "author_name": "Celine Castets-Renard", + "author_inst": "University of Ottawa" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2021.10.05.21264555", "rel_title": "Seropositivity to Nucleoprotein to detect SARS-CoV-2 infections: a tool to detect breakthrough infections after COVID-19 vaccination", @@ -540966,81 +543064,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.10.06.21264573", - "rel_title": "Structural inequalities in the pathway to COVID-19 immunity", - "rel_date": "2021-10-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.06.21264573", - "rel_abs": "BackgroundAs COVID-19 vaccines continue to be rolled-out, the \"double burden\" of health disparities in both exposure to infection and vaccination coverage intersect to determine the current and future patterns of infection, immunity, and mortality. Serology provides a unique opportunity to measure biomarkers of infection and vaccination simultaneously, and to relate these metrics to demographic and geographic factors.\n\nMethodsLeveraging algorithmically selected residual serum samples from two hospital networks in San Francisco, we sampled 1014 individuals during February 2021, capturing transmission during the first 11 months of the epidemic and the early roll out of vaccination. These samples were tested using two serologic assays: one detecting antibodies elicited by infection, and not by vaccines, and one detecting antibodies elicited by both infection and vaccination. We used Bayesian statistical models to estimate the proportion of the population that was naturally infected and the proportion protected due to vaccination.\n\nFindingsWe estimated that the risk of prior infection of Latinx residents was 5.3 (95% CI: 3.2 - 10.3) times greater than the risk of white residents aged 18-64 and that white San Francisco residents over the age of 65 were twice as likely (2.0, 95% CI: 1.1 - 4.6) to be vaccinated as Black residents. We also found socioeconomically deprived zipcodes in the city had high probabilities of natural infections and lower vaccination coverage than wealthier zipcodes.\n\nInterpretationUsing a platform we created for SARS-CoV-2 serologic data collection in San Francisco, we characterized and quantified the stark disparities in infection rates and vaccine coverage by demographic groups over the first year of the pandemic. While the arrival of the SARS-CoV-2 vaccine has created a light at the end of the tunnel for this pandemic, ongoing challenges in achieving and maintaining equity must also be considered.\n\nFundingNIH, NIGMS, Schmidt Science Fellows in partnership with the Rhodes Trust and the Chan Zuckerberg Biohub.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Isobel Routledge", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Saki Takahashi", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Adrienne Epstein", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Jill Hakim", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Owen Janson", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Kierstinne Turcios", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Joanna Vinden", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "John Tomas Risos", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Margaret Rose Banquied", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Lori Pham", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Clara Di Germano", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Michael Paul Busch", - "author_inst": "VITALANT RESEARCH INSTITUTE" - }, - { - "author_name": "Margot B Kushel", - "author_inst": "University of California, San Francisco/Benioff Homelessness and Housing Initiative" - }, - { - "author_name": "Bryan Greenhouse", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Isabel Rodriguez-Barranquer", - "author_inst": "University of California, San Francisco" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.10.05.21264598", "rel_title": "Inactivated Poliovirus Vaccine Induces Antibodies that Inhibit RNA Synthesis of SARS-CoV-2: An open-label, pre-post vaccine clinical trial", @@ -541904,6 +543927,217 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.10.06.21264648", + "rel_title": "TITLE: Randomised Controlled Trial of Intravenous Nafamostat Mesylate in COVID pneumonitis: Phase 1b/2a Experimental Study to Investigate Safety, Pharmacokinetics and Pharmacodynamics", + "rel_date": "2021-10-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.06.21264648", + "rel_abs": "Despite the success of vaccines and selected repurposed treatments, COVID-19 is likely to remain a global health problem and further chemotherapeutics are required. Many repurposed drugs have progressed rapidly to Phase 2 and 3 trials without characterisation of Pharmacokinetics (PK)/Pharmacodynamics (PD) including safety in COVID-19. One such drug is Nafamostat Mesylate (Nafamostat), a synthetic serine protease inhibitor with anticoagulant and anti-inflammatory properties. Preclinical data has demonstrated that it is has potent antiviral activity against SARS-CoV-2 by directly inhibiting the transmembrane protease serine 2 (TMPRSS2) dependent stage of host cell entry.\n\nMethodsWe present the findings of a phase Ib/II open label, platform randomised controlled trial (RCT), exploring the safety of intravenous Nafamostat in hospitalised patients with confirmed COVID-19 pneumonitis. Patients were assigned randomly to standard of care (SoC), Nafamostat or an alternative therapy. Secondary endpoints included clinical endpoints such as number of oxygen free days and clinical improvement/ deterioration, PK/PD, thromboelastometry, D Dimers, cytokines, immune cell flow cytometry and viral load.\n\nResultsData is reported from 42 patients, 21 of which were randomly assigned to receive intravenous Nafamostat. The Nafamostat group developed significantly higher plasma creatinine levels, more adverse events and a lower number of oxygen free days. There were no other statistically significant differences in the primary or secondary endpoints between Nafamostat and SoC. PK data demonstrated that intravenous Nafamostat was rapidly broken down to inactive metabolites. We observed an antifibrinolytic profile, and no significant anticoagulant effects in thromboelastometry. Participants in the Nafamostat group had higher D Dimers compared to SoC. There were no differences in cytokine profile and immune cell phenotype and viral loads between the groups.\n\nConclusionIn hospitalised patients with COVID-19, we did not observe evidence of anti-inflammatory, anticoagulant or antiviral activity with intravenous Nafamostat. Given the number of negative trials with repurposed drugs, our experimental medicine trial highlights the value of PK/PD studies prior to selecting drugs for efficacy trials. Given the mechanism of action, further evaluation of Nafamostat delivered via a different route may be warranted. This trial demonstrates the importance of experimental trials in new disease entities such as COVID-19 prior to selecting drugs for larger trials.", + "rel_num_authors": 49, + "rel_authors": [ + { + "author_name": "Tom Michael Quinn", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Erin E Gaughan", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Annya Bruce", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Jean Antonelli", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Richard O'Connor", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Feng Li", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Sarah McNamara", + "author_inst": "NHS Lothian" + }, + { + "author_name": "Oliver Koch", + "author_inst": "NHS Lothian" + }, + { + "author_name": "Claire MacIntosh", + "author_inst": "NHS Lothian" + }, + { + "author_name": "David Dockrell", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Timothy Walsh", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Kevin Blyth", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Colin Church", + "author_inst": "University of Glasgow" + }, + { + "author_name": "J\u00fcrgen Schwarze", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Cecilia Boz", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Asta Valanciute", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Matthew Burgess", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Philip Emanuel", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Bethany Mills", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Giulia Rinaldi", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Gareth Hardisty", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Ross Mills", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Emily Findlay", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Sunny Jabbal", + "author_inst": "NHS Lothian" + }, + { + "author_name": "Andrew Duncan", + "author_inst": "NHS Lothian" + }, + { + "author_name": "Sin\u00e9ad Plant", + "author_inst": "NHS Lothian" + }, + { + "author_name": "Adam D.L. Marshall", + "author_inst": "NHS Lothian" + }, + { + "author_name": "Irene Young", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Kay Russell", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Emma Scholefield", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Alastair F Nimmo", + "author_inst": "NHS Lothian" + }, + { + "author_name": "Islom B. Nazarov", + "author_inst": "University of Oxford" + }, + { + "author_name": "Grant C Churchill", + "author_inst": "University of Oxford" + }, + { + "author_name": "James S.O. McCullagh", + "author_inst": "University of Oxford" + }, + { + "author_name": "Kourosh Ebrahimi", + "author_inst": "Institute of Pharmaceutical Science, King's College London" + }, + { + "author_name": "Colin Ferrett", + "author_inst": "Oxford University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Kate Templeton", + "author_inst": "NHS Lothian" + }, + { + "author_name": "Steve Rannard", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Andrew Owen", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Anne Moore", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Keith Finlayson", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Manu Shankar-Hari", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "John Norrie", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Richard A Parker", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Ahsan R Akram", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Daniel C Anthony", + "author_inst": "University of Oxford" + }, + { + "author_name": "James W Dear", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Nik Hirani", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Kevin Dhaliwal", + "author_inst": "University of Edinburgh" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2021.10.07.21264626", "rel_title": "Protection Across Age Groups of BNT162b2 Vaccine Booster against Covid-19", @@ -542904,141 +545138,6 @@ "type": "new results", "category": "pathology" }, - { - "rel_doi": "10.1101/2021.10.05.461434", - "rel_title": "Immunogenicity of trimetric spike protein associated to Poly(I:C) plus Alum", - "rel_date": "2021-10-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.05.461434", - "rel_abs": "The SARS-CoV-2 pandemic has had a social and economic impact worldwide, and vaccination is an efficient strategy for diminishing those damages. New adjuvant formulations are required for the high vaccine demands, especially adjuvant formulations that induce a Th1 phenotype. Herein we assess a vaccination strategy using a combination of Alum and polyinosinic:polycytidylic acid (Poly(I:C)) adjuvants plus the SARS-CoV-2 spike protein in a prefusion trimeric conformation by an intradermal (ID) route. We found high levels of IgG anti-spike antibodies in the serum by enzyme linked immunosorbent assay (ELISA) and high neutralizing titers against SARS-CoV-2 in vitro by neutralization assay, after one or two boosts. By evaluating the production of IgG subtypes, as expected, we found that formulations containing Poly(I:C) induced IgG2a whereas Alum did not. The combination of these two adjuvants induced high levels of both IgG1 and IgG2a. In addition, cellular immune responses of CD4+ and CD8+ T cells producing interferon-gamma were equivalent, demonstrating that the Alum + Poly(I:C) combination supported a Th1 profile. Based on the high neutralizing titers, we evaluated B cells in the germinal centers, which are specific for receptor-binding domain (RBD) and spike, and observed that more positive B cells were induced upon the Alum + Poly(I:C) combination. Moreover, these B cells produced antibodies against both RBD and non-RBD sites. We also studied the impact of this vaccination preparation (spike protein with Alum + Poly(I:C)) in the lungs of mice challenged with inactivated SARS-CoV-2 virus. We found a production of IgG, but not IgA, and a reduction in neutrophil recruitment in the bronchoalveolar lavage fluid (BALF) of mice, suggesting that our immunization scheme reduced lung inflammation. Altogether, our data suggest that Alum and Poly(I:C) together is a possible adjuvant combination for vaccines against SARS-CoV-2 by the intradermal route.", - "rel_num_authors": 30, - "rel_authors": [ - { - "author_name": "J\u00falio dos Santos", - "author_inst": "UFRJ" - }, - { - "author_name": "Luan Firmino Cruz", - "author_inst": "UFRJ" - }, - { - "author_name": "Alessandra Marcia da Fonseca-Martins", - "author_inst": "UFRJ" - }, - { - "author_name": "Diogo Oliveira Maciel", - "author_inst": "UFRJ" - }, - { - "author_name": "Gustavo Guadagnini Perez", - "author_inst": "UFRJ" - }, - { - "author_name": "Victor Augusto Roncaglia-Pereira", - "author_inst": "UFRJ" - }, - { - "author_name": "Carlos H. Dumard", - "author_inst": "UFRJ" - }, - { - "author_name": "Francisca H. Guedes da Silva", - "author_inst": "UFRJ" - }, - { - "author_name": "Ana Clara Vicente dos Santos", - "author_inst": "UFRJ" - }, - { - "author_name": "Monique Santos Leandro", - "author_inst": "UFRJ" - }, - { - "author_name": "Jesuino Rafael Machado Ferreira", - "author_inst": "UFRJ" - }, - { - "author_name": "Kamila Guimaraes Pinto", - "author_inst": "UFRJ" - }, - { - "author_name": "Luciana Conde", - "author_inst": "UFRJ" - }, - { - "author_name": "Danielle A. S. Rodrigues", - "author_inst": "UFRJ" - }, - { - "author_name": "Marcus Vinicius Mattos Silva", - "author_inst": "UFRJ" - }, - { - "author_name": "Renata G. F. Alvim", - "author_inst": "UFRJ" - }, - { - "author_name": "Tulio Macedo Lima", - "author_inst": "UFRJ" - }, - { - "author_name": "Frederico Francisco Marsili", - "author_inst": "UFRJ" - }, - { - "author_name": "Daniel Paiva Barros de Abreu", - "author_inst": "UFRJ" - }, - { - "author_name": "Orlando C. Ferreira Jr.", - "author_inst": "UFRJ" - }, - { - "author_name": "Ronaldo da Silva Mohana Borges", - "author_inst": "UFRJ" - }, - { - "author_name": "Amilcar Tanuri", - "author_inst": "UFRJ" - }, - { - "author_name": "Thiago Moreno L. Souza", - "author_inst": "Fiocruz and CDTS" - }, - { - "author_name": "Bartira Rossi-Bergmann", - "author_inst": "UFRJ" - }, - { - "author_name": "Andre M. Vale", - "author_inst": "UFRJ" - }, - { - "author_name": "Jerson Lima Silva", - "author_inst": "UFRJ" - }, - { - "author_name": "Andrea Cheble de Oliveira", - "author_inst": "UFRJ" - }, - { - "author_name": "Alessandra Almeida Filardy", - "author_inst": "UFRJ" - }, - { - "author_name": "Andre Marco Oliveira Gomes", - "author_inst": "UFRJ" - }, - { - "author_name": "Herbert L. de Matos Guedes", - "author_inst": "UFRJ" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.10.04.462902", "rel_title": "SARS-CoV-2 PLpro whole human proteome cleavage prediction and enrichment/depletion analysis", @@ -544206,6 +546305,85 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.10.04.463106", + "rel_title": "A high throughput screening assay for inhibitors of SARS-CoV-2 pseudotyped particle entry", + "rel_date": "2021-10-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.04.463106", + "rel_abs": "Effective small molecule therapies to combat the SARS-CoV-2 infection are still lacking as the COVID-19 pandemic continues globally. High throughput screening assays are needed for lead discovery and optimization of small molecule SARS-CoV-2 inhibitors. In this work, we have applied viral pseudotyping to establish a cell-based SARS-CoV-2 entry assay. Here, the pseudotyped particles (PP) contain SARS-CoV-2 spike in a membrane enveloping both the murine leukemia virus (MLV) gag-pol polyprotein and luciferase reporter RNA. Upon addition of PP to HEK293-ACE2 cells, the SARS-CoV-2 spike protein binds to the ACE2 receptor on the cell surface, resulting in priming by host proteases to trigger endocytosis of these particles, and membrane fusion between the particle envelope and the cell membrane. The internalized luciferase reporter gene is then expressed in cells, resulting in a luminescent readout as a surrogate for spike-mediated entry into cells. This SARS-CoV-2 PP entry assay can be executed in a biosafety level 2 containment lab for high throughput screening. From a collection of 5,158 approved drugs and drug candidates, our screening efforts identified 7 active compounds that inhibited the SARS-CoV-2-S PP entry. Of these seven, six compounds were active against live replicating SARS-CoV-2 virus in a cytopathic effect assay. Our results demonstrated the utility of this assay in the discovery and development of SARS-CoV-2 entry inhibitors as well as the mechanistic study of anti-SARS-CoV-2 compounds. Additionally, particles pseudotyped with spike proteins from SARS-CoV-2 B.1.1.7 and B.1.351 variants were prepared and used to evaluate the therapeutic effects of viral entry inhibitors.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Miao Xu", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Manisha Pradhan", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Kirill Gorshkov", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Jennifer D Petersen", + "author_inst": "Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH" + }, + { + "author_name": "Min Shen", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Hui Guo", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Wei Zhu", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Carleen Klumpp-Thomas", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Sam Michael", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Misha Itkin", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Zina Itkin", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Marco R Straus", + "author_inst": "Department of Microbiology and Immunology, Cornell University" + }, + { + "author_name": "Joshua Zimmerberg", + "author_inst": "Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH" + }, + { + "author_name": "Wei Zheng", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Gary Whittaker", + "author_inst": "Department of Microbiology and Immunology, Cornell University" + }, + { + "author_name": "Catherine Z Chen", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2021.10.04.463121", "rel_title": "Longitudinal characterization of circulating neutrophils uncovers distinct phenotypes associated with disease severity in hospitalized COVID-19 patients", @@ -545150,45 +547328,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.10.02.462862", - "rel_title": "In Vitro Activity of Cysteamine Against SARS-CoV-2 Variants Alpha, Beta, Gamma and Delta", - "rel_date": "2021-10-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.02.462862", - "rel_abs": "Global COVID-19 pandemic is caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Continuous emergence of new variants and their rapid spread are jeopardizing vaccine countermeasures to a significant extent. While currently available vaccines are effective at preventing illness associated with SARS-CoV-2 infection, these have been shown to be less effective at preventing breakthrough infection and transmission from a vaccinated individual to others. Here we demonstrate broad antiviral activity of cysteamine HCl in vitro against major emergent infectious variants of SARS-CoV-2 in a highly permissible Vero cell line. Cysteamine HCl inhibited infection of wild type, alpha, beta, gamma, delta, lambda, and omicron variants effectively. Cysteamine is a very well-tolerated US FDA-approved drug used chronically as a topical ophthalmic solution to treat ocular cystinosis in patients who receive it hourly or QID lifelong at concentrations 6 to 10 times higher than that required to completely inhibit SARS CoV-2 in tissue culture. Application of cysteamine as a topical nasal treatment can potentially1) mitigate existing infection 2) prevent infection in exposed individuals, and 3) limit the contagion in vulnerable populations.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Jess G Thoene", - "author_inst": "University of Michigan" - }, - { - "author_name": "Robert F Gavin", - "author_inst": "Michigan Trans Tech" - }, - { - "author_name": "Aaron Towne", - "author_inst": "Department of Mechanical Engineering, University of Michigan" - }, - { - "author_name": "Lauren Wattay", - "author_inst": "BIOQUAL, Rockville, MD, USA" - }, - { - "author_name": "Maria Grazia Ferrari", - "author_inst": "BIOQUAL, Rockville, MD, USA" - }, - { - "author_name": "Ranajit Pal", - "author_inst": "BIOQUAL, Rockville, MD, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.10.01.21264385", "rel_title": "COVID-19 data reporting systems in Africa reveal insights for pandemic preparedness", @@ -545888,6 +548027,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.09.30.21264339", + "rel_title": "The importance of the population age-structure: insights from Covid-19 dynamics model structured by age, time since infection and acquired immunity", + "rel_date": "2021-10-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.30.21264339", + "rel_abs": "The Covid-19 pandemic outbreak was followed by a huge amount of modelling studies in order to rapidly gain insights to implement the best public health policies. Most of these compartmental models involved ordinary differential equations (ODEs) systems. Such a formalism implicitly assumes that the time spent in each compartment does not depend on the time already spent in it, which is at odds with the clinical data. To overcome this \"memoryless\" issue, a widely used solution is to increase and chain the number of compartments of a unique reality (e.g. have infected individual move between several compartments). This allows for greater heterogeneity and thus be closer to the observed situation, but also tends to make the whole model more difficult to apprehend and parameterize. We develop a non-Markovian alternative formalism based on partial differential equations (PDEs) instead of ODEs, which, by construction, provides a memory structure for each compartment thereby allowing us to limit the number of compartments. We apply our model to the French 2021 SARS-CoV-2 epidemic and, while accounting for vaccine-induced and natural immunity, we analyse and determine the major components that contributed to the Covid-19 hospital admissions. The results indicate that the observed vaccination rate alone is not enough to control the epidemic, and a global sensitivity analysis highlights a huge uncertainty attributable to the age-structured contact matrix. Our study shows the flexibility and robustness of PDE formalism to capture national COVID-19 dynamics and opens perspectives to study medium or long-term scenarios involving immune waning or virus evolution.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Bastien Reyn\u00e9", + "author_inst": "MIVEGEC, Univ Montpellier, CNRS, IRD, Montpellier, France" + }, + { + "author_name": "Quentin Richard", + "author_inst": "MIVEGEC, Univ Montpellier, CNRS, IRD, Montpellier, France" + }, + { + "author_name": "Camille No\u00fbs", + "author_inst": "Laboratoire Cogitamus" + }, + { + "author_name": "Christian Selinger", + "author_inst": "MIVEGEC, Univ Montpellier, CNRS, IRD, Montpellier, France and Swiss Tropical and Public Health Institute, Basel, Swiss" + }, + { + "author_name": "Mircea T. Sofonea", + "author_inst": "MIVEGEC, Univ Montpellier, CNRS, IRD, Montpellier, France" + }, + { + "author_name": "Rams\u00e8s Djidjou-Demasse", + "author_inst": "MIVEGEC, Univ Montpellier, CNRS, IRD, Montpellier, France" + }, + { + "author_name": "Samuel Alizon", + "author_inst": "MIVEGEC, Univ Montpellier, CNRS, IRD, Montpellier, France" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.09.30.21264344", "rel_title": "Development and validation of a questionnaire to measure attitudes toward COVID-19 vaccination and pandemic", @@ -546888,93 +549070,6 @@ "type": "new results", "category": "neuroscience" }, - { - "rel_doi": "10.1101/2021.09.29.21263685", - "rel_title": "Mini-XT, a miniaturized tagmentation-based protocol for efficient sequencing of SARS-CoV-2", - "rel_date": "2021-10-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.29.21263685", - "rel_abs": "IntroductionThe COVID-19 pandemic has highlighted the importance of whole genome sequencing (WGS) of SARS-CoV-2 to inform public health policy. By enabling definition of lineages it facilitates tracking of the global spread of the virus. The evolution of new variants can be monitored and knowledge of specific mutations provides insights into the mechanisms through which the virus increases transmissibility or evades immunity. To date almost one million SARS-CoV-2 genomes have been sequenced by members of the COVID-19 Genomics UK (COG-UK) Consortium. To achieve similar feats in a more cost-effective and sustainable manner in future, improved high throughput virus sequencing protocols are required. We have therefore developed a miniaturized library preparation protocol with drastically reduced consumable use and costs.\n\nMethodsSARS-CoV-2 RNA was amplified using the ARTIC nCov-2019 multiplex RT-PCR protocol and purified using a conventional liquid handling system. Acoustic liquid transfer (Echo 525) was employed to reduce reaction volumes and the number of tips required for a Nextera XT library preparation. Sequencing was performed on an Illumina MiSeq.\n\nResultsWe present the Mini-XT miniaturized tagmentation-based library preparation protocol available on protocols.io (https://dx.doi.org/10.17504/protocols.io.bvntn5en). The final version of Mini-XT has been used to sequence 4,384 SARS-CoV-2 samples from N. Ireland with a COG-UK QC pass rate of 97.4%. Sequencing quality was comparable and lineage calling consistent for replicate samples processed with full volume Nextera DNA Flex (333 samples) or using nanopore technology (20 samples). SNP calling between Mini-XT and these technologies was consistent and sequences from replicate samples paired together in maximum likelihood phylogenetic trees.\n\nConclusionThe Mini-XT protocol maintains sequence quality while reducing library preparation reagent volumes 8-fold and halving overall tip usage from sample to sequence to provide concomitant cost savings relative to standard protocols. This will enable more efficient high-throughput sequencing of SARS-CoV-2 isolates and future pathogen WGS.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Marc Fuchs", - "author_inst": "Genomics Core Technology Unit, Faculty of Medicine and Health Sciences, Queen's University Belfast, Belfast, UK" - }, - { - "author_name": "Clara Radulescu", - "author_inst": "The Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast" - }, - { - "author_name": "Miao Tang", - "author_inst": "The Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast" - }, - { - "author_name": "Arun Mahesh", - "author_inst": "The Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast" - }, - { - "author_name": "Deborah Lavin", - "author_inst": "The Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast" - }, - { - "author_name": "Syed Umbreen", - "author_inst": "The Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast" - }, - { - "author_name": "James McKenna", - "author_inst": "Regional Virus Laboratory, Belfast Health and Social Care Trust, Belfast, UK" - }, - { - "author_name": "Mark Smyth", - "author_inst": "Regional Virus Laboratory, Belfast Health and Social Care Trust, Belfast, UK" - }, - { - "author_name": "Eil\u00eds McColgan", - "author_inst": "Regional Virus Laboratory, Belfast Health and Social Care Trust, Belfast, UK" - }, - { - "author_name": "Zoltan Molnar", - "author_inst": "Regional Virus Laboratory, Belfast Health and Social Care Trust, Belfast, UK" - }, - { - "author_name": "Chris Baxter", - "author_inst": "Genomics Core Technology Unit, Faculty of Medicine and Health Sciences, Queen's University Belfast, Belfast, UK" - }, - { - "author_name": "Timofey Skvortsov", - "author_inst": "School of Pharmacy, Queen's University Belfast, Belfast, UK" - }, - { - "author_name": "Aditi Singh", - "author_inst": "The Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast" - }, - { - "author_name": "Fiona Rogan", - "author_inst": "The Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast" - }, - { - "author_name": "Julia Miskelly", - "author_inst": "Genomics Core Technology Unit, Faculty of Medicine and Health Sciences, Queen's University Belfast, Belfast, UK" - }, - { - "author_name": "Stephen Bridgett", - "author_inst": "The Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast" - }, - { - "author_name": "Derek Fairley", - "author_inst": "Regional Virus Laboratory, Belfast Health and Social Care Trust, Belfast, UK" - }, - { - "author_name": "David Arthur Simpson", - "author_inst": "The Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.29.21264328", "rel_title": "Endemic Seasonal Coronavirus Neutralisation and COVID-19 severity", @@ -547646,6 +549741,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, + { + "rel_doi": "10.1101/2021.09.29.21264298", + "rel_title": "A HOME-TREATMENT ALGORITHM BASED ON ANTI-INFLAMMATORY DRUGS TO PREVENT HOSPITALIZATION OF PATIENTS WITH EARLY COVID-19: A MATCHED-COHORT STUDY (COVER 2)", + "rel_date": "2021-10-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.29.21264298", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSBackground and AimC_ST_ABSWhile considerable success has been achieved in the management of patients hospitalized with severe coronavirus disease 2019 (COVID-19), far less progress has been made with early outpatient treatment. We assessed whether the implementation of a home treatment algorithm - designed based upon on a pathophysiologic and pharmacologic rationale - during the initial, mild phase of COVID-19, could effectively reduce hospital admissions.\n\nMethodsThis fully academic, matched-cohort study evaluated outcomes in 108 consecutive consenting patients with mild COVID-19 managed at home by their family doctors from January 2021 to May 2021, according to the proposed treatment algorithm and in 108 age-, sex-, and comorbidities-matched patients who were given other therapeutic schedules (ClinicalTrials.gov: NCT04854824). The primary outcome was COVID-19-related hospitalization. Analyses were by intention-to-treat.\n\nResultsOne (0.9%) patient in the recommended cohort and 12 (11.1%) in the control cohort were admitted to hospital (P=0.0136). The proposed algorithm reduced, by 85%, the cumulative length of hospital stays (from 141 to 19 days) and related costs (from {euro} 60.316 to {euro} 9.058). Only 9.8 patients needed to be treated with the recommended algorithm to prevent one hospitalization event. The rate of resolution of major symptoms was numerically, but not significantly, higher in the recommended compared to the control cohort (97.2% versus 93.5%, respectively; P=0.322). Other symptoms lingered in a lower proportion of patients in the recommended than in the control cohort (20.4% versus 63.9%, respectively; P<0.001), and for a shorter period.\n\nConclusionThe adoption of the proposed outpatient treatment algorithm during the early, mild phase of COVID-19 reduced the incidence of subsequent hospitalization and related costs.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Elena Consolaro", + "author_inst": "ATS Insubria, Varese, Italy" + }, + { + "author_name": "Fredy Suter", + "author_inst": "Azienda Socio-Sanitaria Territoriale (ASST) Papa Giovanni XXIII, Bergamo, Italy" + }, + { + "author_name": "Nadia Rubis", + "author_inst": "Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy" + }, + { + "author_name": "Stefania Pedroni", + "author_inst": "ATS Insubria, Varese, Italy" + }, + { + "author_name": "Chiara Moroni", + "author_inst": "ATS Insubria, Varese, Italy" + }, + { + "author_name": "Elena Pasto", + "author_inst": "ATS Insubria, Varese, Italy" + }, + { + "author_name": "Maria Vittoria Paganini", + "author_inst": "ATS Insubria, Varese, Italy" + }, + { + "author_name": "Grazia Pravettoni", + "author_inst": "Ospedale Circolo di Busto Arsizio, Varese, Italy" + }, + { + "author_name": "Umberto Cantarelli", + "author_inst": "ASL Teramo, Teramo, Italy" + }, + { + "author_name": "Norberto Perico", + "author_inst": "Istituto di Ricerche Farmacologiche Mario Negri IRCCS" + }, + { + "author_name": "Annalisa Perna", + "author_inst": "Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy" + }, + { + "author_name": "Tobia Peracchi", + "author_inst": "Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy" + }, + { + "author_name": "Piero Ruggenenti", + "author_inst": "Azienda Socio-Sanitaria Territoriale (ASST) Papa Giovanni XXIII, Bergamo, Italy" + }, + { + "author_name": "Giuseppe Remuzzi", + "author_inst": "Istituto di Ricerche Farmacologiche Mario Negri IRCCS" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.30.21264363", "rel_title": "SARS-CoV-2 infections elicit higher levels of original antigenic sin antibodies compared to SARS-CoV-2 mRNA vaccinations", @@ -548530,45 +550696,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.09.29.21264312", - "rel_title": "A cross-sectional study of COVID-19 knowledge, beliefs and prevention behaviors among adults in Senegal", - "rel_date": "2021-09-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.29.21264312", - "rel_abs": "BackgroundCOVID-19 is an ongoing threat to global public health since its emergence at the end of 2019, yet little is known about how populations in francophone West Africa have responded to COVID-19 in their daily lives. Senegal, in particular, has been noted for its relative success in mitigating the spread and impact of COVID-19. We report original research findings on COVID-19 beliefs and prevention behaviors in a sample of Senegalese adults.\n\nMethodsA multi-modal cross-sectional study was conducted to describe COVID-19 beliefs and prevention behaviors in a sample of Senegalese adults and to identify potential predictors of prevention behaviors. Univariate, bivariate, and multivariate statistics were generated to describe the sample and explore potential correlations.\n\nResultsMask wearing, hand washing, and use of hand sanitizer were most frequently reported. Social distancing and staying at home were also reported albeit to a lower degree. We also identified a range of psychosocial and demographic predictors for COVID-19 prevention behaviors. Men, compared to women, had lower odds (OR=0.59) of reporting prevention behaviors. Rural residents (vs. urban; OR=1.49) and participants with at least a high school education (vs. less than high school education; OR=1.33) were more likely to report COVID-19 prevention behaviors.\n\nDiscussionStakeholders and decision makers in Senegal and across Africa can use place-based evidence like ours to address COVID-19 risk factors and intervene effectively with policies and programming. Use of both phone and online surveys enhances representation and study generalizability and should be considered in future research with hard-to-reach populations.\n\nArticle SummaryO_ST_ABSStrengths and limitations of this studyC_ST_ABSO_LIThe main strength of our study is the use of a multi-modal data collection strategy, online and via telephone. Had we relied on a single method, our samples demographic characteristics would likely have differed while also introducing selection bias.\nC_LIO_LIOur recruitment strategy may have also increased the potential for selection bias because participants were recruited online and on-the-ground in Senegal; thus, all participants, by the nature of the recruitment methods, had access to the internet and/or a cell phone. To address potential confounding between recruitment methods, we controlled for recruitment method in our multivariate regression modelling.\nC_LIO_LIPrior to our study, little evidence was available about how populations in francophone West Africa have responded to COVID-19 in their daily lives. We adapted pre-existing research panels and developed novel data collection instruments to capture information about COVID-19, and this may serve as a model for the responsiveness of ongoing scholarship to future global events.\nC_LIO_LIA study with a larger sample may have been able to identify relationships between knowledge and behaviors, and our study was not design with enough statistical power to detect significant differences.\nC_LIO_LIThe findings of our study may not be generalizable beyond Senegal, or more specifically Senegalese adults.\nC_LI", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Matthew Kearney", - "author_inst": "University of Pennsylvania Perelman School of Medicine" - }, - { - "author_name": "Marta Bornstein", - "author_inst": "Ohio State University College of Public Health" - }, - { - "author_name": "Marieme Fall", - "author_inst": "African Health and Education Network (RAES)" - }, - { - "author_name": "Roch Nianogo", - "author_inst": "UCLA Fielding School of Public Health" - }, - { - "author_name": "Deborah Glik", - "author_inst": "UCLA Fielding School of Public Health" - }, - { - "author_name": "Philip M Massey", - "author_inst": "University of Arkansas Fayetteville" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.09.28.21264242", "rel_title": "Clinical Trial of Efficacy and Toxicity of Disoproxil Tenofovir Fumarate and Emtricitabine for Mild to Moderate SARS-CoV-2 Infections", @@ -549952,6 +552079,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.09.28.21264260", + "rel_title": "The impact of SARS-CoV-2 vaccination on Alpha and Delta variant transmission", + "rel_date": "2021-09-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.28.21264260", + "rel_abs": "BackgroundPre-Delta, vaccination reduced SARS-CoV-2 transmission from individuals infected despite vaccination, potentially via reducing viral loads. While vaccination still lowers the risk of infection, similar viral loads in vaccinated and unvaccinated individuals infected with Delta question how much vaccination prevents transmission.\n\nMethodsWe performed a retrospective observational cohort study of adult contacts of SARS-CoV-2-infected adult index cases using English contact testing data. We used multivariable Poisson regression to investigate associations between transmission and index case and contact vaccination, and how these vary with Alpha and Delta variants (classified using S-gene detection/calendar trends) and time since second vaccination.\n\nResults54,667/146,243(37.4%) PCR-tested contacts of 108,498 index cases were PCR-positive. Two doses of BNT162b2 or ChAdOx1 vaccines in Alpha index cases were independently associated with reduced PCR-positivity in contacts (aRR, adjusted rate ratio vs. unvaccinated=0.32[95%CI 0.21-0.48] and 0.48[0.30-0.78] respectively). The Delta variant attenuated vaccine-associated reductions in transmission: two BNT162b2 doses reduced Delta transmission (aRR=0.50[0.39-0.65]), more than ChAdOx1 (aRR=0.76[0.70-0.82]). Variation in Ct values (indicative of viral load) explained 7-23% of vaccine-associated transmission reductions. Transmission reductions declined over time post-second vaccination, for Delta reaching similar levels to unvaccinated individuals by 12 weeks for ChAdOx1 and attenuating substantially for BNT162b2. Protection in contacts also declined in the 3 months post-second vaccination.\n\nConclusionsVaccination reduces transmission of Delta, but by less than the Alpha variant. The impact of vaccination decreased over time. Factors other than PCR Ct values at diagnosis are important in understanding vaccine-associated transmission reductions. Booster vaccinations may help control transmission together with preventing infections.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "David W Eyre", + "author_inst": "University of Oxford" + }, + { + "author_name": "Donald Taylor", + "author_inst": "Department of Health and Social Care" + }, + { + "author_name": "Mark Purver", + "author_inst": "Department of Health and Social Care" + }, + { + "author_name": "David Chapman", + "author_inst": "Deloitte MCS Ltd" + }, + { + "author_name": "Tom Fowler", + "author_inst": "Department of Health and Social Care" + }, + { + "author_name": "Koen Pouwels", + "author_inst": "University of Oxford" + }, + { + "author_name": "Ann Sarah Walker", + "author_inst": "University of Oxford" + }, + { + "author_name": "Tim EA Peto", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.29.21264061", "rel_title": "A PTX3/LDH/CRP signature correlates with lung injury CTs scan severity and disease progression in paucisymptomatic COVID-19", @@ -550696,53 +552870,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.09.24.21264081", - "rel_title": "SARS-CoV-2 vaccine effectiveness and breakthrough infections in maintenance dialysis patients", - "rel_date": "2021-09-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.24.21264081", - "rel_abs": "Among patients receiving maintenance dialysis with a national US dialysis provider, fully vaccinated dialysis patients were significantly less likely to be diagnosed with COVID-19 or be hospitalized than unvaccinated patients. Ad26.COV2.S/Janssen vaccine had significantly worse outcomes, and mRNA-1273/Moderna the best. Among the 27 patients with breakthrough COVID-19 and anti-spike IgG antibodies measured, 23/27 (85%) breakthrough COVID-19 cases occurred at titers <2 U/L (lower limit of a positive response); 14 of these patients never developing Ab titers above 2 U/L. Only 3/27 were receiving immunosuppression. The potential use of antibody titers to guide vaccinations should be explored.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Harold J Manley", - "author_inst": "Dialysis Clinic Inc" - }, - { - "author_name": "Gideon N Aweh", - "author_inst": "Dialysis Clinic, Inc" - }, - { - "author_name": "Caroline M Hsu", - "author_inst": "Tufts Medical Center" - }, - { - "author_name": "Daniel E Weinder", - "author_inst": "Tufts Medical Center" - }, - { - "author_name": "Dana Miskulin", - "author_inst": "Tufts Medical Center" - }, - { - "author_name": "Antonia Harford", - "author_inst": "Dialysis Clinic, Inc." - }, - { - "author_name": "Doug Johnson", - "author_inst": "Dialysis Clinic, Inc" - }, - { - "author_name": "Eduardo Lacson", - "author_inst": "Dialysis Clinic, Inc" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "nephrology" - }, { "rel_doi": "10.1101/2021.09.28.21262976", "rel_title": "Phylodynamics Of A Regional, SARS-CoV-2 Rapid Spreading Event In Colorado", @@ -551934,6 +554061,81 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.09.29.462202", + "rel_title": "A virus-specific monocyte inflammatory phenotype is induced by SARS-CoV2 at the immune-epithelial interface", + "rel_date": "2021-09-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.29.462202", + "rel_abs": "Infection by SARS-CoV2 provokes a potentially fatal pneumonia with multiorgan failure, and high systemic inflammation. To gain mechanistic insight and ferret out the root of this immune dysregulation, we modeled by in vitro co-culture the interactions between infected epithelial cells and immunocytes. A strong response was induced in monocytes and B cells, with a SARS-CoV2-specific inflammatory gene cluster distinct from that seen in influenza-A or Ebola virus-infected co-cultures, and which reproduced deviations reported in blood or lung myeloid cells from COVID-19 patients. A substantial fraction of the effect could be reproduced after individual transfection of several SARS-CoV2 proteins (Spike and some non-structural proteins), mediated by soluble factors, but not via transcriptional induction. This response was greatly muted in monocytes from healthy children, perhaps a clue to the age-dependency of COVID-19. These results suggest that the inflammatory malfunction in COVID-19 is rooted in the earliest perturbations that SARS-CoV2 induces in epithelia.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Juliette Leon", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Daniel A Michelson", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Judith Olejnik", + "author_inst": "Boston University School of Medicine" + }, + { + "author_name": "Kaitavjeet Chowdhary", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Hyung Suk Oh", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Adam J Hume", + "author_inst": "Boston University School of Medicine" + }, + { + "author_name": "Silvia Galvan-Pena", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Yangyang Zhu", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Felicia Chen", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Brinda Vijaykumar", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Liang Yang", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Lael M Yonker", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "David M Knipe", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Elke Muhlberger", + "author_inst": "Boston University School of Medicine" + }, + { + "author_name": "Christophe Benoist", + "author_inst": "Harvard Medical School" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.09.28.462109", "rel_title": "Use of eVLP-based vaccine candidates to broaden immunity against SARS-CoV-2 variants", @@ -552862,93 +555064,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.26.21264129", - "rel_title": "Large-scale seroepidemiologic surveillance of COVID-19 - Cross-sectional study in Hyogo prefecture of Japan in August, 2021", - "rel_date": "2021-09-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.26.21264129", - "rel_abs": "The situation of the COVID-19 pandemic in Japan is drastically changing in the 2nd year, 2021, due to the appearance of SARS-CoV-2 variants of concern and the roll-out of mass vaccination. In addition to PCR diagnosis, periodic seroepidemiologic surveillance is important to analyze the epidemic situation. In this study, we analyzed the rate of seropositivity for the SARS-CoV-2 N and S antigens in Hyogo prefecture, Japan in August 2021. Sera collected from people who received a health check-up in a clinic of the Hyogo Prefecture Health Promotion Association were subjected to analysis of reactivity to the SARS-CoV-2 N and S antigens by electrochemiluminescence immunoassay (ECLIA) and enzyme-linked immunosorbent assay (ELISA), respectively. For a total 1,000 sera, the positive rates to N and S antigens were 2.1% and 38.7%, respectively. The infectious rate estimated by serological analysis based on the presence of the anti-N antibody was 2.5-fold higher than the value reported based on PCR-based analysis, and it increased five-fold compared to the rate determined by our previous seroepidemiologic study in October, 2020. The anti-S positive rate was almost consistent with the vaccination rate in this area. The observed high anti-S antibody level in the seropositive population may indicate that the mass vaccination in Japan is being performed smoothly at this time point, although the infectious rate has also increased.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Zhenxiao Ren", - "author_inst": "Kobe University" - }, - { - "author_name": "Koichi Furukawa", - "author_inst": "Kobe University" - }, - { - "author_name": "Mitsuhiro Nishimura", - "author_inst": "Kobe University" - }, - { - "author_name": "Yukiya Kurahashi", - "author_inst": "Kobe University" - }, - { - "author_name": "Silvia Sutandhio", - "author_inst": "Kobe University" - }, - { - "author_name": "Lidya Handayani Tjan", - "author_inst": "Kobe University" - }, - { - "author_name": "Kaito Aoki", - "author_inst": "Kobe University" - }, - { - "author_name": "Natsumi Hasegawa", - "author_inst": "Kobe University" - }, - { - "author_name": "Jun Arii", - "author_inst": "Kobe University" - }, - { - "author_name": "Kenichi Uto", - "author_inst": "Kobe University" - }, - { - "author_name": "Keiji Matsui", - "author_inst": "Kobe University" - }, - { - "author_name": "Itsuko Sato", - "author_inst": "Kobe University" - }, - { - "author_name": "Jun Saegusa", - "author_inst": "Kobe University" - }, - { - "author_name": "Nonoka Godai", - "author_inst": "Laboratory of Macromolecular Dynamics and X-ray Crystallography, Department of Life Science, University of Hyogo" - }, - { - "author_name": "Kohei Takeshita", - "author_inst": "Life Science Research Infrastructure Group, Advanced Photon Technology Division, RIKEN SPring-8 Center" - }, - { - "author_name": "Masaki Yamamoto", - "author_inst": "Life Science Research Infrastructure Group, Advanced Photon Technology Division, RIKEN SPring-8 Center" - }, - { - "author_name": "Tatsuya Nagashima", - "author_inst": "Hyogo Prefecture Health Promotion Association" - }, - { - "author_name": "Yasuko Mori", - "author_inst": "Kobe University Graduate School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.21.21263227", "rel_title": "A standardized instrument quantifying risk factors associated with bi-directional transmission of SARS-CoV-2 and other zoonotic pathogens: The COVID-19 Human-Animal Interactions Survey (CHAIS)", @@ -553532,6 +555647,65 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.09.28.461924", + "rel_title": "Nasopharyngeal Microbiota as an early severity biomarker in COVID-19 hospitalised patients: a retrospective cohort study in a Mediterranean area.", + "rel_date": "2021-09-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.28.461924", + "rel_abs": "BackgroundThere is mounting evidence suggesting that the microbiome composition could be different in COVID-19 patients. However, the relationship between microbiota and COVID-19 severity progression is still being assessed. This study aimed to analyse the diversity and taxonomic composition of the nasopharyngeal microbiota, to determine its association with COVID-19 clinical outcome.\n\nMethods and FindingsSamples came from a retrospective cohort of adult patients with COVID-19, hospitalised in a tertiary centre. To study the nasopharyngeal microbiota, we utilized 16S rRNA sequencing. Raw sequences were processed by QIIME2. The associations between the microbiota, invasive mechanical ventilation (IMV), and all-cause mortality were analysed by multiple logistic regression (OR; 95%CI), adjusted for age, gender, and comorbidity. 177 patients were included: median age 68.0 years, 57.6% males, 59.3% had a Charlson comorbidity index [≥]3, and 89.2% with pneumonia. The microbiota diversity indexes were lower in patients with a fatal outcome, and this association persisted after adjustment for the main confounders; whereas the {beta} diversity analysis showed a significant clustering, grouping the patients with a fatal outcome. After multivariate adjustment, the presence of Selenomonas spp., Filifactor spp., Actinobacillus spp., or Chroococcidiopsis spp., was associated with a reduced risk of IMV (adjusted OR 0.06[95%CI 0.01-0.0.47], p = 0.007).\n\nConclusionsThe microbiota diversity and taxonomic composition are related to COVID-19 severity. Higher diversity and the presence of certain genera in the nasopharyngeal microbiota seem to be early biomarkers of a favourable clinical evolution in hospitalised patients with moderate to severe SARS-CoV-2 infections.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Maria Paz Ventero", + "author_inst": "Microbiology Service, Alicante General University Hospital - Alicante Institute of Health and Biomedical Research (ISABIAL), Alicante, Spain" + }, + { + "author_name": "Oscar Moreno-Perez", + "author_inst": "Endocrinology and Nutrition department, Alicante General University Hospital - Alicante Institute of Health and Biomedical Research (ISABIAL), Alicante, Spain" + }, + { + "author_name": "Carmen Molina-Pardines", + "author_inst": "Microbiology Service, Alicante General University Hospital - Alicante Institute of Health and Biomedical Research (ISABIAL), Alicante, Spain" + }, + { + "author_name": "Andreu Paytuvi-Gallart", + "author_inst": "Sequentia Biotech, Carrer Comte dUrgell 240, 08036 Barcelona, Spain" + }, + { + "author_name": "Vicente Boix", + "author_inst": "Clinical Medicine department, Miguel Hernandez University, Elche, Spain" + }, + { + "author_name": "Irene Galan", + "author_inst": "Pneumology department, Alicante General University Hospital - Alicante Institute of Health and Biomedical Research (ISABIAL), Alicante, Spain" + }, + { + "author_name": "Pilar Gonzalez-delaAleja", + "author_inst": "Unit of Infectious Diseases, Alicante General University Hospital - Alicante Institute of Health and Biomedical Research (ISABIAL), Alicante, Spain" + }, + { + "author_name": "Mario Lopez-Perez", + "author_inst": "Universidad Miguel Hernandez de Elche - Campus San Juan de Alicante" + }, + { + "author_name": "Rosario Sanchez-Martinez", + "author_inst": "Internal Medicine department, Alicante General University Hospital - Alicante Institute of Sanitary and Biomedical Research (ISABIAL), Alicante, Spain" + }, + { + "author_name": "Esperanza Merino", + "author_inst": "Unit of Infectious Diseases, Alicante General University Hospital - Alicante Institute of Health and Biomedical Research (ISABIAL), Alicante, Spain" + }, + { + "author_name": "Juan Carlos Rodriguez", + "author_inst": "Microbiology Service, Alicante General University Hospital - Alicante Institute of Health and Biomedical Research (ISABIAL), Alicante, Spain" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.09.27.461930", "rel_title": "Milk casein prevents inactivation effect of black tea galloylated theaflavins on SARS-CoV-2 in vitro", @@ -554396,65 +556570,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2021.09.18.460924", - "rel_title": "Spike independent replication of human coronavirus in bat cells", - "rel_date": "2021-09-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.18.460924", - "rel_abs": "Bats are the reservoir for numerous human pathogens including coronaviruses. The factors leading to the emergence and sustained transmission of coronaviruses in humans are poorly understood. An outstanding question is how coronaviruses can accomplish a host switch with a likely mismatch between the surface protein spike of a bat virus and the human cellular receptor at the time of zoonotic virus transmission. To identify potential novel evolutionary pathways for zoonotic virus emergence, we serially passaged six human 229E isolates in a newly established Rhinolophus lepidus (horseshoe bat) kidney cells and analyzed viral genetic changes. Here we observed extensive deletions within the spike and ORF4 genes of five 229E viruses after passaging in bat cells. As a result, spike protein expression and infectivity of human cells was lost in 5 of 6 viruses but the capability to infect bat cells was maintained. Only viruses that expressed the spike protein could be neutralized by 229E spike-specific antibodies in human cells, whereas there was no neutralizing effect on viruses that do not express the spike protein inoculated on bat cells. However, one isolate acquired an early stop codon abrogating spike expression but maintaining infection in bat cells. Upon passaging this isolate in human cells, spike expression was restored due to acquisition of nucleotide insertions amongst virus subpopulations. Spike-independent infection of coronaviruses provides an alternative mechanism for viral maintenance in bats that does not rely on the compatibility of viral surface proteins and cellular entry receptors.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Marcus G Mah", - "author_inst": "Duke-NUS Medical School, Singapore" - }, - { - "author_name": "Martin Linster", - "author_inst": "Duke-NUS Medical School, Singapore" - }, - { - "author_name": "Dolyce HW Low", - "author_inst": "Duke-NUS Medical School, Singapore" - }, - { - "author_name": "Zhuang Yan", - "author_inst": "Duke-NUS Medical School, Singapore" - }, - { - "author_name": "Jayanthi Jayakumar", - "author_inst": "Duke-NUS Medical School, Singapore" - }, - { - "author_name": "Firdaus Samsudin", - "author_inst": "Bioinformatics Institute, Agency for Science, Technology, and Research, Singapore" - }, - { - "author_name": "Foong Ying Wong", - "author_inst": "Duke-NUS Medical School, Singapore" - }, - { - "author_name": "Peter J Bond", - "author_inst": "Bioinformatics Institute, Agency for Science, Technology, and Research, Singapore" - }, - { - "author_name": "Ian HW Mendenhall", - "author_inst": "Duke-NUS Medical School, Singapore" - }, - { - "author_name": "Yvonne CF Su", - "author_inst": "Duke-NUS Medical School, Singapore" - }, - { - "author_name": "Gavin JD Smith", - "author_inst": "Duke-NUS Medical School, Singapore" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.09.24.461732", "rel_title": "SARS-CoV-2 spike-specific memory B cells express markers of durable immunity after non-severe COVID-19 but not after severe disease", @@ -555674,6 +557789,57 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.09.20.21263866", + "rel_title": "Cohort Study: The Accuracy of Screening Methods of COVID-19 in Pregnancy: Practical Approach in Low Resources Health Services", + "rel_date": "2021-09-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.20.21263866", + "rel_abs": "BackgroundAll pregnant women in labor should be universally screened for Coronavirus Disease 2019 (COVID-19) during pandemic periods using Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) test. In many low-middle income countries, screening method was developed as an initial examination because of limited availability of RT-PCR tests.\n\nObjectivesThis study aims to evaluate the screening methods of COVID-19 accuracy in pregnant women.\n\nMaterial and MethodsWe recruited all pregnant women with suspicion of COVID-19 from April - August 2020 at Universitas Airlangga hospital, Surabaya, Indonesia. The participant was divided into two groups based on RT-PCR results: COVID-19 and non-COVID-19 group. The proportion of positive signs & symptoms, rapid antibody test, abnormal findings in chest x-ray, and neutrophil to lymphocyte ratio (NLR) value were then compared between both groups. The sensitivity, specificity, positive predictive value (PPV), negative predictive values (NPV), and diagnostic accuracy (DOR) were calculated.\n\nResultsA total 141 pregnant women with suspected COVID-19 cases were recruited for this study. This consist of 62 COVID-19 cases (43.9%) and 79 non COVID-19 pregnant women (56.1%). The sensitivity, spesificity, PPV, NPV, and diagnostic accuracy of each parameter are as follow: clinical sign & symptoms (24.19%, 75.95%, 3.92%, 96.11%, 65.87%), rapid antibody test (72.73%, 35.06%, 4.35%, 96.94%, 36.53%), chest x-ray (40.68%, 59.45%, 3.92%, 96.11%, 58.76%), and NLR > 5.8 (41.38%, 72%, 5.66%, 96.80%, 70.81%).\n\nConclusionsThe use of combined screening methods can classify pregnant women with high-risk COVID-19 before definitively diagnosed with RT-PCR. This practice will help to reduce RT-PCR need in a limited resources country.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Muhammad Ilham Aldika Akbar", + "author_inst": "Faculty of Medicine Universitas Airlangga" + }, + { + "author_name": "Khanizyah Erza Gumilar", + "author_inst": "Universitas Airlangga Hospital" + }, + { + "author_name": "Eccita Rahestyningtyas", + "author_inst": "Universitas Airlangga Hospital" + }, + { + "author_name": "Manggala Pasca Wardhana", + "author_inst": "Faculty of Medicine Universitas Airlangga" + }, + { + "author_name": "Pungky Mulawardhana", + "author_inst": "Faculty of Medicine Universitas Airlangga" + }, + { + "author_name": "Jimmy Yanuar Anas", + "author_inst": "Faculty of Medicine Universitas Airlangga" + }, + { + "author_name": "Ernawati Ernawati", + "author_inst": "Faculty of Medicine Universitas Airlangga" + }, + { + "author_name": "Muhammad Ardian Cahya Laksana", + "author_inst": "Faculty of Medicine Universitas Airlangga" + }, + { + "author_name": "Hermanto Tri Joewono", + "author_inst": "Universitas Airlangga Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "obstetrics and gynecology" + }, { "rel_doi": "10.1101/2021.09.21.21263898", "rel_title": "The Impact of New SARS-CoV-2 Variants on Vaccine Breakthrough: a pilot study on spreading infection in the communities", @@ -556586,57 +558752,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.09.23.21263920", - "rel_title": "Relationship between support for workers with illness and work functioning impairment in Japan during the COVID-19 pandemic", - "rel_date": "2021-09-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.23.21263920", - "rel_abs": "ObjectiveThis study examined the relationship between job accommodations for workers with poor health and work functioning impairment during the COVID-19 pandemic.\n\nMethodsAn internet survey was conducted in December 2020. We included 24,429 subjects for analysis. One question was used to determine whether subjects needed job accommodations from their company to continue working in their current health condition. The odds ratios (ORs) of the necessity of job accommodations for sick workers associated with work functioning impairment were estimated using multilevel logistic regression analysis.\n\nResultsThe OR of work functioning impairment among sick workers not receiving job accommodations was 5.75 (95% confidence interval (CI) 5.34-6.20, p<0.001) and those receiving job accommodations was 1.88 (95% CI 1.69-2.08, p<0.001) compared to healthy workers.\n\nConclusionsThis study suggests that providing job accommodations to workers with poor health may improve their work functioning impairment.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Igarashi Yu", - "author_inst": "Department of Occupational Medicine, School of Medicine, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Seiichiro Tateishi", - "author_inst": "Department of Occupational Medicine, School of Medicine, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Arisa Harada", - "author_inst": "Department of Occupational Medicine, School of Medicine, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Ayako Hno", - "author_inst": "Department of Mental Health, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Mayumi Tsuji", - "author_inst": "Department of Environmental Health, School of Medicine, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Akira Ogami", - "author_inst": "Department of Work Systems and Health, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Koji Mori", - "author_inst": "Department of Occupational Health Practice and Management, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Jap" - }, - { - "author_name": "Ryutaro Matsugaki", - "author_inst": "Department of Preventive Medicine and Community Health, School of Medicine, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Yoshihisa Fujino", - "author_inst": "Department of Environmental Epidemiology, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2021.09.23.21263927", "rel_title": "Antibody titers against the Alpha, Beta, Gamma, and Delta variants of SARS-CoV-2 induced by BNT162b2 vaccination measured using automated chemiluminescent enzyme immunoassay", @@ -557272,6 +559387,169 @@ "type": "new results", "category": "systems biology" }, + { + "rel_doi": "10.1101/2021.09.24.461743", + "rel_title": "Caspase-4/11 exacerbates disease severity in SARS-CoV-2 infection by promoting inflammation and thrombosis", + "rel_date": "2021-09-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.24.461743", + "rel_abs": "SARS-CoV-2 is a worldwide health concern, and new treatment strategies are needed 1. Targeting inflammatory innate immunity pathways holds therapeutic promise, but effective molecular targets remain elusive. Here, we show that human caspase-4 (CASP4), and its mouse homologue, caspase-11 (CASP11), are upregulated in SARS-CoV-2 infections, and that CASP4 expression correlates with severity of SARS-CoV-2 infection in humans. SARS-CoV-2-infected Casp11-/- mice were protected from severe weight loss and lung pathology, including blood vessel damage, compared to wild-type (WT) and gasdermin-D knock out (Gsdmd-/-) mice. GSDMD is a downstream effector of CASP11 and CASP1. Notably, viral titers were similar in the three genotypes. Global transcriptomics of SARS-CoV-2-infected WT, Casp11-/- and Gsdmd-/- lungs identified restrained expression of inflammatory molecules and altered neutrophil gene signatures in Casp11-/- mice. We confirmed that protein levels of inflammatory mediators IL-1{beta}, IL6, and CXCL1, and neutrophil functions, were reduced in Casp11-/- lungs. Additionally, Casp11-/- lungs accumulated less von Willebrand factor, a marker for endothelial damage, but expressed more Kruppel-Like Factor 2, a transcription factor that maintains vascular integrity. Overall, our results demonstrate that CASP4/11, promotes detrimental SARS-CoV-2-associated inflammation and coagulopathy, largely independently of GSDMD, identifying CASP4/11 as a promising drug target for treatment and prevention of severe COVID-19.", + "rel_num_authors": 37, + "rel_authors": [ + { + "author_name": "Mostafa Eltobgy", + "author_inst": "Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, OH, USA" + }, + { + "author_name": "Ashley Zani", + "author_inst": "Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, OH, USA" + }, + { + "author_name": "Adam Kenney", + "author_inst": "Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, OH, USA" + }, + { + "author_name": "Shady Estfanous", + "author_inst": "Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, OH, USA" + }, + { + "author_name": "Eunsoo Kim", + "author_inst": "Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA" + }, + { + "author_name": "Asmaa Badr", + "author_inst": "Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, OH, USA" + }, + { + "author_name": "Cierra Carafice", + "author_inst": "Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, OH, USA" + }, + { + "author_name": "Kylene Daily", + "author_inst": "Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, OH, USA" + }, + { + "author_name": "Owen Whitham", + "author_inst": "Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, OH, USA" + }, + { + "author_name": "Maciej Pietrzak", + "author_inst": "Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA" + }, + { + "author_name": "Amy Webb", + "author_inst": "Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA" + }, + { + "author_name": "Jeffrey Kawahara", + "author_inst": "Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, OH, USA" + }, + { + "author_name": "Adrian Eddy", + "author_inst": "Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, OH, USA" + }, + { + "author_name": "Parker Denz", + "author_inst": "Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, OH, USA" + }, + { + "author_name": "Mijia Lu", + "author_inst": "Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA" + }, + { + "author_name": "Mahesh KC", + "author_inst": "Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA" + }, + { + "author_name": "Mark Peeples", + "author_inst": "Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA" + }, + { + "author_name": "Jianrong Li", + "author_inst": "Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA" + }, + { + "author_name": "Jian Zhu", + "author_inst": "Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA" + }, + { + "author_name": "Jianwen Que", + "author_inst": "Division of Digestive and Liver Diseases and Center for Human Development, Department of Medicine, Columbia University, New York, NY, USA" + }, + { + "author_name": "Richard Robinson", + "author_inst": "Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, OH, USA" + }, + { + "author_name": "Oscar Rosas Mejia", + "author_inst": "Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, OH, USA" + }, + { + "author_name": "Rachael Rayner", + "author_inst": "Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA" + }, + { + "author_name": "Luanne Hall-Stoodley", + "author_inst": "Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, OH, USA" + }, + { + "author_name": "Stephanie Seveau", + "author_inst": "Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, OH, USA" + }, + { + "author_name": "Mikhail A Gavrilin", + "author_inst": "Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA" + }, + { + "author_name": "Andrea Tedeschi", + "author_inst": "Department of Neuroscience, Chronic Brain Injury Discovery Theme, The Ohio State University, Columbus, OH, USA" + }, + { + "author_name": "Santiago Partida-Sanchez", + "author_inst": "Abigail Wexner Research Institute at Nationwide Childrens Hospital" + }, + { + "author_name": "Frank Roberto", + "author_inst": "Abigail Wexner Research Institute at Nationwide Childrens Hospital, Columbus, OH, USA" + }, + { + "author_name": "Emily Hemann", + "author_inst": "Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, OH, USA" + }, + { + "author_name": "Eman Abdelrazik", + "author_inst": "Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, OH, USA" + }, + { + "author_name": "Adriana Forero", + "author_inst": "Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, OH, USA" + }, + { + "author_name": "Shahid Nimjee", + "author_inst": "Department of Neurological Surgery, The Ohio State University, Columbus, OH, USA" + }, + { + "author_name": "Prosper Boyaka", + "author_inst": "Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA" + }, + { + "author_name": "Estelle Cormet-Boyaka", + "author_inst": "Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA" + }, + { + "author_name": "Jacob Yount", + "author_inst": "Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, OH, USA" + }, + { + "author_name": "Amal Amer", + "author_inst": "Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, OH, USA" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.09.25.461776", "rel_title": "LRRC15 mediates an accessory interaction with the SARS-CoV-2 spike protein", @@ -558220,125 +560498,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2021.09.14.21263564", - "rel_title": "Divergence of delta and beta variants and SARS-CoV-2 evolved in prolonged infection into distinct serological phenotypes", - "rel_date": "2021-09-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.14.21263564", - "rel_abs": "Characterizing SARS-CoV-2 evolution in specific geographies may help predict the properties of variants coming from these regions. We mapped neutralization of a SARS-CoV-2 strain that evolved over 6 months from the ancestral virus in a person with advanced HIV disease. Infection was before the emergence of the Beta variant first identified in South Africa, and the Delta variant. We compared early and late evolved virus to the ancestral, Beta, Alpha, and Delta viruses and tested against convalescent plasma from ancestral, Beta, and Delta infections. Early virus was similar to ancestral, whereas late virus was similar to Beta, exhibiting vaccine escape and, despite pre-dating Delta, strong escape of Delta-elicited neutralization. This example is consistent with the notion that variants arising in immune-compromised hosts, including those with advanced HIV disease, may evolve immune escape of vaccines and enhanced escape of Delta immunity, with implications for vaccine breakthrough and reinfections.\n\nHighlightsO_LIA prolonged ancestral SARS-CoV-2 infection pre-dating the emergence of Beta and Delta resulted in evolution of a Beta-like serological phenotype\nC_LIO_LISerological phenotype includes strong escape from Delta infection elicited immunity, intermediate escape from ancestral virus immunity, and weak escape from Beta immunity\nC_LIO_LIEvolved virus showed substantial but incomplete escape from antibodies elicited by BNT162b2 vaccination\nC_LI\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC=\"FIGDIR/small/21263564v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (18K):\norg.highwire.dtl.DTLVardef@1194bfdorg.highwire.dtl.DTLVardef@1cbe318org.highwire.dtl.DTLVardef@aa74f8org.highwire.dtl.DTLVardef@e57969_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Sandile Cele", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "Farina Karim", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "Gila Lustig", - "author_inst": "Centre for the AIDS Programme of Research in South Africa" - }, - { - "author_name": "San Emmanuel James", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform" - }, - { - "author_name": "Tandile Hermanus", - "author_inst": "National Institute for Communicable Diseases" - }, - { - "author_name": "Eduan Wilkinson", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform" - }, - { - "author_name": "Jumari Snyman", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "Mallory Bernstein", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "Khadija Khan", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "Shi-Hsia Hwa", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "Houriiyah Tegally", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform" - }, - { - "author_name": "Sasha W Tilles", - "author_inst": "Center for Emerging and Re-emerging Infectious Diseases" - }, - { - "author_name": "Jennifer Giandhari", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform" - }, - { - "author_name": "Ntombifuthi Mthabela", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "Matilda Mazibuko", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "Yashica Ganga", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "Bernadett I Gosnell", - "author_inst": "University of KwaZulu-Natal" - }, - { - "author_name": "Salim Abdool Karim", - "author_inst": "Centre for the AIDS Programme of Research in South Africa" - }, - { - "author_name": "Willem Hanekom", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "Wesley C Van Voorhis", - "author_inst": "University of Washington" - }, - { - "author_name": "Thumbi Ndungu", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "Richard J Lessells", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform" - }, - { - "author_name": "Penny L Moore", - "author_inst": "National Institute for Communicable Diseases" - }, - { - "author_name": "Mahomed-Yunus S Moosa", - "author_inst": "University of KwaZulu-Natal" - }, - { - "author_name": "Tulio de Oliveira", - "author_inst": "University of KwaZulu-Natal" - }, - { - "author_name": "Alex Sigal", - "author_inst": "Africa Health Research Institute" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.18.21263755", "rel_title": "Unusual SARS-CoV-2 intra-host diversity reveals lineages superinfection", @@ -559006,6 +561165,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.09.22.461447", + "rel_title": "Deciphering the role of the Pancreatic Secretome in Covid-19 associated Multi-Organ Dysfunctions", + "rel_date": "2021-09-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.22.461447", + "rel_abs": "Emerging evidence indicates an intricate relationship between the SARS-CoV-2 infection and Multi-Organ Dysfunctions (MODs). Here, we have investigated the role of the Secretome of the SARS-CoV-2 infected pancreas and mechanistically linked it with the multi-organ dysfunction using the scRNA-seq analysis. We found that acinar-specific PRSS2, REG3A, REG1A, SPINK1, and ductal-specific SPP1, MMP7 genes are upregulated in alpha, beta, delta, and mesenchyme cells. Using extensive documented experimental evidence, we validated the association of upregulated pancreatic Secretome with coagulation cascade, complement activation, renin angiotensinogen system dysregulation, endothelial cell injury and thrombosis, immune system dysregulation, and fibrosis. Our finding suggests the influence of upregulated Secretome on multi-organ systems such as Nervous, Cardiovascular, Immune, Digestive, and Urogenital systems. In addition, we report that the secretory proteins IL1B, AGT, ALB, SPP1, CRP, SERPINA1, C3, TFRC, TNFSF10, and MIF are associated with diverse diseases. Thus, suggest the role of the pancreatic Secretome in SARS-CoV-2 associated MODs.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Ekta Pathak", + "author_inst": "Banaras Hindu University, Varanasi, India" + }, + { + "author_name": "Rajeev Mishra", + "author_inst": "Banaras Hindu University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "systems biology" + }, { "rel_doi": "10.1101/2021.09.22.461286", "rel_title": "Inducible CRISPR activation screen for interferon-stimulated genes identifies OAS1 as a SARS-CoV-2 restriction factor", @@ -559882,37 +562064,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.09.12.21263462", - "rel_title": "Thrombotic adverse events reported for Moderna, Pfizer and Oxford-AstraZeneca COVID-19 vaccines: comparison of occurrence and clinical outcomes in the EudraVigilance database", - "rel_date": "2021-09-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.12.21263462", - "rel_abs": "BackgroundVaccination against COVID-19 is the cornerstone to control and mitigate the ongoing pandemic. Thrombotic adverse events linked to Moderna, Pfizer and the Oxford-AstraZeneca vaccine have been documented and described as extremely rare. While the Oxford-AstraZeneca vaccine has received much of the attention, the other vaccines should not go unchallenged. This study aimed to determine the frequency of reported thrombotic adverse events and clinical outcomes for these three COVID-19 vaccines, namely, Moderna, Pfizer and Oxford-AstraZeneca\n\nMethodsA retrospective descriptive analysis was conducted of spontaneous reports for Moderna, Pfizer and Oxford-AstraZeneca COVID-19 vaccines submitted to the EudraVigilance database in the period from 17 February to 14 June 2021.\n\nFindingsThere were 729,496 adverse events for the three vaccines, of which 3,420 were thrombotic, mainly Oxford-AstraZeneca (n=1,988, 58{middle dot}1%) followed by Pfizer (n=1,096, 32{middle dot}0%) and Moderna (n=336, 9{middle dot}8%). As serious adverse events, there were 705 reports of pulmonary embolism for the three vaccines, of which 130 reports (18{middle dot}4%) were for Moderna, 226 reports (32{middle dot}1%) for Pfizer and 349 (49{middle dot}5%) for Oxford-AstraZeneca vaccines. The occurrence of pulmonary embolism is significantly associated with a fatal outcome (P=<0{middle dot}001). Sixty-three fatalities were recorded (63/3420, 1.8%), of which Moderna (n=6), Pfizer (n=25) and Oxford-AstraZeneca (n=32).\n\nInterpretationThrombotic adverse events reported for the three vaccines remains extremely rare with multiple causative factors reported elsewhere as precipitating these events. Practicing vigilance and proper clinical management for the affected vaccines, as well as continuing to report adverse events, are essential.\n\nFundingNo funding was sought for this study.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSDuring the first quarter of 2021, several European countries suspended the use of the Oxford-AstraZeneca vaccine amid reports of blood clot events and the death of a vaccinated person. This was followed by several reports of fatalities related to pulmonary embolism and other thrombotic events including thrombocytopenia which has been referred to as vaccine-induced immune thrombotic thrombocytopenia (VITT). The European Medicines Agency on 18 March 2021 concluded that the Oxford- AstraZeneca vaccine was safe, effective and the benefits outweighed the risks.\n\nAdded value of this studyThis study investigated the occurrence of thrombotic adverse events and their clinical outcomes of the three approved and most used COVID-19 vaccines namely Moderna, Pfizer and Oxford-AstraZeneca, using one of the largest spontaneous adverse events databases, namely EudraVigilance. Out of 729,496 adverse events reported for the three vaccines in the study period, only 3420 (0.47%) potential thrombotic adverse events were reported, the majority associated with Oxford-AstraZeneca (n=1,988, 58.1%).\n\nImplications of all the available evidenceMore than 4{middle dot}89 billion doses of different COVID-19 vaccines have been administered across the globe.\n\nDespite thrombotic adverse events reported for the three vaccines in focus for this study - Moderna, Pfizer and Oxford-AstraZeneca - being extremely rare, so continuing to report adverse events is essential. On the basis of scientific evidence showing that benefit outweighs risk, people continue to be urged to accept the vaccination when offered.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Mansour Tobaiqy", - "author_inst": "Department of Pharmacology, College of Medicine, University of Jeddah, PO Box 45311, Jeddah 21512, Kingdom of Saudi Arabia" - }, - { - "author_name": "Katie MacLure", - "author_inst": "Independent Research Consultant, Aberdeen, UK AB32 6RU" - }, - { - "author_name": "Hajer Elkout", - "author_inst": "Department of Family and Community Medicine, Medical Faculty, University of Tripoli, Tripoli 13275, Libya" - }, - { - "author_name": "Derek Stewart", - "author_inst": "College of Pharmacy, QU Health, Qatar University, Doha, Qatar, P.O. Box 2713" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.09.20.21263757", "rel_title": "Potential COVID-19 vaccination opportunities in primary care practices in the United States", @@ -560948,6 +563099,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.21.21263879", + "rel_title": "Viral loads and profile of the patients infected with SARS-CoV-2 Delta, Alpha or R.1 variants in Tokyo", + "rel_date": "2021-09-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.21.21263879", + "rel_abs": "The rapid spread of the Delta variant of SARS-CoV-2 became a serious concern worldwide in summer 2021. We examined the copy number and variant types of all SARS-CoV-2-positive patients who visited our hospital from February to August 2021 using PCR tests. Whole genome sequencing was performed for some samples. The R.1 variant (B.1.1.316) was responsible for most infections in March, replacing the previous variant (B.1.1.214); the Alpha (B.1.1.7) variant caused most infections in April and May; and the Delta variant (B.1.617.2) was the most prevalent in July and August. There was no significant difference in copy numbers among the previous variant cases (n=29, median 3.0x104 copies/L), R.1 variant cases (n=28, 2.1x105 copies/L), Alpha variant cases (n=125, 4.1x105 copies/L), and Delta variant cases (n=106, 2.4x105 copies/L). Patients with Delta variant infection were significantly younger than those infected with R.1 and the previous variants, possibly because many elderly individuals in Tokyo were vaccinated between May and August. There was no significant difference in mortality among the four groups. Our results suggest that the increased infectivity of Delta variant may be caused by factors other than the higher viral loads. Clarifying these factors is important to control the spread of Delta variant infection.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Chihiro Tani-Sassa", + "author_inst": "Tokyo Medical and Dental University" + }, + { + "author_name": "Yumi Iwasaki", + "author_inst": "Tokyo Medical and Dental University" + }, + { + "author_name": "Naoya Ichimura", + "author_inst": "Tokyo Medical and Dental University" + }, + { + "author_name": "Katsutoshi Nagano", + "author_inst": "Tokyo Medical and Dental University" + }, + { + "author_name": "Yuna Takatsuki", + "author_inst": "Tokyo Medical and Dental University" + }, + { + "author_name": "Sonoka Yuasa", + "author_inst": "Tokyo Medical and Dental University" + }, + { + "author_name": "Yuta Takahashi", + "author_inst": "Tokyo Medical and Dental University" + }, + { + "author_name": "Jun Nakajima", + "author_inst": "Tokyo Medical and Dental University" + }, + { + "author_name": "Kazunari Sonobe", + "author_inst": "Tokyo Medical and Dental University" + }, + { + "author_name": "Yoko Nukui", + "author_inst": "Tokyo Medical and Dental University" + }, + { + "author_name": "Hiroaki Takeuchi", + "author_inst": "Tokyo Medical and Dental University" + }, + { + "author_name": "Kousuke Tanimoto", + "author_inst": "Tokyo Medical and Dental University" + }, + { + "author_name": "Yukie Tanaka", + "author_inst": "Tokyo Medical and Dental University" + }, + { + "author_name": "Akinori Kimura", + "author_inst": "Tokyo Medical and Dental University" + }, + { + "author_name": "Shuji Tohda", + "author_inst": "Tokyo Medical and Dental University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.20.21263836", "rel_title": "HUMORAL AND CELLULAR IMMUNOGENICITY and SAFETY UP TO 4 MONTHS AFTER VACCINATION WITH BNT162B2 mRNA COVID-19 VACCINE IN HEART AND LUNG TRANSPLANTED YOUNG ADULTS", @@ -561715,20 +563941,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, - { - "rel_doi": "10.1101/2021.09.18.21263262", - "rel_title": "Effectiveness of COVID-19 Vaccines: Eight Months Post Single Dose Vaccination", - "rel_date": "2021-09-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.18.21263262", - "rel_abs": "ObjectivesTo describe the real-world data on the effectiveness of Pfizer-BioNtech BNT162b2 and AstraZeneca-Oxford AZD1222 vaccines against COVID-19 in a large cohort in the Kingdom of Saudi Arabia (KSA).\n\nMethodsA total of 18,543 subjects received a single-dose of either of the vaccines at one vaccination centre in KSA, and were followed up for three to eight months. Clinical data from medical records, adverse events (AEs) from a self-reporting system, and COVID-19 infection data from the national databases were retrieved and analysed.\n\nResultsSubjects median age was 33 years old with an average of 27.3 body mass index and the majority were male (60.1%). 92.17% of the subjects had no COVID-19 infection post-vaccination. Diabetes mellitus (p=0.0325), organ transplantation (p=0.0254), and morbid obesity (p=0.0014) were risk factors for infection post-vaccination. Unlike vaccine type, being Saudi, male, or obese was more likely to get the infection earlier. AE reports from 1084 subjects included injection site pain, fatigue, fever, myalgia, headache.\n\nConclusionSingle-dose COVID-19 vaccines in KSA showed an effectiveness rate of 92.17% up to eight months follow-up. The rate for AZD1222 was higher than what have been previously reported. Side effects and AEs were within what has been reported in clinical trials.", - "rel_num_authors": 0, - "rel_authors": null, - "version": "1", - "license": "", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.17.21263708", "rel_title": "Modeling SARS-CoV-2 RNA Degradation in Small and Large Sewersheds", @@ -562407,6 +564619,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.16.21263629", + "rel_title": "Access to personal protective equipment in healthcare workers during the COVID-19 pandemic in the United Kingdom: results from a nationwide cohort study (UK-REACH)", + "rel_date": "2021-09-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.16.21263629", + "rel_abs": "ObjectivesTo determine the prevalence and predictors of self-reported access to appropriate personal protective equipment (aPPE) for healthcare workers (HCWs) in the United Kingdom (UK) during the first UK national COVID-19 lockdown (March 2020) and at the time of questionnaire response (December 2020 - February 2021).\n\nDesignTwo cross sectional analyses using data from a questionnaire-based cohort study.\n\nSettingNationwide questionnaire from 4th December 2020 to 28th February 2021.\n\nParticipantsA representative sample of HCWs or ancillary workers in a UK healthcare setting aged 16 or over, registered with one of seven main UK healthcare regulatory bodies.\n\nMain outcome measureBinary measure of self-reported aPPE (access all of the time vs access most of the time or less frequently) at two timepoints: the first national lockdown in the UK (primary analysis) and at the time of questionnaire response (secondary analysis).\n\nResults10,508 HCWs were included in the primary analysis, and 12,252 in the secondary analysis. 3702 (35.2%) of HCWs reported aPPE at all times in the primary analysis; 6806 (83.9%) reported aPPE at all times in the secondary analysis. After adjustment (for age, sex, ethnicity, migration status, occupation, aerosol generating procedure exposure, work sector, work region, working hours, night shift frequency and trust in employing organisation), older HCWs (per decade increase in age: aOR 1.2, 95% CI 1.16-1.26, p<0.001) and those working in Intensive Care Units (1.61, 1.38 - 1.89, p<0.001) were more likely to report aPPE at all times. Those from Asian ethnic groups compared to White (0.77, 0.67-0.89, p<0.001), those in allied health professional (AHPs) and dental roles (vs those in medical roles; AHPs: 0.77, 0.68 - 0.87, p<0.001; dental: 0.63, 0.49-0.81, p<0.001), and those who saw a higher number of COVID-19 patients compared to those who saw none ([≥]21 patients 0.74, 0.61-0.90, p=0.003) were less likely to report aPPE at all times in the primary analysis. aPPE at all times was also not uniform across UK regions (reported access being better in South West and North East England than London). Those who trusted their employing organisation to deal with concerns about unsafe clinical practice, compared to those who did not, were twice as likely to report aPPE at all times (2.18, 1.97-2.40, p<0.001). With the exception of occupation, these factors were also significantly associated with aPPE at all times in the secondary analysis.\n\nConclusionsWe found that only a third of HCWs in the UK reported aPPE at all times during the period of the first lockdown and that aPPE had improved later in the pandemic. We also identified key sociodemographic and occupational determinants of aPPE during the first UK lockdown, the majority of which have persisted since lockdown was eased. These findings have important public health implications for HCWs, particularly as cases of infection and long-COVID continue to rise in the UK.\n\nTrial registrationISRCTN 11811602\n\nWhat is already known on this topicAccess to personal protective equipment (PPE) is crucial to protect healthcare workers (HCWs) from infection. Limited data exist concerning the prevalence of, and factors relating to, PPE access for HCWs in the United Kingdom (UK) during the COVID-19 pandemic.\n\nWhat this study addsOnly a third of HCWs reported having access to appropriate PPE all of the time during the first UK national lockdown. Older HCWs, those working in Intensive Care Units and those who trusted their employing organisation to deal with concerns about unsafe clinical practice, were more likely to report access to adequate PPE. Those from Asian ethnic groups (compared to White ethnic groups) and those who saw a high number of COVID-19 were less likely to report access to adequate PPE. Our findings have important implications for the mental and physical health of HCWs working during the pandemic in the UK.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Christopher A Martin", + "author_inst": "University of Leicester" + }, + { + "author_name": "Daniel Pan", + "author_inst": "University of Leicester" + }, + { + "author_name": "Joshua Nazareth", + "author_inst": "University of Leicester" + }, + { + "author_name": "Avinash Aujayeb", + "author_inst": "Northumbria Specialist Emergency Care Hospital" + }, + { + "author_name": "Luke Bryant", + "author_inst": "University of Leicester" + }, + { + "author_name": "Sue Carr", + "author_inst": "University Hospitals of Leicester NHS Trust" + }, + { + "author_name": "Laura J Gray", + "author_inst": "University of Leicester" + }, + { + "author_name": "Bindu Gregary", + "author_inst": "Royal Preston Hospital" + }, + { + "author_name": "Amit Gupta", + "author_inst": "Oxford University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Anna Louise Guyatt", + "author_inst": "University of Leicester" + }, + { + "author_name": "Alan Gopal", + "author_inst": "Hull University Teaching Hospitals NHS Trust" + }, + { + "author_name": "Thomas Hine", + "author_inst": "Oxford University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Catherine John", + "author_inst": "University of Leicester" + }, + { + "author_name": "Ian Christopher McManus", + "author_inst": "University College London" + }, + { + "author_name": "Carl Melbourne", + "author_inst": "University of Leicester" + }, + { + "author_name": "Laura B Nellums", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Rubina Reza", + "author_inst": "Derbyshire Healthcare NHS Foundation Trust" + }, + { + "author_name": "Sandra Simpson", + "author_inst": "Nottinghamshire Healthcare NHS Foundation Trust" + }, + { + "author_name": "Martin D Tobin", + "author_inst": "University of Leicester" + }, + { + "author_name": "Katherine Woolf", + "author_inst": "University College London" + }, + { + "author_name": "Stephen Zingwe", + "author_inst": "Berkshire Healthcare NHS Foundation Trust" + }, + { + "author_name": "Kamlesh Khunti", + "author_inst": "University of Leicester" + }, + { + "author_name": "Manish Pareek", + "author_inst": "University of Leicester" + }, + { + "author_name": "- the UK-REACH Study Collaborative Group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.09.16.21263678", "rel_title": "Association of inflammatory markers with severity of disease and mortality in COVID-19 patients: a systematic review and meta-analysis", @@ -563087,37 +565410,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.09.17.460870", - "rel_title": "Gene networks under circadian control exhibit diurnal organization in primate organs", - "rel_date": "2021-09-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.17.460870", - "rel_abs": "Mammalian organs are individually controlled by autonomous circadian clocks. At the molecular level, this process is defined by the cyclical co-expression of both core transcription factors and off-target genes across time. While interactions between these molecular clocks are likely necessary for proper homeostasis, these features remain undefined. Here, we utilize integrative analysis of a baboon diurnal transcriptome atlas to characterize the properties of gene networks under circadian control. We found that 53.4% (8,120) of baboon genes are rhythmically expressed body-wide. In addition, >30% of gene-gene interactions exhibit periodic co-expression patterns, with core circadian genes more cyclically co-expressed than others. Moreover, two basic network modes were observed at the systems level: daytime and nighttime mode. Daytime networks were enriched for genes involved in metabolism, while nighttime networks were enriched for genes associated with growth and cellular signaling. A substantial number of diseases only form significant disease modules at either daytime or nighttime. In addition, we found that 216 of 313 genes encoding products that interact with SARS-CoV-2 are rhythmically expressed throughout the body. Importantly, more than 80% of SARS-CoV-2 related genes enriched modules are rhythmically expressed, and have significant network proximities with circadian regulators. Our data suggest that synchronization amongst circadian gene networks is necessary for proper homeostatic functions and circadian regulators have close interactions with SARS-CoV-2 infection.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Jie Li", - "author_inst": "Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, China" - }, - { - "author_name": "Pengxing Nie", - "author_inst": "Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, China" - }, - { - "author_name": "Christoph Turck", - "author_inst": "Max Planck Institute of Psychiatry, Germany" - }, - { - "author_name": "Guang-Zhong Wang", - "author_inst": "Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, China" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "systems biology" - }, { "rel_doi": "10.1101/2021.09.20.461023", "rel_title": "SARS-CoV-2 preS dTM vaccine booster candidates increase functional antibody responses and cross-neutralization against SARS-CoV-2 variants of concern in non-human primates", @@ -563829,6 +566121,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.09.10.21263398", + "rel_title": "Computational systematics of nutritional support of vaccination against viral and bacterial pathogens as prolegomena to vaccinations against COVID-19", + "rel_date": "2021-09-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.10.21263398", + "rel_abs": "A total of 6,628 PUBMED-registered publications on the relationships between the effects of vaccination and the provision of micronutrients have been studied by methods of topological analysis of text data. In case of insufficient intake of certain micronutrients, the functioning of the acquired immunity is disrupted resulting in an imbalance of populations of T-cells CD4+/CD8+ and of B-lymphocytes. Nutritional supplements of folate, vitamins A, D and B12, which are recognized regulators of cell division, support a wide range of lymphocyte populations. Trace elements zinc, iron, selenium, manganese and omega-3 polyunsaturated fatty acids are also important for supporting the mechanisms of acquired immunity. The data presented show that a course intake of these micronutrients by patients planning vaccination can significantly improve its effectiveness. In particular, these micronutrients can increase the titers of antibodies to pathogens, and to reduce the percentage of patients who still contract infection after vaccination. Supplements of these micronutrients can also contribute to the safety of vaccination: to prevent malaise and, in the unfortunate case of contracting infection despite the vaccine, to reduce the severity of the course and the mortality from the corresponding infection.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ivan Y. Torshin", + "author_inst": "FIC IU RAN" + }, + { + "author_name": "Olga A. Gromova", + "author_inst": "FIC IU RAN" + }, + { + "author_name": "Alexander G. Chuchalin", + "author_inst": "RSMU" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2021.09.16.21263704", "rel_title": "Real-world serologic responses to Extended-interval and Heterologous COVID-19 mRNA vaccination in Frail Elderly - Interim report from a prospective observational cohort study", @@ -565057,33 +567376,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.09.15.21263648", - "rel_title": "Environmental factors and mobility predict COVID-19 seasonality", - "rel_date": "2021-09-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.15.21263648", - "rel_abs": "BackgroundWe recently showed that seasonal patterns of COVID-19 incidence and Influenza-Like Illnesses incidence are highly similar, in a country in the temperate climate zone, such as the Netherlands (latitude: 52{degrees}N). We hypothesize that in The Netherlands the same environmental factors and mobility trends that are associated with the seasonality of flu-like illnesses are predictors of COVID-19 seasonality as well.\n\nMethodsWe used meteorological, pollen/hay fever and mobility data from the Netherlands with its 17.4 million inhabitants. For the reproduction number of COVID-19 (Rt), we used data from the Dutch State Institute for Public Health. This Rt metric is a daily estimate that is based on positive COVID-19 tests in the Netherlands in hospitals and municipalities. For all datasets we selected the overlapping period of COVID-19 and the first allergy season: from February 17, 2020 till September 21, 2020 (total number of measurements: n = 218), the end of pollen season. Backward stepwise multiple linear regression was used to develop an environmental prediction model of the Rt of COVID-19. Next, we studied whether adding mobility trends to an environmental model improved the predictive power.\n\nResultsBy means of stepwise backward multiple linear regression four highly significant (p value < 0.01) predictive factors are selected in our combined model: temperature, solar radiation, hay fever incidence, and mobility to indoor recreation locations. Our combined model explains 87.5% of the variance of Rt of COVID-19 and has a good and highly significant fit: F(4, 213) = 374.2, p-value < 0.00001. The combined model had a better overall predictive performance compared to a solely environmental model, which still explains 77.3% of the variance of Rt, and a good and highly significant fit: F(4, 213) = 181.3, p < 0.00001.\n\nConclusionsWe conclude that the combined mobility and environmental model can adequately predict the seasonality of COVID-19 in a country with a temperate climate like the Netherlands. In this model higher solar radiation, higher temperature and hay fever are related to lower COVID-19 reproduction, and mobility to indoor recreation locations with increased COVID-19 spread.\n\nHighlightsO_LIThe seasonality of COVID-19 can be well-explained by environmental factors and mobility.\nC_LIO_LIA combined model explains 87.5% of the variance of the reproduction number of COVID-19\nC_LIO_LIInhibitors of the reproduction number of COVID-19 are higher solar radiation, and seasonal allergens/allergies.\nC_LIO_LIMobility, especially to indoor recreation locations, increases the reproduction number of COVID-19.\nC_LIO_LITemperature has no direct effect on the reproduction number of COVID-19, but affects mobility and seasonal allergens.\nC_LIO_LIAdding mobility trends to an environmental model improves the predictive value regarding the reproduction number of COVID-19.\nC_LI", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Martijn J Hoogeveen", - "author_inst": "Open University Netherlands" - }, - { - "author_name": "Aloys C.M. Kroes", - "author_inst": "Leiden University Medical Center" - }, - { - "author_name": "Ellen K Hoogeveen", - "author_inst": "Jeroen Bosch Ziekenhuis" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.09.10.21262933", "rel_title": "Impact of multiple sclerosis disease-modifying therapies on SARS-CoV-2 vaccine-induced antibody and T cell immunity", @@ -566175,6 +568467,117 @@ "type": "new results", "category": "pathology" }, + { + "rel_doi": "10.1101/2021.09.14.21263541", + "rel_title": "Dysregulated immune responses in COVID-19 patients correlating with disease severity and invasive oxygen requirements", + "rel_date": "2021-09-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.14.21263541", + "rel_abs": "The prognosis of severe COVID-19 patients has motivated research communities to uncover mechanisms of SARS-CoV-2 pathogenesis also on a regional level. In this work, we aimed to understand the immunological dynamics of severe COVID-19 patients with different degrees of illness, and upon long-term recovery.\n\nWe analyzed immune cellular subsets and SARS-CoV-2-specific antibody isotypes of 66 COVID-19 patients admitted to the Hospital Clinico Universidad de Chile, which were categorized according to the WHO ten-point clinical progression score. These included 29 moderate patients (score 4-5) and 37 severe patients under either high flow oxygen nasal cannula (18 patients, score 6), or invasive mechanical ventilation (19 patients, score 7-9), plus 28 convalescent patients and 28 healthy controls. Furthermore, six severe patients that recovered from the disease were longitudinally followed over 300 days.\n\nOur data indicate that severe COVID-19 patients display increased frequencies of plasmablasts, activated T cells and SARS-CoV-2-specific antibodies compared to moderate and convalescent patients. Remarkably, within the severe COVID-19 group, patients rapidly progressing into invasive mechanical ventilation show higher frequencies of plasmablasts, monocytes, eosinophils, Th1 cells and SARS-CoV-2-specific IgG than patients under high flow oxygen nasal cannula. These findings demonstrate that severe COVID-19 patients progressing into invasive mechanical ventilation show a distinctive type of immunity. In addition, patients that recover from severe COVID-19 begin to regain normal proportions of immune cells 100 days after hospital discharge and maintain high levels of SARS-CoV-2-specific IgG throughout the study, which is an indicative sign of immunological memory. Thus, this work can provide a useful benchmark for improvement of disease outcomes.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Paulina Garcia-Gonzalez Ph.D", + "author_inst": "Laboratory of Immunology and Cellular Stress, Program of Immunology, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chil" + }, + { + "author_name": "Fabian Tempio", + "author_inst": "Laboratory of Cancer Immunoregulation, Program of Immunology, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile" + }, + { + "author_name": "Camila Fuentes", + "author_inst": "Laboratory of Cancer Immunoregulation, Program of Immunology, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile" + }, + { + "author_name": "Consuelo Merino", + "author_inst": "Laboratory of Cancer Immunoregulation, Program of Immunology, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile" + }, + { + "author_name": "Leonardo Vargas", + "author_inst": "Laboratory of Immunology, Biology Department, Faculty of Sciences, Universidad de Chile, Santiago, Chile" + }, + { + "author_name": "Valeska Simon", + "author_inst": "Laboratory of Immunology, Biology Department, Faculty of Sciences, Universidad de Chile, Santiago, Chile" + }, + { + "author_name": "Mirliana Ramirez", + "author_inst": "Nursing Department, Faculty of Medicine. Universidad de Chile, Santiago, Chile" + }, + { + "author_name": "Veronica Rojas MD", + "author_inst": "Critical Care Unit, Department of Medicine, Hospital ClInico Universidad de Chile, Santiago, Chile" + }, + { + "author_name": "Eduardo Tobar MD", + "author_inst": "Critical Care Unit, Department of Medicine, Hospital ClInico Universidad de Chile, Santiago, Chile" + }, + { + "author_name": "Glauben Landskron Ph.D", + "author_inst": "Laboratory of Innate Immunity, Program of Immunology, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile" + }, + { + "author_name": "Juan Pablo Araya", + "author_inst": "Laboratory of Antitumoral Immunology, Program of Immunology, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile. Mille" + }, + { + "author_name": "Mariela Navarrete", + "author_inst": "Laboratory of Antitumoral Immunology, Program of Immunology, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile. Mille" + }, + { + "author_name": "Carla Bastias MD", + "author_inst": "HIV Immunology and Allergies Unit, Department of Medicine. Hospital ClInico Universidad de Chile, Santiago, Chile" + }, + { + "author_name": "Rocio Tordecilla MD", + "author_inst": "HIV Immunology and Allergies Unit, Department of Medicine. Hospital ClInico Universidad de Chile, Santiago, Chile" + }, + { + "author_name": "Macarena Varas Ph.D", + "author_inst": "Integrative Microbiology Group, Biology Department, Faculty of Sciences, Universidad de Chile, Santiago, Chile. Center for Genome Regulation (CGR), Biology Depa" + }, + { + "author_name": "Pablo Maturana", + "author_inst": "Laboratory of Biochemistry and Molecular Biology, Biology Department, Faculty of Sciences, Universidad de Chile, Santiago, Chile" + }, + { + "author_name": "Andres Marcoleta Ph.D", + "author_inst": "Integrative Microbiology Group, Biology Department, Faculty of Sciences, Universidad de Chile, Santiago, Chile" + }, + { + "author_name": "Miguel Allende Ph.D", + "author_inst": "Center for Genome Regulation (CGR), Biology Department, Faculty of Sciences, Universidad de Chile, Santiago, Chile" + }, + { + "author_name": "Rodrigo Naves Ph.D", + "author_inst": "Laboratory of Neuroimmunology, Program of Immunology, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile" + }, + { + "author_name": "Marcela Hermoso Ph.D", + "author_inst": "Laboratory of Innate Immunity, Program of Immunology, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile" + }, + { + "author_name": "Flavio Salazar-Onfray Ph.D", + "author_inst": "Laboratory of Antitumoral Immunology, Program of Immunology, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile. Mille" + }, + { + "author_name": "Mercedes Lopez Ph.D", + "author_inst": "Laboratory of Cancer Immunoregulation, Program of Immunology, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile" + }, + { + "author_name": "MarIa Rosa Bono Ph.D", + "author_inst": "Laboratory of Immunology, Biology Department, Faculty of Sciences, Universidad de Chile, Santiago, Chile" + }, + { + "author_name": "Fabiola Osorio Ph.D", + "author_inst": "Laboratory of Immunology and Cellular Stress, Program of Immunology, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chil" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2021.09.14.21263545", "rel_title": "Widening Disparities in Online Information Access during the COVID-19 Pandemic", @@ -567259,61 +569662,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2021.09.13.21263437", - "rel_title": "Platelet polyphosphate and SARS-Cov-2 mRNA-vaccine-induced inflammatory side-effects: a pilot study", - "rel_date": "2021-09-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.13.21263437", - "rel_abs": "BackgroundPlatelets have recently been recognized as immune cells. Platelets first contact invading pathogens and then induce immune reactions in cooperation with white blood cells. Platelet polyphosphate (polyP), which is classically recognized as a thrombotic and hemostatic biomolecule, has recently attracted attention as a cytokine that modulates inflammation and is involved in intercellular communication between platelets and major immune cells.\n\nObjectiveTo determine the involvement of polyP in SARS-Cov-2-mRNA vaccine-induced immune responses, this pilot study examined the effects of mRNA vaccines on platelet polyP levels.\n\nMethodsBefore and after vaccination (BNT162b2), blood samples were obtained from healthy, non-smoking individuals (relatively older male group, n=6 vs. younger female group, n=23), who did not have systemic diseases that required continuous treatment. Washed platelets were prepared and subjected to a fluorometric determination of platelet polyP levels using 4,6-diamidino-2-phenylindole. The side effects of vaccination were recorded as scores.\n\nResultsCompared with the male group, platelet polyP levels decreased in the relatively younger female group after the initial dose, while the side effect score increased in the female group after the second dose. Moderate correlation coefficients were observed between the reduction in polyP levels and the side effect scores or the original polyP levels.\n\nConclusionsDespite being a pilot study using a small sample size, this study suggests the possibility that platelet polyP may suppress the side effects induced by the mRNA vaccines after the initial dose, but not the second dose, in relatively young female subjects who generally have high immune responsiveness.\n\nEssentialsO_LIThe COVID-19 mRNA vaccines (BNT162b2) reduced platelet polyP levels after the initial dose, but not after the 2nd dose, in relatively younger female subjects.\nC_LIO_LIRelatively older male subjects did not respond to the vaccination by reducing platelet polyP.\nC_LIO_LIThese findings suggest that platelets release polyP to suppress vaccine-induced reactions, for example, inflammation, which is usually recognized as a side effect.\nC_LIO_LIHowever, such suppression could be observed in subjects with higher immune responses, generally in relatively younger female subjects.\nC_LI", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Takashi Uematsu", - "author_inst": "Tokyo Plastic Dental Society" - }, - { - "author_name": "Atsushi Sato", - "author_inst": "Tokyo Plastic Dental Society" - }, - { - "author_name": "Hachidai Aizawa", - "author_inst": "Tokyo Plastic Dental Society" - }, - { - "author_name": "Tetsuhiro Tsujino", - "author_inst": "Tokyo Plastic Dental Society" - }, - { - "author_name": "Taisuke Watanabe", - "author_inst": "Tokyo Plastic Dental Society" - }, - { - "author_name": "Kazushige Isobe", - "author_inst": "Tokyo Plastic Dental Society" - }, - { - "author_name": "Hideo Kawabata", - "author_inst": "Tokyo Plastic Dental Society" - }, - { - "author_name": "Yutaka Kitamura", - "author_inst": "Tokyo Plastic Dental Society" - }, - { - "author_name": "Takaaki Tanaka", - "author_inst": "Niigata Univeristy" - }, - { - "author_name": "Tomoyuki Kawase", - "author_inst": "Institute of Medicine and Dentistry, Niigata University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "hematology" - }, { "rel_doi": "10.1101/2021.09.13.21263504", "rel_title": "Aging-related cell type-specific pathophysiologic immune responses that exacerbate disease severity in aged COVID-19 patients", @@ -568197,6 +570545,57 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.09.15.459215", + "rel_title": "Signatures of adaptive evolution during human to mink SARS CoV2 cross species transmission inform estimates of the COVID19 pandemic timing", + "rel_date": "2021-09-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.15.459215", + "rel_abs": "One of the unique features of SARS-CoV-2 is that it mainly evolved neutrally or under purifying selection during the early pandemic. This contrasts with the preceding epidemics of the closely related SARS-CoV and MERS-CoV, both of which evolved adaptively. It is possible that the SARS-CoV-2 exhibits a unique or adaptive feature which deviates from other coronaviruses. Alternatively, the virus may have been cryptically circulating in humans for a sufficient time to have acquired adaptive changes for efficient transmission before the onset of the current pandemic. In order to test the above scenarios, we analyzed the SARS-CoV-2 sequences from minks (Neovision vision) and parenteral human strains. In the early phase of the mink epidemic (April to May 2020), nonsynonymous to synonymous mutation ratios per site within the spike protein was 2.93, indicating a selection process favoring adaptive amino acid changes. In addition, mutations within this protein concentrated within its receptor binding domain and receptor binding motif. Positive selection also left a trace on linked neutral variation. An excess of high frequency derived variants produced by genetic hitchhiking was found during middle (June to July 2020) and early late (August to September 2020) phases of the mink epidemic, but quickly diminished in October and November 2020. Strong positive selection found in SARS-CoV-2 from minks implies that the virus may be not unique in super-adapting to a wide range of new hosts. The mink study suggests that SARS-CoV-2 already went through adaptive evolution in humans, and likely been circulating in humans at least six months before the first case found in Wuhan, China. We also discuss circumstances under which the virus can be well-adapted to its host but fail to induce an outbreak.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Jui-Hung Tai", + "author_inst": "National Taiwan University" + }, + { + "author_name": "Shu-Miaw Chaw", + "author_inst": "Academia Sinica" + }, + { + "author_name": "Hsiao-Yu Sun", + "author_inst": "Taipei Municipal Zhongshan Girls High School, Taipei, Taiwan." + }, + { + "author_name": "Yi-Cheng Tseng", + "author_inst": "National Taiwan University" + }, + { + "author_name": "Guanghao Li", + "author_inst": "Chinese Academy of Science" + }, + { + "author_name": "Sui-Yuan Chang", + "author_inst": "National Taiwan University" + }, + { + "author_name": "Shiou-Hwei Yeh", + "author_inst": "National Taiwan University College of Medicine" + }, + { + "author_name": "Pei-Jer Chen", + "author_inst": "National Taiwan University" + }, + { + "author_name": "Hurng-Yi Wang", + "author_inst": "National Taiwan University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2021.09.16.460663", "rel_title": "Neutralizing antibody-independent immunity to SARS-CoV-2 in hamsters and hACE-2 transgenic mice immunized with a RBD/Nucleocapsid fusion protein", @@ -569225,41 +571624,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.09.14.460264", - "rel_title": "Characterizing flexibility and mobility in the natural mutations of the SARS-CoV-2 spikes", - "rel_date": "2021-09-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.14.460264", - "rel_abs": "We use in silico modelling of the SARS-CoV-2 spike protein and its mutations, as deposited on the Protein Data Bank (PDB), to ascertain their dynamics, flexibility and rigidity. Identifying the precise nature of the dynamics for the spike proteins enables, in principle, the use of further in silico design methods to quickly screen for existing and novel drug molecules that might prohibit the natural protein dynamics. We employ a recent protein flexibility modeling approach, combining methods for deconstructing a protein structure into a network of rigid and flexible units with a method that explores the elastic modes of motion of this network, and a geometric modeling of flexible motion. Our results thus far indicate that the overall motion of wild-type and mutated spike protein structures remains largely the same.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "James Panayis", - "author_inst": "University of Warwick" - }, - { - "author_name": "Navodya Sophie Roemer", - "author_inst": "University of Lincoln" - }, - { - "author_name": "Dom Bellini", - "author_inst": "MRC Laboratory of Molecular Biology" - }, - { - "author_name": "Katrine Wallis", - "author_inst": "University of Warwick" - }, - { - "author_name": "Rudolf Andreas Roemer", - "author_inst": "University of Warwick" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.09.15.460487", "rel_title": "Synthetic Multiantigen MVA Vaccine COH04S1 Protects Against SARS-CoV-2 in Syrian Hamsters and Non-Human Primates", @@ -570023,6 +572387,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.12.21263373", + "rel_title": "Robust induction of B cell and T cell responses by a third dose of inactivated SARS-CoV-2 vaccine", + "rel_date": "2021-09-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.12.21263373", + "rel_abs": "SARS-CoV-2 inactivated vaccines have shown remarkable efficacy in clinical trials, especially in reducing severe illness and casualty. However, the waning of humoral immunity over time has raised concern over the durability of immune memory following vaccination. Thus, we conducted a non-randomized trial among the healthcare professionals (HCWs) to investigate the long-term sustainability of SARS-CoV-2-specific B cells and T cells stimulated by inactivated vaccines and the potential need for a third booster dose. Although neutralizing antibodies elicited by the standard two-dose vaccination schedule dropped from a peak of 29.3 AU/ml to 8.8 AU/ml 5 months after the second vaccination, spike-specific memory B and T cells were still detectable, forming the basis for a quick recall response. As expected, the faded humoral immune response was vigorously elevated to 63.6 AU/ml by 7.2 folds 1 week after the third dose along with abundant spike-specific circulating follicular helper T cells in parallel. Meanwhile, spike-specific CD4+ and CD8+ T cells were also robustly elevated by 5.9 and 2.7 folds respectively. Robust expansion of memory pools by the third dose potentiated greater durability of protective immune responses. Another key finding in this trial was that HCWs with low serological response to 2 doses were not truly \"non-responders\" but fully equipped with immune memory that could be quickly recalled by a third dose even 5 months after the second vaccination. Collectively, these data provide insights into the generation of long-term immunological memory by the inactivated vaccine, which could be rapidly recalled and further boosted by a third dose.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Yihao Liu", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Qin Zeng", + "author_inst": "First Affiliated Hospital, Sun Yat-sen University" + }, + { + "author_name": "Caiguanxi Deng", + "author_inst": "First Affiliated Hospital, Sun Yat-sen University" + }, + { + "author_name": "Mengyuan Li", + "author_inst": "First Affiliated Hospital, Sun Yat-sen University" + }, + { + "author_name": "Liubing Li", + "author_inst": "First Affiliated Hospital, Sun Yat-sen University" + }, + { + "author_name": "Dayue Liu", + "author_inst": "First Affiliated Hospital, Sun Yat-sen University" + }, + { + "author_name": "Ming Liu", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Xinyuan Ruan", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Jie Mei", + "author_inst": "First Affiliated Hospital, Sun Yat-sen University" + }, + { + "author_name": "Ruohui Mo", + "author_inst": "First Affiliated Hospital, Sun Yat-sen University" + }, + { + "author_name": "Qian Zhou", + "author_inst": "First Affiliated Hospital, Sun Yat-sen University" + }, + { + "author_name": "Min Liu", + "author_inst": "First Affiliated Hospital, Sun Yat-sen University" + }, + { + "author_name": "Sui Peng", + "author_inst": "First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Ji Wang", + "author_inst": "First Affiliated Hospital, Sun Yat-sen University" + }, + { + "author_name": "Hui Zhang", + "author_inst": "The First Affiliated Hospital, Sun Yat-sen University" + }, + { + "author_name": "Haipeng Xiao", + "author_inst": "First Affiliated Hospital, Sun Yat-sen University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.12.21263291", "rel_title": "Olfactory Bulb and Amygdala Gene Expression Changes in Subjects Dying with COVID-19", @@ -571195,97 +573638,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2021.09.09.21263049", - "rel_title": "Calibration of Two Validated SARS-CoV-2 Pseudovirus Neutralization Assays for COVID-19 Vaccine Evaluation", - "rel_date": "2021-09-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.09.21263049", - "rel_abs": "Vaccine-induced neutralizing antibodies (nAbs) are key biomarkers considered to be associated with vaccine efficacy. In United States Government-sponsored phase 3 efficacy trials of COVID-19 vaccines, nAbs are measured by two different validated pseudovirus-based SARS-CoV-2 neutralization assays, with each trial using one of the two assays. Here we describe and compare the nAb titers obtained in the two assays. We observe that one assay consistently yielded higher nAb titers than the other when both assays were performed on the World Health Organizations anti-SARS-CoV-2 immunoglobulin International Standard, COVID-19 convalescent sera, and mRNA-1273 vaccinee sera. To overcome the challenge this difference in readout poses in comparing/combining data from the two assays, we evaluate three calibration approaches and show that readouts from the two assays can be calibrated to a common scale. These results may aid decision-making based on data from these assays for the evaluation and licensure of new or adapted COVID-19 vaccines.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Yunda Huang", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Oleg Borisov", - "author_inst": "Biomedical Advanced Research and Development Authority" - }, - { - "author_name": "Jia Jin Kee", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Lindsay N. Carpp", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Terri Wrin", - "author_inst": "LabCorp-Monogram Biosciences" - }, - { - "author_name": "Suqin Cai", - "author_inst": "LabCorp-Monogram Biosciences" - }, - { - "author_name": "Marcella Sarzotti-Kelsoe", - "author_inst": "Duke University" - }, - { - "author_name": "Charlene McDanal", - "author_inst": "Duke University" - }, - { - "author_name": "Amanda Eaton", - "author_inst": "Duke University" - }, - { - "author_name": "Rolando Pajon", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "John Hural", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Christine M. Posavad", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Katherine Gill", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Shelly Karuna", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Lawrence Corey", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "M. Juliana McElrath", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Peter B. Gilbert", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Christos J. Petropoulos", - "author_inst": "LabCorp-Monogram Biosciences" - }, - { - "author_name": "David C. Montefiori", - "author_inst": "Duke University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.07.21262911", "rel_title": "The evolutionary landscape of SARS-CoV-2 variant B.1.1.519 and its clinical impact in Mexico City", @@ -572221,6 +574573,33 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.09.14.460211", + "rel_title": "Mitoxantrone dihydrochloride, an FDA approved drug, binds with SARS-CoV-2 NSP1 C-terminal", + "rel_date": "2021-09-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.14.460211", + "rel_abs": "One of the major virulence factors of SARS-CoV-2, NSP1, is a vital drug target due to its role in host immune evasion through multiple pathways. NSP1 protein is associated with inhibiting host mRNA translation by binding to the small subunit of ribosome through its C-terminal region. Previously, we have shown the structural dynamics of NSP1 C-terminal region (NSP1-CTR) in different physiological environments. So, it would be very interesting to investigate the druggable compounds that could bind with NSP1-CTR. Here, in this article, we have performed the different spectroscopic technique-based binding assays of an anticancer drug Mitoxantrone dihydrochloride (MTX) against the NSP1-CTR. We have also performed molecular docking followed by computational simulations with two different forcefields up to one microsecond. Overall, our results have suggested good binding between NSP1-CTR and MTX and may have implications in developing therapeutic strategies targeting NSP1 protein of SARS-CoV-2.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Prateek Kumar", + "author_inst": "Indian Institute of Technology Mandi" + }, + { + "author_name": "Taniya Bhardwaj", + "author_inst": "Indian Institute of Technology Mandi" + }, + { + "author_name": "Rajanish Giri", + "author_inst": "Indian Institute of Technology Mandi" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.09.08.21263296", "rel_title": "SARS-CoV-2 infection fatality rates in India: systematic review, meta-analysis and model-based estimation", @@ -573161,53 +575540,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rehabilitation medicine and physical therapy" }, - { - "rel_doi": "10.1101/2021.09.13.460054", - "rel_title": "The key features of SARS-CoV-2 leader and NSP1 required for viral escape of NSP1-mediated repression", - "rel_date": "2021-09-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.13.460054", - "rel_abs": "SARS-CoV-2, responsible for the ongoing global pandemic, must overcome a conundrum faced by all viruses. To achieve its own replication and spread, it simultaneously depends on and subverts cellular mechanisms. At the early stage of infection, SARS-CoV-2 expresses the viral nonstructural protein 1 (NSP1), which inhibits host translation by blocking the mRNA entry tunnel on the ribosome; this interferes with the binding of cellular mRNAs to the ribosome. Viral mRNAs, on the other hand, overcome this blockade. We show that NSP1 enhances expression of mRNAs containing the SARS-CoV-2 leader. The first stem-loop (SL1) in viral leader is both necessary and sufficient for this enhancement mechanism. Our analysis pinpoints specific residues within SL1 (three cytosine residues at the positions 15, 19 and 20) and another within NSP1 (R124) which are required for viral evasion, and thus might present promising drug targets. Additionally, we carried out analysis of a functional interactome of NSP1 using BioID and identified components of anti-viral defense pathways. Our analysis therefore suggests a mechanism by which NSP1 inhibits the expression of host genes while enhancing that of viral RNA. This analysis helps reconcile conflicting reports in the literature regarding the mechanisms by which the virus avoids NSP1 silencing.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Lucija Bujanic", - "author_inst": "Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrueck Center (MDC) for Molecular Medicine in the Helmholtz Association" - }, - { - "author_name": "Olga Shevchuk", - "author_inst": "Leibniz-Institut fuer Analytische Wissenschaften, ISAS, Dortmund, Germany" - }, - { - "author_name": "Nicolai von Kuegelgen", - "author_inst": "Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrueck Center (MDC) for Molecular Medicine in the Helmholtz Association" - }, - { - "author_name": "Katarzyna Ludwik", - "author_inst": "Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrueck Center (MDC) for Molecular Medicine in the Helmholtz Association" - }, - { - "author_name": "David Koppstein", - "author_inst": "Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrueck Center (MDC) for Molecular Medicine in the Helmholtz Association" - }, - { - "author_name": "Nadja Zerna", - "author_inst": "Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrueck Center (MDC) for Molecular Medicine in the Helmholtz Association" - }, - { - "author_name": "Albert Sickmann", - "author_inst": "Leibniz-Institut fuer Analytische Wissenschaften, ISAS, Dortmund, Germany" - }, - { - "author_name": "Marina Chekulaeva", - "author_inst": "Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrueck Center (MDC) for Molecular Medicine in the Helmholtz Association" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2021.09.13.460076", "rel_title": "Elicitation of potent SARS-CoV-2 neutralizing antibody responses through immunization using a versatile adenovirus-inspired multimerization platform", @@ -573951,6 +576283,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.09.08.21263310", + "rel_title": "Citizens' Attitudes Under Covid19: a cross-country panel survey of public opinion in 11 democracies", + "rel_date": "2021-09-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.08.21263310", + "rel_abs": "This article introduces data collected in the Citizens Attitudes Under Covid-19 Project (CAUCP), which surveyed public opinion throughout the Covid-19 pandemic in 11 countries between March to December 2020. In this paper, we present a unique cross-country panel survey of citizens attitudes and behaviors during a worldwide unprecedented health, governance, and economic crisis. This dataset allows to examine the behavioral and attitudinal consequences of crisis across time and contexts. In this paper, we describe the set-up of the CAUCP and the main features of the dataset and we present promising research prospects.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Brouard Sylvain", + "author_inst": "Sciences Po" + }, + { + "author_name": "Martial Foucault", + "author_inst": "Sciences Po" + }, + { + "author_name": "Elie Michel", + "author_inst": "Sciences Po" + }, + { + "author_name": "Michael Becher", + "author_inst": "School of Global and Public Affairs (IE University)" + }, + { + "author_name": "Pavlos Vasilopoulos", + "author_inst": "University of York" + }, + { + "author_name": "Pierre-Henri Bono", + "author_inst": "Sciences Po" + }, + { + "author_name": "Nicolas Sormani", + "author_inst": "Sciences Po" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.09.09.21262542", "rel_title": "Indirect effects of peaks in COVID admissions on access to surgery in the English NHS, differential effects by operation type, ethnicity and socio-economic status: a database study", @@ -574703,49 +577078,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.09.08.21263264", - "rel_title": "University of Texas at Arlington (UTA) in-house COVID-19 testing program", - "rel_date": "2021-09-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.08.21263264", - "rel_abs": "The pandemic caused by the spread of the virus SARS-CoV-2 threatened to severely disrupt the activities of student-athletes. (REF) In order to provide a safe environment for athletic competition, the National Collegiate Athletic Association (NCAA) mandated testing of student-athletes. The goal was to rapidly identify student-athletes and the athletic staff member who either tested positive for SARS-CoV-2 or were in contact with individuals who tested positive. Rapid identification of infected individuals and their contacts allowed the University to implement quarantine standards and quarantine facilities quickly as needed. The University of Texas at Arlington (UTA) developed an in-house testing program and was quickly able to meet the NCAA requirements, allowing UTA to continue its athletic participation with minimal forfeiture of scheduled games. The purpose of this paper is to report the implementation UTAs COVID prevention program for the universitys athletic program. This program will provide valuable information to other universities planning for the management of COVID prevention in their athletic programs. Challenges and solutions are identified.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Roy Rudwick", - "author_inst": "University of Texas at Arlington" - }, - { - "author_name": "Florence P Haseltine", - "author_inst": "University of Texas at Arlington" - }, - { - "author_name": "Anajane Gey Smith", - "author_inst": "University of Texas at Arlington" - }, - { - "author_name": "Necole Cox", - "author_inst": "University of Texas at Arlington" - }, - { - "author_name": "Angela Middleton", - "author_inst": "University of Texas at Arlington" - }, - { - "author_name": "Zibiao Guo", - "author_inst": "University of Texas at Arlington" - }, - { - "author_name": "Taylor Gunby", - "author_inst": "University of Texas at Arlington" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "sports medicine" - }, { "rel_doi": "10.1101/2021.09.07.21263244", "rel_title": "COVID-19 Outcomes in Patients with Cancer: Findings from the University of California Health System Database", @@ -575481,6 +577813,141 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.09.08.21263232", + "rel_title": "Determinants of early antibody responses to COVID-19 mRNA vaccines in exposed and naive healthcare workers", + "rel_date": "2021-09-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.08.21263232", + "rel_abs": "BackgroundTwo doses of mRNA vaccination have shown >94% efficacy at preventing COVID-19 mostly in naive adults, but it is not clear if the second dose is needed to maximize effectiveness in those previously exposed to SARS-CoV-2 and what other factors affect responsiveness.\n\nMethodsWe measured IgA, IgG and IgM levels against SARS-CoV-2 spike (S) and nucleocapsid (N) antigens from the wild-type and S from the Alpha, Beta and Gamma variants of concern, after BNT162b2 (Pfizer/BioNTech) or mRNA-1273 (Moderna) vaccination in a cohort of health care workers (N=578). Neutralizing capacity and antibody avidity were evaluated. Data were analyzed in relation to COVID-19 history, comorbidities, vaccine doses, brand and adverse events.\n\nFindingsVaccination induced robust IgA and IgG levels against all S antigens. Neutralization capacity and S IgA and IgG levels were higher in mRNA-1273 vaccinees, previously SARS-CoV-2 exposed, particularly if symptomatic, and in those experiencing systemic adverse effects. A second dose in pre-exposed did not increase antibody levels. Smoking and comorbidities were associated with lower neutralization and antibody levels. Among fully vaccinated, 6.3% breakthroughs were detected up to 189 days post-vaccination. Among pre-exposed non-vaccinated, 90% were IgG seropositive more than 300 days post-infection.\n\nInterpretationOur data support administering a single-dose in pre-exposed healthy individuals. However, heterogeneity of responses suggests that personalized recommendations may be necessary depending on COVID-19 history and life-style. Higher mRNA-1273 immunogenicity would be beneficial for those expected to respond worse to vaccination. Persistence of antibody levels in pre-exposed unvaccinated indicates maintenance of immunity up to one year.\n\nFundingThis work was supported by Institut de Salut Global de Barcelona (ISGlobal) internal funds, in-kind contributions from Hospital Clinic de Barcelona, the Fundacio Privada Daniel Bravo Andreu, and European Institute of Innovation and Technology (EIT) Health (grant number 20877), supported by the European Institute of Innovation and Technology, a body of the European Union receiving support from the H2020 Research and Innovation Programme. We acknowledge support from the Spanish Ministry of Science and Innovation and State Research Agency through the \"Centro de Excelencia Severo Ochoa 2019-2023\" Program (CEX2018-000806-S), and support from the Generalitat de Catalunya through the CERCA Program. L. I. work was supported by PID2019-110810RB-I00 grant from the Spanish Ministry of Science & Innovation. Development of SARS-CoV-2 reagents was partially supported by the National Institute of Allergy and Infectious Diseases Centers of Excellence for Influenza Research and Surveillance (contract number HHSN272201400008C). The funders had no role in study design, data collection and analysis, the decision to publish, or the preparation of the manuscript.", + "rel_num_authors": 30, + "rel_authors": [ + { + "author_name": "Gemma Moncunill", + "author_inst": "ISGlobal" + }, + { + "author_name": "Ruth Aguilar", + "author_inst": "ISGlobal" + }, + { + "author_name": "Marta Ribes", + "author_inst": "ISGlobal" + }, + { + "author_name": "Natalia Ortega", + "author_inst": "ISGlobal" + }, + { + "author_name": "Roc\u00edo Rubio", + "author_inst": "ISGlobal" + }, + { + "author_name": "Gemma Salmeron", + "author_inst": "Hospital Clinic de Barcelona" + }, + { + "author_name": "Mar\u00eda Jos\u00e9 Molina", + "author_inst": "ISGlobal" + }, + { + "author_name": "Marta Vidal", + "author_inst": "ISGlobal" + }, + { + "author_name": "Diana Barrios", + "author_inst": "ISGlobal" + }, + { + "author_name": "Robert A. Mitchell", + "author_inst": "ISGlobal" + }, + { + "author_name": "Alfons Jimenez", + "author_inst": "ISGlobal" + }, + { + "author_name": "Cristina Castellana", + "author_inst": "ISGlobal" + }, + { + "author_name": "Pablo Hern\u00e1ndez-Luis", + "author_inst": "Universitat de Barcelona" + }, + { + "author_name": "Pau Rodo", + "author_inst": "ISGlobal" + }, + { + "author_name": "Susana M\u00e9ndez", + "author_inst": "ISGlobal" + }, + { + "author_name": "Anna Llupi\u00e1", + "author_inst": "ISGlobal" + }, + { + "author_name": "Laura Puyol", + "author_inst": "ISGlobal" + }, + { + "author_name": "Natalia Rodrigo Melero", + "author_inst": "CRG" + }, + { + "author_name": "Carlo Carolis", + "author_inst": "CRG" + }, + { + "author_name": "Alfredo Mayor", + "author_inst": "ISGlobal" + }, + { + "author_name": "Luis Izquierdo", + "author_inst": "ISGlobal" + }, + { + "author_name": "Pilar Varela", + "author_inst": "Hospital Clinic de Barcelona" + }, + { + "author_name": "Antoni Trilla", + "author_inst": "Hospital Clinic de Barcelona" + }, + { + "author_name": "Anna Vilella", + "author_inst": "Hospital Clinic de Barcelona" + }, + { + "author_name": "Sonia Barroso", + "author_inst": "Hospital Clinic de Barcelona" + }, + { + "author_name": "Ana Angulo", + "author_inst": "Universitat de Barcelona" + }, + { + "author_name": "Pablo Engel", + "author_inst": "Universitat de Barcelona" + }, + { + "author_name": "Marta Tortajada", + "author_inst": "Hospital Clinic de Barcelona" + }, + { + "author_name": "Alberto L. Garc\u00eda-Basteiro", + "author_inst": "ISGlobal" + }, + { + "author_name": "Carlota Doba\u00f1o", + "author_inst": "ISGlobal" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.08.21263027", "rel_title": "Autoantibodies against IL-1-receptor-antagonist in multisystem inflammatory syndrome in children", @@ -576773,57 +579240,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.09.10.459410", - "rel_title": "Pharmacological perturbation of intracellular dynamics as a SARS-CoV-2 antiviral strategy", - "rel_date": "2021-09-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.10.459410", - "rel_abs": "SARS-CoV-2 (CoV2) is the viral agent responsible for the pandemic of the coronavirus disease 2019 (COVID-19). Vaccines are being deployed all over the world with good efficacy, but there is no approved antiviral treatment to date. This is particularly needed since the emergence of variants and the potential immune escape may prolong pandemic spreading of the infection for much longer than anticipated. Here, we developed a series of small molecules and identified RG10 as a potent antiviral compound against SARS-CoV-2 in cell lines and human airway epithelia (HAE). RG10 localizes to endoplasmic reticulum (ER) membranes, perturbing ER morphology and inducing ER stress. Yet, RG10 does not associate with SARS-CoV-2 replication sites although preventing virus replication. To further investigate the antiviral properties of our compound, we developed fluorescent SARS-CoV-2 viral particles allowing us to track virus arrival to ER membranes. Live cell imaging of replication-competent virus infection revealed that RG10 stalls the intracellular virus-ER dynamics. Finally, we synthesized RG10b, a stable version of RG10, that showed increased potency in vitro and in HAE with a pharmacokinetic half-life greater than 2 h. Together, our work reports on a novel fluorescent virus model and innovative antiviral strategy consisting of the perturbation of ER/virus dynamics, highlighting the promising antiviral properties of RG10 and RG10b.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "William Bakhache", - "author_inst": "CNRS" - }, - { - "author_name": "Emma Partiot", - "author_inst": "CNRS" - }, - { - "author_name": "Vincent Lucansky", - "author_inst": "Comenius University in Bratislava, the Jessenius Faculty of Medicine in Martin (JFMED CU), Biomedical Center Martin" - }, - { - "author_name": "Yonis Bare", - "author_inst": "CNRS" - }, - { - "author_name": "Boris Bonaventure", - "author_inst": "CNRS" - }, - { - "author_name": "Caroline Goujon", - "author_inst": "CNRS, Montpellier university" - }, - { - "author_name": "Cedric Bories", - "author_inst": "AGV discovery" - }, - { - "author_name": "Maika S Deffieu", - "author_inst": "CNRS" - }, - { - "author_name": "Raphael Gaudin", - "author_inst": "CNRS" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.09.10.459744", "rel_title": "Clinical grade ACE2 as a universal agent to block SARS-CoV-2 variants", @@ -577831,6 +580247,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.05.21262678", + "rel_title": "Epidemiological, clinical Characteristics and mortality of patients Infected with SARS-CoV-2 Admitted of Kinshasa University Hospital, Democratic Republic of the Congo from March 24, 2020 to January 30, 2021: Two waves, two faces?", + "rel_date": "2021-09-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.05.21262678", + "rel_abs": "BackgroundThe objective of our retrospective study was to establish a comparison between the first and the second waves of demographic and clinical characteristics as well as mortality and its determinants.\n\nMethodsA total of 411 COVID-19 patients were enrolled in Kinshasa University Hospital and categorized into two groups according to the pandemic pattern, demographics, and disease severity. The clinical characteristics were compared according to the two waves. To describe survival from the first day of hospitalization until death, we used Kaplan Meiers method. We used the Log Rank test to compare the survival curves between the two waves. The Cox regression was used to identify independent predictors of mortality.\n\nResultsDuring the study period, 411 patients with confirmed COVID-19 were admitted to the hospital. The average age of patients in the 2nd wave was higher than in the first wave (52.4 {+/-}17.5 vs 58.1 {+/-}15.7, p=0.026). The mean saturation was lower in the first wave than in the second. The death rate of patients in the first wave was higher than in the second wave (p=0.009). Survival was reduced in the first wave compared to the second wave. In the first wave, age over 60 years, respiratory distress, law oxygen saturation ([≤]89%) and severe stage of COVID-19 emerged as factors associated with death, while in the second wave it was mainly respiratory distress, law oxygen saturation ([≤] 89%) and severe stage. The predictors of mortality present in both the first and second waves were respiratory distress and severe COVID-19 stage.\n\nConclusionMortality decreased in the second wave. Age no longer emerged as a factor in mortality in the second wave. Health system strengthening and outreach to those at high risk of mortality should continue to maintain and improve gains.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Madone Mandina", + "author_inst": "1.\tKinshasa University Hospital, Faculty of Medicine, University of Kinshasa, DRC" + }, + { + "author_name": "jean robert Makulo", + "author_inst": "1.\tKinshasa University Hospital, Faculty of Medicine, University of Kinshasa, DRC" + }, + { + "author_name": "Roger Wumba", + "author_inst": "1.\tKinshasa University Hospital, Faculty of Medicine, University of Kinshasa, DRC" + }, + { + "author_name": "Ben Bepouka", + "author_inst": "1.\tKinshasa University Hospital, Faculty of Medicine, University of Kinshasa, DRC" + }, + { + "author_name": "jerome odio", + "author_inst": "1. Kinshasa University Hospital, Faculty of Medicine, University of Kinshasa, DRC" + }, + { + "author_name": "Aliocha Nkodila", + "author_inst": "2.\tUnit of Vaccinology, World Health Organization, Kinshasa, Democratic Republic of the Congo" + }, + { + "author_name": "Murielle Longokolo", + "author_inst": "1.\tKinshasa University Hospital, Faculty of Medicine, University of Kinshasa, DRC" + }, + { + "author_name": "Nadine Mayasi", + "author_inst": "1.\tKinshasa University Hospital, Faculty of Medicine, University of Kinshasa, DRC" + }, + { + "author_name": "Donatien Mangala", + "author_inst": "1.\tKinshasa University Hospital, Faculty of Medicine, University of Kinshasa, DRC" + }, + { + "author_name": "Guyguy Kamwiziku", + "author_inst": "1.\tKinshasa University Hospital, Faculty of Medicine, University of Kinshasa, DRC" + }, + { + "author_name": "Augustin Luzayadio Longo", + "author_inst": "1.\tKinshasa University Hospital, Faculty of Medicine, University of Kinshasa, DRC" + }, + { + "author_name": "Guillome Mpia", + "author_inst": "1.\tKinshasa University Hospital, Faculty of Medicine, University of Kinshasa, DRC" + }, + { + "author_name": "Yamine Kokusa", + "author_inst": "1.\tKinshasa University Hospital, Faculty of Medicine, University of Kinshasa, DRC" + }, + { + "author_name": "Herve Keke", + "author_inst": "1.\tKinshasa University Hospital, Faculty of Medicine, University of Kinshasa, DRC" + }, + { + "author_name": "Marcel Mbula", + "author_inst": "1.\tKinshasa University Hospital, Faculty of Medicine, University of Kinshasa, DRC" + }, + { + "author_name": "Hippolyte Situakibanza", + "author_inst": "1.\tKinshasa University Hospital, Faculty of Medicine, University of Kinshasa, DRC" + }, + { + "author_name": "Ernest Sumaili", + "author_inst": "1.\tKinshasa University Hospital, Faculty of Medicine, University of Kinshasa, DRC" + }, + { + "author_name": "Jean Marie Kayembe", + "author_inst": "3.\tTechnical Secretariat of the Multisectoral Committee for the Response to Covid-19, DRC" + } + ], + "version": "1", + "license": "cc0_ng", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.04.21262907", "rel_title": "Perceptions towards mask use in school children during the SARS-CoV-2 pandemic: the Ciao Corona Study", @@ -578935,93 +581438,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.03.21263091", - "rel_title": "Greater Covid-19 Severity and Mortality in Hospitalized Patients in Second (Delta Variant) Wave Compared to the First: Single Centre Prospective Study in India", - "rel_date": "2021-09-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.03.21263091", - "rel_abs": "Background & ObjectiveCovid-19 pandemic has led to multiple waves secondary to mutations in SARS-CoV-2 and emergence of variants of concern (VOC). Clinical characteristics of delta (B.1.617.2) VOC are not well reported. To compare demographic, clinical and laboratory features and outcomes in the second Covid-19 wave in India (delta VOC) with the previous wave we performed a registry-based study.\n\nMethodsSuccessive SARS-CoV-2 reverse transcriptase-polymerase chain reaction (RT-PCR) confirmed Covid-19 patients presenting to our Advanced Covid Care hospital were prospectively recruited. In the first phase (wave) from March-December 2020, 1395 of 7476 (18.7%) suspected patients tested positive and 863 (61.89%) hospitalized, while in second wave from January-July 2021 out of 1641 confirmed cases out of 8680 (19.4%) suspected 388 (23.6%) were hospitalized. Details of clinical and laboratory features at admission to hospital, management and outcomes in the two waves have been compared.\n\nResultsIn both cohorts, majority were men and 20% less than 40 years. Prevalence of hypertension, diabetes and cardiovascular diseases was more than 20%. Second wave patients had similar pre-hospitalization symptom duration but had significantly greater cough, fever and shortness of breath and lower SpO2 at presentation with greater lymphopenia, C-reactive proteins, interleukin-6, ferritin, lactic dehydrogenase and transaminases. In the second vs first wave patients, requirement of supplementary oxygen (47.9% vs 34.3%), prone positioning (89.2 vs 38.6%), high flow nasal oxygen(15.7 vs 9.1%), non-invasive ventilation (14.4 vs 9.5%), invasive ventilation (16.2 vs 9.5%), steroids (94.1 vs 85.9%), remdesivir (91.2 vs 76.0%) and anticoagulants (94.3 vs 76.0%) was greater (p<0.001). Median (IQR) length of stay [8 (6-10) vs 7 (5-10) days] as well as ICU stay [9 (5-13) vs 6 (2-10) days] was more in second wave (p<0.001). In-hospital deaths occurred in 173 patients (13.9%) and were significantly more in the second wave, 75 (19.3%), compared to the first, 98 (11.5%); unadjusted odds ratio (95% CI) 1.84 (1.32-2.55) which did not change significantly with adjustment for age and sex (2.03, 1.44-2.86), and age, sex and comorbidities (2.09, 1.47-2.95). Greater disease severity at presentation was associated with mortality in both the waves.\n\nConclusionsCovid-19 patients hospitalized during the second wave of the epidemic (delta variant) had more severe disease with greater dyspnea, hypoxia, hematological and biochemical abnormalities compared to first wave patients. They had greater length of stay in intensive care unit, oxygen requirement, non-invasive and invasive ventilatory support. The in-hospital mortality in the second wave was double of the first.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Raghubir S Khedar", - "author_inst": "Eternal Heart Care Centre & Research Institute, Jaipur, India" - }, - { - "author_name": "Kartik Mittal", - "author_inst": "Eternal Heart Care Centre & Research Institute, Jaipur, India" - }, - { - "author_name": "Harshad C Ambaliya", - "author_inst": "Eternal Heart Care Centre & Research Institute, Jaipur, India" - }, - { - "author_name": "Alok Mathur", - "author_inst": "Eternal Heart Care Centre & Research Institute, Jaipur, India" - }, - { - "author_name": "Jugal B Gupta", - "author_inst": "Eternal Heart Care Centre & Research Institute, Jaipur, India" - }, - { - "author_name": "Krishna K Sharma", - "author_inst": "Eternal Heart Care Centre & Research Institute, Jaipur, India" - }, - { - "author_name": "Yogendra Singh", - "author_inst": "Eternal Heart CAre Centre & Research Institute, Jaipur, India" - }, - { - "author_name": "Gunjan Sharma", - "author_inst": "Eternal Heart Care Centre & Research Institute, Jaipur, India" - }, - { - "author_name": "Akhil Gupta", - "author_inst": "Eternal Heart Care Centre & Research Institute, Jaipur, India" - }, - { - "author_name": "Vaibhav Bhargava", - "author_inst": "Eternal Heart Care Centre & Research Institute, Jaipur, India" - }, - { - "author_name": "Kishore Mangal", - "author_inst": "Eternal Heart Care Centre & Research Institute, Jaipur, India" - }, - { - "author_name": "Anil K Sharma", - "author_inst": "Eternal Heart Care Centre & Research Institute, Jaipur, India" - }, - { - "author_name": "Yatendra K Gupta", - "author_inst": "Eternal Heart Care Centre & Research Institute, Jaipur, India" - }, - { - "author_name": "Pramod Sarwa", - "author_inst": "Eternal Heart Care Centre & Research Institute, Jaipur, India" - }, - { - "author_name": "Bhawani S Mishra", - "author_inst": "Eternal Heart Care Centre & Research Institute, Jaipur, India" - }, - { - "author_name": "Swati Sharma", - "author_inst": "Eternal Heart Care Centre ,& Research Institute, Jaipur, India" - }, - { - "author_name": "Krishnakumar Sharma", - "author_inst": "LBS College of Pharmacy, Rajasthan University of Health Sciences, Jaipur, India" - }, - { - "author_name": "Rajeev Gupta", - "author_inst": "Eternal Heart Care Centre & Research Institute, Jaipur, India & Rajasthan University of Health Sciences, Jaipur, India" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.03.21263078", "rel_title": "Development and validation of an enzyme immunoassay for detection and quantification of SARS-CoV-2 salivary IgA and IgG", @@ -579825,6 +582241,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.06.459196", + "rel_title": "Both Simulation and Sequencing Data Reveal Multiple SARS-CoV-2 Variants Coinfection in COVID-19 Pandemic", + "rel_date": "2021-09-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.06.459196", + "rel_abs": "SARS-CoV-2 is a single-stranded RNA betacoronavirus with a high mutation rate. The rapidly emerged SARS-CoV-2 variants could increase the transmissibility, aggravate the severity, and even fade the vaccine protection. Although the coinfections of SARS-CoV-2 with other respiratory pathogens have been reported, whether multiple SARS-CoV-2 variants coinfection exists remains controversial. This study collected 12,986 and 4,113 SARS-CoV-2 genomes from the GISAID database on May 11, 2020 (GISAID20May11) and April 1, 2021 (GISAID21Apr1), respectively. With the single-nucleotide variants (SNV) and network clique analysis, we constructed the single-nucleotide polymorphism (SNP) coexistence networks and noted the SNP number of the maximal clique as the coinfection index. The coinfection indices of GISAID20May11 and GISAID21Apr1 datasets were 16 and 34, respectively. Simulating the transmission routes and the mutation accumulations, we discovered the linear relationship between the coinfection index and the coinfected variant number. Based on the linear relationship, we deduced that the COVID-19 cases in the GISAID20May11 and GISAID21Apr1 datasets were coinfected with 2.20 and 3.42 SARS-CoV-2 variants on average. Additionally, we performed Nanopore sequencing on 42 COVID-19 patients to explore the virus mutational characteristics. We found the heterozygous SNPs in 41 COVID-19 cases, which support the coinfection of SARS-CoV-2 variants and challenge the accuracy of phylogenetic analysis. In conclusion, our findings reported the coinfection of SARS-CoV-2 variants in COVID-19 patients, demonstrated the increased coinfected variants number in the epidemic, and provided clues for the prolonged viral shedding and severe symptoms in some cases.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Yinhu Li", + "author_inst": "City University of Hong Kong" + }, + { + "author_name": "Yiqi Jiang", + "author_inst": "City University of Hong Kong" + }, + { + "author_name": "Zhengtu Li", + "author_inst": "The First Affiliated Hospital of Guangzhou Medical University" + }, + { + "author_name": "Yonghan Yu", + "author_inst": "City University of Hong Kong" + }, + { + "author_name": "Jiaxing Chen", + "author_inst": "City University of Hong Kong" + }, + { + "author_name": "Wenlong Jia", + "author_inst": "City University of Hong Kong" + }, + { + "author_name": "Yen Kaow Ng", + "author_inst": "Universiti Tunku Abdul Rahman" + }, + { + "author_name": "Feng Ye", + "author_inst": "The First Affiliated Hospital of Guangzhou Medical University" + }, + { + "author_name": "Bairong Shen", + "author_inst": "West China Hospital, Sichuan University" + }, + { + "author_name": "Shuai Cheng Li", + "author_inst": "City University of Hong Kong" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.09.04.21263115", "rel_title": "Durability analysis of the highly effective BNT162b2 vaccine against COVID-19", @@ -580593,45 +583064,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.03.21263064", - "rel_title": "UTTARAKHAND COVID-19 CASES AND DEATHS: COMPARING THE DEMOGRAPHICS AND SUGGESTIVE STRATEGY TO PREVENT SIMILAR PANDEMICS IN FUTURE", - "rel_date": "2021-09-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.03.21263064", - "rel_abs": "Coronavirus disease 19 (Covid-19) is causing a dramatic impact on human life worldwide. As of June 11 2021, later one has attributed more than 174 million confirmed cases and over 3.5 million deaths globally. Nonetheless, a World Bank Group flagship report features Covid-19 induced global crisis as the strongest post-recession since World WarII. Currently, all approved therapeutics or vaccines are strictly allowed for emergency use. Hence, in the absence of pharmaceutical interventions, it is vital to analyze data set covering the growth rates of positive human cases, number of recoveries, other factors, and future strategies to manage the growth of fatal Covid-19 effectively. The Uttarakhand state of India is snuggled in the lap of the Himalayas and occupies more people than Israel, Switzerland, Hong Kong, etc. This study analyzed state Covid-19 data, fetched from an authenticated government repository using Python 3.9 from April 1, 2020, to February 28, 2021. In the first wave, plain areas of Uttarakhand covering the districts Dehradun, Haridwar, Nainital, and U. S. Nagar were severely affected and reported peak positive cases during the 21st - 26th week. Other hands, the hilly terrains of Uttarakhand districts, including Chamoli, Pauri Garhwal, and Rudraprayag, reported a high number of positive cases between the 30th and 31st week, and other hilly districts reported an increase in Covid-19 cases during the 34th to 38th week. The highest recovery rate was attributed to the hilly district Rudraprayag. The analysis also revealed that a very high doubling rate was seen during the last week of May to the first week of Jun 2020. At last, based on this blueprint, we have suggested 6-points solutions for preventing the next pandemic.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Gaurav Joshi", - "author_inst": "Graphic Era Hill University" - }, - { - "author_name": "Akshara Pande", - "author_inst": "Graphic Era Hill University" - }, - { - "author_name": "Omdeep Gupta", - "author_inst": "Graphic Era Hill University" - }, - { - "author_name": "Anoop Nautiyal", - "author_inst": "SDC Foundation Dehradun" - }, - { - "author_name": "Sanjay Jasola", - "author_inst": "Graphic Era Hill University" - }, - { - "author_name": "Prashant Gahtori", - "author_inst": "Graphic Era Hill University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.02.21262995", "rel_title": "A semi-parametric, state-space compartmental model with time-dependent parameters for forecasting COVID-19 cases, hospitalizations, and deaths", @@ -581331,6 +583763,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.08.25.21262155", + "rel_title": "How Informative were Early SARS-CoV-2 Treatment and Prevention Trials? A longitudinal cohort analysis of trials registered on clinicaltrials.gov", + "rel_date": "2021-09-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.25.21262155", + "rel_abs": "BackgroundEarly in the SARS-CoV-2 pandemic, commentators warned that some COVID trials were inadequately conceived, designed and reported. Here, we retrospectively assess the prevalence of informative COVID trials launched in the first 6 months of the pandemic.\n\nMethodsWe created a cohort of SARS-CoV-2 treatment and prevention efficacy trials that were initiated from 2020-01-01 to 2020-06-30 using ClinicalTrials.gov registration records. We evaluated trials on 3 criteria of informativeness: potential redundancy, design quality and feasibility of patient-participant recruitment. The study protocol was prospectively registered with the Open Science Framework (https://osf.io/fp726/).\n\nResultsWe included 500 trials in our cohort, 58% of which were Phase 2 and 84.8% were directed towards the treatment of SARS-CoV-2. Close to one third of trials met all three criteria and were deemed informative (29.9% (95% Confidence Interval 23.7 - 36.9)). The proportion of potentially redundant trials in our cohort was 4.1%. Over half of the trials in our cohort (56.2%) did not meet our criteria for high quality trial design. The proportion of trials with infeasible patient-participant recruitment was 22.6%.\n\nConclusionsLess than one third of COVID-19 trials registered on ClinicalTrials.gov during the first six months met all three criteria for informativeness. Shortcomings in trial design, recruitment feasibility and redundancy reflect longstanding weaknesses in the clinical research enterprise that were likely amplified by the exceptional circumstances of a pandemic.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Nora Hutchinson", + "author_inst": "Studies of Translation, Ethics, and Medicine (STREAM), Biomedical Ethics Unit, McGill University, Montreal, Quebec, Canada" + }, + { + "author_name": "Katarzyna Klas", + "author_inst": "Research Ethics in Medicine Study Group (REMEDY), Faculty of Health Sciences, Jagiellonian University Medical College, Krakow, Poland" + }, + { + "author_name": "Benjamin Gregory Carlisle", + "author_inst": "Berlin Institute of Health at Charite (BIH), BIH QUEST Center for Transforming Biomedical Research, Berlin, Germany" + }, + { + "author_name": "Jonathan Kimmelman", + "author_inst": "Studies of Translation, Ethics, and Medicine (STREAM), Biomedical Ethics Unit, McGill University, Montreal, Quebec, Canada" + }, + { + "author_name": "Marcin Waligora", + "author_inst": "Research Ethics in Medicine Study Group (REMEDY), Faculty of Health Sciences, Jagiellonian University Medical College, Krakow, Poland" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "medical ethics" + }, { "rel_doi": "10.1101/2021.09.02.21263019", "rel_title": "The association between SARS-CoV-2 infection and neuronal damage: A population-based nested case-control study", @@ -582163,33 +584630,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.30.21262851", - "rel_title": "Tracking Covid-19 Cases and Deaths in the United States Distribution of Events by Day of Pandemic", - "rel_date": "2021-09-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.30.21262851", - "rel_abs": "In this paper, we analyze the progression of COVID-19 in the United States over a nearly one-year period beginning March 1, 2020, with a novel metric representing the partial-average day-of-event, where events are new cases and new deaths. The metric is calculated as a function of date and location to illustrate patterns of disease, showing growing or waning cases and deaths. The metrics enable the direct comparison of the time distribution of cases and deaths, revealing data coherence and how patterns varied over a one-year period. We also compare different methods of estimating actual infections and deaths to better understand on the timing and dynamics of the pandemic by state. We used three example states to graphically compare metrics as functions of date and also compared statistics derived from all 50 states. Over the period studied, average case day and average death day vary by two to five months among the 50 states, depending on data source, with the earliest averages in New York and surrounding states, as well as Louisiana. The average day of death has preceded the average day of case in Centers for Disease Control (CDC) data for most states and most dates since June of 2020. In contrast, \"COVID-19 Projections\" more closely align deaths and cases, which are similarly distributed.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Andrew Moore", - "author_inst": "University of Southern California" - }, - { - "author_name": "Mingdong Lyu", - "author_inst": "University of Southern California" - }, - { - "author_name": "Randolph Hall", - "author_inst": "University of Southern California" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.09.01.21262696", "rel_title": "The COVID-19 pandemic and ophthalmic care: a qualitative study of patients with neovascular age-related macular degeneration (nAMD)", @@ -583053,6 +585493,53 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.08.30.21262875", + "rel_title": "Early versus late third trimester maternal SARS-CoV-2 BNT162b2 mRNA immunization maximizes transplacental antibody transfer and neonatal neutralizing antibody levels", + "rel_date": "2021-09-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.30.21262875", + "rel_abs": "ObjectiveWe aimed to assess the impact of early versus late third trimester maternal SARS-CoV-2 vaccination on transplacental transfer and neonatal levels of SARS-CoV-2 antibodies.\n\nMethodsMaternal and cord blood sera were collected following term delivery after antenatal SARS-CoV-2 BNT162b2 mRNA vaccination, with the first vaccine dose administered during 27-36 weeks gestation. SARS-CoV-2 spike protein (S) and receptor binding domain (RBD)- specific, IgG levels and neutralizing potency were evaluated in maternal and cord blood samples.\n\nResultsThe study cohort consisted of 171 parturients (median age, 31 years; median gestational age, 39.7 weeks): 83 (48.5%) immunized at early 3rd trimester (1st dose at 27-31 weeks), and 88 (51.5%) immunized at late 3rd trimester (1st dose at 32-36 weeks). All mother-infant paired sera were positive for anti S- and anti-RBD-specific IgG. Anti-RBD-specific IgG concentrations in neonatal sera were higher following early versus late 3rd trimester vaccination and were positively correlated with increasing time since vaccination (r={square}0.26; P=0.001). The median placental transfer ratios of anti-S and anti-RBD specific IgG were increased following early versus late 3rd trimester immunization (anti-S ratio:1.3 vs. 0.9, anti-RBD-specific ratio:2.3 vs. 0.7, P<0.001). Neutralizing antibodies placental transfer ratio was greater following early versus late 3rd trimester immunization (1.9 vs. 0.8, P<0.001), and was positively associated with longer duration from vaccination (r={square}0.77; P<0.001).\n\nConclusionsEarly- as compared to late third trimester maternal SARS-CoV-2 immunization enhanced transplacental antibody transfer and increased neonatal neutralizing antibody levels. Our findings highlight that vaccination of pregnant women early in the third trimester may optimize neonatal seroprotection.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Amihai Rottenstreich", + "author_inst": "Hadassah Medical Center" + }, + { + "author_name": "Gila Zarbiv", + "author_inst": "Hadassah Medical Center" + }, + { + "author_name": "Esther Oiknine-Djian", + "author_inst": "Hadassah Medical Center" + }, + { + "author_name": "Olesya Vorontsov", + "author_inst": "Hadassah Medical Center" + }, + { + "author_name": "Roy Zigron", + "author_inst": "Hadassah Medical Center" + }, + { + "author_name": "Geffen Kleinstern", + "author_inst": "University of Haifa" + }, + { + "author_name": "Dana Wolf", + "author_inst": "Hadassah Medical Center" + }, + { + "author_name": "Shay Porat", + "author_inst": "Hadassah Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.28.21262692", "rel_title": "Pharmacokinetic /Pharmacodynamic Considerations of Alternate Dosing Strategies of Tocilizumab in COVID-19", @@ -584133,41 +586620,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.31.21262943", - "rel_title": "Ensemble forecast of COVID-19 in Karnataka for vulnerability assessment and policy interventions", - "rel_date": "2021-09-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.31.21262943", - "rel_abs": "We present an ensemble forecast for Wave-3 of COVID-19 in the state of Karnataka, India, using the IISc Population Balance Model for infectious disease spread. The reported data of confirmed, recovered, and deceased cases in Karnataka from 1 July 2020 to 4 July 2021 is utilized to tune the models parameters, and an ensemble forecast is done from 5 July 2021 to 30 June 2022. The ensemble is built with 972 members by varying seven critical parameters that quantify the uncertainty in the spread dynamics (antibody waning, viral mutation) and interventions (pharmaceutical, non-pharmaceutical). The probability of Wave-3, the peak date distribution, and the peak caseload distribution are estimated from the ensemble forecast. Our analysis shows that the most significant causal factors are compliance to Covid-appropriate behavior, daily vaccination rate, and the immune escape new variant emergence-time. These causal factors determine when and how severe the Wave-3 of COVID-19 would be in Karnataka. We observe that when compliance to Covid-Appropriate Behavior is good (i.e., lockdown-like compliance), the emergence of new immune-escape variants beyond Sep 21 is unlikely to induce a new wave. A new wave is inevitable when compliance to Covid-Appropriate Behavior is only partial. Increasing the daily vaccination rates reduces the peak active caseload at Wave-3. Consequently, the hospitalization, ICU, and Oxygen requirements also decrease. Compared to Wave-2, the ensemble forecast indicates that the number of daily confirmed cases of children (0-17 years) at Wave-3s peak could be seven times more on average. Our results provide insights to plan science-informed policy interventions and public health response.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Sashikumaar Ganesan", - "author_inst": "Indian Institute of Science" - }, - { - "author_name": "Deepak Subramani", - "author_inst": "Indian Institute of Science" - }, - { - "author_name": "Thivin Anandh", - "author_inst": "Indian Institute of Science" - }, - { - "author_name": "Divij Ghose", - "author_inst": "Indian Institute of Science" - }, - { - "author_name": "Giridhara R Babu", - "author_inst": "Indian Institute of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.09.02.458740", "rel_title": "Distinct neutralizing kinetics and magnitudes elicited by different SARS-CoV-2 variant spikes", @@ -585183,6 +587635,65 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.09.01.458544", + "rel_title": "The SARS-CoV-2 spike (S) and the orthoreovirus p15 cause neuronal and glial fusion", + "rel_date": "2021-09-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.01.458544", + "rel_abs": "Numerous enveloped viruses use specialized surface molecules called fusogens to enter host cells1. During virus replication, these fusogens decorate the host cells membrane enabling them the ability to fuse with neighboring cells, forming syncytia that the viruses use to propagate while evading the immune system. Many of these viruses, including the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), infect the brain and may cause serious neurological symptoms through mechanisms which remain poorly understood2-4. Here we show that expression of either the SARS-CoV-2 spike (S) protein or p15 protein from the baboon orthoreovirus is sufficient to induce fusion between interconnected neurons, as well as between neurons and glial cells. This phenomenon is observed across species, from nematodes to mammals, including human embryonic stem cells-derived neurons and brain organoids. We show that fusion events are progressive, can occur between distant neurites, and lead to the formation of multicellular syncytia. Finally, we reveal that in addition to intracellular molecules, fusion events allow diffusion and movement of large organelles such as mitochondria between fused neurons. Our results provide important mechanistic insights into how SARS-CoV-2 and other viruses could affect the nervous system circuitries causing neurological symptoms.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Ramon Martinez-Marmol", + "author_inst": "Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Australia" + }, + { + "author_name": "Rosina Giordano-Santini", + "author_inst": "Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Australia" + }, + { + "author_name": "Eva Kaulich", + "author_inst": "Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Australia" + }, + { + "author_name": "Ann-Na Cho", + "author_inst": "Dementia Research Centre, Department of Biomedical Sciences, Faculty of Medicine Health and Human Sciences, Macquarie University, Sydney, Australia." + }, + { + "author_name": "Md Asrafuzzaman Riyadh", + "author_inst": "Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Australia" + }, + { + "author_name": "Emilija Robinson", + "author_inst": "Dementia Research Centre, Department of Biomedical Sciences, Faculty of Medicine Health and Human Sciences, Macquarie University, Sydney, Australia" + }, + { + "author_name": "Giuseppe Balistreri", + "author_inst": "Faculty of Biological and Environmental Sciences, Molecular and Integrative Biosciences Research Program, University of Helsinki, Helsinki, Finland" + }, + { + "author_name": "Frederic A Meunier", + "author_inst": "Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Australia" + }, + { + "author_name": "Yazi D. Ke", + "author_inst": "Dementia Research Centre, Department of Biomedical Sciences, Faculty of Medicine Health and Human Sciences, Macquarie University, Sydney, Australia" + }, + { + "author_name": "Lars M Ittner", + "author_inst": "Dementia Research Centre, Department of Biomedical Sciences, Faculty of Medicine Health and Human Sciences, Macquarie University, Sydney, Australia" + }, + { + "author_name": "Massimo A Hilliard", + "author_inst": "Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Australia." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "neuroscience" + }, { "rel_doi": "10.1101/2021.09.01.457774", "rel_title": "Mapping interindividual dynamics of innate immune response at single-cell resolution", @@ -585991,73 +588502,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rheumatology" }, - { - "rel_doi": "10.1101/2021.08.24.21262376", - "rel_title": "Real-world evaluation of AI driven COVID-19 triage for emergency admissions: External validation & operational assessment of lab-free and high-throughput screening solutions", - "rel_date": "2021-08-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.24.21262376", - "rel_abs": "BackgroundUncertainty in patients COVID-19 status contributes to treatment delays, nosocomial transmission, and operational pressures in hospitals. However, typical turnaround times for batch-processed laboratory PCR tests remain 12-24h. Although rapid antigen lateral flow testing (LFD) has been widely adopted in UK emergency care settings, sensitivity is limited. We recently demonstrated that AI-driven triage (CURIAL-1.0) allows high-throughput COVID-19 screening using clinical data routinely available within 1h of arrival to hospital. Here we aimed to determine operational and safety improvements over standard-care, performing external/prospective evaluation across four NHS trusts with updated algorithms optimised for generalisability and speed, and deploying a novel lab-free screening pathway in a UK emergency department.\n\nMethodsWe rationalised predictors in CURIAL-1.0 to optimise separately for generalisability and speed, developing CURIAL-Lab with vital signs and routine laboratory blood predictors (FBC, U&E, LFT, CRP) and CURIAL-Rapide with vital signs and FBC alone. Models were calibrated during training to 90% sensitivity and validated externally for unscheduled admissions to Portsmouth University Hospitals, University Hospitals Birmingham and Bedfordshire Hospitals NHS trusts, and prospectively during the second-wave of the UK COVID-19 epidemic at Oxford University Hospitals (OUH). Predictions were generated using first-performed blood tests and vital signs and compared against confirmatory viral nucleic acid testing. Next, we retrospectively evaluated a novel clinical pathway triaging patients to COVID-19-suspected clinical areas where either model prediction or LFD results were positive, comparing sensitivity and NPV with LFD results alone. Lastly, we deployed CURIAL-Rapide alongside an approved point-of-care FBC analyser (OLO; SightDiagnostics, Israel) to provide lab-free COVID-19 screening in the John Radcliffe Hospitals Emergency Department (Oxford, UK), as trust-approved service improvement. Our primary improvement outcome was time-to-result availability; secondary outcomes were sensitivity, specificity, PPV, and NPV assessed against a PCR reference standard. We compared CURIAL-Rapides performance with clinician triage and LFD results within standard-care.\n\nResults72,223 patients met eligibility criteria across external and prospective validation sites. Model performance was consistent across trusts (CURIAL-Lab: AUROCs range 0.858-0.881; CURIAL-Rapide 0.836-0.854), with highest sensitivity achieved at Portsmouth University Hospitals (CURIAL-Lab:84.1% [95% Wilsons score CIs 82.5-85.7]; CURIAL-Rapide:83.5% [81.8 - 85.1]) at specificities of 71.3% (95% Wilsons score CIs: 70.9 - 71.8) and 63.6% (63.1 - 64.1). For 3,207 patients receiving LFD-triage within routine care for OUH admissions between December 23, 2021 and March 6, 2021, a combined clinical pathway increased sensitivity from 56.9% for LFDs alone (95% CI 51.7-62.0) to 88.2% with CURIAL-Rapide (84.4-91.1; AUROC 0.919) and 85.6% with CURIAL-Lab (81.6-88.9; AUROC 0.925). 520 patients were prospectively enrolled for point-of-care FBC analysis between February 18, 2021 and May 10, 2021, of whom 436 received confirmatory PCR testing within routine care and 10 (2.3%) tested positive. Median time from patient arrival to availability of CURIAL-Rapide result was 45:00 min (32-64), 16 minutes (26.3%) sooner than LFD results (61:00 min, 37-99; log-rank p<0.0001), and 6:52 h (90.2%) sooner than PCR results (7:37 h, 6:05-15:39; p<0.0001). Sensitivity and specificity of CURIAL-Rapide were 87.5% (52.9-97.8) and 85.4% (81.3-88.7), therefore achieving high NPV (99.7%, 98.2-99.9). CURIAL-Rapide correctly excluded COVID-19 for 58.5% of negative patients who were triaged by a clinician to COVID-19-suspected (amber) areas.\n\nImpactCURIAL-Lab & CURIAL-Rapide are generalisable, high-throughput screening tests for COVID-19, rapidly excluding the illness with higher NPV than LFDs. CURIAL-Rapide can be used in combination with near-patient FBC analysis for rapid, lab-free screening, and may reduce the number of COVID-19-negative patients triaged to enhanced precautions ( amber) clinical areas.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Andrew AS Soltan", - "author_inst": "John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust; RDM Division of Cardiovascular Medicine, University of Oxford" - }, - { - "author_name": "Jenny Yang", - "author_inst": "Institute of Biomedical Engineering, Dept. Engineering Science, University of Oxford" - }, - { - "author_name": "Ravi Pattanshetty", - "author_inst": "John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Alex Novak", - "author_inst": "John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Omid Rohanian", - "author_inst": "Institute of Biomedical Engineering, Dept. Engineering Science, University of Oxford" - }, - { - "author_name": "Sally Beer", - "author_inst": "John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Marina A Soltan", - "author_inst": "The Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust; Institute of Inflammation and Ageing, University of Birmingham" - }, - { - "author_name": "David R Thickett", - "author_inst": "The Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust; Institute of Inflammation and Ageing, University of Birmingham" - }, - { - "author_name": "Rory Fairhead", - "author_inst": "University of Oxford Medical School" - }, - { - "author_name": "- CURIAL Translational Collaborative", - "author_inst": "" - }, - { - "author_name": "Tingting Zhu", - "author_inst": "Institute of Biomedical Engineering, Dept. Engineering Science, University of Oxford" - }, - { - "author_name": "David W Eyre", - "author_inst": "John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust; Big Data Institute, Nuffield Department of Population Health, University of Oxford; N" - }, - { - "author_name": "David A Clifton", - "author_inst": "Institute of Biomedical Engineering, Dept. Engineering Science, University of Oxford" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2021.08.28.21262748", "rel_title": "Projected resurgence of COVID-19 in the United States in July-December 2021 resulting from the increased transmissibility of the Delta variant and faltering vaccination", @@ -587105,6 +589549,97 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.08.30.21262863", + "rel_title": "Single-cell transcriptomic atlas of individuals receiving inactivated COVID-19 vaccines reveals distinct immunological responses between vaccine and natural SARS-CoV-2 infection", + "rel_date": "2021-08-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.30.21262863", + "rel_abs": "To control the ongoing COVID-19 pandemic, CoronaVac (Sinovac), an inactivated vaccine, has been granted emergency use authorization by many countries. However, the underlying mechanisms of the inactivated COVID-19 vaccine-induced immune response remain unclear, and little is known about its features compared to SARS-CoV-2 infection. Here, we implemented single-cell RNA sequencing (scRNA-seq) to profile longitudinally collected PBMCs (peripheral blood mononuclear cells) in six individuals immunized with CoronaVac and compared these to the profiles of COVID-19 infected patients from a Single Cell Consortium. Both inactivated vaccines and SARS-CoV-2 infection drove changes in immune cell type proportions, caused B cell activation and differentiation, and induced the expression of genes associated with antibody production in the plasma. The inactivated vaccine and SARS-COV-2 infection also caused alterations in peripheral immune activity such as interferon response, inflammatory cytokine expression, innate immune cell apoptosis and migration, effector T cell exhaustion and cytotoxicity, however, the magnitude of change was greater in COVID-19 patients, especially those with severe disease, than in immunized individuals. Further analyses revealed a distinct peripheral immune cell phenotype associated with CoronaVac immunization (HLA class II upregulation and IL21R upregulation in naive B cells) versus SARS-CoV-2 infection (HLA class II downregulation and IL21R downregulation in naive B cells severe disease). There were also differences in the expression of important genes associated with proinflammatory cytokines and thrombosis. In conclusion, this study provides a single-cell atlas of the systemic immune response to CoronaVac immunization and reveals distinct immune responses between inactivated vaccines and SARS-CoV-2 infection.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Yi Wang", + "author_inst": "Experimental Research Center, Capital Institute of Pediatrics, Beijing, 100020, P.R. China" + }, + { + "author_name": "Xiaoxia Wang", + "author_inst": "Central & Clinical Laboratory of Sanya People's Hospital, Sanya, Hainan 572000, P. R. China" + }, + { + "author_name": "Laurence Don Wai Luu", + "author_inst": "School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, Australia" + }, + { + "author_name": "Jieqiong Li", + "author_inst": "Department of Respiratory Disease, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's" + }, + { + "author_name": "Xiaodai Cui", + "author_inst": "Experimental Research Center, Capital Institute of Pediatrics, Beijing, 100020, P.R. China" + }, + { + "author_name": "Hailan Yao", + "author_inst": "Department of Biochemistry and Immunology, Capital Institute of Pediatrics, Beijing 100020, P. R. China" + }, + { + "author_name": "Xin Zhang", + "author_inst": "Beijing Engineering Research Center of Pediatric Surgery, Engineering and Transformation Center, Beijing Childrens Hospital, Capital Medical University, Nationa" + }, + { + "author_name": "Shaojin Chen", + "author_inst": "Central & Clinical Laboratory of Sanya People's Hospital, Sanya, Hainan 572000, P. R. China" + }, + { + "author_name": "Jin Fu", + "author_inst": "Experimental Research Center, Capital Institute of Pediatrics, Beijing, 100020, P.R. China" + }, + { + "author_name": "Licheng Wang", + "author_inst": "Central & Clinical Laboratory of Sanya People's Hospital, Sanya, Hainan 572000, P. R. China" + }, + { + "author_name": "Chongzhen Wang", + "author_inst": "Central & Clinical Laboratory of Sanya People's Hospital, Sanya, Hainan 572000, P. R. China" + }, + { + "author_name": "Rui Yuan", + "author_inst": "Central & Clinical Laboratory of Sanya People's Hospital, Sanya, Hainan 572000, P. R. China" + }, + { + "author_name": "Qinguo Cai", + "author_inst": "Central & Clinical Laboratory of Sanya People's Hospital, Sanya, Hainan 572000, P. R. China" + }, + { + "author_name": "Xiaolan Huang", + "author_inst": "Experimental Research Center, Capital Institute of Pediatrics, Beijing, 100020, P.R. China" + }, + { + "author_name": "Junfei Huang", + "author_inst": "Laboratory of Infectious Disease of Experimental Center, Guizhou Provincial Center for Disease Control and Prevention, Guiyang 550050, P. R. China." + }, + { + "author_name": "Wenjian Xu", + "author_inst": "Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Ce" + }, + { + "author_name": "Shijun Li", + "author_inst": "Laboratory of Infectious Disease of Experimental Center, Guizhou Provincial Center for Disease Control and Prevention, Guiyang 550050, P. R. China." + }, + { + "author_name": "Xiong Zhu", + "author_inst": "Central & Clinical Laboratory of Sanya People's Hospital, Sanya, Hainan 572000, P. R. China" + }, + { + "author_name": "Jun Tai", + "author_inst": "Department of Otolaryngology, Head and Neck Surgery, Children's Hospital Capital Institute of Pediatrics, Beijing 100020, P. R. China" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.30.21262865", "rel_title": "Total Infectomes Characterization of Respiratory Infections in pre-COVID-19 Wuhan, China", @@ -588081,45 +590616,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.22.21262392", - "rel_title": "Localized and Whole-Room Effects of Portable Air Filtration Units on Aerosol Particle Deposition and Concentration in a Classroom Environment", - "rel_date": "2021-08-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.22.21262392", - "rel_abs": "In indoor environments with limited ventilation, recirculating portable air filtration (PAF) units may reduce COVID-19 infection risk via not only the direct aerosol route (i.e., inhalation) but also via an indirect aerosol route (i.e., contact with the surface where particles deposited). We systematically investigated the impact of PAF units in a mock classroom, as a supplement to background ventilation, on localized and whole-room surface deposition and particle concentration. Fluorescently tagged particles with a volumetric mean diameter near two micrometers were continuously introduced into the classroom environment via a breathing simulator with a prescibed inhalation-exhalation waveform. Deposition velocities were inferred on >50 horizontal and vertical surfaces throughout the classroom, while aerosol concentrations were spatially monitored via optical particle spectrometry. Results revealed a particle decay rate consistent with expectations based upon the reported clean air delivery rates of the PAF units. Additionally, the PAF units reduced peak concentrations by a factor of around 2.5 compared to the highest concentrations observed and led to a statistically significant reduction in deposition velocities for horizontal surfaces >2.5 m from the aerosol source. Our results not only confirm PAF units can reduce particle concentrations but also demonstrate that they may lead to reduced particle deposition throughout an indoor environment when properly positioned.\n\nPractical ImplicationsO_LIPortable air filtration units should be prioritized in classrooms as part of a multi-layed strategy to mitigate potentially infectious particle transmission by direct aerosol transmission via inhalation and indirect aerosol transmission via particle deposition to surfaces and later contact with said surfaces.\nC_LIO_LIWhen placing portable air filtration unit(s) within a classrom space, one should consider the airflow field within the classroom, the characteristic operational mode (heating vs. cooling) of the heating, ventilation, and air conditioning system, the predominantly occupied areas of the classroom, and interference with the regular teaching and learning activities.\nC_LI", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Meng Kong", - "author_inst": "Well Living Lab" - }, - { - "author_name": "Linhao Li", - "author_inst": "Well Living Lab" - }, - { - "author_name": "Stephanie Eilts", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Li Li", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Christopher J. Hogan Jr.", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Zachary C. Pope", - "author_inst": "Well Living Lab; Mayo Clinic" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.29.21262788", "rel_title": "Barrier gesture relaxation during vaccination campaign in France: modelling impact of waning immunity", @@ -588987,6 +591483,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.08.27.21262737", + "rel_title": "Analysis of daily reproduction rates of COVID-19 using Current Health Expenditure as Gross Domestic Product percentage (CHE/GDP) across countries", + "rel_date": "2021-08-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.27.21262737", + "rel_abs": "(1) BackgroundImpact and severity of coronavirus pandemic on health infrastructure vary across countries. We examine the role percentage health expenditure plays in various countries in terms of their preparedness and see how countries improved their public health policy in the first and second wave of the coronavirus pandemic;\n\n(2) MethodsWe considered the infectious period during the first and second wave of 195 countries with their Current Health Expenditure as Gross Domestic Product percentage (CHE/GDP). Exponential model was used to calculate the slope of the regression line while the ARIMA model was used to calculate the initial autocorrelation slope and also to forecast new cases for both waves. The relationship between epidemiologic and CHE/GDP data was used for processing ordinary least square multivariate modeling and classifying countries into different groups using PC analysis, K-means and Hierarchical clustering;\n\n(3) ResultsResults show that some countries with high CHE/GDP improved their public health strategy against virus during the second wave of the pandemic;\n\n(4) ConclusionsResults revealed that countries who spend more on health infrastructure improved in the tackling of the pandemic in the second wave as they were worst hit in the first wave. This research will help countries to decide on how to increase their CHE/GDP in order to tackle properly other pandemic waves of the present Covid-19 outbreak and future diseases that may occur. We are also opening up a debate on the crucial role socio-economic determinants play during the exponential phase of the pandemic modelling.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Kayode Oshinubi", + "author_inst": "University Grenoble Alpes" + }, + { + "author_name": "Mustapha Rachdi", + "author_inst": "University Grenoble Alpes" + }, + { + "author_name": "Jacques Demongeot", + "author_inst": "University Grenoble Alpes" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2021.08.25.21262417", "rel_title": "Prolonged SARS-CoV-2 infection in patients with lymphoid malignancies", @@ -589891,61 +592414,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2021.08.26.21262219", - "rel_title": "Erytra Blood Group Analyser and Kode Technology testing of SARS-CoV-2 antibodies among convalescent patients and vaccinated individuals", - "rel_date": "2021-08-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.26.21262219", - "rel_abs": "Surveillance of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic requires tests to monitor antibody formation and prevalence. We detected SARS-CoV-2 antibodies using red cells coated by Kode technology with short peptides derived from the SARS-CoV-2 spike protein. Such modified red cells, called C19-kodecytes, can be used as reagent cells in any manual or automated column agglutination assay. We investigated the presence of SARS-CoV-2 antibodies in 130 samples from COVID-19 convalescent plasma donors using standard manual technique, two FDA authorized ELISA assays and a virus neutralisation assay. The sensitivity of the C19-kodecyte assay was 88%, comparable to the anti-SP and anti-NCP ELISAs (86% and 83%) and the virus neutralisation assay (88%). The specificity of the C19-kodecyte assay was 90% (anti-SP 100% and anti-NCP 97%). Likewise, 231 samples from 73 vaccinated individuals were tested with an automated analyser and we monitored the appearance and persistence of SARS-CoV-2 antibodies. The C19-kodecyte assay is a robust tool for SARS-CoV-2 antibody detection. Automated blood group analyser use enables large-scale SARS-CoV-2 antibody testing for vaccination monitoring in population surveys.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Christof Weinstock", - "author_inst": "German Red Cross Blood Service Baden-Wuerttemberg - Hessen" - }, - { - "author_name": "Willy A Flegel", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Kshitij Srivastava", - "author_inst": "NIH Clinical Center" - }, - { - "author_name": "Sabine Kaiser", - "author_inst": "Institute of Clinical Transfusion Medicine and Immunogenetics, Ulm, and Department of Transfusion Medicine, Ulm University, Germany" - }, - { - "author_name": "Hubert Schrezenmeier", - "author_inst": "Institute of Clinical Transfusion Medicine and Immunogenetics, Ulm, and Department of Transfusion Medicine, Ulm University, Germany" - }, - { - "author_name": "Chrysanthi Tsamadou", - "author_inst": "Institute of Clinical Transfusion Medicine and Immunogenetics, Ulm, and Department of Transfusion Medicine, Ulm University, Germany" - }, - { - "author_name": "Carolin Ludwig", - "author_inst": "Institute of Clinical Transfusion Medicine and Immunogenetics, Ulm, and Department of Transfusion Medicine, Ulm University, Germany" - }, - { - "author_name": "Bernd Jahrsdoerfer", - "author_inst": "Institute of Clinical Transfusion Medicine and Immunogenetics, Ulm, and Department of Transfusion Medicine, Ulm University, Germany" - }, - { - "author_name": "Nicolai V Bovin", - "author_inst": "Centre for Kode Technology Innovation, School of Engineering, Computer and Mathematical Sciences, Faculty of Design and Creative Technologies, Auckland, Univers" - }, - { - "author_name": "Stephen M Henry", - "author_inst": "AUT University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.25.21262623", "rel_title": "Effect of losartan on hospitalized patients with COVID-19-induced lung injury: A randomized clinical trial", @@ -591089,6 +593557,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.26.457782", + "rel_title": "Structural remodeling of SARS-CoV-2 spike protein glycans reveals the regulatory roles in receptor binding affinity", + "rel_date": "2021-08-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.26.457782", + "rel_abs": "Glycans of the SARS-CoV-2 spike protein are speculated to play functional roles in the infection processes as they extensively cover the protein surface and are highly conserved across the variants. To date, the spike protein has become the principal target for vaccine and therapeutic development while the exact effects of its glycosylation remain elusive. Experimental reports have described the heterogeneity of the spike protein glycosylation profile. Subsequent molecular simulation studies provided a knowledge basis of the glycan functions. However, there are no studies to date on the role of discrete glycoforms on the spike protein pathobiology. Building an understanding of its role in SARS-CoV-2 is important as we continue to develop effective medicines and vaccines to combat the disease. Herein, we used designed combinations of glycoengineering enzymes to simplify and control the glycosylation profile of the spike protein receptor-binding domain (RBD). Measurements of the receptor binding affinity revealed the regulatory effects of the RBD glycans. Remarkably, opposite effects were observed from differently remodeled glycans, which presents a potential strategy for modulating the spike protein behaviors through glycoengineering. Moreover, we found that the reported anti-SARS-CoV-(2) antibody, S309, neutralizes the impact of different RBD glycoforms on the receptor binding affinity. Overall, this work reports the regulatory roles that glycosylation plays in the interaction between the viral spike protein and host receptor, providing new insights into the nature of SARS-CoV-2. Beyond this study, enzymatic remodeling of glycosylation offers the opportunity to understand the fundamental role of specific glycoforms on glycoconjugates across molecular biology.\n\nCovert art LegendsThe glycosylation of the SARS-CoV-2 spike protein receptor-binding domain has regulatory effects on the receptor binding affinity. Sialylation or not determines the \"stabilizing\" or \"destabilizing\" effect of the glycans. (Protein structure model is adapted from Protein Data Bank: 6moj. The original model does not contain the glycan structure.)\n\nSignificanceGlycans extensively cover the surface of SARS-CoV-2 spike (S) protein but the relationships between the glycan structures and the protein pathological behaviors remain elusive. Herein, we simplified and harmonized the glycan structures in the S protein receptor-binding domain and reported their regulatory roles in human receptor interaction. Opposite regulatory effects were observed and were determined by discrete glycan structures, which can be neutralized by the reported S309 antibody binding to the S protein. This report provides new insight into the mechanism of SARS-CoV-2 S protein infection as well as S309 neutralization.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Yen-Pang Hsu", + "author_inst": "Merck" + }, + { + "author_name": "Debopreeti Mukherjee", + "author_inst": "Merck" + }, + { + "author_name": "Vladimir Shchurik", + "author_inst": "Merck" + }, + { + "author_name": "Alexey Makarov", + "author_inst": "Merck" + }, + { + "author_name": "Benjamin F. Mann", + "author_inst": "Merck" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2021.08.21.21262401", "rel_title": "An in-depth statistical analysis of the COVID-19 pandemic's initial spread in the WHO African region", @@ -592149,101 +594652,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.25.457693", - "rel_title": "Protective activity of mRNA vaccines against ancestral and variant SARS-CoV-2 strains", - "rel_date": "2021-08-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.25.457693", - "rel_abs": "Although mRNA vaccines prevent COVID-19, variants jeopardize their efficacy as immunity wanes. Here, we assessed the immunogenicity and protective activity of historical (mRNA-1273, designed for Wuhan-1 spike) or modified (mRNA-1273.351, designed for B.1.351 spike) preclinical Moderna mRNA vaccines in 129S2 and K18-hACE2 mice. Immunization with high or low dose formulations of mRNA vaccines induced neutralizing antibodies in serum against ancestral SARS-CoV-2 and several variants, although levels were lower particularly against the B.1.617.2 (Delta) virus. Protection against weight loss and lung pathology was observed with all high-dose vaccines against all viruses. Nonetheless, low-dose formulations of the vaccines, which produced lower magnitude antibody and T cell responses, and serve as a possible model for waning immunity, showed breakthrough lung infection and pneumonia with B.1.617.2. Thus, as levels of immunity induced by mRNA vaccines decline, breakthrough infection and disease likely will occur with some SARS-CoV-2 variants, suggesting a need for additional booster regimens.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Baoling Ying", - "author_inst": "Washington University" - }, - { - "author_name": "Bradley Whitener", - "author_inst": "Washington University" - }, - { - "author_name": "Laura A VanBlargan", - "author_inst": "Washington University" - }, - { - "author_name": "Ahmed O Hassan", - "author_inst": "Washington University" - }, - { - "author_name": "Swathi Shrihari", - "author_inst": "Washington University" - }, - { - "author_name": "Chieh-Yu Liang", - "author_inst": "Washington University" - }, - { - "author_name": "Courtney E Karl", - "author_inst": "Washington University" - }, - { - "author_name": "Samantha Mackin", - "author_inst": "Washington University" - }, - { - "author_name": "Rita E Chen", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Natasha M Kafai", - "author_inst": "Washington University" - }, - { - "author_name": "Samuel H Wilks", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Derek J. Smith", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Juan Manuel Carreno", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Gagandeep Singh", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Florian Krammer", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Andrea Carfi", - "author_inst": "Moderna" - }, - { - "author_name": "Sayda Elbashir", - "author_inst": "Moderna" - }, - { - "author_name": "Darin K Edwards", - "author_inst": "Moderna Inc" - }, - { - "author_name": "Larissa B Thackray", - "author_inst": "Washington University" - }, - { - "author_name": "Michael S Diamond", - "author_inst": "Washington University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.08.25.457711", "rel_title": "Structural Analysis of Receptor Binding Domain Mutations in SARS-CoV-2 Variants of Concern that Modulate ACE2 and Antibody Binding", @@ -592903,6 +595311,73 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2021.08.23.21262241", + "rel_title": "The Yale Department of Medicine COVID-19 Data Explorer and Repository (DOM-CovX): An Innovative Approach to Promoting Collaborative Scholarship During a Pandemic", + "rel_date": "2021-08-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.23.21262241", + "rel_abs": "BackgroundThe COVID-19 pandemic has led to an explosion of research publications spanning epidemiology, basic and clinical science. While a digital revolution has allowed for open access to large datasets enabling real-time tracking of the epidemic, detailed, locally-specific clinical data has been less readily accessible to a broad range of academic faculty and their trainees. This perpetuates the separation of the primary missions of clinically-focused and primary research faculty resulting in lost opportunities for improved understanding of the local epidemic; expansion of the scope of scholarship; limitation of the diversity of the research pool; lack of creation of initiatives for growth and dissemination of research skills needed for the training of the next generation of clinicians and faculty.\n\nObjectivesCreate a common, easily accessible and up-to-date database that would promote access to local COVID-19 clinical data, thereby increasing efficiency, streamlining and democratizing the research enterprise. By providing a robust dataset, a broad range of researchers (faculty, trainees) and clinicians are encouraged to explore and collaborate on novel clinically relevant research questions.\n\nMethodsWe constructed a research platform called the Yale Department of Medicine COVID-19 Explorer and Repository (DOM-CovX), to house cleaned, highly granular, de-identified, continually-updated data from over 7,000 patients hospitalized with COVID-19 (1/2020-present) across the Yale New Haven Health System. This included a front-end user interface for simple data visualization of aggregate data and more detailed clinical datasets for researchers after a review board process. The goal is to promote access to local COVID-19 clinical data, thereby increasing efficiency, streamlining and democratizing the research enterprise.\n\nExpected OutcomesO_LIAccelerate generation of new knowledge and increase scholarly productivity with particular local relevance\nC_LIO_LIImprove the institutional academic climate by:\nO_LIBroadening research scope\nC_LIO_LIExpanding research capability to more diverse group of stakeholders including clinical and research-based faculty and trainees\nC_LIO_LIEnhancing interdepartmental collaborations\nC_LI\nC_LI\n\nConclusionsThe DOM-CovX Data Explorer and Repository have great potential to increase academic productivity. By providing an accessible tool for simple data analysis and access to a consistently updated, standardized and large-scale dataset, it overcomes barriers for a wide variety of researchers. Beyond academic productivity, this innovative approach represents an opportunity to improve the institutional climate by fostering collaboration, diversity of scholarly pursuits and expanding medical education. It provides a novel approach that can be expanded to other diseases beyond COVID 19.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Tanima Arora", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Michael S. Simonov", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Jameel Alausa", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Labeebah Subair", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Brett Gerber", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Andrew Nguyen", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Allen Hsaio", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Richard Hintz", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Yu Yamamoto", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Robert Soufer", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Gary Desir", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Francis P Wilson", + "author_inst": "Yale University" + }, + { + "author_name": "Merceditas S. Villanueva", + "author_inst": "Yale University School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2021.08.26.21262468", "rel_title": "Long-term immunogenicity of BNT162b2 vaccination in the elderly and in younger health care workers", @@ -594183,61 +596658,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hiv aids" }, - { - "rel_doi": "10.1101/2021.08.23.21262472", - "rel_title": "Discordant humoral and T cell immune responses to SARS-CoV-2 vaccination in people with multiple sclerosis on anti-CD20 therapy", - "rel_date": "2021-08-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.23.21262472", - "rel_abs": "BackgroundSphingosine-1-phosphate receptor (S1P) modulators and antiCD20 therapies impair humoral responses to SARS-CoV-2 mRNA vaccines. Whether disease modifying therapies (DMTs) for multiple sclerosis (MS) also impact T cell immune response to vaccination is unknown.\n\nMethodsIn 101 people with MS, we measured humoral responses via an immunoassay to measure IgG against the COVID-19 spike S1 glycoprotein in serum. We also measured T cell responses using FluoroSpot assay for interferon gamma (IFN-{gamma}) (Mabtech,Sweden) using cryopreserved rested PBMCs and then incubated in cRPMI with 1{micro}g/ml of pooled peptides spanning the entire spike glycoprotein (Genscript, 2 pools; 158 peptides each). Plates were read on an AID iSpot Spectrum to determine number of spot forming cells (SFC)/106 PBMCs. We tested for differences in immune responses across DMTs using linear models.\n\nFindingsHumoral responses were detected in 22/39 (56.4%) participants on anti-CD20 and in 59/63 (93.6%) participants on no or other DMTs. In a subset with immune cell phenotyping (n=88; 87%), T cell responses were detected in 76/88 (86%), including 32/33 (96.9%) participants on anti-CD20 therapies. AntiCD20 therapies were associated with an increase in IFN-{gamma} SFC counts relative to those on no DMT or other DMTs (for antiCD20 vs. no DMT: 425.9% higher [95%CI: 109.6%, 1206.6%] higher; p<0.001; for antiCD20 vs. other DMTs: 289.6% [95%CI: 85.9%, 716.6%] higher; p<0.001).\n\nInterpretationWe identified a robust T cell response in individuals on anti-CD20 therapies despite a reduced humoral response to SARS-CoV-2 vaccination. Follow up studies are needed to determine if this translates to protection against COVID-19 infection.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Sachin P Gadani", - "author_inst": "Johns Hopkins School of Medicine" - }, - { - "author_name": "Maria Reyes-Mantilla", - "author_inst": "Johns Hopkins School of Medicine" - }, - { - "author_name": "Larissa Jank", - "author_inst": "Johns Hopkins School of Medicine" - }, - { - "author_name": "Samantha Harris", - "author_inst": "Johns Hopkins School of Medicine" - }, - { - "author_name": "Morgan Douglas", - "author_inst": "Johns Hopkins School of Medicine" - }, - { - "author_name": "Matthew D Smith", - "author_inst": "Johns Hopkins School of Medicine" - }, - { - "author_name": "Peter A Calabresi", - "author_inst": "Johns Hopkins School of Medicine" - }, - { - "author_name": "Ellen M Mowry", - "author_inst": "Johns Hopkins School of Medicine" - }, - { - "author_name": "Kathryn C Fitzgerald", - "author_inst": "Johns Hopkins School of Medicine" - }, - { - "author_name": "Pavan Bhargava", - "author_inst": "Johns Hopkins School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.19.21262275", "rel_title": "Hydroxychloroquine for pre-exposure prophylaxis of COVID-19 in health care workers: a randomized, multicenter, placebo-controlled trial (HERO-HCQ)", @@ -595136,6 +597556,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.16.21262073", + "rel_title": "Urban Tertiary Care Centre Experience of Characteristics of Severe COVID-19 Pneumonia", + "rel_date": "2021-08-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.16.21262073", + "rel_abs": "IntroductionThe global pandemic of novel coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) began in Wuhan, China, in December 2019, and has since spread worldwide.[1] This study attempts to summarize current evidence regarding major inflammatory markers, severity predictors and its impact on outcome, which provide current clinical experience and treatment guidance for this novel coronavirus.\n\nMethodsThis is a retrospective observational study done at an urban teaching covid-19 designated hospital. Hospital data were analysed with aim of studying inflammatory markers, predictors and outcome. Patients were classified in Mild, Moderate, Severe & Critical categories of COVID cases. Their clinical parameters, laboratory investigations, radiological findings & Outcome measures were studied. Strength of association & correlation of those parameters with severity and in-hospital mortality were studied.\n\nResultsA total 204 (N) patients were clinically classified into different severity groups, as per MOHFW and qCSI(quick Covid Severity Index) guidelines, as Mild (34), Moderate (56), Severe (39) and Critical (75). The mean(SD) age of the cohort was 55.1+13.2 years; 74.02% were male. Severe COVID-19 illness is seen more in patients more than 50 years of age. COVID-19 patients having IHD develop worse disease with excess early in-hospital mortality. Respiratory rate & Heart Rate on admission are correlated with severe and stormy disease. Among Inflammatory markers, on admission LDH, D-Dimer and CRP are related with severity and excess in-hospital death rate.\n\nConclusionAdvanced age, male gender, IHD, Respiratory Rate & Heart Rate on admission were associated with severe covid-19 illness. S. Lactate Dehydrogenase & D-dimer was associated with severe covid-19 illness and early in-hospital death.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Nehal M Shah", + "author_inst": "Smt NHL Municipal Medical College & Sardar Vallabhbhai Patel Institute of Medical Sciences and Research" + }, + { + "author_name": "Janakkumar R Khambholja", + "author_inst": "Smt NHL Municipal Medical College & Sardar Vallabhbhai Patel Institute of Medical Sciences and Research" + }, + { + "author_name": "Nilay N Suthar", + "author_inst": "Smt NHL Municipal Medical College & Sardar Vallabhbhai Patel Institute of Medical Sciences and Research" + }, + { + "author_name": "Hemant Tiwari", + "author_inst": "Smt NHL Municipal Medical College" + }, + { + "author_name": "Vandit Desai", + "author_inst": "Smt NHL Municipal Medical College & Sardar Vallabhbhai Patel Institute of Medical Sciences and Research" + }, + { + "author_name": "Vishal Beriwala", + "author_inst": "Smt NHL Municipal Medical College & Sardar Vallabhbhai Patel Institute of Medical Sciences and Research" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.16.21262135", "rel_title": "Assessing the impact of adherence to Non-pharmaceutical interventions and indirect transmission on the dynamics of COVID-19: a mathematical modelling study", @@ -596060,89 +598519,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.08.23.457419", - "rel_title": "Discovery of Antiviral Cyclic Peptides Targeting the Main Protease of SARS-CoV-2 via mRNA Display", - "rel_date": "2021-08-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.23.457419", - "rel_abs": "Antivirals that specifically target SARS-CoV-2 are needed to control the COVID-19 pandemic. The main protease (Mpro) is essential for SARS-CoV-2 replication and is an attractive target for antiviral development. Here we report the use of the Random nonstandard Peptide Integrated Discovery (RaPID) mRNA display on a chemically cross-linked SARS-CoV-2 Mpro dimer, which yielded several high-affinity thioether-linked cyclic peptide inhibitors of the protease. Structural analysis of Mpro complexed with a selenoether analogue of the highest-affinity peptide revealed key binding interactions, including glutamine and leucine residues in sites S1 and S2, respectively, and a binding epitope straddling both protein chains in the physiological dimer. Several of these Mpro peptide inhibitors possessed antiviral activity against SARS-CoV-2 in vitro with EC50 values in the low micromolar range. These cyclic peptides serve as a foundation for the development of much needed antivirals that specifically target SARS-CoV-2.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Jason Johansen-Leete", - "author_inst": "The University of Sydney" - }, - { - "author_name": "Sven Ullrich", - "author_inst": "Australian National University" - }, - { - "author_name": "Sarah Fry", - "author_inst": "The University of Sydney" - }, - { - "author_name": "Rebecca Frkic", - "author_inst": "Australian National University" - }, - { - "author_name": "Max Bedding", - "author_inst": "The University of Sydney" - }, - { - "author_name": "Anupriya Aggarwal", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Anneliese Ashhurst", - "author_inst": "The University of Sydney School of Medicine" - }, - { - "author_name": "Kasuni Ekanayake", - "author_inst": "Australian National University" - }, - { - "author_name": "Mithun Mahawaththa", - "author_inst": "Australian National University" - }, - { - "author_name": "Vishnu Sasi", - "author_inst": "Australian National University" - }, - { - "author_name": "Toby Passioura", - "author_inst": "The University of Sydney" - }, - { - "author_name": "Mark Larance", - "author_inst": "The University of Sydney" - }, - { - "author_name": "Gottfried Otting", - "author_inst": "Australian National University" - }, - { - "author_name": "Stuart Grant Turville", - "author_inst": "Kirby Institute" - }, - { - "author_name": "Colin J Jackson", - "author_inst": "Australian National University" - }, - { - "author_name": "Christoph Nitsche", - "author_inst": "Australian National University" - }, - { - "author_name": "Richard J Payne", - "author_inst": "The University of Sydney" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.08.24.457521", "rel_title": "Gene Expression Risk Scores for COVID-19 Illness Severity", @@ -597034,6 +599410,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2021.08.13.21261910", + "rel_title": "Gene-environment interaction analysis incorporating sex, cardiometabolic diseases, and multiple deprivation index reveals novel genetic associations with COVID-19 severity", + "rel_date": "2021-08-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.13.21261910", + "rel_abs": "Increasing evidence indicates that specific genetic variants influence the severity of outcomes after infection with COVID-19. However, it is not clear whether the effect of these genetic factors is independent of the risk due to more established non-genetic demographic and metabolic risk factors such as male sex, poor cardiometabolic health, and low socioeconomic status. We sought to identify interactions between genetic variants and non-genetic risk factors influencing COVID-19 severity via a genome-wide interaction study in the UK Biobank. Of 378,051 unrelated individuals of European ancestry, 2,402 were classified as having experienced severe COVID-19, defined as hospitalization or death due to COVID-19. Exposures included sex, cardiometabolic risk factors (obesity and type 2 diabetes [T2D], tested jointly), and multiple deprivation index. Multiplicative interaction was tested using a logistic regression model, conducting both an interaction test and a joint test of genetic main and interaction effects. Five independent variants reached genome-wide significance in the joint test, one of which also reached significance in the interaction test. One of these, rs2268616 in the PGF gene, showed stronger effects in males and in individuals with T2D. None of the five variants showed effects on a similarly-defined phenotype in a lookup in the COVID-19 Host Genetics Initiative. These results reveal potential additional genetic loci contributing to COVID-19 severity and demonstrate the value of including non-genetic risk factors in an interaction testing approach for genetic discovery.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Kenneth E Westerman", + "author_inst": "Broad Institute" + }, + { + "author_name": "Joanna Lin", + "author_inst": "Mass General Hospital" + }, + { + "author_name": "Magda Sevilla-Gonzalez", + "author_inst": "Broad Institute" + }, + { + "author_name": "Beza Tadess", + "author_inst": "Mass General Hospital" + }, + { + "author_name": "Alisa K Manning", + "author_inst": "Broad Institute" + }, + { + "author_name": "Casey J Marchek", + "author_inst": "Mass General Hospital" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.15.21262074", "rel_title": "Comparison of the inhomogeneous SEPIR model and data from the COVID-19 outbreak in South Carolina", @@ -598314,77 +600729,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, - { - "rel_doi": "10.1101/2021.08.19.21262249", - "rel_title": "Intention to receive a COVID-19 vaccine by HIV status among a population-based sample of women and gender diverse individuals in British Columbia, Canada", - "rel_date": "2021-08-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.19.21262249", - "rel_abs": "IntroductionCOVID-19 vaccination is recommended for people living with HIV (PLWH), among whom social inequities and co-morbidities may drive risks of COVID-19 infection and outcome severity. Among a provincial (British Columbia) sample, we determined the prevalence of COVID-19 vaccine intention by HIV status and assessed socio-demographic, vaccine hesitancy, and psychological predictors of vaccine intention.\n\nMethodsIndividuals (25-69y) recruited from province-wide research cohorts completed an online survey examining COVID-19 impacts (August/2020-March/2021). Among women and gender diverse participants, we compared intention to receive a recommended COVID-19 vaccine (Very likely/Likely vs Neutral/Unlikely/Very Unlikely) by self-reported HIV status. Logistic regression models assessed the independent effect of HIV status and other factors on vaccine intention.\n\nResultsOf 5,588 participants, 69 (1.2%) were PLWH, of whom 79.7% were on antiretroviral therapy. Intention to vaccinate was significantly lower among PLWH compared to participants not living with HIV (65.2% vs 79.6%; OR: 0.44; 95%CI: 0.32-0.60). However, this association was attenuated after adjustment for social disparities (aOR:0.85; 95%CI: 0.48-1.55). Among PLWH, those with greater vaccine confidence, positive attitudes towards the COVID-19 vaccine, and more strongly influenced by direct and indirect social norms to vaccinate had significantly higher odds of vaccine intention.\n\nDiscussionTailored messaging is needed to build vaccine confidence, address questions about vaccine benefits, and support informed vaccination decision-making to promote COVID-19 vaccine uptake among women and gender diverse PLWH.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Angela Kaida", - "author_inst": "Simon Fraser University (SFU), Faculty of Health Sciences, Burnaby, British Columbia, Canada ; Women's Health Research Institute (WHRI), Vancouver, British Colu" - }, - { - "author_name": "Lori A. Brotto", - "author_inst": "Women's Health Research Institute (WHRI), Vancouver, British Columbia, Canada ; University of British Columbia (UBC), Vancouver, British Columbia, Canada" - }, - { - "author_name": "Melanie C.M. Murray", - "author_inst": "Women's Health Research Institute (WHRI), Vancouver, British Columbia, Canada ; University of British Columbia (UBC), Vancouver, British Columbia, Canada ; Oa" - }, - { - "author_name": "Helene C.F. Cote", - "author_inst": "Women's Health Research Institute (WHRI), Vancouver, British Columbia, Canada ; University of British Columbia (UBC), Vancouver, British Columbia, Canada" - }, - { - "author_name": "Arianne Y. Albert", - "author_inst": "Women's Health Research Institute (WHRI), Vancouver, British Columbia, Canada" - }, - { - "author_name": "Valerie Nicholson", - "author_inst": "Simon Fraser University (SFU), Faculty of Health Sciences, Burnaby, British Columbia, Canada ; BC Centre for Excellence in HIV/AIDS, Vancouver, British Columbi" - }, - { - "author_name": "Rebecca Gormley", - "author_inst": "Simon Fraser University (SFU), Faculty of Health Sciences, Burnaby, British Columbia, Canada ; BC Centre for Excellence in HIV/AIDS, Vancouver, British Columbia" - }, - { - "author_name": "Shanlea Gordon", - "author_inst": "Women's Health Research Institute (WHRI), Vancouver, British Columbia, Canada" - }, - { - "author_name": "Amy Booth", - "author_inst": "Women's Health Research Institute (WHRI), Vancouver, British Columbia, Canada ; University of British Columbia (UBC), Vancouver, British Columbia, Canada" - }, - { - "author_name": "Laurie W. Smith", - "author_inst": "Women's Health Research Institute (WHRI), Vancouver, British Columbia, Canada ; Cancer Control Research, BC Cancer, Vancouver, British Columbia, Canada" - }, - { - "author_name": "Ally Baaske", - "author_inst": "Women's Health Research Institute (WHRI), Vancouver, British Columbia, Canada" - }, - { - "author_name": "Liisa A.M. Galea", - "author_inst": "Women's Health Research Institute (WHRI), Vancouver, British Columbia, Canada ; University of British Columbia (UBC), Vancouver, British Columbia, Canada" - }, - { - "author_name": "Manish Sadarangani", - "author_inst": "University of British Columbia (UBC), Vancouver, British Columbia, Canada ; Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, B" - }, - { - "author_name": "Gina S. Ogilvie", - "author_inst": "Women's Health Research Institute (WHRI), Vancouver, British Columbia, Canada ; University of British Columbia (UBC), Vancouver, British Columbia, Canada ; " - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "hiv aids" - }, { "rel_doi": "10.1101/2021.08.19.21262111", "rel_title": "Large-scale study of antibody titer decay following BNT162b2 mRNA vaccine or SARS-CoV-2 infection", @@ -599016,6 +601360,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2021.08.20.21262158", + "rel_title": "Virological characteristics of SARS-CoV-2 vaccine breakthrough infections in health care workers", + "rel_date": "2021-08-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.20.21262158", + "rel_abs": "BackgroundSARS-CoV-2 vaccines are highly effective at preventing COVID-19-related morbidity and mortality. As no vaccine is 100% effective, breakthrough infections are expected to occur.\n\nMethodsWe analyzed the virological characteristics of 161 vaccine breakthrough infections in a population of 24,706 vaccinated healthcare workers (HCWs), using RT-PCR and virus culture.\n\nResultsThe delta variant (B.1.617.2) was identified in the majority of cases. Despite similar Ct-values, we demonstrate lower probability of infectious virus detection in respiratory samples of vaccinated HCWs with breakthrough infections compared to unvaccinated HCWs with primary SARS-CoV-2 infections. Nevertheless, infectious virus was found in 68.6% of breakthrough infections and Ct-values decreased throughout the first 3 days of illness.\n\nConclusionsWe conclude that rare vaccine breakthrough infections occur, but infectious virus shedding is reduced in these cases.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Marc Conrad Shamier", + "author_inst": "Erasmus Medical Center" + }, + { + "author_name": "Alma Tostmann", + "author_inst": "Radboud Centre for Infectious Diseases, Radboud university medical centre" + }, + { + "author_name": "Susanne Bogers", + "author_inst": "Erasmus Medical Center" + }, + { + "author_name": "Janet De Wilde", + "author_inst": "Erasmus Medical Center" + }, + { + "author_name": "Jeroen IJpelaar", + "author_inst": "Erasmus Medical Center" + }, + { + "author_name": "Willemijn Van Der Kleij", + "author_inst": "Erasmus Medical Center" + }, + { + "author_name": "Herbert De Jager", + "author_inst": "Erasmus Medical Center" + }, + { + "author_name": "Bart Haagmans", + "author_inst": "Erasmus Medical Center" + }, + { + "author_name": "Richard Molenkamp", + "author_inst": "Erasmus Medical Center" + }, + { + "author_name": "Bas Oude Munnink", + "author_inst": "Erasmus Medical Center" + }, + { + "author_name": "Carsten van Rossum", + "author_inst": "Radboud university medical center" + }, + { + "author_name": "Janette Rahamat-Langendoen", + "author_inst": "Radboud university medical center" + }, + { + "author_name": "Nannet Van Der Geest", + "author_inst": "Radboud university medical center" + }, + { + "author_name": "Chantal Bleeker-Rovers", + "author_inst": "Radboud university medical center" + }, + { + "author_name": "Heiman Wertheim", + "author_inst": "Radboud university medical center" + }, + { + "author_name": "Marion Koopmans", + "author_inst": "Erasmus Medical Center" + }, + { + "author_name": "Corine GeurtsvanKessel", + "author_inst": "Erasmus Medical Center" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.19.21262304", "rel_title": "Bias as a source of inconsistency in ivermectin trials for COVID-19: A systematic review", @@ -599824,49 +602251,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.17.21262177", - "rel_title": "Do Covid-19 patients needing ICU admission have worse 6 months follow up outcomes when compared with hospitalized non-ICU patients? A prospective cohort study", - "rel_date": "2021-08-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.17.21262177", - "rel_abs": "IntroductionStudies focus on pathogenesis, clinical manifestations, and complications during the early phase of the coronavirus disease-19 (COVID-19). Long-term outcomes of COVID-19 patients who discharge intensive care unit (ICU) are unclear.\n\nObjectivesWe investigated the effect of COVID-19 on lung structure, pulmonary functional, exercise capacity and quality of life in patients discharge from ICU and medical ward.\n\nMethodsA prospective single-centre study conducted in PCR confirmed COVID-19 patients who has been discharged from University of Health Sciences, Dr. Suat Seren Chest Disease and Thoracic Surgery Teaching and Research Hospital between 15 January and 5 March 2021. Patients who followed up for more than 48 hours in ICU and more than 72 hours in medical ward were included the study. Computed tomography scores, pulmonary functional tests (PFT), 6-min walking distance and health related quality of life by SF-36 were compared between ICU and medical ward patients at 6 months after discharge.\n\nResultsSeventy patients were included final analyses and 31 of them discharged from ICU. ICU patients had higher CT scores than non-ICU patients at admission (17 vs 11) and follow up visit (6 vs 0). Two-three of ICU patients had at least one abnormal finding at control CT. Advanced age (OR 1.08, 95% CI 1.02-1.15) and higher CT score at admission (OR 1.13, 95% CI 1.01-1.27) were risk factors for having radiological abnormalities at control CT.\n\nConclusionA number of COVID-19 survivors especially with severe disease could not fully recover after 6 months of hospital discharge.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Suleyman Yildirim", - "author_inst": "University of Health Sciences Turkey, Dr. Suat Seren Chest Disease and Chest Surgery Training and Research Hospital, Intensive Care Unit, Izmir, Turkey" - }, - { - "author_name": "Seher Susam", - "author_inst": "University of Health Sciences Turkey, Dr. Suat Seren Chest Disease and Chest Surgery Training and Research Hospital, Department of Radiology, Izmir, Turkey" - }, - { - "author_name": "Pinar Cimen", - "author_inst": "University of Health Sciences Turkey, Dr. Suat Seren Chest Disease and Chest Surgery Training and Research Hospital, Department of Chest Disease, Izmir, Turkey" - }, - { - "author_name": "Sena Yapicioglu", - "author_inst": "University of Health Sciences Turkey, Dr. Suat Seren Chest Disease and Chest Surgery Training and Research Hospital, Department of Chest Disease, Izmir, Turkey" - }, - { - "author_name": "Onur Sunecli", - "author_inst": "University of Health Sciences Turkey, Dr. Suat Seren Chest Disease and Chest Surgery Training and Research Hospital, Department of Physiotherapy, Izmir, Turkey" - }, - { - "author_name": "Ozlem Ediboglu", - "author_inst": "University of Health Sciences Turkey, Dr. Suat Seren Chest Disease and Chest Surgery Training and Research Hospital, Intensive Care Unit, Izmir, Turkey" - }, - { - "author_name": "Cenk Kirakli", - "author_inst": "University of Health Sciences Turkey, Dr. Suat Seren Chest Disease and Chest Surgery Training and Research Hospital, Intensive Care Unit, Izmir, Turkey" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2021.08.17.21262170", "rel_title": "The Rapid Assessment of Aggregated Wastewater Samples for Genomic Surveillance of SARS-CoV-2 on a City-Wide Scale", @@ -600674,6 +603058,85 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2021.08.19.456951", + "rel_title": "Pandemic, epidemic, endemic: B cell repertoire analysis reveals unique anti-viral responses to SARS-CoV-2, Ebola and Respiratory Syncytial Virus", + "rel_date": "2021-08-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.19.456951", + "rel_abs": "Immunoglobulin gene heterogeneity reflects the diversity and focus of the humoral immune response towards different infections, enabling inference of B cell development processes. Detailed compositional and lineage analysis of long read IGH repertoire sequencing, combining examples of pandemic, epidemic and endemic viral infections with control and vaccination samples, demonstrates general responses including increased use of IGHV4-39 in both EBOV and COVID-19 infection cohorts. We also show unique characteristics absent in RSV infection or yellow fever vaccine samples: EBOV survivors show unprecedented high levels of class switching events while COVID-19 repertoires from acute disease appear underdeveloped. Despite the high levels of clonal expansion in COVID-19 IgG1 repertoires there is a striking lack of evidence of germinal centre mutation and selection. Given the differences in COVID-19 morbidity and mortality with age, it is also pertinent that we find significant differences in repertoire characteristics between young and old patients. Our data supports the hypothesis that a primary viral challenge can result in a strong but immature humoral response where failures in selection of the repertoire risks off-target effects.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Alexander Stewart", + "author_inst": "University of Surrey" + }, + { + "author_name": "Emma Sinclair", + "author_inst": "University of Surrey" + }, + { + "author_name": "Ilaria Serangeli", + "author_inst": "Sapienza Universita di Roma" + }, + { + "author_name": "Nora Kasar", + "author_inst": "University of Surrey" + }, + { + "author_name": "Katherine Longman", + "author_inst": "University of Surrey" + }, + { + "author_name": "Cecile Frampas", + "author_inst": "University of Surrey" + }, + { + "author_name": "Holly-May Lewis", + "author_inst": "University of Surrey" + }, + { + "author_name": "Catia Costa", + "author_inst": "University of Surrey" + }, + { + "author_name": "David Kipling", + "author_inst": "University of Surrey" + }, + { + "author_name": "Peter Openshaw", + "author_inst": "Imperial College London" + }, + { + "author_name": "Christopher Chiu", + "author_inst": "Imperial College London" + }, + { + "author_name": "J Kenneth Baillie", + "author_inst": "Roslin Institute, University of Edinburgh" + }, + { + "author_name": "Janet Scott", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Malcolm Semple", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Melanie Bailey", + "author_inst": "University of Surrey" + }, + { + "author_name": "Deborah Dunn-Walters", + "author_inst": "University of Surrey" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.08.19.456973", "rel_title": "Modeling Coronavirus Spike Protein Dynamics: Implications for Immunogenicity and Immune Escape", @@ -601658,113 +604121,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.08.16.21262126", - "rel_title": "DeepSARS: simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2", - "rel_date": "2021-08-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.16.21262126", - "rel_abs": "The continued spread of SARS-CoV-2 and emergence of new variants with higher transmission rates and/or partial resistance to vaccines has further highlighted the need for large-scale testing and genomic surveillance. However, current diagnostic testing (e.g., PCR) and genomic surveillance methods (e.g., whole genome sequencing) are performed separately, thus limiting the detection and tracing of SARS-CoV-2 and emerging variants. Here, we developed DeepSARS, a high-throughput platform for simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2 by the integration of molecular barcoding, targeted deep sequencing, and computational phylogenetics. DeepSARS enables highly sensitive viral detection, while also capturing genomic diversity and viral evolution. We show that DeepSARS can be rapidly adapted for identification of emerging variants, such as alpha, beta, gamma, and delta strains, and profile mutational changes at the population level. DeepSARS sets the foundation for quantitative diagnostics that capture viral evolution and diversity.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC=\"FIGDIR/small/21262126v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (31K):\norg.highwire.dtl.DTLVardef@befa4corg.highwire.dtl.DTLVardef@22d496org.highwire.dtl.DTLVardef@b2da7dorg.highwire.dtl.DTLVardef@265657_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO DeepSARS uses molecular barcodes (BCs) and multiplexed targeted deep sequencing (NGS) to enable simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2.\n\nC_FIG", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Alexander Yermanos", - "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland, Institute of Microbiology, ETH Zurich, Zurich, Switzerland, Department of Path" - }, - { - "author_name": "Kai-Lin Hong", - "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland" - }, - { - "author_name": "Andreas Agrafiotis", - "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland" - }, - { - "author_name": "Jiami Han", - "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland" - }, - { - "author_name": "Sarah Nadeau", - "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland" - }, - { - "author_name": "Cecilia Valenzuela", - "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland" - }, - { - "author_name": "Asli Azizoglu", - "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland" - }, - { - "author_name": "Roy Ehling", - "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland" - }, - { - "author_name": "Beichen Gao", - "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland" - }, - { - "author_name": "Michael Spahr", - "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland" - }, - { - "author_name": "Daniel Neumeier", - "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland" - }, - { - "author_name": "Ching-Hsiang Chang", - "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland" - }, - { - "author_name": "Andreas Dounas", - "author_inst": "Institute for Biomedical Engineering, University and ETH Zurich, Zurich, Switzerland" - }, - { - "author_name": "Ezequiel Petrillo", - "author_inst": "Instituto de Fisiologia, Biologia Molecular y Neurociencias, Ciudad Universitaria, Buenos Aires, Argentina. Facultad de Ciencias Exactas y Naturales, Universida" - }, - { - "author_name": "Ina Nissen", - "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland" - }, - { - "author_name": "Elodie Burcklen", - "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland" - }, - { - "author_name": "Mirjam Feldkamp", - "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland" - }, - { - "author_name": "Christian Beisel", - "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland" - }, - { - "author_name": "Annette Oxenius", - "author_inst": "Institute of Microbiology, ETH Zurich, Zurich, Switzerland" - }, - { - "author_name": "Miodrag Savic", - "author_inst": "Department of Health, Economics and Health Directorate Canton Basel-Landschaft." - }, - { - "author_name": "Tanja Stadler", - "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland" - }, - { - "author_name": "Fabian Rudolf", - "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland" - }, - { - "author_name": "Sai T. Reddy", - "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.16.21262153", "rel_title": "The Impact of COVID-19 Testing on College Campuses", @@ -602476,6 +604832,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.15.21262095", + "rel_title": "Proactive COVID-19 testing in a partially vaccinated population", + "rel_date": "2021-08-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.15.21262095", + "rel_abs": "During the initial stages of the COVID-19 pandemic, many workplaces and universities implemented institution-wide proactive testing programs of all individuals, ir-respective of symptoms. These measures have proven effective in mitigating outbreaks. As a greater fraction of the population becomes vaccinated, we need to understand what continued benefit, if any, proactive testing can contribute. Here, we address this problem with two distinct modeling approaches: a simple analytical model and a more simulation using the SEIRS+ platform. Both models indicate that proactive testing remains useful until a threshold level of vaccination is reached. This threshold depends on the transmissibility of the virus and the scope of other control measures in place. If a community is able to reach the threshold level of vaccination, testing can cease. Otherwise, continued testing will be an important component of disease control. Because it is usually difficult or impossible to precisely estimate key parameters such as the basic reproduction number for a specific workplace or other setting, our results are more useful for understanding general trends than for making precise quantitative predictions.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Ryan Seamus McGee", + "author_inst": "Department of Physics, Washington University" + }, + { + "author_name": "Julian R. Homburger", + "author_inst": "Maze Therapeutics, South San Francisco, CA" + }, + { + "author_name": "Hannah E. Williams", + "author_inst": "Color Health, Burlingame, CA" + }, + { + "author_name": "Carl T. Bergstrom", + "author_inst": "University of Washington" + }, + { + "author_name": "Alicia Y. Zhou", + "author_inst": "Color Health, Burlingame, CA" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.17.456707", "rel_title": "An Endogenously activated antiviral state restricts SARS-CoV-2 infection in differentiated primary airway epithelial cells", @@ -603364,145 +605755,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2021.08.13.456316", - "rel_title": "Optimization of Non-Coding Regions Improves Protective Efficacy of an mRNA SARS-CoV-2 Vaccine in Nonhuman Primates", - "rel_date": "2021-08-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.13.456316", - "rel_abs": "The CVnCoV (CureVac) mRNA vaccine for SARS-CoV-2 has recently been evaluated in a phase 2b/3 efficacy trial in humans. CV2CoV is a second-generation mRNA vaccine with optimized non-coding regions and enhanced antigen expression. Here we report a head-to-head study of the immunogenicity and protective efficacy of CVnCoV and CV2CoV in nonhuman primates. We immunized 18 cynomolgus macaques with two doses of 12 ug of lipid nanoparticle formulated CVnCoV, CV2CoV, or sham (N=6/group). CV2CoV induced substantially higher binding and neutralizing antibodies, memory B cell responses, and T cell responses as compared with CVnCoV. CV2CoV also induced more potent neutralizing antibody responses against SARS-CoV-2 variants, including B.1.351 (beta), B.1.617.2 (delta), and C.37 (lambda). While CVnCoV provided partial protection against SARS-CoV-2 challenge, CV2CoV afforded robust protection with markedly lower viral loads in the upper and lower respiratory tract. Antibody responses correlated with protective efficacy. These data demonstrate that optimization of non-coding regions can greatly improve the immunogenicity and protective efficacy of an mRNA SARS-CoV-2 vaccine in nonhuman primates.", - "rel_num_authors": 31, - "rel_authors": [ - { - "author_name": "Makda Gebre", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Susanne Rauch", - "author_inst": "CureVac AG" - }, - { - "author_name": "Nicole Roth", - "author_inst": "CureVac AG" - }, - { - "author_name": "Jingyou Yu", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Abishek Chandrashekar", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Noe Mercado", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Xuan He", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Jinyan Liu", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Katherine McMahan", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Amanda Martinot", - "author_inst": "Tufts University" - }, - { - "author_name": "Tori Giffin", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "David Hope", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Shivani Patel", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Daniel Sellers", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Owen Sanborn", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Julia Barrett", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Xiaowen Liu", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Andrew Cole", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Laurent Pessaint", - "author_inst": "Bioqual Inc" - }, - { - "author_name": "Daniel Valentin", - "author_inst": "Bioqual Inc." - }, - { - "author_name": "Zack Flinchbaugh", - "author_inst": "Bioqual Inc." - }, - { - "author_name": "Jake Yalley-Ogunro", - "author_inst": "Bioqual Inc." - }, - { - "author_name": "Jeanne Muench", - "author_inst": "Bioqual Inc." - }, - { - "author_name": "Renita Brown", - "author_inst": "Bioqual Inc." - }, - { - "author_name": "Anthony Cook", - "author_inst": "Bioqual Inc." - }, - { - "author_name": "Elyse Teow", - "author_inst": "Bioqual Inc." - }, - { - "author_name": "Hanne Andersen", - "author_inst": "Bioqual Inc" - }, - { - "author_name": "Mark G. Lewis", - "author_inst": "Bioqual Inc" - }, - { - "author_name": "Stefan Mueller", - "author_inst": "CureVac AG" - }, - { - "author_name": "Benjamin Petsch", - "author_inst": "CureVac AG" - }, - { - "author_name": "Dan H. Barouch", - "author_inst": "Beth Israel Deaconess Medical Center" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.08.13.456164", "rel_title": "Comparison of Wild Type DNA Sequence of Spike Protein from SARS-CoV-2 with Optimized Sequence on The Induction of Protective Responses Against SARS-Cov-2 Challenge in Mouse Model", @@ -604194,6 +606446,49 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.08.14.456330", + "rel_title": "Next generation infection prevention clothing: Non-woven Fabrics Coated with Cranberry Extracts Capable of Inactivating Enveloped Viruses such as SARS-CoV-2 and Multidrug-resistant Bacteria", + "rel_date": "2021-08-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.14.456330", + "rel_abs": "The Coronavirus Disease (COVID-19) pandemic is demanding rapid action of the authorities and scientific community in order to find new antimicrobial solutions that could inactivate the pathogen SARS-CoV-2 that causes this disease. Gram-positive bacteria contribute to severe pneumonia associated with COVID-19, and their resistance to antibiotics is increasing at an alarming rate. In this regard, non-woven fabrics are currently used for the fabrication of infection prevention clothing such as face masks, caps, scrubs, shirts, trousers, disposable gowns, overalls, hoods, aprons and shoe covers as protective tools against viral and bacterial infections. However, these non-woven fabrics are made of materials that do not possess antimicrobial activity. Thus, we have developed here non-woven fabrics with antimicrobial coatings of cranberry extracts capable of inactivating enveloped viruses such as SARS-CoV-2 and the phage phi 6, and two multidrug-resistant bacteria: the methicillin-resistant Staphylococcus aureus and Staphylococcus epidermidis. The non-toxicity of these advanced technology was ensured using a Caenorhabditis elegans in vivo model. These results open up a new prevention path using natural and biodegradable compounds for the fabrication of infection prevention clothing in the current COVID-19 and future pandemics.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Alberto Tunon-Molina", + "author_inst": "Universidad Catolica de Valencia San Vicente Martir" + }, + { + "author_name": "Alba Cano-Vicent", + "author_inst": "Universidad Catolica de Valencia San Vicente Martir" + }, + { + "author_name": "Miguel Marti", + "author_inst": "Universidad Catolica de Valencia San Vicente Martir" + }, + { + "author_name": "Yukiko Muramoto", + "author_inst": "Kyoto University" + }, + { + "author_name": "Takeshi Noda", + "author_inst": "Kyoto University" + }, + { + "author_name": "Kazuo Takayama", + "author_inst": "Kyoto University" + }, + { + "author_name": "Angel Serrano-Aroca", + "author_inst": "Universidad Catolica de Valencia San Vicente Martir" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2021.08.09.21261738", "rel_title": "Beneficial Effects of novel Aureobasidium Pullulans strains produced Beta-1,3-1,6 Glucans on Interleukin-6 and D-Dimer levels in COVID-19 patients; results of a randomized multiple-arm pilot clinical study", @@ -605094,109 +607389,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.12.21261921", - "rel_title": "Clinical course impacts early kinetics and long-term magnitude and amplitude of SARS-CoV-2 neutralizing antibodies beyond one year after infection", - "rel_date": "2021-08-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.12.21261921", - "rel_abs": "BackgroundUnderstanding the determinants of long-term immune responses to SARS-CoV-2 and the concurrent impact of vaccination and emerging variants of concern will guide optimal strategies to achieve global protection against the COVID-19 pandemic.\n\nMethodsA prospective cohort of 332 COVID-19 patients was followed beyond one year. Plasma neutralizing activity was evaluated using HIV-based reporter pseudoviruses expressing different SARS-CoV-2 spikes and was longitudinally analyzed using mixed-effects models.\n\nFindingsLong-term neutralizing activity was stable beyond one year after infection in mild/asymptomatic and hospitalized participants. However, longitudinal models suggest that hospitalized individuals generate both short- and long-lived memory B cells, while outpatient responses were dominated by long-lived B cells. In both groups, vaccination boosted responses to natural infection, although viral variants, mainly B.1.351, reduced the efficacy of neutralization. Importantly, despite showing higher neutralization titers, hospitalized patients showed lower cross-neutralization of B.1.351 variant compared to outpatients. Multivariate analysis identified severity of primary infection as the factor that independently determines both the magnitude and the inferior cross-neutralization activity of long-term neutralizing responses.\n\nConclusionsNeutralizing response induced by SARS-CoV-2 is heterogeneous in magnitude but stable beyond one year after infection. Vaccination boosts these long-lasting natural neutralizing responses, counteracting the significant resistance to neutralization of new viral variants. Severity of primary infection determines higher magnitude but poorer quality of long-term neutralizing responses.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Edwards Pradenas", - "author_inst": "IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916, Badalona, Catalonia, Spain" - }, - { - "author_name": "Benjamin Trinit\u00e9", - "author_inst": "IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916, Badalona, Catalonia, Spain" - }, - { - "author_name": "V\u00edctor Urrea", - "author_inst": "IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916, Badalona, Catalonia, Spain" - }, - { - "author_name": "Silvia Marfil", - "author_inst": "IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916, Badalona, Catalonia, Spain" - }, - { - "author_name": "Ferran Tarr\u00e9s-Freixas", - "author_inst": "IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916, Badalona, Catalonia, Spain" - }, - { - "author_name": "Raquel Ortiz", - "author_inst": "IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916, Badalona, Catalonia, Spain" - }, - { - "author_name": "Carla Rovirosa", - "author_inst": "IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916, Badalona, Catalonia, Spain" - }, - { - "author_name": "Jordi Rodon", - "author_inst": "IRTA Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la UAB, 08193, Bellaterra, Catalonia, Spain" - }, - { - "author_name": "J\u00falia Vergara-Alert", - "author_inst": "IRTA Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la UAB, 08193, Bellaterra, Catalonia, Spain" - }, - { - "author_name": "Joaquim Segal\u00e9s", - "author_inst": "UAB, Centre de Recerca en Sanitat Animal (IRTA-UAB), Campus de la UAB, 08193, Bellaterra, Catalonia, Spain" - }, - { - "author_name": "Victor Guallar", - "author_inst": "Barcelona Supercomputing Center, 08034, Barcelona, Catalonia, Spain" - }, - { - "author_name": "Alfonso Valencia", - "author_inst": "Barcelona Supercomputing Center, 08034, Barcelona, Catalonia, Spain" - }, - { - "author_name": "Nuria Izquierdo-Useros", - "author_inst": "IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916, Badalona, Catalonia, Spain" - }, - { - "author_name": "Marc Noguera-Julian", - "author_inst": "IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916, Badalona, Catalonia, Spain" - }, - { - "author_name": "Jorge Carrillo", - "author_inst": "IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916, Badalona, Catalonia, Spain" - }, - { - "author_name": "Roger Paredes", - "author_inst": "IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916, Badalona, Catalonia, Spain" - }, - { - "author_name": "Lourdes Mateu", - "author_inst": "Infectious Diseases Department, Fight against AIDS Foundation (FLS), Germans Trias i Pujol Hospital, 08916, Badalona, Catalonia, Spain" - }, - { - "author_name": "Anna Chamorro", - "author_inst": "Infectious Diseases Department, Fight against AIDS Foundation (FLS), Germans Trias i Pujol Hospital, 08916, Badalona, Catalonia, Spain" - }, - { - "author_name": "Ruth Toledo", - "author_inst": "Infectious Diseases Department, Fight against AIDS Foundation (FLS), Germans Trias i Pujol Hospital, 08916, Badalona, Catalonia, Spain" - }, - { - "author_name": "Marta Massanella", - "author_inst": "IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916, Badalona, Catalonia, Spain" - }, - { - "author_name": "Bonaventura Clotet", - "author_inst": "IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916, Badalona, Catalonia, Spain" - }, - { - "author_name": "Juli\u00e0 Blanco", - "author_inst": "IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916, Badalona, Catalonia, Spain" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.11.21261915", "rel_title": "Molecular and serological investigation of the 2021 COVID-19 case surge in Mongolian vaccinees", @@ -605992,6 +608184,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, + { + "rel_doi": "10.1101/2021.08.12.21261929", + "rel_title": "Seroprevalence of anti-SARS-CoV-2 antibodies six months into the vaccination campaign in Geneva, Switzerland", + "rel_date": "2021-08-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.12.21261929", + "rel_abs": "BackgroundUp-to-date seroprevalence estimates are critical to describe the SARS-CoV-2 immune landscape in the population and guide public health measures. We aimed to estimate the seroprevalence of anti-SARS-CoV-2 antibodies 15 months into the COVID-19 pandemic and six months into the vaccination campaign.\n\nMethodsWe conducted a population-based cross-sectional serosurvey between June 1 and July 7, 2021, recruiting participants from age- and sex-stratified random samples of the general population. We tested participants for anti-SARS-CoV-2 antibodies targeting the spike (S) or nucleocapsid (N) proteins (Roche Elecsys immunoassays). We estimated the anti-SARS-CoV-2 antibodies seroprevalence following vaccination and/or infection (anti-S antibodies), or infection only (anti-N antibodies).\n\nResultsWe included 3355 individuals, of which 1814 (54.1%) were women, 697 (20.8%) were aged <18 years and 449 (13.4%) were aged [≥]65 years, 2161 (64.4%) tested positive for anti-S antibodies, and 906 (27.0%) tested positive for anti-N antibodies. The total seroprevalence of anti-SARS-CoV-2 antibodies was 66.1% (95% credible interval, 64.1-68.0). We estimated that 29.9% (28.0-31.9) of the population developed antibodies after infection; the rest having developed antibodies only via vaccination. Seroprevalence estimates were similar across sexes, but differed markedly across age groups, being lowest among children aged 0-5 years (20.8% [15.5-26.7]) and highest among older adults aged [≥]75 years (93.1% [89.6-96.0]). Seroprevalence of antibodies developed via infection and/or vaccination was higher among participants with a higher educational level.\n\nConclusionsMost adults have developed anti-SARS-CoV-2 antibodies, while most teenagers and children remain vulnerable to infection. As the SARS-CoV-2 Delta variant spreads and vaccination rates stagnate, efforts are needed to address vaccine hesitancy, particularly among younger individuals and socioeconomically disadvantaged groups, and to minimize spread among children.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Silvia Stringhini", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Mar\u00eda-Eugenia Zaballa", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Nick Pullen", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Javier Perez-Saez", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Carlos de Mestral", + "author_inst": "Geneva University Hospitals (HUG)" + }, + { + "author_name": "Andrea Loizeau", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Julien Lamour", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Francesco Pennacchio", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Ania Wisniak", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Roxane Dumont", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "H\u00e9l\u00e8ne Baysson", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Viviane Richard", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Elsa Lorthe", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Claire Semaani", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Jean-Fran\u00e7ois Balavoine", + "author_inst": "University of Geneva" + }, + { + "author_name": "Didier Pittet", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Nicolas Vuilleumier", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Fran\u00e7ois Chappuis", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Omar Kherad", + "author_inst": "H\u00f4pital de la Tour" + }, + { + "author_name": "Andrew S Azman", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Klara Posfay-Barbe", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Laurent Kaiser", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Idris Guessous", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "- the Specchio-COVID19 Study Group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.12.21261981", "rel_title": "COVID-19 vaccine uptake among older people in relation to sociodemographic factors: cohort results from southern Sweden", @@ -606872,121 +609175,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.08.13.456228", - "rel_title": "A diabetic milieu increases cellular susceptibility to SARS-CoV-2 infections in engineered human kidney organoids and diabetic patients", - "rel_date": "2021-08-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.13.456228", - "rel_abs": "SARS-CoV-2 infections lead to a high risk of hospitalization and mortality in diabetic patients. Why diabetic individuals are more prone to develop severe COVID-19 remains unclear. Here, we established a novel human kidney organoid model that mimics early hallmarks of diabetic nephropathy. High oscillatory glucose exposure resulted in metabolic changes, expansion of extracellular membrane components, gene expression changes determined by scRNAseq, and marked upregulation of angiotensin-converting enzyme 2 (ACE2). Upon SARS-CoV-2 infection, hyperglycemic conditions lead to markedly higher viral loads in kidney organoids compared to normoglycemia. Genetic deletion of ACE2, but not of the candidate receptor BSG/CD147, in kidney organoids demonstrated the essential role of ACE2 in SARS-CoV-2 infections and completely prevented SARS-CoV-2 infection in the diabetogenic microenvironment. These data introduce a novel organoid model for diabetic kidney disease and show that diabetic-induced ACE2 licenses the diabetic kidney to enhanced SARS-CoV-2 replication.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Elena Garreta", - "author_inst": "Institute for Bioengineering of Catalonia" - }, - { - "author_name": "Praticia Prado", - "author_inst": "Institute for Bioengineering of Catalonia" - }, - { - "author_name": "Megan L. Stanifer", - "author_inst": "Universitatsklinikum Heidelberg" - }, - { - "author_name": "Vanessa Monteil", - "author_inst": "Karolinska Institute" - }, - { - "author_name": "Carmen Hurtado del Pozo", - "author_inst": "Institute for Bioengineering of Catalonia" - }, - { - "author_name": "Asier Ullate-Agote", - "author_inst": "University of Navarra" - }, - { - "author_name": "Amaia Vilas-Zornoza", - "author_inst": "University of Navarra" - }, - { - "author_name": "Juan Pablo Romero", - "author_inst": "University of Navarra" - }, - { - "author_name": "Gustav Jonsson", - "author_inst": "Institute of Molecular Biotechnology (IMBA)" - }, - { - "author_name": "Roger Oria", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Alexandra Leopoldi", - "author_inst": "Institute of Molecular Biotechnology of the Austrian Academy of Sciences" - }, - { - "author_name": "Astrid Hagelkrueys", - "author_inst": "Institute of Molecular Biotechnology (IMBA)" - }, - { - "author_name": "Daniel Moya-Rull", - "author_inst": "Institute for Bioengineering of Catalonia" - }, - { - "author_name": "Federico Gonzalez", - "author_inst": "Institute for Bioengineering of Catalonia" - }, - { - "author_name": "Andres Marco", - "author_inst": "Institute for Bioengineering of Catalonia" - }, - { - "author_name": "Carolina Tarantino", - "author_inst": "Institute for Bioengineering of Catalonia" - }, - { - "author_name": "Pere Domingo-Pedrol", - "author_inst": "Hospital de la Santa Creu i Sant Pau" - }, - { - "author_name": "Omar HasanAli", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Pedro Ventura-Aguiar", - "author_inst": "Hospital Clinic de Barcelona" - }, - { - "author_name": "Josep Maria Campistol", - "author_inst": "Hospital Clinic de Barcelona" - }, - { - "author_name": "Felipe Prosper", - "author_inst": "Clinica Universidad de Navarra" - }, - { - "author_name": "Ali Mirazimi", - "author_inst": "Karolinska Institute" - }, - { - "author_name": "Steeve Boulant", - "author_inst": "University Heidelberg" - }, - { - "author_name": "Josef Penninger", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Nuria Montserrat", - "author_inst": "Institute for Bioengineering of Catalonia" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2021.08.13.456190", "rel_title": "Screening of cell-virus, cell-cell, gene-gene interactions among kingdoms of life at single cell resolution", @@ -608126,6 +610314,97 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.08.12.456077", + "rel_title": "Hybrid immunity improves B cell frequency, antibody potency and breadth against SARS-CoV-2 and variants of concern", + "rel_date": "2021-08-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.12.456077", + "rel_abs": "To understand the nature of the antibody response to SARS-CoV-2 vaccination, we analyzed at single cell level the B cell responses of five naive and five convalescent people immunized with the BNT162b2 mRNA vaccine. Convalescents had higher frequency of spike protein specific memory B cells and by cell sorting delivered 3,532 B cells, compared with 2,352 from naive people. Of these, 944 from naive and 2,299 from convalescents produced monoclonal antibodies against the spike protein and 411 of them neutralized the original Wuhan SARS-CoV-2 virus. More than 75% of the monoclonal antibodies from naive people lost their neutralization activity against the B.1.351 (beta) and B.1.1.248 (gamma) variants while this happened only for 61% of those from convalescents. The overall loss of neutralization was lower for the B.1.1.7 (alpha) and B.1.617.2 (delta) variants, however it was always significantly higher in those of naive people. In part this was due to the IGHV2-5;IGHJ4-1 germline, which was found only in convalescents and generated potent and broadly neutralizing antibodies. Overall, vaccination of seropositive people increases the frequency of B cells encoding antibodies with high potency and that are not susceptible to escape by any of the four variants of concern. Our data suggest that people that are seropositive following infection or primary vaccination will produce antibodies with increased potency and breadth and will be able to better control SARS-CoV-2 emerging variants.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Emanuele Andreano", + "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy" + }, + { + "author_name": "Ida Paciello", + "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy" + }, + { + "author_name": "Giulia Piccini", + "author_inst": "VisMederi S.r.l, Siena, Italy" + }, + { + "author_name": "Noemi Manganaro", + "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy" + }, + { + "author_name": "Piero Pileri", + "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy" + }, + { + "author_name": "Inesa Hyseni", + "author_inst": "VisMederi S.r.l, Siena, Italy; VisMederi Research S.r.l., Siena, Italy" + }, + { + "author_name": "Margherita Leonardi", + "author_inst": "VisMederi S.r.l, Siena, Italy; VisMederi Research S.r.l., Siena, Italy" + }, + { + "author_name": "Elisa Pantano", + "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy" + }, + { + "author_name": "Valentina Abbiento", + "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy" + }, + { + "author_name": "Linda Benincasa", + "author_inst": "VisMederi Research S.r.l., Siena, Italy" + }, + { + "author_name": "Ginevra Giglioli", + "author_inst": "VisMederi Research S.r.l., Siena, Italy" + }, + { + "author_name": "Concetta De Santi", + "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy" + }, + { + "author_name": "Massimiliano Fabbiani", + "author_inst": "Department of Medical Biotechnologies, University of Siena, Siena, Italy" + }, + { + "author_name": "Ilaria Rancan", + "author_inst": "Department of Medical Biotechnologies, University of Siena, Siena, Italy; Department of Medical Sciences, Infectious and Tropical Diseases Unit, Siena Universit" + }, + { + "author_name": "Mario Tumbarello", + "author_inst": "Department of Medical Biotechnologies, University of Siena, Siena, Italy; Department of Medical Sciences, Infectious and Tropical Diseases Unit, Siena Universit" + }, + { + "author_name": "Francesca Montagnani", + "author_inst": "Department of Medical Biotechnologies, University of Siena, Siena, Italy; Department of Medical Sciences, Infectious and Tropical Diseases Unit, Siena Universit" + }, + { + "author_name": "Claudia Sala", + "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy" + }, + { + "author_name": "Emanuele Montomoli", + "author_inst": "VisMederi S.r.l, Siena, Italy; VisMederi Research S.r.l., Siena, Italy; Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy" + }, + { + "author_name": "Rino Rappuoli", + "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy; Department of Biotechnology, Chemistry and Pharmacy, University of Sien" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.08.12.21261943", "rel_title": "The impact of school closures on adolescent health-related outcomes during the COVID-19 pandemic: A natural experiment in South Korea", @@ -609302,97 +611581,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.08.11.455956", - "rel_title": "Molecular basis of immune evasion by the delta and kappa SARS-CoV-2 variants", - "rel_date": "2021-08-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.11.455956", - "rel_abs": "Worldwide SARS-CoV-2 transmission leads to the recurrent emergence of variants, such as the recently described B.1.617.1 (kappa), B.1.617.2 (delta) and B.1.617.2+ (delta+). The B.1.617.2 (delta) variant of concern is causing a new wave of infections in many countries, mostly affecting unvaccinated individuals, and has become globally dominant. We show that these variants dampen the in vitro potency of vaccine-elicited serum neutralizing antibodies and provide a structural framework for describing the impact of individual mutations on immune evasion. Mutations in the B.1.617.1 (kappa) and B.1.617.2 (delta) spike glycoproteins abrogate recognition by several monoclonal antibodies via alteration of key antigenic sites, including an unexpected remodeling of the B.1.617.2 (delta) N-terminal domain. The binding affinity of the B.1.617.1 (kappa) and B.1.617.2 (delta) receptor-binding domain for ACE2 is comparable to the ancestral virus whereas B.1.617.2+ (delta+) exhibits markedly reduced affinity. We describe a previously uncharacterized class of N-terminal domain-directed human neutralizing monoclonal antibodies cross-reacting with several variants of concern, revealing a possible target for vaccine development.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Matthew McCallum", - "author_inst": "University of Washington" - }, - { - "author_name": "Alexandra C Walls", - "author_inst": "University of Washington" - }, - { - "author_name": "Kaitlin R Sprouse", - "author_inst": "University of Washington" - }, - { - "author_name": "John E Bowen", - "author_inst": "University of Washington" - }, - { - "author_name": "Laura Rosen", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Ha V Dang", - "author_inst": "University of Washington" - }, - { - "author_name": "Anna deMarco", - "author_inst": "Humabs" - }, - { - "author_name": "Nicholas Franko", - "author_inst": "University of Washington" - }, - { - "author_name": "Sasha W Tilles", - "author_inst": "University of Washington" - }, - { - "author_name": "Jennifer Logue", - "author_inst": "University of Washington" - }, - { - "author_name": "Marcos C Miranda", - "author_inst": "University of Washington" - }, - { - "author_name": "Margaret Ahlrichs", - "author_inst": "University of Washington" - }, - { - "author_name": "Lauren Carter", - "author_inst": "University of Washington" - }, - { - "author_name": "Gyorgy Snell", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Matteo Samuele Pizzuto", - "author_inst": "Humabs" - }, - { - "author_name": "Helen Y Chu", - "author_inst": "University of Washington" - }, - { - "author_name": "Wesley C Van Voorhis", - "author_inst": "University of Washington" - }, - { - "author_name": "Davide Corti", - "author_inst": "Humabs" - }, - { - "author_name": "David Veesler", - "author_inst": "University of Washington" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.08.11.455960", "rel_title": "SARS-CoV-2 Spike Affinity and Dynamics Exclude the Strict Requirement of an Intermediate Host", @@ -610087,6 +612275,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.09.21261554", + "rel_title": "Progress of the Delta variant and erosion of vaccine effectiveness, a warning from Utah", + "rel_date": "2021-08-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.09.21261554", + "rel_abs": "Since the emergence of SARS-CoV-2, vaccines have been heralded as the best way to curtail the pandemic. Clinical trials have shown SARS-CoV-2 vaccines to be highly efficacious against both disease and infection. However, those currently in use were primarily tested against early lineages. Data on vaccine effectiveness (VE) against variants of concern (VOC), including the Delta variant (B.1.617.2), remain limited. To examine the effectiveness of vaccination in Utah we compared the proportion of cases reporting vaccination to that expected at different VEs, then estimated the combined daily vaccine effectiveness using a field evaluation approach. Delta has rapidly outcompeted all other variants and, as of June 20th, represents 70% of all SARS-CoV-2 viruses sequenced in Utah. If we attribute the entire change in VE to the Delta variant, the estimated vaccine effectiveness against Delta would be 82% (95% CI: 78%, 85%). We show a modest reduction in vaccine effectiveness against COVID-19 in Utah corresponding to the expansion of the Delta lineage in the state. This reduction in the effectiveness of available vaccines correlated with the arrival of novel VOCs, rather than waning immunity, is highly concerning.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Lindsay Keegan", + "author_inst": "University of Utah" + }, + { + "author_name": "Shaun A Truelove", + "author_inst": "Johns Hopksin Bloomberg School of Public Health" + }, + { + "author_name": "Justin Lessler", + "author_inst": "University of North Carolina at Chapel Hill" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.09.21261754", "rel_title": "Use of health care services during the Covid-19 pandemic in Ethiopia: Evidence from a health facility survey", @@ -610995,61 +613210,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.09.455472", - "rel_title": "Neutrophil-epithelial interactions augment infectivity and pro-inflammatory responses to SARS-CoV-2 infection", - "rel_date": "2021-08-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.09.455472", - "rel_abs": "In response to viral infection, neutrophils release inflammatory mediators as part of the innate immune response, contributing to pathogen clearance through virus internalization and killing. Pre-existing co- morbidities correlating to incidence of severe COVID-19 are associated with chronic airway neutrophilia. Furthermore, examination of COVID-19 explanted lung tissue revealed a series of epithelial pathologies associated with the infiltration and activation of neutrophils, indicating neutrophil activity in response to SARS- CoV-2 infection. To determine the impact of neutrophil-epithelial interactions on the infectivity and inflammatory responses to SARS-CoV-2 infection, we developed a co-culture model of airway neutrophilia. SARS-CoV-2 infection of the airway epithelium alone does not result in a notable pro-inflammatory response from the epithelium. The addition of neutrophils induces the release of proinflammatory cytokines and stimulates a significantly augmented pro-inflammatory response subsequent SARS-CoV-2 infection. The resulting inflammatory response is polarized with differential release from the apical and basolateral side of the epithelium. Additionally, the integrity of the epithelial barrier is impaired with notable epithelial damage and infection of basal stem cells. This study reveals a key role for neutrophil-epithelial interactions in determining inflammation and infectivity in response to SARS-CoV-2 infection.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Ben A Calvert", - "author_inst": "University of Southern California" - }, - { - "author_name": "Erik J Quiroz", - "author_inst": "University of Southern California" - }, - { - "author_name": "Zareeb Lorenzana", - "author_inst": "University of Southern California" - }, - { - "author_name": "Ngan Doan", - "author_inst": "University of Southern California" - }, - { - "author_name": "Seongjae Kim", - "author_inst": "The Salk Institute for Biological Studies" - }, - { - "author_name": "Christiana N Senger", - "author_inst": "University of Southern California" - }, - { - "author_name": "William D Wallace", - "author_inst": "University of Southern California" - }, - { - "author_name": "Matthew Salomon", - "author_inst": "University of Southern California" - }, - { - "author_name": "Jill Henley", - "author_inst": "University of Southern California" - }, - { - "author_name": "Amy L Ryan", - "author_inst": "University of Southern California" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2021.08.09.455715", "rel_title": "Cryo-EM structure determination of small proteins by nanobody-binding scaffolds (Legobodies)", @@ -611881,6 +614041,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rheumatology" }, + { + "rel_doi": "10.1101/2021.08.06.21261696", + "rel_title": "Safety and Immunogenicity of Inactivated SARS-CoV-2 Vaccine in High-Risk Occupational Population: a randomized, parallel, controlled clinical trial", + "rel_date": "2021-08-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.06.21261696", + "rel_abs": "Vaccination is urgently needed to prevent the global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we conducted a randomized, parallel, controlled clinical trial for assessment of the immunogenicity and safety of an inactivated SARS-CoV-2 vaccine, aiming to determine an appropriate vaccination interval for high-risk occupational population. Participants were randomly assigned to receive two doses of inactivated SARS-CoV-2 vaccine (4 {micro}g per dose) at an interval of either 14 days, 21 days or 28 days. The primary immunogenicity endpoints were neutralization antibody seroconversion and geometric mean titer (GMT) at 28 days after the second dose. Our results showed that the seroconversion rates (GMT [≥] 16) were all 100% in the three groups and the 0-21 and 0-28 groups elicited significantly higher SARS-CoV-2 neutralizing antibody level. All reported adverse reactions were mild. (Chinese Clinical Trial Registry: ChiCTR2100041705, ChiCTR2100041706)", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Yongliang Feng", + "author_inst": "Shanxi Medical University" + }, + { + "author_name": "Jing Chen", + "author_inst": "Shanxi Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Tian Yao", + "author_inst": "Shanxi Medical University" + }, + { + "author_name": "Yue Chang", + "author_inst": "Shanxi Medical University" + }, + { + "author_name": "Xiaoqing Li", + "author_inst": "Shanxi Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Rongqin Xing", + "author_inst": "Outpatient Department of Shanxi Aviation Industry Group Co. LTD" + }, + { + "author_name": "Hong Li", + "author_inst": "Shanxi Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Ruixue Xie", + "author_inst": "Shanxi Medical University" + }, + { + "author_name": "Xiaohong Zhang", + "author_inst": "Shanxi Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Zhiyun Wei", + "author_inst": "Shanxi Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Shengcai Mu", + "author_inst": "Shanxi Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Ling Liu", + "author_inst": "Shanxi Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Lizhong Feng", + "author_inst": "Shanxi Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Suping Wang", + "author_inst": "Shanxi Medical University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.06.21261689", "rel_title": "Internet Use impact on Physical Health during COVID-19 pandemic in Bangladesh: A Web-based Cross-sectional study", @@ -612917,77 +615148,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.06.21261725", - "rel_title": "Modelling the effectiveness and social costs of daily lateral flow antigen tests versus quarantine in preventing onward transmission of COVID-19 from traced contacts", - "rel_date": "2021-08-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.06.21261725", - "rel_abs": "Quarantining close contacts of individuals infected with SARS-CoV-2 for 10 to 14 days is a key strategy in reducing transmission. However, quarantine requirements are often unpopular, with low adherence, especially when a large fraction of the population has been vaccinated. Daily contact testing (DCT), in which contacts are required to isolate only if they test positive, is an alternative to quarantine for mitigating the risk of transmission from traced contacts. In this study, we developed an integrated model of COVID-19 transmission dynamics and compared the strategies of quarantine and DCT with regard to reduction in transmission and social/economic costs (days of quarantine/self-isolation). Specifically, we compared 10-day quarantine to 7 days of self-testing using rapid lateral flow antigen tests, starting 3 days after exposure to a case. We modelled both incomplete adherence to quarantine and incomplete adherence to DCT. We found that DCT reduces transmission from contacts with similar effectiveness, at much lower social/economic costs, especially for highly vaccinated populations. The findings were robust across a spectrum of scenarios with varying assumptions on the speed of contact tracing, sensitivity of lateral flow antigen tests, adherence to quarantine and uptake of testing. Daily tests would also allow rapid initiation of a new round of tracing from infected contacts.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Luca Ferretti", - "author_inst": "Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK" - }, - { - "author_name": "Chris Wymant", - "author_inst": "Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK" - }, - { - "author_name": "Anel Nurtay", - "author_inst": "Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK" - }, - { - "author_name": "Lele Zhao", - "author_inst": "Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK" - }, - { - "author_name": "Robert Hinch", - "author_inst": "Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK" - }, - { - "author_name": "David Bonsall", - "author_inst": "Wellcome Centre for Human Genetics, Nuffield Departmentof Medicine, University of Oxford, Oxford, UK" - }, - { - "author_name": "Michelle Kendall", - "author_inst": "Department of Statistics, University of Warwick, Coventry, UK" - }, - { - "author_name": "Joanna Masel", - "author_inst": "Department of Ecology and Evolutionary Biology, University of Arizona, Tucson AZ, USA" - }, - { - "author_name": "John Bell", - "author_inst": "Nuffield Department of Medicine, University of Oxford, Oxford, UK" - }, - { - "author_name": "Susan Hopkins", - "author_inst": "National Infection Service, Public Health England, London, UK" - }, - { - "author_name": "A. Marm Kilpatrick", - "author_inst": "Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California, USA" - }, - { - "author_name": "Tim Peto", - "author_inst": "Nuffield Department of Medicine, University of Oxford, Oxford, UK" - }, - { - "author_name": "Lucie Abeler-D\u00f6rner", - "author_inst": "Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK" - }, - { - "author_name": "Christophe Fraser", - "author_inst": "Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.08.06.21261721", "rel_title": "Neutralizing antibody responses to SARS-CoV-2 variants in vaccinated Ontario long-term care home residents and workers", @@ -614023,6 +616183,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.08.04.21261235", + "rel_title": "MFDNN: Multi-channel feature deep neural network algorithm to identify Covid19 chest X-ray images", + "rel_date": "2021-08-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.04.21261235", + "rel_abs": "The use of chest X-ray images (CXI) to detect Severe Acute Respiratory Syndrome Coronavirus 2 (SARS CoV-2) caused by Coronavirus Disease 2019 (COVID-19) is life-saving important for both patients and doctors. This research proposed a multi-channel feature deep neural network algorithm to screen people infected with COVID-19. The algorithm integrates data oversampling technology and a multi-channel feature deep neural network model to carry out the training process in an end-to-end manner. In the experiment, we used a publicly available CXI database with 10,192 Normal, 6012 Lung Opacity (Non-COVID lung infection), and 1345 Viral Pneumonia images. Compared with traditional deep learning models (Densenet201, ResNet50, VGG19, GoogLeNet), the MFDNN model obtains an average test accuracy of 93.19% in all data. Furthermore, in each type of screening, the precision, recall, and F1 Score of the MFDNN model are also better than traditional deep learning networks. Secondly, compared with the latest CoroDet model, the MFDNN algorithm is 1.91% higher than the CoroDet model in the experiment of detecting the four categories of COVID19 infected persons. Finally, our experimental code will be placed at https://github.com/panliangrui/covid19.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Liangrui Pan", + "author_inst": "prince of songkla university" + }, + { + "author_name": "boya ji", + "author_inst": "HuNan university" + }, + { + "author_name": "Xiaoqi wang", + "author_inst": "HuNan university" + }, + { + "author_name": "shaoliang peng", + "author_inst": "HuNan university" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2021.08.06.455441", "rel_title": "VPS29 exerts opposing effects on endocytic viral entry", @@ -614951,41 +617142,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.08.05.21261683", - "rel_title": "Rapid transmission of coronavirus disease 2019 within a religious sect in South Korea: a mathematical modeling study", - "rel_date": "2021-08-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.05.21261683", - "rel_abs": "Rapid transmission of coronavirus disease 2019 (COVID-19) was observed in the Shincheonji Church of Jesus, a religious sect in South Korea. The index case was confirmed on February 18, 2020 in Daegu City, and within two weeks, 3,081 connected cases were identified. Doubling times during these initial stages (i.e., February 18 - March 2) of the outbreak were less than 2 days. A stochastic model fitted to the time series of confirmed cases suggests that the basic reproduction number (R0) of COVID-19 was 8.5 [95% credible interval (CrI): 6.3, 10.9] among the church members, whereas (R0 = 1.9 [95% CrI: 0.4, 4.4]) in the rest of the population of Daegu City. The model also suggests that there were already 4 [95% CrI: 2, 11] undetected cases of COVID-19 on February 7 when the index case reportedly presented symptoms. The Shincheonji Church cluster is likely to be emblematic of other outbreak-prone populations where R0 of COVID-19 is higher. Understanding and subsequently limiting the risk of transmission in such high-risk places is key to effective control.\n\nHighlightsO_LIBasic reproduction number (R0) of COVID-19 in a religious community of Shincheonji Church of Jesus was estimated to be 8.5 [95% credible interval (CrI): 6.3, 10.9], which is more than 4 times larger than the general population (R0 = 1.9 [95% CrI: 0.4, 4.4])\nC_LIO_LIThere were estimated 4 [95% CrI: 2, 11] undetected cases when the index case from the religious community reported symptom on February 7.\nC_LIO_LIThe Shincheonji Church cluster is likely to be emblematic of other outbreak-prone populations where R0 of COVID-19 is higher. Understanding and subsequently limiting the risk of transmission in such high-risk places is key to effective control.\nC_LI", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Jong-Hoon Kim", - "author_inst": "International Vaccine Institute" - }, - { - "author_name": "Hyojung Lee", - "author_inst": "National Institute for Mathematical Sciences, Daejeon, South Korea; Department of Statistics, Kyungpook National University, Daegu 41566, South Korea" - }, - { - "author_name": "Yong Sul Won", - "author_inst": "National Institute for Mathematical Sciences, Daejeon, South Korea" - }, - { - "author_name": "Woo-Sik Son", - "author_inst": "National Institute for Mathematical Sciences, Daejeon, South Korea" - }, - { - "author_name": "Justin Im", - "author_inst": "International Vaccine Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.05.21261663", "rel_title": "COVID-19 & Mental Health: Impact on Working people and Students", @@ -615857,6 +618013,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.05.21261633", + "rel_title": "COVID-19 vaccination coverage and hesitancy among groups prioritised in Australia's vaccine rollout", + "rel_date": "2021-08-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.05.21261633", + "rel_abs": "BackgroundCOVID-19 vaccination is the cornerstone of managing Australias COVID-19 pandemic and the success of the vaccination program depends on high vaccination coverage. This paper examined differences in COVID-19 vaccination coverage and vaccine hesitancy for people with disability, long-term health conditions, and carers - subgroups that were prioritised in the vaccination program.\n\nMethodsUsing data from 2,400 Australians who participated in two waves of the Taking the Pulse of the Nation survey in April and May 2021, we described vaccination coverage and hesitancy among people with disability, severe mental health conditions, severe long-term health conditions, frequent need for assistance with everyday activities, and carers, disaggregated by age group and gender.\n\nFindingsVaccination coverage was estimated to be 8.2% in the sample overall and was similar for people with disability, those with frequent need for assistance, and carers. It was higher for people with severe long-term health conditions (13.4%) and lower for people with severe mental health conditions (4.3%). Vaccine hesitancy was high overall (35.6%) and was similarly high across the priority groups.\n\nInterpretationThis study highlights the lack of a difference in vaccination coverage and vaccine hesitancy for people with disability, long-term health conditions, and carers compared to the general population. Sub-optimal vaccination coverage for people in the priority population groups leaves many people at significant risk of serious disease or death if exposed to COVID-19, particularly in light of the easing of disease-control restrictions across Australia and the emergence of new COVID-19 variants.\n\nFundingNational Health and Medical Research Council", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Zoe Aitken", + "author_inst": "The University of Melbourne" + }, + { + "author_name": "Eric Emerson", + "author_inst": "Lancaster University" + }, + { + "author_name": "Anne Kavanagh", + "author_inst": "The University of Melbourne" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.06.21261711", "rel_title": "Preterm birth rates during the COVID-19 lockdown in Queensland Australia", @@ -616945,89 +619128,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, - { - "rel_doi": "10.1101/2021.08.04.21261471", - "rel_title": "Integrated miRNA/cytokine/chemokine profiling reveals immunopathological step changes associated with COVID-19 severity", - "rel_date": "2021-08-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.04.21261471", - "rel_abs": "Circulating microRNAs (miRNAs) are exceptional mechanism-based correlates of disease, yet their potential remains largely untapped in COVID-19. Here, we determined circulating miRNA and cytokine and chemokine (CC) profiles in 171 blood plasma samples from 58 hospitalised COVID-19 patients. Thirty-two miRNAs were differentially expressed in severe cases when compared to moderate and mild cases. These miRNAs and their predicted targets reflected key COVID-19 features including cell death and hypoxia. Compared to mild cases, moderate and severe cases were characterised by a global decrease in circulating miRNA levels. Partial least squares regression using miRNA and CC measurements allowed for discrimination of severe cases with greater accuracy (87%) than using miRNA or CC levels alone. Correlation analysis revealed severity group-specific associations between CC and miRNA levels. Importantly, the miRNAs that correlated with IL6 and CXCL10, two cardinal COVID-19-associated cytokines, were distinct between severity groups, providing a novel qualitative way to stratify patients with similar levels of proinflammatory cytokines but different disease severity. Integration of miRNA and CC levels with clinical parameters revealed severity-specific signatures associated with clinical hallmarks of COVID-19. Our study highlights the existence of severity-specific circulating CC/miRNA networks, providing insight into COVID-19 pathogenesis and a novel approach for monitoring COVID-19 progression.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Julie C. WIlson", - "author_inst": "University of York" - }, - { - "author_name": "David Kealy", - "author_inst": "University of York" - }, - { - "author_name": "Sally R. James", - "author_inst": "University of York" - }, - { - "author_name": "Katherine Newling", - "author_inst": "University of York" - }, - { - "author_name": "Christopher Jagger", - "author_inst": "University of Manchester" - }, - { - "author_name": "Kara Filbey", - "author_inst": "University of Manchester" - }, - { - "author_name": "Elizabeth Mann", - "author_inst": "University of Manchester" - }, - { - "author_name": "Joanne Konkel", - "author_inst": "University of Manchester" - }, - { - "author_name": "Madhvi Menon", - "author_inst": "University of Manchester" - }, - { - "author_name": "Sean B. Knight", - "author_inst": "University of Manchester" - }, - { - "author_name": "Angela Simspon", - "author_inst": "University of Manchester" - }, - { - "author_name": "- CIRCO collaborative group", - "author_inst": "" - }, - { - "author_name": "John R. Grainger", - "author_inst": "University of Manchester" - }, - { - "author_name": "Tracy Hussell", - "author_inst": "University of Manchester" - }, - { - "author_name": "Paul M Kaye", - "author_inst": "University of York" - }, - { - "author_name": "Nathalie Signoret", - "author_inst": "University of York" - }, - { - "author_name": "Dimitris Lagos", - "author_inst": "University of York" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.03.21260940", "rel_title": "Symptom Persistence Despite Improvement in Cardiopulmonary Health - Insights from longitudinal CMR, CPET and lung function testing post-COVID-19", @@ -617623,6 +619723,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.01.21261397", + "rel_title": "Study protocol for the Innovative Support for Patients with SARS-COV-2 Infections Registry (INSPIRE): a longitudinal study of the medium and long-term sequelae of SARS-CoV-2 infection", + "rel_date": "2021-08-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.01.21261397", + "rel_abs": "BACKGROUNDReports on medium and long-term sequelae of SARS-CoV-2 infections largely lack quantification of incidence and relative risk. We describe the rationale and methods of the Innovative Support for Patients with SARS-CoV-2 Registry (INSPIRE) that combines patient-reported outcomes with data from digital health records to understand predictors and impacts of SARS-CoV-2 infection.\n\nMETHODSINSPIRE is a prospective, multicenter, longitudinal study of individuals with symptoms of SARS-CoV-2 infection in eight regions across the US. Adults are eligible for enrollment if they are fluent in English or Spanish, reported symptoms suggestive of acute SARS-CoV-2 infection, and if they are within 42 days of having a SARS-CoV-2 viral test (i.e., nucleic acid amplification test or antigen test), regardless of test results. Recruitment occurs in-person, by phone or email, and through online advertisement. A secure online platform is used to facilitate the collation of consent-related materials, digital health records, and responses to self-administered surveys. Participants are followed for up to 18 months, with patient-reported outcomes collected every three months via survey and linked to concurrent digital health data; follow-up includes no in-person involvement. Our planned enrollment is 4,800 participants, including 2,400 SARS-CoV-2 positive and 2,400 SARS-CoV-2 negative participants (as a concurrent comparison group). These data will allow assessment of longitudinal outcomes from SARS-CoV-2 infection and comparison of the relative risk of outcomes in individuals with and without infection. Patient-reported outcomes include self-reported health function and status, as well as clinical outcomes including health system encounters and new diagnoses.\n\nRESULTSParticipating sites obtained institutional review board approval. Enrollment and follow-up are ongoing.\n\nCONCLUSIONSThis study will characterize medium and long-term sequelae of SARS-CoV-2 infection among a diverse population, predictors of sequelae, and their relative risk compared to persons with similar symptomatology but without SARS-CoV-2 infection. These data may inform clinical interventions for individuals with sequelae of SARS-CoV-2 infection.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Kelli N. O'Laughlin", + "author_inst": "University of Washington" + }, + { + "author_name": "Matthew Thompson", + "author_inst": "University of Washington" + }, + { + "author_name": "Bala Hota", + "author_inst": "Rush University Medical Center" + }, + { + "author_name": "Michael Gottlieb", + "author_inst": "Rush University Medical Center" + }, + { + "author_name": "Ian D. Plumb", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Anna Marie Chang", + "author_inst": "Thomas Jefferson University" + }, + { + "author_name": "Lauren E. Wisk", + "author_inst": "David Geffen School of Medicine at UCLA" + }, + { + "author_name": "Aron J. Hall", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Ralph C. Wang", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Erica S. Spatz", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Kari A. Stephens", + "author_inst": "University of Washington" + }, + { + "author_name": "Ryan M. Heubinger", + "author_inst": "Rush University" + }, + { + "author_name": "Samuel A. McDonald", + "author_inst": "UT Southwestern" + }, + { + "author_name": "Arjun Venkatesh", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Nikki Gentile", + "author_inst": "University of Washington" + }, + { + "author_name": "Benjamin H. Slovis", + "author_inst": "Thomas Jefferson University" + }, + { + "author_name": "Mandy Hill", + "author_inst": "UTHealth McGovern Medical School" + }, + { + "author_name": "Sharon Saydah", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Ahamed H. Idris", + "author_inst": "UT Southwestern" + }, + { + "author_name": "Robert Rodriquez", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Harlan M. Krumholz", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Joann G. Elmore", + "author_inst": "Yale University" + }, + { + "author_name": "Robert A. Weinstein", + "author_inst": "Rush University Medical Center" + }, + { + "author_name": "Graham Nichol", + "author_inst": "University of Washington" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.01.21261309", "rel_title": "Multiple-time measurements of multidimensional psychiatric states from immediately before the COVID-19 pandemic to one year later: A longitudinal online survey of the Japanese population", @@ -619219,45 +621430,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2021.08.04.455042", - "rel_title": "But Mouse, you are not alone: On some severe acute respiratory syndrome coronavirus 2 variants infecting mice", - "rel_date": "2021-08-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.04.455042", - "rel_abs": "In silico predictions combined with in vitro, in vivo and in situ observations collectively suggest that mouse adaptation of the SARS-CoV-2 virus requires an aromatic substitution in position 501 or position 498 (but not both) of the spike proteins receptor binding domain. This effect could be enhanced by mutations in positions 417, 484, and 493 (especially K417N, E484K, Q493K and Q493R), and to a lesser extent by mutations in positions 486 and 499 (such as F486L and P499T). Such enhancements due to more favourable binding interactions with residues on the complementary angiotensin-converting enzyme 2 (ACE2) interface, are however, unlikely to sustain mouse infectivity on their own based on theoretical and experimental evidence to date. Our current understanding thus points to the Alpha, Beta, Gamma, and Omicron variants of concern infecting mice, while Delta and Delta Plus lack a similar biomolecular basis to do so. This paper identifies eleven countries (Brazil, Chile, Djibouti, Haiti, Malawi, Mozambique, Reunion, Suriname, Trinidad and Tobago, Uruguay and Venezuela) where targeted local field surveillance of mice is encouraged because they may have come in contact with humans who had the virus with adaptive mutation(s). It also provides a systematic methodology to analyze the potential for other animal reservoirs and their likely locations.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Michael J Kuiper", - "author_inst": "Commonwealth Scientific and Industrial Research Organisation" - }, - { - "author_name": "Laurence Wilson", - "author_inst": "CSIRO" - }, - { - "author_name": "Shruthi Mangalaganesh", - "author_inst": "Monash University" - }, - { - "author_name": "Carol Lee", - "author_inst": "Commonwealth Scientific and Industrial Research Organisation" - }, - { - "author_name": "Daniel Reti", - "author_inst": "Centre for Population Genomics" - }, - { - "author_name": "Seshadri S Vasan", - "author_inst": "Commonwealth Scientific and Industrial Research Organisation" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "confirmatory results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.08.05.455126", "rel_title": "Optical nanoscopy reveals SARS-CoV-2-induced remodeling of human airway cells", @@ -619909,6 +622081,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.02.21261502", + "rel_title": "SARS-CoV-2 viral load monitoring by extraction-free testing of saliva", + "rel_date": "2021-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.02.21261502", + "rel_abs": "Real-time quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) remains the foundation of SARS-CoV-2 testing due to its accessibility, scalability, and superior assay performance. Variability in specimens and methods prevent standardization of RT-qPCR assays and reliable quantitative reporting to assess viral load. We developed an extraction-free RT-qPCR assay for detection of SARS-CoV-2 in saliva and monitored viral load until convalescence in COVID-19 patients. Comparison of 231 matched anterior nares swab and saliva specimens demonstrated that extraction-free testing of saliva has equivalent analytical and clinical assay performance compared to testing of RNA extracts from either anterior nares or saliva specimens. Analysis of specimen pairs revealed higher viral loads in the nasal cavity compared to the oral cavity, although this difference did not impact clinical sensitivity for COVID-19. Extraction-free testing of a combination specimen consisting of both nasal swab and saliva is also demonstrated. Assessment of viral load by RT-qPCR and parallel digital droplet PCR (ddPCR) revealed that cycle threshold (Ct) values less than approximately 30 correlated well with viral load, whereas Ct values greater than 30 correspond to low viral loads <10 copies/{micro}L. Therefore, extraction-free saliva testing maximizes testing efficiency without compromising assay performance and approximates viral loads >10 copies/{micro}L. This technology can facilitate high-throughput laboratory testing for SARS-CoV-2, monitor viral load in individual patients, and assess efficacy of therapies for COVID-19.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Yue Qiu", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Ling Lu", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Dexiang Gao", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Patrick McGrath", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Chann Han", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Igor Kogut", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Bob Blomquist", + "author_inst": "Summit Biolabs, Inc" + }, + { + "author_name": "Xin Yao", + "author_inst": "Summit Biolabs, Inc" + }, + { + "author_name": "Jose P Zevallos", + "author_inst": "Washington University in St. Louis" + }, + { + "author_name": "Brian Harry", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Shi-long Lu", + "author_inst": "University of Colorado Anschutz Medical Campus" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.03.21261545", "rel_title": "Domestic and international mobility trends in the United Kingdom during the COVID-19 pandemic: An analysis of Facebook data", @@ -621041,29 +623272,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.01.21261458", - "rel_title": "Aspergillosis and Mucormycosis in COVID-19 Patients; a Systematic Review and Meta-analysis.", - "rel_date": "2021-08-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.01.21261458", - "rel_abs": "Fungal infections have increased in number since the onset of this lethal pandemic. The aim of this study is to assess risk factors and case fatality in COVID-19 cases with aspergillosis or mucormycosis. Systematic review and meta-analysis was done according to PRISMA guidelines. Data bases used were Google scholar, Pakmedinet, PUBMED and MEDLINE. 21 case reports and case series of mucormycosis in COVID-19 patients were identified and mean age was 56.3 years (36 males and 12 females). The most common comorbidity was diabetes and site was Rhino orbital mucormycosis. Case fatality of 48 combined cases was calculated to be 52%. 19 articles of aspergillosis were included. Diabetes was the most common comorbidity in cases. The number of male cases were more than females. Incidence of aspergillosis in critically sick COVID-19 patients was calculated to be 9.3%. Case fatality was calculated to be 51.2%. Screening can be a beneficial tool for decreasing the morbidity and mortality.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Prof. Saira Afzal", - "author_inst": "King Edward Medical University" - }, - { - "author_name": "Mehreen Nasir", - "author_inst": "King Edward Medical University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.23.21261029", "rel_title": "Adverse events following COVID-19 virus vaccination in Japanese young population: The first cross-sectional study conducted by a questionnaire survey after the first-time-injection", @@ -622075,6 +624283,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.31.21261425", + "rel_title": "Performance of three molecular tests for SARS-CoV-2 on a university campus estimated jointly with Bayesian latent class modeling", + "rel_date": "2021-08-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.31.21261425", + "rel_abs": "Accurate tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been critical in efforts to control its spread. The accuracy of molecular tests for SARS-CoV-2 has been assessed numerous times, usually in reference to a gold standard diagnosis. One major disadvantage of that approach is the possibility of error due to inaccuracy of the gold standard, which is especially problematic for evaluating testing in a real-world surveillance context. We used an alternative approach known as Bayesian latent class modeling (BLCM), which circumvents the need to designate a gold standard by simultaneously estimating the accuracy of multiple tests. We applied this technique to a collection of 1,716 tests of three types applied to 853 individuals on a university campus during a one-week period in October 2020. We found that reverse transcriptase polymerase chain reaction (RT-PCR) testing of saliva samples performed at a campus facility had higher sensitivity (median: 0.923; 95% credible interval: 0.732-0.996) than RT-PCR testing of nasal samples performed at a commercial facility (median: 0.859; 95% CrI: 0.547-0.994). The reverse was true for specificity, although the specificity of saliva testing was still very high (median: 0.993; 95% CrI: 0.983-0.999). An antigen test was less sensitive and specific than both of the RT-PCR tests. These results suggest that RT-PCR testing of saliva samples at a campus facility can be an effective basis for surveillance screening to prevent SARS-CoV-2 transmission in a university setting.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Alex Perkins", + "author_inst": "University of Notre Dame" + }, + { + "author_name": "Melissa Stephens", + "author_inst": "University of Notre Dame" + }, + { + "author_name": "Wendy Alvarez Barrios", + "author_inst": "University of Notre Dame" + }, + { + "author_name": "Sean M. Cavany", + "author_inst": "University of Notre Dame" + }, + { + "author_name": "Liz Rulli", + "author_inst": "University of Notre Dame" + }, + { + "author_name": "Michael E. Pfrender", + "author_inst": "University of Notre Dame" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.31.21261422", "rel_title": "COVID-19 Mortality in Women and Men in Sub-Saharan Africa: A Cross Sectional Study", @@ -623043,89 +625290,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.07.30.21261288", - "rel_title": "TREATMENTS, RESOURCE UTILIZATION, AND OUTCOMES OF COVID-19 PATIENTS PRESENTING TO EMERGENCY DEPARTMENTS ACROSS PANDEMIC WAVES: AN OBSERVATIONAL STUDY BY THE CANADIAN COVID-19 EMERGENCY DEPARTMENT RAPID RESPONSE NETWORK (CCEDRRN)", - "rel_date": "2021-08-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.30.21261288", - "rel_abs": "BackgroundTreatment strategies for coronavirus disease 2019 (COVID-19) evolved between pandemic waves. Our objective was to compare treatments, acute care resource utilization, and outcomes of COVID-19 patients presenting to Emergency Departments across two pandemic waves.\n\nMethodsThis observational study enrolled consecutive eligible COVID-19 patients presenting to 46 Emergency Departments participating in the Canadian COVID-19 Emergency Department Rapid Response Network (CCEDRRN) between March 1 and December 31, 2020. We collected data by retrospective chart review. Our primary outcome was in-hospital mortality. We used logistic regression modeling to assess the impact of pandemic wave on outcomes.\n\nResultsWe enrolled 9,967 patients in 8 provinces, 3,336 from the first and 6,631 from the second wave. Patients in the second wave were younger, fewer met criteria for severe COVID-19, and more were discharged from the Emergency Department. Adjusted for patient characteristics and disease severity, steroid use increased (odds ratio [OR] 8.0; 95% confidence interval [CI] 6.4 - 10.0), while the use of invasive mechanical ventilation decreased (OR 0.5; 95%CI 0.4 - 0.6) in the second wave. After adjusting for differences in patient characteristics and disease severity, the odds of hospitalization (OR 0.7; 95%CI 0.6 - 0.8) and critical care admission (OR 0.6; 95%CI 0.4 - 0.7) decreased, while mortality remained unchanged (OR 1.0; 95%CI 0.7-1.4).\n\nInterpretationIn patients presenting to Canadian acute care facilities, rapid uptake of steroid therapy was evident. Mortality was stable despite lower critical care utilization in the second wave.\n\nTrial RegistrationClinicaltrials.gov, NCT04702945", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Corinne M Hohl", - "author_inst": "Department of Emergency Medicine, University of British Columbia, Vancouver, Canada" - }, - { - "author_name": "Rhonda J Rosychuk", - "author_inst": "Department of Pediatrics, University of Alberta, Edmonton, Canada" - }, - { - "author_name": "Jeffrey P Hau", - "author_inst": "Department of Emergency Medicine, University of British Columbia, Vancouver, Canada" - }, - { - "author_name": "Jake Hayward", - "author_inst": "Department of Emergency Medicine, University of Alberta, Edmonton, Canada" - }, - { - "author_name": "Megan Landes", - "author_inst": "Division of Emergency Medicine, University of Toronto, Toronto, Canada" - }, - { - "author_name": "Justin W Yan", - "author_inst": "Division of Emergency Medicine, London Health Sciences Centre, London, Canada" - }, - { - "author_name": "Daniel K Ting", - "author_inst": "Department of Emergency Medicine, University of British Columbia, Vancouver, Canada" - }, - { - "author_name": "Michelle Welsford", - "author_inst": "Division of Emergency Medicine, McMaster University, Hamilton, Canada" - }, - { - "author_name": "Patrick M Archambault", - "author_inst": "Department of Family Medicine and Emergency Medicine, Universit\u00e9 Laval, Qu\u00e9bec, Canada." - }, - { - "author_name": "Eric Mercier", - "author_inst": "Centre de recherche, CHU de Qu\u00e9bec, Universit\u00e9 Laval, Qu\u00e9bec, Canada" - }, - { - "author_name": "Kavish Chandra", - "author_inst": "Department of Emergency Medicine, Dalhousie Medicine New Brunswick, Saint John, Canada" - }, - { - "author_name": "Philip Davis", - "author_inst": "Department of Emergency Medicine, University of Saskatchewan, Saskatoon, Canada." - }, - { - "author_name": "Samuel Vaillancourt", - "author_inst": "Department of Emergency Medicine, St Michael's Hospital, Unity Health Toronto, Toronto, Canada" - }, - { - "author_name": "Murdoch Leeies", - "author_inst": "Department of Emergency Medicine, University of Manitoba, Winnipeg, Canada" - }, - { - "author_name": "Serena Small", - "author_inst": "Department of Emergency Medicine, University of British Columbia, Vancouver, Canada" - }, - { - "author_name": "Laurie J Morrison", - "author_inst": "Department of Emergency Medicine, St Michael's Hospital, Unity Health Toronto, Toronto, Canada" - }, - { - "author_name": "- Canadian COVID-19 Emergency Department Rapid Response Network", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "emergency medicine" - }, { "rel_doi": "10.1101/2021.07.29.21261308", "rel_title": "Decline in pneumococcal disease in young children during the COVID-19 pandemic associated with suppression of seasonal respiratory viruses, despite persistent pneumococcal carriage: A prospective cohort study", @@ -624029,6 +626193,57 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.07.28.21261254", + "rel_title": "Transmission of SARS-CoV-2 from pre and asymptomatic infected individuals. A systematic review", + "rel_date": "2021-07-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.28.21261254", + "rel_abs": "BackgroundThe transmission role of SARS-Cov-2 infected persons who develop symptoms post testing (pre symptomatics) or not at all throughout the course of positivity (asymptomatics) is unknown. We carried out a systematic review of available evidence to determine whether they were infectious or not and if so for how long and their probable contribution to the pandemic spread of SARS-CoV-2.\n\nMethodsWe searched LitCovid, medRxiv, Google Scholar and the WHO Covid-19 databases and reference lists of included studies. Search terms were COVID-19, SARS-CoV-2, transmission, asymptomatic, presymptomatic and appropriate synonyms. Searches were carried out to 31 March 2021. We included studies on people exposed to SARS CoV-2 within 2-14 days (incubation time) of close contact or suspected community or institutional exposure to index asymptomatic (at the time of observation) infected individuals, as defined in the study. We included studies with a proven or hypothesised chain of transmission with secondary case infected based on fulfilling a confirmed or probable case definition and confirmation of infectiousness and transmission outcome based either on serial PCR cycle threshold readings or viral culture or gene sequencing or any combination thereof and adequate follow up. We assessed the reliability of eliciting symptom and signs compatible with contemporary knowledge and extracted documentation of the likelihood of transmission, presence of replicating virus and/or documentation of phylodynamics (genetic sequence lineage) and/or adequate follow-up and reporting of symptoms and signs. We wrote to all included studies corresponding authors to request further details and assessed likelihood of transmission using adapted causality criteria.\n\nResultsWe included 18 studies from a variety of settings. Because of the current lack of standardized methodology and clear reporting criteria there was substantial methodological variation in transmission studies. Asymptomatic prevalence at the time of initial testing varied from 12.5% to 100% and of these 6% to 100% were pre-symptomatic cases, depending on the setting and the methods of case ascertainment and the population. Nursing/care home facilities reported high rates of presymptomatic: 50% - 100% (n=3 studies). Fifteen studies were classified as high risk and three studies at moderate risk of symptom ascertainment bias. In practice, this assessment means that high-risk studies may be less likely to distinguish between pre-symptomatic and asymptomatic cases. Six of the asymptomatic studies and four presymptomatic studies reported growing infectious virus although the data was too sparse to determine duration of infectiousness. Three studies were judged as providing possible and three of probable/likely evidence of asymptomatic transmission of SARs-CoV-2. Five studies provided evidence of possible and two of probable/likely presymptomatic transmission of SARs-CoV-2. Author response rate was 100%.\n\nConclusionsReliable studies included here provide probable evidence of transmission of SARS-CoV-2 from presymptomatic and asymptomatic individuals. Single point in time estimates and binary PCR testing alone cannot provide reliable information on symptom status and information on infectivity. The number of studies and asymptomatic and presymptomatic cases eligible for inclusion was low, with more data and international standardisation of methods needed to further reduce uncertainty.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Tom Jefferson", + "author_inst": "University of Oxford" + }, + { + "author_name": "Elizabeth A Spencer", + "author_inst": "University of Oxford" + }, + { + "author_name": "Jon Brassey", + "author_inst": "Trip Database Ltd" + }, + { + "author_name": "Igho Onakpoya", + "author_inst": "UNIVERSITY OF OXFORD" + }, + { + "author_name": "Elena Rosca", + "author_inst": "University of Oxford" + }, + { + "author_name": "Annette Pluddeman", + "author_inst": "University of Oxford" + }, + { + "author_name": "David Evans", + "author_inst": "University of Alberta" + }, + { + "author_name": "John Conly", + "author_inst": "University of Calgary" + }, + { + "author_name": "Carl Heneghan", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.28.21261261", "rel_title": "Predictors of COVID-19 vaccination uptake and reasons for decline of vaccination: a systematic review", @@ -625129,73 +627344,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.28.21261304", - "rel_title": "Promoting resilience in healthcare workers during the COVID-19 pandemic with a brief online intervention", - "rel_date": "2021-07-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.28.21261304", - "rel_abs": "IntroductionThe psychological wellbeing of healthcare workers has been impacted by the high levels of stress many have experienced during the COVID-19 pandemic. This study aimed to examine the feasibility and acceptability of a brief online course focused on introducing skills that could increase resilience and decreases emotional distress in healthcare workers during the pandemic.\n\nMaterials and MethodsEmployees of a large healthcare system completed a survey at baseline, one month, and two months later. The online course, called Resilience Training for Healthcare Workers, consists of three 12-20 minute videos focused on evidence-based skills that support aspects of emotional resilience: mindfulness, mentalization, and self-compassion.\n\nResultsA total of 554 participants completed the baseline survey, endorsing moderate to high levels of emotional distress. Of those who completed all three assessments and participated in the course (n = 38), significant improvements in resilience and reductions in emotional distress were found across two months, in comparison to those who did not participate in the course.\n\nDiscussionThese findings suggest that a brief, online intervention can improve the mental health of healthcare workers during a crisis such as the COVID-19 pandemic.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Nicole R DeTore", - "author_inst": "Massachusetts General Hospital, Harvard Medical School" - }, - { - "author_name": "Louisa Sylvia", - "author_inst": "Massachusetts General Hospital, Harvard Medical School" - }, - { - "author_name": "Elyse R Park", - "author_inst": "Massachusetts General Hospital, Harvard Medical School" - }, - { - "author_name": "Anne Burke", - "author_inst": "Massachusetts General Hospital, Harvard Medical School" - }, - { - "author_name": "Julie H Levison", - "author_inst": "Massachusetts General Hospital, Harvard Medical School" - }, - { - "author_name": "Alec Shannon", - "author_inst": "Massachusetts General Hospital, Harvard Medical School" - }, - { - "author_name": "Karmel W Choi", - "author_inst": "Massachusetts General Hospital, Harvard Medical School" - }, - { - "author_name": "Felipe A Jain", - "author_inst": "Massachusetts General Hospital, Harvard Medical School" - }, - { - "author_name": "Drew C Coman", - "author_inst": "Massachusetts General Hospital, Harvard Medical School" - }, - { - "author_name": "John Herman", - "author_inst": "Massachusetts General Hospital, Harvard Medical School" - }, - { - "author_name": "Roy Perlis", - "author_inst": "Massachusetts General Hospital, Harvard Medical School" - }, - { - "author_name": "Maurizio Fava", - "author_inst": "Massachusetts General Hospital, Harvard Medical School" - }, - { - "author_name": "Daphne J Holt", - "author_inst": "Massachusetts General Hospital, Harvard Medical School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.07.29.21261190", "rel_title": "Right Ventricular Dysfunction in Ventilated Patients with COVID-19 (COVID-RV)", @@ -625999,6 +628147,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.30.21261265", + "rel_title": "Accuracy verification of low-cost CO2 concentration measuring devices for general use as a countermeasure against COVID-19", + "rel_date": "2021-07-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.30.21261265", + "rel_abs": "Within the context of the COVID-19 pandemic, CO2 sensors that measure ventilation conditions and thereby reduce the risk of airborne infection, are gaining increasing attention. We investigated and verified the accuracy of 12 relatively low-cost sensor models that retail for less than $45 and are advertised as infection control measures on a major e-commerce site. Our results indicate that 25% of the tested sensors can be used to identify trends in CO2 concentration, if correctly calibrated. However, 67% of sensors did not respond to the presence of CO2, which suggests that a type of pseudo-technique is used to display the CO2 concentration. We recommend that these sensors are not suitable for infection prevention purposes. We also found that all 67% of the sensors that did not respond to CO2 responded strongly to alcohol. Owing to the widespread use of alcohol in preventing the spread of infectious diseases, sensors that react to alcohol can display inaccurate values, resulting in inappropriate ventilation behavior. Therefore, we strongly recommended that these sensors not be used. Based on our results, we offer practical recommendations to the average consumer, who does not have special measuring equipment, on how to identify inaccurate CO2 sensors.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Yo Ishigaki", + "author_inst": "University of Electro-Communications" + }, + { + "author_name": "Koji Enoki", + "author_inst": "Graduate School of Informatics and Engineering, The University of Electro-communications, Chofu, Tokyo, Japan." + }, + { + "author_name": "Shinji Yokogawa", + "author_inst": "The University of Electro-Communications" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.07.28.21261219", "rel_title": "Effects of Various Policy Options on COVID-19 Cases in Nova Scotia including Vaccination Rollout Schedule: A Modelling Study", @@ -626919,37 +629094,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.27.21261226", - "rel_title": "Overlapping Time Scales Obscure Early Warning Signals for the Second COVID-19 Wave", - "rel_date": "2021-07-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.27.21261226", - "rel_abs": "Early warning indicators based on critical slowing down have been suggested as a model-independent and low-cost tool to anticipate the (re)emergence of infectious diseases. We studied whether such indicators could reliably have anticipated the second COVID-19 wave in European countries. Contrary to theoretical predictions, we found that characteristic early warning indicators generally decreased rather than increased prior to the second wave. A model explains this unexpected finding as a result of transient dynamics and the multiple time scales of relaxation during a non-stationary epidemic. Particularly, if an epidemic that seems initially contained after a first wave does not fully settle to its new quasi-equilibrium prior to changing circumstances or conditions that force a second wave, then indicators will show a decreasing rather than an increasing trend as a result of the persistent transient trajectory of the first wave. Our simulations show that this lack of time scale separation was to be expected during the second European epidemic wave of COVID-19. Overall, our results emphasize that the theory of critical slowing down applies only when the external forcing of the system across a critical point is slow relative to the internal system dynamics.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Fabian Dablander", - "author_inst": "University of Amsterdam" - }, - { - "author_name": "Hans Heesterbeek", - "author_inst": "Utrecht University" - }, - { - "author_name": "Denny Borsboom", - "author_inst": "University of Amsterdam" - }, - { - "author_name": "John M. Drake", - "author_inst": "University of Georgia" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.29.454404", "rel_title": "Photosensitized Electrospun Nanofibrous Filters for Capturing and Killing Airborne Coronaviruses under Visible Light Irradiation", @@ -627765,6 +629909,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.26.21261146", + "rel_title": "Laboratory Study of Physical Barrier Efficiency for Worker Protection against SARS-CoV-2 while Standing or Sitting", + "rel_date": "2021-07-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.26.21261146", + "rel_abs": "Transparent barriers were installed as a response to the SARS-COV-2 pandemic in many customer-facing industries. Transparent barriers are an engineering control that are utilized to intercept air traveling between customers to workers. Information on the effectiveness of these barriers against aerosols is limited. In this study, a cough simulator was used to represent a cough from a customer. Two optical particle counters were used (one on each side of the barrier, labeled reference and worker) to determine the number of particles that migrated around a transparent barrier. Nine barrier sizes and a no barrier configuration were tested with six replicates each. Tests of these 10 configurations were conducted for both sitting and standing scenarios to represent configurations common to nail salons and grocery stores, respectively. Barrier efficiency was calculated using a ratio of the particle count results (reference/worker). Barriers had better efficiency when they were 9 to 39 cm (3.5 to 15.5\") above cough height and at least 91 cm (36\") wide, 92% and 93% respectively. Barriers that were 91 cm (36\") above table height for both scenarios blocked 71% or more of the particles between 0.35-0.725 {micro}m and 68% for particles between 1 to 3 {micro}m. A barrier that blocked an initial cough was effective at reducing particle counts. While the width of barriers was not as significant as height in determining barrier efficiency it was important that a barrier be placed where interactions between customers and workers are most frequent.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Jacob Bartels", + "author_inst": "NIOSH" + }, + { + "author_name": "Cheryl Fairfield Estill", + "author_inst": "NIOSH" + }, + { + "author_name": "I-Chen Chen", + "author_inst": "NIOSH" + }, + { + "author_name": "Dylan Neu", + "author_inst": "NIOSH" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2021.07.27.21261031", "rel_title": "Prognostic accuracy of triage tools for adults with suspected COVID-19 in a pre-hospital setting: an observational cohort study", @@ -628809,45 +630984,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, - { - "rel_doi": "10.1101/2021.07.26.21250865", - "rel_title": "Cash versus Lotteries: COVID-19 Vaccine Incentives Experiment", - "rel_date": "2021-07-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.26.21250865", - "rel_abs": "Governments are considering financial incentives to increase vaccine uptake to end the COVID-19 pandemic. Incentives being offered include cash-equivalents such as vouchers or being entered into lotteries. Our experiment involved random assignment of 1,628 unvaccinated participants in the United States to one of three 45 second informational videos promoting vaccination with messages about: (a) health benefits of COVID-19 vaccines (control); (b) being entered into lotteries; or (c) receiving cash equivalent vouchers. After seeing the control health information video, 16% of individuals wanted information on where to get vaccinated. This compared with 14% of those assigned to the lottery video (odds ratio of 0.82 relative to control: 95% credible interval 0.57-1.17) and 22% of those assigned to the cash voucher video (odds ratio of 1.53 relative to control: 95% credible interval 1.11-2.11). These results support greater use of cash vouchers to promote COVID-19 vaccine uptake and do not support the use of lottery incentives.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Raymond M Duch", - "author_inst": "University of Oxford" - }, - { - "author_name": "Adrian Barnett", - "author_inst": "Queensland University of Technology" - }, - { - "author_name": "Maciej Filipek", - "author_inst": "Vienna University of Economics and Business" - }, - { - "author_name": "Laurence Roope", - "author_inst": "University of Oxford" - }, - { - "author_name": "Mara Violato", - "author_inst": "University of Oxford" - }, - { - "author_name": "Philip Clarke", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2021.07.24.21261037", "rel_title": "Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant dependent manner", @@ -629999,6 +632135,105 @@ "type": "new results", "category": "synthetic biology" }, + { + "rel_doi": "10.1101/2021.07.28.453844", + "rel_title": "The human nose organoid respiratory virus model: an ex-vivo human challenge model to study RSV and SARS-CoV-2 pathogenesis and evaluate therapeutics", + "rel_date": "2021-07-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.28.453844", + "rel_abs": "There is an unmet need for pre-clinical models to understand the pathogenesis of human respiratory viruses; and predict responsiveness to immunotherapies. Airway organoids can serve as an ex-vivo human airway model to study respiratory viral pathogenesis; however, they rely on invasive techniques to obtain patient samples. Here, we report a non-invasive technique to generate human nose organoids (HNOs) as an alternate to biopsy derived organoids. We made air liquid interface (ALI) cultures from HNOs and assessed infection with two major human respiratory viruses, respiratory syncytial virus (RSV) and severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Infected HNO-ALI cultures recapitulate aspects of RSV and SARS-CoV-2 infection, including viral shedding, ciliary damage, innate immune responses, and mucus hyper-secretion. Next, we evaluated the feasibility of the HNO-ALI respiratory virus model system to test the efficacy of palivizumab to prevent RSV infection. Palivizumab was administered in the basolateral compartment (circulation) while viral infection occurred in the apical ciliated cells (airways), simulating the events in infants. In our model, palivizumab effectively prevented RSV infection in a concentration dependent manner. Thus, the HNO-ALI model can serve as an alternate to lung organoids to study respiratory viruses and testing therapeutics.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Anubama Rajan", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Ashley Morgan Weaver", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Gina Marie Alosio", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Joseph Jelinski", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Hannah L Johnson", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Susan F. Venable", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Trevor McBride", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Letisha Aideyan", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Felipe-Andres Piedra", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Xunyan Ye", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Ernestina Melicoff-Portillo", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Malli Rama Kanthi Yerramilli", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Xi-Lei Zeng", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Michael A Mancini", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Fabio Stossi", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Anthony W Maresso", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Shalaka A. Kotkar", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Mary K. Estes", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Sarah Blutt", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Vasanthi Avadhanula", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Pedro A. Piedra", + "author_inst": "Baylor College of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.07.15.21260606", "rel_title": "The Costs and Benefits of Covid-19 Lockdowns in New Zealand", @@ -630811,33 +633046,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2021.07.23.21261030", - "rel_title": "Breakthrough Symptomatic COVID-19 Infections Leading to Long Covid: Report from Long Covid Facebook Group Poll", - "rel_date": "2021-07-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.23.21261030", - "rel_abs": "Vaccines have been shown to be extremely effective in preventing COVID-19 hospitalizations and deaths. However, a question remains whether vaccine breakthrough cases can still lead to Post-Acute Sequelae of SARS-CoV-2 (PASC), also known as Long Covid. To address this question, the Survivor Corps group, a grassroots COVID-19 organization focused on patient support and research, posted a poll to its 169,900 members that asked about breakthrough cases, Long Covid, and hospitalizations. 1,949 people who self-report being fully vaccinated have responded to date. While robust data are needed in a larger, unbiased sample to extrapolate rates to the population, we analyzed the results of this public poll to determine what people were reporting regarding Long Covid after breakthrough infection and to prompt discussion of how breakthrough cases are measured. The poll was posted in the Survivor Corps Facebook group ([~]169,900 members). Of the 1,949 participants who responded to the poll, 44 reported a symptomatic breakthrough case and 24 of those reported that the case led to symptoms of Long Covid. 1 of these 24 cases was reported to have led to hospitalization in addition to Long Covid.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Daisy Massey", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Diana Berrent", - "author_inst": "Survivor Corps" - }, - { - "author_name": "Harlan Krumholz", - "author_inst": "Yale University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.23.21261039", "rel_title": "Geographical concentration of COVID-19 cases by social determinants of health in 16 large metropolitan areas in Canada - a cross-sectional study", @@ -631921,6 +634129,57 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.07.26.453518", + "rel_title": "Increased aerosol transmission for B.1.1.7 (alpha variant) over lineage A variant of SARS-CoV-2", + "rel_date": "2021-07-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.26.453518", + "rel_abs": "Airborne transmission, a term combining both large droplet and aerosol transmission, is thought to be the main transmission route of SARS-CoV-2. Here we investigated the relative efficiency of aerosol transmission of two variants of SARS-CoV-2, B.1.1.7 (alpha) and lineage A, in the Syrian hamster. A novel transmission caging setup was designed and validated, which allowed the assessment of transmission efficiency at various distances. At 2 meters distance, only particles <5 {micro}m traversed between cages. In this setup, aerosol transmission was confirmed in 8 out of 8 (N = 4 for each variant) sentinels after 24 hours of exposure as demonstrated by respiratory shedding and seroconversion. Successful transmission occurred even when exposure time was limited to one hour, highlighting the efficiency of this transmission route. Interestingly, the B.1.1.7 variant outcompeted the lineage A variant in an airborne transmission chain after mixed infection of donors. Combined, this data indicates that the infectious dose of B.1.1.7 required for successful transmission may be lower than that of lineage A virus. The experimental proof for true aerosol transmission and the increase in the aerosol transmission potential of B.1.1.7 underscore the continuous need for assessment of novel variants and the development or preemptive transmission mitigation strategies.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Julia Port", + "author_inst": "NIAID" + }, + { + "author_name": "Kwe Claude Yinda", + "author_inst": "NIAID" + }, + { + "author_name": "Victoria Avanzato", + "author_inst": "NIAID" + }, + { + "author_name": "Jonathan Schulz", + "author_inst": "NIAID" + }, + { + "author_name": "Myndi Holbrook", + "author_inst": "NIAID" + }, + { + "author_name": "Neeltje van Doremalen", + "author_inst": "NIH" + }, + { + "author_name": "Carl Shaia", + "author_inst": "NIAID" + }, + { + "author_name": "Robert Fischer", + "author_inst": "NIAID" + }, + { + "author_name": "Vincent Munster", + "author_inst": "NIAID" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.07.25.453717", "rel_title": "ETAS(R)50 Attenuates SARS-CoV-2 Spike Protein-Induced IL-6 and IL-1\u03b2 Production by Suppressing p44/42 MAPK and Akt Phosphorylation in Murine Primary Macrophages", @@ -632789,297 +635048,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.07.23.21260280", - "rel_title": "A Multi-Site Analysis of the Prevalence of Food Security in the United States, before and during the COVID-19 Pandemic", - "rel_date": "2021-07-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.23.21260280", - "rel_abs": "BackgroundThe COVID-19 pandemic profoundly affected food systems including food security. Understanding how the COVID-19 pandemic impacted food security is important to provide support, and identify long-term impacts and needs.\n\nObjectiveOur team- the National Food Access and COVID research Team (NFACT) was formed to assess food security over different U.S. study sites throughout the pandemic, using common instruments and measurements. Here we present results from 18 study sites across 15 states and nationally over the first year of the COVID-19 pandemic.\n\nMethodsA validated survey instrument was developed and implemented in whole or part across the sites throughout the first year of the pandemic, representing 22 separate surveys. Sampling methods for each study site were convenience, representative, or high-risk targeted. Food security was measured using the USDA six-item module. Food security prevalence was analyzed using analysis of variance by sampling method to statistically significant differences.\n\nResultsIn total, more than 27,000 people responded to the surveys. We find higher prevalence of food insecurity (low or very low food security) since the COVID-19 pandemic, as compared to before the pandemic. In nearly all study sites, we find higher prevalence of food insecurity among Black, Indigenous, and People of Color (BIPOC), households with children, and those with job disruptions. We also demonstrate lingering food insecurity, with high or increased prevalence over time in sites with repeat surveys. We find no statistically significant differences between convenience and representative surveys, but statistically higher prevalence of food insecurity among high-risk compared to convenience surveys.\n\nConclusionsThis comprehensive multi-study site effort demonstrates higher prevalence of food insecurity since the beginning of the COVID-19 pandemic, which in multiple survey sites continues throughout the first year of the pandemic. These impacts were prevalent for certain demographic groups, and most pronounced for surveys targeting high-risk populations.", - "rel_num_authors": 69, - "rel_authors": [ - { - "author_name": "Meredith T. Niles", - "author_inst": "University of Vermont" - }, - { - "author_name": "Alyssa W. Beavers", - "author_inst": "Wayne State University" - }, - { - "author_name": "Lauren A. Clay", - "author_inst": "DYouville College" - }, - { - "author_name": "Marcelle M. Dougan", - "author_inst": "San Jose State University" - }, - { - "author_name": "Giselle A. Pignotti", - "author_inst": "San Jose State University" - }, - { - "author_name": "Stephanie Rogus", - "author_inst": "New Mexico State University" - }, - { - "author_name": "Mateja R. Savoie-Roskos", - "author_inst": "Utah State University" - }, - { - "author_name": "Rachel E. Schattman", - "author_inst": "University of Maine, Orono" - }, - { - "author_name": "Rachel M. Zack", - "author_inst": "The Greater Boston Food Bank" - }, - { - "author_name": "Francesco Acciai", - "author_inst": "Arizona State University" - }, - { - "author_name": "Deanne Allegro", - "author_inst": "Auburn University at Montgomery" - }, - { - "author_name": "Emily H. Belarmino", - "author_inst": "University of Vermont" - }, - { - "author_name": "Farryl Bertmann", - "author_inst": "University of Vermont" - }, - { - "author_name": "Erin Biehl", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Nick Birk", - "author_inst": "The Greater Boston Food Bank" - }, - { - "author_name": "Jessica Bishop-Royse", - "author_inst": "DePaul University" - }, - { - "author_name": "Christine Bozlak", - "author_inst": "University at Albany- State University of New York" - }, - { - "author_name": "Brianna Bradley", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Barrett P. Brenton", - "author_inst": "Binghamton University" - }, - { - "author_name": "James Buszkiewicz", - "author_inst": "University of Washington" - }, - { - "author_name": "Brittney N. Cavaliere", - "author_inst": "Connecticut Food Bank/Foodshare" - }, - { - "author_name": "Young Cho", - "author_inst": "University of Wisconsin-Milwaukee" - }, - { - "author_name": "Eric M. Clark", - "author_inst": "University of Vermont" - }, - { - "author_name": "Kathryn Coakley", - "author_inst": "University of New Mexico" - }, - { - "author_name": "Jeanne Coffin-Schmitt", - "author_inst": "Cornell University" - }, - { - "author_name": "Sarah M. Collier", - "author_inst": "University of Washington" - }, - { - "author_name": "Casey Coombs", - "author_inst": "Utah State University" - }, - { - "author_name": "Anne Dressel", - "author_inst": "University of Wisconsin-Milwaukee" - }, - { - "author_name": "Adam Drewnowski", - "author_inst": "University of Washington" - }, - { - "author_name": "Tom Evans", - "author_inst": "University of Arizona" - }, - { - "author_name": "Beth J. Feingold", - "author_inst": "University at Albany- State University of New York" - }, - { - "author_name": "Lauren Fiechtner", - "author_inst": "MassGeneral Hospital for Children" - }, - { - "author_name": "Kathryn J. Fiorella", - "author_inst": "Cornell University" - }, - { - "author_name": "Katie Funderburk", - "author_inst": "Auburn University" - }, - { - "author_name": "Preety Gadhoke", - "author_inst": "St. John's University (at the time of study administration)" - }, - { - "author_name": "Diana Gonzales-Pacheco", - "author_inst": "University of New Mexico" - }, - { - "author_name": "Amelia Greiner Safi", - "author_inst": "Cornell University" - }, - { - "author_name": "Sen Gu", - "author_inst": "St. John's University" - }, - { - "author_name": "Karla L. Hanson", - "author_inst": "Cornell University" - }, - { - "author_name": "Amy Harley", - "author_inst": "University of Wisconsin-Milwaukee" - }, - { - "author_name": "Kaitlyn Harper", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Akiko S. Hosler", - "author_inst": "University at Albany- State University of New York" - }, - { - "author_name": "Alan Ismach", - "author_inst": "University of Washington" - }, - { - "author_name": "Anna Josephson", - "author_inst": "University of Arizona" - }, - { - "author_name": "Linnea Laestadius", - "author_inst": "University of Wisconsin-Milwaukee" - }, - { - "author_name": "Heidi LeBlanc", - "author_inst": "Utah State University" - }, - { - "author_name": "Laura R. Lewis", - "author_inst": "Washington State University" - }, - { - "author_name": "Michelle M. Litton", - "author_inst": "Wayne State University" - }, - { - "author_name": "Katie S. Martin", - "author_inst": "Connecticut Food Bank/Foodshare" - }, - { - "author_name": "Shadai Martin", - "author_inst": "New Mexico State University" - }, - { - "author_name": "Sarah Martinelli", - "author_inst": "Arizona State University" - }, - { - "author_name": "John Mazzeo", - "author_inst": "DePaul University" - }, - { - "author_name": "Scott C. Merrill", - "author_inst": "University of Vermont" - }, - { - "author_name": "Roni Neff", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Esther Nguyen", - "author_inst": "University of Washington" - }, - { - "author_name": "Punam Ohri-Vachaspati", - "author_inst": "Arizona State University" - }, - { - "author_name": "Abigail Orbe", - "author_inst": "Connecticut Food Bank/Foodshare" - }, - { - "author_name": "Jennifer J. Otten", - "author_inst": "University of Washington" - }, - { - "author_name": "Sondra Parmer", - "author_inst": "Auburn University" - }, - { - "author_name": "Salome Pemberton", - "author_inst": "Hunter College, City University of New York" - }, - { - "author_name": "Zain Al Abdeen Qusair", - "author_inst": "DePaul University" - }, - { - "author_name": "Victoria Rivkina", - "author_inst": "DePaul University" - }, - { - "author_name": "Joelle Robinson", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Chelsea M. Rose", - "author_inst": "University of Washington" - }, - { - "author_name": "Saloumeh Sadeghzadeh", - "author_inst": "Binghamton University" - }, - { - "author_name": "Brinda Sivaramakrishnan", - "author_inst": "Tacoma Community College" - }, - { - "author_name": "Mariana Torres Arroyo", - "author_inst": "University at Albany- State University of New York" - }, - { - "author_name": "McKenna Voorhees", - "author_inst": "Utah State University" - }, - { - "author_name": "Kathryn Yerxa", - "author_inst": "University of Maine, Orono" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "nutrition" - }, { "rel_doi": "10.1101/2021.07.23.21260909", "rel_title": "A cross-sectional study of socioeconomic status and sickness presenteeism in Japanese workers during the COVID-19 pandemic", @@ -633915,6 +635883,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.21.21260913", + "rel_title": "Hospitalization Data Supports Correlation of Lower Covid-19 Severity vs. Universal BCG Immunization in the Early Phase of the Pandemic", + "rel_date": "2021-07-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.21.21260913", + "rel_abs": "The possibility of a correlation between universal administration of the bacillus Calmette-Guerin (BCG) tuberculosis vaccine and lower severity of Covid-19 by national jurisdiction has been pointed out previously. In this work we examined hospitalization data attributed to Covid-19 cause reported by European national jurisdictions with the conclusion of a clear negative correlation between current or recent BCG vaccination program and reduced impact of the epidemics on the population measured in hospital admissions per capita in the early phase of the pandemic, before variants and vaccines. While there is no evidence that BCG vaccination provides strong individual level protection, the results of this work in combination with the results of other studies appear to support the hypothesis of a certain population-wide protection effect that is correlated with BCG immunization.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Serge Dolgikh", + "author_inst": "National Aviation University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.07.22.21260972", "rel_title": "The mystery of COVID-19 reinfections: A global systematic review and meta-analysis of 577 cases", @@ -636119,41 +638106,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.07.20.21260869", - "rel_title": "Sensitivity of excess mortality due to the COVID-19 pandemic to the choice of the mortality index, method, reference period, and the time unit of the death series", - "rel_date": "2021-07-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.20.21260869", - "rel_abs": "Estimating excess mortality is challenging. The metric depends on the expected mortality level, which can differ based on given choices, such as the method and the time series length used to estimate the baseline. However, these choices are often arbitrary, and are not subject to any sensitivity analysis. We bring to light the importance of carefully choosing the inputs and methods used to estimate excess mortality. Drawing on data from 26 countries, we investigate how sensitive excess mortality is to the choice of the mortality index, the number of years included in the reference period, the method, and the time unit of the death series. We employ two mortality indices, three reference periods, two data time units, and four methods for estimating the baseline. We show that excess mortality estimates can vary substantially when these factors are changed, and that the largest variations stem from the choice of the mortality index and the method. We also find that the magnitude of the variation in excess mortality can change markedly within countries, resulting in different cross-country rankings. We conclude that the inputs and method used to estimate excess mortality should be chosen carefully based on the specific research question.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Marilia R. Nepomuceno", - "author_inst": "Max Planck Institute for Demographic Research" - }, - { - "author_name": "Ilya Klimkin", - "author_inst": "National Research University Higher School of Economics" - }, - { - "author_name": "Dmitry A. Jdanov", - "author_inst": "Max Planck Institute for Demographic Research" - }, - { - "author_name": "Ainhoa Alustiza Galarza", - "author_inst": "Max Planck Institute for Demographic Research" - }, - { - "author_name": "Vladimir Shkolnikov", - "author_inst": "Max Planck Institute for Demographic Research" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.07.21.21260823", "rel_title": "Protocol for a prospective, hospital-based registry of pregnant women with SARS-CoV-2 infection in India: PregCovid Registry study", @@ -636889,6 +638841,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.07.23.453505", + "rel_title": "SARS-CoV-2 Exploits Sexually Dimorphic and Adaptive IFN and TNFa Signaling to Gain Entry into Alveolar Epithelium", + "rel_date": "2021-07-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.23.453505", + "rel_abs": "Infection of the alveolar epithelium constitutes a bottleneck in the progression of COVID-19 to SARS presumably due to the paucity of viral entry receptors in alveolar epithelial type 1 and 2 cells. We have found that the male alveolar epithelial cells express twice as many ACE2 and TMPRSS2 entry receptors as the female ones. Intriguingly, IFN and TNF- signaling are preferentially active in male alveolar cells and induce binding of the cognate transcription factors to the promoters and lung-active enhancers of ACE2 and TMPRSS2. Cotreatment with IFN-I and III dramatically increases expression of the receptors and viral entry in alveolar epithelial cells. TNF and IFN-II, typically overproduced during the cytokine storm, similarly collaborate to induce these events. Whereas JAK inhibitors suppress viral entry induced by IFN-I/III, simultaneous inhibition of IKK/NF-{kappa}B is necessary to block viral entry induced by TNF and IFN-II. In addition to explaining the increased incidence of SARS in males, these findings indicate that SARS-Cov-2 hijacks epithelial immune signaling to promote infection of the alveolar epithelium and suggest that JAK inhibitors, singly and in combination with NF-KB inhibitors, may exhibit efficacy in preventing or treating COVID-19 SARS.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Filippo Giancotti", + "author_inst": "The University of Texas MD Anderson Cancer Center" + }, + { + "author_name": "Yan Wang", + "author_inst": "The University of Texas MD Anderson Cancer Center" + }, + { + "author_name": "Sreeharsha Gurrapu", + "author_inst": "The University of Texas MD Anderson Cancer Center" + }, + { + "author_name": "Hong Chen", + "author_inst": "The University of Texas MD Anderson Cancer Center" + }, + { + "author_name": "Sara Laudato", + "author_inst": "The University of Texas MD Anderson Cancer Center" + }, + { + "author_name": "Emily Caggiano", + "author_inst": "The University of Texas MD Anderson Cancer Center" + }, + { + "author_name": "Yan Jiang", + "author_inst": "The University of Texas MD Anderson Cancer Center" + }, + { + "author_name": "Hsiang-Hsi Ling", + "author_inst": "The University of Texas MD Anderson Cancer Center" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.07.22.453309", "rel_title": "A Highly Potent SARS-CoV-2 Blocking Lectin Protein", @@ -637889,209 +639888,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.20.21260863", - "rel_title": "Typically asymptomatic but with robust antibody formation: Childrens unique humoral immune response to SARS-CoV-2", - "rel_date": "2021-07-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.20.21260863", - "rel_abs": "BackgroundLong-term persistence of antibodies against SARS-CoV-2, particularly the SARS-CoV-2 Spike Trimer, determines individual protection against infection and potentially viral spread. The quality of childrens natural humoral immune response following SARS-CoV-2 infection is yet incompletely understood but crucial to guide pediatric SARS-CoV-2 vaccination programs.\n\nMethodsIn this prospective observational multi-center cohort study, we followed 328 households, consisting of 548 children and 717 adults, with at least one member with a previous laboratory-confirmed SARS-CoV-2 infection. The serological response was assessed at 3-4 months and 11-12 months after infection using a bead-based multiplex immunoassay for 23 human coronavirus antigens including SARS-CoV-2 and its Variants of Concern (VOC) and endemic human coronaviruses (HCoVs), and additionally by three commercial SARS-CoV-2 antibody assays.\n\nResultsOverall, 33.76% of SARS-CoV-2 exposed children and 57.88% adults were seropositive. Children were five times more likely to have seroconverted without symptoms compared to adults. Despite the frequently asymptomatic course of infection, children had higher specific antibody levels, and their antibodies persisted longer than in adults (96.22% versus 82.89% still seropositive 11-12 months post infection). Of note, symptomatic and asymptomatic infections induced similar humoral responses in all age groups. In symptomatic children, only dysgeusia was found as diagnostic indicator of COVID-19. SARS-CoV-2 infections occurred independent of HCoV serostatus. Antibody binding responses to VOCs were similar in children and adults, with reduced binding for the Beta variant in both groups.\n\nConclusionsThe long-term humoral immune response to SARS-CoV-2 infection in children is robust and may provide long-term protection even after asymptomatic infection.\n\n(Study ID at German Clinical Trials Register: 00021521)", - "rel_num_authors": 47, - "rel_authors": [ - { - "author_name": "Hanna Renk", - "author_inst": "Department of Haematology and Oncology, University Children's Hospital Tuebingen, Tuebingen, Germany" - }, - { - "author_name": "Alex Dulovic", - "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany" - }, - { - "author_name": "Matthias Becker", - "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany" - }, - { - "author_name": "Dorit Fabricius", - "author_inst": "Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm University, Ulm, Germany," - }, - { - "author_name": "Maria Zernickel", - "author_inst": "Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm University, Ulm, Germany" - }, - { - "author_name": "Daniel Junker", - "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany" - }, - { - "author_name": "Alina Seidel", - "author_inst": "Institute of Molecular Virology, Ulm University, Ulm, Germany" - }, - { - "author_name": "Ruediger Gross", - "author_inst": "Institute of Molecular Virology, Ulm University, Ulm, Germany" - }, - { - "author_name": "Alexander Hilger", - "author_inst": "Center for Pediatrics and Adolescent Medicine, Medical Center Freiburg, Germany and Faculty of Medicine, University of Freiburg, Freiburg, Germany" - }, - { - "author_name": "Sebastian Bode", - "author_inst": "Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm University, Ulm, Germany" - }, - { - "author_name": "Linus Fritsch", - "author_inst": "Center for Pediatrics and Adolescent Medicine, Medical Center Freiburg, Germany and Faculty of Medicine, University of Freiburg, Freiburg, Germany" - }, - { - "author_name": "Pauline Frieh", - "author_inst": "Center for Pediatrics and Adolescent Medicine, Medical Center Freiburg, Germany and Faculty of Medicine, University of Freiburg, Freiburg, Germany" - }, - { - "author_name": "Anneke Haddad", - "author_inst": "Center for Pediatrics and Adolescent Medicine, Medical Center Freiburg, Germany and Faculty of Medicine, University of Freiburg, Freiburg, Germany" - }, - { - "author_name": "Tessa Goerne", - "author_inst": "Center for Pediatrics and Adolescent Medicine, Medical Center Freiburg, Germany and Faculty of Medicine, University of Freiburg, Freiburg, Germany" - }, - { - "author_name": "Jonathan Remppis", - "author_inst": "University Childrens Hospital Tuebingen, Tuebingen, Germany" - }, - { - "author_name": "Tina Ganzenmueller", - "author_inst": "Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany" - }, - { - "author_name": "Andrea Dietz", - "author_inst": "Institute of Virology, Ulm University Medical Center, Ulm, Germany" - }, - { - "author_name": "Daniela Huzly", - "author_inst": "Institute of Virology, Medical Center - University of Freiburg, Faculty of Medicine, University of F" - }, - { - "author_name": "Hartmut Hengel", - "author_inst": "Institute of Virology, University Medical Center Freiburg, Germany and Faculty of Medicine, University of Freiburg, Freiburg, Germany" - }, - { - "author_name": "Klaus Kaier", - "author_inst": "Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg" - }, - { - "author_name": "Susanne Weber", - "author_inst": "Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany" - }, - { - "author_name": "Eva-Maria Jacobsen", - "author_inst": "Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm University, Ulm, Germany" - }, - { - "author_name": "Philipp Kaiser", - "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany" - }, - { - "author_name": "Bjoern Traenkle", - "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany" - }, - { - "author_name": "Ulrich Rothbauer", - "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany" - }, - { - "author_name": "Maximilian Stich", - "author_inst": "Department of Pediatrics I, University Childrens Hospital Heidelberg, Heidelberg, Germany" - }, - { - "author_name": "Burkhard Toenshoff", - "author_inst": "Department of Pediatrics I, University Childrens Hospital Heidelberg, Heidelberg, Germany" - }, - { - "author_name": "Georg Friedrich Hoffmann", - "author_inst": "Department of Pediatrics I, University Childrens Hospital Heidelberg, Heidelberg, Germany" - }, - { - "author_name": "Barbara Mueller", - "author_inst": "Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany" - }, - { - "author_name": "Bernd Jahrsdoerfer", - "author_inst": "Department of Transfusion Medicine, Ulm University, Ulm, Germany" - }, - { - "author_name": "Carolin Ludwig", - "author_inst": "Department of Transfusion Medicine, Ulm University, Ulm, Germany" - }, - { - "author_name": "Hubert Schrezenmeier", - "author_inst": "Department of Transfusion Medicine, Ulm University, Ulm, Germany" - }, - { - "author_name": "Andreas Peter", - "author_inst": "Institute for Clinical Chemistry and Pathobiochemistry, University Hospital Tuebingen, Tuebingen, Germany" - }, - { - "author_name": "Sebastian Hoerber", - "author_inst": "Institute for Clinical Chemistry and Pathobiochemistry, University Hospital Tuebingen, Tuebingen, Germany" - }, - { - "author_name": "Thomas Iftner", - "author_inst": "Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany" - }, - { - "author_name": "Jan Muench", - "author_inst": "Institute of Molecular Virology, Ulm University, Ulm, Germany" - }, - { - "author_name": "Thomas Stamminger", - "author_inst": "Institute of Virology, Ulm University Medical Center, Ulm, Germany" - }, - { - "author_name": "Martin Wolkewitz", - "author_inst": "Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany" - }, - { - "author_name": "Corinna Engel", - "author_inst": "University Childrens Hospital Tuebingen, Tuebingen, Germany" - }, - { - "author_name": "Marta Rizzi", - "author_inst": "Department of Rheumatology and Clinical Immunology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany" - }, - { - "author_name": "Hans-Juergen Gross", - "author_inst": "Institute of Clinical Chemistry, Ulm University, Ulm, Germany" - }, - { - "author_name": "Axel Franz", - "author_inst": "Centre for Paediatric Clinical Studies at the University Children's Hospital Tuebingen, Tuebingen, Germany" - }, - { - "author_name": "Philipp Henneke", - "author_inst": "Center for Pediatrics and Adolescent Medicine, Medical Center Freiburg, Germany and Faculty of Medicine, University of Freiburg, Freiburg, Germany" - }, - { - "author_name": "Klaus-Michael Debatin", - "author_inst": "Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm University, Ulm, Germany" - }, - { - "author_name": "Nicole Schneiderhan-Marra", - "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen" - }, - { - "author_name": "Ales Janda", - "author_inst": "Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm University, Ulm, Germany" - }, - { - "author_name": "Roland Elling", - "author_inst": "University Medial Center Freiburg, Center of Pediatrics and Adolescent Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2021.07.19.21260782", "rel_title": "Does COVID-19 vaccination improve mental health? A difference-in-difference analysis of the UnderstandingCoronavirus in America study", @@ -638843,6 +640639,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.18.21260708", + "rel_title": "State-dependent patterns and coupling between the vaccination schedule, population mobility and the COVID epidemic outline, in the US states", + "rel_date": "2021-07-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.18.21260708", + "rel_abs": "We study the evolution of the COVID-19 epidemic in the US, since January 2020 until May 2021. Our primary goal is to understand some of the complex coupled dynamics between factors that ultimately regulate the epidemic case load. As potentially crucial factors, we focus on population mobility and vaccination patters (both related to risk of contracting the SARS-Cov2 virus). These factors may in turn depend on demographic parameters (which are unrelated to the epidemic evolution), but also on the population response to the epidemic outbreak itself. In our work, we use correlation analyses, in conjunction with open source data from US states, to investigate the type and strength (1) of the relationships between demographic measures and epidemic, mobility and vaccination timelines during our established time window; (2) of the bidirectional coupling between these timelines.\n\nWe showed that the wide between-state differences in epidemic outcome correspond to between-state differences in demographic measures (such as density, income, political affiliation). As a potential underlying mechanism, we found that demographic measures are also predictive of the degree of coupling between epidemic timelines (on one hand) and vaccination and mobility timelines (on the other hand), coupling which can be broadly interpreted as the populations behavioral response to the epidemic. In support of this idea, our analysis shows this response to be tightly correlated with epidemic outcome.\n\nThis suggests that a states demographic profile may be invaluable to generating predictions on the epidemic evolution in the respective state, and that this information may be used to understand the weaknesses of a state and how to compensate for them to improve epidemic outcome (e.g., via state centralized incentives, and customized mitigation strategies).", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Anca Radulescu", + "author_inst": "SUNY New Paltz" + }, + { + "author_name": "Tatiana Alonso", + "author_inst": "Mathematics, State University of New York, New Paltz" + }, + { + "author_name": "Norman Reid", + "author_inst": "Biology, State University of New York, New Paltz" + }, + { + "author_name": "Johanna Sanchez", + "author_inst": "Biology, State University of NewYork, New Paltz" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.07.18.21259093", "rel_title": "COVID-19 mortality across selected states in India: the role of age structure.", @@ -640219,105 +642046,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.19.21260767", - "rel_title": "Children with SARS-CoV-2 in the National COVID Cohort Collaborative (N3C)", - "rel_date": "2021-07-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.19.21260767", - "rel_abs": "ImportanceSARS-CoV-2\n\nObjectiveTo determine the characteristics, changes over time, outcomes, and severity risk factors of SARS-CoV-2 affected children within the National COVID Cohort Collaborative (N3C)\n\nDesignProspective cohort study of patient encounters with end dates before May 27th, 2021.\n\nSetting45 N3C institutions\n\nParticipantsChildren <19-years-old at initial SARS-CoV-2 testing\n\nMain Outcomes and MeasuresCase incidence and severity over time, demographic and comorbidity severity risk factors, vital sign and laboratory trajectories, clinical outcomes, and acute COVID-19 vs MIS-C contrasts for children infected with SARS-CoV-2.\n\nResults728,047 children in the N3C were tested for SARS-CoV-2; of these, 91,865 (12.6%) were positive. Among the 5,213 (6%) hospitalized children, 685 (13%) met criteria for severe disease: mechanical ventilation (7%), vasopressor/inotropic support (7%), ECMO (0.6%), or death/discharge to hospice (1.1%). Male gender, African American race, older age, and several pediatric complex chronic condition (PCCC) subcategories were associated with higher clinical severity (p[≤]0.05). Vital signs (all p[≤]0.002) and many laboratory tests from the first day of hospitalization were predictive of peak disease severity. Children with severe (vs moderate) disease were more likely to receive antimicrobials (71% vs 32%, p<0.001) and immunomodulatory medications (53% vs 16%, p<0.001).\n\nCompared to those with acute COVID-19, children with MIS-C were more likely to be male, Black/African American, 1-to-12-years-old, and less likely to have asthma, diabetes, or a PCCC (p<0.04). MIS-C cases demonstrated a more inflammatory laboratory profile and more severe clinical phenotype with higher rates of invasive ventilation (12% vs 6%) and need for vasoactive-inotropic support (31% vs 6%) compared to acute COVID-19 cases, respectively (p<0.03).\n\nConclusionsIn the largest U.S. SARS-CoV-2-positive pediatric cohort to date, we observed differences in demographics, pre-existing comorbidities, and initial vital sign and laboratory test values between severity subgroups. Taken together, these results suggest that early identification of children likely to progress to severe disease could be achieved using readily available data elements from the day of admission. Further work is needed to translate this knowledge into improved outcomes.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Blake Martin", - "author_inst": "Section of Critical Care Medicine, Department of Pediatrics, University of Colorado School of Medicine, University of Colorado, Aurora, CO, USA" - }, - { - "author_name": "Peter E DeWitt", - "author_inst": "Section of Informatics and Data Science, Department of Pediatrics, University of Colorado School of Medicine, University of Colorado, Aurora, CO, USA" - }, - { - "author_name": "Seth Russell", - "author_inst": "Section of Informatics and Data Science, Department of Pediatrics, University of Colorado School of Medicine, University of Colorado, Aurora, CO, USA" - }, - { - "author_name": "Adit Anand", - "author_inst": "Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA" - }, - { - "author_name": "Katie R Bradwell", - "author_inst": "Palantir Technologies, Denver, CO, USA" - }, - { - "author_name": "Carolyn Bremer", - "author_inst": "Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA" - }, - { - "author_name": "Davera Gabriel", - "author_inst": "Johns Hopkins University School of Medicine, Baltimore, MD, USA" - }, - { - "author_name": "Andrew T Girvin", - "author_inst": "Palantir Technologies, Denver, CO, USA" - }, - { - "author_name": "Janos G Hajagos", - "author_inst": "Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA" - }, - { - "author_name": "Julie A McMurry", - "author_inst": "Translational and Integrative Sciences Center, University of Colorado, Aurora, CO, USA; Center for Health AI, University of Colorado, Aurora, CO, USA" - }, - { - "author_name": "Andrew J Neumann", - "author_inst": "Translational and Integrative Sciences Center, University of Colorado, Aurora, CO, USA; Center for Health AI, University of Colorado, Aurora, CO, USA" - }, - { - "author_name": "Emily R Pfaff", - "author_inst": "North Carolina Translational and Clinical Sciences Institute (NC TraCS), University of North Carolina at Chapel Hill, Chapel Hill, NC, USA" - }, - { - "author_name": "Anita Walden", - "author_inst": "Center for Health AI, University of Colorado, Aurora, CO, USA" - }, - { - "author_name": "Jacob T Wooldridge", - "author_inst": "Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA" - }, - { - "author_name": "Yun Jae Yoo", - "author_inst": "Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA" - }, - { - "author_name": "Joel Saltz", - "author_inst": "Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA" - }, - { - "author_name": "Ken R Gersing", - "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA" - }, - { - "author_name": "Christopher G Chute", - "author_inst": "Johns Hopkins University School of Medicine, Baltimore, MD, USA; Schools of Public Health, and Nursing, Johns Hopkins University, Baltimore, MD, USA" - }, - { - "author_name": "Melissa A Haendel", - "author_inst": "Center for Health AI, University of Colorado, Aurora, CO, USA" - }, - { - "author_name": "Richard Moffitt", - "author_inst": "Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA" - }, - { - "author_name": "Tellen D Bennett", - "author_inst": "Section of Critical Care Medicine, Department of Pediatrics, University of Colorado School of Medicine, University of Colorado, Aurora, CO, USA; Section of Info" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2021.07.19.21260559", "rel_title": "Clinical and Virological Response to a Neutralizing Monoclonal Antibody for Hospitalized Patients with COVID-19", @@ -640969,6 +642697,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, + { + "rel_doi": "10.1101/2021.07.21.21260691", + "rel_title": "Spread of infection and treatment interruption among Japanese workers during the COVID-19 pandemic: a cross-sectional study", + "rel_date": "2021-07-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.21.21260691", + "rel_abs": "ObjectivesThis study aimed to examine the relationship between regional infection level and treatment interruption for chronic diseases.\n\nMethodsA cross-sectional Internet monitoring survey was performed between December 22 and 26, 2020. Data from 9,510 (5,392 males and 4,118 females) participants needing regular treatment or hospital visits were analyzed. We determined the age-sex- and multivariate-adjusted odds ratios (ORs) of treatment interruption associated with various indices of infection level by nesting multilevel logistic models in prefecture of residence. In the multivariate model, sex, age, marital status, job type, equivalent household income, education, self-rated health, and anxiety were adjusted.\n\nResultsThe ORs of treatment interruption for the lowest versus highest levels of infection were 1.32 (95% CI: 1.09-1.59) for the overall incidence rate (per 1,000 population), 1.34 (95% CI: 1.10-1.63) for the overall number of people infected, 1.28 (95% CI: 1.06-1.54) for the monthly incidence rate (per 1,000 population), and 1.38 (95% CI: 1.14-1.67) for the number of people infected per month. For each index of infection level, higher infection was linked to more workers experiencing treatment interruption.\n\nConclusionHigher local infection levels were linked to more workers experiencing treatment interruption. Our results suggest that apart from individual characteristics such as socioeconomic and health status, treatment interruptions during the pandemic were also subject to contextual effects related to regional infection levels. Preventing community spread of COVID-19 may thus protect individuals from indirect effects of the pandemic, such as treatment interruption.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Jun Akashi", + "author_inst": "School of Medicine, University of Occupational and Environmental Health, JapanSchool of Medicine, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Ayako HIno", + "author_inst": "Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Seiichiro Tateishi", + "author_inst": "School of Medicine, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Tomohisa Nagata", + "author_inst": "Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Mayumi Tsuji", + "author_inst": "School of Medicine, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Akira Ogami", + "author_inst": "Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Shinya Matsuda", + "author_inst": "School of Medicine, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Masaharu Kataoka", + "author_inst": "School of Medicine, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Yoshihisa Fujino", + "author_inst": "Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.07.21.21260905", "rel_title": "A Wastewater-based Epidemiology tool for COVID-19 Surveillance in Portugal", @@ -641881,89 +643660,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2021.07.19.21260770", - "rel_title": "Uptake of infant and pre-school immunisations in Scotland and England during the COVID-19 pandemic: an observational study of routinely collected data", - "rel_date": "2021-07-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.19.21260770", - "rel_abs": "BackgroundIn 2020, the COVID-19 pandemic and control measures such as national lockdowns threatened to disrupt routine childhood immunisation programmes. Initial reports from the early weeks of lockdown in the UK and worldwide suggested that uptake could fall putting children at risk from multiple other infectious diseases. In Scotland and England, enhanced surveillance of national data for childhood immunisations was established to inform and rapidly assess the impact of the pandemic on infant and preschool immunisation uptake rates.\n\nMethods and findingsWe undertook an observational study using routinely collected data for the year prior to the pandemic (2019), and immediately before, during and after the first period of the UK lockdown in 2020. Data were obtained for Scotland from the Public Health Scotland \"COVID19 wider impacts on the health care system\" dashboard (https://scotland.shinyapps.io/phs-covid-wider-impact/) and for England from ImmForm.\n\nFive vaccinations delivered at different ages were evaluated; three doses of the 6-in-1 DTaP/IPV/Hib/HepB vaccine and two doses of MMR. Uptake in the periods in 2020 compared to that in the baseline year of 2019 using binary logistic regression analysis. For Scotland, we analysed timely uptake of immunisations, defined as uptake within four weeks of the child becoming eligible by age for each immunisation and data were also analysed by geographical region and indices of deprivation. For both Scotland and England, we assessed whether immunisations were up to date at approximately 6 months (all doses 6-in-1) and 16-18 months (first MMR) of age.\n\nWe found that uptake rates within four weeks of eligibility in Scotland for all the five vaccine visits were higher during the 2020 lockdown period than in 2019. The difference ranged from 1.3% for the first dose of the 6-in-1 vaccine (95.3 vs 94%, OR 1.28, CI 1.18-1.39) to 14.3% for the second MMR dose (66.1 vs 51.8 %, OR 1.8, CI 1.74-1.87). Significant increases in uptake were seen across all deprivation levels, though, for MMR, there was evidence of greater improvement for children living in the least deprived areas.\n\nIn England, fewer children who had been due to receive their immunisations during the lockdown period were up to date at 6 months (6-in-1) or 18 months (first dose MMR). The fall in percentage uptake ranged from 0.5% for first 6-in1 (95.8 vs 96.3%, OR 0.89, CI 0.86-0.91) to 2.1% for third 6-in-1 (86.6 vs 88.7%, OR 0.82, CI 0.81-0.83).\n\nConclusionsThis study suggests that the national lockdown in Scotland was associated with a positive effect on timely childhood immunisation uptake, however in England a lower percentage of children were up to date at 6 and 18 months. Reason for the improve uptake in Scotland may include active measures taken to promote immunisation at local and national level during this period. Promoting immunisation uptake and addressing potential vaccine hesitancy is particularly important given the ongoing pandemic and COVID-19 vaccination campaigns.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Fiona McQuaid", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Rachel Mulholland", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Yuma Sangpang Rai", - "author_inst": "Public Health England" - }, - { - "author_name": "Utkarsh Agrawal", - "author_inst": "University of St Andrews" - }, - { - "author_name": "Helen Bedford", - "author_inst": "UCL Great Ormond Street Institute of Child Health" - }, - { - "author_name": "Claire Cameron", - "author_inst": "Public Health Scotland" - }, - { - "author_name": "Cheryl Gibbon", - "author_inst": "Public Health Scotland" - }, - { - "author_name": "Partho Roy", - "author_inst": "Public Health England" - }, - { - "author_name": "Aziz Sheikh", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Ting Shi", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Colin Simpson", - "author_inst": "Victoria University of Wellington" - }, - { - "author_name": "Judith Tait", - "author_inst": "Public Health Scotland" - }, - { - "author_name": "Elise Tessier", - "author_inst": "Public Health England" - }, - { - "author_name": "Steve Turner", - "author_inst": "University of Aberdeen" - }, - { - "author_name": "Jaime Villacampa Ortega", - "author_inst": "Public Health Scotland" - }, - { - "author_name": "Joanne White", - "author_inst": "Public Health England" - }, - { - "author_name": "Rachael Wood", - "author_inst": "University of Edinburgh" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2021.07.17.21260662", "rel_title": "Determinants of SARS-CoV-2 Vaccine Engagement in Algeria: A Population-based Study with Systematic Review of Studies from Arab Countries of the MENA Region", @@ -642547,6 +644243,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.20.21260827", + "rel_title": "Potentially effective drugs for the treatment of COVID-19 in children: a systematic review", + "rel_date": "2021-07-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.20.21260827", + "rel_abs": "IntroductionThe purpose of this systematic review is to evaluate the efficacy and safety of using potential drugs: remdesivir and glucocorticoid in treating children and adolescents with COVID-19 and intravenous immunoglobulin (IVIG) in treating MIS-C.\n\nMethodsWe searched seven databases, three preprint platform, ClinicalTrials.gov, and Google from December 1, 2019, to August 5, 2021, to collect evidence of remdesivir, glucocorticoid, and IVIG which were used in children and adolescents with COVID-19 or MIS-C.\n\nResultsA total of six cohort studies and one case series study were included in this systematic review. In terms of remdesivir, the meta-analysis of single-arm cohort studies have shown that, after the treatment, 37.1% (95%CI, 0.0% to 74.5%) experienced adverse events, 5.9% (95%CI, 1.5% to 10.2%) died, 37.2% (95%CI, 0% to 76.0%) needed extracorporeal membrane oxygenation or invasive mechanical ventilation. As for glucocorticoids, the results of the meta-analysis showed that the fixed-effect summary odds ratio for the association with mortality was 2.79 (95%CI, 0.13 to 60.87), and the mechanical ventilation rate was 3.12 (95%CI, 0.80 to 12.08) for glucocorticoids compared with the control group. In terms of IVIG, the two included cohort studies showed that for MIS-C patients with more severe clinical symptoms, IVIG combined with methylprednisolone could achieve better clinical efficacy than IVIG alone.\n\nConclusionsOverall, the current evidence in the included studies is insignificant and of low quality. It is recommended to conduct high-quality randomized controlled trials of remdesivir, glucocorticoids, and IVIG in children and adolescents with COVID-19 or MIS-C to provide substantial evidence for the development of guidelines.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Zijun Wang", + "author_inst": "Lanzhou University" + }, + { + "author_name": "Siya Zhao", + "author_inst": "School of Public Health, Lanzhou University" + }, + { + "author_name": "Yuyi Tang", + "author_inst": "Department of Respiratory Medicine, Childrens Hospital of Chongqing Medical University" + }, + { + "author_name": "Zhili Wang", + "author_inst": "Department of Respiratory Medicine, Childrens Hospital of Chongqing Medical University" + }, + { + "author_name": "Qianling Shi", + "author_inst": "The First School of Clinical Medicine, Lanzhou University" + }, + { + "author_name": "Xiangyang Dang", + "author_inst": "Department of Respiratory Medicine, Childrens Hospital of Chongqing Medical University" + }, + { + "author_name": "Lidan Gan", + "author_inst": "Department of Respiratory Medicine, Childrens Hospital of Chongqing Medical University" + }, + { + "author_name": "Shuai Peng", + "author_inst": "Department of Respiratory Medicine, Childrens Hospital of Chongqing Medical University" + }, + { + "author_name": "Weiguo Li", + "author_inst": "Department of Respiratory Medicine, Childrens Hospital of Chongqing Medical University" + }, + { + "author_name": "Qi Zhou", + "author_inst": "Evidence-based Medicine Center, School of Basic Medical Sciences, Lanzhou University" + }, + { + "author_name": "Qinyuan Li", + "author_inst": "Department of Respiratory Medicine, Childrens Hospital of Chongqing Medical University" + }, + { + "author_name": "Joy James Mafiana", + "author_inst": "School of Public Health, Lanzhou University" + }, + { + "author_name": "Rafael Gonzalez Cortes", + "author_inst": "Paediatric Intensive Care Unit, Hospital General Universitario Gregorio Maranon" + }, + { + "author_name": "Zhengxiu Luo", + "author_inst": "Department of Respiratory Medicine, Childrens Hospital of Chongqing Medical University" + }, + { + "author_name": "Enmei Liu", + "author_inst": "Department of Respiratory Medicine, Childrens Hospital of Chongqing Medical University" + }, + { + "author_name": "Yaolong Chen", + "author_inst": "Evidence-based Medicine Center, School of Basic Medical Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.19.21260791", "rel_title": "Role of Multi-resolution Vulnerability Indices in COVID-19 spread: A Case Study in India", @@ -643679,61 +645454,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2021.07.20.453079", - "rel_title": "CoVizu: Rapid analysis and visualization of the global diversity of SARS-CoV-2 genomes", - "rel_date": "2021-07-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.20.453079", - "rel_abs": "Phylogenetics has played a pivotal role in the genomic epidemiology of SARS-CoV-2, such as tracking the emergence and global spread of variants, and scientific communication. However, the rapid accumulation of genomic data from around the world -- with over two million genomes currently available in the GISAID database -- is testing the limits of standard phylogenetic methods. Here, we describe a new approach to rapidly analyze and visualize large numbers of SARS-CoV-2 genomes. Using Python, genomes are filtered for problematic sites, incomplete coverage, and excessive divergence from a strict molecular clock. All differences from the reference genome, including indels, are extracted using minimap2, and compactly stored as a set of features for each genome. For each Pango lineage (https://cov-lineages.org), we collapse genomes with identical features into variants, generate 100 bootstrap samples of the feature set union to generate weights, and compute the symmetric differences between the weighted feature sets for every pair of variants. The resulting distance matrices are used to generate neigihbor-joining trees in RapidNJ and converted into a majority-rule consensus tree for the lineage. Branches with support values below 50% or mean lengths below 0.5 differences are collapsed, and tip labels on affected branches are mapped to internal nodes as directly-sampled ancestral variants. Currently, we process about million genomes in approximately nine hours on 34 cores. The resulting trees are visualized using the JavaScript framework D3.js as beadplots, in which variants are represented by horizontal line segments, annotated with beads representing samples by collection date. Variants are linked by vertical edges to represent branches in the consensus tree. These visualizations are published at https://filogeneti.ca/CoVizu. All source code was released under an MIT license at https://github.com/PoonLab/covizu.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Roux-Cil Ferreira", - "author_inst": "Western University, Canada" - }, - { - "author_name": "Emmanuel Wong", - "author_inst": "Western University, Canada" - }, - { - "author_name": "Gopi Gugan", - "author_inst": "Western University, Canada" - }, - { - "author_name": "Kaitlyn Wade", - "author_inst": "Western University, Canada" - }, - { - "author_name": "Molly Liu", - "author_inst": "Western University, Canada" - }, - { - "author_name": "Laura Munoz Baena", - "author_inst": "Western University, Canada" - }, - { - "author_name": "Connor Chato", - "author_inst": "Western University, Canada" - }, - { - "author_name": "Bonnie Lu", - "author_inst": "Western University, Canada" - }, - { - "author_name": "Abayomi Samuel Olabode", - "author_inst": "Western University, Canada" - }, - { - "author_name": "Art Poon", - "author_inst": "Western University, Canada" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.07.21.453244", "rel_title": "Lung Epithelial Regulation of BCL2 Related Protein A1 (BCL2A1) by Coronaviruses (SARS-CoV) and Type I Interferon Signaling", @@ -644581,6 +646301,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.16.21260200", + "rel_title": "Forecasting admissions in psychiatric hospitals before and during Covid-19", + "rel_date": "2021-07-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.16.21260200", + "rel_abs": "IntroductionThe COVID-19 pandemic has strong effects on most health care systems and individual services providers. Forecasting of admissions can help for the efficient organisation of hospital care. We aimed to forecast the number of admissions to psychiatric hospitals before and during the COVID-19 pandemic and we compared the performance of machine learning models and time series models. This would eventually allow to support timely resource allocation for optimal treatment of patients.\n\nMethodsWe used admission data from 9 psychiatric hospitals in Germany between 2017 and 2020. We compared machine learning models with time series models in weekly, monthly and yearly forecasting before and during the COVID-19 pandemic. Our models were trained and validated with data from the first two years and tested in prospectively sliding time-windows in the last two years.\n\nResultsA total of 90,686 admissions were analysed. The models explained up to 90% of variance in hospital admissions in 2019 and 75% in 2020 with the effects of the COVID-19 pandemic. The best models substantially outperformed a one-step seasonal naive forecast (seasonal mean absolute scaled error (sMASE) 2019: 0.59, 2020: 0.76). The best model in 2019 was a machine learning model (elastic net, mean absolute error (MAE): 7.25). The best model in 2020 was a time series model (exponential smoothing state space model with Box-Cox transformation, ARMA errors and trend and seasonal components, MAE: 10.44), which adjusted more quickly to the shock effects of the COVID-19 pandemic. Models forecasting admissions one week in advance did not perform better than monthly and yearly models in 2019 but they did in 2020. The most important features for the machine learning models were calendrical variables.\n\nConclusionModel performance did not vary much between different modelling approaches before the COVID-19 pandemic and established forecasts were substantially better than one-step seasonal naive forecasts. However, weekly time series models adjusted quicker to the COVID-19 related shock effects. In practice, different forecast horizons could be used simultaneously to allow both early planning and quick adjustments to external effects.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Jan Wolff", + "author_inst": "Peter L. Reichertz Institute for Medical Informatics, Hannover Medical School" + }, + { + "author_name": "Ansgar Klimke", + "author_inst": "Vitos Klinikum Hochtaunus" + }, + { + "author_name": "Michael Marschollek", + "author_inst": "Peter L. Reichertz Institute for Medical Informatics, Hannover Medical School" + }, + { + "author_name": "Tim Kacprowski", + "author_inst": "Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics Braunschweig, Integrated Centre of Systems Biology (BRICS), TU Brauns" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2021.07.16.21260611", "rel_title": "SARS-CoV-2 seroprevalence in Chattogram, Bangladesh before a National Lockdown, March-April 2021", @@ -645389,149 +647140,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2021.07.16.21260628", - "rel_title": "Overall and cause-specific hospitalisation and death after COVID-19 hospitalisation in England: cohort study in OpenSAFELY using linked primary care, secondary care and death registration data", - "rel_date": "2021-07-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.16.21260628", - "rel_abs": "BackgroundThere is concern about medium to long-term adverse outcomes following acute COVID-19, but little relevant evidence exists. We aimed to investigate whether risks of hospital admission and death, overall and by specific cause, are raised following discharge from a COVID-19 hospitalisation.\n\nMethods and FindingsWorking on behalf of NHS-England, we used linked primary care and hospital data in OpenSAFELY to compare risks of hospital admission and death, overall and by specific cause, between people discharged from COVID-19 hospitalisation (February-December 2020), and (i) demographically-matched controls from the 2019 general population; (ii) people discharged from influenza hospitalisation in 2017-19. We used Cox regression adjusted for personal and clinical characteristics.\n\n24,673 post-discharge COVID-19 patients, 123,362 general population controls, and 16,058 influenza controls were followed for [≤]315 days. Overall risk of hospitalisation or death (30968 events) was higher in the COVID-19 group than general population controls (adjusted-HR 2.23, 2.14-2.31) but similar to the influenza group (adjusted-HR 0.94, 0.91-0.98). All-cause mortality (7439 events) was highest in the COVID-19 group (adjusted-HR 4.97, 4.58-5.40 vs general population controls and 1.73, 1.60-1.87 vs influenza controls). Risks for cause-specific outcomes were higher in COVID-19 survivors than general population controls, and largely comparable between COVID-19 and influenza patients. However, COVID-19 patients were more likely than influenza patients to be readmitted/die due to their initial infection/other lower respiratory tract infection (adjusted-HR 1.37, 1.22-1.54), and to experience mental health or cognitive-related admission/death (adjusted-HR 1.36, 1.01-2.83); in particular, COVID-19 survivors with pre-existing dementia had higher risk of dementia death. One limitation of our study is that reasons for hospitalisation/death may have been misclassified in some cases due to inconsistent use of codes.\n\nConclusionsPeople discharged from a COVID-19 hospital admission had markedly higher risks for rehospitalisation and death than the general population, suggesting a substantial extra burden on healthcare. Most risks were similar to those observed after influenza hospitalisations; but COVID-19 patients had higher risks of all-cause mortality, readmissions/death due to the initial infection, and dementia death, highlighting the importance of post-discharge monitoring.", - "rel_num_authors": 32, - "rel_authors": [ - { - "author_name": "Krishnan Bhaskaran", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Christopher T Rentsch", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "George Hickman", - "author_inst": "University of Oxford" - }, - { - "author_name": "William J Hulme", - "author_inst": "University of Oxford" - }, - { - "author_name": "Anna Schultze", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Helen J Curtis", - "author_inst": "University of Oxford" - }, - { - "author_name": "Kevin Wing", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Charlotte Warren-Gash", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Laurie Tomlinson", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Christopher Bates", - "author_inst": "TPP" - }, - { - "author_name": "Rohini Mathur", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Brian MacKenna", - "author_inst": "University of Oxford" - }, - { - "author_name": "Viyaasan Mahalingasivam", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Angel YS Wong", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Alex J Walker", - "author_inst": "University of Oxford" - }, - { - "author_name": "Caroline E Morton", - "author_inst": "University of Oxford" - }, - { - "author_name": "Daniel Grint", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Amir Mehrkar", - "author_inst": "University of Oxford" - }, - { - "author_name": "Rosalind M Eggo", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Peter Inglesby", - "author_inst": "University of Oxford" - }, - { - "author_name": "Ian J Douglas", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Helen I McDonald", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Jonathan Cockburn", - "author_inst": "TPP" - }, - { - "author_name": "Elizabeth J Williamson", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "David Evans", - "author_inst": "University of Oxford" - }, - { - "author_name": "John Parry", - "author_inst": "TPP" - }, - { - "author_name": "Frank Hester", - "author_inst": "TPP" - }, - { - "author_name": "Sam Harper", - "author_inst": "TPP" - }, - { - "author_name": "Stephen JW Evans", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Sebastian CJ Bacon", - "author_inst": "University of Oxford" - }, - { - "author_name": "Liam Smeeth", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Ben Goldacre", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.16.21260337", "rel_title": "Exposition to airborne SARS-CoV-2 in household and hospitals settings as studied by a vacuum cleaner as a high-powered air sampler", @@ -646471,6 +648079,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, + { + "rel_doi": "10.1101/2021.07.19.21260762", + "rel_title": "Low seropositivity and sub-optimal neutralisation rates in patients fully vaccinated against COVID-19 with B cell malignancies.", + "rel_date": "2021-07-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.19.21260762", + "rel_abs": "Patients with haematological malignancies are at increased risk of severe disease and death from COVID-19 and are less likely to mount humoral immune responses to COVID-19 vaccination, with the B cell malignancies a particularly high-risk group.\n\nOur COV-VACC study is evaluating the immune response to COVID-19 vaccination in patients with B cell malignancies. Eligible patients were either receiving active treatment or had received treatment within the last 24 months. Patients were vaccinated with either the BNT162b2 (Pfizer-BioNTech) (n=41) or ChAdOx1 nCoV-19 (Oxford-AstraZeneca) (n=14) vaccines. The median age of participants was 60 years (range: 27-82) and 50% were receiving systemic anti-cancer therapy (SACT) at the time of vaccination. This interim analysis from the first 55 participants describes anti-S seropositivity rates, neutralising antibody activity and association with peripheral lymphocyte subsets.\n\nAfter the first vaccine dose, 36% overall had detectable anti-S antibodies rising to 42% after the second dose. Sera from seropositive patients was assessed for neutralisation activity in vitro. Of the seropositive patients after first dose (n=17), only 41% were able to neutralise SARS-CoV-2 pseudotyped virus with a 50% inhibitory dilution factor (ID50) of >1:50. After two doses (n=21) 57% of the seropositive patients had detectable neutralisation activity (median ID50 of 1:469, range 1:70 - 1:3056). Total blood lymphocyte, CD19, CD4 and CD56 counts were significantly associated with seropositivity. Patients vaccinated more than 6 months after completing therapy were significantly more likely to develop antibodies than those within 6 months of treatment or on active treatment; OR: 5.93 (1.29 - 27.28).\n\nOur data has important implications for patients with B cell malignancies as we demonstrate a disconnect between anti-S seropositivity and virus neutralisation in vitro following vaccination against COVID-19.\n\nUrgent consideration should be given to revaccinating patients with B-cell malignancies after completion of anti-cancer treatment as large numbers currently remain at high risk of infection with the increasing transmission of SARS-CoV-2 in many countries.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Thomas A Fox", + "author_inst": "University College London" + }, + { + "author_name": "Amy A Kirkwood", + "author_inst": "CR UK & UCL Cancer Trials Centre, UCL Cancer Institute, UCL, London, UK." + }, + { + "author_name": "Louise Enfield", + "author_inst": "Department of Clinical Haematology, University College London Hospitals NHS Foundation Trust, London, UK." + }, + { + "author_name": "Suzanne Arulogun", + "author_inst": "Department of Clinical Haematology, University College London Hospitals NHS Foundation Trust, London, UK." + }, + { + "author_name": "Janki Kavi", + "author_inst": "Immunology, Royal Free London Hospitals NHS Foundation Trust, London, UK." + }, + { + "author_name": "Evan Vitsaras", + "author_inst": "Health Services Laboratories, London, UK." + }, + { + "author_name": "William Townsend", + "author_inst": "Department of Clinical Haematology, University College London Hospitals NHS Foundation Trust, London, UK." + }, + { + "author_name": "Siobhan O Burns", + "author_inst": "UCL Institute of Immunity & Transplantation, University College London, London, UK." + }, + { + "author_name": "Satyen H Gohil", + "author_inst": "Department of Clinical Haematology, University College London Hospitals NHS Foundation Trust, London, UK." + }, + { + "author_name": "Kate Cwynarski", + "author_inst": "Department of Clinical Haematology, University College London Hospitals NHS Foundation Trust, London, UK." + }, + { + "author_name": "Kirsty J Thomson", + "author_inst": "Department of Clinical Haematology, University College London Hospitals NHS Foundation Trust, London, UK." + }, + { + "author_name": "Mahdad Noursadeghi", + "author_inst": "Research Department of Infection, University College London, London, UK." + }, + { + "author_name": "Robert S. Heyderman", + "author_inst": "Research Department of Infection, University College London, London, UK." + }, + { + "author_name": "Tommy Rampling", + "author_inst": "Department of Infectious Disease, University College London Hospitals NHS Foundation Trust, London, UK." + }, + { + "author_name": "Kirit M Ardeshna", + "author_inst": "Department of Clinical Haematology, University College London Hospitals NHS Foundation Trust, London, UK." + }, + { + "author_name": "Laura E McCoy", + "author_inst": "UCL Institute of Immunity & Transplantation, University College London, London, UK." + }, + { + "author_name": "Emma C Morris", + "author_inst": "UCL Institute of Immunity & Transplantation, University College London, London, UK." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.16.21260638", "rel_title": "Social determinants of health exacerbate disparities in COVID-19 illness severity and lasting symptom complaints", @@ -647467,125 +649158,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.07.16.452721", - "rel_title": "Single-dose respiratory mucosal delivery of next-generation viral-vectored COVID-19 vaccine provides robust protection against both ancestral and variant strains of SARS-CoV-2", - "rel_date": "2021-07-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.16.452721", - "rel_abs": "The emerging SARS-CoV-2 variants of concern (VOC) increasingly threaten the effectiveness of current first-generation COVID-19 vaccines that are administered intramuscularly and are designed to only target the spike protein. There is thus a pressing need to develop next-generation vaccine strategies to provide more broad and long-lasting protection. By using adenoviral vectors (Ad) of human and chimpanzee origin, we developed Ad-vectored trivalent COVID-19 vaccines expressing Spike-1, Nucleocapsid and RdRp antigens and evaluated them following single-dose intramuscular or intranasal immunization in murine models. We show that respiratory mucosal immunization, particularly with chimpanzee Ad-vectored vaccine, is superior to intramuscular immunization in induction of the three-arm immunity, consisting of local and systemic antibody responses, mucosal tissue-resident memory T cells, and mucosal trained innate immunity. We further show that single-dose intranasal immunization provides robust protection against not only the ancestral strain of SARS-CoV-2, but also two emerging VOC, B.1.1.7 and B.1.351. Our findings indicate that single-dose respiratory mucosal delivery of an Ad-vectored multivalent vaccine represents an effective next-generation COVID-19 vaccine strategy against current and future VOC. This strategy has great potential to be used not only to boost first-generation vaccine-induced immunity but also to expand the breadth of protective T cell immunity at the respiratory mucosa.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Sam Afkhami", - "author_inst": "McMaster University" - }, - { - "author_name": "Ali Zhang", - "author_inst": "McMaster University" - }, - { - "author_name": "Hannah D. Stacey", - "author_inst": "McMaster University" - }, - { - "author_name": "Art Marzok", - "author_inst": "McMaster University" - }, - { - "author_name": "Alisha Kang", - "author_inst": "McMaster University" - }, - { - "author_name": "Ramandeep Singh", - "author_inst": "McMaster University" - }, - { - "author_name": "Jegarubee Bavananthasivam", - "author_inst": "McMaster University" - }, - { - "author_name": "Gluke Ye", - "author_inst": "McMaster University" - }, - { - "author_name": "Xiangqian Luo", - "author_inst": "McMaster University" - }, - { - "author_name": "Fuan Wang", - "author_inst": "McMaster University" - }, - { - "author_name": "Jann C. Ang", - "author_inst": "McMaster University" - }, - { - "author_name": "Anna Zganiacz", - "author_inst": "McMaster University" - }, - { - "author_name": "Uma Sankar", - "author_inst": "McMaster University" - }, - { - "author_name": "Natallia Kazhdan", - "author_inst": "McMaster University" - }, - { - "author_name": "Joshua F.E. Koenig", - "author_inst": "McMaster University" - }, - { - "author_name": "Allyssa Phelps", - "author_inst": "McMaster University" - }, - { - "author_name": "Manel Jordana", - "author_inst": "McMaster University" - }, - { - "author_name": "Yonghong Wan", - "author_inst": "McMaster University" - }, - { - "author_name": "Karen L. Mossman", - "author_inst": "McMaster University" - }, - { - "author_name": "Mangalakumari Jeyanathan", - "author_inst": "McMaster University" - }, - { - "author_name": "Amy Gillgrass", - "author_inst": "McMaster University" - }, - { - "author_name": "Maria Fe C. Medina", - "author_inst": "McMaster University" - }, - { - "author_name": "Fiona Smaill", - "author_inst": "McMaster University" - }, - { - "author_name": "Brian D. Lichty", - "author_inst": "McMaster University" - }, - { - "author_name": "Matthew S. Miller", - "author_inst": "McMaster University" - }, - { - "author_name": "Zhou Xing", - "author_inst": "McMaster University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.07.15.21260603", "rel_title": "Paradoxical Sex-Specific Patterns of Autoantibodies Response to SARS-CoV-2 Infection", @@ -648357,6 +649929,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2021.07.14.21260481", + "rel_title": "Lives saved and hospitalizations averted by COVID-19 vaccination in New York City", + "rel_date": "2021-07-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.14.21260481", + "rel_abs": "Despite the emergence of highly transmissible variants, the number of cases in NYC has fallen from over 5,500 average daily cases in January, 2020 to less than 350 average daily cases in July, 2021. The impact of vaccination in saving lives and averting hospitalizations in NYC has not been formally investigated yet. We used an age-stratified agent-based model calibrated to COVID-19 transmission and vaccination in NYC to evaluate the impact of the vaccination campaign in suppressing the COVID-19 burden. We found that the vaccination campaign has prevented over 250,000 COVID-19 cases, 44,000 hospitalizations and 8,300 deaths from COVID-19 infection since the start of vaccination through July 1, 2021. Notably, the swift vaccine rollout suppressed another wave of COVID-19 that would have led to sustained increase in cases, hospitalizations and deaths during spring triggered by highly transmissible variants. As the Delta variant sweeps across the city, the findings of this study underscore the urgent need to accelerate vaccination and close the vaccine coverage gaps across the city.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Affan Shoukat", + "author_inst": "Yale University" + }, + { + "author_name": "Thomas Nogueira Vilches", + "author_inst": "IMECC-UNICAMP" + }, + { + "author_name": "Seyed Moghadas", + "author_inst": "York University" + }, + { + "author_name": "Pratha Sah", + "author_inst": "Yale University" + }, + { + "author_name": "Eric C Schneider", + "author_inst": "The Commonwealth Fund" + }, + { + "author_name": "Jaimie Shaff", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Jane Zucker", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Celia Quinn", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Dave A Chokshi", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Alison P Galvani", + "author_inst": "Yale University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.07.16.21260079", "rel_title": "Relative Ratios of Human Seasonal Coronavirus Antibodies Predict the Efficiency of Cross-Neutralization of SARS-CoV-2 Spike Binding to ACE2", @@ -649441,25 +651068,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.08.21260081", - "rel_title": "Variants of SARS-COV-2 and the Death Toll", - "rel_date": "2021-07-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.08.21260081", - "rel_abs": "New variants of SARS-COV-2 have been found in various countries. Especially, the UK has been attacked by Indias Delta Plus, and the spread of infection has been very rapid, since it is extremely infectious. Fortunately, however, the number of deaths has been stayed flat, where deaths are reported to be those who are not yet received a shot of COVID-19 vaccine. In this short not, we would like to consider why the number of deaths is so small, compared with high cases, around the infection peak, when the basic reproduction number is very large.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Takesi Saito", - "author_inst": "Kwansei Gakuin University" - } - ], - "version": "1", - "license": "cc0_ng", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.13.21260412", "rel_title": "Gut microbiota alterations in patients with persistent respiratory dysfunction three months after severe COVID-19", @@ -650159,6 +651767,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.13.21260484", + "rel_title": "THE COMPARISON OF THREE REAL-TIME PCR KITS FOR SARS-COV-2 DIAGNOSIS REVEALS DISCREPANCIES ON THE IDENTIFICATION OF POSITIVE COVID-19 CASES AND DISPERSION ON THE VALUES OBTAINED FOR THE DETECTION OF SARS-COV-2 VARIANTS", + "rel_date": "2021-07-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.13.21260484", + "rel_abs": "The COVID-19 pandemic has generated a huge challenge and threat to public health throughout the world population. Reverse transcription associated with real-time Polymerase Chain Reaction (RT-qPCR) has been the gold-standard molecular tool for diagnosis and detection of the SARS-CoV-2. Currently, it is used as the main strategy for testing, traceability, and control of positive cases For this reason, the on-top high demand for reagents has produced stock-out on several occasions and the only alternative to keep population diagnosis has been the use of different RT-qPCR kits. Therefore, we evaluate the performance of three of the commercial RT-qPCR kits currently in use for SARS-CoV-2 diagnosis in Chile, consisting in: TaqMan 2019-nCoV Assay Kit v1 (Thermo). Real-Time Fluorescent RT-PCR Kit for Detecting SARS-CoV-2 (BGI), and LightCycler(R) Multiplex RNA Virus Master (Roche). Results of quantification cycle (Cq) and relative fluorescence units (RFU) obtained from their RT-qPCR reactions revealed important discrepancies on the total RNA required for the identification of SARS-CoV-2 genes and diagnosis. Marked differences between kits in samples with 30>Cq value< 34 was observed. Samples with positive diagnoses for Covid-19 using the Thermo Fisher kit had different results when the same samples were evaluated with Roche and BGI kits. The displacement on the Cq value for SARS-CoV-2 identification between the three different RT-qPCR kits was also evident when the presence of single nucleotide variants was evaluated in the context of genomic surveillance. Taken together, this study emphasizes the special care adjusting RT-qPCR reaction conditions of the different kits must be taken by all the laboratories before carrying out the detection of SARS-CoV-2 genes from total RNA nasopharyngeal swab (NPS) samples.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Alvaro Santibanez", + "author_inst": "Universidad de Santiago de Chile Facultad de Quimica y Biologia" + }, + { + "author_name": "Roberto Luraschi", + "author_inst": "Universidad de Santiago de Chile Facultad de Quimica y Biologia" + }, + { + "author_name": "Carlos Barrera-Avalos", + "author_inst": "Universidad de Santiago de Chile Facultad de Quimica y Biologia" + }, + { + "author_name": "Eva Vallejos-Vidal", + "author_inst": "Universidad de Santiago de Chile Facultad de Quimica y Biologia" + }, + { + "author_name": "Javiera Alarcon", + "author_inst": "Universidad de Santiago de Chile Facultad de Quimica y Biologia" + }, + { + "author_name": "Javiera Cayunao", + "author_inst": "Universidad de Santiago de Chile Facultad de Quimica y Biologia" + }, + { + "author_name": "Andrea Mella", + "author_inst": "Universidad de Santiago de Chile Facultad de Quimica y Biologia" + }, + { + "author_name": "Maximiliano Figueroa", + "author_inst": "Universidad de Santiago de Chile Facultad de Quimica y Biologia" + }, + { + "author_name": "Felipe Hernandez", + "author_inst": "Universidad de Santiago de Chile Facultad de Quimica y Biologia" + }, + { + "author_name": "Barbara Plaza", + "author_inst": "Universidad de Santiago de Chile Facultad de Quimica y Biologia" + }, + { + "author_name": "Ailen Inostroza-Molina", + "author_inst": "Universidad de Santiago de Chile Facultad de Quimica y Biologia" + }, + { + "author_name": "Daniel Valdes", + "author_inst": "Universidad de Santiago de Chile Facultad de Quimica y Biologia" + }, + { + "author_name": "Monica Imarai", + "author_inst": "Universidad de Santiago de Chile Facultad de Quimica y Biologia" + }, + { + "author_name": "Claudio Acuna-Castillo", + "author_inst": "Universidad de Santiago de Chile Facultad de Quimica y Biologia" + }, + { + "author_name": "Felipe E Reyes-Lopez", + "author_inst": "Universitat Autonoma de Barcelona; Universidad de Santiago de Chile Facultad de Quimica y Biologia" + }, + { + "author_name": "Ana Maria Sandino", + "author_inst": "Universidad de Santiago de Chile Facultad de Quimica y Biologia" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.16.452441", "rel_title": "A single de novo substitution in SARS-CoV-2 spike informs enhanced adherence to human ACE2.", @@ -650959,45 +652646,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.12.21260390", - "rel_title": "Modeling COVID-19 vaccine efficacy and coverage towards herd-immunity in the Basque Country, Spain", - "rel_date": "2021-07-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.12.21260390", - "rel_abs": "Vaccines have measurable efficacies, obtained first from vaccine trials. However, vaccine efficacy is not a static measure upon licensing, and the long term population studies are very important to evaluate vaccine performance and impact. COVID-19 vaccines were developed in record time and although the extent of sterilizing immunity is still under evaluation, the currently licensed vaccines are extremely effective against severe disease, with vaccine efficacy significantly higher after the full immunization schedule. We investigate the impact of vaccines which have different efficacies after first dose and after the second dose administration schedule, eventually considering different efficacies against severe disease as opposed to overall infection. As a proof of concept, we model the vaccine performance of hospitalization reduction at the momentary scenario of the Basque Country, Spain, with population in a mixed vaccination setting, giving insights into the population coverage needed to achieve herd immunity in the current vaccination context.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Nico Stollenwerk", - "author_inst": "BCAM" - }, - { - "author_name": "Javier Mar", - "author_inst": "Osakidetza Basque Health Service; Biodonostia Health Research Institute" - }, - { - "author_name": "Joseba Bidaurrazaga Van-Dierdonck", - "author_inst": "Basque Health Department" - }, - { - "author_name": "Oliver Ibarrondo", - "author_inst": "Osakidetza Basque Health Service" - }, - { - "author_name": "Carlo Estadilla", - "author_inst": "BCAM" - }, - { - "author_name": "Maira Aguiar", - "author_inst": "BCAM; UNITN; Ikerbasque" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.12.21260365", "rel_title": "Birth during the COVID-19 pandemic, but not maternal SARS-CoV-2 infection during pregnancy, is associated with lower neurodevelopmental scores at 6-months", @@ -651865,6 +653513,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.07.13.21260402", + "rel_title": "EVALUATION OF THE PANBIO SARS-COV-2 RAPID ANTIGEN DETECTION TEST IN THE BAHAMAS", + "rel_date": "2021-07-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.13.21260402", + "rel_abs": "Identification and isolation of persons infected with SARS-COV-2 are key mitigation strategies in the current pandemic, and rapid antigen detection tests (RADTs) offer the promise of decreased turnaround time to diagnosis when compared with gold standard RT-PCR testing. We evaluated the analytical performance of the Abbott(R) Panbio RADT on nasopharyngeal samples stored at the Ministry of Health National Reference Lab in Nassau, Bahamas. The Panbio demonstrated a test sensitivity of 94% and a specificity of 100% on 50 PCR negative samples and 50 samples presumed to be infectious based on having PCR cycle threshold values below 30. Additionally, in our examination of operator results there was low interpersonal variation (1%) among three blind operators and significant correlation between sample Ct value and perceived signal strength on the RADT device. However, three PCR positive samples below Ct 30 were misdiagnosed by RADT, including one sample with Ct value less than 20. These results support the use of the Panbio in symptomatic persons to detect active SARS-COV-2 infections, with the caveat that RADT-negative samples should be confirmed by RT-PCR.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Christoph Johnson", + "author_inst": "National Reference Lab, The Bahamas Ministry of Health" + }, + { + "author_name": "Kirvina Ferguson", + "author_inst": "National Reference Lab, The Bahamas Ministry of Health" + }, + { + "author_name": "Tavion Smith", + "author_inst": "National Reference Lab, The Bahamas Ministry of Health" + }, + { + "author_name": "Dashaunette Wallace", + "author_inst": "National Reference Lab, The Bahamas Ministry of Health" + }, + { + "author_name": "Keith McConnell", + "author_inst": "National Reference Lab, The Bahamas Ministry of Health" + }, + { + "author_name": "Donaldson Conserve", + "author_inst": "The George Washington University Milken School of Public Health" + }, + { + "author_name": "indira martin", + "author_inst": "Ministry of health" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.07.15.452488", "rel_title": "Monitoring the spread of SARS-CoV-2 variants in Moscow and the Moscow region using targeted high-throughput sequencing", @@ -652952,93 +654643,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.07.09.21260192", - "rel_title": "Comparison of humoral and cellular responses in kidney transplant recipients receiving BNT162b2 and ChAdOx1 SARS-CoV-2 vaccines", - "rel_date": "2021-07-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.09.21260192", - "rel_abs": "BackgroundAttenuated immune responses to mRNA SARS-CoV-2 vaccines have been reported in solid organ transplant recipients. Most studies have assessed serological responses alone, and there is limited immunological data on vector-based vaccines in this population. This study compares the immunogenicity of BNT162b2 with ChAdOx1 in a cohort of kidney transplant patients, assessing both serological and cellular responses.\n\nMethods920 patients were screened for spike protein antibodies (anti-S) following 2 doses of either BNT162b2 (n=490) or ChAdOx1 (n=430). 106 patients underwent assessment with T-cell ELISpot assays. 65 health care workers were used as a control group.\n\nResultsAnti-S was detected in 569 (61.8%) patients. Seroconversion rates in infection-naive patients who received BNT162b2 were higher compared with ChAdOx1, at 269/410 (65.6%) and 156/358 (43.6%) respectively, p<0.0001. Anti-S concentrations were higher following BNT162b, 58(7.1-722) BAU/ml, compared with ChAdOx1, 7.1(7.1-39) BAU/ml, p<0.0001. Calcineurin inhibitor monotherapy, vaccination occurring >1st year post-transplant and receiving BNT162b2 was associated with seroconversion.\n\nOnly 28/106 (26.4%) of patients had detectable T-cell responses. There was no difference in detection between infection-naive patients who received BNT162b2, 7/40 (17.5%), versus ChAdOx1, 2/39 (5.1%), p=0.15. There was also no difference in patients with prior infection who received BNT162b2, 8/11 (72.7%), compared with ChAdOx1, 11/16 (68.8%), p=0.83.\n\nConclusionsEnhanced humoral responses were seen with BNT162b2 compared with ChAdOx1 in kidney transplant patients. T-cell responses to both vaccines were markedly attenuated. Clinical efficacy data is still required but immunogenicity data suggests weakened responses to both vaccines in transplant patients, with ChAdOx1 less immunogenic compared with BNT162b2.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Maria Prendecki", - "author_inst": "Imperial College London" - }, - { - "author_name": "Tina Thomson", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Candice L Clarke", - "author_inst": "Imperial College London" - }, - { - "author_name": "Paul Martin", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Sarah Gleeson", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Rute c De aguiar", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Helena Edwards", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Paige Mortimer", - "author_inst": "Imperial College London" - }, - { - "author_name": "Stacey McIntyre", - "author_inst": "Imperial College London" - }, - { - "author_name": "Shanice Lewis", - "author_inst": "Imperial College London" - }, - { - "author_name": "Jaid Deborah", - "author_inst": "Imperial College London" - }, - { - "author_name": "Alison Cox", - "author_inst": "Northwest London Pathology NHS Trust" - }, - { - "author_name": "Graham Pickard", - "author_inst": "Northwest London Pathology NHS Trust" - }, - { - "author_name": "Liz Lightstone", - "author_inst": "Imperial College London" - }, - { - "author_name": "Stephen P McAdoo", - "author_inst": "Imperial College London" - }, - { - "author_name": "Peter Kelleher", - "author_inst": "Imperial College London, Northwest London Pathology NHS Trust" - }, - { - "author_name": "Michelle Willicombe", - "author_inst": "Imperial College London, Imperial College Healthcare NHS Trust" - }, - { - "author_name": "- OCTAVE Study Consortium", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "transplantation" - }, { "rel_doi": "10.1101/2021.07.10.21260232", "rel_title": "SARS-CoV-2 variants of concern exhibit reduced sensitivity to live-virus neutralization in sera from CoronaVac vaccinees and naturally infected COVID-19 patients", @@ -653922,6 +655526,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2021.07.12.21260409", + "rel_title": "Understanding COVID-19 vaccine hesitancy in Pakistan: The paradigm of Confidence, Convenience and Complacency; A Cross-sectional study.", + "rel_date": "2021-07-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.12.21260409", + "rel_abs": "Background and objectivesVaccine hesitancy is a big obstacle for vaccination programs, as is anticipated for the COVID-19 vaccination program, resulting in low uptake of vaccines thereby hindering the process of reaching herd immunity. Bearing this in mind the current study was aimed to explore the determinants of vaccine hesitancy amongst the Pakistani population.\n\nMethodologyA cross-sectional study was carried out from November 2020 to March 2021. The conceptual framework of the study was based on the 3Cs (Confidence, Convenience, Complacency) model. The google-forms-based questionnaire was disseminated amongst the general population. Data collected were entered into SPSS version 26 and analyzed.\n\nResultsOf the 421 participants, 68.4% were women. Non-healthcare workers were 55.8% of respondents. Of vaccine-hesitant individuals, 26.13% reported they were very unlikely to get vaccinated. The vaccine was not safe as it came out too fast was agreed upon by 12.6% of individuals, 50.6% were worried about experiencing side-effects, 18% believed the vaccine will not offer protection and 5.9% believed the vaccine would cause death. Low Practice of SOP in non-Healthcare workers was the strongest contributor to vaccine hesitancy (OR: 5.338, p=0.040, 95% CI: 1.082-26.330) followed by High complacency (p=0.026) and Moderate Complacency (OR: 0.212, p=0.007, 95% CI: 0.069-0.654) towards COVID-19 vaccination. In Healthcare workers the strongest contributor to vaccine hesitancy was having a Moderate Confidence (OR: 0.323, p=0.042, 95% CI: 0.109-0.958) in the vaccine followed by Moderate Convenience (OR: 0.304, p=0.049, 95% CI: 0.093-0.993) for vaccination\n\nConclusionCampaigning and communication strategies to reaffirm confidence in the COVID-19 vaccine and educating the general population about the vaccine could lead to increased perception of vaccine safety and effectiveness thereby restoring confidence in vaccine and decreasing vaccine hesitancy. Likewise, working to increase vaccine convenience and decreasing complacency towards the COVID-19 vaccine would translate into high vaccine uptake.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Naveen Siddique Sheikh", + "author_inst": "CMH Lahore Medical College and Institute of Dentistry, Lahore, Pakistan." + }, + { + "author_name": "Mumtaz Touseef", + "author_inst": "CMH Lahore Medical College and Institute of Dentistry, Lahore, Pakistan." + }, + { + "author_name": "Riddah Sultan", + "author_inst": "CMH Lahore Medical College and Institute of Dentistry, Lahore, Pakistan." + }, + { + "author_name": "Kanwal Hassan Cheema", + "author_inst": "CMH Lahore Medical College and Institute of Dentistry, Lahore, Pakistan." + }, + { + "author_name": "Sidra Shafiq Cheema", + "author_inst": "CMH Lahore Medical College and Institute of Dentistry, Lahore, Pakistan." + }, + { + "author_name": "Afia Sarwar", + "author_inst": "CMH Lahore Medical College and Institute of Dentistry, Lahore, Pakistan." + }, + { + "author_name": "Haniya Zainab Siddique", + "author_inst": "2Institute of Environmental Engineering and Sciences (IESE), National University Of Sciences and Technology (NUST), Islamabad, Pakistan." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.07.09.21260089", "rel_title": "Comparison of immunogenicity between BNT162b2 and ChAdOx1 SARS-CoV-2 vaccines in a large haemodialysis population", @@ -654978,45 +656625,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2021.07.09.21260251", - "rel_title": "Heterologous immunisation with vector vaccine as prime followed by mRNA vaccine as boost leads to humoral immune response against SARS-CoV-2, which is comparable to that according to a homologous mRNA vaccination scheme", - "rel_date": "2021-07-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.09.21260251", - "rel_abs": "BackgroundThe humoral immune response after primary immunisation with a SARS-CoV-2 vector vaccine (AstraZeneca AZD1222, ChAdOx1 nCoV-19, Vaxzevria) followed by an mRNA vaccine boost (Pfizer/BioNTech, BNT162b2; Moderna, m-1273) was examined and compared with the antibody response after homologous vaccination schemes (AZD1222/AZD1222 or BNT162b2/BNT162b2).\n\nMethodsSera from 59 vaccinees were tested for anti-SARS-CoV-2 immunoglobulin G (IgG) and virus-neutralising antibodies (VNA) with four IgG assays, a surrogate neutralisation test (sVNT), and a Vero cell-based neutralisation test (cVNT) using the B.1.1.7 variant of concern (VOC; alpha) as antigen. Investigation was done before and after heterologous (n=31 and 42) or homologous booster vaccination (AZD1222/AZD1222, n=8/9; BNT162b2/BNT162b2, n=8/8). After the second immunisation, 26 age and gender matched sera (AZD1222/mRNA, n=9; AZD1222/AZD1222, n=9; BNT162b2/BNT162b2, n=8) were also tested for VNA against VOC B.1.617.2 (delta) in the cVNT. The strength of IgG binding to separate SARS-CoV-2 antigens was measured by avidity.\n\nResultsAfter the first vaccination, prevalence of IgG directed against (trimeric) SARS-CoV-2 spike (S)-protein and its receptor-binding domain (RBD) varied from 55-95 % (AZD1222) to 100% (BNT162b2), depending on the vaccine used and the SARS-CoV-2 antigen used. The booster vaccination resulted in 100 percent seroconversion and appearance of highly avid IgG as well as VNA against VOC B.1.1.7. The results of the anti-SARS-CoV-2 IgG tests showed an excellent correlation to the VNA titres against this VOC. The agreement of cVNT and sVNT results was good. However, the sVNT seems to overestimate non and weak B.1.1.7-neutralising titres. The mean anti-SARS-CoV-2 IgG and B.1.1.7-neutralising titres were significantly higher after heterologous vaccination compared to the homologous AZD1222 scheme. If VOC B.1.617.2 was used as antigen, significantly lower mean VNAs were measured in the cVNT, and three (33.3%) vector vaccine recipients had a VNA titre <1:10.\n\nConclusionsThe heterologous SARS-CoV-2 vaccination leads to a strong antibody response with anti-SARS-CoV-2 IgG and VNA titres at a level comparable to that of a homologous BNT162b2 vaccination scheme. Irrespectively of the chosen immunisation regime, highly avid IgG antibodies can be detected just two weeks after the second vaccine dose indicating the development of a robust humoral immunity. The observed reduction in the VNA titre against VOC B.1.617.2 is remarkable and may be attributed to a partial immune escape of the delta variant.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Ruben Rose", - "author_inst": "Institut fuer Infektionsmedizin, Christian-Albrechts-Universitaet zu Kiel und Universitaetsklinikum Schleswig Holstein, Campus Kiel, Brunswiker Strasse 4, D-241" - }, - { - "author_name": "Franziska Neumann", - "author_inst": "Labor Dr. Krause und Kollegen MVZ GmbH, Steenbeker Weg 23, D-24106 Kiel, Germany" - }, - { - "author_name": "Olaf Grobe", - "author_inst": "Labor Dr. Krause und Kollegen MVZ GmbH, Steenbeker Weg 23, D-24106 Kiel, Germany" - }, - { - "author_name": "Thomas Lorentz", - "author_inst": "Labor Dr. Krause und Kollegen MVZ GmbH Kiel, Steenbeker Weg 23, D-24106 Kiel" - }, - { - "author_name": "Helmut Fickenscher", - "author_inst": "Institut fuer Infektionsmedizin, Christian-Albrechts-Universitaet zu Kiel und Universitaetsklinikum Schleswig Holstein, Campus Kiel, Brunswiker Strasse 4, D-241" - }, - { - "author_name": "Andi Krumbholz", - "author_inst": "Institut fuer Infektionsmedizin, Christian-Albrechts-Universitaet zu Kiel und Universitaetsklinikum Schleswig Holstein, Campus Kiel, Brunswiker Strasse 4, D-241" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.09.21260250", "rel_title": "Utilization of health care services before and after media attention about fatal side effects of the AstraZeneca vaccine", @@ -655616,6 +657224,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.09.21260106", + "rel_title": "Risk of Severe COVID-19 Outcomes Among Patients with Rheumatoid Arthritis in the United States", + "rel_date": "2021-07-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.09.21260106", + "rel_abs": "IntroductionCoronavirus disease 2019 (COVID-19) has infected over 22 million individuals worldwide. It remains unclear whether patients with COVID-19 and Rheumatoid Arthritis (RA) experience worse clinical outcomes compared to similar patients with COVID-19 without RA.\n\nAimThe aim of this study is to provide insights on how COVID-19 impacted patients with RA given the nature of the disease and medication used.\n\nMethodsRA cases were identified via International Classification of Diseases (ICD) codes and COVID-19 cases by laboratory results in the U.S. based TriNetX network. Patients with COVID-19 and RA were propensity-score matched based on demographics with patients with COVID-19 without RA at a 1:3 ratio. A hospitalized sub-population was defined by procedure codes.\n\nResultsWe identified 1,014 COVID-19 patients with RA and 3,042 non-RA matches selected from 137,757 patients. The odds of hospitalization (non-RA:23%, RA:24.6%, OR:1.08, 95% CI: 0.88 to 1.33) or mortality (non-RA:5.4%, RA:6%, OR:0.93, 95% CI: 0.65 to 1.34) were not significantly different.\n\nThe hospitalized sub-population included 249 patients with COVID-19 and RA and 745 non-RA matches selected from 21,435 patients. The risk of intensive care unit (ICU) admission (non-RA:18.8%, RA:18.1%, OR:0.94, 95% CI: 0.60 to 1.45), and inpatient mortality (non-RA:14.4%, RA:14.5%, OR:0.86, 95% CI: 0.53 to 1.40) were not significantly different.\n\nConclusionWe didnt find evidence suggesting patients with COVID-19 and RA are more likely to have severe outcomes than patients with COVID-19 without RA.\n\nKey Messages- Patients with Rheumatoid Arthritis (RA) tend to be older, and often have co-morbidities which could put them at greater risk of severe COVID-19 outcomes.\n- This study is one of the largest studies of COVID-19 infected RA populations to date. We did not find increased risk of hospitalization, ICU admission, or mortality among RA patients vs. matched non-RA patients.\n- Patients previously exposed to anti-coagulants experienced higher risks of hospitalization and overall mortality. Extra attention is needed for treating such patients.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Ching-Yi Chuo", + "author_inst": "Genentech inc" + }, + { + "author_name": "Vince Yau", + "author_inst": "Genentech" + }, + { + "author_name": "Sriraman Madhavan", + "author_inst": "Genentech" + }, + { + "author_name": "Larry Tsai", + "author_inst": "Genentech" + }, + { + "author_name": "Jenny Chia", + "author_inst": "Genentech" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.07.09.21260277", "rel_title": "Predicted Norovirus Resurgence in 2021-2022 Due to the Relaxation of Nonpharmaceutical Interventions Associated with COVID-19 Restrictions in England: A Mathematical Modelling Study", @@ -656752,65 +658395,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.08.21260236", - "rel_title": "Aspirin Use is Associated with Decreased Mortality in Patients with COVID-19: A Systematic Review and Meta-analysis", - "rel_date": "2021-07-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.08.21260236", - "rel_abs": "BackgroundNovel Corona Virus Disease 2019 (COVID-19) has resulted in more than three and half million deaths worldwide as of June 6, 2021. The role of aspirin in prevention of COVID-19 mortality has not been much studied. We aimed to study the relationship between aspirin use and covid-19 mortality.\n\nMethodsWe searched PubMed, MEDLINE, EMBASE, and Cochrane database for studies from January 2019 till June 6, 2021 with inclusion criteria of RCT, Cohort study, studies reporting mortality, and comparison studies on aspirin versus non-aspirin. Statistical analysis was done with Review Manager 5.4 statistical software using the inverse variance method. We assessed the pooled hazard ratio (HR), and 95% confidence interval using the random effect model and I-squared test was used to determine statistical heterogeneity.\n\nResultsWe included five retrospective cohort studies which met our inclusion criteria with total of 14065 participants in both groups. There were 6797 participants in the aspirin group and 7268 participants in the non-aspirin group. Our results show that the use of aspirin was associated with 53% decrease in mortality compared to non-aspirin in patients with COVID-19 (adjusted HR 0.47, 95% CI 0.35-0.63, P< 0.001, I2= 47%). In the analysis restricted to patients hospitalized for COVID-19, the use of aspirin was associated with a 49% reduction in the risk for in-hospital mortality (adjusted HR 0.51, 95% CI 0.33-0.80, P = 0.004, I2= 39%).\n\nConclusionsOur results show that aspirin is associated with decrease in both overall mortality and in-hospital mortality in patients with COVID-19.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Pramod savarapu", - "author_inst": "McLaren Flint/MSU" - }, - { - "author_name": "Nischit Baral", - "author_inst": "McLaren Flint/Michigan State University College of Human Medicine" - }, - { - "author_name": "Govinda Adhikari", - "author_inst": "Govinda.adhikari@mclaren.org" - }, - { - "author_name": "Maxwell Akanbi", - "author_inst": "McLaren Flint/MSU" - }, - { - "author_name": "Basel Abdelazeem", - "author_inst": "McLaren Flint/MSU" - }, - { - "author_name": "Sakiru O. Isa", - "author_inst": "McLaren Flint/MSU" - }, - { - "author_name": "Ashiya Khan", - "author_inst": "McLaren Flint/MSU" - }, - { - "author_name": "Maham Ali", - "author_inst": "McLaren Flint/MSU" - }, - { - "author_name": "Sravanthi Jenumula", - "author_inst": "McLaren Flint/MSU" - }, - { - "author_name": "Kavitha Kesari", - "author_inst": "McLaren Flint/MSU" - }, - { - "author_name": "Arvind Kunadi", - "author_inst": "McLaren Flint/MSU" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.08.21260181", "rel_title": "The Lived Experience of Implementing Infection Control Measures in Care Homes during two waves of the COVID-19 Pandemic. A mixed-methods study", @@ -657458,6 +659042,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.09.451812", + "rel_title": "Impact of temperature on the affinity of SARS-CoV-2 Spike for ACE2", + "rel_date": "2021-07-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.09.451812", + "rel_abs": "The seasonal nature in the outbreaks of respiratory viral infections with increased transmission during low temperatures has been well established. The current COVID-19 pandemic makes no exception, and temperature has been suggested to play a role on the viability and transmissibility of SARS-CoV-2. The receptor binding domain (RBD) of the Spike glycoprotein binds to the angiotensin-converting enzyme 2 (ACE2) to initiate viral fusion. Studying the effect of temperature on the receptor-Spike interaction, we observed a significant and stepwise increase in RBD-ACE2 affinity at low temperatures, resulting in slower dissociation kinetics. This translated into enhanced interaction of the full Spike to ACE2 receptor and higher viral attachment at low temperatures. Interestingly, the RBD N501Y mutation, present in emerging variants of concern (VOCs) that are fueling the pandemic worldwide, bypassed this requirement. This data suggests that the acquisition of N501Y reflects an adaptation to warmer climates, a hypothesis that remains to be tested.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Jeremie Prevost", + "author_inst": "CRCHUM / Universite de Montreal" + }, + { + "author_name": "Jonathan Richard", + "author_inst": "CRCHUM / Universite de Montreal" + }, + { + "author_name": "Romain Gasser", + "author_inst": "CRCHUM / Universite de Montreal" + }, + { + "author_name": "Shilei Ding", + "author_inst": "CRCHUM" + }, + { + "author_name": "Clement Fage", + "author_inst": "CRCHUQ / Universite Laval" + }, + { + "author_name": "Sai Priya Anand", + "author_inst": "CRCHUM / McGill University" + }, + { + "author_name": "Damien Adam", + "author_inst": "CRCHUM / Universite de Montreal" + }, + { + "author_name": "Natasha Gupta Vergara", + "author_inst": "Drexel University" + }, + { + "author_name": "Alexandra Tauzin", + "author_inst": "CRCHUM / Universite de Montreal" + }, + { + "author_name": "Mehdi Benlarbi", + "author_inst": "CRCHUM" + }, + { + "author_name": "Shang Yu Gong", + "author_inst": "CRCHUM / McGill University" + }, + { + "author_name": "Guillaume Goyette", + "author_inst": "CRCHUM" + }, + { + "author_name": "Anik Prive", + "author_inst": "CRCHUM" + }, + { + "author_name": "Sandrine Moreira", + "author_inst": "INSPQ" + }, + { + "author_name": "Hugues Charest", + "author_inst": "INSPQ" + }, + { + "author_name": "Michel Roger", + "author_inst": "INSPQ" + }, + { + "author_name": "Walther Mothes", + "author_inst": "Yale University" + }, + { + "author_name": "Marzena Pazgier", + "author_inst": "USUHS" + }, + { + "author_name": "Emanuelle Brochiero", + "author_inst": "CRCHUM / Universite de Montreal" + }, + { + "author_name": "Guy Boivin", + "author_inst": "CRCHUQ / Universite Laval" + }, + { + "author_name": "Cameron F Abrams", + "author_inst": "Drexel University" + }, + { + "author_name": "Arne Schon", + "author_inst": "The Johns Hopkins University" + }, + { + "author_name": "Andres Finzi", + "author_inst": "CRCHUM / Universite de Montreal" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.07.09.451732", "rel_title": "Reduced neutralization of SARS-CoV-2 B.1.617 variant by inactivated and RBD-subunit vaccine", @@ -658554,57 +660245,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.07.21260130", - "rel_title": "Loneliness among people with severe mental ill health during the COVID-19 pandemic: results from a linked UK population cohort study", - "rel_date": "2021-07-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.07.21260130", - "rel_abs": "PurposePopulation surveys underrepresent people with severe mental ill health. This paper aims to explore perceived social support and loneliness and factor associations during the Covid-19 pandemic in a sample of individuals with severe mental ill health.\n\nDesign/methodology/approachWe sampled an already existing cohort of people with severe mental ill health. Researchers contacted participants by phone or by post to invite them to take part in a survey about how the pandemic restrictions had impacted health, Covid-19 experiences, perceived social support, employment and loneliness. Loneliness was measured by the three item UCLA loneliness scale.\n\nFindingsIn the pandemic sub-cohort, 367 adults with a severe mental ill health diagnosis completed a remote survey. 29-34% of participants reported being lonely. Loneliness was associated with being younger in age (adjusted OR = -.98, p = .02), living alone (adjusted OR = 2.04, p = .01), high levels of social and economic deprivation (adjusted OR = 2.49, p = .04), and lower perceived social support (B = -5.86, p < .001). Living alone was associated with lower perceived social support. Being lonely was associated with a self-reported deterioration in mental health during the pandemic (adjusted OR = 3.46, 95%CI 2.03-5.91).\n\nPractical implicationsIntervention strategies to tackle loneliness in the severe mental ill health population are needed. Further research is needed to follow-up the severe mental ill health population after pandemic restrictions are lifted to understand perceived social support and loneliness trends.\n\nOriginalityLoneliness was a substantial problem for the severe mental ill health population before the Covid-19 pandemic but there is limited evidence to understand perceived social support and loneliness trends during the pandemic.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Paul N Heron", - "author_inst": "University of York" - }, - { - "author_name": "Panagiotis Spanakis", - "author_inst": "University of York" - }, - { - "author_name": "Suzanne Crosland", - "author_inst": "University of York" - }, - { - "author_name": "Gordon Johnston", - "author_inst": "Independent peer researcher" - }, - { - "author_name": "Elizabeth Newbronner", - "author_inst": "University of York" - }, - { - "author_name": "Ruth Wadman", - "author_inst": "University of York" - }, - { - "author_name": "Lauren Walker", - "author_inst": "University of York" - }, - { - "author_name": "Simon Gilbody", - "author_inst": "Mental Health and Addictions Research Group" - }, - { - "author_name": "Emily Peckham", - "author_inst": "University of York" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.07.07.21260158", "rel_title": "The Impact of Sampling Type, Frequency and Scale of Collection System on SARS-CoV-2 Quantification Fidelity", @@ -659500,6 +661140,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.06.21260115", + "rel_title": "Elucidating Post-COVID-19 manifestations in India", + "rel_date": "2021-07-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.06.21260115", + "rel_abs": "BackgroundIn India, a large number of patients with coronavirus disease-2019 (COVID-19), presented with common symptoms including fever, dyspnea, cough, musculoskeletal symptoms (fatigue, myalgia, joint pain) and gastrointestinal symptoms. However, information is lacking on symptoms that persist after recovery from COVID-19. In this study we assessed symptoms that persisted in patients even after their recovery and discharged from the hospital after one month from COVID-19.\n\nMethodsThis study is an observational cohort study. Participants in this study were enrolled between 30 to 40 days after recovery from COVID-19 of [≥]18 years of age, who were hospitalized with laboratory-confirmed RT-PCR COVID-19 disease. Outcomes from post COVID-19 participants were elicited through questionnaire that consisted of three main parts beginning from subjects demographical data, depicting about the status of COVID-19 and other co-morbidities of the subject, and about post-COVID-19 symptoms and manifestations.\n\nResultsAll subjects have reported some manifestation after recovery from COVID-19 whereas numerous symptoms and diseases were experienced by a great percentage of participants. Fatigue (56.25%), dyspnea (74.3%) and disturbed sleep (64.3%) were among the most common symptoms. However, more critical manifestations like renal failure and pulmonary fibrosis were reported by only a few percent of the subjects. Rating of worse physical and mental health after post-COVID recovery was also reported by subjects. There was a strong relationship found in between the presence of other co-morbidities before infection like diabetes, hypertension and in disease severity after infection. A total of 280 patients were enrolled and 160 completed the survey.\n\nConclusionsPost COVID-19 sufferers often experience symptoms that cause a disturbance in their physical health, mental health and their respiratory status for several weeks even after recovery from COVID-19. Therefore, all subjects after recovering from COVID-19 should undergo long-term monitoring programme for their symptoms and condition improvement.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Ghizal Fatima", + "author_inst": "Eras Lucknow Medical College and Hospital, Era University, Lucknow" + }, + { + "author_name": "Divyansh Bhatt", + "author_inst": "Eras Lucknow Medical College and Hospital, Era University, Lucknow" + }, + { + "author_name": "Jaserah Idrees", + "author_inst": "Eras Lucknow Medical College and Hospital, Era University, Lucknow" + }, + { + "author_name": "Bushra Khalid", + "author_inst": "Eras Lucknow Medical College and Hospital, Era University, Lucknow" + }, + { + "author_name": "Farzana Mahdi", + "author_inst": "Eras Lucknow Medical College and Hospital, Era University, Lucknow" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.07.21260142", "rel_title": "First detection of SARS-CoV-2 Delta variant (B.1.617.2) in the wastewater of (Ahmedabad), India", @@ -660492,45 +662167,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.06.451294", - "rel_title": "Impairment Of Aversive Episodic Memories During COVID-19 Pandemic: The Impact Of Emotional Context On Memory Processes", - "rel_date": "2021-07-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.06.451294", - "rel_abs": "The threatening context of the COVID-19 pandemic provided a unique setting to study the effects of negative psychological symptoms on memory processes. Episodic memory is an essential function of the human being related to the ability to store and remember experiences and anticipate possible events in the future. Studying this function in this context is crucial to help understand what effects the pandemic will have on the formation of episodic memories. To study this, the formation of episodic memories was evaluated by free recall, recognition, and episode order tasks for an aversive and neutral content. The results indicated that aversive episodic memory is impaired both in the free recall task and in the recognition task. Even the beneficial effect that emotional memory usually has for the episodic order was undermined as there were no differences between the neutral and aversive condition. The present work adds to the evidence that indicates that the level of activation does not modify memory processes in a linear way, which also depends on the type of evocation that people are asked and the characteristics of the content to be encoded.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Candela S Leon", - "author_inst": "Laboratorio de Sueno y memoria, Departamento de Ciencias de la Vida, Instituto Tecnologico de Buenos Aires" - }, - { - "author_name": "Matias Bonilla", - "author_inst": "Laboratorio de Sueno y memoria, Departamento de Ciencias de la Vida, Instituto Tecnologico de Buenos Aires" - }, - { - "author_name": "Facundo A Urreta Benitez", - "author_inst": "Laboratorio de Sueno y Memoria, Departamento de Ciencias de la Vida, Instituto Tecnologico de Buenos Aires" - }, - { - "author_name": "Luis I Brusco", - "author_inst": "Centro de Neuropsiquiatria y Neurologia de la Conducta, Facultad de Medicina, Universidad de Buenos Aires." - }, - { - "author_name": "Jingyi Wang", - "author_inst": "State Key Laboratory of Cognitive Neuroscience and Learning & IDG McGovern Institute for Brain Research, Faculty of Psychology at Beijing Normal University, Bei" - }, - { - "author_name": "Cecilia Forcato", - "author_inst": "Laboratorio de Sueno y Memoria, Departamento de Ciencias de la Vida, Instituto Tecnologico de Buenos Aires" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "animal behavior and cognition" - }, { "rel_doi": "10.1101/2021.07.05.451203", "rel_title": "Mouse Antibodies with Activity Against the SARS-CoV-2 D614G and B.1.351 Variants", @@ -661294,6 +662930,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.02.21258881", + "rel_title": "Breakthrough COVID-19 infection rate with Indian strain in Single-center Healthcare Workers: A real world data.", + "rel_date": "2021-07-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.02.21258881", + "rel_abs": "IntroductionIt is observed that many healthcare workers got COVID-19 infection despite of completing both doses of Covishield vaccine. This study aimed to find real incidence of vaccine breakthrough infection.\n\nMaterial and methodsAll hospital employees, who were fully vaccinated were included in study. Details about their vaccine side effects, infection prior to vaccination, post vaccination infection, severity of infection, hospital and ICU admission were noted.\n\nResultsNone encountered any significant side effects of vaccine. Of the 461 participants - 86 (18.65%) got infection average 38 days (range 14-70days) after vaccination. As per the NIH classification, out of 86, disease was mild in 69(80.2%), moderate in 10(11.62%), severe in 6(6.97%) and critical in 1(1.16%). Of these, 10(11.62%) required hospital admission. Of these 10, 2 were shifted to ICU. Of the 2, One recovered while one died. Thus mortality was 1/86(1.6%).\n\nConclusionBreakthrough infection rate in health care workers was 18.65%. Moderate, severe or critical disease occurred in 19.7% participants even after two doses of vaccine. Mortality due to disease cannot be completely obviated due to vaccine. The vaccine was safe without any significant adverse events.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "RAVINDRA SABNIS", + "author_inst": "Muljibhai Patel Urological Hospital, India" + }, + { + "author_name": "Abhijit Patil", + "author_inst": "Muljibhai Patel Urological Hospital, Nadiad, India" + }, + { + "author_name": "Nitiraj Shete", + "author_inst": "Muljibhai Patel Urological Hospital, Nadiad, India" + }, + { + "author_name": "Arun Kumar Rastogi", + "author_inst": "Muljibhai Patel Urological Hospital, Nadiad, India" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.03.21259957", "rel_title": "The rise and fall of an emerging SARS-CoV-2 variant with the spike protein mutation L452R", @@ -662358,41 +664025,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.03.21259976", - "rel_title": "Incidence of Severe Acute Respiratory Syndrome Coronavirus-2 infection among previously infected or vaccinated employees", - "rel_date": "2021-07-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.03.21259976", - "rel_abs": "IntroductionThe protective effect of previous infection versus vaccination is poorly studied. Among a clinical laboratory that has been conducting routine workforce screening since the beginning of the pandemic, we aimed to assess the relative risk of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infection among individuals who were SARS-CoV-2 naive, previously infected, or vaccinated.\n\nMethodsUsing an electronic laboratory information system, employees were divided into three groups: (1) SARS-CoV-2 naive and unvaccinated, (2) previous SARS-CoV-2 infection, and (3) vaccinated. Person-days were measured from the date of the employee first test and truncated at the end of the observation period. SARS-CoV-2 infection was defined as two positive SARS-CoV-2 PCR tests in a 30-day period. Individuals with fewer than 14 days of follow up were excluded. Incidence estimates and the 95% confidence intervals were calculated using the Poisson Exact equation. The incidence rate ratio (IRR) was used as a measure of association between groups. Analyses were performed on StataSE (StataCorp, College Station, TX).\n\nResultsWe identified 4313, 254 and 739 employee records for groups 1, 2, and 3, respectively. The median age of employees was 29.0 years (interquartile range: 23.6, 39.9). During the observation period, 254, 0, and 4 infections were identified among groups 1, 2, and 3, respectively. Group 1 had an incidence of 25.9 per 100 person-years (95% CI: 22.8-29.3). Group 2 had an incidence of 0 per 100 person-years (95% CI: 0-5.0). Group 3 had an incidence of 1.6 per 100 person-years (95% CI: 0.04-4.2). The IRR of reinfection among those with previous infection compared to SARS-CoV-2 naive was 0 (95% CI: 0-0.19). The IRR of those vaccinated compared to SARS-CoV-2 naive was 0.06 (95% CI: 0.02-0.16). The IRR of those vaccinated compared to prior SARS-CoV-2 was 0 (95% CI: 0-4.98).\n\nConclusionPrevious SARS-CoV-2 infection and vaccination for SARS-CoV-2 were associated with decreased risk for infection or re-infection with SARS-CoV-2 in a routinely screened workforce. The was no difference in the infection incidence between vaccinated individuals and individuals with previous infection. Further research is needed to determine whether our results are consistent with the emergence of new SARS-CoV-2 variants.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Noah Kojima", - "author_inst": "UCLA" - }, - { - "author_name": "Arash Roshani", - "author_inst": "Curative" - }, - { - "author_name": "Matthew Brobeck", - "author_inst": "Curative" - }, - { - "author_name": "Arthur Baca", - "author_inst": "Curative" - }, - { - "author_name": "Jeffrey D Klausner", - "author_inst": "USC" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.05.21259786", "rel_title": "Excess years of life lost to COVID-19 and other causes of death by sex, neighbourhood deprivation and region in England & Wales during 2020", @@ -663116,6 +664748,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.05.21259999", + "rel_title": "Sustaining effective COVID-19 control in Malaysia through large-scale vaccination", + "rel_date": "2021-07-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.05.21259999", + "rel_abs": "IntroductionAs of 3rd June 2021, Malaysia is experiencing a resurgence of COVID-19 cases. In response, the federal government has implemented various non-pharmaceutical interventions (NPIs) under a series of Movement Control Orders and, more recently, a vaccination campaign to regain epidemic control. In this study, we assessed the potential for the vaccination campaign to control the epidemic in Malaysia and four high-burden regions of interest, under various public health response scenarios.\n\nMethodsA modified susceptible-exposed-infectious-recovered compartmental model was developed that included two sequential incubation and infectious periods, with stratification by clinical state. The model was further stratified by age and incorporated population mobility to capture NPIs and micro-distancing (behaviour changes not captured through population mobility). Emerging variants of concern (VoC) were included as an additional strain competing with the existing wild-type strain. Several scenarios that included different vaccination strategies (i.e. vaccines that reduce disease severity and/or prevent infection, vaccination coverage) and mobility restrictions were implemented.\n\nResultsThe national model and the regional models all fit well to notification data but underestimated ICU occupancy and deaths in recent weeks, which may be attributable to increased severity of VoC or saturation of case detection. However, the true case detection proportion showed wide credible intervals, highlighting incomplete understanding of the true epidemic size. The scenario projections suggested that under current vaccination rates complete relaxation of all NPIs would trigger a major epidemic. The results emphasise the importance of micro-distancing, maintaining mobility restrictions during vaccination roll-out and accelerating the pace of vaccination for future control. Malaysia is particularly susceptible to a major COVID-19 resurgence resulting from its limited population immunity due to the countrys historical success in maintaining control throughout much of 2020.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Pavithra Jayasundara", + "author_inst": "School of Public Health and Preventive Medicine, Monash University, Australia" + }, + { + "author_name": "Kalaiarasu M. Peariasamy", + "author_inst": "Institute for Clinical Research, National Institutes of Health, Ministry of Health Malaysia" + }, + { + "author_name": "Kian Boon Law", + "author_inst": "Institute for Clinical Research, National Institutes of Health, Ministry of Health Malaysia." + }, + { + "author_name": "Ku Nurhasni Ku Abd Rahim", + "author_inst": "Malaysian Health Technology Assessment Section, Medical Development Division, Ministry of Health, Malaysia" + }, + { + "author_name": "Sit Wai Lee", + "author_inst": "Malaysian Health Technology Assessment Section, Medical Development Division, Ministry of Health, Malaysia" + }, + { + "author_name": "Izzuna Mudla M. Ghazali", + "author_inst": "Malaysian Health Technology Assessment Section, Medical Development Division, Ministry of Health, Malaysia" + }, + { + "author_name": "Milinda Abayawardana", + "author_inst": "School of Public Health and Preventive Medicine, Monash University, Australia" + }, + { + "author_name": "Linh-Vi Le", + "author_inst": "World Health Organization, Regional Office for the Western Pacific, the Philippines" + }, + { + "author_name": "Rukun K.S. Khalaf", + "author_inst": "World Health Organization Representative Office to Malaysia, Brunei Darussalam and Singapore, Cyberjaya, Malaysia" + }, + { + "author_name": "Karina Razali", + "author_inst": "World Health Organization Representative Office to Malaysia, Brunei Darussalam and Singapore, Cyberjaya, Malaysia" + }, + { + "author_name": "Xuan Le", + "author_inst": "School of Public Health and Preventive Medicine, Monash University, Australia" + }, + { + "author_name": "Zhuo Lin Chong", + "author_inst": "Institute for Public Health, National Institutes of Health, Ministry of Health, Malaysia" + }, + { + "author_name": "Emma S McBryde", + "author_inst": "Australian Institute of Tropical Health and Medicine, James Cook University, Queensland, Australia" + }, + { + "author_name": "Michael T Meehan", + "author_inst": "Australian Institute of Tropical Health and Medicine, James Cook University, Queensland, Australia" + }, + { + "author_name": "Jamie M. Caldwell", + "author_inst": "Department of Biology, University of Hawaii at Manoa, Hawaii, USA" + }, + { + "author_name": "Romain Ragonnet", + "author_inst": "School of Public Health and Preventive Medicine, Monash University, Australia" + }, + { + "author_name": "James M Trauer", + "author_inst": "School of Public Health and Preventive Medicine, Monash University, Australia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.06.21260059", "rel_title": "Initial SARS-CoV-2 vaccination response can predict booster response for BNT162b2 but not for AZD1222", @@ -664148,33 +665863,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.06.21260093", - "rel_title": "Evaluation of Clinical Job Demands, Job Resources, and a Novel Intervention on Measures of Health Care Worker Stress at a Community Hospital Pre and Post COVID-19", - "rel_date": "2021-07-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.06.21260093", - "rel_abs": "ObjectiveTo explore the relationship and identity of Health Care Worker stressors to a measure of perceived burnout and to a novel intervention tool.\n\nParticipants and MethodsFrom July 2019 to June 2020, we surveyed Health Care Workers (HCW) pre and post COVID19 in an independent local community hospital for burnout with the Health Care Provider Wellness Assessment tool. Linear regression and means comparison were used to identify overall job demand and resource perception with burnout, unique stressor portraits by provider subtype and mean survey scores between those who did or did not voluntarily complete at least 14 days of a 28 day novel self-help intervention tool.\n\nResultsRegarding the pre COVID-19 data, of 73 respondents, there was statistically significant (p<.01) correlation between overall job demands (directly) and resources (inversely) with burnout intensity. With respect to the HCW stressor characteristic analyses there was statistical significance (p<.05) between the mean frequency occurrence of the top 5 stressors identified by respondent subtype when compared to the mean occurrence of overall individual responses within the corresponding subtype. Finally, although limited by a low number of respondents, the intervention tool analysis suggested a therapeutic trend toward disruption of the stress-burnout relationship. Regarding the post COVID-19 data, 18 respondents did not show statistically significant characterizable stressor portraits (ie stressors were present but not patternable).\n\nConclusionUnique stressor portraits were identified by HCW subtype which correlated with more intense burnout self-perception. Additionally, there was a trend toward self-help tool efficacy in mitigating burnout.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Jessica Sels", - "author_inst": "Parkview Medical Center Department of Graduate Medical Education" - }, - { - "author_name": "Dylan Carroll", - "author_inst": "Parkview Medical Center Department of Graduate Medical Education" - }, - { - "author_name": "Douglas Duffee", - "author_inst": "Parkview Medical Center Department of Graduate Medical Education" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "primary care research" - }, { "rel_doi": "10.1101/2021.07.06.21259924", "rel_title": "Effectiveness of Ivermectin-Based Multidrug Therapy in Severe Hypoxic Ambulatory COVID-19 Patients", @@ -665162,6 +666850,141 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.01.21259687", + "rel_title": "High Seroprevalence of anti-SARS-CoV-2 antibodies among Ethiopian healthcare workers", + "rel_date": "2021-07-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.01.21259687", + "rel_abs": "BackgroundCOVID-19 pandemic has a devastating impact on the economies and health care system of sub-Saharan Africa. Healthcare workers (HWs), the main actors of the health system, are at higher-risk because of their occupation. Serology-based estimates of SARS-CoV-2 infection among HWs represent a measure of HWs exposure to the virus and a guide to the prevalence of SARS-CoV-2 in the community. This information is currently lacking in Ethiopia and other African countries. This study aimed to develop an in-house antibody testing assay, assess the prevalence of SARS-CoV-2 antibodies among Ethiopian high-risk frontline HWs.\n\nMethods and findingsA cross-sectional seroprevalence study was conducted among HWs in five public hospitals located in different geographic regions of Ethiopia. Socio-demographic and clinical data were collected using questionnaire-based interviews. From consenting HWs, blood samples were collected between December 2020 and February 2021, the period between the two peaks of COVID-19 in Ethiopia. The collected sera were tested using an in-house immunoglobin G (IgG) enzyme-linked immunosorbent assay (ELISA) for SARS-CoV-2 specific antibodies on sera collected from HWs. Of 1,997 HWs who provided a blood sample, demographic and clinical data, 50.5% were female, 74.0% had no symptoms compatible with COVID-19, and 29.0% had history of contact with suspected or confirmed patient with SARS-CoV-2 infection. The overall seroprevalence was 39.6%. The lowest (24.5%) and the highest (48.0%) seroprevalence rates were found in Hiwot Fana Specialized Hospital in Harar and ALERT Hospital in Addis Ababa, respectively. Of the 821 seropositive HWs, 224(27.3%) had history of symptoms consistent with COVID-19. A history of close contact with suspected/confirmed COVID-19 cases was strongly associated with seropositivity (Adjusted odds Ratio (AOR) =1.4, 95% CI 1.1-1.8; p=0.015).\n\nConclusionHigh SARS-CoV-2 seroprevalence levels were observed in the five Ethiopian hospitals. These findings highlight the significant burden of asymptomatic infection in Ethiopia, and may reflect the scale of transmission in the general population.\n\nAuthor summaryO_ST_ABSWhy was this study done?C_ST_ABSO_LISevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global public health threat, including Africa\nC_LIO_LIThe actual morbidity and mortality associated with SARS-CoV-2 infection in Ethiopia underestimated due to the limited molecular testing capacity.\nC_LIO_LIWe have limited knowledge about the seroprevalence of COVID-19 among health workers in Ethiopia.\nC_LIO_LIThis study aimed to develop an in-house immunoglobin G (IgG) enzyme-linked immunosorbent assay (ELISA) for SARS-CoV-2 specific antibodies on sera collected from HWs and to find out the proportion of healthcare workers who have developed antibodies specific to SARS-CoV-2 from five public hospitals located in the different regions of Ethiopia.\nC_LI\n\nWhat did the researchers do and find?O_LIA cross-sectional seroprevalence study was conducted among HWs in five public hospitals located in different geographic regions of Ethiopia.\nC_LIO_LISocio-demographic and clinical data were collected from recruited and consented participants using questionnaire-based interviews.\nC_LIO_LIBlood samples were collected from participants between December 2020 and February 2021, the period between the two peaks of COVID-19 in Ethiopia.\nC_LIO_LIThe collected sera were tested using an in-house ELISA for SARS-CoV-2 specific antibodies on sera collected from HWs.\nC_LIO_LIApproximately 40% of the 1,997 healthcare workers who participated in this study had antibodies against SARS-CoV-2 infection.\nC_LIO_LINo association between seropositivity and study participants age, gender, occupation, and comorbid medical conditions.\nC_LI\n\nWhat do these findings mean?O_LIThe observed high seroprevalence among healthcare workers regardless of their occupation suggests the cryptic but massive SARS-CoV-2 transmission in urban hospital settings.\nC_LIO_LIMost of the seropositive healthcare workers in the present study were asymptomatic, and might pose a threat to the most vulnerable populations such as individuals with comorbid medical conditions.\nC_LIO_LIGiven the low level of vaccine roll-out (1%), this study highlights the need to strengthen health workers adherence to personal protection practices such as wearing face masks to protect individuals at high risk of developing severe COVID-19 illness after SARS-CoV-2 infection.\nC_LI", + "rel_num_authors": 30, + "rel_authors": [ + { + "author_name": "Tesfaye Gelanew", + "author_inst": "Armauer Hansen Research Institute, Addis Ababa Ethiopia" + }, + { + "author_name": "Berhanu Seyoum", + "author_inst": "Armauer Hansen Research Institute, Addis Ababa Ethiopia" + }, + { + "author_name": "Andargachew Mulu", + "author_inst": "Armauer Hansen Research Institute, Addis Ababa Ethiopia" + }, + { + "author_name": "Adane Mihret", + "author_inst": "Armauer Hansen Research Institute, Addis Ababa Ethiopia" + }, + { + "author_name": "Markos Abebe", + "author_inst": "Armauer Hansen Research Institute, Addis Ababa Ethiopia" + }, + { + "author_name": "Liya Wassie", + "author_inst": "Armauer Hansen Research Institute, Addis Ababa Ethiopia" + }, + { + "author_name": "Baye Gelaw", + "author_inst": "Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopi" + }, + { + "author_name": "Abebe Sorsa", + "author_inst": "Arsi University, Asella College of Health Sciences, Asella, Ethiopia" + }, + { + "author_name": "Yared Merid", + "author_inst": "Hawassa University, College of Medicine and Health Sciences, Department of Medical Microbiology, Hawassa, Ethiopia" + }, + { + "author_name": "Yilkal Muchie", + "author_inst": "All Africa Leprosy and Tuberculosis Rehabilitation and Training Center (ALERT Center) Hospital, Addis Ababa, Ethiopia" + }, + { + "author_name": "Zelalem Teklemariam", + "author_inst": "College of Health and Medical Sciences, Department of Medical Laboratory Sciences, Haramaya University, Harar, Ethiopia" + }, + { + "author_name": "Bezalem Tesfaye", + "author_inst": "Armauer Hansen Research Institute, Addis Ababa Ethiopia" + }, + { + "author_name": "Mahlet Osman", + "author_inst": "Armauer Hansen Research Institute, Addis Ababa Ethiopia" + }, + { + "author_name": "Gutema Jebessa", + "author_inst": "Armauer Hansen Research Institute, Addis Ababa Ethiopia" + }, + { + "author_name": "Abay Atinafu", + "author_inst": "Armauer Hansen Research Institute, Addis Ababa Ethiopia" + }, + { + "author_name": "Tsegaye Hailu", + "author_inst": "Armauer Hansen Research Institute, Addis Ababa Ethiopia" + }, + { + "author_name": "Antenehe Habte", + "author_inst": "Armauer Hansen Research Institute, Addis Ababa Ethiopia" + }, + { + "author_name": "Dagag Kenea", + "author_inst": "Arsi University, Asella College of Health Sciences, Asella, Ethiopia" + }, + { + "author_name": "Anteneh Gadissa", + "author_inst": "Hawassa University, College of Medicine and Health Sciences, Department of Medical Microbiology, Hawassa, Ethiopia" + }, + { + "author_name": "Desalegn Admasu", + "author_inst": "College of Health and Medical Sciences, Department of Medical Laboratory Sciences, Haramaya University, Harar, Ethiopia" + }, + { + "author_name": "Emmet Tesfaye", + "author_inst": "Hawassa University, College of Medicine and Health Sciences, Department of Medical Microbiology, Hawassa, Ethiopia" + }, + { + "author_name": "Timothy A Bates", + "author_inst": "Department of Molecular Microbiology & Immunology, Oregon Health & Sciences University, OR, USA" + }, + { + "author_name": "Jote Bulcha", + "author_inst": "Horae Gene Therapy Center, University of Massachusetts Medical School, MA, USA" + }, + { + "author_name": "Rea Tschopp", + "author_inst": "Armauer Hansen Research Institute, Addis Ababa Ethiopia" + }, + { + "author_name": "Dareskedar Tsehay", + "author_inst": "Armauer Hansen Research Institute, Addis Ababa Ethiopia" + }, + { + "author_name": "kim Mullholand", + "author_inst": "London School of Hygiene and Tropical Medicine, London, UK" + }, + { + "author_name": "Rawleigh Howe", + "author_inst": "Armauer Hansen Research Institute, Addis Ababa Ethiopia" + }, + { + "author_name": "Abebe Gentu", + "author_inst": "Armauer Hansen Research Institute, Addis Ababa Ethiopia" + }, + { + "author_name": "Fikadu G Tafesse", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Alemseged Abdissa", + "author_inst": "Armauer Hansen Research Institute, Addis Ababa Ethiopia" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.03.21257942", "rel_title": "Whole-genome sequencing of SARS-COV-2 reveals a substantially lower frequency of the UK variant than previously announced in Libya", @@ -665906,49 +667729,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.05.21259882", - "rel_title": "Assessment of COVID-19 risk and prevention effectiveness among spectators of mass gathering events", - "rel_date": "2021-07-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.05.21259882", - "rel_abs": "There is a need to evaluate and minimise the risk of novel coronavirus infections at mass gathering events, such as sports. In particular, to consider how to hold mass gathering events, it is important to clarify how the local infection prevalence, the number of spectators, the capacity proportion, and the implementation of preventions affect the infection risk. In this study, we used an environmental exposure model to analyse the relationship between infection risk and infection prevalence, the number of spectators, and the capacity proportion at mass gathering events in football and baseball games. In addition to assessing risk reduction through the implementation of various preventive measures, we assessed how face-mask-wearing proportion affects infection risk. Furthermore, the model was applied to estimate the number of infectors who entered the stadium and the number of newly infected individuals, and to compare them with actual reported cases. The model analysis revealed an 86%-95% reduction in the infection risk due to the implementation of face-mask wearing and hand washing. Among the individual measures, face-mask wearing was particularly effective, and the infection risk increased as the face-mask-wearing proportion decreased. A linear relationship was observed between infection risk at mass gathering events and the infection prevalence. Furthermore, the number of newly infected individuals was also dependent on the number of spectators and the capacity proportion independent of the infection prevalence, confirming the importance of considering spectator capacity in infection risk management. These results highlight that it is beneficial for organisers to ensure prevention compliance and to mitigate or limit the number of spectators according to the prevalence of local infection. Both the estimated and reported numbers of newly infected individuals after the events were small, below 10 per 3-4 million spectators, despite a small gap between these numbers.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Tetsuo Yasutaka", - "author_inst": "Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST)" - }, - { - "author_name": "Michio Murakami", - "author_inst": "Department of Health Risk Communication, Fukushima Medical University School of Medicine" - }, - { - "author_name": "Yuichi Iwasaki", - "author_inst": "Research Institute of Science for Safety and Sustainability, National Institute of Advanced Industrial Science and Technology (AIST)" - }, - { - "author_name": "Wataru Naito", - "author_inst": "Research Institute of Science for Safety and Sustainability, National Institute of Advanced Industrial Science and Technology (AIST)" - }, - { - "author_name": "Masaki Onishi", - "author_inst": "Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST)" - }, - { - "author_name": "Tsukasa Fujita", - "author_inst": "Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST)" - }, - { - "author_name": "Seiya Imoto", - "author_inst": "Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.30.21259811", "rel_title": "If we cannot eliminate them, should we tame them? Mathematics underpinning the dose effect of virus infection and its application on covid-19 virulence evolution", @@ -666688,6 +668468,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2021.07.01.21259404", + "rel_title": "Epidemiological dynamics of SARS-CoV-2 VOC Gamma in Rio de Janeiro, Brazil", + "rel_date": "2021-07-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.01.21259404", + "rel_abs": "The emergence and widespread circulation of SARS-CoV-2 variants of concern (VOC) or interest (VOI) imposes an enhanced threat to global public health. In Brazil, one of the countries most severely impacted throughout the pandemic, a complex dynamics involving variants co-circulation and turnover events has been recorded with the emergence and spread of VOC Gamma in Manaus in late 2020. In this context, we present a genomic epidemiology investigation based on samples collected between December 2020 and May 2021 in the second major Brazilian metropolis, Rio de Janeiro. By sequencing 244 novel genomes through all epidemiological weeks in this period, we were able to document the introduction and rapid dissemination of VOC Gamma in the city, driving the rise of the third local epidemic wave. Molecular clock analysis indicates this variant has circulated locally since the first weeks of 2021 and only seven weeks were necessary for it to achieve a frequency above 70%, consistent with rates of growth observed in Manaus and other states. Moreover, a Bayesian phylogeographic reconstruction indicates VOC Gamma spread throughout Brazil between December 2020 and January 2021, and that it was introduced in Rio de Janeiro through at least 13 events coming from nearly all regions of the country. Comparative analysis of RT-qPCR cycle threshold (Ct) values provides further evidence that VOC Gamma induces higher viral loads (N1 target; mean reduction of Ct: 2.7, 95% CI = {+/-}0.7). This analysis corroborates the previously proposed mechanistic basis for this variant enhanced transmissibility and distinguished epidemiological behavior. Our results document the evolution of VOC Gamma and provide independent assessment of scenarios previously studied in Manaus, therefore contributing to the better understanding of the epidemiological dynamics currently being surveyed in other Brazilian regions.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Filipe Romero Rebello Moreira", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Mirela D'arc", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Diana Mariani", + "author_inst": "Federal University of Rio de Janeiro" + }, + { + "author_name": "Alice Laschuk Herlinger", + "author_inst": "Federal University of Rio de Janeiro" + }, + { + "author_name": "Francine Bittencourt Schiffler", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Atila Duque Rossi", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Isabela de Carvalho Leitao", + "author_inst": "Federal University of Rio de Janeiro" + }, + { + "author_name": "Thamiris dos Santos Miranda", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Matheus Augusto Calvano Cosentino", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Marcelo Calado de Paula Torres", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Raissa Mirella dos Santos Cunha da Costa", + "author_inst": "Federal University of Rio de Janeiro; Hospital Naval Marcilio Dias" + }, + { + "author_name": "Cassia Cristina Alves Goncalves", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Debora Souza Faffe", + "author_inst": "Federal University of Rio de Janeiro" + }, + { + "author_name": "Rafael de Mello Galiez", + "author_inst": "Federal University of Rio de Janeiro" + }, + { + "author_name": "Orlando Costa Ferreira Jr.", + "author_inst": "Federal University of Rio de Janeiro" + }, + { + "author_name": "Renato Santana Aguiar", + "author_inst": "Universidade Federal de Minas Gerais" + }, + { + "author_name": "Andre Felipe Andrade dos Santos", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Carolina Moreira Voloch", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Terezinha Marta Pereira Pinto Castineiras", + "author_inst": "Federal University of Rio de Janeiro" + }, + { + "author_name": "Amilcar Tanuri", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "- COVID-19-UFRJ Workgroup", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.07.01.21259132", "rel_title": "A Cross Sectional Study To Assess The Attitude Regarding Online Lecture Among Nursing College Students After Impact of Covid-19 At Selected College of Nursing, Nadiad.", @@ -667672,61 +669551,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.30.21259770", - "rel_title": "Incidence of outbreak-associated COVID-19 cases by industry in Ontario, Canada, April 1, 2020- March 31, 2021", - "rel_date": "2021-07-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.30.21259770", - "rel_abs": "ObjectivesThe objective of our study was to estimate the rate of workplace outbreak-associated cases of COVID-19 by industry in labour market participants aged 15-69 years who reported working the majority of hours outside the home in Ontario, Canada.\n\nMethodsWe conducted a population based cross-sectional study of COVID-19 workplace outbreaks and associated-cases reported in Ontario between April 1, 2020 and March 31, 2021. All outbreaks were manually classified into two digit North American Industry Classification System (NAICS) codes. We obtained denominator data from the Statistics Canada Labour Force Survey in order to estimate the incidence of outbreak-associated cases per 100,000,000 hours amongst individuals who reported the majority of hours were worked outside the home. We performed this analysis across industries and in three distinct time periods.\n\nResultsOverall, 12% of cases were attributed to workplace outbreaks among working age adults across our study period. While incidence varied across the time periods, the five industries with the highest incidence rates across our study period were agriculture; healthcare and social assistance; food manufacturing; educational services; and, transportation and warehousing.\n\nConclusionsCertain industries have consistently increased incidence of COVID-19 over the course of the pandemic. These results may assist in ongoing efforts to reduce transmission of COVID-19, by prioritizing resources, as well as industry-specific guidance, vaccination, and public health messaging.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Sarah A Buchan", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Peter M Smith", - "author_inst": "Institute for Work and Health" - }, - { - "author_name": "Christine Warren", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Michelle Murti", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Cameron Mustard", - "author_inst": "Institute for Work and Health" - }, - { - "author_name": "JinHee Kim", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Sandya Menon", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Kevin Antoine Brown", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Trevor van Ingen", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Brendan T Smith", - "author_inst": "Public Health Ontario" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.30.21259769", "rel_title": "Disinfection of SARS-CoV-2 using UVC reveals wavelength sensitivity contributes towards rapid virucidal activity", @@ -668418,6 +670242,73 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2021.07.05.451071", + "rel_title": "Construction of a new chromosome-scale, long-read reference genome assembly of the Syrian hamster, Mesocricetus auratus", + "rel_date": "2021-07-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.05.451071", + "rel_abs": "BackgroundThe Syrian hamster (Mesocricetus auratus) has been suggested as a useful mammalian model for a variety of diseases and infections, including infection with respiratory viruses such as SARS-CoV-2. The MesAur1.0 genome assembly was generated in 2013 using whole-genome shotgun sequencing with short-read sequence data. Current more advanced sequencing technologies and assembly methods now permit the generation of near-complete genome assemblies with higher quality and greater continuity.\n\nFindingsHere, we report an improved assembly of the M. auratus genome (BCM_Maur_2.0) using Oxford Nanopore Technologies long-read sequencing to produce a chromosome-scale assembly. The total length of the new assembly is 2.46 Gbp, similar to the 2.50 Gbp length of a previous assembly of this genome, MesAur1.0. BCM_Maur_2.0 exhibits significantly improved continuity with a scaffold N50 that is 6.7 times greater than MesAur1.0. Furthermore, 21,616 protein coding genes and 10,459 noncoding genes are annotated in BCM_Maur_2.0 compared to 20,495 protein coding genes and 4,168 noncoding genes in MesAur1.0. This new assembly also improves the unresolved regions as measured by nucleotide ambiguities, where approximately 17.11% of bases in MesAur1.0 were unresolved compared to BCM_Maur_2.0 in which the number of unresolved bases is reduced to 3.00%.\n\nConclusionsAccess to a more complete reference genome with improved accuracy and continuity will facilitate more detailed, comprehensive, and meaningful research results for a wide variety of future studies using Syrian hamsters as models.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "R. Alan Harris", + "author_inst": "Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030" + }, + { + "author_name": "Muthuswamy Raveendran", + "author_inst": "Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030" + }, + { + "author_name": "Dustin T Lyfoung", + "author_inst": "Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53711" + }, + { + "author_name": "Fritz J Sedlazeck", + "author_inst": "Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030" + }, + { + "author_name": "Medhat Mahmoud", + "author_inst": "Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030" + }, + { + "author_name": "Trent Prall", + "author_inst": "Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53711" + }, + { + "author_name": "Julie Karl", + "author_inst": "Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53711" + }, + { + "author_name": "Harshavardhan Doddapaneni", + "author_inst": "Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030" + }, + { + "author_name": "Qingchang Meng", + "author_inst": "Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030" + }, + { + "author_name": "Yi Han", + "author_inst": "Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030" + }, + { + "author_name": "Donna Muzny", + "author_inst": "Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030" + }, + { + "author_name": "Roger W. Wiseman", + "author_inst": "Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53711, Department of Pathology and Laboratory Medicine, University of Wisconsin" + }, + { + "author_name": "Jeffrey Rogers", + "author_inst": "Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2021.07.03.450992", "rel_title": "Increased Histone-DNA Complexes and Endothelial-Dependent Thrombin Generation in Severe COVID-19", @@ -669250,49 +671141,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2021.07.01.21259887", - "rel_title": "Risk factors for SARS-CoV-2 infection and hospitalisation in children and adolescents in Norway: A nationwide population-based study.", - "rel_date": "2021-07-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.01.21259887", - "rel_abs": "ObjectiveTo determine risk factors for SARS-CoV-2 infection and hospitalisation among children and adolescents.\n\nDesignNationwide, population-based cohort study. Setting: Norway from 1 March 2020 to 31 April 2021. Participants: All Norwegian residents <18 years of age.\n\nMain outcome measuresPopulation-based health care and population registries were used to study risk factors for SARS-CoV-2 infection, including socioeconomic factors, country of origin, and pre-existing chronic comorbidities. All residents were followed until age 18, emigration, death, or end of follow-up. Hazard ratios (HR) estimated by Cox regression models were adjusted for testing frequency. Further, risk factors for admission to the hospital among the infected were investigated.\n\nResultsOf 1 182 796 residents, 22608 (1.9%) tested positive by polymerase chain reaction or lateral flow tests, of whom 107 (0.5%) were admitted to a hospital. Low family income (aHR 1.40, 95% confidence interval 1.36 to 1.46), crowded housing (1.35, 1.30 to 1.39), household size, age, and area of living were independent risk factors for infection. A non-Nordic country of origin was the strongest risk factor (aHR 2.37, 95% CI 2.30 to 2.49), whereas chronic comorbidity was not associated with the risk of infection. Chronic comorbidity was associated with hospitalisation (aHR 4.15, 2.63 to 6.56), in addition to age, whereas socioeconomic status and country of origin did not predict hospitalisation among those infected.\n\nConclusionsSocioeconomic factors, country of origin, and area of living were associated with the risk of SARS-CoV-2 infection. However, these factors did not predict hospitalisation among those infected. Chronic comorbidity was associated with the risk of admission but not with the overall risk of acquiring SARS-CoV-2.\n\nWhat is already known on this topicHospital admissions rates for covid-19 among children and adolescents are low compared to adults. Admission rates to hospitals and intensive care units for covid-19 have been higher in minority groups and in children and adolescents with chronic comorbidity.\n\nWhether underlying differences in susceptibility for severe disease or the incidence of infections are driving these associations have not been investigated.\n\nWhat this study addsLow family income, crowded housing and household size, and country of origin outside the Nordic countries were associated with increased risk of infection with SARS-CoV-2.\n\nNone of these factors, but chronic comorbidities, were associated with the risk of hospital admission among those infected.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Ketil Stordal", - "author_inst": "University of Oslo" - }, - { - "author_name": "Paz Lopez-Doriga Ruiz", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Margrethe Greve-Isdahl", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Pal Suren", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Per Kristian Knudsen", - "author_inst": "Oslo University Hospital" - }, - { - "author_name": "Hanne Lovdal Gulseth", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "German Tapia", - "author_inst": "Norwegian Institute of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2021.06.29.21259741", "rel_title": "Perceptions and acceptance of COVID-19 vaccine among pregnant and lactating women in Singapore: A cross-sectional study", @@ -670116,6 +671964,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.27.21259530", + "rel_title": "Modeling robust COVID-19 intensive care unit occupancy thresholds for imposing mitigation to prevent exceeding capacities", + "rel_date": "2021-07-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.27.21259530", + "rel_abs": "In managing COVID-19 with non-pharmaceutical interventions, occupancy of intensive care units (ICU) is often used as an indicator to inform when to intensify mitigation and thus reduce SARS-CoV-2 transmission, strain on ICUs, and deaths. However, ICU occupancy thresholds at which action should be taken are often selected arbitrarily. We propose a quantitative approach using mathematical modeling to identify ICU occupancy thresholds at which mitigation should be triggered to avoid exceeding the ICU capacity available for COVID-19 patients. We used a stochastic compartmental model to simulate SARS-CoV-2 transmission and disease progression, including critical cases that would require intensive care. We calibrated the model for the United States city of Chicago using daily COVID-19 ICU and hospital census data between March and August 2020. We projected ICU occupancies from September to May 2021 under two possible levels of transmission increase. The effect of combined mitigation measures was modeled as a decrease in the transmission rate that took effect when projected ICU occupancy reached a specified threshold. We found that mitigation did not immediately eliminate the risk of exceeding ICU capacity. Delaying action by 7 days increased the probability of exceeding ICU capacity by 10-60% and this increase could not be counteracted by stronger mitigation. Even under modest transmission increase, a threshold occupancy no higher than 60% was required when mitigation reduced the reproductive number Rt to just below 1. At higher transmission increase, a threshold of at most 40% was required with mitigation that reduced Rt below 0.75 within the first two weeks after mitigation. Our analysis demonstrates a quantitative approach for the selection of ICU occupancy thresholds that considers parameter uncertainty and compares relevant mitigation and transmission scenarios. An appropriate threshold will depend on the location, number of ICU beds available for COVID-19, available mitigation options, feasible mitigation strengths, and tolerated durations of intensified mitigation.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Manuela Runge", + "author_inst": "Department of Preventive Medicine and Institute for Global Health, Northwestern University, Chicago IL USA" + }, + { + "author_name": "Reese A.K. Richardson", + "author_inst": "Department of Chemical and Biological Engineering, Northwestern University, Evanston IL USA" + }, + { + "author_name": "Patrick Clay", + "author_inst": "Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor MI USA" + }, + { + "author_name": "Arielle Eagan", + "author_inst": "Department of Preventive Medicine and Institute for Global Health, Northwestern University, Chicago IL USA" + }, + { + "author_name": "Tobias M Holden", + "author_inst": "Northwestern University Feinberg School of Medicine, Chicago IL USA" + }, + { + "author_name": "Manisha Singam", + "author_inst": "Northwestern University Feinberg School of Medicine, Chicago IL USA" + }, + { + "author_name": "Natsumi Tsuboyama", + "author_inst": "Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago IL USA" + }, + { + "author_name": "Philip Arevalo", + "author_inst": "Department of Ecology and Evolution, University of Chicago, Chicago IL USA" + }, + { + "author_name": "Jane Fornoff", + "author_inst": "Illinois Department of Public Health, Springfield IL USA" + }, + { + "author_name": "Sarah Patrick", + "author_inst": "Illinois Department of Public Health, Springfield IL USA" + }, + { + "author_name": "Ngozi O. Ezike", + "author_inst": "Illinois Department of Public Health, Springfield IL USA" + }, + { + "author_name": "Jaline Gerardin", + "author_inst": "Department of Preventive Medicine and Institute for Global Health, Northwestern University, Chicago IL USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.29.21259726", "rel_title": "Prominent Spatiotemporal Waves of COVID-19 Incidence in the United States: Implications for Causality, Forecasting, and Control", @@ -671100,25 +673011,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.29.21259698", - "rel_title": "Characterizing parametric differences between the two waves of COVID-19 in India", - "rel_date": "2021-07-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.29.21259698", - "rel_abs": "The first case of COVID-19 in India was reported on January 30, 2020 [1]. The number of infections rose steeply and preventative measures such as lockdowns were implemented to slow down the spread of the disease. Infections peaked around mid-September the same year and the cases gradually started declining. Following the relaxation of lockdown and the appearance of mutant strains of the virus, a much severe second wave of COVID-19 emerged starting mid-February. For characterization and comparison of both the waves, a SIQR (Susceptible-Infected-Quarantined-Removed) model is used in this paper. The results indicate that a single patient can infect approximately 2.44 individuals in the population. The epidemic doubling time was calculated to be 11.8 days. It is predicted that the actual number of infected patients is grossly underestimated (by a factor of 16) by current testing methods.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Arpit Omprakash", - "author_inst": "Indian Institute of Science Education and Research Mohali" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.26.21259487", "rel_title": "The Emergence of SARS-CoV-2 Variant Lambda (C.37) in South America", @@ -671894,6 +673786,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2021.06.24.21259435", + "rel_title": "Change in disease dynamics and health care utilization in children during COVID19 in a tertiary care hospital of Eastern India.", + "rel_date": "2021-07-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.24.21259435", + "rel_abs": "This retrospective, observational study was conducted by collecting data from medical records during COVID 19 pandemic from March 2020 till August 2020. This was compared with the data of 2019 during similar months. The impact of COVID 19 on use of preventive and curative paediatric health care service units like outpatient department, casualty, intensive care and immunization clinic were assessed. Data from 2019 to 2020 were compared using standard parametric and nonparametric tests. There was a significant decline in routine OPD (68%) attendance during the COVID 19 period as compared to pre-COVID period. Paediatric ward admissions and PICU admissions were decreased by 55% and 42% respectively. We also observed a significant 43% decline in the number of children attending immunization clinic in the year 2020. The fear of COVID 19 pandemic and the measures taken to control the pandemic has affected the health seeking behaviour of patients. This evaluation of trends in healthcare use may help in planning the delivery of healthcare service delivery in future.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Bandya Sahoo", + "author_inst": "Kalinga Institute of Medical Sciences, Bhubaneswar" + }, + { + "author_name": "Suneeti Kanyari S", + "author_inst": "Kalinga Institute of Medical Sciences, Bhubaneswar" + }, + { + "author_name": "Deepti Damayanty Pradhan", + "author_inst": "Kalinga Institute of Medical Sciences, Bhubaneswar" + }, + { + "author_name": "Sibabratta Patnaik", + "author_inst": "Kalinga Institute of Medical Sciences, Bhubaneswar" + }, + { + "author_name": "Manas Ranjan Behera", + "author_inst": "Kalinga Institute of Medical Sciences, Bhubaneswar" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2021.06.24.21255875", "rel_title": "Genomic epidemiology of SARS-CoV-2 in Pakistan", @@ -673098,25 +675025,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.29.21257965", - "rel_title": "Estimating the death toll of the Covid-19 pandemic in India", - "rel_date": "2021-07-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.29.21257965", - "rel_abs": "The absence of reliable registration of Covid-19 deaths in India has prevented the proper assessment and monitoring of coronavirus pandemic. Indias relatively young age structure tends to conceal the severity of Covid-19 mortality, which is concentrated in older age groups. In this paper, we present four different demographic samples of Indian populations for which we have information on both their demographic structures and death outcomes. We show that we can model the age gradient of Covid-19 mortality in India and use this modeling for estimating the level of Covid-19 mortality in the country. Our findings point to a death toll of about 2.2 million persons by late May 2021. Once Indias age structure is taken into account, these figures correspond to one of the most severe cases of Covid-19 mortality in the world.\n\nBackgroundIndia has recorded after February a second outbreak of coronavirus that has affected the entire country. The accuracy of official statistics of Covid-19 mortality has been called in question and the real number of Covid-19 deaths is thought to be several times higher than reported. In this paper, we assembled four independent population samples to model and estimate the level of Covid-19 mortality in India.\n\nMethodsWe first used a first population sample with age and sex of Covid-19 victims to develop a Gompertz model of Covid-19 mortality in India. We applied and adjusted this mortality model on two other national population samples after factoring in the demographic characteristics of these samples. We finally derive from one of these samples the most reasonable estimate of Covid-19 mortality level in India and confirm this result with the use of a fourth population sample.\n\nFindingsOur findings point to a death toll of about 2.2 million persons by late May 2021. This is the largest number of Covid-19 deaths in the world. Once standardized for its age and sex structure, Indias Covid-19 mortality rate is above that of Brazil or the USA.\n\nInterpretationOur analysis shows that existing population samples allow for an alternative estimation of deaths due to Covid-19 in India. The results confirm that only one out 7 Covid-19 deaths appear to be registered in India. The estimates point to a very Covid-19 mortality rate, which is even higher after age and sex standardization. The magnitude of the pandemic in India requires immediate attention and calls for a strong response based on a combination of non-pharmaceutical interventions and the scale-up of vaccination to make them accessible to all, with an improved surveillance system to monitor the progression of the pandemic.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Christophe Z Guilmoto", - "author_inst": "IRD/CEPED CSH New Delhi" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.07.01.21259656", "rel_title": "Proxalutamide (GT0918) Improves Lung Injury in Hospitalized COVID-19 Patients - an Analysis of the Radiological Findings of the Proxa-Rescue AndroCoV Trial", @@ -674108,6 +676016,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.07.01.21259838", + "rel_title": "The safety and efficacy of mesenchymal stem cells in the treatment of COVID-19-associated pneumonia: a systematic review and meta-analysis", + "rel_date": "2021-07-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.01.21259838", + "rel_abs": "Mesenchymal stem cells (MSCs) therapy is considered one of the most promising treatments in the context of the coronavirus disease 2019 (COVID-19) pandemic. However, the safety and effectiveness of MSCs in the treatment of COVID-19-associated pneumonia patients need to be systematically reviewed and analyzed. Two independent researchers searched for the relevant studies published between October 2019 and April 2021 in PubMed, Embase, Cochrane Library, WAN FANG, and CNKI databases. A total of 22 studies involving 371 patients were included in the present study. MSCs were administered in 247 participants, and MSCs were allogeneic from umbilical cord, adipose tissue, menstrual blood, placenta, Whartons jelly, or unreported sources. Combined results found that MSCs group significantly reduced the incidence of adverse events (OR = 0.43, 95%CI. = 0.22[~]0.84, P = 0.01) and mortality (OR = 0.17, 95%CI. = 0.06[~]0.49, P < 0.01), and the difference compared with control group was statistically significant. No MSCs treat-related serious adverse events were reported. The lung function and radiographic outcomes, and biomarker levels of inflammation and immunity all showed improvement trends. Therefore, MSCs therapy is an effective and safe method in the treatment of COVID-19-associated pneumonia and shows advantages in less adverse events and mortality. However, a standard and effective MSCs treatment program needs to be developed.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Junwu Wang", + "author_inst": "Clinical Medical College of Yangzhou University" + }, + { + "author_name": "Pengzhi Shi", + "author_inst": "Graduate School of Dalian Medical University" + }, + { + "author_name": "Dong Chen", + "author_inst": "Clinical Medical College of Yangzhou University" + }, + { + "author_name": "Shuguang Wang", + "author_inst": "Graduate School of Dalian Medical University" + }, + { + "author_name": "Pingchuan Wang", + "author_inst": "Clinical Medical College of Yangzhou University" + }, + { + "author_name": "Xinmin Feng", + "author_inst": "Clinical Medical College of Yangzhou University" + }, + { + "author_name": "Liang Zhang", + "author_inst": "Clinical Medical College of Yangzhou University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2021.06.30.21259439", "rel_title": "Efficacy, safety, and lot to lot immunogenicity of an inactivated SARS-CoV-2 vaccine (BBV152): a double-blind, randomised, controlled phase 3 trial", @@ -675360,73 +677311,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.07.01.450701", - "rel_title": "Thiol-based mucolytics exhibit antiviral activity against SARS-CoV-2 through allosteric disulfide disruption in the spike glycoprotein", - "rel_date": "2021-07-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.01.450701", - "rel_abs": "Small molecule therapeutics targeting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have lagged far behind the development of vaccines in the fight to control the COVID-19 pandemic. Here, we show that thiol-based mucolytic agents, P2119 and P2165, potently inhibit infection by human coronaviruses, including SARS-CoV-2, and decrease the binding of spike glycoprotein to its receptor, angiotensin-converting enzyme 2 (ACE2). Proteomics and reactive cysteine profiling link the antiviral activity of repurposed mucolytic agents to the reduction of key disulfides, specifically, by disruption of the Cys379-Cys432 and Cys391-Cys525 pairs distal to the receptor binding motif (RBM) in the receptor binding domain (RBD) of the spike glycoprotein. Computational analyses provide insight into conformation changes that occur when these disulfides break or form, consistent with an allosteric role, and indicate that P2119/P2165 target a conserved hydrophobic binding pocket in the RBD with the benzyl thiol warhead pointed directly towards Cys432. These collective findings establish the vulnerability of human coronaviruses to repurposed thiol-based mucolytics and lay the groundwork for developing these compounds as a potential treatment, preventative and/or adjuvant against infection.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Yunlong Shi", - "author_inst": "Scripps Research, Florida Campus" - }, - { - "author_name": "Ari Zeida", - "author_inst": "Facultad de Medicina, Universidad de la Republica" - }, - { - "author_name": "Caitlin E Edwards", - "author_inst": "Department of Epidemiology, University of North Carolina at Chapel Hill" - }, - { - "author_name": "Michael L Mallory", - "author_inst": "Department of Epidemiology, University of North Carolina at Chapel Hill" - }, - { - "author_name": "Santiago Sastre", - "author_inst": "Facultad de Medicina, Universidad de la Republica" - }, - { - "author_name": "Matias R Machado", - "author_inst": "Institut Pasteur de Montevideo" - }, - { - "author_name": "Raymond J Pickles", - "author_inst": "UNC School of Medicine Marsico Lung Institute" - }, - { - "author_name": "Ling Fu", - "author_inst": "National Center for Protein Sciences - Beijing" - }, - { - "author_name": "Keke Liu", - "author_inst": "National Center for Protein Sciences - Beijing" - }, - { - "author_name": "Jing Yang", - "author_inst": "National Center for Protein Sciences - Beijing" - }, - { - "author_name": "Richard C Boucher", - "author_inst": "UNC School of Medicine Marsico Lung Institute" - }, - { - "author_name": "Rafael Radi", - "author_inst": "Facultad de Medicina, Universidad de la Republica" - }, - { - "author_name": "Kate S Carroll", - "author_inst": "Scripps Research" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.07.01.450475", "rel_title": "CRISPRa screening with real world evidence identifies potassium channels as neuronal entry factors and druggable targets for SARS-CoV-2", @@ -676242,6 +678126,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.06.29.21259504", + "rel_title": "Relating in vitro neutralisation level and protection in the CVnCoV (CUREVAC) trial.", + "rel_date": "2021-06-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.29.21259504", + "rel_abs": "A recent study analysed the relationship between neutralising antibody response and protection from SARS-CoV-2 infection across eight vaccine platforms1. The efficacy results from a phase 2b/3 trial of a ninth vaccine candidate, CVnCoV (CUREVAC), was announced on 16 June 20212. The low efficacy of this new mRNA vaccine, which showed only 47% protection from symptomatic SARS-CoV-2 infection, was surprising given the high efficacy of two previous mRNA-based vaccines3,4. A number of factors have been suggested to play a role in the low efficacy in the CVnCoV study, particularly around the dose and immunogenicity of the vaccine (which uses an unmodified mRNA construct5,6) and the potential role of infection with SARS-CoV-2 variants (which were the dominant strains observed in the CVnCoV trial)2.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Deborah Cromer", + "author_inst": "Kirby Institute, University of New South Wales, Sydney, Australia" + }, + { + "author_name": "Arnold Reynaldi", + "author_inst": "Kirby Institute, University of New South Wales, Sydney, Australia" + }, + { + "author_name": "Megan Steain", + "author_inst": "School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia" + }, + { + "author_name": "James A Triccas", + "author_inst": "School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia" + }, + { + "author_name": "Miles Philip Davenport", + "author_inst": "Kirby Institute, UNSW Sydney" + }, + { + "author_name": "David S Khoury", + "author_inst": "Kirby Institute, University of New South Wales, Sydney, Australia" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.29.450378", "rel_title": "Comparative computational modeling of the bat and human immune response to viral infection with the Comparative Biology Immune Agent Based Model", @@ -677186,81 +679109,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.24.21259441", - "rel_title": "Accuracy of telephone triage for predicting adverse outcome in suspected COVID-19: An observational cohort study", - "rel_date": "2021-06-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.24.21259441", - "rel_abs": "ObjectiveTo assess accuracy of telephone triage in identifying patients who need emergency care amongst those with suspected COVID-19 infection and identify factors which affect triage accuracy.\n\nDesignObservational cohort study\n\nSettingCommunity telephone triage in the Yorkshire and Humber, Bassetlaw, North Lincolnshire and North East Lincolnshire region.\n\nParticipants40, 261 adults who contacted NHS 111 telephone triage services provided by Yorkshire Ambulance Service NHS Trust between the 18th March 2020 and 29th June 2020 with symptoms indicating possible COVID-19 infection were linked to Office for National Statistics death registration data, hospital and general practice electronic health care data collected by NHS Digital.\n\nOutcomeAccuracy of triage disposition (self-care/non-urgent clinical assessment versus ambulance dispatch/urgent clinical assessment) was assessed in terms of death or need for organ support at 30, 7 and 3 days from first contact with the telephone triage service.\n\nResultsCallers had a 3% (1, 200/40, 261) risk of adverse outcome. Telephone triage recommended self-care or non-urgent assessment for 60% (24, 335/40, 261), with a 1.3% (310/24, 335) risk of subsequent adverse outcome. Telephone triage had 74.2% sensitivity (95% CI: 71.6 to 76.6%) and 61.5% specificity (61% to 62%) for adverse outcomes at 30 days from first contact. Multivariable analysis suggested some co-morbidities (such as chronic respiratory disease) may be over-estimated as predictors of adverse outcome, while the association of diabetes with adverse outcome may be under-estimated. Repeat contact with the service appears to be an important under recognised predictor of adverse outcomes with both 2 contacts (OR 1.77 95% CI: 1.14 to 2.75) and 3 or more contacts (OR 4.02 95% CI: 1.68 to 9.65) associated with clinical deterioration when not provided with an ambulance or urgent clinical assessment.\n\nConclusionPatients advised to self-care or receive non-urgent clinical assessment had a small but non-negligible risk of serious clinical deterioration. The sensitivity and specificity of telephone triage was comparable to other tools used to triage patient acuity in emergency and urgent care. Repeat contact with telephone services needs recognition as an important predictor of subsequent adverse outcomes.\n\nWhat is already known on this topicO_LITelephone triage has been used to divert patients with suspected COVID-19 to self care or for non-urgent clinical assessments, and thereby help mitigate the risk of health services being overwhelmed by patients who require no speficic treatment.\nC_LIO_LIConcerns have been raised that telephone triage may not be sufficiently accurate in identifying need for emergency care. However, no previous evaluation of accuracy of telephone triage in patients with suspected COVID-19 infection has been completed.\nC_LI\n\nWhat this study addsO_LIPatients advised to self care or receive non-urgent clinical assessment had a small but non-negligible risk of deterioration and significant adverse outcomes.\nC_LIO_LITelephone triage has comparable performance to methods used to triage patient acuity in other emergency and urgent care settings.\nC_LIO_LIAccuracy of triage may be improved by better recognition of multiple contact with services as a predictor of adverse outcomes.\nC_LI", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Carl Marincowitz", - "author_inst": "Centre for Urgent and Emergency Care Research (CURE), Health Services Research School of Health and Related Research," - }, - { - "author_name": "Tony Stone", - "author_inst": "Centre for Urgent and Emergency Care Research (CURE), Health Services Research School of Health and Related Research, University of Sheffield" - }, - { - "author_name": "Peter Bath", - "author_inst": "Information School, University of Sheffield" - }, - { - "author_name": "Richard Richard Campbell", - "author_inst": "Centre for Urgent and Emergency Care Research (CURE), Health Services Research School of Health and Related Research, University of Sheffield" - }, - { - "author_name": "Janette Turner", - "author_inst": "Centre for Urgent and Emergency Care Research (CURE), Health Services Research School of Health and Related Research, University of Sheffield" - }, - { - "author_name": "Madina Hussein", - "author_inst": "Information School, The University of Sheffield" - }, - { - "author_name": "Richard Pilbery", - "author_inst": "Yorkshire Ambulance Service NHS Trust" - }, - { - "author_name": "Benjamin Thomas", - "author_inst": "Centre for Urgent and Emergency Care Research (CURE), Health Services Research School of Health and Related Research, University of Sheffield" - }, - { - "author_name": "Laura Sutton", - "author_inst": "Clinical Trials Research Unit (CTRU), Health Services Research School of Health and Related Research, University of Sheffield" - }, - { - "author_name": "Fiona Bell", - "author_inst": "Yorkshire Ambulance Service NHS Trust" - }, - { - "author_name": "Katie Biggs", - "author_inst": "Clinical Trials Research Unit (CTRU), Health Services Research School of Health and Related Research, University of Sheffield" - }, - { - "author_name": "Frank Hopfgartner", - "author_inst": "Information School, University of Sheffield" - }, - { - "author_name": "Suvodeep Mazumdar", - "author_inst": "Information School, University of Sheffield" - }, - { - "author_name": "Jennifer Petrie", - "author_inst": "Clinical Trials Research Unit (CTRU), Health Services Research School of Health and Related Research" - }, - { - "author_name": "Steve Goodacre", - "author_inst": "Centre for Urgent and Emergency Care Research (CURE), Health Services Research School of Health and Related Research, University of Sheffield" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "emergency medicine" - }, { "rel_doi": "10.1101/2021.06.17.21259122", "rel_title": "Tracking SARS-CoV-2 in rivers as a tool for epidemiological surveillance", @@ -678316,6 +680164,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.06.21.21258579", + "rel_title": "Detection of B.1.351 and B.1.1.7 SARS-CoV-2 variants in Monterrey metropolitan area in Northeast Mexico", + "rel_date": "2021-06-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.21.21258579", + "rel_abs": "SARS-CoV-2 variants of concern (VOC) have spread throughout the world. In Mexico, VOC B.1.351 has been detected on one occasion and B.1.1.7 several times. We detected lineages B.1.351 and B.1.1.7 in patients who traveled to USA and B.1.1.7 in a patient with no travel history.\n\nArticle summary lineIntroduction of B.1.351 and B.1.1.7 S ARS-CoV-2 variants in Monterrey, Mexico.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Kame Alberto Gal\u00e1n-Huerta", + "author_inst": "Centro de Investigaci\u00f3n e Innovaci\u00f3n en Virolog\u00eda M\u00e9dica, Departamento de Bioqu\u00edmica y Medicina Molecular, Facultad de Medicina, Universidad Aut\u00f3noma de Nuevo L" + }, + { + "author_name": "Eduardo Garza-de-la-Pe\u00f1a", + "author_inst": "Laboratorio de Patolog\u00eda Cl\u00ednica y Gen\u00e9tica Molecular" + }, + { + "author_name": "Gabriela Viridiana Elizondo-Valdez", + "author_inst": "Laboratorio de Patolog\u00eda Cl\u00ednica y Gen\u00e9tica Molecular" + }, + { + "author_name": "Maria Fernanda Herrera-Saldivar", + "author_inst": "Centro de Investigaci\u00f3n e Innovaci\u00f3n en Virolog\u00eda M\u00e9dica, Departamento de Bioqu\u00edmica y Medicina Molecular, Facultad de Medicina, Universidad Aut\u00f3noma de Nuevo L" + }, + { + "author_name": "Ana Maria Rivas-Estilla", + "author_inst": "Centro de Investigaci\u00f3n e Innovaci\u00f3n en Virolog\u00eda M\u00e9dica, Departamento de Bioqu\u00edmica y Medicina Molecular, Facultad de Medicina, Universidad Aut\u00f3noma de Nuevo L" + }, + { + "author_name": "Sonia Amelia Lozano-Sep\u00falveda", + "author_inst": "Centro de Investigaci\u00f3n e Innovaci\u00f3n en Virolog\u00eda M\u00e9dica, Departamento de Bioqu\u00edmica y Medicina Molecular, Facultad de Medicina, Universidad Aut\u00f3noma de Nuevo L" + }, + { + "author_name": "Natalia Martinez-Acu\u00f1a", + "author_inst": "Centro de Investigaci\u00f3n e Innovaci\u00f3n en Virolog\u00eda M\u00e9dica, Departamento de Bioqu\u00edmica y Medicina Molecular, Facultad de Medicina, Universidad Aut\u00f3noma de Nuevo L" + }, + { + "author_name": "Daniel Arellanos-Soto", + "author_inst": "Centro de Investigaci\u00f3n e Innovaci\u00f3n en Virolog\u00eda M\u00e9dica, Departamento de Bioqu\u00edmica y Medicina Molecular, Facultad de Medicina, Universidad Aut\u00f3noma de Nuevo L" + }, + { + "author_name": "Javier Ramos-Jim\u00e9nez", + "author_inst": "Centro de Investigaci\u00f3n e Innovaci\u00f3n en Virolog\u00eda M\u00e9dica, Departamento de Bioqu\u00edmica y Medicina Molecular, Facultad de Medicina, Universidad Aut\u00f3noma de Nuevo L" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.21.21259299", "rel_title": "Meta-analytical evidence on mental disorder symptoms during the COVID-19 pandemic in Latin America", @@ -679844,77 +681743,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.06.28.450153", - "rel_title": "Myeloid cell interferon responses correlate with clearance of SARS-CoV-2", - "rel_date": "2021-06-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.28.450153", - "rel_abs": "The emergence of mutant SARS-CoV-2 strains associated with an increased risk of COVID-19-related death necessitates better understanding of the early viral dynamics, host responses and immunopathology. While studies have reported immune profiling using single cell RNA sequencing in terminal human COVID-19 patients, performing longitudinal immune cell dynamics in humans is challenging. Macaques are a suitable model of SARS-CoV-2 infection. We performed longitudinal single-cell RNA sequencing of bronchoalveolar lavage (BAL) cell suspensions from adult rhesus macaques infected with SARS-CoV-2 (n=6) to delineate the early dynamics of immune cells changes. The bronchoalveolar compartment exhibited dynamic changes in transcriptional landscape 3 days post-SARS-CoV-2-infection (3dpi) (peak viremia), relative to 14-17dpi (recovery phase) and pre-infection (baseline). We observed the accumulation of distinct populations of both macrophages and T-lymphocytes expressing strong interferon-driven inflammatory gene signature at 3dpi. Type I IFN response was highly induced in the plasmacytoid dendritic cells. The presence of a distinct HLADR+CD68+CD163+SIGLEC1+ macrophage population exhibiting higher angiotensin converting enzyme 2 (ACE2) expression was also observed. These macrophages were significantly recruited to the lungs of macaques at 3dpi and harbored SARS-CoV-2, while expressing a strong interferon-driven innate anti-viral gene signature. The accumulation of these responses correlated with decline in viremia and recovery. The recruitment of a myeloid cell-mediated Type I IFN response is associated with the rapid clearance of SARS-CoV-2 infection in macaques.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Dhiraj K. Singh", - "author_inst": "Texas Biomedical Research Institute" - }, - { - "author_name": "Ekaterina Aladyeva", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "Shibali Das", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "Bindu Singh", - "author_inst": "Texas Biomedical Research Institute" - }, - { - "author_name": "Ekaterina Esaulova", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "Amanda Swain", - "author_inst": "Washington Univ in St Louis" - }, - { - "author_name": "Mushtaq Ahmed", - "author_inst": "Washington Univ in St Louis" - }, - { - "author_name": "Journey Cole", - "author_inst": "Texas Biomedical Research Institute" - }, - { - "author_name": "Chivonne Moodley", - "author_inst": "Tulane Univ" - }, - { - "author_name": "Smriti Mehra", - "author_inst": "Tulane Univ" - }, - { - "author_name": "Larry Schlesinger", - "author_inst": "Texas Biomedical Research Institute" - }, - { - "author_name": "Maxim Artyomov", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Shabaana A. Khader", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "Deepak Kaushal", - "author_inst": "Texas Biomedical Research Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.06.28.450211", "rel_title": "A SARS-CoV-2 mini-genome assay based on negative-sense RNA to study replication inhibitors and emerging mutations", @@ -680950,6 +682778,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.22.21259273", + "rel_title": "More complaints than findings - Long-term pulmonary function in children and adolescents after COVID-19", + "rel_date": "2021-06-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.22.21259273", + "rel_abs": "BackgroundThe frequency of persistent symptoms after coronavirus disease 2019 (COVID-19) in adults varies from 4.5% to 87%. Pulmonary function can also show long-term impairment in adults: 10% of hospitalised adults had reduced spirometry values, and 24% had decreased diffusion capacity. To date, only preliminary evidence is available on persistent respiratory sequelae in children and adolescents, therefore our objective was to examine the long-term effects of COVID-19 on pulmonary function in this age group.\n\nMethodsMultiple-breath washout, body plethysmography, and diffusion capacity testing were performed after an average of 2.6 months (range 0.4-6.0) following COVID-19 in 73 children and adolescents (age 5-18 years) with different disease severity. Cases were compared to 45 controls with and without infection within six months prior to assessment after exclusion of severe acute respiratory coronavirus-2 infection (SARS-CoV-2).\n\nResultsOf the 19 patients (27.1%) who complained about persistent or newly emerged symptoms since COVID-19, 8 (11.4%) reported respiratory symptoms. Comparing patients with COVID-19 to controls, no significant differences were detected in frequency of abnormal pulmonary function (COVID-19: 12, 16.4%; controls: 12, 27.7%; OR 0.54, 95% CI 0.22-1.34). Only two patients with persistent respiratory symptoms showed abnormal pulmonary function. Multivariate analysis revealed reduced forced vital capacity (p=0.045) in patients with severe infection regardless of SARS-CoV-2 infection.\n\nDiscussionPulmonary function is rarely impaired in children and adolescents after COVID-19, except of those with severe infection. The discrepancy between persistent respiratory symptoms and normal pulmonary function suggests a different underlying pathology such as dysfunctional breathing.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Leona Knoke", + "author_inst": "University Children's Hospital, Ruhr-University Bochum" + }, + { + "author_name": "Anne Schlegtendal", + "author_inst": "University Children's Hospital, Ruhr-University Bochum" + }, + { + "author_name": "Christoph Maier", + "author_inst": "University Children's Hospital, Ruhr-University Bochum" + }, + { + "author_name": "Lynn Eitner", + "author_inst": "University Children's Hospital, Ruhr-University Bochum" + }, + { + "author_name": "Thomas Luecke", + "author_inst": "University Children's Hospital, Ruhr-University Bochum" + }, + { + "author_name": "Folke Brinkmann", + "author_inst": "University Children's Hospital, Ruhr-University Bochum" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2021.06.20.21259177", "rel_title": "The evaluation of factors affecting antibody response after administration of the BNT162b2 vaccine: A prospective study in Japan", @@ -682106,49 +683973,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.24.21258842", - "rel_title": "Pulmonary thromboembolism in patients after COVID-19 - predictive indicators for correct diagnosis", - "rel_date": "2021-06-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.24.21258842", - "rel_abs": "IntroductionInfection caused by SARS-CoV-2 has been shown to lead to significant procoagulant events, in some cases involving life-threatening pulmonary thromboembolism (PE). Additional conditions complicating the diagnosis are the presence of risk factors for PE in almost all patients with COVID-19, as well as the overlap of the clinical presentation between PE and COVID-19. Materials and Methods: [T]herefore we conducted a single-center study at the Heart and Brain Hospital, Pleven in the period December 2020-February 2021. It included 27 consecutively hospitalized patients with recent pneumonia caused by Covid-19 and clinical presentation referring to PE. The cohort was divided into two groups - with and without a definitive diagnosis of PE, proven by CT pulmoangiography. The aim was to find the indicators that predict the presence of PE in patients with acute or Post-acute COVID-19 conditions. Results: Our results show that part of the ECG criteria - S-wave over 1.5 mm in I lead and aVL (p = 0.007), Q-wave in III and aVF (p = 0.020), as well as the D-dimer as quantitative variable (p = 0.025) proved to be independent predictors of PE. The RV/ LV diameter ratios [≥]1.0 as well as right ventricular dysfunction showed sensitivity 62.5%, specificity 100%, positive predictive value 100% and negative such 86.4% to verify the PE diagnosis[Lcy] We suggest that the cut-off value of D-dimer of 1032 ng/ml has an optimal sensitivity (Se) of 87.5%, specificity (Sp) 57.9%, positive a predictive value (PPV) 46.7% and negative predictive value (NPV) of 91.7% for the diagnosis of PE (p = 0.021). Conclusion: Against the background of acute and Post-acute COVID-19 conditions ECG and EchoCG criteria remain predictive of PE. We suggest that a higher D-dimer cut-off value should be applied in COVID-19 and post-COVID-19 patients in order to confirm/dismiss the diagnosis PE.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Dilyana Yakova-Hristova", - "author_inst": "Heart and Brain Centre of Excellence, University Hospital, Pleven, Bulgaria" - }, - { - "author_name": "Iana Simova", - "author_inst": "Heart and Brain Centre of Excellence, University Hospital; Medical University, Pleven, Bulgaria; Bulgarian Cardiac Institute" - }, - { - "author_name": "Plamen Pavlov", - "author_inst": "Heart and Brain Centre of Excellence, University Hospital, Pleven, Bulgaria" - }, - { - "author_name": "Martin Hristov", - "author_inst": "Cardiology Hospital Pleven, Bulgaria" - }, - { - "author_name": "Todor Kundurzhiev", - "author_inst": "Faculty of Public Health, Medical University, Sofia, Bulgaria" - }, - { - "author_name": "Nikolai Dimitrov", - "author_inst": "Heart and Brain Centre of Excellence, University Hospital, Pleven, Bulgaria; Bulgarian Cardiac Institute" - }, - { - "author_name": "Toni Vekov", - "author_inst": "Medical University, Pleven, Bulgaria; Bulgarian Cardiac Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2021.06.22.21259295", "rel_title": "Into the thirteenth Month: A Case Study on the Outbreak Analytics and Modeling the spread of SARS-CoV-2 Infection in Pune City, India", @@ -682836,6 +684660,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.06.25.21259256", + "rel_title": "Pre-existing anxiety, depression, and neurological disability are associated with long COVID: A prospective and longitudinal cohort study of the United Kingdom Multiple Sclerosis Register", + "rel_date": "2021-06-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.25.21259256", + "rel_abs": "ObjectivesTo assess the prevalence of long COVID among people with multiple sclerosis (MS) and its predictors, including their pre-COVID-19 functional status.\n\nDesignCommunity-based prospective and longitudinal cohort study\n\nSettingThe United Kingdom (UK) MS Register (UKMSR) COVID-19 study\n\nParticipantsA national cohort of people with MS and COVID-19\n\nMain outcome measuresParticipants used the online questionnaire-based platform of the UKMSR to update their COVID-19 symptoms, recovery status, and duration of symptoms for those who had fully recovered. Questionnaires were date-stamped for estimation of COVID-19 symptom duration for those who had not recovered at their last follow-up. The UKMSR holds demographic and up-to-date clinical data on participants as well as their web-based Expanded Disability Status Scale (a measure of physical disability in MS) and Hospital Anxiety and Depression Scale scores. The association between these factors and recovery from COVID-19 was assessed using multivariable Cox regression analysis.\n\nResultsOut of 7,977 people with MS who participated in the UKMSR COVID-19 study, 599 had COVID-19 and updated their recovery status prospectively. At least 181 participants (31.1%) had long-standing COVID-19 symptoms for [≥]4 weeks and 76 (13.1 %) for [≥]12 weeks. Participants with higher levels of pre-COVID-19 physical disability, participants with anxiety and/or depression prior to COVID-19 onset, and women were less likely to report recovery from COVID-19.\n\nConclusionsLong COVID appears to disproportionately affect people with pre-existing mental health problems or physical disabilities. As post-COVID-19 rehabilitation services are being developed, individualised pathways should be considered to accommodate the needs of these vulnerable populations.\n\nTrial RegistrationClinicalTrials.gov: NCT04354519", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Afagh Garjani", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Rodden M Middleton", + "author_inst": "Swansea University" + }, + { + "author_name": "Richard Nicholas", + "author_inst": "Imperial College London" + }, + { + "author_name": "Nikos Evangelou", + "author_inst": "University of Nottingham" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.06.23.21259176", "rel_title": "Averting an outbreak of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in a university residence hall through wastewater surveillance", @@ -683764,25 +685619,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.20.21259222", - "rel_title": "COVID-19 Susceptibility, Mortality, and Length of hospitalization based on age-sex composition: Evidence from Davao Region Philippines", - "rel_date": "2021-06-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.20.21259222", - "rel_abs": "The coronavirus disease is spreading continuously worldwide with an unprecedented amount of impact on every human society. In order to reduce the risks of infections and mortality, several interventions such as mobility restrictions for different age groups and vaccination prioritization programs are implemented in the Philippines. Identifying age-sex composition with greater susceptibility, longer hospitalization, and higher fatality is useful to guide the targeted intervention and establish risk stratification for patients infected with COVID-19 within communities and localities. Furthermore, it is also helpful in the allocation of medical resources and assessment of vaccination priority. We analyzed the COVID-19 data provided by the Davao Center for Health Development of the Department of Health Davao Region in the Philippines. The dataset contains records of COVID-19 cases reported from March 2020 to April 2021. Methods that were used include descriptive statistics, graphical presentations, and nonparametric statistical methods. The study reveals that male children and female senior citizens are the most susceptible age-sex composition while male senior citizen is the subgroup with the highest case fatality and mortality. Furthermore, regardless of sex groups, the senior citizen is the subgroup with the longest hospitalization. Susceptibility due to exposure should be included as a criterion in determining the age-sex compositions for vaccination priority against COVID-19 and other potentially deadly viruses. Further, Proper planning and allocation of medical resources for the elderly should be prioritized in the provincial levels.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Roel Ceballos", - "author_inst": "University of Southeastern Philippines" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.06.21.21259227", "rel_title": "Meta-Analytic Evidence of Depression and Anxiety in Eastern Europe during the COVID-19 Pandemic", @@ -684438,6 +686274,93 @@ "type": "new results", "category": "physiology" }, + { + "rel_doi": "10.1101/2021.06.25.449893", + "rel_title": "Enhanced Fc\u03b3RIII/CD16 activation by discrete ligands as independent correlates of disease severity in COVID-19 patients", + "rel_date": "2021-06-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.25.449893", + "rel_abs": "A dysregulated immune response with high levels of SARS-CoV-2 specific IgG antibodies characterizes patients with severe or critical COVID-19. Although a robust IgG response is traditionally considered to be protective, excessive triggering of activating Fc-gamma-receptors (Fc{gamma}Rs) could be detrimental and cause immunopathology. Here, we document that patients who develop soluble circulating IgG immune complexes (sICs) during infection are subject to enhanced immunopathology driven by Fc{gamma}R activation. Utilizing cell-based reporter systems we provide evidence that sICs are predominantly formed prior to a specific humoral response against SARS-CoV-2. sIC formation, together with increased afucosylation of SARS-CoV-2 specific IgG eventually leads to an enhanced CD16 (Fc{gamma}RIII) activation of immune cells reaching activation levels comparable active systemic lupus erythematosus (SLE) disease. Our data suggest a vicious cycle of escalating immunopathology driven by an early formation of sICs in predisposed patients. These findings reconcile the seemingly paradoxical findings of high antiviral IgG responses and systemic immune dysregulation in severe COVID-19.\n\nClinical implicationsThe identification of sICs as drivers of an escalating immunopathology in predisposed patients opens new avenues regarding intervention strategies to alleviate critical COVID-19 progression.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC=\"FIGDIR/small/449893v4_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (17K):\norg.highwire.dtl.DTLVardef@b4616corg.highwire.dtl.DTLVardef@682d1aorg.highwire.dtl.DTLVardef@16946cborg.highwire.dtl.DTLVardef@a6ef7d_HPS_FORMAT_FIGEXP M_FIG C_FIG A vicious cycle of immunopathology in COVID-19 patients is driven by soluble multimeric immune complexes (sICs). SARS-CoV-2 infection triggers sIC formation in prone individuals. Activation of Fc{gamma}RIII/CD16 expressing immune cells by sICs precedes a humoral response to SARS-CoV2 infection. sICs and infection add to IgG afucosylation, further enhancing Fc{gamma}RIII/CD16 activation by opsonized targets. High inflammation induces further sIC mediated immune cell activation ultimately leading to an escalating immunopathology.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Jakob Ankerhold", + "author_inst": "Institute of Virology, University Medical Center, Albert-Ludwigs-University Freiburg, Hermann-Herder-Str. 11, 79104 Freiburg, Germany" + }, + { + "author_name": "Sebastian Giese", + "author_inst": "Institute of Virology, University Medical Center, Albert-Ludwigs-University Freiburg, Hermann-Herder-Str. 11, 79104 Freiburg, Germany" + }, + { + "author_name": "Philipp Kolb", + "author_inst": "Institute of Virology, University Medical Center, Albert-Ludwigs-University Freiburg, Hermann-Herder-Str. 11, 79104 Freiburg, Germany" + }, + { + "author_name": "Andrea Maul-Pavicic", + "author_inst": "Department of Rheumatology and Clinical Immunology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Hugstetterstr. 55, 79106" + }, + { + "author_name": "Reinhard Edmund Voll", + "author_inst": "Department of Rheumatology and Clinical Immunology, Freiburg University Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Ge" + }, + { + "author_name": "Nathalie Goeppert", + "author_inst": "Institute of Virology, University Medical Center, Albert-Ludwigs-University Freiburg, Hermann-Herder-Str. 11, 79104 Freiburg, Germany" + }, + { + "author_name": "Kevin Ciminski", + "author_inst": "Institute of Virology, University Medical Center, Albert-Ludwigs-University Freiburg, Hermann-Herder-Str. 11, 79104 Freiburg, Germany" + }, + { + "author_name": "Clemens Kreutz", + "author_inst": "Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Stefan Meier Str. 26, 79104 Freiburg, Germany" + }, + { + "author_name": "Achim Lother", + "author_inst": "Heart Center Freiburg University, Department of Cardiology and Angiology I, Faculty of Medicine, University of Freiburg, Hugstetterstr. 55, 79106 Freiburg, Germ" + }, + { + "author_name": "Ulrich Salzer", + "author_inst": "Department of Rheumatology and Clinical Immunology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Hugstetterstr. 55, 79106" + }, + { + "author_name": "Wolfgang Bildl", + "author_inst": "Institute of Physiology II, Faculty of Medicine, University of Freiburg, Hermann-Herder-Str. Freiburg, Germany" + }, + { + "author_name": "Tim Welsink", + "author_inst": "InVivo BioTech Services GmbH, 16761 Hennigsdorf, Germany" + }, + { + "author_name": "Nils Morgenthaler", + "author_inst": "InVivo BioTech Services GmbH, 16761 Hennigsdorf, Germany" + }, + { + "author_name": "Andrea Busse Grawitz", + "author_inst": "Institute of Clinical Chemistry and Laboratory Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hugstetterstr. 55" + }, + { + "author_name": "Daniela Huzly", + "author_inst": "Institute of Virology, University Medical Center, Albert-Ludwigs-University Freiburg, Hermann-Herder-Str. 11, 79104 Freiburg, Germany" + }, + { + "author_name": "Martin Schwemmle", + "author_inst": "Institute of Virology, University Medical Center, Albert-Ludwigs-University Freiburg, Hermann-Herder-Str. 11, 79104 Freiburg, Germany" + }, + { + "author_name": "Hartmut Hengel", + "author_inst": "Institute of Virology, University Medical Center, Albert-Ludwigs-University Freiburg, Hermann-Herder-Str. 11, 79104 Freiburg, Germany" + }, + { + "author_name": "Valeria Falcone", + "author_inst": "Institute of Virology, University Medical Center, Albert-Ludwigs-University Freiburg, Hermann-Herder-Str. 11, 79104 Freiburg, Germany" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.06.21.21257822", "rel_title": "Identification of driver genes for severe forms of COVID-19 in a deeply phenotyped young patient cohort", @@ -685454,109 +687377,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.21.21258528", - "rel_title": "Correlates of Protection against symptomatic and asymptomatic SARS-CoV-2 infection", - "rel_date": "2021-06-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.21.21258528", - "rel_abs": "BackgroundAlthough 6 COVID-19 vaccines have been approved by the World Health Organisation as of 16th June 2021, global supply remains limited. An understanding of the immune response associated with protection could facilitate rapid licensure of new vaccines.\n\nMethodsData from a randomised efficacy trial of ChAdOx1 nCoV-19 (AZD1222) vaccine in the UK was analysed to determine the antibody levels associated with protection against SARS-CoV-2. Anti-spike and anti-RBD IgG by multiplex immunoassay, pseudovirus and live neutralising antibody at 28 days after the second dose were measured in infected and non-infected vaccine recipients. Weighted generalised additive models for binary data were applied to symptomatic and asymptomatic SARS-CoV-2 infection data from ChAdOx1 nCoV-19 recipients. Cubic spline smoothed log antibody levels, and weights were applied to account for potential selection bias in sample processing. Models were adjusted for baseline risk of exposure to SARS-CoV-2 infection.\n\nResultsHigher levels of all immune markers were correlated with a reduced risk of symptomatic infection. Vaccine efficacy of 80% against primary symptomatic COVID-19 was achieved with an antibody level of 40923 (95% CI: 16748, 125017) and 63383 (95% CI: 16903, not computed (NC)) for anti-spike and anti-RBD, and 185 (95% CI: NC, NC) and 247 (95% CI: 101, NC) for pseudo- and live-neutralisation assays respectively. Antibody responses did not correlate with overall protection against asymptomatic infection.\n\nConclusionsCorrelates of protection can be used to bridge to new populations using validated assays. The data can be used to extrapolate efficacy estimates for new vaccines where large efficacy trials cannot be conducted. More work is needed to assess correlates for emerging variants.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Shuo Feng", - "author_inst": "Oxford Vaccine Group, Department of Paediatrics, University of Oxford, UK" - }, - { - "author_name": "Daniel Phillips", - "author_inst": "Oxford Vaccine Group, Department of Paediatrics, University of Oxford, UK" - }, - { - "author_name": "Thomas White", - "author_inst": "AstraZeneca BioPharmaceuticals PLC" - }, - { - "author_name": "Homesh Sayal", - "author_inst": "AstraZeneca BioPharmaceuticals PLC" - }, - { - "author_name": "Parvinder K Aley", - "author_inst": "Oxford Vaccine Group, Department of Paediatrics, University of Oxford" - }, - { - "author_name": "Sagida Bibi", - "author_inst": "Oxford Vaccine Group, Department of Paediatrics, University of Oxford, UK" - }, - { - "author_name": "Christina Dold", - "author_inst": "Oxford Vaccine Group, Department of Paediatrics, University of Oxford, UK" - }, - { - "author_name": "Michelle Fuskova", - "author_inst": "Jenner Institute, Nuffield Department of Medicine, University of Oxford, UK" - }, - { - "author_name": "Sarah C Gilbert", - "author_inst": "Jenner Institute, Nuffield Department of Medicine, University of Oxford, UK" - }, - { - "author_name": "Ian Hirsch", - "author_inst": "AstraZeneca BioPharmaceuticals PLC" - }, - { - "author_name": "Holly E Humphries", - "author_inst": "National Infection Service, Public Health England, Salisbury, UK" - }, - { - "author_name": "Brett Jepson", - "author_inst": "AstraZeneca BioPharmaceuticals PLC and Cytel Inc, Chapel Hill, North Carolina, United States" - }, - { - "author_name": "Elizabeth J Kelly", - "author_inst": "AstraZeneca BioPharmaceuticals PLC" - }, - { - "author_name": "Emma Plested", - "author_inst": "Oxford Vaccine Group, Department of Paediatrics, University of Oxford, UK" - }, - { - "author_name": "Kathryn Shoemaker", - "author_inst": "AstraZeneca BioPharmaceuticals PLC" - }, - { - "author_name": "Kelly M Thomas", - "author_inst": "National Infection Service, Public Health England, Salisbury, UK" - }, - { - "author_name": "Johan Vekemans", - "author_inst": "AstraZeneca BioPharmaceuticals PLC" - }, - { - "author_name": "Tonya L Villafana", - "author_inst": "AstraZeneca BioPharmaceuticals PLC" - }, - { - "author_name": "Teresa Lambe", - "author_inst": "Jenner Institute, Nuffield Department of Medicine, University of Oxford, UK" - }, - { - "author_name": "Andrew J Pollard", - "author_inst": "Oxford Vaccine Group, Department of Paediatrics, University of Oxford, UK" - }, - { - "author_name": "Merryn Voysey", - "author_inst": "Oxford Vaccine Group, Department of Paediatrics, University of Oxford, UK" - }, - { - "author_name": "- Oxford Vaccine Trial Team", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.22.21259336", "rel_title": "Population disruption: estimating changes in population distribution in the UK during the COVID-19 pandemic", @@ -686288,6 +688108,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, + { + "rel_doi": "10.1101/2021.06.18.21259143", + "rel_title": "Seroprevalence of SARS-CoV-2 infection in the Colombo Municipality region, Sri Lanka", + "rel_date": "2021-06-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.18.21259143", + "rel_abs": "BackgroundAs the Municipality Council area in Colombo (CMC) experienced the highest number of cases until end of January 2021, in Sri Lanka, we carried out a serosurvey prior to initiation of the vaccination program to understand the extent of the SARS-CoV-2 outbreak.\n\nMethodsSARS-CoV-2 seropositivity was determined in 2547 individuals between the ages of 10 to 86 years, by the Wantai total antibody ELISA. We also compared to seroprevalence using the haemagglutination test (HAT) to evaluate its usefulness in carrying out serosurveys.\n\nResultsThe overall seropositivity rate was 24.46%, while seropositivity by HAT was 18.9%. Although the SARS-CoV-2 infection detection rates by PCR were highest in the population between the ages of 20 to 60 years of age, the seropositivity rates were equal among all age groups. The seropositivity rate was highest in the 10 to 20 age group (34.03%), whereas the PCR positivity rates was 9.8%. Differences in the PCR positivity rates and seropositivity rates were also seen in 60- to 70-year-olds (8.9% vs 30.4%) and in individuals >70 year (4.1% vs 1.2%). The seropositivity rates of the females was 29.7% (290/976), which was significantly higher (p<0.002) than in males 21.2% (333/1571).\n\nConclusionsA high seroprevalence rate (24.5%) was seen in all age groups in the CMC suggesting that a high level of transmission was seen during this area. The PCR positivity rates, appear to underestimate the true extent of the outbreak and the age groups which were infected.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Chandima Jeewandara", + "author_inst": "University of Sri Jayewardenepura" + }, + { + "author_name": "Dinuka Guruge", + "author_inst": "Colombo Municipal Council" + }, + { + "author_name": "Inoka S Aberathna", + "author_inst": "University of Sri Jayewardenepura" + }, + { + "author_name": "Saubhagya Danasekara", + "author_inst": "University of Sri Jayewardenepura" + }, + { + "author_name": "Banuri Gunasekara", + "author_inst": "University of Sri Jayewardenepura" + }, + { + "author_name": "Pradeep D Pushpakumara", + "author_inst": "University of Sri Jayewardenepura" + }, + { + "author_name": "Deshan Madushanka", + "author_inst": "University of Sri Jayewardenepura" + }, + { + "author_name": "Deshni Jayathilaka", + "author_inst": "University of Sri Jayewardenepura" + }, + { + "author_name": "Thushali Ranasinghe", + "author_inst": "University of Sri Jayewardenepura" + }, + { + "author_name": "Gayasha Somathilaka", + "author_inst": "University of Sri Jayewardenepura" + }, + { + "author_name": "Shyrar Tanussiya", + "author_inst": "University of Sri Jayewardenepura" + }, + { + "author_name": "Tibutius Jayadas", + "author_inst": "University of Sri Jayewardenepura" + }, + { + "author_name": "Heshan Kuruppu", + "author_inst": "University of Sri Jayewardenepura" + }, + { + "author_name": "Nimasha Thashmi", + "author_inst": "University of Sri Jayewardenepura" + }, + { + "author_name": "Michael Harvie", + "author_inst": "University of Sri Jayewardenepura" + }, + { + "author_name": "Ruwan Wijayamuni", + "author_inst": "Colombo Municipal Council" + }, + { + "author_name": "Lisa Schimanski", + "author_inst": "University of Oxford" + }, + { + "author_name": "Tiong Tan", + "author_inst": "University of Oxford" + }, + { + "author_name": "Pramila Rijal", + "author_inst": "University of Oxford" + }, + { + "author_name": "Julie Xiao", + "author_inst": "University of Oxford" + }, + { + "author_name": "Graham Ogg", + "author_inst": "University of Oxford" + }, + { + "author_name": "Alain Townsend", + "author_inst": "University of Oxford" + }, + { + "author_name": "Gathsaurie Neelika Malavige", + "author_inst": "University of Sri Jayewardenepura" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.19.21259172", "rel_title": "Molecular Genetic Analysis of SARS-CoV-2 Lineages in Armenia", @@ -687328,53 +689255,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.10.21258526", - "rel_title": "Evidence-based pandemic preparedness: an infrastructure for population-scale genome-based based testing for COVID-19", - "rel_date": "2021-06-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.10.21258526", - "rel_abs": "Our lives (and deaths) have been dominated for more than a year by COVID-19, a pandemic that has caused hundreds of millions of disease cases, millions of deaths, trillions in economic costs, and major restrictions on our freedom. We argue that much of this could have been avoided by repeated and systematic population-scale PCR-based testing and targeted quarantine. We describe key elements of the current implementations of such a system and demonstrate (with Germany as an example), that this strategy could have suppressed the pandemic within weeks, eliminating the vast majority of its overall impact in terms of deaths, economic costs and restrictions. It can, however, still play a major role in further reducing the worldwide impact of the current phase of the pandemic, and remain as a key protection against similar dangers in the future.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Hans R Lehrach", - "author_inst": "Max Planck Institute for Molecular Genetics" - }, - { - "author_name": "Jon Curtis", - "author_inst": "Alacris Theranostics GmbH" - }, - { - "author_name": "Bodo Lange", - "author_inst": "Alacris Theranostics GmbH" - }, - { - "author_name": "Lesley Ogilvie", - "author_inst": "Alacris Theranostics GmbH" - }, - { - "author_name": "Richard Gauss", - "author_inst": "State Sanitary Directorate, City Government, Vienna, Austria" - }, - { - "author_name": "Christoph Steininger", - "author_inst": "Medical University of Vienna, Department of Medicine I, Division of Infectious Diseases, Vienna, Austria; LEAD Horizon, Vienna, Austria" - }, - { - "author_name": "Erhard Scholz", - "author_inst": "University of Wuppertal" - }, - { - "author_name": "Matthias Kreck", - "author_inst": "University of Bonn, Germany; University of Frankfurt, Germany" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.20.21259220", "rel_title": "A Continuous Bayesian Model for the Stimulation COVID-19 Epidemic Dynamics", @@ -687782,6 +689662,41 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2021.06.17.21259116", + "rel_title": "COVID-19 Vaccine Coverage Index: Identifying barriers to COVID-19 vaccine uptake across U.S. counties", + "rel_date": "2021-06-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.17.21259116", + "rel_abs": "ImportanceThe United States is in a race against time to vaccinate its population to contain the COVID-19 pandemic. With limited resources, a proactive, targeted effort is needed to reach widespread community immunity.\n\nObjectiveIdentify county-level barriers to achieving rapid COVID-19 vaccine coverage and validate the index against vaccine rollout data.\n\nDesignEcological study\n\nSettingPopulation-based\n\nParticipantsLongitudinal COVID-19 vaccination coverage data for 50 states and the District of Columbia and 3118 counties from January 12 through May 25, 2021.\n\nExposure(s)The COVID-19 Vaccine Coverage index (CVAC) ranks states and counties on barriers to coverage through 28 indicators across 5 themes: historic undervaccination, sociodemographic barriers, resource-constrained health system, healthcare accessibility barriers, and irregular care-seeking behaviors. A score of 0 indicates the lowest level of concern, whereas a score of 1 indicates the highest level of concern.\n\nMain Outcome(s) and Measure(s)State-level vaccine administrations from January 12 through May 25, 2021, provided by the Centers for Disease Control and Prevention (CDC) and Our World In Data. County-level vaccine coverage as of May 25, 2021, provided by the CDC.\n\nResultsAs of May 25, 2021, the CVAC strongly correlated with the percentage of population fully vaccinated against COVID-19 by county (r = -0.39, p=2.2x10-16) and state (r=-0.77, p=4.9x10-11). Low-concern states and counties have fully vaccinated 26.5% [t=6.8, p=1.7x10-7] and 26% (t=22.0, p=2.2x10-16) more people, respectively, compared to their high-concern counterparts. This vaccination gap is at its highest point since the start of vaccination and continues to grow. Higher concern on each of the five themes predicts a lower rate of vaccination at the county level (all p<.001). We identify five types of counties with distinct barrier profiles.\n\nConclusions and RelevanceThe CVAC measures underlying barriers to vaccination and is strongly associated with the speed of rollout. As the coverage gap between high- and low-concern regions continues to grow, the CVAC can inform a precision public health response targeted to underlying barriers.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSWhich U.S. counties face barriers to COVID-19 vaccine rollout, and are these communities vaccinating fewer individuals?\n\nFindingsThe COVID-19 Vaccine Coverage Index (CVAC) comprises five themes reflecting county-level concern for low coverage. We report rural, regional, and racial divides in exposure to these vaccination barriers. The top third of states and counties of highest concern have vaccinated 19% and 20% fewer people, respectively, compared to regions of least concern.\n\nMeaningThe CVAC can help contextualize progress to widespread COVID-19 vaccine coverage, identifying underlying community-level factors that could be driving suboptimal rollout to inform precision solutions.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Anubhuti Mishra", + "author_inst": "Surgo Ventures" + }, + { + "author_name": "Staci Sutermaster", + "author_inst": "Surgo Ventures" + }, + { + "author_name": "Peter Smittenaar", + "author_inst": "Surgo Ventures" + }, + { + "author_name": "Nicholas Stewart", + "author_inst": "Surgo Ventures" + }, + { + "author_name": "Sema Sgaier", + "author_inst": "Surgo Ventures" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2021.06.18.21258798", "rel_title": "Impact of vaccination in reducing Hospital expenses, Mortality and Average length of stay among COVID 19 patients. A retrospective cohort study from India", @@ -688434,49 +690349,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.06.18.21259164", - "rel_title": "Rural prioritization may increase the impact of COVID-19 vaccines in Sub-Saharan Africa due to ongoing internal migration: A modeling study", - "rel_date": "2021-06-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.18.21259164", - "rel_abs": "How COVID-19 vaccine is distributed within low- and middle-income countries has received little attention outside of equity or logistical concerns but may ultimately affect campaign impact in terms of infections, severe cases, or deaths averted. In this study we examined whether subnational (urban-rural) prioritization may affect the cumulative two-year impact on disease transmission and burden of a vaccination campaign using an agent-based model of COVID-19 in a representative Sub-Saharan Africa country setting. We simulated a range of vaccination strategies that differed by urban-rural prioritization, age group prioritization, timing of introduction, and final coverage level. Urban prioritization averted more infections in only a narrow set of scenarios, when internal migration rates were low and vaccination was started by day 30 of an outbreak. Rural prioritization was the optimal strategy for all other scenarios, e.g., with higher internal migration rates or later start dates, due to the presence of a large immunological naive rural population. Among other factors, timing of the vaccination campaign was important to determining maximum impact, and delays as short as 30 days prevented larger campaigns from having the same impact as smaller campaigns that began earlier. The optimal age group for prioritization depended on choice of metric, as prioritizing older adults consistently averted more deaths across all of the scenarios. While guidelines exist for these latter factors, urban-rural allocation is an orthogonal factor that we predict to affect impact and warrants consideration as countries plan the scale-up of their vaccination campaigns.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Prashanth Selvaraj", - "author_inst": "Bill and Melinda Gates Foundation" - }, - { - "author_name": "Bradley G Wagner", - "author_inst": "Bill and Melinda Gates Foundation" - }, - { - "author_name": "Dennis L Chao", - "author_inst": "Bill and Melinda Gates Foundation" - }, - { - "author_name": "Maina L'Azou Jackson", - "author_inst": "Coalition for Epidemic Preparedness Innovations" - }, - { - "author_name": "J. Gabrielle Breugelmans", - "author_inst": "Coalition for Epidemic Preparedness Innovations" - }, - { - "author_name": "Nicholas Jackson", - "author_inst": "Coalition for Epidemic Preparedness Innovations" - }, - { - "author_name": "Stewart T Chang", - "author_inst": "Bill and Melinda Gates Foundation" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.15.21258920", "rel_title": "Observed and self-reported COVID-19 health protection behaviours on a university campus and the impact of a single simple intervention.", @@ -689172,6 +691044,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, + { + "rel_doi": "10.1101/2021.06.17.21259095", + "rel_title": "Use of the Internet and digital devices among people with severe mental ill health during the COVID-19 pandemic restrictions.", + "rel_date": "2021-06-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.17.21259095", + "rel_abs": "BackgroundRestrictions due to the COVID-19 pandemic have led to everyday reliance on digitalisation of life, including access to health care services. People with severe mental ill health (SMI - e.g., bipolar or psychosis spectrum disorders) are at greater risk for digital exclusion and it is unknown to what extent they are able to adapt to online service delivery. This cross-sectional survey study explored use of the Internet and digital devices during the pandemic restrictions and its association with physical and mental health changes.\n\nMethods367 adults with an SMI diagnosis completed a survey (online or offline) and provided information on access to Internet connection and devices, internet skills, online activities, and barriers to using the Internet. They also self-reported changes in mental and physical health.\n\nResultsDuring the pandemic restrictions 61.6% were limited or non-users of the Internet. The majority had access to the Internet and digital devices but around half reported knowledge deficits. Most common activities were accessing information and entertainment (88.9%), staying in touch with friends and families (84.8%), and purchasing goods (other than food) (84.3%). Most common barriers were finding the Internet not interesting (28.3%) or too difficult (27.9%), as well as security concerns (22.1% to 24.3%). Using the Internet a lot (vs just a bit or not at all) during the pandemic was associated with younger age (Adj ORs = 4.76 - 6.39, Ps < .001), having a diagnosis of bipolar disorder (compared to psychosis; Adj OR = 3.88, P < .001), or reporting a decline in mental health (compared to no decline; Adj OR = 1.92, P = .01).\n\nConclusionMost people with SMI were limited or non-users of the Internet during the pandemic, which seems to be mainly attributable to lack of interest and skills, rather than lack of devices or connectivity. Older adults with psychosis should be the focus of interventions to support digital engagement in people with SMI.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Panagiotis Spanakis", + "author_inst": "University of York" + }, + { + "author_name": "Paul Heron", + "author_inst": "University of York" + }, + { + "author_name": "Lauren Walker", + "author_inst": "University of York" + }, + { + "author_name": "Susanne Crosland", + "author_inst": "University of York" + }, + { + "author_name": "Ruth Wadman", + "author_inst": "University of York" + }, + { + "author_name": "Elizabeth Newbronner", + "author_inst": "University of York" + }, + { + "author_name": "Gordon Johnston", + "author_inst": "Independent peer researcher" + }, + { + "author_name": "Simon Gilbody", + "author_inst": "University of York" + }, + { + "author_name": "Emily Peckham", + "author_inst": "University of York" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.06.17.21257667", "rel_title": "\"It's hard to keep a distance when you're with someone you really care about\" -a qualitative study of adolescents' pandemic-related health literacy and how Covid-19 affects their lives", @@ -690192,65 +692115,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.06.18.21258899", - "rel_title": "Increased Risk of Severe COVID-19 Disease in Pregnancy in a Multicenter Propensity Score-Matched Study.", - "rel_date": "2021-06-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.18.21258899", - "rel_abs": "BackgroundRespiratory infections have long been associated with higher maternal and perinatal morbidity. Early data did not report an increased risk of SARS-CoV-2 infection or disease severity in pregnancy. However, surveillance data from the Center for Disease Control and Prevention (CDC) indicates a higher risk of severe disease and death in pregnant women with symptomatic SARS-CoV-2 infection, although this data is subject to ascertainment bias.\n\nObjectiveTo explore the association between COVID-19 disease severity and pregnancy in our university-based hospital system using measures such as COVID-19 ordinal scale severity score, hospitalization, intensive care unit admission, oxygen supplementation, invasive mechanical ventilation, and death.\n\nStudy designWe conducted a retrospective, multicenter case-control study to understand the association between COVID-19 disease severity and pregnancy. We reviewed consecutive charts of adult females, ages 18-45, with laboratory-confirmed SARS-CoV-2 infection in six months between March 1, 2020, and August 31, 2020. Cases were patients diagnosed with COVID-19 during pregnancy, whereas controls were not pregnant at the time of COVID-19 diagnosis. Primary endpoints were the COVID-19 severity score at presentation (within four hours) and the nadir of the clinical course. The secondary endpoints were the proportion of patients requiring hospitalization, intensive care unit admission, oxygen supplementation, invasive mechanical ventilation, and death.\n\nResultsA higher proportion of pregnant women had moderate to severe COVID-19 disease at the nadir of the clinical course than nonpregnant women (25% vs. 16.1%, p=0.04, respectively). While there was a higher rate of hospitalization (25.6% vs. 17.2%), ICU admission (8.9% vs. 4.4%), need for vasoactive substances (5.0% vs. 2.8%), and invasive mechanical ventilation (5.6% vs. 2.8%) in the pregnant group, this difference was not significant after the propensity score matching was applied.\n\nWe found a high rate of pregnancy complications in our population (40.7%). The most worrisome is the rate of hypertensive disorders of pregnancy (20.1%).\n\nConclusionsIn our propensity score-matched study, COVID-19 in pregnancy is associated with an increased risk of disease severity and an increased risk of pregnancy complications.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Liviu Cojocaru", - "author_inst": "Division of Maternal-Fetal Medicine. Department of Obstetrics, Gynecology and Reproductive Science. University of Maryland School of Medicine, Baltimore, MD, US" - }, - { - "author_name": "Myint Noe", - "author_inst": "Division of Clinical Care and Research. Institute of Human Virology. University of Maryland School of Medicine, Baltimore, MD, USA." - }, - { - "author_name": "Autusa Pahlavan", - "author_inst": "University of Maryland School of Medicine, Baltimore, MD, USA." - }, - { - "author_name": "Alissa Werzen", - "author_inst": "Division of Clinical Care and Research. Institute of Human Virology. University of Maryland School of Medicine, Baltimore, MD, USA." - }, - { - "author_name": "Hyunuk Seung", - "author_inst": "School of Pharmacy. University of Maryland Baltimore, Baltimore, MD, USA." - }, - { - "author_name": "Young Chae Jessica Yoo", - "author_inst": "Division of Clinical Care and Research. Institute of Human Virology. University of Maryland School of Medicine, Baltimore, MD, USA." - }, - { - "author_name": "Patricia Tyson", - "author_inst": "University of Maryland School of Medicine, Baltimore, MD, USA." - }, - { - "author_name": "Shivakumar Narayanan", - "author_inst": "Division of Clinical Care and Research. Institute of Human Virology. University of Maryland School of Medicine, Baltimore, MD, USA." - }, - { - "author_name": "Shifa Turan", - "author_inst": "Division of Maternal-Fetal Medicine. Department of Obstetrics, Gynecology and Reproductive Science. University of Maryland School of Medicine, Baltimore, MD, US" - }, - { - "author_name": "Ozhan M. Turan", - "author_inst": "Division of Maternal-Fetal Medicine. Department of Obstetrics, Gynecology and Reproductive Science. University of Maryland School of Medicine, Baltimore, MD, US" - }, - { - "author_name": "Joel V. Chua", - "author_inst": "Division of Clinical Care and Research. Institute of Human Virology. University of Maryland School of Medicine, Baltimore, MD, USA." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "obstetrics and gynecology" - }, { "rel_doi": "10.1101/2021.06.20.21259195", "rel_title": "Rapid displacement of SARS-CoV-2 variant B.1.1.7 by B.1.617.2 and P.1 in the United States", @@ -691213,6 +693077,233 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.17.21259078", + "rel_title": "Understanding the Potential Impact of Different Drug Properties On SARS-CoV-2 Transmission and Disease Burden: A Modelling Analysis", + "rel_date": "2021-06-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.17.21259078", + "rel_abs": "BackgroundThe unprecedented public health impact of the COVID-19 pandemic has motivated a rapid search for potential therapeutics, with some key successes. However, the potential impact of different treatments, and consequently research and procurement priorities, have not been clear.\n\nMethods and FindingsWe develop a mathematical model of SARS-CoV-2 transmission, COVID-19 disease and clinical care to explore the potential public-health impact of a range of different potential therapeutics, under a range of different scenarios varying: i) healthcare capacity, ii) epidemic trajectories; and iii) drug efficacy in the absence of supportive care. In each case, the outcome of interest was the number of COVID-19 deaths averted in scenarios with the therapeutic compared to scenarios without. We find the impact of drugs like dexamethasone (which are delivered to the most critically-ill in hospital and whose therapeutic benefit is expected to depend on the availability of supportive care such as oxygen and mechanical ventilation) is likely to be limited in settings where healthcare capacity is lowest or where uncontrolled epidemics result in hospitals being overwhelmed. As such, it may avert 22% of deaths in high-income countries but only 8% in low-income countries (assuming R=1.35). Therapeutics for different patient populations (those not in hospital, early in the course of infection) and types of benefit (reducing disease severity or infectiousness, preventing hospitalisation) could have much greater benefits, particularly in resource-poor settings facing large epidemics.\n\nConclusionsThere is a global asymmetry in who is likely to benefit from advances in the treatment of COVID-19 to date, which have been focussed on hospitalised-patients and predicated on an assumption of adequate access to supportive care. Therapeutics that can feasibly be delivered to those earlier in the course of infection that reduce the need for healthcare or reduce infectiousness could have significant impact, and research into their efficacy and means of delivery should be a priority.", + "rel_num_authors": 53, + "rel_authors": [ + { + "author_name": "Charles Whittaker", + "author_inst": "MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, United Kingdom" + }, + { + "author_name": "Oliver Watson", + "author_inst": "MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, United Kingdom" + }, + { + "author_name": "Carlos Alvarez-Moreno", + "author_inst": "Clinica Universitaria Colombia, Clinica Colsanitas. Facultad de Medicina, Universidad Nacional de Colombia, Bogota, Colombia" + }, + { + "author_name": "Nasikarn Angkasekwinai", + "author_inst": "Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand" + }, + { + "author_name": "Adhiratha Boonyasiri", + "author_inst": "Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand" + }, + { + "author_name": "Luis Carlos-Triana", + "author_inst": "Hospital Universitario San Ignacio -Pontificia Universidad Javeriana, Bogota, Colombia" + }, + { + "author_name": "Duncan Chanda", + "author_inst": "Adult Infectious Diseases Centre, University Teaching Hospital, Lusaka, Zambia; Department of Internal Medicine, University of Zambia School of Medicine, Lusaka" + }, + { + "author_name": "Lantharita Charoenpong", + "author_inst": "Bamrasnaradura Infectious Diseases Institute, Department of Diseases Control, Ministry of Public Health, Nonthaburi, Thailand" + }, + { + "author_name": "Methee Chayakulkeeree", + "author_inst": "Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand" + }, + { + "author_name": "Graham Cooke", + "author_inst": "Department of Infectious Diseases, Imperial College London, London, United Kingdom; NIHR Biomedical Research Centre, Imperial College NHS Trust, London, United " + }, + { + "author_name": "Julio Croda", + "author_inst": "Oswaldo Cruz Foudantion, Mato Grosso do Sul, Campo Grande, Brazil; School of Medicine, Federal University of Mato Grosso do Sul, Campo Grande, Brazil; Yale Scho" + }, + { + "author_name": "Zulma Cucunuba", + "author_inst": "MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, United Kingdom; Faculty of Medicine, Pontificia Universidad Javeriana, Bogot" + }, + { + "author_name": "Bimandra Djafaara", + "author_inst": "MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, United Kingdom; Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia" + }, + { + "author_name": "Cassia Estofolete", + "author_inst": "Faculdade de Medicina de Sao Jose do Rio Preto (FAMERP), Sao Jose do Rio Preto, Brazil" + }, + { + "author_name": "Maria Eugenia-Grillet", + "author_inst": "Instituto de Zoologia y Ecologia Tropical, Facultad de Ciencias, Universidad Central de Venezuela, Caracas, Venezuela" + }, + { + "author_name": "Nuno Faria", + "author_inst": "MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, United Kingdom; Departamento de Molestias Infecciosas e Parasitarias and Ins" + }, + { + "author_name": "Silva Figueiredo-Costa", + "author_inst": "Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "David Forero-Pena", + "author_inst": "Biomedical Research and Therapeutic Vaccines Institute, Ciudad Bolivar, Venezuela." + }, + { + "author_name": "Diana Gibb", + "author_inst": "MRC Clinical Trials Unit at University College London, London, United Kingdom" + }, + { + "author_name": "Anthony Gordon", + "author_inst": "Division of Anaesthetics, Pain Medicine and Intensive Care, Imperial College London, London, United Kingdom" + }, + { + "author_name": "Raph Hamers", + "author_inst": "Centre for Tropical Medicine and Global Health, Nuffield Dept of Medicine, University of Oxford, Oxford, UK; Eijkman-Oxford Clinical Research Unit, Jakarta, Ind" + }, + { + "author_name": "Arran Hamlet", + "author_inst": "MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, United Kingdom" + }, + { + "author_name": "Vera Irawany", + "author_inst": "Fatmawati General Hospital, Faculty of Medicine University of Indonesia" + }, + { + "author_name": "Anupop Jitmuang", + "author_inst": "Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand" + }, + { + "author_name": "Nukool Keurueangkul", + "author_inst": "Samutprakan Hospital, Bangkok, Thailand" + }, + { + "author_name": "Teresia Njoki Kimani", + "author_inst": "Kenyan Ministry of Health, Nairobi, Kenya" + }, + { + "author_name": "Margarita Lampo", + "author_inst": "Instituto Venezolano de Investigaciones Cientifica, Caracas, Venezuela" + }, + { + "author_name": "Anna Levin", + "author_inst": "Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Gustavo Lopardo", + "author_inst": "Hospital Bernardo Houssay, Buenos Aires, Argentina" + }, + { + "author_name": "Rima Mustafa", + "author_inst": "Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom" + }, + { + "author_name": "Shevanthi Nayagam", + "author_inst": "MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, United Kingdom" + }, + { + "author_name": "Thundon Ngamprasertchai", + "author_inst": "Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand" + }, + { + "author_name": "Ng'ang'a Irene Hannah Njeri", + "author_inst": "Kenyan Ministry of Health, Kiambu County, Kenya" + }, + { + "author_name": "Mauricio Nogueira", + "author_inst": "Faculdade de Medicina de Sao Jose do Rio Preto (FAMERP), Sao Jose do Rio Preto, Brazil" + }, + { + "author_name": "Esteban Ortiz-Prado", + "author_inst": "OneHealth Global Research Group, Universidad de las Americas, Quito, Ecuador" + }, + { + "author_name": "Mauricio Perroud", + "author_inst": "School of Medical Sciences; University of Campinas, Campinas, Brazil" + }, + { + "author_name": "Andrew Phillips", + "author_inst": "Institute for Global Health, University College London, London, United Kingdom" + }, + { + "author_name": "Panuwat Promsin", + "author_inst": "Critical Care Division, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand" + }, + { + "author_name": "Ambar Qavi", + "author_inst": "School of Public Health, Imperial College London, London, United Kingdom" + }, + { + "author_name": "Alison Rodger", + "author_inst": "Institute for Global Health, University College London, London, United Kingdom" + }, + { + "author_name": "Ester Sabino", + "author_inst": "Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Sorawat Sangkaew", + "author_inst": "Section of Adult Infectious Disease, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK" + }, + { + "author_name": "Djayanti Sari", + "author_inst": "Department of Anesthesiology and Intensive Theraphy, Faculty of Medicine, Public Health and Nursing Universitas Gadjah Mada. Public Hospital Dr. Sardjito, Yogya" + }, + { + "author_name": "Rujipas Sirijatuphat", + "author_inst": "Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand" + }, + { + "author_name": "Andrei Sposito", + "author_inst": "Atherosclerosis and Vascular Biology Laboratory, State University of Campinas, Campinas, Brazil" + }, + { + "author_name": "Pratthana Srisangthong", + "author_inst": "Bangkok Christian Hospital, Bangkok, Thailand" + }, + { + "author_name": "Hayley Thompson", + "author_inst": "MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, United Kingdom" + }, + { + "author_name": "Zarir Udwadia", + "author_inst": "Hinduja Hospital and Research Centre, Mumbai, India" + }, + { + "author_name": "Sandra Valderrama-Beltran", + "author_inst": "Division of Infectious Diseases. School of Medicine. Pontificia Universidad Javeriana, Hospital Universitario San Ignacio. Bogota, Colombia." + }, + { + "author_name": "Peter Winskill", + "author_inst": "MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, United Kingdom" + }, + { + "author_name": "Azra Ghani", + "author_inst": "MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, United Kingdom" + }, + { + "author_name": "Patrick Walker", + "author_inst": "MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, United Kingdom" + }, + { + "author_name": "Timothy Hallett", + "author_inst": "MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, United Kingdom" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.17.21259100", "rel_title": "COVID-19 Transmission Dynamics Underlying Epidemic Waves in Kenya", @@ -692297,29 +694388,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2021.06.11.21258733", - "rel_title": "Impact estimation on COVID-19 infections following school reopening in September 2020 in Italy", - "rel_date": "2021-06-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.11.21258733", - "rel_abs": "BackgroundSince its outbreak, CoViD-19 (formally known as 2019-nCoV) has been triggering many questions among public authorities, social organisms and school officials, as to when students should be allowed to return to school. Such a decision is critical and must take into account, other than its beneficial effects, also those associated with an increased exposition of the students to the virus, which, as a result, might spread at a faster rate. To date, in Italy, a few studies have rigorously investigated the correlation between school reopening and number of people tested positive to CoViD-19. Therefore, this paper aims to provide an assessment of such an impact as well as to illustrate the methodology followed.\n\nMethodsOfficial daily data on the cumulative number of people tested positive to CoViD-19 - in conjunction with external information accounting for the different points in time schools reopened in the various Italian regions - have been employed to build a stochastic model of the type Seasonal Autoregressive Moving Average embodying external information.\n\nResultsThere was a statistically significant increase in the number of positive cases in all the Italian regions related to schools reopening. Such an increase occurred, in average, about 18.9 days after the schools have been reopened. Schools reopening have been significantly contributed to the diffusion of the pandemic, with an overall estimated impact of about 228,724 positive cases.\n\nConclusionsThe results suggest the need for strict control of all in-school activities. This could be done by using, to a variable extent, all the non-pharmaceutical interventions available, such as limited access to school spaces, no overlapping practices between different sports in the same space, universal masking, bubble-size classroom. However, in many cases, such measures might not be a viable option, at least in the short run, nor be reasonably applicable. Therefore, whenever the established safety criteria could not be met, school buildings should remain closed.\n\nKey MessagesO_LIDue to CoViD-19 pandemic, physical school attendance is at the center of an intense political and social debates;\nC_LIO_LIschools reopening decision should be based on reliable and well maintained data-sets;\nC_LIO_LIin the lack of quality data, it is advisable to use a portion of them, to reduce uncertainty.\nC_LI", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Livio Fenga", - "author_inst": "Istat" - }, - { - "author_name": "Massimo Galli", - "author_inst": "University of Milan" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.13.21258838", "rel_title": "Visible and real dynamics of the COVID-19 pandemic in Ukraine in the spring of 2021", @@ -693111,6 +695179,53 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.06.18.448982", + "rel_title": "Influence of viral transport media and freeze-thaw cycling on the sensitivity of qRT-PCR detection of SARS-CoV-2 nucleic acids", + "rel_date": "2021-06-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.18.448982", + "rel_abs": "The events of the last year have highlighted the complexity of implementing large-scale molecular diagnostic testing for novel pathogens. The purpose of this study was to determine the chemical influences of sample collection media and storage on the stability and detection of viral nucleic acids by qRT-PCR. We studied the mechanism(s) through which viral transport media (VTM) and number of freeze-thaw cycles influenced the analytical sensitivity of qRT-PCR detection of SARS-CoV-2. Our goal is to reinforce testing capabilities and identify weaknesses that could arise in resource-limited environments that do not have well-controlled cold chains. The sensitivity of qRT-PCR analysis was studied in four VTM for synthetic single-stranded RNA (ssRNA) and double-stranded DNA (dsDNA) simulants of the SARS-CoV-2 genome. The sensitivity and reproducibility of qRT-PCR for the synthetic ssRNA and dsDNA were found to be highly sensitive to VTM with the best results observed for ssRNA in HBSS and PBS-G. Surprisingly, the presence of epithelial cellular material with the ssRNA increased the sensitivity of the qRT-PCR assay. Repeated freeze-thaw cycling decreased the sensitivity of the qRT-PCR with two noted exceptions. The choice of VTM is critically important to defining the sensitivity of COVID-19 molecular diagnostics assays and this study suggests they can impact upon the stability of the SARS-CoV-2 viral genome. This becomes increasingly important if the virus structure is destabilised before analysis, which can occur due to poor storage conditions. This study suggests that COVID-19 testing performed with glycerol-containing PBS will produce a high level of stability and sensitivity. These results are in agreement with clinical studies reported for patient-derived samples.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Cian Holohan", + "author_inst": "School of Chemistry and Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Republic of Ireland." + }, + { + "author_name": "Sophia Hanrahan", + "author_inst": "School of Chemistry and Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Republic of Ireland." + }, + { + "author_name": "Nathan Feely", + "author_inst": "School of Chemistry and Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Republic of Ireland." + }, + { + "author_name": "Peng Li", + "author_inst": "Magnostics Ltd, Monkstown, Co. Dublin, Republic of Ireland." + }, + { + "author_name": "Catherine Moss", + "author_inst": "School of Chemistry and Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Republic of Ireland." + }, + { + "author_name": "Michael J. Carr", + "author_inst": "National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Republic of Ireland." + }, + { + "author_name": "Oya Tagit", + "author_inst": "Magnostics Ltd, Monkstown, Co. Dublin, Republic of Ireland." + }, + { + "author_name": "Gil U Lee", + "author_inst": "School of Chemistry and Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Republic of Ireland." + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2021.06.18.448958", "rel_title": "Structure and computation-guided design of a mutation-integrated trimeric RBD candidate vaccine with broad neutralization against SARS-CoV-2", @@ -693955,81 +696070,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.06.16.448754", - "rel_title": "A stem-loop RNA RIG-I agonist confers prophylactic and therapeutic protection against acute and chronic SARS-CoV-2 infection in mice", - "rel_date": "2021-06-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.16.448754", - "rel_abs": "As SARS-CoV-2 continues to cause morbidity and mortality around the world, there is an urgent need for the development of effective medical countermeasures. Here, we assessed the antiviral capacity of a minimal RIG-I agonist, stem-loop RNA 14 (SLR14), in viral control, disease prevention, post-infection therapy, and cross-variant protection in mouse models of SARS-CoV-2 infection. A single dose of SLR14 prevented viral replication in the lower respiratory tract and development of severe disease in a type I interferon (IFN-I) dependent manner. SLR14 demonstrated remarkable protective capacity against lethal SARS-CoV-2 infection when used prophylactically and retained considerable efficacy as a therapeutic agent. In immunodeficient mice carrying chronic SARS-CoV-2 infection, SLR14 elicited near-sterilizing innate immunity by inducing IFN-I responses in the absence of the adaptive immune system. In the context of infection with variants of concern (VOC), SLR14 conferred broad protection and uncovered an IFN-I resistance gradient across emerging VOC. These findings demonstrate the therapeutic potential of SLR14 as a host-directed, broad-spectrum antiviral for early post-exposure treatment and for treatment of chronically infected immunosuppressed patients.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Tianyang Mao", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Benjamin Israelow", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Carolina Lucas", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Chantal B. F. Vogels", - "author_inst": "Yale University School of Public Health" - }, - { - "author_name": "Olga Fedorova", - "author_inst": "Yale University" - }, - { - "author_name": "Mallery I. Breban", - "author_inst": "Yale University School of Public Health" - }, - { - "author_name": "Bridget L. Menasche", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Huiping Dong", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Melissa Linehan", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "- Yale SARS-CoV-2 Genome Surveillance Initiative", - "author_inst": "" - }, - { - "author_name": "Craig B. Wilen", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Marie L. Landry", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Nathan D. Grubaugh", - "author_inst": "Yale University School of Public Health" - }, - { - "author_name": "Anna M. Pyle", - "author_inst": "Yale University" - }, - { - "author_name": "Akiko Iwasaki", - "author_inst": "Yale University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.06.16.448777", "rel_title": "Specificity and Mechanism of Coronavirus, Rotavirus and Mammalian Two-Histidine-Phosphoesterases That Antagonize Antiviral Innate Immunity", @@ -695129,6 +697169,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.11.21258743", + "rel_title": "Baseline Characteristics and Outcomes of 180 Egyptian COVID-19 Patients Admitted to Quarantine Hospitals of Ain Shams University: A Retrospective Comparative Study", + "rel_date": "2021-06-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.11.21258743", + "rel_abs": "Background and study aimCOVID-19 mortality, severity, and recovery are major global concerns, but they are still insufficiently understood, particularly in the Middle East. This study focused on evaluating if there was a link between COVID-19 patients clinical and laboratory findings at hospital admission and disease severity and mortality.\n\nPatients and methodsA total of 180 adult Egyptian COVID-19 patients were included in this study then were categorized and compared.\n\nResultsOf all, 27.8% had severe disease, and 13.9% died during their hospital stay. Diabetes (46.7%), hypertension (36.1%), and chronic obstructive pulmonary disease (COPD) (33.3%) were the most frequent associated co-morbidities. Severe patients and non-survivors were significantly older compared to their corresponding groups. Their neutrophil count, PCT, ESR, C-reactive protein (CRP), AST, ALT, LDH, D-dimer, and ferritin levels were significantly higher (P [≤] 0.05). In contrast, their absolute lymphocyte count was significantly lower (P [≤] 0.05). COPD (OR: 3.294; 95% CI: 1.199-9.053), diabetes (OR: 2.951; 95% CI:1.070- 8.137), ferritin [≥] 350 ng/mL (OR: 11.08; 95% CI: 2.796-41.551), AST [≥] 40 IU/L (OR: 3.07; 95% CI: 1.842-7.991), CT-scoring system (CT-SS) [≥] 17 (OR: 1.205; 95% CI: 1.089-1.334) and lymphocyte count < 1x103/{micro}L (OR: 4.002; 95% CI: 1.537-10.421), were all linked to a higher risk of COVID-19 severity. While mortality was predicted by dyspnea (OR: 4.006; 95% CI: 1.045-15.359), CT-SS [≥] 17 (OR: 1.271; 95% CI: 1.091-1.482) and AST [≥] 40 IU/L (OR: 2.89; 95% CI: 1.091-7.661).\n\nConclusionsClinical and laboratory data of COVID-19 patients at their hospital admission may aid in identifying early risk factors for severe illness and a high mortality rate.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Sara I. Taha", + "author_inst": "Department of Clinical Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt." + }, + { + "author_name": "Sara F. Samaan", + "author_inst": "Department of Internal Medicine, Faculty of Medicine, Ain Shams University, Cairo, Egypt." + }, + { + "author_name": "Aalaa K. Shata", + "author_inst": "Department of Pulmonary Medicine, Faculty of Medicine, Ain Shams University, Cairo, Egypt." + }, + { + "author_name": "Shereen A. Baioumy", + "author_inst": "Department of Microbiology and Immunology, Faculty of Medicine, Zagazig University, Egypt." + }, + { + "author_name": "Shaimaa A. Abdalgeleel", + "author_inst": "Department of Biostatistics and Epidemiology, National Cancer Institute, Cairo University, Cairo, Egypt." + }, + { + "author_name": "Mariam K. Youssef", + "author_inst": "Department of Clinical Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.10.21258715", "rel_title": "Role of Hemogram-Derived Ratios and Systemic-Immune Inflammation Index in Prediction of COVID-19 Progression in Egyptian Patients", @@ -696617,77 +698696,6 @@ "type": "confirmatory results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.06.11.21257717", - "rel_title": "SARS-CoV-2 shedding, infectivity and evolution in an immunocompromised adult patient", - "rel_date": "2021-06-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.11.21257717", - "rel_abs": "This report describes a persistent SARS-CoV-2 infection of at least 218 days in a male, in his 40s who had undergone a prior autologous hematopoietic stem cell transplant due to a diffuse large B-cell lymphoma. He did not manifest a humoral immune response to the virus. Whole-genome sequencing and viral cultures confirmed a continual infection with a replication-positive virus that had undergone genetic variation for at least 196 days following symptom onset.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Maria Cassia Mendes-Correa", - "author_inst": "Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil." - }, - { - "author_name": "Fabio Ghilardi", - "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo- Departamento de Molestias Infecciosas e Parasitarias" - }, - { - "author_name": "Matias Chiarastelli Salomao", - "author_inst": "Hospital 9 de Julho" - }, - { - "author_name": "Lucy S Villas-Boas", - "author_inst": "Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil." - }, - { - "author_name": "Anderson Vincente de Paula", - "author_inst": "Instituto de Medicina Tropical,Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil." - }, - { - "author_name": "Tania Regina Tozetto-Mendoza", - "author_inst": "Instituto de Medicina Tropical de Sao Paulo ,Faculdade de Medicina da Universidade de Sao Paulo,Sao Paulo,Brazil" - }, - { - "author_name": "Wilton Freire", - "author_inst": "Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil." - }, - { - "author_name": "Flavia Cristina da Silva Sales", - "author_inst": "Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil." - }, - { - "author_name": "Camila Malta Romano", - "author_inst": "Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil." - }, - { - "author_name": "Ingra Morales Claro", - "author_inst": "Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil." - }, - { - "author_name": "Leandro Menezes de Souza", - "author_inst": "Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil." - }, - { - "author_name": "Jessica F Ramos", - "author_inst": "Departamento de Molestias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de Sao Paulo" - }, - { - "author_name": "Heuder Gustavo de Oliveira Paiao", - "author_inst": "Departamento de Molestias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de Sao Paulo" - }, - { - "author_name": "Roberta Shcoinik Szor", - "author_inst": "Centro de Oncologia Hospital Sirio Libanes" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.08.21258551", "rel_title": "NHS CHECK: protocol for a cohort study investigating the psychosocial impact of the COVID-19 pandemic on healthcare workers", @@ -697454,6 +699462,77 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.06.14.448436", + "rel_title": "Molecular dynamics analysis of fast-spreading severe acute respiratory syndrome coronavirus 2 variants and their effects in the interaction with human angiotensin-converting enzyme 2", + "rel_date": "2021-06-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.14.448436", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is evolving with mutations in the Spike protein, especially in the receptor-binding domain (RBD). The failure of public health measures to contain the spread of the disease in many countries has given rise to novel viral variants with increased transmissibility. However, key questions about how quickly the variants can spread and whether they can cause a more severe disease remain unclear. Herein, we performed a structural investigation using molecular dynamics simulations and determined dissociation constant (KD) values using surface plasmon resonance (SPR) assays of three fastspreading SARS-CoV-2 variants, Alpha, Beta and Gamma ones, as well as genetic factors in the host cells that may be related to the viral infection. Our results suggest that the SARS-CoV-2 variants facilitate their entry into the host cell by moderately increased binding affinities to the human ACE2 receptor, different torsions in hACE2 mediated by RBD variants, and an increased Spike exposure time to proteolytic enzymes. We also found that other host cell aspects, such as gene and isoform expression of key genes for the infection (ACE2, FURIN and TMPRSS2), may have few contributions to the SARS-CoV-2 variants infectivity. In summary, we concluded that a combination of viral and host cell factors allows SARS-CoV-2 variants to increase their abilities to spread faster than wild-type.\n\nO_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Anacleto Silva de Souza Sr.", + "author_inst": "University of Sao Paulo" + }, + { + "author_name": "Vitor Martins de Freitas Amorim", + "author_inst": "Universidade de Sao Paulo" + }, + { + "author_name": "Gabriela D. A. Guardia", + "author_inst": "Hospital Sirio Libanes" + }, + { + "author_name": "Felipe R C dos Santos", + "author_inst": "Hospital Sirio Libanes" + }, + { + "author_name": "Filipe F dos Santos", + "author_inst": "Hospital Sirio Libanes" + }, + { + "author_name": "Robson F de Souza", + "author_inst": "Universidade de Sao Paulo" + }, + { + "author_name": "Guilherme de Araujo Juvenal", + "author_inst": "Universidade de Sao Paulo" + }, + { + "author_name": "Yihua Huang", + "author_inst": "ACROBiosystems Inc." + }, + { + "author_name": "Pingju Ge", + "author_inst": "ACROBiosystems Inc." + }, + { + "author_name": "Yinan Jiang", + "author_inst": "ACROBiosystems Inc." + }, + { + "author_name": "Prajwal Paudel", + "author_inst": "ACROBiosystems Inc." + }, + { + "author_name": "Henning Ulrich", + "author_inst": "Instituto de Quimica, Universidade de Sao Paulo" + }, + { + "author_name": "Pedro A.F. Galante", + "author_inst": "Hospital Sirio-Libanes" + }, + { + "author_name": "Cristiane Rodrigues Guzzo", + "author_inst": "Universidade de Sao Paulo" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2021.06.13.21258862", "rel_title": "Similar Rates of AKI during the First Two Waves of COVID-19 in Northern Italy: a single-center study", @@ -698214,41 +700293,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2021.06.13.21258864", - "rel_title": "Electoral processes and COVID-19 infections in Japan", - "rel_date": "2021-06-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.13.21258864", - "rel_abs": "Election campaigns and polling stations might be areas of potential infections; however, it is unknown whether elections can impact the spread of coronavirus disease (COVID-19). This study aimed to evaluate the association between election process and COVID-19 infection in Japan. Quasi-experimental design using time-series COVID-19 cases data with an election intervention. We chose the cities where elections for major and/or city/ward assembly members were held in 2021 January in Japan. The study period for each city spans one weeks before the start date of the election campaign and three weeks after the voting day (36 days). The daily number of patients testing positive for COVID-19. We used Poisson regression analysis with sandwich estimator to evaluate the association between election and the spread of COVID-19 infections. For Miyakojima City, we assessed the relationship between election and COVID-19 infections by using the Box-Jenkins autoregressive integrated moving average (ARIMA) model. We also estimated the instantaneous reproduction number (Rt) in the city. There were 17 cities that met the inclusion criteria. In all models with three types of different lag effects (i.e., 4, 9, and 14 days), election was not a significant predictor of COVID-19 infections in the 17 cities. For Miyakojima City, the autoregressive integrated moving average (0, 0, 0) with a lag of 14 (=14) was the best model. The partial coefficient ({omega}) of the election was 11.91 (95% confidence interval: 3.10-20.72, P<0.001), indicating that the election was associated with an increase in the number of COVID-19 cases 14 days after the election campaign (mean: 12 cases/day). Rt hovered far above 1 during and after the election campaign in Miyakojima. Although elections were associated with an increased number of COVID-19 cases in Miyakojima, this association was not verified in the analysis including all 17 cities. Therefore, if preventive measures prescribed by election guidelines are followed, elections do not necessarily relate to a spread of COVID-19 as long as the election process does not involve activities necessitating close contact.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Shunsuke Murata", - "author_inst": "National Cerebral And Cardiovascular Center Research Institute" - }, - { - "author_name": "Takashi Nagata", - "author_inst": "Kyushu University Graduate School of Medical Sciences" - }, - { - "author_name": "Soshiro Ogata", - "author_inst": "National Cerebral And Cardiovascular Center Research Institute" - }, - { - "author_name": "Kunihiro Nishimura", - "author_inst": "National Cerebral And Cardiovascular Center Research Institute" - }, - { - "author_name": "Akihito Hagihara", - "author_inst": "National Cerebral And Cardiovascular Center Research Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.10.21258694", "rel_title": "Are We There Yet? Big Data Significantly Overestimates COVID-19 Vaccination in the US", @@ -698663,6 +700707,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.06.12.21258835", + "rel_title": "Predicted domination of variant Delta of SARS-CoV-2 before Tokyo Olympic games, Japan", + "rel_date": "2021-06-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.12.21258835", + "rel_abs": "Using numbers of SARS-CoV-2 variants detected in Japan, the relative instantaneous reproduction numbers of the R.1, Alpha, and Delta variants with respect to other strains circulating in Japan were estimated at 1.245, 1.437, and 1.948, respectively. The numbers can vary within 1.190-1.319 for R.1, 1.335-1.580 for Alpha, and 1.703-2.30 for Delta depending on the assumed serial interval distributions. The frequency of the Delta is expected to take over the Alpha in Japan around July 12, 2021.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Kimihito Ito", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Chayada Piantham", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Hiroshi Nishiura", + "author_inst": "Kyoto University" + } + ], + "version": "1", + "license": "", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.13.21258845", "rel_title": "Importance of adequate COVID-19 case definitions in the SARS-CoV-2 pandemic", @@ -699541,29 +701612,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.06.11.21258749", - "rel_title": "The NICE COVID-19 search strategy for Ovid MEDLINE and Embase: developing and maintaining a strategy to support rapid guidelines", - "rel_date": "2021-06-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.11.21258749", - "rel_abs": "Introduction The United Kingdom's (UK) National Institute for Health and Care Excellence (NICE) needs access to evidence on COVID-19 to develop rapid guidelines for healthcare professionals. This paper reports on how the NICE COVID-19 search strategy for identifying references in Ovid MEDLINE and Embase has been developed and maintained. Methods Each free-text line from the June 2020 version of the NICE COVID-19 search strategy was categorised as Critical, High, Medium, Low or Zero priority, according to the number of results and their relevance to NICE. Five search options were devised and tested by combining them with a search for drug treatments. The two prioritised options were compared to the COVID-19 Limit available in Ovid. New subject headings were tested and added. The selected option was refined to make the strategy simpler to use. Results The updated strategy combines free-text terms, categorised as Critical, High and Medium priority for NICE, with appropriate subject headings. Discussion The paper describes the challenges of maintaining a search strategy during the COVID-19 pandemic, as terminology continues to evolve. Conclusions A search strategy for identifying COVID-19 references, within the remit of NICE, has been developed. The recommended strategy could be considered for validation at an appropriate point in the pandemic. It is hoped that understanding how NICE has maintained its COVID-19 strategy will encourage further discussion on the challenges.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Paul Levay", - "author_inst": "National Institute for Health and Care Excellence" - }, - { - "author_name": "Amy Finnegan", - "author_inst": "National Institute for Health and Care Excellence" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2021.06.14.21258619", "rel_title": "A pilot feasibility study on SARS-CoV-2 detection method based on nasopharyngeal lavage fluid", @@ -700455,6 +702503,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.09.21258634", + "rel_title": "Determinants of adherence to COVID-19 preventive behaviours in Canada: Results from the iCARE Study", + "rel_date": "2021-06-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.09.21258634", + "rel_abs": "ObjectiveKey to slowing the spread of SARS-Cov-2 is adherence to preventive behaviours promoted through government policies, which may be influenced by policy awareness, attitudes and concerns about the virus and its impacts. This study assessed determinants of adherence to major coronavirus preventive behaviours, including demographics, attitudes and concerns, among Canadians during the first pandemic wave.\n\nMethodsAs part of the iCARE study (www.iCAREstudy.com), we weighted data from two population-based, online surveys (April and June, 2020) of Canadian adults. Questions tapped into behaviour change constructs. Multivariate regression models identified determinants of adherence.\n\nResultsData from 6,008 respondents (51% female) were weighted for age, sex, and province. Awareness of government policies was high at both time points (80-99%), and adherence to prevention behaviours was high in April (87.5%-93.5%) but decreased over time, particularly for avoiding social gatherings (68.1%). Adherence was worse among men, those aged 25 and under, and those currently working. Aligned with the Health Beliefs Model, perceptions of the importance of prevention behaviours and the nature of peoples COVID-19-related concerns were highly predictive of adherence. Interestingly, health and social/economic concerns predicted better adherence, but having greater personal financial concerns predicted worse adherence at both time points.\n\nConclusionAdherence to COVID-19 prevention behaviours was worse among men, younger adults, and workers, and deteriorated over time. Perceived importance of prevention behaviours measures and health and social/economic concerns predicted better adherence, but personal financial concerns predicted worse adherence. Results have implications for tailoring policy and communication strategies during subsequent pandemic waves.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Kim L. Lavoie", + "author_inst": "Montreal Behavioural Medicine Centre, Research Centre, CIUSSS-NIM, Montreal, Quebec, Canada" + }, + { + "author_name": "Vincent Gosselin Boucher", + "author_inst": "Department of Psychology, University of Quebec at Montreal (UQAM), Montreal, Quebec, Canada" + }, + { + "author_name": "Jovana Stojanovic", + "author_inst": "Department of Health, Kinesiology and Applied Physiology, Concordia University, Montreal, Quebec, Canada" + }, + { + "author_name": "Brigitte Voisard", + "author_inst": "Department of Psychology, University of Quebec at Montreal (UQAM), Montreal, Quebec, Canada;" + }, + { + "author_name": "Genevieve Szczepanik", + "author_inst": "Montreal Behavioural Medicine Centre, Research Centre, CIUSSS-NIM, Montreal, Quebec, Canada" + }, + { + "author_name": "Jacqueline A. Boyle", + "author_inst": "Monash Centre for Health Research and Implementation, Monash University, VIC, Australia" + }, + { + "author_name": "Ariane Belanger-Gravel", + "author_inst": "Department of Information and Communication, Laval University, Quebec City, Quebec, Canada" + }, + { + "author_name": "Simon L. Bacon", + "author_inst": "Montreal Behavioural Medicine Centre, Research Centre, CIUSSS-NIM, Montreal, Quebec, Canada; Department of Health, Kinesiology and Applied Physiology, Concordia" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.06.07.21258488", "rel_title": "Risk factors for hospitalization, disease severity and mortality in children and adolescents with COVID-19: Results from a nationwide German registry", @@ -701391,41 +703486,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "dentistry and oral medicine" }, - { - "rel_doi": "10.1101/2021.06.09.21258537", - "rel_title": "Increased risk of death in covid-19 hospital admissions during the second wave as compared to the first epidemic wave. A prospective dynamic cohort study in South London, UK.", - "rel_date": "2021-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.09.21258537", - "rel_abs": "ObjectiveTo assess whether mortality of patients admitted for covid-19 treatment was different in the second UK epidemic wave of covid-19 compared to the first wave accounting for improvements in the standard of care available and differences in the distribution of risk factors between the two waves.\n\nDesignSingle-centre, analytical, dynamic cohort study.\n\nParticipants2,701 adults ([≥]18 years) with SARS-CoV-2 infection confirmed by polymerase chain reaction (PCR) and/or clinico-radiological diagnosis of covid-19, who required hospital admission to covid-19 specific wards, between January 2020 and March 2021. There were 884 covid-19 admissions during the first wave (before 30 Jun 2020) and 1,817 during the second wave.\n\nOutcome measuresin-hospital covid-19 associated mortality, ascertained from clinical records and Medical Certificate Cause of Death.\n\nResultsThe crude mortality rate was 25% lower during the second wave (2.23 and 1.66 deaths per 100 person-days in first and second wave respectively). However, after accounting for age, sex, dexamethasone, oxygen requirements, symptoms at admission and Charlson Comorbidity Index, mortality hazard ratio associated with covid-19 hospital admissions was 1.62 (95% confidence interval 1.26, 2.08) times higher in the second wave compared to the first.\n\nConclusionsAnalysis of covid-19 admissions recorded in St. Georges Hospital, shows a larger second epidemic wave, with a lower crude mortality in hospital admissions. Nevertheless, after accounting for other factors underlying risk of death for covid-19 admissions was higher in the second wave. These findings are temporally and ecologically correlated with an increased circulation of SARS-CoV-2 variant of concern 202012/1 (alpha).", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Martina Cusinato", - "author_inst": "St. Georges University of London, London, UK" - }, - { - "author_name": "Jessica Gates", - "author_inst": "St. Georges Hospital, London, UK" - }, - { - "author_name": "Danyal Jajbhay", - "author_inst": "St. Georges Hospital, London, UK" - }, - { - "author_name": "Tim Planche", - "author_inst": "St. Georges University of London, London, UK" - }, - { - "author_name": "Yee-Ean Ong", - "author_inst": "St. Georges University of London, and St. Georges Hospital, London, UK." - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.09.21257809", "rel_title": "Vaccination history for diphtheria and tetanus is associated with less severe COVID-19", @@ -702153,6 +704213,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2021.06.08.21258587", + "rel_title": "The effect of obesity-related traits on COVID-19 severe respiratory symptoms is mediated by socioeconomic status: a multivariable Mendelian randomization study", + "rel_date": "2021-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.08.21258587", + "rel_abs": "BackgroundObesity has been associated with more severe clinical manifestations of coronavirus disease 2019 (COVID-19). However, this association can be affected by many correlates of these traits. Due to its large impact on human health, socioeconomic status (SES) could at least partially influence the association between obesity and COVID-19 severity. To estimate the independent effect of traits related to body size and SES on the clinical manifestations of COVID-19, we conducted a Mendelian randomization (MR) study analyzing the effect of obesity-related anthropometric traits on COVID-19 outcomes.\n\nMethodsApplying two-sample MR approaches, we evaluated the effects of body mass index (BMI), waist circumference (WC), hip circumference, (HIP) and waist-hip ratio (WHR) studied in up to 234,069 participants from the Genetic Investigation of ANthropometric Traits (GIANT) consortium with respect to three COVID-19 outcomes: severe respiratory COVID-19 (5,101 cases vs. 1,383,241 controls), hospitalized COVID-19 (9,986 cases vs. 1,877,672 controls), and COVID-19 infection (38,984 cases vs. 1,644,784 controls) obtained from the COVID-19 Host Genetics Initiative (HGI). Finally, to test the effect of SES using multivariable MR methods, we analyzed genetic data related to self-reported household income (HI) information from 286,301 UK Biobank (UKB) participants.\n\nResultsBMI and WC were associated with severe respiratory COVID-19 (BMI: OR=1.68 p=0.0004; WC: OR=1.72, p=0.007) and COVID-19 hospitalization (BMI: OR=1.62, p=1.35e-06; WC: OR=1.62, p=0.0001). Also, HIP influenced hospitalized COVID-19 (OR=1.31, p=0.012) and COVID-19 infection (OR=1.18, p=0.002). Conversely, HI was associated with lower odds of severe respiratory COVID-19 (OR=0.57, p=0.011) and hospitalized COVID-19 (OR=0.71, p=0.045). Testing these effects in multivariable MR models, we observed that the effect of these obesity-related anthropometric traits on COVID-19 outcomes is not independent of SES effect assessed as HI.\n\nConclusionsOur findings indicate that low SES is a contributor to the observed association between body size and COVID-19 outcomes.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Brenda Cabrera Mendoza", + "author_inst": "Yale" + }, + { + "author_name": "Frank Wendt", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Gita A Pathak", + "author_inst": "Yale University" + }, + { + "author_name": "Flavio De Angelis", + "author_inst": "Yale Univeristy" + }, + { + "author_name": "Antonella De Lillo", + "author_inst": "Yale" + }, + { + "author_name": "Dora Koller", + "author_inst": "Yale" + }, + { + "author_name": "Renato Polimanti", + "author_inst": "Yale University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.06.08.21258546", "rel_title": "Inequalities in healthcare disruptions during the Covid-19 pandemic: Evidence from 12 UK population-based longitudinal studies", @@ -703233,61 +705336,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.08.21258421", - "rel_title": "Wastewater-based epidemiology for tracking COVID-19 trend and variants of concern in Ohio, United States", - "rel_date": "2021-06-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.08.21258421", - "rel_abs": "The global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in more than 129 million confirm cases. Many health authorities around the world have implemented wastewater-based epidemiology as a rapid and complementary tool for the COVID-19 surveillance system and more recently for variants of concern emergence tracking. In this study, three SARS-CoV-2 target genes (N1, N2, and E) were quantified from wastewater influent samples (n = 250) obtained from the capital city and 7 other cities in various size in central Ohio from July 2020 to January 2021. To determine human-specific fecal strength in wastewater samples more accurately, two human fecal viruses (PMMoV and crAssphage) were quantified to normalize the SARS-CoV-2 gene concentrations in wastewater. To estimate the trend of new case numbers from SARS-CoV-2 gene levels, different statistical models were built and evaluated. From the longitudinal data, SARS-CoV-2 gene concentrations in wastewater strongly correlated with daily new confirmed COVID-19 cases (average Spearmans r = 0.70, p < 0.05), with the N2 gene being the best predictor of the trend of confirmed cases. Moreover, average daily case numbers can help reduce the noise and variation from the clinical data. Among the models tested, the quadratic polynomial model performed best in correlating and predicting COVID-19 cases from the wastewater surveillance data, which can be used to track the effectiveness of vaccination in the later stage of the pandemic. Interestingly, neither of the normalization methods using PMMoV or crAssphage significantly enhanced the correlation with new case numbers, nor improved the estimation models. Whole-genome sequencing result showed that those detected SARS-CoV-2 variants of concern from the wastewater matched with the clinical isolates from the communities. The findings from this study suggest that wastewater surveillance is effective in COVID-19 trend tracking and variant emergence and transmission within a community.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Yuehan Ai", - "author_inst": "Ohio State University" - }, - { - "author_name": "Angela Davis", - "author_inst": "Ohio State University" - }, - { - "author_name": "Daniel Jones", - "author_inst": "Ohio State University" - }, - { - "author_name": "Stanley Lemeshow", - "author_inst": "Ohio State University" - }, - { - "author_name": "Huolin Tu", - "author_inst": "Ohio State University" - }, - { - "author_name": "Fan He", - "author_inst": "Ohio State University" - }, - { - "author_name": "Peng Ru", - "author_inst": "Ohio State University" - }, - { - "author_name": "Xiaokang Pan", - "author_inst": "Ohio State University" - }, - { - "author_name": "Zazuna Bohrerova", - "author_inst": "Ohio State University" - }, - { - "author_name": "Jiyoung Lee", - "author_inst": "Ohio State University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.06.08.21258480", "rel_title": "SARS-CoV-2 infection in pregnancy in Denmark - characteristics and outcomes after confirmed infection in pregnancy: a nationwide, prospective, population-based cohort study", @@ -703979,6 +706027,33 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2021.06.06.21258177", + "rel_title": "The mental health impact of COVID-19 racial and ethnic discrimination against Asian American and Pacific Islanders", + "rel_date": "2021-06-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.06.21258177", + "rel_abs": "Hate crimes against Asian American/ Pacific Islanders (AAPIs) have surged in the United States during the COVID-19 pandemic to alarming new levels. We analyzed data from the Healthy Minds Study, and found that COVID-19 related racial/ethnic discrimination was associated with greater odds of having depression, anxiety, non-suicidal self-injury, binge drinking, and suicidal ideation among AAPI university students (N=1697). Findings suggest that the COVID-19 pandemic precipitated discrimination, which has been linked to mental health problems, calling for more preventive interventions to address the AAPI population, especially given their low rates of formal treatment utilization.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Sasha Zhou", + "author_inst": "Wayne State University" + }, + { + "author_name": "Rachel Banawa", + "author_inst": "The Milken Institute School of Public Health, The George Washington University" + }, + { + "author_name": "Hans Oh", + "author_inst": "University of Southern California" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.06.07.21258230", "rel_title": "A multi-component, community-based strategy to facilitate COVID-19 vaccine uptake among Latinx populations: from theory to practice", @@ -705171,57 +707246,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.06.08.21258584", - "rel_title": "Association between Preventive Measures against Workplace Infection and Preventive Behavior against Personal Infection", - "rel_date": "2021-06-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.08.21258584", - "rel_abs": "ObjectivesTo prevent the spread of coronavirus disease 2019 (COVID-19) infection, it is necessary for each individual to adopt infection prevention behavior. We investigated the effect of infection control measures implemented in the workplace on personal infection prevention behavior.\n\nMethodsWe conducted a self-administered questionnaire survey through the Internet from December 22 to 25, 2020, during which period COVID-19 was spreading. Among respondents aged 20 to 65 years (n=27,036), a total of 21,915 workers were included in the analysis after excluding self-employed workers (n=2,202), workers in small/home offices (n=377), and agriculture, forestry, and fisheries workers (n=212), etc., whose personal infection prevention behavior was almost the same as infection control measures taken in the workplace.\n\nResultsThe results showed that as the number of infection control measures in the workplace increased, implementation of infection prevention behavior by individuals also significantly increased. However, the relationship differed depending on the type of personal infection prevention behavior. Specifically, infection control measures against COVID-19 in the workplace may affect personal infection prevention behavior.\n\nConclusionImplementation of infection control measures in the workplace appears to deepen personal understanding of infection prevention behaviors, and increases awareness of the importance of individual infection prevention behavior and its implementation by all individuals. These findings may be applicable not only to COVID-19 measures but also to responses to other emerging infections and seasonal influenza.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Mika Kawasumi", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Tomohisa Nagata", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Hajime Ando", - "author_inst": "Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Ayako Hino", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Seiichiro Tateishi", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Mayumi Tsuji", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Shinya Matsuda", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Yoshihisa Fujino", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Koji Mori", - "author_inst": "University of Occupational and Environmental Health, Japan" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2021.06.04.21258335", "rel_title": "A Chinese host genetic study discovered type I interferons and causality of cholesterol levels and WBC counts on COVID-19 severity", @@ -706073,6 +708097,105 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.06.08.447631", + "rel_title": "Immunogenicity and In vivo protection of a variant nanoparticle vaccine that confers broad protection against emerging SARS-CoV-2 variants", + "rel_date": "2021-06-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.08.447631", + "rel_abs": "The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) continues to spread globally. As SARS-CoV-2 has transmitted from person to person, variant viruses have emerged with elevated transmission rates and higher risk of infection for vaccinees. We present data showing that a recombinant prefusion-stabilized Spike (rS) protein based on the B.1.351 sequence (rS-B.1.351) was highly immunogenic in mice and produced neutralizing antibodies against SARS-CoV-2/WA1, B.1.1.7, and B.1.351. Mice vaccinated with our prototype vaccine NVX-CoV2373 (rS-WU1) or rS-B.1.351 alone, in combination, or as a heterologous prime boost, were protected when challenged with live SARS-CoV-2/B.1.1.7 or SARS-CoV-2/B.1.351. Virus titer was reduced to undetectable levels in the lungs post-challenge in all vaccinated mice, and Th1-skewed cellular responses were observed. A strong anamnestic response was demonstrated in baboons boosted with rS-B.1.351 approximately one year after immunization with NVX-CoV2373 (rS-WU1). An rS-B.1.351 vaccine alone or in combination with prototype rS-WU1 induced protective antibody- and cell-mediated responses that were protective against challenge with SARS-CoV-2 variant viruses.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "James Logue", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "Robert Johnson", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "Nita Patel", + "author_inst": "Novavax" + }, + { + "author_name": "Bin Zhou", + "author_inst": "Novavax" + }, + { + "author_name": "Sonia Maciejewski", + "author_inst": "Novavax" + }, + { + "author_name": "Haixia Zhou", + "author_inst": "Novavax" + }, + { + "author_name": "Alyse Portnoff", + "author_inst": "Novavax" + }, + { + "author_name": "Jing-Hui Tian", + "author_inst": "Novavax" + }, + { + "author_name": "Marisa McGrath", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "Robert Haupt", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "Stuart Weston", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "Holly Hammod", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "Mimi Guebre-Xabier", + "author_inst": "Novavax" + }, + { + "author_name": "Carly Dillen", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "Joyce Plested", + "author_inst": "Novavax" + }, + { + "author_name": "Shane Cloney-Clark", + "author_inst": "Novavax" + }, + { + "author_name": "Anne Greene", + "author_inst": "Novavax" + }, + { + "author_name": "Mike Massare", + "author_inst": "Novavax" + }, + { + "author_name": "Greg Glenn", + "author_inst": "Novavax" + }, + { + "author_name": "Gale Smith", + "author_inst": "Novavax" + }, + { + "author_name": "Matthew Frieman", + "author_inst": "University of Maryland School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.06.09.447662", "rel_title": "Intranasal administration of a monoclonal neutralizing antibody protects mice against SARS-CoV-2 infection", @@ -707209,125 +709332,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2021.06.07.21258350", - "rel_title": "Recognition and inhibition of SARS-CoV-2 by humoral innate immunity pattern recognition molecules", - "rel_date": "2021-06-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.07.21258350", - "rel_abs": "The humoral arm of innate immunity includes diverse molecules with antibody-like functions, some of which serve as disease severity biomarkers in COVID-19. The present study was designed to conduct a systematic investigation of the interaction of humoral fluid phase pattern recognition molecules (PRM) with SARS-CoV-2. Out of 10 PRM tested, the long pentraxin PTX3 and Mannose Binding Lectin (MBL) bound the viral Nucleoprotein and Spike, respectively. MBL bound trimeric Spike, including that of variants of concern, in a glycan- dependent way and inhibited SARS-CoV-2 in three in vitro models. Moreover, upon binding to Spike, MBL activated the lectin pathway of complement activation. Genetic polymorphisms at the MBL locus were associated with disease severity. These results suggest that selected humoral fluid phase PRM can play an important role in resistance to, and pathogenesis of, COVID-19, a finding with translational implications.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Matteo Stravalaci", - "author_inst": "IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano (Milan), Italy; Dept. Biomedical Sciences, Humanitas University, via Rita Levi Montalcini 4, 2" - }, - { - "author_name": "Isabel Pagani", - "author_inst": "Viral Pathogenesis and Biosafety Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy" - }, - { - "author_name": "Elvezia Maria Paraboschi", - "author_inst": "IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano (Milan), Italy; Dept. Biomedical Sciences, Humanitas University, via Rita Levi Montalcini 4, 20" - }, - { - "author_name": "Mattia Pedotti", - "author_inst": "Institute for Research in Biomedicine, Universita della Svizzera Italiana, Bellinzona, Switzerland" - }, - { - "author_name": "Andrea Doni", - "author_inst": "IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano (Milan), Italy;" - }, - { - "author_name": "Francesco Scavello", - "author_inst": "IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano (Milan), Italy;" - }, - { - "author_name": "Sarah N. Mapelli", - "author_inst": "IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano (Milan), Italy;" - }, - { - "author_name": "Marina Sironi", - "author_inst": "IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano (Milan), Italy;" - }, - { - "author_name": "Luca Varani", - "author_inst": "Institute for Research in Biomedicine, Universita della Svizzera Italiana, Bellinzona, Switzerland" - }, - { - "author_name": "Milos Matkovic", - "author_inst": "Institute for Research in Biomedicine, Universita della Svizzera italiana (USI), Bellinzona, Switzerland" - }, - { - "author_name": "Andrea Cavalli", - "author_inst": "Institute for Research in Biomedicine, Universita della Svizzera italiana (USI), Bellinzona, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerla" - }, - { - "author_name": "Daniela Cesana", - "author_inst": "San Raffaele Telethon Institute for Gene Therapy (SR-Tiget); IRCCS, San Raffaele Scientific Institute, Milan, Italy" - }, - { - "author_name": "Pierangela Gallina", - "author_inst": "San Raffaele Telethon Institute for Gene Therapy (SR-Tiget); IRCCS, San Raffaele Scientific Institute, Milan, Italy" - }, - { - "author_name": "Nicoletta Pedemonte", - "author_inst": "UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gaslini 5, 16147 Genova" - }, - { - "author_name": "Valeria Capurro", - "author_inst": "UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gaslini 5, 16147 Genova" - }, - { - "author_name": "Nicola Clementi", - "author_inst": "Laboratory of Microbiology and Virology, IRCCS Scientific Institute and Vita-Salute San Raffaele University, Milan Italy" - }, - { - "author_name": "Nicasio Mancini", - "author_inst": "Laboratory of Microbiology and Virology, IRCCS Scientific Institute and Vita-Salute San Raffaele University, Milan Italy" - }, - { - "author_name": "Pietro Invernizzi", - "author_inst": "9Division of Gastroenterology, Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Re" - }, - { - "author_name": "Rino Rappuoli", - "author_inst": "Monoclonal Antibody Discovery Lab, Fondazione Toscana Life Sciences, Siena, Italy; Faculty of Medicine, Imperial College London, London, UK" - }, - { - "author_name": "Stefano Duga", - "author_inst": "IRCCS Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano (Milan), Italy; Dept Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 200" - }, - { - "author_name": "Barbara Bottazzi", - "author_inst": "IRCCS Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano (Milan), Italy" - }, - { - "author_name": "Mariagrazia Uguccioni", - "author_inst": "Institute for Research in Biomedicine, Universita della Svizzera italiana (USI), Bellinzona, Switzerland; Dept Biomedical Sciences, Humanitas University, Via Ri" - }, - { - "author_name": "Rosanna Asselta", - "author_inst": "IRCCS Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano (Milan), Italy; Dept Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 200" - }, - { - "author_name": "Elisa Vicenzi", - "author_inst": "Viral Pathogenesis and Biosafety Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy" - }, - { - "author_name": "Alberto Mantovani", - "author_inst": "IRCCS Humanitas Research Hospital, Rozzano (Milan), Italy; Dept Biomedical Sciences, Humanitas University, Pieve Emanuele (Milan), Italy; The William Harvey Res" - }, - { - "author_name": "Cecilia Garlanda", - "author_inst": "IRCCS Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano (Milan), Italy; Dept Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 200" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2021.06.06.21258423", "rel_title": "A Cross-sectional Study of Clinical COVID-19 Myocarditis", @@ -708155,6 +710159,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.06.21258406", + "rel_title": "Anti-spike protein receptor-binding domain IgG levels after COVID-19 infection or vaccination against SARS-CoV-2 in a seroprevalence study", + "rel_date": "2021-06-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.06.21258406", + "rel_abs": "PurposeIn a country-wide seroprevalence study of COVID-19 in Estonia we aimed to determine the seroprevalence and the dynamics of IgG against SARS-CoV-2 after vaccination or positive PCR-test.\n\nMethodsLeftover blood samples were selected between February 8 to March 25, 2021, by SYNLAB Estonia from all counties and age groups (0-9, 10-19, 20-59, 60-69, 70-79, 80-100 years) proportionally to the whole Estonian population and tested for IgG against SARS-CoV-2 spike protein receptor-binding domain (anti-S-RBD IgG) using Abbott SARS-CoV-2 IgG II Quant assay. Antibody levels after positive PCR-test or vaccination were described by nonlinear model.\n\nResultsA total of 2517 samples were tested. Overall seroprevalence (95% CI) was 20.1% (18.5-21.7%), similar in all age groups. If all individuals vaccinated with the first dose at least 14 days before antibody measurement were assumed to be seronegative, the overall seroprevalence was 15.8% (14.4-17.3%), 4-fold larger than the proportion of confirmed COVID-19 cases. According to nonlinear models, age increased anti-S-RBD IgG production after positive PCR-test but decreased after vaccination. The peak of anti-S-RBD IgG in a 52-year-old (median age of PCR-positive and/or vaccinated individuals) was significantly higher after vaccination compared with positive PCR-test (22082 (12897...26875) vs 6732 (2321...8243) AU/mL), but half-life was similar (26.5 (6.9...46.1) vs 38.3 (8.2...68.5) days).\n\nConclusionOne year after the start of COVID-19 pandemic the actual prevalence of infection is still underestimated compared with confirmed COVID-19 cases, underlining the importance of seroepidemiological studies. Older individuals have lower anti-S-RBD IgG level after vaccination, but similar decline rate to younger.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Hiie Soeorg", + "author_inst": "University of Tartu" + }, + { + "author_name": "Piia Jogi", + "author_inst": "University of Tartu" + }, + { + "author_name": "Paul Naaber", + "author_inst": "SYNLAB Eesti" + }, + { + "author_name": "Aigar Ottas", + "author_inst": "University of Tartu" + }, + { + "author_name": "Karolin Toompere", + "author_inst": "University of Tartu" + }, + { + "author_name": "Irja Lutsar", + "author_inst": "University of Tartu" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.30.21257913", "rel_title": "Highly sensitive scent-detection of COVID-19 patients in vivo by trained dogs", @@ -709075,153 +711118,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2021.06.06.446826", - "rel_title": "Evolution of enhanced innate immune evasion by the SARS-CoV-2 B.1.1.7 UK variant", - "rel_date": "2021-06-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.06.446826", - "rel_abs": "Emergence of SARS-CoV-2 variants, including the globally successful B.1.1.7 lineage, suggests viral adaptations to host selective pressures resulting in more efficient transmission. Although much effort has focused on Spike adaptation for viral entry and adaptive immune escape, B.1.1.7 mutations outside Spike likely contribute to enhance transmission. Here we used unbiased abundance proteomics, phosphoproteomics, mRNA sequencing and viral replication assays to show that B.1.1.7 isolates more effectively suppress host innate immune responses in airway epithelial cells. We found that B.1.1.7 isolates have dramatically increased subgenomic RNA and protein levels of Orf9b and Orf6, both known innate immune antagonists. Expression of Orf9b alone suppressed the innate immune response through interaction with TOM70, a mitochondrial protein required for RNA sensing adaptor MAVS activation, and Orf9b binding and activity was regulated via phosphorylation. We conclude that B.1.1.7 has evolved beyond the Spike coding region to more effectively antagonise host innate immune responses through upregulation of specific subgenomic RNA synthesis and increased protein expression of key innate immune antagonists. We propose that more effective innate immune antagonism increases the likelihood of successful B.1.1.7 transmission, and may increase in vivo replication and duration of infection.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Lucy G Thorne", - "author_inst": "UCL" - }, - { - "author_name": "Mehdi Bouhaddou", - "author_inst": "UCSF" - }, - { - "author_name": "Ann-Kathrin Reuschl", - "author_inst": "UCL" - }, - { - "author_name": "Lorena Zuliani-Alvarez", - "author_inst": "UCSF" - }, - { - "author_name": "Benjamin J. Polacco", - "author_inst": "UCSF" - }, - { - "author_name": "Adrian Pelin", - "author_inst": "UCSF" - }, - { - "author_name": "Jyoti Batra", - "author_inst": "UCSF" - }, - { - "author_name": "Matthew V.X. Whelan", - "author_inst": "UCL" - }, - { - "author_name": "Manisha Ummadi", - "author_inst": "UCSF" - }, - { - "author_name": "Ajda Roic", - "author_inst": "UCSF" - }, - { - "author_name": "Jane Turner", - "author_inst": "UCL" - }, - { - "author_name": "Kirsten Obernier", - "author_inst": "UCSF" - }, - { - "author_name": "Hannes Braberg", - "author_inst": "UCSF" - }, - { - "author_name": "Margaret Soucheray", - "author_inst": "UCSF" - }, - { - "author_name": "Alicia L. Richards", - "author_inst": "UCSF" - }, - { - "author_name": "Kuei-Ho Chen", - "author_inst": "UCSF" - }, - { - "author_name": "Bhavya Harjai", - "author_inst": "UCSF" - }, - { - "author_name": "Danish Memon", - "author_inst": "EMBL EBI" - }, - { - "author_name": "Myra Hosmillo", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Joseph Hiatt", - "author_inst": "UCSF" - }, - { - "author_name": "Aminu S. Jahun", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Ian G. Goodfellow", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Mahdad Noursadeghi", - "author_inst": "UCL" - }, - { - "author_name": "Jacqueline Fabius", - "author_inst": "UCSF" - }, - { - "author_name": "Kevan Shokat", - "author_inst": "UCSF" - }, - { - "author_name": "Natalia Jura", - "author_inst": "UCSF" - }, - { - "author_name": "Kliment A Verba", - "author_inst": "UCSF" - }, - { - "author_name": "Pedro Beltrao", - "author_inst": "EMBL EBI" - }, - { - "author_name": "Danielle L. Swaney", - "author_inst": "UCSF" - }, - { - "author_name": "Adolfo Garcia-Sastre", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Clare Jolly", - "author_inst": "UCL" - }, - { - "author_name": "Greg J. Towers", - "author_inst": "UCL" - }, - { - "author_name": "Nevan J. Krogan", - "author_inst": "UCSF" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.06.02.21258233", "rel_title": "Revealing public opinion towards COVID-19 vaccines using Twitter data in the United States: a spatiotemporal perspective", @@ -709869,6 +711765,77 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.06.06.447293", + "rel_title": "Comprehensive analysis of RNA-seq and whole genome sequencing data reveals no evidence for SARS-CoV-2 integrating into host genome", + "rel_date": "2021-06-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.06.447293", + "rel_abs": "SARS-CoV-2, as the causation of severe epidemic of COVID-19, is one kind of positive single-stranded RNA virus with high transmissibility. However, whether or not SARS-CoV-2 can integrate into host genome needs thorough investigation. Here, we performed both RNA sequencing (RNA-seq) and whole genome sequencing on SARS-CoV-2 infected human and monkey cells, and investigated the presence of host-virus chimeric events. Through RNA-seq, we did detect the chimeric host-virus reads in the infected cells. But further analysis using mixed libraries of infected cells and uninfected zebrafish embryos demonstrated that these reads are falsely generated during library construction. In support, whole genome sequencing also didnt identify the existence of chimeric reads in their corresponding regions. Therefore, the evidence for SARS-CoV-2s integration into host genome is lacking.\n\nOne-Sentence SummarySARS-CoV-2 does not integrate into host genome through whole genome sequencing.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Yu-Sheng Chen", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Shuaiyao Lu", + "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College" + }, + { + "author_name": "Bing Zhang", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Tingfu Du", + "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College" + }, + { + "author_name": "Wen-Jie Li", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Meng Lei", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Yanyan Zhou", + "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College" + }, + { + "author_name": "Yong Zhang", + "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College" + }, + { + "author_name": "Penghui Liu", + "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College" + }, + { + "author_name": "Yong-Qiao Sun", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Yong-Liang Zhao", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Ying Yang", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Xiaozhong Peng", + "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College" + }, + { + "author_name": "Yun-Gui Yang", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "contradictory results", + "category": "genomics" + }, { "rel_doi": "10.1101/2021.06.07.447286", "rel_title": "Dual roles of a novel oncolytic viral vector-based SARS-CoV-2 vaccine: preventing COVID-19 and treating tumor progression", @@ -710785,97 +712752,6 @@ "type": "new results", "category": "physiology" }, - { - "rel_doi": "10.1101/2021.06.03.21258289", - "rel_title": "Implementation of COVID-19 Preventive Measures in Primary and Secondary Schools Following Reopening of Schools in Autumn 2020; A Cross-Sectional Study of Parents' and Teachers' Experiences in England", - "rel_date": "2021-06-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.03.21258289", - "rel_abs": "ObjectiveThe main objective was to assess implementation of and ease of implementation of control measures in schools as reported by staff and parents.\n\nDesignCross-sectional study.\n\nSettingStaff and parents/guardian participants in the 132 primary schools and 20 secondary schools participating in sKIDs and sKIDsPLUS surveillances.\n\nMain outcome measurePrevalence of control measures implemented in Autumn 2020, parental and staff perception of ease of implementation and acceptability of conducting school surveillance studies.\n\nResultsIn total, 56/152 (37%) schools participating in Public Health Englands sKIDs study of COVID in schools accepted the invitation to participate in the survey. By 28 December 2020, 1,953 parent and 986 staff respondents had completed the online questionnaire. While more than half the parents were positive about their children returning to school, roughly a third reported being a little anxious. 90% and 82% of primary and secondary school parents were either completely or partly reassured by the preventive measures implemented in their schools. Among staff, 80% of primary staff and 87% of secondary school staff felt that they were at higher risk of COVID-19 because of their profession; only 52% of primary school staff and 38% of secondary school staff reportedly felt safe. According to the teaching staff, most preventive measures were well-implemented apart from requiring 2-metre distancing between staff. For students, maintaining the 2-metre distance was reported to be particularly difficult. By extension, secondary schools also struggled to maintain small groups at all times or ensuring that the same staff were assigned to each student group (a problem also commonly reported by parents).\n\nConclusionsVariable implementation of infection control measures was reported by staff and parents. Whilst the majority were not worried about returning to school, some parents and staff, were concerned about returning to school and the risks posed to children, staff and household members.\n\nStrengths and limitations of this studyO_ST_ABSStrengthsC_ST_ABSO_LIThis study is one of the few to investigate school staff and parents perceptions of the implementation of control measures implemented following the reopening of schools in England.\nC_LIO_LIThe early establishment of COVID-19 surveillance in primary and secondary schools in the summer term 2020 provided a cohort to rapidly evaluate the experiences of parents and school staff during the autumn term before schools were required to close for the subsequent national lockdown.\nC_LI\n\nLimitationsO_LIAs the questionnaire and information provided was available in English only, there is likely to be an under-representation of families for whom English was not their main language.\nC_LIO_LISome school responses were only provided by one participant so may not necessarily be representative of the whole school.\nC_LIO_LIAlthough the surveillance included schools recruited nationally, a convenience sample was used and as such may not be representative of all primary and secondary schools in England.\nC_LI", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Zahin Amin-Chowdhury", - "author_inst": "Public Health England" - }, - { - "author_name": "Marta Bertran", - "author_inst": "Public Health England" - }, - { - "author_name": "Meaghan Kall", - "author_inst": "Public Health England" - }, - { - "author_name": "Georgina Ireland", - "author_inst": "Public Health England" - }, - { - "author_name": "Felicity Aiano", - "author_inst": "Public Health England" - }, - { - "author_name": "Annabel Powell", - "author_inst": "Public Health England" - }, - { - "author_name": "Samuel E Jones", - "author_inst": "Public Health England" - }, - { - "author_name": "Andrew Brent", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Bernadette Brent", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Frances Baawuah", - "author_inst": "Public Health England" - }, - { - "author_name": "Ifeanychukwu Okike", - "author_inst": "University Hospitals of Derby and Burton NHS foundation Trust" - }, - { - "author_name": "Joanne Beckmann", - "author_inst": "Specialist Children & Young People's Services, East London NHS Foundation Trust" - }, - { - "author_name": "Joanna Garstang", - "author_inst": "Birmingham Community Healthcare Trust" - }, - { - "author_name": "Shazaad Ahmed", - "author_inst": "Public Health England" - }, - { - "author_name": "Neisha Sundaram", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Chris Bonell", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Sinead Langan", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "James Hargreaves", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Shamez N Ladhani", - "author_inst": "Public Health England" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.06.03.21258283", "rel_title": "Safety of COVID-19 vaccines, their components or their platforms for pregnant women: A rapid review", @@ -711527,6 +713403,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.03.21258276", + "rel_title": "Virtual care and the impact of COVID-19 on nursing: A single centre evaluation", + "rel_date": "2021-06-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.03.21258276", + "rel_abs": "AimsThe overall aim of this evaluation was to look at the impact of the changes in working practices during the pandemic on nurses. This secondary analysis provided an evaluation of virtual care and being able/required to work from home.\n\nDesignThis was secondary analysis of an evaluation using semi-structured interviews.\n\nMethodsConducted at a single National Health Service (NHS) university hospital in the United Kingdom between May-July 2020. Forty-eight operational leads and nurses participated in semi-structured interviews which were digitally recorded, transcribed verbatim and analysed using a framework analysis.\n\nResultsTwo overarching themes emerged relating to the patient experience and nursing experience. There were both positive and negative elements associated with virtual care and remote working related to these themes. However, the majority of nurses found virtual clinics were useful when proper resources were provided, and managerial strategies were put in place to support them. Participants felt virtual care could benefit many but not all patient groups moving forward, and that flexibility around working from home would be desirable in the future.\n\nConclusionVirtual care and remote working were implemented to accommodate the restrictions imposed because of the pandemic. The benefits of these changes to nurses and patients support these being business as usual. However, clear policies are needed to ensure nurses feel supported when working remotely and there are robust assessments in place to ensure virtual care is provided to patients who have access to the necessary technology.\n\nImpactThis was a study of the move to virtual care and remote working during the COVID-19 pandemic. Telemedicine and flexible working were not common in the NHS prior to the pandemic but the current evaluation supports the role out of these as standard care with policies in place to ensure nurses and patients are appropriately supported.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Luke Hughes", + "author_inst": "University College London Hospitals NHS Foundation Trust" + }, + { + "author_name": "Anika Petrella", + "author_inst": "University College London Hospitals NHS Foundation Trust" + }, + { + "author_name": "Natasha Phillips", + "author_inst": "NHSx" + }, + { + "author_name": "Rachel M Taylor", + "author_inst": "University College London Hospitals NHS Foundation Trust" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "nursing" + }, { "rel_doi": "10.1101/2021.06.03.21258302", "rel_title": "Comparative Household Secondary Attack Rates associated with B.1.1.7, B.1.351, and P.1 SARS-CoV-2 Variants", @@ -712407,41 +714314,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.04.21258205", - "rel_title": "Serial intervals observed in SARS-CoV-2 B.1.617.2 variant cases", - "rel_date": "2021-06-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.04.21258205", - "rel_abs": "Rapid growth of the SARS-CoV-2 variant B.1.617.2 has been observed in many countries. The factors driving the recent rapid growth of COVID-19 cases could be attributed to shorten generation intervals or higher transmissibility (effective reproduction number, R), or both. Establishing the reasons for the observed rapid growth is key for outbreak control. In this study, we analysed the serial interval of household transmission pairs infected with SARS-CoV-2 B.1.617.2 variant and compared with those who were infected prior to the occurrence of the major global SARS-CoV-2 variants. After controlling for confounding factors, our findings suggest no significant changes in the serial intervals for SARS-CoV-2 cases infected with the B.1.617.2 variant. This, in turn, lends support for the hypothesis of a higher R in B.1.617.2 cases.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Rachael Pung", - "author_inst": "Ministry of Health, Singapore; Centre for the Mathematical Modelling of infectious Diseases, and Department of Infectious Disease Epidemiology, London School of" - }, - { - "author_name": "Tze Minn Mak", - "author_inst": "National Public Health Laboratory, National Centre for Infectious Diseases, Singapore" - }, - { - "author_name": "- CMMID COVID-19 Working Group", - "author_inst": "" - }, - { - "author_name": "Adam J Kucharski", - "author_inst": "Centre for the Mathematical Modelling of infectious Diseases, and Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine," - }, - { - "author_name": "Vernon J Lee", - "author_inst": "Ministry of Health, Singapore; Saw Swee Hock School of Public Health, National University of Singapore, Singapore" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.01.21258185", "rel_title": "2020 SARS-CoV-2 diversification in the United States: Establishing a pre-vaccination baseline", @@ -713201,6 +715073,45 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2021.05.31.446403", + "rel_title": "Irradiation of UVC LED at 277 nm inactivates coronaviruses by photodegradation of spike protein.", + "rel_date": "2021-06-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.31.446403", + "rel_abs": "To interrupt SARS-CoV-2 transmission chains, Ultraviolet-C (UVC) irradiation has emerged as a potential disinfection tool to aid in blocking the spread of coronaviruses. While conventional 254-nm UVC mercury lamps have been used for disinfection purposes, other UVC wavelengths have emerged as attractive alternatives but a direct comparison of these tools is lacking with the inherent mechanistic properties unclear. Our results using human coronaviruses, hCoV-229E and hCoV-OC43, have indicated that 277-nm UVC LED is most effective in viral inactivation, followed by 222-nm far UVC and 254-nm UVC mercury lamp. While UVC mercury lamp is more effective in degrading viral genomic content compared to 277-nm UVC LED, the latter results in a pronounced photo-degradation of spike proteins which potentially contributed to the higher efficacy of coronavirus inactivation. Hence, inactivation of coronaviruses by 277-nm UVC LED irradiation constitutes a more promising method for disinfection.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Qunxiang Ong", + "author_inst": "Institute of Molecular and Cell Biology, A*STAR" + }, + { + "author_name": "J.W. Ronnie Teo", + "author_inst": "Singapore Institute of Manufacturing Technology (SIMTech), A*STAR" + }, + { + "author_name": "Joshua Dela Cruz", + "author_inst": "Institute of Molecular and Cell Biology, A*STAR" + }, + { + "author_name": "Elijah Wee", + "author_inst": "Institute of Molecular and Cell Biology, A*STAR" + }, + { + "author_name": "Winson Wee", + "author_inst": "Institute of Molecular and Cell Biology, A*STAR" + }, + { + "author_name": "Weiping Han", + "author_inst": "Institute of Molecular and Cell Biology, A*STAR" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2021.06.02.21257981", "rel_title": "COVID-19 Sniffer Dog experimental training: which protocol and which implications for reliable identification?", @@ -714425,61 +716336,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.03.21258128", - "rel_title": "What most influences severity and death of COVID-19 patients in Brazil? Is it clinical, social, or demographic factors? An observational study.", - "rel_date": "2021-06-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.03.21258128", - "rel_abs": "ObjectiveThis study aimed to assess the space distribution and factors associated with the risk of severe acute respiratory syndrome (SARS) and death in COVID-19 patients, based on routine register data; and to develop and validate a predictive model of the risk of death from COVID-19.\n\nMethodsA cross-sectional, epidemiological study of positive SARS-CoV-2 cases, reported in the south region of the city of Sao Paulo, SP, Brazil, from March 2020 to February 2021. Data were obtained from the official reporting databases of the Brazilian Ministry of Health for influenza-like illness (ILI) (esus-VE, in Portuguese) and for patients hospitalized for SARS (SIVEP-Gripe). The space distribution of cases is described by 2D kernel density. To assess potential factors associated with the outcomes of interest, generalized linear and additive logistic models were adjusted. To evaluate the discriminatory power of each variable studied as well as the final model, C-statistic was used (area under the receiver operating characteristics curve). Moreover, a predictive model for risk of death was developed and validated with accuracy measurements in the development, internal and temporal (March and April 2021) validation samples.\n\nResultsA total of 16,061 patients with confirmed COVID-19 were enrolled. Morbidities associated with a higher risk of SARS were obesity (OR=25.32) and immunodepression (OR=12.15). Morbidities associated with a higher risk of death were renal disease (OR=11.8) and obesity (OR=8.49), and clinical and demographic data were more important than the territory per se. Based on the data, a calculator was developed to predict the risk of death from COVID-19, with 92.2% accuracy in the development sample, 92.3% in the internal validation sample, and 80.0% in the temporal validation sample.\n\nConclusionsThe risk factors for SARS and death in COVID-19 patients seeking health care, in order of relevance, were age, comorbidities, and socioeconomic factors, considering each discriminatory power.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Ana Carolina Cintra Nunes Mafra", - "author_inst": "Hospital Israelita Albert Einstein" - }, - { - "author_name": "R\u00e9gis Rodrigues Vieira", - "author_inst": "Hospital Israelita Albert Einstein" - }, - { - "author_name": "Camila Nascimento Monteiro", - "author_inst": "Hospital Israelita Albert Einstein" - }, - { - "author_name": "Denise de Fatima Barros Cavalcante", - "author_inst": "Hospital Israelita Albert Einstein" - }, - { - "author_name": "Jo\u00e3o Luiz Miraglia", - "author_inst": "Hospital Israelita Albert Einstein" - }, - { - "author_name": "Daiana Bonfim", - "author_inst": "Hospital Israelita Albert Einstein" - }, - { - "author_name": "Danielle Costa Palacio", - "author_inst": "Hospital Israelita Albert Einstein" - }, - { - "author_name": "Alessandra Cristina Ferreira Martins", - "author_inst": "Hospital Israelita Albert Einstein" - }, - { - "author_name": "Leticia Yamawaka de Almeida", - "author_inst": "Hospital Israelita Albert Einstein" - }, - { - "author_name": "Jo\u00e3o Peres Neto", - "author_inst": "Hospital Israelita Albert Einstein" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.02.21258203", "rel_title": "The INDSCI-SIM model for COVID-19 in India", @@ -715395,6 +717251,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2021.05.28.21258022", + "rel_title": "Is my cough a cold or covid? A qualitative study of COVID-19 symptom recognition and attitudes towards testing in the UK", + "rel_date": "2021-06-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.28.21258022", + "rel_abs": "ObjectiveKey to reducing the spread of COVID-19 in the UK is increased use of the NHS Test and Trace (NHSTT) system. This study explored one of the main issues that determine whether people engage with NHSTT, how people understand symptoms that may indicate the presence of COVID-19 and that should trigger a request for a test.\n\nMethodsIn this qualitative study, a series of semi-structured telephone interviews were conducted with 40 people (21 members of the general population, 19 students). There was nearly an equal split between male and female participants in both populations. Data were collected between 30 November and 11 December 2020 and explored using thematic analysis. There was substantial similarity in responses for both populations so we combined our results and highlighted where differences were present.\n\nResultsParticipants generally had good knowledge of the main symptoms of COVID-19 (high temperature, new, persistent cough, anosmia) but had low confidence in their ability to differentiate them from symptoms of other illnesses. Attribution of symptoms to COVID-19 was most likely where the symptoms were severe, many symptoms were present, symptoms had lasted for some time and when perceived risk of exposure to infection was high due to previous contact with others. Participants felt encouraged to engage in testing where symptoms were present and had persisted for several days, though many had concerns about the safety of testing centres and the accuracy of test results. Students had mixed feelings about mass asymptomatic testing, seeing it as a way to access a more normal student experience, but also a potential waste of resources.\n\nConclusionsThis study offers novel insights into how people attribute symptoms to COVID-19 and barriers and facilitators to engaging with testing. Participants had positive views of testing, but there is a need to improve not just recognition of each main symptom, but also understanding that even single, mild symptoms may necessitate a test rather than a \"wait and see\" approach, and to address concerns around test accuracy to increase testing uptake.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Fiona Mowbray", + "author_inst": "King's College London" + }, + { + "author_name": "Lisa Woodland", + "author_inst": "King's College London" + }, + { + "author_name": "Louise E Smith", + "author_inst": "King's College London" + }, + { + "author_name": "Richard Amlot", + "author_inst": "Public Health England" + }, + { + "author_name": "G James Rubin", + "author_inst": "King's College London" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.05.31.21256946", "rel_title": "Confirmed COVID-19 cases per economic activity during Autumn wave in Belgium", @@ -716387,33 +718278,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.05.30.21258074", - "rel_title": "COVID-19 vaccine acceptance and its socio-demographic and emotional determinants: a multi-country cross-sectional study", - "rel_date": "2021-06-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.30.21258074", - "rel_abs": "BackgroundMultiple COVID-19 vaccines have now been licensed for human use, with other candidate vaccines in different stages of development. Effective and safe vaccines against COVID-19 are essential to achieve global control of the pandemic caused by severe acute respiratory coronavirus 2 (SARS-CoV-2), but multiple factors, including vaccine supply and vaccine confidence, will be key for high rates of global uptake. Confidence in COVID-19 vaccines, socio-demographic status, and recent emotional status are likely to be key drivers of COVID-19 vaccine acceptance. In this study, we explore these determinants of COVID-19 vaccination intent across17 countries worldwide.\n\nMethodsIn this large-scale multi-country study, we explore intent to accept a COVID-19 vaccine and the socio-demographic and emotional determinants of uptake for 17 countries and over 19,000 individuals surveyed in June and July 2020 via nationally representative samples. We used Bayesian ordinal logistic regressions to probe the relationship between intent to accept a COVID-19 vaccine and individuals socio-demographic status, their confidence in COVID-19 vaccines, and their recent emotional status. Gibbs sampling was used for Bayesian model inference, with 95% Bayesian highest posterior density intervals used to capture uncertainty.\n\nFindingsIntent to accept a COVID-19 vaccine is highest in India, where 77.8% (95% HPD, 75.5 to 80.0%) of respondents strongly agreeing that they would take a new COVID-19 vaccine if it were available. The Democratic Republic of Congo (15.5%, 12.2 to 18.6%) and France (26.4%, 23.7 to 29.2%) have the lowest share of respondents who strongly agree that they would accept a COVID-19. Confidence in the safety, importance, and effectiveness of COVID-19 vaccines are the most widely informative determinants of vaccination intent. Socio-demographic and emotional determinants played a lesser role, with being male and having higher education was associated with increased uptake intent in five countries and being fearful of catching COVID-19 also a strong determinant of uptake intent.\n\nInterpretationBarriers to COVID-19 vaccine acceptance will be highly country and context dependent. These findings highlight the importance of regular monitoring of COVID-19 vaccine confidence to identify groups less likely to vaccinate and to monitor the impact of vaccination policies on uptake behaviour.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Alex de Figueiredo", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Clarissa Simas", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Heidi J Larson", - "author_inst": "London School of Hygiene and Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.05.29.21257899", "rel_title": "COVID Oximetry @home: evaluation of patient outcomes", @@ -717077,6 +718941,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.05.31.21258031", + "rel_title": "The COVID-19 pandemic shifted the Veterans Affairs System toward being a payer and virtual care provider: is it sustainable?", + "rel_date": "2021-06-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.31.21258031", + "rel_abs": "Structured AbstractO_ST_ABSObjectiveC_ST_ABSTo examine how VA shifted care delivery methods one year into the pandemic.\n\nStudy SettingAll encounters paid or provided by VA between January 1, 2019 and February 27, 2021.\n\nStudy DesignWe aggregated all VA paid or provided encounters and classified them into community (non-VA) acute and non-acute visits, VA acute and non-acute visits, and VA virtual visits. We then compared the number of encounters by week over time to pre-pandemic levels.\n\nData Extraction MethodsAggregation of administrative VA claims and health records.\n\nPrincipal FindingsVA has experienced a dramatic and persistent shift to providing virtual care and purchasing care from non-VA providers. Before the pandemic, a majority (63%) of VA care was provided in-person at a VA facility. One year into the pandemic, in-person care at VAs constituted just 33% of all visits. Most of the difference made up by large expansions of virtual care; total VA provided visits (in person and virtual) declined (4.9 million to 4.2 million) while total visits of all types declined only 3.5%. Community provided visits exceeded prepandemic levels (2.3 million to 2.9 million, +26%).\n\nConclusionUnlike private health care, VA has resumed in-person care slowly at its own facilities, and more rapidly in purchased care with different financial incentives a likely driver. The very large expansion of virtual care nearly made up the difference. With a widespread physical presence across the U.S., this has important implications for access to care and future allocation of medical personnel, facilities, and resources.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Liam Rose", + "author_inst": "Department of Veterans Affairs" + }, + { + "author_name": "Linda Diem Tran", + "author_inst": "Department of Veterans Affairs" + }, + { + "author_name": "Steven M Asch", + "author_inst": "Stanford University/Department of Veterans Affairs" + }, + { + "author_name": "Anita Vashi", + "author_inst": "Department of Veterans Affairs / University of California, San Francisco" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2021.05.31.21257367", "rel_title": "A one-step real-time RT-PCR assay for simultaneous typing of SARS-CoV-2 mutations associated with the E484K and N501Y spike protein amino-acid substitutions", @@ -718217,29 +720112,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.30.21257992", - "rel_title": "Reliability of wastewater analysis for monitoring COVID-19 incidence revealed by a long-term follow-up study", - "rel_date": "2021-06-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.30.21257992", - "rel_abs": "BackgroundWastewater-based epidemiology has been used for monitoring human activities and waterborne pathogens. Although wastewaters can also be used for tracking SARS-CoV-2 at the population level, the reliability of this approach remains to be established, especially for early warning of outbreaks.\n\nMethodsWe collected 377 samples from different treatment plants processing wastewaters of >1 million inhabitants in Valencia, Spain, between April 2020 and March 2021. Samples were cleaned, concentrated, and subjected to RT-qPCR to determine SARS-CoV-2 concentrations. These data were compared with cumulative disease notification rates over 7 and 14 day periods.\n\nResultsWe amplified SARS-CoV-2 RNA in 75% of the RT-qPCRs, with an estimated detection limit of 100 viral genome copies per liter (gc/L). SARS-CoV-2 RNA concentration correlated strongly with disease notification rates over 14-day periods (Pearson r = 0.962, P < 0.001). A concentration >1000 gc/L showed >95% sensitivity and specificity as an indicator of more than 25 new cases per 100,000 inhabitants. Albeit with slightly higher uncertainty, these figures were reproduced using a 7-day period. Time series were similar for wastewaters data and declared cases, but wastewater RNA concentrations exhibited transient peaks that were not observed in declared cases and preceded major outbreaks by several weeks.\n\nInterpretationWastewater analysis provides a reliable tool for monitoring COVID-19, particularly at low incidence values, and is not biased by asymptomatic cases. Moreover, this approach might reveal previously unrecognized features of COVID-19 transmission.\n\nFundingConselleria dAgricultura, Desenvolupament Rural, Emergencia Climatica i Transicio Ecologica of the Generalitat Valenciana (project OTR2020-20593SUBDI), Instituto de Salud Carlos III (FONDO-COVID19 COV20/00210), CSIC (Salud Global CSIC 202020E292), and Ministerio de Ciencia e Innovacion (Ramon y Cajal contract, Call 2019).", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Rafael Sanjuan", - "author_inst": "Insitute for Integrative Systems Biology (Universitat de Valencia-CSIC)" - }, - { - "author_name": "Pilar Domingo-Calap", - "author_inst": "Institute for Integrative Systems Biology (Universitat de Valencia-CSIC)" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.05.30.21258079", "rel_title": "Stopping the misinformation: BNT16b2 COVID-19 vaccine has no negative effect on women's fertility", @@ -718879,6 +720751,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2021.06.01.446555", + "rel_title": "Endomembrane systems are reorganized by ORF3a and Membrane (M) of SARS-CoV-2", + "rel_date": "2021-06-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.01.446555", + "rel_abs": "The endomembrane reticulum (ER) is largely reorganized by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 ORF3a and membrane (M) protein expression affects ER-derived structures including cubic membrane and double membrane vesicles in coronavirus-infected cells; however, the molecular mechanisms underlying ER remodeling remain unclear. We introduced a \"plug and playable\" proximity labeling tool (TurboID-GBP) for interactome mapping of GFP-tagged SARS-CoV-2 ORF3a and M proteins. Through mass spectrometric identification of the biotinylated lysine residue (K+226 Da) on the viral proteins using Spot-TurboID workflow, 117 and 191 proteins were robustly determined as ORF3a and M interactomes, respectively, and many, including RNF5 (E3 ubiquitin ligase), overlap with the mitochondrial-associated membrane (MAM) proteome. RNF5 expression was correlated to ORF3a ubiquitination. MAM formation and secreted proteome profiles were largely affected by ORF3a expression. Thus, SARS-CoV-2 may utilize MAM as a viral assembly site, suggesting novel anti-viral treatment strategies for blocking viral replication in host cells.\n\nHighlightsO_LISARS-CoV-2 proteins ORF3a and M alter endoplasmic reticulum proteome profile\nC_LIO_LIORF3a affects mitochondrial-associated membrane formation\nC_LIO_LISARS-CoV-2 may utilize mitochondrial-associated membrane as viral assembly site\nC_LIO_LIORF3a and M interactome proteins may serve as targets for COVID-19 treatment\nC_LI\n\neTOC BlurbER remodelling by SARS-CoV-2 ORF3a and M protein", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Yun-Bin Lee", + "author_inst": "Seoul National University" + }, + { + "author_name": "Minkyo Jung", + "author_inst": "Korea Brain Research Institute" + }, + { + "author_name": "Jeesoo Kim", + "author_inst": "Seoul National University" + }, + { + "author_name": "Myeong-Gyun Kang", + "author_inst": "Seoul National University" + }, + { + "author_name": "Chulhwan Kwak", + "author_inst": "Seoul National University" + }, + { + "author_name": "Jong-Seo Kim", + "author_inst": "Seoul National University" + }, + { + "author_name": "Ji-Young Mun", + "author_inst": "Korea Brain Research Institute" + }, + { + "author_name": "Hyun-Woo Rhee", + "author_inst": "Seoul National University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2021.06.01.446181", "rel_title": "Characterization of SARS2 Nsp15 Nuclease Activity Reveals it's Mad About U", @@ -719627,33 +721546,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.05.29.446272", - "rel_title": "Kite-shaped molecules block SARS-CoV-2 cell entry at a post-attachment step", - "rel_date": "2021-05-31", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.29.446272", - "rel_abs": "Anti-viral small molecules are currently lacking for treating coronavirus infection. The long development timescales for such drugs are a major problem, but could be shortened by repurposing existing drugs. We therefore screened a small library of FDA-approved compounds for potential severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) antivirals using a pseudovirus system that allows a sensitive read-out of infectivity. A group of structurally-related compounds, showing moderate inhibitory activity with IC50 values in the 1-5{micro}M range, were identified. Further studies demonstrated that these kite-shaped molecules were surprisingly specific for SARS-CoV and SARS-CoV-2 and that they acted early in the entry steps of the viral infectious cycle, but did not affect virus attachment to the cells. Moreover the compounds were able to prevent infection in both kidney- and lung-derived human cell lines. The structural homology of the hits allowed the production of a well-defined pharmacophore that was found to be highly accurate in predicting the anti-viral activity of the compounds in the screen. We discuss the prospects of repurposing these existing drugs for treating current and future coronavirus outbreaks.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Shiu-Wan Chan", - "author_inst": "The University of Manchester" - }, - { - "author_name": "Talha Shafi", - "author_inst": "The University of Manchester" - }, - { - "author_name": "Robert Ford", - "author_inst": "The University of Manchester" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.05.31.21258081", "rel_title": "Favorable outcome on viral load and culture viability using Ivermectin in early treatment of non-hospitalized patients with mild COVID-19, A double-blind, randomized placebo-controlled trial.", @@ -720352,6 +722244,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2021.05.27.21257931", + "rel_title": "Estimates of cases and hospitalizations averted by COVID-19 case investigation and contact tracing in 14 health jurisdictions in the United States", + "rel_date": "2021-05-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.27.21257931", + "rel_abs": "ContextThe implementation of case investigation and contact tracing (CICT) for controlling COVID-19 (caused by SARS-Cov-2 virus) has proven challenging due to varying levels of public acceptance and initially constrained resources, especially enough trained staff. Evaluating the impacts of CICT will aid efforts to improve such programs.\n\nObjectivesEstimate the number of COVID-19 cases and hospitalizations averted by CICT and identify CICT processes that could improve overall effectiveness.\n\nDesignWe used data on proportion of cases interviewed, contacts notified or monitored, and days from testing to contact notification from 14 jurisdictions to model the impact of CICT on cumulative cases counts and hospitalizations over a 60-day period. Using the Centers for Disease Control and Prevention (CDC)s COVIDTracer tool, we estimated a range of impacts by assuming either contacts would quarantine only if monitored or would do so upon notification of potential exposure. We also varied the observed program metrics to assess their relative influence.\n\nResultsPerformance by jurisdictions varied widely. Jurisdictions isolated between 12 and 86% of cases (including contacts which became cases) within 6 to 10 days after exposure-and-infection. We estimated that CICT-related reductions in transmission ranged from 0.4% to 32%. For every 100 cases prevented by nonpharmaceutical interventions, CICT averted between 4 and 97 additional cases. Reducing time to case isolation by one day increased averted case estimates by up to 15 percentage points. Increasing the proportion of cases interviewed or contacts notified by 20 percentage points each resulted in at most 3 or 6 percentage point improvements in averted cases.\n\nConclusionsWe estimated that case investigation and contact tracing reduced the number of COVID-19 cases and hospitalizations among all jurisdictions studied. Reducing time to isolation produced the greatest improvements in impact of CICT.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Seonghye Jeon", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Gabriel Rainisch", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Ryan Lash", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Patrick K Moonan", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "John E Oeltmann", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Bradford Greening Jr.", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Bishwa B Adhikari", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Martin I Meltzer", + "author_inst": "Centers for Disease Control and Prevention" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2021.05.28.21257973", "rel_title": "CoMix: Changes in social contacts as measured by the contact survey during the 1 COVID-19 pandemic in England between March 2020 and March 2021", @@ -721288,45 +723227,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2021.05.27.21257940", - "rel_title": "The rapid reemergence of seasonal respiratory viruses in Houston, Texas, after relaxing COVID-19 restrictions", - "rel_date": "2021-05-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.27.21257940", - "rel_abs": "Brief abstractImplementation of measures to limit the spread of the SARS-CoV-2 virus at the start of the COVID-19 pandemic resulted in a rapid decrease in all other respiratory pathogens. As COVID-19 containment measures were relaxed, the first non-COVID respiratory viruses to return to prepandemic levels were members of the rhinovirus/enterovirus, followed by the rapid return of seasonal coronaviruses, parainfluenza, and respiratory syncytial virus after the complete removal of COVID-19 precautions at the state level, including an end to mask mandates. Inasmuch as COVID-19 has dominated the landscape of respiratory infections since early 2020, it is important for clinicians to recognize the return of non-COVID respiratory pathogens may be rapid and significant when COVID-19 containment measures are removed.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Parsa Hodjat", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Paul Christensen", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Sishir Subedi", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Randall James Olsen", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "David W Bernard", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Scott Wesley Long", - "author_inst": "Houston Methodist Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pathology" - }, { "rel_doi": "10.1101/2021.05.27.21257896", "rel_title": "The indirect effect of mRNA-based Covid-19 vaccination on unvaccinated household members", @@ -722034,6 +723934,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2021.05.26.21257862", + "rel_title": "Spatially refined time-varying reproduction numbers of SARS-CoV-2 in Arkansas and Kentucky and their relationship to population size and public health policy, March - November, 2020", + "rel_date": "2021-05-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.26.21257862", + "rel_abs": "PurposeTo examine the time-varying reproduction number, Rt, for COVID-19 in Arkansas and Kentucky and investigate the impact of policies and preventative measures on the variability in Rt.\n\nMethodsArkansas and Kentucky county-level COVID-19 cumulative case count data (March 6-November 7, 2020) were obtained. Rt was estimated using the R package EpiEstim, by county, region (Delta, non-Delta, Appalachian, non-Appalachian), and policy measures.\n\nResultsThe Rt was initially high, falling below 1 in May or June depending on the region, before stabilizing around 1 in the later months. The median Rt for Arkansas and Kentucky at the end of the study were 1.15 (95% credible interval [CrI], 1.13, 1.18) and 1.10 (95% CrI, 1.08, 1.12), respectively, and remained above 1 for the non-Appalachian region. Rt decreased when facial coverings were mandated, changing by -10.64% (95% CrI, -10.60%, -10.70%) in Arkansas and -5.93% (95% CrI, -4.31%, -7.65%) in Kentucky. The trends in Rt estimates were mostly associated with the implementation and relaxation of social distancing measures.\n\nConclusionsArkansas and Kentucky maintained a median Rt above 1 during the entire study period. Changes in Rt estimates allows quantitative estimates of potential impact of policies such as facemask mandate.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Maria D. Politis", + "author_inst": "University of Arkansas for Medical Sciences" + }, + { + "author_name": "Xinyi Hua", + "author_inst": "Georgia Southern University Jiann-Ping Hsu College of Public Health" + }, + { + "author_name": "Chigozie A. Ogwara", + "author_inst": "Georgia Southern University Jiann-Ping Hsu College of Public Health" + }, + { + "author_name": "Margaret R. Davies", + "author_inst": "Georgia Southern University Jiann-Ping Hsu College of Public Health" + }, + { + "author_name": "Temitayo M. Adebile", + "author_inst": "Georgia Southern University Jiann-Ping Hsu College of Public Health" + }, + { + "author_name": "Maya P. Sherman", + "author_inst": "Georgia Southern University Jiann-Ping Hsu College of Public Health" + }, + { + "author_name": "Xiaolu Zhou", + "author_inst": "Texas Christian University" + }, + { + "author_name": "Gerardo Chowell", + "author_inst": "Georgia State University School of Public Health" + }, + { + "author_name": "Anne C. Spaulding", + "author_inst": "Emory University Rollins School of Public Health" + }, + { + "author_name": "Isaac Chun-Hai Fung", + "author_inst": "Georgia Southern University Jiann-Ping Hsu College of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.05.26.21257844", "rel_title": "The real-life impact of vaccination on COVID-19 mortality in Europe and Israel", @@ -723014,37 +724969,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.05.28.446137", - "rel_title": "Mutational hotspot in the SARS-CoV-2 Spike protein N-terminal domain conferring immune escape potential", - "rel_date": "2021-05-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.28.446137", - "rel_abs": "Global efforts are being taken to monitor the evolution of SARS-CoV-2, aiming at early identification of mutations with the potential of increasing viral infectivity or virulence. We report a striking increase in the frequency of recruitment of diverse substitutions at a critical residue (W152), positioned in the N-terminal domain (NTD) of the Spike protein, observed repeatedly across independent phylogenetic and geographical contexts. We investigate the impact these mutations might have on the evasion of neutralizing antibodies. Finally, we uncover that NTD is a region exhibiting particularly high frequency of mutation recruitments, suggesting an evolutionary path on which the virus maintains optimal efficiency of ACE2 binding combined with the flexibility facilitating the immune escape.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Slawomir Kubik", - "author_inst": "SOPHiA GENETICS" - }, - { - "author_name": "Nils Arrigo", - "author_inst": "SOPHiA GENETICS" - }, - { - "author_name": "Jaume Bonet", - "author_inst": "SOPHiA GENETICS" - }, - { - "author_name": "Zhenyu Xu", - "author_inst": "SOPHiA GENETICS" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2021.05.28.446149", "rel_title": "Decomposition of the SARS-CoV-2-ACE2 interface reveals a common trend among emerging viral variants", @@ -723591,6 +725515,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.25.21257770", + "rel_title": "Early transfusion of convalescent plasma improves the clinical outcome in severe SARS-CoV2 infection", + "rel_date": "2021-05-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.25.21257770", + "rel_abs": "Plasma harvested from convalescent COVID-19 patients (CCP) has been applied as first-line therapy in the early phase of the SARS-CoV2 pandemic through clinical studies using various protocols. We present data from a cohort of 267 hospitalized, severe COVID-19 patients who received CCP. No transfusion-related complications were reported, indicating the overall safety of CCP therapy. Patients who eventually died from COVID-19 received CCP significantly later (3.95 versus 5.22 days after hospital admission) and had higher interleukin 6 (IL-6) levels (28.9 pg/ml versus 102.5 pg/ml) than those who survived. In addition, CCP-transfusion caused a significant reduction in the overall inflammatory status of the patients regardless of the severity of disease or outcome, as evidenced by decreasing C-reactive protein, IL6 and ferritin levels. We conclude that, CCP-transfusion is a safe and effective supplementary treatment modality for hospitalized COVID-19 patients characterized by better expected outcome if applied as early as possible. We also observed that, IL-6 may be a suitable laboratory parameter for patient selection and monitoring of CCP therapy effectiveness.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Eszter Fodor", + "author_inst": "University of Physical Education" + }, + { + "author_name": "Veronika Muller", + "author_inst": "Semmelweis University, Department of Pulmonology" + }, + { + "author_name": "Zsolt Ivanyi", + "author_inst": "Semmelweis University, Department of Anesthesiology and Intensive Therapy" + }, + { + "author_name": "Timea Berki", + "author_inst": "University of Pecs, Department of Immunology and Biotechnology" + }, + { + "author_name": "Olga Pella Kuten", + "author_inst": "Orthosera kft." + }, + { + "author_name": "Mira Ambrus", + "author_inst": "University of Physical Education" + }, + { + "author_name": "Agnes Sarkany", + "author_inst": "Szent Gyorgy University Teaching Hospital" + }, + { + "author_name": "Arpad Skazel", + "author_inst": "Szent Gyorgy University Teaching Hospital" + }, + { + "author_name": "Agnes Madar", + "author_inst": "University of Physical Education" + }, + { + "author_name": "Dorottya Kardos", + "author_inst": "Research Center Natural Sciences" + }, + { + "author_name": "Gabor Kemenesi", + "author_inst": "University of Pecs" + }, + { + "author_name": "Fanni Foldes", + "author_inst": "Univesity of Pecs, Szentagothai Research Center, National Laboratory of Virology," + }, + { + "author_name": "Sandor Nagy", + "author_inst": "Hungarian National Blood Transfusion Service" + }, + { + "author_name": "Andrea Matusovits", + "author_inst": "Hungarian National Blood Transfusion Service" + }, + { + "author_name": "Janos Nacsa", + "author_inst": "Hungarian National Blood Transfusion Service" + }, + { + "author_name": "Attila Tordai", + "author_inst": "Semmelweis University, Department of Translational Medicine" + }, + { + "author_name": "Ferenc Jakab", + "author_inst": "University of Pecs, Szentagothai Research Centre" + }, + { + "author_name": "Zsombor Lacza", + "author_inst": "University of Physical Education" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.25.21257783", "rel_title": "Development and performance of a population-based risk stratification model for COVID-19", @@ -724675,129 +726686,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.25.21257772", - "rel_title": "SARS-CoV-2 Antibody Testing in Healthcare Workers: a comparison of the clinical performance of three commercially available antibody assays", - "rel_date": "2021-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.25.21257772", - "rel_abs": "SARS-CoV-2 antibodies are an excellent indicator of past COVID-19 infection. As the COVID-19 pandemic progresses, retained sensitivity over time is an important quality in an antibody assay that is to be used for the purpose of population seroprevalence studies.\n\nWe compared 5788 healthcare worker (HCW) serum samples on two serological assays (Abbott SARS-CoV-2 anti-nucleocapsid IgG and Roche Anti-SARS-CoV-2 anti-nucleocapsid Total Antibody) and a subset of samples (all Abbott assay positive or grayzone, n=485) on Wantai SARS-CoV-2 anti-spike Antibody ELISA. For 367 samples from HCW with previous PCR-confirmed SARS-CoV-2 infection we correlated the timing of infection with assay results.\n\nOverall seroprevalence was 4.2% on Abbott, 9.5% on Roche. Of those with previously confirmed infection, 41% (150/367) and 95% (348/367) tested positive on Abbott and Roche respectively. At 21 weeks (150 days) after confirmed infection, positivity on Abbott started to decline. Roche positivity was retained for the entire study period (33 weeks). Factors associated (P[≤] 0.050) with Abbott seronegativity in those with previous PCR-confirmed infection included sex (male OR0.30;95%CI0.15-0.60), symptom severity (OR0.19 severe symptoms;95%CI0.05-0.61), ethnicity (OR0.28 Asian ethnicity;95%CI0.12-0.60) and time since PCR diagnosis (OR2.06 for infection 6 months previously;95%CI1.01-4.30. Wantai detected all previously confirmed infections.\n\nIn our population, Roche detected antibodies up to at least seven months after natural infection with SARS-CoV-2. This may indicate that Roche is better suited than Abbott to population-based studies. Wantai demonstrated high sensitivity but sample selection was biased. The relationship between serological response and functional immunity to SARS-CoV-2 infection needs to be delineated.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Niamh Allen", - "author_inst": "St. James's Hospital" - }, - { - "author_name": "Melissa Brady", - "author_inst": "European Programme for Intervention Epidemiology Training (EPIET), European Centre for Disease Prevention and Control (ECDC)" - }, - { - "author_name": "Antonio Isidro Carrion Martin", - "author_inst": "University of Murcia School of Medicine" - }, - { - "author_name": "Lisa Domegan", - "author_inst": "Health Protection Surveillance Centre" - }, - { - "author_name": "Cathal Walsh", - "author_inst": "University of Limerick" - }, - { - "author_name": "Elaine Houlihan", - "author_inst": "University Hospital Galway" - }, - { - "author_name": "Colm Kerr", - "author_inst": "St. James's Hospital" - }, - { - "author_name": "Lorraine Doherty", - "author_inst": "Health Protection Surveillance Centre" - }, - { - "author_name": "Joanne King", - "author_inst": "University Hospital Galway" - }, - { - "author_name": "Martina Doheny", - "author_inst": "University Hospital Galway" - }, - { - "author_name": "Damian Griffin", - "author_inst": "University Hospital Galway" - }, - { - "author_name": "Maria Molloy", - "author_inst": "University Hospital Galway" - }, - { - "author_name": "Jean Dunne", - "author_inst": "St. James's Hospital" - }, - { - "author_name": "Vivion Crowley", - "author_inst": "St. James's Hospital" - }, - { - "author_name": "Philip Holmes", - "author_inst": "St. James's Hospital" - }, - { - "author_name": "Evan Keogh", - "author_inst": "St. James's Hospital" - }, - { - "author_name": "Sean Naughton", - "author_inst": "St. James's Hospital" - }, - { - "author_name": "Fiona O'Rourke", - "author_inst": "St. James's Hospital" - }, - { - "author_name": "Martina Kelly", - "author_inst": "St. James's Hospital" - }, - { - "author_name": "Yvonne Lynagh", - "author_inst": "St. James's Hospital" - }, - { - "author_name": "Brendan Crowley", - "author_inst": "St. James Hospital" - }, - { - "author_name": "Cillian De Gascun", - "author_inst": "National Virus Reference Laboratory" - }, - { - "author_name": "Paul Holder", - "author_inst": "National Virus Reference Laboratory" - }, - { - "author_name": "Colm Bergin", - "author_inst": "St James hospital, Dublin." - }, - { - "author_name": "Catherine Fleming", - "author_inst": "University Hospital Galway" - }, - { - "author_name": "Una Ni Riain", - "author_inst": "University Hospital Galway" - }, - { - "author_name": "Niall Conlon", - "author_inst": "St. James's Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.25.21257788", "rel_title": "Influence of past infection with SARS-CoV-2 on the response to the BioTech/ Pfizer BNT162b2 mRNA vaccine in health care workers: kinetics and durability of the humoral response", @@ -725849,6 +727737,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.24.21257752", + "rel_title": "Multi-level multi-state modelling applied to hospital admission in mexican patients with COVID-19", + "rel_date": "2021-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.24.21257752", + "rel_abs": "Since the beginning of the SARS-CoV 2 pandemic, healthcare authorities have made clear that it is crucial to track and identify COVID-19 symptoms and seek medical attention in the presence of the first warning signs, as immediate medical attention can improve the patients prognosis. Therefore the present work aims to analyze the risks associated with the time between the patients first symptoms and hospitalization followed by death. A cross-sectional study was performed among Mexican population diagnosed with COVID-19 and hospitalized from March to January 2021. Four different Bayesian models were developed to asses the risk associated with different patient trajectories: symptoms-hospitalization and hospitalization-death. Comorbidities that could worsen the patient outcome were included as linear predictions; these analyses were further broken down to the different states of the Mexican Republic and the healthcare providers within. Model III was chosen as the best performance through a validation of leaving one out (LOO). Increased risk for hospitalization was observed at the global population level for chronic renal disease, whereas for death such was the case for COPD and the interaction of diabetes:hypertension:obesity. Our results show that there are differences in mortality between the states without accounting for institution and it is related to the prompt time of death or viceversa. Regarding the 6 healthcare providers included in the analysis differences were also found. While state-managed hospitals and private sector showed lower risks, in contrast the IMSS seems to be the one with the highest risk. The proposed modelling can be helpful to improve healthcare assistance at a regional level, additionally it could inform statistical parameter inference in epidemiological models.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Juan Pablo Diaz-Martinez", + "author_inst": "University of Toronto" + }, + { + "author_name": "Karen Janik Orozco-Becerril", + "author_inst": "UNAM" + }, + { + "author_name": "Marco Antonio Gallegos-Herrada", + "author_inst": "UNAM" + }, + { + "author_name": "Ruth Fuentes-Garcia", + "author_inst": "UNAM" + }, + { + "author_name": "Mayra Alejandra Gutierrez-Garcia", + "author_inst": "UNAM" + }, + { + "author_name": "Osvaldo Espin-Garcia", + "author_inst": "University of Toronto" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.05.26.445880", "rel_title": "Evidence of neutralizing antibodies against SARS-CoV-2 in domestic cats living with owners with a history of COVID-19 in Lima, Peru", @@ -726597,41 +728524,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.05.19.21257317", - "rel_title": "Adverse events and their association with comorbidities after first and second doses of Covishield vaccination among healthcare workers of Government owned medical colleges in Kerala", - "rel_date": "2021-05-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.19.21257317", - "rel_abs": "BackgroundA bridging study in the population was not existing at the time of introduction of Covishield vaccine in the state of Kerala A monitoring network for adverse events which was already in place ensured the reporting of serious adverse events following vaccination, but the recording of symptom profile and timeline of symptoms along with the comorbidity status of the individual recipients needed a further database.\n\nAimsTo find the proportion of vaccine recipients with adverse events following the first and second doses of Covishield vaccination along with assessment of the symptom profile and timeline of appearance of symptoms following vaccination with each dose along with association of adverse events with comorbidity status of the respondents.\n\nMaterials & MethodsCross-sectional study with secondary data taken from the AEFI database of the Covid Cell, Directorate of Medical Education of the Kerala state.The database is formed with responses collected as online self-reporting forms collected from the health workers (doctors, nurses, students, paramedical, housekeeping and clerical staff) who received vaccination from vaccination centres in government owned Medical Colleges in Kerala for a period of three months from the date of rolling out vaccination in the state.\n\nResultsA total of 4402 healthworkers submitted the forms after taking the vaccination,either first dose or second dose.Out of this 3656(83.1%)responders were after first dose and 746(16.9%)participants responded after second dose 63.3% respondents after first dose & 24.3% after second dose reported they had experienced adverse events following vaccination with first or second dose of the vaccine respectively.The first symptom to be noticed in those who reported the adverse event after first dose was body ache (17.9%) followed by headache in 15.1 % of participants. 11% (403 out of 3656)of the responders after first dose were having comorbidities and 8.3 % were taking concomitant medications. History of being an asthmatic was found to be of increased risk for developing symptoms following first dose of vaccination(p value 0.004, OR-1.269,95% CI 1.127-1.429) whereas diabetes mellitus is not identified as a risk factor for development of adverse events though a significant association is found,might be due to a decreased reactogenicity.Among those who responded after receiving second dose of vaccination,24.3% reported they had adverse events(at least one post vaccination symptom),of which the first symptom experienced was headache (25.5%),followed by fever(20.9%) as compared to bodyache and headache after the first dose.\n\nConclusions56.7% of those who responded after receiving either first or second dose of the vaccine developed at least one symptom afterwards (63.3% after first and 24.3% after second dose of the vaccine respectively)with mean duration of appearance of symptoms being 8.5 hours and for majority of respondents the symptoms lasted for a day only.The first symptom to appear was bodyache (first dose),fever(in second dose) Though 8.5% respondents had a history of previous Covid infection it had no association with adverse events.Symptoms like chestpain,dry mouth, breathing difficulty which are not being spelled out in Covishield factsheet, has also been reported by the study respondents.Seizures were also reported as an adverse event by the responders", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Remlabeevi A", - "author_inst": "Directorate of Medical Education Kerala" - }, - { - "author_name": "Thomas Mathew", - "author_inst": "Directorate of Medical Education Kerala" - }, - { - "author_name": "Harikumaran Nair", - "author_inst": "Directorate of Medical Education Kerala" - }, - { - "author_name": "Greeshma Lathika Rajasekharan Nair", - "author_inst": "Govt Medical College Thiruvananthapuram" - }, - { - "author_name": "Mariyam Rajee Alex", - "author_inst": "Govt Medical College Konni" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.05.21.21257440", "rel_title": "How COVID-19 challenged care for women and their newborns: a qualitative case study of the experience of Belgian midwives during the first wave of the pandemic", @@ -727283,6 +729175,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2021.05.25.21257637", + "rel_title": "Fear among Syrians: a Proposed Cutoff Score and Validation of the Arabic Fear of COVID-19 Scale- A National Survey", + "rel_date": "2021-05-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.25.21257637", + "rel_abs": "COVID-19 pandemic has led to psychological health issues one of which is fear. This study validates the Arabic version of the fear of COVID-19 scale and suggests a new cutoff score to measure fear of COVID-19 among the Syrian Population. A total of 3989 participants filled an online survey consisting of socio-demographic information, the fear of COVID-19 scale, the patient health questionnaire 9-item, and the generalized anxiety disorder 7-item. Receiver operating characteristic analysis was used to define cutoff scores for the fear of COVID-19 scale in relation to generalized anxiety disorder 7-item and the patient health questionnaire 9-item. The Cronbach value of the Arabic fear of COVID-19 scale was 0.896, revealing good stability and internal consistency. The inter-item correlations were between [0.420 - 0.868] and the corrected item-total correlations were between [0.614 - 0.768]. A cutoff point of 17.5 was deduced from analysis. According to the deduced cutoff point, 2111(52.9%) were classified as cases with extreme fear. This cutoff score deduced from this study can be used for screening purposes to identify individuals that may be most vulnerable towards developing extreme fear of COVID-19. Therefore, early preventive and supportive measures can then be delivered.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Fatema Mohsen", + "author_inst": "Syrian Private University" + }, + { + "author_name": "Batoul Bakkar", + "author_inst": "Syrian Private University" + }, + { + "author_name": "Salma Khadem alsrouji", + "author_inst": "Syrian Private University" + }, + { + "author_name": "Esraa Abbas", + "author_inst": "Syrian Private University" + }, + { + "author_name": "Alma Najjar", + "author_inst": "Syrian Private University" + }, + { + "author_name": "Marah Marrawi", + "author_inst": "Syrian Private University" + }, + { + "author_name": "Youssef Latifeh", + "author_inst": "Syrian Private University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.05.25.21257644", "rel_title": "Engagement with daily testing instead of self-isolating in contacts of confirmed cases of SARS-CoV-2: A qualitative analysis", @@ -728447,25 +730382,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2021.05.20.21257387", - "rel_title": "Deep Covid - Coronavirus Diagnosis Using Deep Neural Networks and Transfer Learning", - "rel_date": "2021-05-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.20.21257387", - "rel_abs": "Coronavirus is a global emergency as of May 2021. If not acted upon by drugs at the right time, coronavirus may result in the death of individuals. Hence early diagnosis is very important along the progress of the disease. This paper focuses on coronavirus detection using x-ray images, for automating the diagnosis pipeline using convolutional neural networks and transfer learning. This could be deployed in places where radiologists are not easily available in order to detect the disease at very early stages. In this study we propose our deep learning architecture for the classification task, which is trained with modified images, through multiple steps of preprocessing. Our classification method uses convolutional neural networks and transfer learning architecture for classifying the images. Our findings yield an accuracy value of 91.03%, precision of 89.76 %, recall value of 96.67% and F1 score of 93.09%.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Abhinav Sagar Jr.", - "author_inst": "Stealth Startup" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2021.05.24.21257020", "rel_title": "EVALUATION OF A RAPID ANTIGEN TEST FOR SARS-COV-2 IN SYMPTOMATIC PATIENTS AND THEIR CONTACTS: A MULTICENTER STUDY", @@ -729357,6 +731273,69 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2021.05.23.445341", + "rel_title": "Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning.", + "rel_date": "2021-05-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.23.445341", + "rel_abs": "Genomic data analysis is a fundamental system for monitoring pathogen evolution and the outbreak of infectious diseases. Based on bioinformatics and deep learning, this study was designed to identify the genomic variability of SARS-CoV-2 worldwide and predict the impending mutation rate. Analysis of 259044 SARS-CoV-2 isolates identify 3334545 mutations (14.01 mutations per isolate), suggesting a high mutation rate. Strains from India showed the highest no. of mutations (48) followed by Scotland, USA, Netherlands, Norway, and France having up to 36 mutations. Besides the most prominently occurring mutations (D416G, F106F, P314L, and UTR:C241T), we identify L93L, A222V, A199A, V30L, and A220V mutations which are in the top 10 most frequent mutations. Multi-nucleotide mutations GGG>AAC, CC>TT, TG>CA, and AT>TA have come up in our analysis which are in the top 20 mutational cohort. Future mutation rate analysis predicts a 17%, 7%, and 3% increment of C>T, A>G, and A>T, respectively in the future. Conversely, 7%, 7%, and 6% decrement is estimated for T>C, G>A, and G>T mutations, respectively. T>G\\A, C>G\\A, and A>T\\C are not anticipated in the future. Since SARS-CoV-2 is evolving continuously, our findings will facilitate the tracking of mutations and help to map the progression of the COVID-19 intensity worldwide.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Md. Shahadat Hossain", + "author_inst": "Noakhali Science and Technology University" + }, + { + "author_name": "A. Q. M. Sala Uddin Pathan", + "author_inst": "Noakhali Science and Technology University" + }, + { + "author_name": "Md. Nur Islam", + "author_inst": "Noakhali Science and Technology University" + }, + { + "author_name": "Mahafujul Islam Quadery Tonmoy", + "author_inst": "Noakhali Science and Technology University" + }, + { + "author_name": "Mahmudul Islam Rakib", + "author_inst": "Noakhali Science and Technology University" + }, + { + "author_name": "Md. Adnan Munim", + "author_inst": "Noakhali Science and Technology University" + }, + { + "author_name": "Otun Saha", + "author_inst": "Dhaka University" + }, + { + "author_name": "Atqiya Fariha", + "author_inst": "Noakhali Science and Technology University" + }, + { + "author_name": "Hasan Al Reza", + "author_inst": "University of Dhaka" + }, + { + "author_name": "Maitreyee Roy", + "author_inst": "University of New South Wales" + }, + { + "author_name": "Newaz Mohammed Bahadur", + "author_inst": "Noakhali Science and Technology University" + }, + { + "author_name": "Md. Mizanur Rahaman", + "author_inst": "University of Dhaka" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.05.23.445305", "rel_title": "Dimerization of SARS-CoV-2 nucleocapsid protein affects sensitivity of ELISA based diagnostics of COVID-19", @@ -730349,57 +732328,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.05.20.21257512", - "rel_title": "Anti-Sars-Cov-2 IgA And IgG In Human Milk After Vaccination Is Dependent On Vaccine Type And Previous Sars-Cov-2 Exposure: A Longitudinal Study.", - "rel_date": "2021-05-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.20.21257512", - "rel_abs": "Structured AbstractO_ST_ABSImportanceC_ST_ABSLimited data are available on COVID-19 vaccine impact in lactating women.\n\nObjectiveTo evaluate the impact of different COVID-19 vaccines on specific anti-SARS-CoV-2 IgA and IgG levels in human milk.\n\nDesign, Settings and ParticipantsIn this prospective observational study in Spain, 75 lactating women from priority groups receiving vaccination against SARS-CoV-2 were included (January to April 2021). Human milk samples were collected at seven-time points. A group with confirmed SARS-CoV-2 infection (n=19) and a group of women from prepandemic time (n=13) were included.\n\nExposuremRNA vaccines (BNT162b2 and mRNA-1273) and adenovirus-vectored vaccine (ChAdOx1 nCoV-19).\n\nMain Outcome(s) and Measure(s)Presence of IgA and IgG against RBD SARS-CoV-2 in breast milk.\n\nResultsSeventy-five vaccinated lactating women [mean age, 34.9 {+/-} 3.7 years] of whom 96% were Caucasic and 92% were health care workers. A total of 417 milk samples were included and vaccine distribution was BioNTech/Pfizer (BNT162b2, n=30), Moderna (mRNA-1273, n=21), and AstraZeneca (ChAdOx1 nCoV-19, n=24). For each vaccine, 7 time points were collected from baseline up to 25 days after the 1st dose and same points were collected for mRNA vaccines 30 days after 2nd dose. A strong reactivity was observed for IgG and IgA after vaccination mainly after the 2nd dose. Presence and the persistence of specific SARS-CoV-2 antibodies in breast milk were dependent on the vaccine-type and, on previous virus exposure. High inter-variability was observed, being relevant for IgA antibodies. IgG levels were significantly higher than those observed in milk from COVID-19 women while IgA levels were lower. Women with previous COVID-19 increased the IgG levels after the 1st dose to a similar level observed in vaccinated women after the 2nd dose.\n\nConclusions and RelevanceBreast milk from vaccinated women contains anti-SARS-CoV-2 IgA and IgG, with highest after the 2nd dose. Levels were dependent on vaccine type and previous exposure to SARS-CoV-2. Previous COVID-19 influenced the vaccine effect after a single dose, which could be especially relevant in the design of vaccination protocols. Further studies are warranted to demonstrate the potential protective role of these antibodies against COVID-19 in infants from vaccinated and infected mothers through breastfeeding.\n\nTrial RegistrationNCT04751734\n\nKey PointsO_ST_ABSQuestionC_ST_ABSWhat is the effect of the different COVID-19 vaccines on the anti-SARS-CoV-2 antibodies in breast milk? Is the vaccine-specific antibody response in milk comparable to a natural infection? What would be the effect of vaccination on human milk antibodies in women with past SARS-CoV-2 infection?\n\nFindingsIn this prospective, observational and multicenter study in Spain, lactating women within the priority groups receiving the vaccination against SARS-CoV-2 were included. Although there is a high intra- and inter-variability in the generation of specific SARS-CoV-2 antibodies in breast milk, they are also dependent on the vaccine-type and previous viral exposure.\n\nMeaningMaternal SARS-CoV-2 vaccination provides anti-SARS-CoV-2 antibodies, both IgA and IgG, in human milk and it depends on vaccines and previous COVID-19.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Marta Selma-Royo", - "author_inst": "IATA-CSIC" - }, - { - "author_name": "Christine Bauerl", - "author_inst": "IATA-CSIC" - }, - { - "author_name": "Desiree Mena-Tudela", - "author_inst": "Department of Nursing, Nursing Research Group, Universitat Jaume I, Castellon, Spain" - }, - { - "author_name": "Laia Aguilar-Camprubi", - "author_inst": "LactApp Women Health, Barcelona, Spain." - }, - { - "author_name": "Francisco Jose Perez-Cano", - "author_inst": "Physiology Section, Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Science and Institute of Research in Nutrition and Food Safety (INSA" - }, - { - "author_name": "Anna Parra-Llorca", - "author_inst": "Health Research Institute La Fe, Neonatal Research Group, Spain and University and Polytechnic Hospital La Fe, Division of Neonatology, 46026 Valencia, Spain" - }, - { - "author_name": "Carles Lerin", - "author_inst": "Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, 08950 Barcelona, Spain." - }, - { - "author_name": "Cecilia Martinez-Costa", - "author_inst": "Department of Pediatrics, Hospital Clinico Universitario, University of Valencia, Spain. Nutrition Research Group of INCLIVA, 46010 Valencia, Spain." - }, - { - "author_name": "Maria Carmen COLLADO", - "author_inst": "IATA-CSIC" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2021.05.20.21257513", "rel_title": "DEFINE: A Phase IIa Randomised Controlled Trial to Evaluate Repurposed Treatments for COVID-19", @@ -731339,6 +733267,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.20.21256197", + "rel_title": "Evaluation of silver nanoparticles for the prevention of SARS-CoV-2 infection in health workers: in vitro and in vivo", + "rel_date": "2021-05-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.20.21256197", + "rel_abs": "SARS-CoV-2 infection in hospital areas is of a particular concern, since the close interaction between health care personnel and patients diagnosed with COVID-19, which allows virus to be easily spread between them and subsequently to their families and communities. Preventing SARS-CoV-2 infection among healthcare personnel is essential to reduce the frequency of infections and outbreaks during the pandemic considering that they work in high-risk areas. In this research, silver nanoparticles (AgNPs) were tested in vitro and shown to have an inhibitory effect on SARS-CoV-2 infection in cultured cells. Subsequently, we assess the effects of mouthwash and nose rinse with ARGOVIT(R) silver nanoparticles (AgNPs), in the prevention of SARS-CoV-2 contagion in health workers consider as high-risk group of acquiring the infection in the General Tijuana Hospital, Mexico, a hospital for the exclusive recruitment of patients diagnosed with COVID-19. We present a prospective randomized study of 231 participants that was carried out for 9 weeks (during the declaration of a pandemic). The \"experimental\" group was instructed to do mouthwash and nose rinse with the AgNPs solution; the \"control\" group was instructed to do mouthwashes and nose rinse in a conventional way. The incidence of SARS-CoV-2 infection was significantly lower in the \"experimental\" group (two participants of 114, 1.8%) compared to the \"control\" group (thirty-three participants of 117, 28.2%), with a 84.8% efficiency. We conclude that the mouth and nasal rinse with AgNPs helps in the prevention of SARS-CoV-2 infection in health personnel who are exposed to patients diagnosed with COVID-19.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Horacio Almanza-Reyes", + "author_inst": "Cluster de Bioeconomia de Baja California, A.C." + }, + { + "author_name": "Sandra Moreno", + "author_inst": "Centro de Investigacion en Sanidad Animal. Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria." + }, + { + "author_name": "Ismael Plascencia-Lopez", + "author_inst": "Faculty of Accounting and Administration, Universidad Autonoma de Baja California" + }, + { + "author_name": "Martha Alvarado-Vera", + "author_inst": "Cluster de Bioeconomia de Baja California, A.C." + }, + { + "author_name": "Leslie Patron-Romero", + "author_inst": "Faculty of Medicine and Psychology, Autonomous University of Baja California" + }, + { + "author_name": "Belen Borrego", + "author_inst": "Centro de Investigacion en Sanidad Animal. Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria" + }, + { + "author_name": "Alberto Reyes-Escamilla", + "author_inst": "Tijuana General Hospital" + }, + { + "author_name": "Daniel Valencia-Manzo", + "author_inst": "Nursing Postgraduate, Iberoamericana University" + }, + { + "author_name": "Alejandro Brun", + "author_inst": "Centro de Investigacion en Sanidad Animal. Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria" + }, + { + "author_name": "Alexey Pestryakov", + "author_inst": "Tomsk Polytechnic University" + }, + { + "author_name": "Nina Bogdanchikova", + "author_inst": "Center of Nanoscience and Nanotechnology; UNAM (CNyN-UNAM)" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.21.20248630", "rel_title": "A Deep Recurrent Reinforced Learning model to compare the efficacy of targeted local vs. national measures on the spread of COVID-19 in the UK", @@ -732407,41 +734394,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2021.05.20.21257550", - "rel_title": "Unusually high risks of COVID-19 mortality with age-related comorbidities: An adjusted method to improve the risk assessment of mortality using the comorbid mortality data.", - "rel_date": "2021-05-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.20.21257550", - "rel_abs": "BackgroundThe pandemic of Coronavirus Disease 2019 (COVID-19) has been a threat to global health in the world. In the US, the Centers for Disease Control and Prevention (CDC) has listed 12 comorbidities within the first tier that increase with the risk of severe illness from COVID-19, including the comorbidities that are common with increasing age (referred to as age-related comorbidities) and other comorbidities. However, the current method compares a population with and without a particular disease (or disorder), which may result in a bias on the results. Thus, comorbidity risks of COVID-19 mortality may be underestimated.\n\nObjectiveTo re-evaluate the mortality data from US States and estimate the odds ratios of death by major comorbidities with COVID-19, we incorporated the control population with no comorbidity reported and assessed the risk of COVID-19 mortality with comorbidity.\n\nMethodsWe collected all the comorbidity data from the Public Health websites of fifty US States and Washington DC accessed on December 2020. The timing of the data collection should allow minimizing a bias from the COVID-19 vaccines and new COVID-19 variants. The comorbidity demographic data were extracted from the State Public Health data made available online. Using the inverse-variance random-effects model, we performed a comparative analysis and estimated the odds ratio of deaths by COVID-19 with pre-existing comorbidities.\n\nResultsA total of 39,451 COVID-19 deaths were identified from four States that had comorbidity data, including Alabama, Louisiana, Mississippi, New York. 92.8% of the COVID-19 deaths were associated with pre-existing comorbidity. The risk of mortality associated with at least one comorbidity combined was 1,113 times higher than that with no comorbidity. The comparative analysis identified nine comorbidities with odds ratios of up to 35 times significantly higher than no comorbidities. Of them, the top four comorbidities were: hypertension (odds ratio 34.73; 95% CI 3.63-331.91; p = 0.002), diabetes (odds ratio 20.16; 95% CI 5.55-73.18; p < 0.00001), cardiovascular disease (odds ratio 18.91; 95% CI 2.88-124.38; p = 0.002); and chronic kidney disease (odds ratio 12.34; 95% CI 9.90-15.39; p < 0.00001). Interestingly, lung disease added only a modest increase in risk (odds ratio 6.69; 95% CI 1.06-42.26; p < 0.00001).\n\nConclusionThe aforementioned comorbidities show surprisingly high risks of COVID-19 mortality when compared to the population with no comorbidity. Major comorbidities were enriched with pre-existing comorbidities that are common with increasing age (cardiovascular disease, diabetes, and hypertension). The COVID-19 deaths were mostly associated with at least one comorbidity, which may be a source of the bias leading to the underestimation of the mortality risks previously reported. Taken together, this type of study is useful to approximate the risks, which most likely provide an updated awareness of age-related comorbidities.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Andrew Antos", - "author_inst": "Touro University California" - }, - { - "author_name": "Ming Lai Kwong", - "author_inst": "Touro University California" - }, - { - "author_name": "Timothy Balmorez", - "author_inst": "Touro University California" - }, - { - "author_name": "Alyssa Villanueva", - "author_inst": "Touro University California" - }, - { - "author_name": "Shin Murakami", - "author_inst": "Touro University California" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.19.21257469", "rel_title": "REGEN-COV Antibody Cocktail Clinical Outcomes Study in Covid-19 Outpatients", @@ -733285,6 +735237,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2021.05.20.21257516", + "rel_title": "A cross-sectional study of the mismatch between telecommuting preference and frequency associated with psychological distress among Japanese workers in the COVID-19 pandemic", + "rel_date": "2021-05-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.20.21257516", + "rel_abs": "ObjectiveTo examine how the mismatch between telecommuting preference and telecommuting frequency was associated with psychological distress during the COVID-19 pandemic.\n\nMethodsData from 33,302 workers throughout Japan were obtained using an Internet survey. Among 33,302 participants, 20,395 who telecommuted were included in the analysis. Participants telecommuting preference and frequency during the COVID-19 pandemic were determined using a questionnaire. Psychological distress was assessed using Kessler 6 (K6).\n\nResultsAmong participants who did and did not prefer to telecommute, those who telecommuted four or more days per week had an OR of psychological distress of 0.67 (p<0.001) and 1.87 (p=0.001), respectively, compared with those who rarely telecommuted.\n\nConclusionsThe association between telecommuting and psychological distress differs depending on telecommuting preference.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Souhei Otsuka", + "author_inst": "University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Tomohiro Ishimaru", + "author_inst": "University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Masako Nagata", + "author_inst": "University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Seiichiro Tateishi", + "author_inst": "University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Hisashi Eguchi", + "author_inst": "University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Mayumi Tsuji", + "author_inst": "University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Akira Ogami", + "author_inst": "University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Shinya Matsuda", + "author_inst": "University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Yoshihisa Fujino", + "author_inst": "University of Occupational and Environmental Health, Japan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2021.05.19.21257237", "rel_title": "SARS-CoV-2 infection of BNT162b2(mRNA)-vaccinated individuals is not restricted to variants of concern or high-risk exposure environments", @@ -734113,153 +736116,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.05.19.21257433", - "rel_title": "One year of SARS-CoV-2: Genomic characterization of COVID-19 outbreak in Qatar", - "rel_date": "2021-05-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.19.21257433", - "rel_abs": "The state of Qatar has emerged as a major transit hub connecting all parts of the globe, making it as a hotspot for infectious disease introduction and providing an ideal setting to monitor the emergence and spread of variants. In this study, we report on 2634 SARS-CoV-2 whole-genome sequences from infected patients in Qatar between March-2020 and March-2021, representing 1.5% of all positive cases in this period. Despite the restrictions on international travel, the viruses sampled from the populace of Qatar mirrored nearly the entire global populations genomic diversity with nine predominant viral lineages that were sustained by local transmission chains and the emergence of mutations that are likely to have originated in Qatar. We reported an increased number in the mutations and deletions in B.1.1.7 and B.1.351 lineages in a short period. This raises the imperative need to continue the ongoing genomic surveillance that has been an integral part of the national response to monitor SARS-CoV-2 profile and re-emergence in Qatar.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Fatiha M. Benslimane", - "author_inst": "Qatar University" - }, - { - "author_name": "Hebah A. AlKhatib", - "author_inst": "Qatar University" - }, - { - "author_name": "Ola Al-Jamal", - "author_inst": "Qatar University" - }, - { - "author_name": "Dana Albatesh", - "author_inst": "Qatar University" - }, - { - "author_name": "Sonia Boughattas", - "author_inst": "Qatar University" - }, - { - "author_name": "Ayeda A. Ahmed", - "author_inst": "Weill Cornell Medicine-Qatar" - }, - { - "author_name": "Meryem Bensaad", - "author_inst": "Weill Cornell Medicine-Qatar" - }, - { - "author_name": "Shameem Younuskunju", - "author_inst": "Weill Cornell Medicine-Qatar" - }, - { - "author_name": "Yasmin A. Mohamoud", - "author_inst": "Weill Cornell Medicine-Qatar" - }, - { - "author_name": "Mashael Al Badr", - "author_inst": "Ministry of Public Health" - }, - { - "author_name": "Abdalla A. Mohamed", - "author_inst": "Ministry of Public Health" - }, - { - "author_name": "Reham A. El Kahlout", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Tasneem Al Hamad", - "author_inst": "Qatar Biobank" - }, - { - "author_name": "Dina Elgakhlab", - "author_inst": "Qatar Biobank" - }, - { - "author_name": "Fatima H. Al-Kuwari", - "author_inst": "Qatar Genome Program" - }, - { - "author_name": "Chadi Saad", - "author_inst": "Qatar Genome Project" - }, - { - "author_name": "Andrew Jeremijenko", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Abdullatif Al-Khal", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Muna A. Al-Maslamani", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Roberto Bertollini", - "author_inst": "Ministry of Public Health" - }, - { - "author_name": "Einas A. Al-Kuwari", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Hamad E. Al-Romaihi", - "author_inst": "Ministry of Public Health" - }, - { - "author_name": "Salih Al-Marri", - "author_inst": "Ministry of Public Health" - }, - { - "author_name": "Mohammed Al-Thani", - "author_inst": "Ministry of Public Health" - }, - { - "author_name": "Radja M. Badji", - "author_inst": "Qatar Genome Project" - }, - { - "author_name": "Hamdi Mbarek", - "author_inst": "Qatar Genome Project" - }, - { - "author_name": "Yasser Al-Sarraj", - "author_inst": "Qatar Genome Project" - }, - { - "author_name": "Joel A Malek", - "author_inst": "Weill Cornell Medicine in Qatar" - }, - { - "author_name": "Said I. Ismail", - "author_inst": "Qatar Genome Project" - }, - { - "author_name": "Laith J Abu-Raddad", - "author_inst": "Weill Cornell Medicine-Qatar" - }, - { - "author_name": "Peter Coyle", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Asmaa A. Althani", - "author_inst": "Qatar University" - }, - { - "author_name": "HADI M. YASSINE", - "author_inst": "Qatar University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.18.21257362", "rel_title": "Vaccination and three non-pharmaceutical interventions determine the end of COVID-19 at 381 metropolitan statistical areas in the US", @@ -735015,6 +736871,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rheumatology" }, + { + "rel_doi": "10.1101/2021.05.18.21256584", + "rel_title": "Critically ill COVID-19 associated trait genetics reveals CDK6 inhibitors as potential treatment", + "rel_date": "2021-05-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.18.21256584", + "rel_abs": "BackgroundDespite recent development of vaccines and monoclonal antibodies to prevent SARS-CoV-2 infection, treatment of critically ill COVID-19 patients remains an important goal. In principle, genome-wide association studies (GWAS) could shortcut the clinical evidence needed to repurpose drugs - the use of an existing drug for a new indication. However, it has been shown that the genes found in GWA studies usually do not encode an established drug target and the causal role for disease, a key requirement for drug efficacy, is unclear. We report here an alternative method for finding and testing causal target candidates for drug repurposing.\n\nMethodsRather than focusing on the genetics of the disease, we looked for disease-causing traits by searching for significant differences in 33 blood cell types, 30 blood biochemistries, and body mass index between an infectious disease phenotype and healthy controls. We then matched critically ill COVID-19 cases with controls that exhibited mild or no symptoms after SARS-CoV-2 infection in order to identify disease-causing traits by applying causal inference methods.\n\nResultsWe found high neutrophil cell count as a causal trait for the immune overreaction in critical illness due to COVID-19. Based on these findings, we identified the enzyme CDK6 as a potential drug target to prevent the immune overreaction in critical illness due to COVID-19.\n\nConclusionsThe genetics of disease-causing traits turns out to be a rich reservoir for the identification of known drug targets. This is due to the usually larger datasets of traits, as they also cover healthy ones. A clinical trial testing CDK6 inhibitor palbociclib in critically ill COVID-19 patients is currently ongoing (ClinicalTrials.gov Identifier: NCT05371275).", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Hannes A. Baukmann", + "author_inst": "biotx.ai GmbH" + }, + { + "author_name": "Justin L. Cope", + "author_inst": "biotx.ai GmbH" + }, + { + "author_name": "Charles N. J. Ravarani", + "author_inst": "biotx.ai GmbH" + }, + { + "author_name": "Colin Bannard", + "author_inst": "University of Manchester" + }, + { + "author_name": "Margaretha R. J. Lamparter", + "author_inst": "biotx.ai GmbH" + }, + { + "author_name": "Alexander R. E. C. Schwinges", + "author_inst": "biotx.ai GmbH" + }, + { + "author_name": "Joern E. Klinger", + "author_inst": "biotx.ai GmbH" + }, + { + "author_name": "Marco F. Schmidt", + "author_inst": "biotx.ai GmbH" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2021.05.19.21257452", "rel_title": "SARS-CoV-2 screening prevalence in educational staff in Berlin, Germany, June-December 2020", @@ -736199,85 +738102,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.17.21257341", - "rel_title": "Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa", - "rel_date": "2021-05-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.17.21257341", - "rel_abs": "COVID-19 disease dynamics have been widely studied in different settings around the globe, but little is known about these patterns in the African continent.\n\nTo investigate the epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa, more than 2400 complete genomes from 33 African countries were retrieved from the GISAID database and analyzed. We investigated their diversity using various clade and lineage nomenclature systems, reconstructed their evolutionary divergence and history using maximum likelihood inference methods, and studied the case and death trends in the continent. We also examined potential repeat patterns and motifs across the sequences.\n\nIn this study, we show that after almost one year of the COVID-19 pandemic, only 143 out of the 782 Pango lineages found worldwide circulated in Africa, with five different lineages dominating in distinct periods of the pandemic. Analysis of the number of reported deaths in Africa also revealed large heterogeneity across the continent. Phylogenetic analysis revealed that African viruses cluster closely with those from all continents but more notably with viruses from Europe. However, the extent of viral diversity observed among African genomes is closest to that of the Oceania outbreak, most likely due to genomic under-surveillance in Africa. We also identified two motifs that could function as integrin-binding sites and N-glycosylation domains.\n\nThese results shed light on the evolutionary dynamics of the circulating viral strains in Africa, elucidate the functions of protein motifs present in the genome sequences, and emphasize the need to expand genomic surveillance efforts in the continent to better understand the molecular, evolutionary, epidemiological, and spatiotemporal dynamics of the COVID-19 pandemic in Africa.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Olayinka S Okoh", - "author_inst": "Anchor University, Lagos, Nigeria" - }, - { - "author_name": "Nicholas Israel Nii-Trebi", - "author_inst": "University of Ghana, Accra, Ghana" - }, - { - "author_name": "Abdulrokeeb Jakkari", - "author_inst": "Lagos State University, Ojo, Lagos, Nigeria" - }, - { - "author_name": "Tosin Titus Olaniran", - "author_inst": "Ladoke Akintola University of Technology, Ogbomoso, Nigeria" - }, - { - "author_name": "Tosin Yetunde Senbadejo", - "author_inst": "Fountain University, Osogbo, Nigeria" - }, - { - "author_name": "Anna Aba Kafintu-kwashie", - "author_inst": "University of Ghana Medical School, Accra, Ghana" - }, - { - "author_name": "Emmanuel Oluwatobi Dairo", - "author_inst": "University of Ibadan, Ibadan, Nigeria" - }, - { - "author_name": "Tajudeen Oladunni Ganiyu", - "author_inst": "Fountain University, Osogbo, Nigeria" - }, - { - "author_name": "Ifiokakaninyene Ekpo Akaninyene", - "author_inst": "Ladoke Akintola University of Technology, Ogbomoso, Nigeria" - }, - { - "author_name": "Louis Odinakaose Ezediuno", - "author_inst": "University of Ilorin, Ilorin, Nigeria" - }, - { - "author_name": "Idowu Jesulayomi Adeosun", - "author_inst": "Adeleke University, Ede, Osun State, Nigeria" - }, - { - "author_name": "Michael Asebake Ockiya", - "author_inst": "Niger Delta University, Wilberforce Island, Bayelsa State, Nigeria" - }, - { - "author_name": "Esther Moradeyo Jimah", - "author_inst": "University of Ilorin, Ilorin, Nigeria" - }, - { - "author_name": "David J Spiro", - "author_inst": "Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA" - }, - { - "author_name": "Elijah Kolawole Oladipo", - "author_inst": "Adeleke University, Ede, Osun State, Nigeria" - }, - { - "author_name": "Nidia S. Trovao", - "author_inst": "Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.18.21257383", "rel_title": "Decline in COPD Admissions During the COVID-19 Pandemic Associated with Lower Burden of Community Respiratory Viral Infections", @@ -737029,6 +738853,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.18.21257397", + "rel_title": "Associations of socioeconomic position and adverse childhood experiences with health-related behaviour changes and changes to employment during the first COVID-19 lockdown in the UK", + "rel_date": "2021-05-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.18.21257397", + "rel_abs": "BackgroundNon-pharmaceutical interventions to reduce the spread of COVID-19 may have disproportionately affected already disadvantaged populations.\n\nMethodsWe analysed data from 2710 young adult participants of the Avon Longitudinal Study of Parents and Children. We assessed the associations of socioeconomic position (SEP) and Adverse Childhood Experiences (ACEs, e.g. abuse, neglect, measures of family dysfunction) with changes to health-related behaviours (meals, snacks, exercise, sleep, alcohol and smoking/vaping), and to financial and employment status during the first UK lockdown between March-June 2020.\n\nResultsExperiencing 4 or more ACEs was associated with reporting decreased sleep quantity during lockdown (OR 1.53, 95% CI: 1.07-2.18) and increased smoking and/or vaping (OR 1.85, 95% CI: 0.99-3.43); no other associations were seen between ACEs or SEP and health-related behaviour changes. Adverse financial and employment changes were more likely for people with low SEP and for people who had experienced multiple ACEs; e.g. people who had been in the never worked or long-term unemployed or routine and manual occupation categories pre-lockdown were almost 3 times more likely to have stopped working during lockdown compared with people who were in a higher managerial, administrative or professional occupation pre-lockdown (OR 2.83, 95% CI: 1.45-5.50 and OR 2.68, 95% CI: 1.63-4.42 respectively).\n\nConclusionAdverse financial and employment consequences of lockdown were more likely to be experienced by people who have already experienced socioeconomic deprivation or childhood adversity, thereby widening social inequalities. Despite this, in this sample of young adults, there was little evidence that lockdown worsened inequalities in health-related behaviours.\n\nBOXO_ST_ABSWhat is already known on this subject?C_ST_ABSO_LINon-pharmaceutical interventions implemented to mitigate the spread of COVID-19 (e.g. nationwide lockdown) have affected the lifestyles and livelihoods of many, with potential consequences for physical health and financial wellbeing.\nC_LIO_LIExisting evidence suggests sociodemographic inequalities in the effects of lockdown, but details of the factors influencing these inequalities remain unclear.\nC_LI\n\nWhat this study adds?O_LIA history of adverse childhood experiences may be associated with decreased sleep and increased smoking/vaping during lockdown. SEP and ACEs were not associated with changes in other health-related behaviours in this cohort of young adults.\nC_LIO_LIAdverse financial and employment consequences of lockdown were more likely to be experienced by people who have already experienced socioeconomic deprivation or childhood adversity, thereby widening social inequalities. Our findings highlight a need for continued support of people who experience ACEs into adulthood, and demonstrate that this need may have increased during the COVID-19 pandemic.\nC_LI", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Madeleine L Smith", + "author_inst": "University of Bristol" + }, + { + "author_name": "Annie Herbert", + "author_inst": "University of Bristol" + }, + { + "author_name": "Amanda Hughes", + "author_inst": "University of Bristol" + }, + { + "author_name": "Kate Northstone", + "author_inst": "University of Bristol" + }, + { + "author_name": "Laura D Howe", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.05.19.21257447", "rel_title": "Analysis of the Second COVID-19 Wave in India Using a Birth-Death Model", @@ -739549,53 +741408,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2021.05.14.21257215", - "rel_title": "SARS-CoV-2 infection risk during delivery of childhood vaccination campaigns: a modelling study", - "rel_date": "2021-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.14.21257215", - "rel_abs": "BackgroundThe COVID-19 pandemic has disrupted delivery of immunisation services globally. Many countries have postponed vaccination campaigns out of concern about infection risks to staff delivering vaccination, the children being vaccinated and their families. The World Health Organization recommends considering both the benefit of preventive campaigns and the risk of SARS-CoV-2 transmission when making decisions about campaigns during COVID-19 outbreaks, but there has been little quantification of the risks.\n\nMethodsWe modelled excess SARS-CoV-2 infection risk to vaccinators, vaccinees and their caregivers resulting from vaccination campaigns delivered during a COVID-19 epidemic. Our model used population age-structure and contact patterns from three exemplar countries (Burkina Faso, Ethiopia, and Brazil). It combined an existing compartmental transmission model of an underlying COVID-19 epidemic with a Reed-Frost model of SARS-CoV-2 infection risk to vaccinators and vaccinees. We explored how excess risk depends on key parameters governing SARS-CoV-2 transmissibility, and aspects of campaign delivery such as campaign duration, number of vaccinations, and effectiveness of personal protective equipment (PPE) and symptomatic screening.\n\nResultsInfection risks differ considerably depending on the circumstances in which vaccination campaigns are conducted. A campaign conducted at the peak of a SARS-CoV-2 epidemic with high prevalence and without special infection mitigation measures could increase absolute infection risk by 32% to 45% for vaccinators, and 0.3% to 0.5% for vaccinees and caregivers. However, these risks could be reduced to 3.6% to 5.3% and 0.1% to 0.2% respectively by use of PPE that reduces transmission by 90% (as might be achieved with N95 respirators or high-quality surgical masks) and symptomatic screening.\n\nConclusionsSARS-CoV-2 infection risks to vaccinators, vaccinees and caregivers during vaccination campaigns can be greatly reduced by adequate PPE, symptomatic screening, and appropriate campaign timing. Our results support the use of adequate risk mitigation measures for vaccination campaigns held during SARS-CoV-2 epidemics, rather than cancelling them entirely.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Simon R Procter", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Kaja Abbas", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Stefan Flasche", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Ulla Griffiths", - "author_inst": "UNICEF" - }, - { - "author_name": "Brittany Hagedorn", - "author_inst": "Bill and Melinda Gates Foundation" - }, - { - "author_name": "Kathleen M O'Reilly", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "- CMMID COVID-19 Working Group", - "author_inst": "" - }, - { - "author_name": "Mark Jit", - "author_inst": "London School of Hygiene & Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.15.21257210", "rel_title": "Persistence of functional memory B cells recognizing SARS-CoV-2 variants despite loss of specific IgG", @@ -740315,6 +742127,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.05.17.444479", + "rel_title": "Viability of MS2 and Phi6 Bacteriophages on Carpet and Dust", + "rel_date": "2021-05-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.17.444479", + "rel_abs": "Respiratory viral illnesses are commonly spread in the indoor environment through multiple transmission routes, including droplets, aerosols, and direct/indirect contact. Indoors, resuspension of dust from flooring is a major source of human exposure. However, it is critical to determine viral persistence on dust and flooring to better characterize human exposure. The goal of this work is to determine viral viability on two carpet types (cut and looped) and house dust over time and after four different cleaning methods. MS2 and Phi6 bacteriophages were used to represent non-enveloped and enveloped viruses, respectively. These viral surrogates were placed in an artificial saliva solution and nebulized onto carpet or dust. Viability was measured at various time points (0, 1, 2, 3, 4, 24, and 48 hours) and after cleaning (vacuuming, hot water extraction with stain remover, steam, and a disinfection spray). Viability decay was modeled as first-order. MS2 bacteriophages showed slower viability decay rates in dust (-0.11 hr-1), cut carpet (-0.20 hr-1), and looped carpet (-0.09 hr-1) compared to Phi6 (-3.36 hr-1, -1.57 hr-1, and - 0.20 hr-1 respectively). The difference between phages was statistically significant in dust and cut carpet (p<0.05). Viral RNA demonstrated minimal degradation that in most cases was not statistically different from zero over the 48 hours measured (p>0.05). Viable viral concentrations were reduced to below the detection limit for steam and disinfection for both MS2 and Phi6 (p<0.05), while vacuuming and hot water extraction with stain remover showed no significant changes in concentration from uncleaned carpet (p>0.05). This study used viral surrogates and did not model risk of viral transmission via dust. Overall, these results demonstrate that MS2 and Phi6 bacteriophages can remain viable in carpet and dust for several hours to days, and cleaning techniques with heat and disinfectants may be more effective than standard vacuuming for viral removal. Future work should model risk from exposure via dust and flooring for various viruses such as influenza, SARS-CoV-2, and RSV.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC=\"FIGDIR/small/444479v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (31K):\norg.highwire.dtl.DTLVardef@1cc0ad9org.highwire.dtl.DTLVardef@dc440corg.highwire.dtl.DTLVardef@f787dcorg.highwire.dtl.DTLVardef@f8bda3_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Nicholas Nastasi", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Nicole Renninger", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Ashleigh Bope", + "author_inst": "Ohio State University" + }, + { + "author_name": "Samuel J Cochran", + "author_inst": "Ohio State University" + }, + { + "author_name": "Justin Greaves", + "author_inst": "University of Notre Dame" + }, + { + "author_name": "Sarah R. Haines", + "author_inst": "Ohio State University" + }, + { + "author_name": "Neeraja Balasubrahmaniam", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Katelyn Stuart", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Jenny Panescu", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Kyle Bibby", + "author_inst": "University of Notre Dame" + }, + { + "author_name": "Natalie M. Hull", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Karen C. Dannemiller", + "author_inst": "Ohio State University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.05.16.21257297", "rel_title": "The effect of smaller classes on infection-related school absence: Evidence from the Project STAR randomized controlled trial", @@ -741279,45 +743154,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.05.18.444646", - "rel_title": "Effects of common mutations in the SARS-CoV-2 Spike RBD domain and its ligand the human ACE2 receptor on binding affinity and kinetics", - "rel_date": "2021-05-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.18.444646", - "rel_abs": "The interaction between the SARS-CoV-2 virus Spike protein receptor binding domain (RBD) and the ACE2 cell surface protein is required for viral infection of cells. Mutations in the RBD domain are present in SARS-CoV-2 variants of concern that have emerged independently worldwide. For example, the more transmissible B.1.1.7 lineage has a mutation (N501Y) in its Spike RBD domain that enhances binding to ACE2. There are also ACE2 alleles in humans with mutations in the RBD binding site. Here we perform a detailed affinity and kinetics analysis of the effect of five common RBD mutations (K417N, K417T, N501Y, E484K and S477N) and two common ACE2 mutations (S19P and K26R) on the RBD/ACE2 interaction. We analysed the effects of individual RBD mutations, and combinations found in new SARS-CoV-2 variants first identified in the UK (B.1.1.7), South Africa (B.1.351) and Brazil (P1). Most of these mutations increased the affinity of the RBD/ACE2 interaction. The exceptions were mutations K417N/T, which decreased the affinity. Taken together with other studies, our results suggest that the N501Y and S477N mutations primarily enhance transmission, the K417N/T mutations facilitate immune escape, and the E484K mutation facilitates both transmission and immune escape.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Michael I Barton", - "author_inst": "University of Oxford" - }, - { - "author_name": "Stuart MacGowan", - "author_inst": "University of Dundee" - }, - { - "author_name": "Mikhail A Kutuzov", - "author_inst": "University of Oxford" - }, - { - "author_name": "Omer Dushek", - "author_inst": "University of Oxford" - }, - { - "author_name": "Geoffrey J Barton", - "author_inst": "University of Dundee" - }, - { - "author_name": "P. Anton van der Merwe", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.05.17.444397", "rel_title": "An intranasal ASO therapeutic targeting SARS-CoV-2", @@ -742085,6 +743921,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.15.21257017", + "rel_title": "Extended interval BNT162b2 vaccination enhances peak antibody generation in older people", + "rel_date": "2021-05-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.15.21257017", + "rel_abs": "ObjectivesTo assess the relative immunogenicity of standard or extended interval BNT162b2 vaccination.\n\nDesignPopulation based cohort study comparing immune responses 2 weeks after the second vaccine, with appropriate time-matched samples in participants who received standard or extended interval double vaccination.\n\nSettingPrimary care networks, Birmingham, UK. December 2020 to April 2021.\n\nParticipants172 people aged over 80 years of age. All donors received the BNT162b2 Pfizer/BioNTech vaccination and were vaccinated with either a standard 3 week interval between doses or an extended interval schedule.\n\nMain outcome measuresPeak quantitative spike-specific antibody and cellular immune responses.\n\nResultsIn donors without evidence of previous infection the peak antibody response was 3.5-fold higher in donors who had undergone delayed interval vaccination. Cellular immune responses were 3.6-fold lower.\n\nConclusionPeak antibody responses after the second BNT162b2 vaccine are markedly enhanced in older people when this is delayed to 12 weeks although cellular responses are lower. Extended interval vaccination may therefore offer the potential to enhance and extend humoral immunity. Further follow up is now required to assess long term immunity and clinical protection.\n\nWhat is already known on this topicThe BNT162b2 vaccine is highly effective against Covid-19 infection and was delivered with a 3-week time interval in registration studies. However, this interval has been extended in many countries in order to extend population coverage with a single vaccine. It is not known how immune responses after the second dose are influenced by delaying the second vaccine.\n\nWhat this study addsWe provide the first assessment of immune responses in the first 14 weeks after standard or extended interval BNT162b2 vaccination and show that delaying the second dose acts to strongly boost the peak antibody response in older people. The extended interval vaccination may offer a longer period of clinical protection. This information will be of value in optimizing vaccine regimens and help guide guide vaccination policies.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Helen M Parry", + "author_inst": "University of Birmingham, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham. B15 2TT, UK" + }, + { + "author_name": "Rachel Bruton", + "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham. B15 2TT, UK" + }, + { + "author_name": "Christine Stephens", + "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham. B15 2TT, UK" + }, + { + "author_name": "Kevin Brown", + "author_inst": "National infection Service, Public Health England, Colindale, London NW9 5EQ, UK" + }, + { + "author_name": "Gayatri Amirthalingam", + "author_inst": "National infection Service, Public Health England, Colindale, London NW9 5EQ, UK" + }, + { + "author_name": "Bassam Hallis", + "author_inst": "National infection Service, Public Health England, Porton Down, Salisbury, SP4 OJG, UK" + }, + { + "author_name": "Ashley Otter", + "author_inst": "National infection Service, Public Health England, Porton Down, Salisbury, SP4 OJG, UK" + }, + { + "author_name": "Jianmin Zuo", + "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham. B15 2TT, UK" + }, + { + "author_name": "Paul Moss", + "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham. B15 2TT, UK" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.14.21257248", "rel_title": "Interim Report of a Phase 2 Randomized Trial of a Plant-Produced Virus-Like Particle Vaccine for Covid-19 in Healthy Adults Aged 18-64 and Older Adults Aged 65 and Older", @@ -743097,69 +744984,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2021.05.13.21257177", - "rel_title": "Current challenges of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seroprevalence studies among blood donors: A scoping review", - "rel_date": "2021-05-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.13.21257177", - "rel_abs": "BackgroundBlood donors are increasingly being recognized as an informative resource for surveillance. We aimed to review and characterize SARS-CoV-2 seroprevalence studies conducted using blood donors to investigate methodology and provide guidance for future research.\n\nMethodsWe conducted a scoping review of peer-reviewed and preprint publications between January 2020 to January 2021. Two reviewers used standardized forms to extract seroprevalence estimates and data on methodology pertaining to population sampling, periodicity, assay characteristics and antibody kinetics. National data on cumulative incidence and social distancing policies were extracted from publicly available sources and summarized.\n\nResultsThirty-three studies representing 1,323,307 blood donations from 20 countries worldwide were included (sample size per study ranged from 22 to 953,926 donations). Seroprevalence rates ranged from 0% to 76% (after adjusting for waning antibodies). Overall, less than 1 in 5 studies reported standardized seroprevalence rates to reflect the demographics of the general population. Stratification by age and sex were most common (64% of studies), followed by region (48%). 52% of studies reported seroprevalence at a single time point. Overall, 27 unique assay combinations were identified, 55% of studies used a single assay and only 39% adjusted seroprevalence rates for imperfect test characteristics. Among the eight nationally representative studies case detection was most underrepresented in Kenya (1:1264).\n\nConclusionAs of December 11, 2020, 79% of studies reported seroprevalence rates <10%; thresholds far from reaching herd immunity. In addition to differences in community transmission and diverse public health policies, study designs and methodology were likely contributing factors to seroprevalence heterogeneity.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Sahar Saeed", - "author_inst": "Canadian Blood Services" - }, - { - "author_name": "Samra Uzicanin", - "author_inst": "Canadian Blood Services" - }, - { - "author_name": "Antoine Lewin", - "author_inst": "Hema Quebec" - }, - { - "author_name": "Ryanne Lieshout-Krikke", - "author_inst": "Sanquin Blood Supply Foundation" - }, - { - "author_name": "Helen Faddy", - "author_inst": "University of the Sunshine Coast" - }, - { - "author_name": "Christian Erikstrup", - "author_inst": "Aarhus University Hospital" - }, - { - "author_name": "Carla Osiowy", - "author_inst": "Public Health Agency of Canada" - }, - { - "author_name": "Clive Seed", - "author_inst": "University of the Sunshine Coast" - }, - { - "author_name": "Whitney Steele", - "author_inst": "American Red Cross" - }, - { - "author_name": "Katy Davidson", - "author_inst": "NHS Blood Transplant" - }, - { - "author_name": "Brian Custer", - "author_inst": "Vitalant" - }, - { - "author_name": "Sheila F O'Brien", - "author_inst": "Canadian Blood Services" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.13.444021", "rel_title": "Global mapping of RNA homodimers in living cells", @@ -743955,6 +745779,165 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.13.21256846", + "rel_title": "Therapeutic Anticoagulation in Non-Critically Ill Patients with Covid-19", + "rel_date": "2021-05-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.13.21256846", + "rel_abs": "BackgroundThrombo-inflammation may contribute to morbidity and mortality in Covid-19. We hypothesized that therapeutic-dose anticoagulation may improve outcomes in non-critically ill patients hospitalized for Covid-19.\n\nMethodsIn an open-label adaptive multiplatform randomized controlled trial, non-critically ill patients hospitalized for Covid-19, defined by the absence of critical care-level organ support at enrollment, were randomized to a pragmatic strategy of therapeutic-dose anticoagulation with heparin or usual care pharmacological thromboprophylaxis. The primary outcome combined survival to hospital discharge and days free of organ support through 21 days, which was evaluated with Bayesian statistical models according to baseline D-dimer.\n\nResultsThe trial was stopped when prespecified criteria for superiority were met for therapeutic-dose anticoagulation in groups defined by high ([≥]2-fold elevated) and low (<2-fold elevated) D-dimer. Among 2219 participants in the final analysis, the probability that therapeutic anticoagulation increased organ support-free days compared to thromboprophylaxis was 99.0% (adjusted odds ratio 1.29, 95% credible interval 1.04 to 1.61). The adjusted absolute increase in survival to hospital discharge without organ support with therapeutic-dose anticoagulation was 4.6% (95% credible interval 0.7 to 8.1). In the primary adaptive stopping groups, the final probabilities of superiority for therapeutic anticoagulation were 97.3% in the high D-dimer group and 92.9% in the low D-dimer group. Major bleeding occurred in 1.9% and 0.9% of participants randomized to therapeutic anticoagulation and thromboprophylaxis, respectively.\n\nConclusionsIn non-critically ill patients with Covid-19, an initial strategy of therapeutic-dose anticoagulation with heparin increases the probability of survival to hospital discharge with reduced use of organ support.\n\nTrial registration numbers: NCT02735707, NCT04505774, NCT04359277, NCT04372589", + "rel_num_authors": 36, + "rel_authors": [ + { + "author_name": "Patrick R. Lawler", + "author_inst": "University of Toronto, Toronto, Canada; Peter Munk Cardiac Centre at University Health Network, Toronto, Canada" + }, + { + "author_name": "Ewan C. Goligher", + "author_inst": "University of Toronto, Toronto, Canada; University Health Network, Toronto, Canada" + }, + { + "author_name": "Jeffrey S. Berger", + "author_inst": "NYU Grossman School of Medicine, New York City, United States" + }, + { + "author_name": "Matthew D. Neal", + "author_inst": "University of Pittsburgh, Pittsburgh, United States, UPMC, Pittsburgh, United States" + }, + { + "author_name": "Bryan J. McVerry", + "author_inst": "University of Pittsburgh, Pittsburgh, United States, UPMC, Pittsburgh, United States" + }, + { + "author_name": "Jose C. Nicolau", + "author_inst": "Instituto do Corao (InCor), Hospital das Clnicas HCFMUSP, Universidade de So Paulo, So Paulo, Brazil" + }, + { + "author_name": "Michelle N. Gong", + "author_inst": "Montefiore Medical Center, Bronx, United States; Albert Einstein College of Medicine, Bronx, United States" + }, + { + "author_name": "Marc Carrier", + "author_inst": "Ottawa Hospital Research Institute, Ottawa, Canada; Institut du Savoir Montfort, Ottawa, Canada" + }, + { + "author_name": "Robert S. Rosenson", + "author_inst": "Icahn School of Medicine at Mount Sinai, New York City, United States" + }, + { + "author_name": "Harmony R. Reynolds", + "author_inst": "NYU Grossman School of Medicine, New York City, United States" + }, + { + "author_name": "Alexis F. Turgeon", + "author_inst": "Universit Laval, Qubec City, Canada; CHU de Qubec Universit Laval Research Center, Qubec City, Canada" + }, + { + "author_name": "Jorge Escobedo", + "author_inst": "Instituto Mexicano del Seguro Social, Mexico City, Mexico" + }, + { + "author_name": "David T. Huang", + "author_inst": "University of Pittsburgh, Pittsburgh, United States" + }, + { + "author_name": "Charlotte Ann Bradbury", + "author_inst": "University of Bristol, Bristol, United Kingdom; University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, United Kingdom" + }, + { + "author_name": "Brett L. Houston", + "author_inst": "University of Manitoba, Winnipeg, Canada; CancerCare Manitoba, Winnipeg, Canada" + }, + { + "author_name": "Lucy Z. Kornblith", + "author_inst": "Zuckerberg San Francisco General Hospital/University of California, San Francisco, United States" + }, + { + "author_name": "Anand Kumar", + "author_inst": "University of Manitoba, Winnipeg, Canada" + }, + { + "author_name": "Susan R. Kahn", + "author_inst": "McGill University, Montreal, Canada" + }, + { + "author_name": "Mary Cushman", + "author_inst": "Larner College of Medicine at the University of Vermont, Burlington, United States" + }, + { + "author_name": "Zoe McQuilten", + "author_inst": "Australian and New Zealand Intensive Care Research Centre, Monash University, Melbourne, Australia" + }, + { + "author_name": "Arthur S. Slutsky", + "author_inst": "University of Toronto, Toronto, Canada; St. Michael's Hospital Unity Health, Toronto, Canada" + }, + { + "author_name": "Keri S. Kim", + "author_inst": "University of Illinois, Chicago, United States" + }, + { + "author_name": "Anthony C. Gordon", + "author_inst": "Imperial College London, London, United Kingdom; Imperial College Healthcare NHS Trust, St. Mary's Hospital, London, United Kingdom" + }, + { + "author_name": "Bridget-Anne Kirwan", + "author_inst": "SOCAR Research SA, Nyon, Switzerland; London School of Hygiene and Tropical Medicine, London, UK" + }, + { + "author_name": "Maria M. Brooks", + "author_inst": "University of Pittsburgh, Pittsburgh, United States" + }, + { + "author_name": "Alisa M. Higgins", + "author_inst": "Australian and New Zealand Intensive Care Research Centre, Monash University, Melbourne, Australia" + }, + { + "author_name": "Roger J. Lewis", + "author_inst": "Berry Consultants, LLC, Austin, United States; Harbor-UCLA Medical Center, Torrance, United States" + }, + { + "author_name": "Elizabeth Lorenzi", + "author_inst": "Berry Consultants, LLC, Austin, United States" + }, + { + "author_name": "Scott M. Berry", + "author_inst": "Berry Consultants, LLC, Austin, United States" + }, + { + "author_name": "Lindsay R. Berry", + "author_inst": "Berry Consultants, LLC, Austin, United States" + }, + { + "author_name": "Derek C. Angus", + "author_inst": "University of Pittsburgh, Pittsburgh, United States; UPMC, Pittsburgh, United States" + }, + { + "author_name": "Colin J. McArthur", + "author_inst": "Australian and New Zealand Intensive Care Research Centre, Monash University, Melbourne, Australia; Auckland City Hospital, Auckland, New Zealand; NHS Blood and" + }, + { + "author_name": "Steven A. Webb", + "author_inst": "Australian and New Zealand Intensive Care Research Centre, Monash University, Melbourne, Australia; St John of God Hospital, Subiaco, Australia" + }, + { + "author_name": "Michael E. Farkouh", + "author_inst": "University of Toronto, Toronto, Canada; Peter Munk Cardiac Centre at University Health Network, Toronto, Canada" + }, + { + "author_name": "Judith S. Hochman", + "author_inst": "NYU Grossman School of Medicine, New York City, United States" + }, + { + "author_name": "Ryan Zarychanski", + "author_inst": "University of Manitoba, Winnipeg, Canada; CancerCare Manitoba, Winnipeg, Canada" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2021.05.12.21257133", "rel_title": "Effect of polymerized type I collagen in hyperinflammation of adult outpatients with symptomatic COVID-19: a double blind, randomised, placebo-controlled clinical trial.", @@ -745102,169 +747085,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.05.14.444111", - "rel_title": "CD147 antibody specifically and effectively inhibits infection and cytokine storm of SARS-CoV-2 variants", - "rel_date": "2021-05-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.14.444111", - "rel_abs": "SARS-CoV-2 and its variants are raging worldwide. Unfortunately, the global vaccination is not efficient enough to attain a vaccine-based herd-immunity and yet no special and effective drug is developed to contain the spread of the disease. Previously we have identified CD147 as a novel receptor for SARS-CoV-2 infection. Here, we demonstrated that CD147 antibody effectively inhibits infection and cytokine storm caused by SARS-CoV-2 variants. In CD147KO VeroE6 cells, infections of SARS-CoV-2, its variants (B.1.1.7, B.1.351) and pseudovirus mutants (B.1.1.7, B.1.351, B.1.525, B.1.526 (S477N), B.1.526 (E484K), P.1, P.2, B.1.617.1, B.1.617.2) were decreased. Meanwhile, CD147 antibody effectively blocked the entry of variants and pseudomutants in VeroE6 cells, and inhibited the expression of cytokines. A model of SARS-CoV-2-infected hCD147 transgenic mice was constructed, which recapitulated the features of exudative diffuse alveolar damage and dynamic immune responses of COVID-19. CD147 antibody could effectively clear the virus and alveolar exudation, resolving the pneumonia. We found the elevated level of cyclophilin A (CyPA) in plasma of severe/critical cases, and identified CyPA as the most important proinflammatory intermediate causing cytokine storm. Mechanistically, spike protein of SARS-CoV-2 bound to CD147 and initiated the JAK-STAT pathway, which induced expression of CyPA. CyPA reciprocally bound to CD147, triggered MAPK pathway and consequently mediated the expression of cytokine and chemokine. In conclusion, CD147 is a critical target for SARS-CoV-2 variants and CD147 antibody is a promising drug to control the new wave of COVID-19 epidemic.", - "rel_num_authors": 37, - "rel_authors": [ - { - "author_name": "Zhi-Nan Chen", - "author_inst": "The Fourth Military Medicial University" - }, - { - "author_name": "Ping Zhu", - "author_inst": "Department of Clinical Immunology, Xijing Hospital, Fourth Military Medical University" - }, - { - "author_name": "Huijie Bian", - "author_inst": "National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University" - }, - { - "author_name": "Jiejie Geng", - "author_inst": "Fourth Military Medical University" - }, - { - "author_name": "Liang Chen", - "author_inst": "School of Medicine, Shanghai University" - }, - { - "author_name": "Yufeng Yuan", - "author_inst": "Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Ruo Chen", - "author_inst": "National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University" - }, - { - "author_name": "Ke Wang", - "author_inst": "National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University" - }, - { - "author_name": "Yongqiang Deng", - "author_inst": "Beijing Institute of Microbiology and Epidemiology" - }, - { - "author_name": "Peng Du", - "author_inst": "Beijing Institute of Biotechnology" - }, - { - "author_name": "Jiangning Liu", - "author_inst": "Institute of Laboratory Animals Science, Chinese Academy of Medical Sciences" - }, - { - "author_name": "Guizhen Wu", - "author_inst": "MHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, China CDC" - }, - { - "author_name": "Youchun Wang", - "author_inst": "National Institutes for Food and Drug Control" - }, - { - "author_name": "Xiuxuan Sun", - "author_inst": "National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University" - }, - { - "author_name": "Ting Guo", - "author_inst": "National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University" - }, - { - "author_name": "Xu Yang", - "author_inst": "National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University" - }, - { - "author_name": "Jiao Wu", - "author_inst": "National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University" - }, - { - "author_name": "Jianli Jiang", - "author_inst": "National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University" - }, - { - "author_name": "Ling Li", - "author_inst": "National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University" - }, - { - "author_name": "Kui Zhang", - "author_inst": "Department of Clinical Immunology, Xijing Hospital, Fourth Military Medical University" - }, - { - "author_name": "Hua Zhu", - "author_inst": "Institute of Laboratory Animals Science, Chinese Academy of Medical Sciences" - }, - { - "author_name": "Zhaohui Zheng", - "author_inst": "Department of Clinical Immunology, Xijing Hospital, Fourth Military Medical University" - }, - { - "author_name": "Xianghui Fu", - "author_inst": "Department of Clinical Immunology, Xijing Hospital, Fourth Military Medical University" - }, - { - "author_name": "Fengfan Yang", - "author_inst": "Department of Clinical Immunology, Xijing Hospital, Fourth Military Medical University" - }, - { - "author_name": "Xiaochun Chen", - "author_inst": "Jiangsu Pacific Meinuoke Biopharmceutical Co. Ltd." - }, - { - "author_name": "Hao Tang", - "author_inst": "Jiangsu Pacific Meinuoke Biopharmceutical Co. Ltd." - }, - { - "author_name": "Zheng Zhang", - "author_inst": "National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University" - }, - { - "author_name": "Ding Wei", - "author_inst": "National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University" - }, - { - "author_name": "Yang Zhang", - "author_inst": "National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University" - }, - { - "author_name": "Ying Shi", - "author_inst": "National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University" - }, - { - "author_name": "Yumeng Zhu", - "author_inst": "National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University" - }, - { - "author_name": "Zhuo Pei", - "author_inst": "National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University" - }, - { - "author_name": "Fei Huo", - "author_inst": "National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University" - }, - { - "author_name": "Shirui Chen", - "author_inst": "National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University" - }, - { - "author_name": "Qingyi Wang", - "author_inst": "Department of Foreign Languages, Fourth Military Medical University" - }, - { - "author_name": "Wen Xie", - "author_inst": "Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Yirong Li", - "author_inst": "Zhongnan Hospital of Wuhan University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.05.12.21257086", "rel_title": "Distinct immune responses in patients infected with influenza or SARS-CoV-2, and in COVID-19 survivors, characterised by transcriptomic and cellular abundance differences in blood.", @@ -746192,6 +748012,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.11.21257060", + "rel_title": "Transmission roles of symptomatic and asymptomatic COVID-19 cases: a modeling study", + "rel_date": "2021-05-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.11.21257060", + "rel_abs": "Key PointsO_ST_ABSQuestionC_ST_ABSWhat is the transmissibility of COVID-19 asymptomatic and symptomatic cases, respectively? To date, they have not been well quantified in existing literature.\n\nFindingsThe transmissibility of asymptomatic and symptomatic COVID-19 increases with patient age. The asymptomatic cases had a 66.72% lower transmissibility rate than symptomatic cases.\n\nMeaningThe transmissibility of asymptomatic COVID-19 cases is not low. Asymptomatic cases are harder to detect compared to symptomatic cases. Consequently, the burden of asymptomatic transmission could potentially dominate the spreading in certain scenarios.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Jianbin Tan", + "author_inst": "Sun Yat-Sen University" + }, + { + "author_name": "Yang Ge", + "author_inst": "University of Georgia" + }, + { + "author_name": "Leonardo Martinez", + "author_inst": "Stanford University" + }, + { + "author_name": "Zhiping Chen", + "author_inst": "Zhejiang Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Changwei Li", + "author_inst": "Tulane University" + }, + { + "author_name": "Adrianna Westbrook", + "author_inst": "University of Georgia" + }, + { + "author_name": "Enfu Chen", + "author_inst": "Zhejiang Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Jinren Pan", + "author_inst": "Zhejiang Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Yang Li", + "author_inst": "Renmin University of China" + }, + { + "author_name": "Feng Ling", + "author_inst": "Zhejiang Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Jimin Sun", + "author_inst": "Zhejiang Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Hui Huang", + "author_inst": "Sun Yat-Sen University" + }, + { + "author_name": "Ye Shen", + "author_inst": "University of Georgia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.11.21257048", "rel_title": "Impact of the COVID-19 pandemic on the provision of routine childhood immunizations in Ontario, Canada", @@ -747176,45 +749063,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "transplantation" }, - { - "rel_doi": "10.1101/2021.05.11.21257047", - "rel_title": "COVID-19 case definitions, diagnostic testing criteria, and surveillance across the pandemic's 25 highest burden countries", - "rel_date": "2021-05-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.11.21257047", - "rel_abs": "ObjectiveWe compared suspect, probable, and confirmed case definitions, as well as diagnostic testing criteria, used in the COVID-19 pandemics 25 highest burden countries to aid interpretation of global and national surveillance data.\n\nMethodsWe identified the COVID-19 pandemics 25 countries with the highest disease burden based on the number of cumulative reported cases to the World Health Organization (WHO) as of 1 October 2020. We searched official websites of these countries for suspect, probable, and confirmed case definitions. Given that confirmation of COVID-19 usually requires diagnostic testing, we also searched for diagnostic testing eligibility criteria in these countries. Extracted case definitions and testing criteria were managed in a database and analyzed in Microsoft Excel.\n\nFindingsWe identified suspect, probable, and confirmed case definitions in 96%, 64%, and 100% of countries, respectively. Testing criteria were identified in 100% of countries. 56% of identified countries followed WHO recommendations for using a combination of clinical and epidemiological criteria as part of the suspect case definition. 75% of identified countries followed WHO recommendations on using clinical, epidemiological, and diagnostic criteria for probable cases. 72% of countries followed WHO recommendations on using PCR testing for confirming a case of COVID-19. Finally, 64% of countries used testing eligibility criteria at least as permissive as WHO.\n\nConclusionThere is marked heterogeneity in who is eligible for testing in countries and how countries define a case of COVID-19. This affects the ability to compare burden, transmission, and response impact estimates derived from case surveillance data across countries.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Amitabh Suthar", - "author_inst": "CDC" - }, - { - "author_name": "Sara Schubert", - "author_inst": "CDC" - }, - { - "author_name": "Julie Garon", - "author_inst": "CDC" - }, - { - "author_name": "Alexia Couture", - "author_inst": "CDC" - }, - { - "author_name": "Amy Brown", - "author_inst": "CDC" - }, - { - "author_name": "Sana Charania", - "author_inst": "CDC" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.11.21256862", "rel_title": "Impact of BNT162b first vaccination on the immune transcriptome of elderly patients infected with the B.1.351 SARS-CoV-2 variant", @@ -747930,6 +749778,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.05.07.21256824", + "rel_title": "Seroconversion rates following COVID-19 vaccination amongst patients with malignant disease- the impact of diagnosis and cancer-directed therapies", + "rel_date": "2021-05-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.07.21256824", + "rel_abs": "As COVID-19 has been shown to adversely affect patients with cancer, prophylactic strategies are critically needed. We determined the immunogenicity of COVID-19 vaccination in a cohort of cancer patients that had received full dosing with one of the FDA-approved COVID-19 vaccines. 201 oncology patients underwent anti-spike protein SARS-CoV-2 IgG testing post vaccination and demonstrated a high rate of seroconversion (94%) overall. When compared to solid tumors (98%), a significantly lower rate of seroconversion was observed in patients with hematological malignancies (85%), particularly recipients of anti-CD20 therapies (70%) and stem cell transplantation (74%). Patients receiving immune checkpoint inhibitor therapy (97%) or hormonal therapies (100%) demonstrated high seroconversion post-vaccination. Patients with prior COVID-19 infection demonstrated higher anti-spike IgG titers post-vaccination. Relatively lower IgG titers were noted following vaccination with the adenoviral when compared to the mRNA-based vaccines. These data demonstrate generally high immunogenicity of COVID-19 vaccination in oncology patients and identify vulnerable cohorts that need novel vaccination or passive immunization strategies.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Astha Thakkar", + "author_inst": "Montefiore Medical Center" + }, + { + "author_name": "Jesus Gonzalez Lugo", + "author_inst": "Montefiore Medical Center" + }, + { + "author_name": "Niyati Goradia", + "author_inst": "Montefiore Medical Center" + }, + { + "author_name": "Radhika Gali", + "author_inst": "Montefiore Medical Center" + }, + { + "author_name": "Lauren C. Shapiro", + "author_inst": "Montefiore Medical Center" + }, + { + "author_name": "Kith Pradhan", + "author_inst": "Montefiore Medical Center" + }, + { + "author_name": "Shafia Rahman", + "author_inst": "Montefiore Medical Center" + }, + { + "author_name": "So Yeon Kim", + "author_inst": "Montefiore Medical Center" + }, + { + "author_name": "Brian Ko", + "author_inst": "Montefiore Medical Center" + }, + { + "author_name": "R.Alejandro Sica", + "author_inst": "Montefiore Medical Center" + }, + { + "author_name": "Noah Kornblum", + "author_inst": "Montefiore Medical Center" + }, + { + "author_name": "Lizamarie Bachier-Rodriguez", + "author_inst": "Montefiore Medical Center" + }, + { + "author_name": "Margaret McCort", + "author_inst": "Montefiore Medical Center" + }, + { + "author_name": "Sanjay Goel", + "author_inst": "Montefiore Medical Center" + }, + { + "author_name": "Roman Perez-Soler", + "author_inst": "Montefiore Medical Center" + }, + { + "author_name": "Stuart Packer", + "author_inst": "Montefiore Medical Center" + }, + { + "author_name": "Joseph Sparano", + "author_inst": "Montefiore Medical Center" + }, + { + "author_name": "Benjamin Gartrell", + "author_inst": "Montefiore Medical Center" + }, + { + "author_name": "Della Makower", + "author_inst": "Montefiore Medical Center" + }, + { + "author_name": "Yitz D Goldstein", + "author_inst": "Montefiore Medical Center" + }, + { + "author_name": "Lucia Wolgast", + "author_inst": "Montefiore Medical Center" + }, + { + "author_name": "Amit Verma", + "author_inst": "Montefiore Medical Center" + }, + { + "author_name": "Balazs Halmos", + "author_inst": "Montefiore Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "oncology" + }, { "rel_doi": "10.1101/2021.05.13.21256973", "rel_title": "A Randomized Placebo-Controlled Trial of Sarilumab in Hospitalized Patients with Covid-19", @@ -749866,65 +751821,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2021.05.06.21256769", - "rel_title": "Pharmacogenomic and drug interaction risk associations with hospital length of stay among Medicare Advantage members with COVID-19", - "rel_date": "2021-05-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.06.21256769", - "rel_abs": "ImportanceCOVID-19 has severely impacted older populations and strained healthcare resources, with many patients requiring long periods of hospitalization. Reducing the hospital length of stay (LOS) reduces patient and hospital burden. Given that adverse drug reactions are known to prolong LOS, unmanaged pharmacogenomic risk and drug interactions among COVID-19 patients may be a risk factor for longer hospital stays.\n\nObjectiveThe objective of this study was to determine if pharmacogenomic and drug interaction risks were associated with longer lengths of stay among high-risk patients hospitalized with COVID-19.\n\nDesignRetrospective cohort study of medical and pharmacy claims\n\nSettingAdministrative database from a large U.S. health insurance company\n\nParticipantsMedicare Advantage members with a first COVID-19 hospitalization between January 2020 and June 2020, who did not die during the stay.\n\nExposures(1) Pharmacogenetic interaction probability (PIP) of [≤]25% (low), 26%-50% (moderate), or >50% (high), which indicate the likelihood that one or more clinically actionable gene-drug or gene-drug-drug interactions would be identified with testing; (2) drug-drug interaction (DDI) severity of minimal, minor, moderate, major, or contraindicated, which indicate the severity of an interaction between two or more active medications.\n\nMain Outcomes and MeasuresThe primary outcome was hospital length of stay. Results were stratified by hierarchical condition categories (HCC) counts and chronic conditions.\n\nResultsA total of 6,025 patients hospitalized with COVID-19 were included in the study. Patients with moderate or high PIP were hospitalized for 9% (CI: 4%-15%; p < 0.001) and 16% longer (CI: 8%-24%; p < 0.001), respectively, compared to those with low PIP, whereas RAF score was not associated with LOS. High PIP was significantly associated with 12%-22% longer lengths of stay compared to low PIP in patients with hypertension, hyperlipidemia, diabetes, or COPD. Finally, among patients with 2 or 3 HCCs, a 10% longer length of stay was observed among patients with moderate or more severe DDI compared to minimal or minor DDI.\n\nConclusions and RelevanceProactively mitigating pharmacogenomic risk has the potential to reduce length of stay in patients hospitalized with COVID-19 especially those with COPD, diabetes, hyperlipidemia, and hypertension.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSWhat is the impact of unmanaged pharmacogenomic risk among patients hospitalized with COVID-19?\n\nFindingsAmong 6,025 patients hospitalized with COVID-19, those with greater unmanaged pharmacogenomic risk for adverse drug reactions had longer hospital stays than those with lower risk, both within the entire cohort and within groups matched by number and type of chronic conditions.\n\nMeaningPreemptive pharmacogenomic testing may shorten hospital stay by reducing adverse drug reactions among seriously ill patients and more broadly improve patient risk classification, care utilization predictions, and health system performance.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Kristine Ashcraft", - "author_inst": "Invitae" - }, - { - "author_name": "Chad Moretz", - "author_inst": "Invitae" - }, - { - "author_name": "Chantelle Schenning", - "author_inst": "Invitae" - }, - { - "author_name": "Susan Rojahn", - "author_inst": "Invitae" - }, - { - "author_name": "Kae Vines Tanudtanud", - "author_inst": "UnitedHealth Group" - }, - { - "author_name": "Gwyn Omar Magoncia", - "author_inst": "UnitedHealth Group" - }, - { - "author_name": "Justine Reyes", - "author_inst": "UnitedHealth Group" - }, - { - "author_name": "Bernardo Marquez", - "author_inst": "UnitedHealth Group" - }, - { - "author_name": "Yinglong Guo", - "author_inst": "UnitedHealth Group" - }, - { - "author_name": "Elif Tokar-Erdemir", - "author_inst": "UnitedHealth Group" - }, - { - "author_name": "Taryn O. Hall", - "author_inst": "UnitedHealth Group" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2021.05.06.21256732", "rel_title": "Optimizing the spatio-temporal allocation of COVID-19 vaccines: Italy as a case study", @@ -750544,6 +752440,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.07.21256745", + "rel_title": "Meta-analysis of rapid direct-to-PCR assays for the qualitative detection of SARS-CoV-2", + "rel_date": "2021-05-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.07.21256745", + "rel_abs": "Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the ensuing COVID-19 pandemic present significant challenges to current diagnostic and therapeutic patient care pathways including whether new in vitro diagnostic tests can accurately identify and rule out current SARS-CoV-2 infection.\n\nThe gold standard diagnostic test to identify a current SARS-CoV-2 infection is a central laboratory-based molecular assay employing reverse transcription polymerase chain reaction (RT-PCR) with very high accuracy of detection; however, which typically requires 1-2 days turn-around for results. Rapid RT-PCR assays and systems have been developed which can be deployed locally (near-patient or point of care (POC)), provide faster results and not impact on already stressed central laboratory capacity. Rapid test results can be returned within the same clinical encounter, facilitating timely decisions that optimise the patient care pathway and support more rapid COVID-19 diagnosis, isolation and contract tracing activities1.\n\nDirect-to-PCR is an evolution of RT-PCR in which the patient sample is added directly to an amplification reaction without being subjected to prior nucleic acid extraction, purification, or quantification to reduce the time and monetary resources required to process samples. Rapid, direct-to-PCR systems further increase the speed of testing by combining rapid PCR instruments with direct-to-PCR assays, to generate results in less than two hours.\n\nThis appears to be the first meta-analysis assessing the accuracy of rapid direct-to-PCR in the detection of SARS-CoV-2. In total, 1,144 unique records were identified and screened using search string evaluation, 49 full-text reports and/or supplemental materials were assessed for inclusion. This resulted in 16 studies, reporting 22 datasets with 5322 patient samples (of which 2220 were identified as positive according to centralised laboratory testing) included in the analysis.\n\nThe overall percentage agreement (OPA) between the rapid direct RT-PCR and gold standard centralised laboratory RT-PCR was 95.10% with 91.22% positive percent agreement (PPA) and 98.16% negative percent agreement (NPA). When compared to commercially available tests were considered, these were assessed to be 96.95% OPA, 94.78 % PPA and 98.34 % NPA. Furthermore, the Cohens kappa statistical coefficient k = 0.94 (0.96 for commercial only), and Youden Index = 0.893 (0.924 for commercial only) indicate an almost perfect agreement. These results therefore indicate that direct-to-PCR assays performance is equivalent to the standard centralised laboratory PCR systems for the detection of SARS-CoV-2.\n\nObjectivesTo assess the efficacy of rapid direct-to-PCR assays and systems for the detection of SARS-CoV-2 in the hospital, care home and medical research population from November 2020 to July 2021.\n\nSearch methodsInitial electronic searches of the Cochrane COVID-19 Study Register (which includes daily updates from PubMed and Embase and preprints from medRxiv and bioRxiv) were undertaken on the 30th of April 2021, with a further search undertaken on 8th July 2021 (PRISMA flow diagram, Figure 2).\n\nO_FIG O_LINKSMALLFIG WIDTH=170 HEIGHT=200 SRC=\"FIGDIR/small/21256745v3_fig2.gif\" ALT=\"Figure 2\">\nView larger version (26K):\norg.highwire.dtl.DTLVardef@14e69fcorg.highwire.dtl.DTLVardef@1105ea2org.highwire.dtl.DTLVardef@1b50b5corg.highwire.dtl.DTLVardef@fce6b7_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 2.C_FLOATNO PRISMA flowchart\n\nC_FIG Selection criteriaStudies, published in English, of subjects with either suspected SARS-CoV-2 infection, known SARS-CoV-2 infection or known absence of infection, or those who were being screened for infection were included. Commercially available and research use only rapid direct-to-PCR assays (without RNA extraction and purification reporting results within two hours) were included in the study.\n\nData collection, extraction and analysisStudies were screened independently, in duplicate with any disagreements resolved by discussion with a third author. Study characteristics were extracted by one author and checked by a second; extraction of study results and assessments of risk of bias and applicability were undertaken independently in duplicate.\n\nWhere studies were not publicly available, sites that undertook in-service evaluations of rapid direct-to-PCR system were contacted and asked to supply anonymised datasets. Both reviewers independently performed data extraction and verification and calculated 2x2 contingency tables with the number of true positives, false positives, false negatives and true negatives. They resolved any disagreements by discussion and by review with the third reviewer.\n\nMain resultsIn total, 22 study cohorts were included (described in 16 study reports, including 5 unpublished reports), reporting results for 5322 samples (of which 2220 were confirmed SARS-CoV-2, as determined by central laboratory testing). Studies were mainly from Europe and North America and evaluated eight commercially available direct-to-PCR assay kits/cartridges, and six developed from other reagents.\n\nConclusionsThis appears to be the first meta-analysis assessing the accuracy of rapid direct-to-PCR in the detection of SARS-CoV-2. In total, 1,144 unique records were identified and screened using search string evaluation, 49 full-text reports and/or supplemental materials were assessed for inclusion. This resulted in 16 studies reporting 21 datasets with 5322 patient samples (2220 positive) included in the analysis.\n\nThe overall agreement between the commercially available rapid direct RT-PCR and gold standard centralised laboratory RT-PCR was 96.9% with 94.8% PPA and 98.4% NPA. Furthermore, the Cohens kappa statistical coefficient k = 0.96, indicating an almost perfect agreement and Youden Index = 0.93. These results show that direct-to-PCR assays performance is equivalent to the gold standard centralised laboratory RT-PCR systems for the detection of SARS-CoV-2.\n\nPlain language summaryO_ST_ABSWhat is a rapid direct-to-PCR test for diagnosing COVID-19?C_ST_ABSRapid direct-to-PCR tests are rapid tests that aim to confirm or rule out the presence of SARS-CoV-2 within 2 hours without complicated processing of the sample.\n\nHow accurate is a rapid direct-to-PCR test for diagnosing COVID-19?We compared the accuracy of rapid direct-to-PCR tests with gold standard centralised laboratory RT-PCR for the detection of SARS-CoV-2 and found that direct-to-PCR was as accurate as standard RT-PCR assays.\n\nWhy is this question important?People with suspected COVID-19 need to know quickly whether they are infected, so that they can self-isolate, inform close contacts and possibly receive treatment. Currently, COVID-19 infection is confirmed by a laboratory test called RT-PCR, which uses specialist equipment and often takes at least 24 hours to produce a result. If they are accurate, faster diagnosis could allow people to take appropriate action more rapidly, with the potential to reduce the spread of COVID-19.1\n\nWhat did we aim to find out?Our goal was to determine if commercially available and research use rapid direct-to-PCR tests are accurate enough to detect SARS-CoV-2 in comparison to gold standard laboratory RT-PCR.\n\nWhat did we do?We looked for studies that measured the accuracy of any commercially produced and research use rapid direct-to-PCR tests, in people tested for COVID-19 using RT-PCR. People could be tested in hospital or in the community. Studies could test people with or without symptoms.\n\nTests had to use minimal equipment, be performed safely without risking infection from the sample, and have results available within two hours of the sample being collected.\n\nWhat we found?We include 22 studies in the review. They investigated a total of 5322 nose or throat samples; COVID-19 was confirmed in 2220 of these samples. The studies investigated 15 different direct-to-PCR tests. They took place mainly in Europe and North America.\n\nWhat did we find?Although overall results for diagnosing and ruling out COVID-19 were good (91.2% of infections correctly diagnosed and 98.3% correctly ruled out), we noted a difference in COVID-19 detection between tests, especially those available as commercial kits versus ones assembled from reagents from different sources. However, we cannot be certain about whether results will remain the same in a real-world setting. We could not investigate differences in people with or without symptoms, nor time since symptoms-onset because the studies did not consistently provide enough clinical information about their participants.\n\nHow reliable were the results of the studies?In general, the studies included followed rigorous methods, in accordance with the tests intended use to detect COVID-19 and included at least two independent results to confirm or rule out COVID-19 infection. The results from different test brands varied and few studies compared multiple rapid-PCR tests. Most of the studies did not provide sufficient information to determine whether the detection levels would vary in people with COVID-19 symptoms versus without symptoms.\n\nWhat does this mean?On average the rapid direct-to-PCR were shown to be equivalent to gold standard laboratory-based RT-PCR tests and several direct-to-PCR tests show very high accuracy. However, for most of the tests, more evidence is needed particularly in people without symptoms, on the accuracy of repeated testing, and testing in non-healthcare settings such as schools (including self-testing).", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "R A Trevor", + "author_inst": "Novacyt Group" + }, + { + "author_name": "Seden Grippon", + "author_inst": "Novacyt Group" + }, + { + "author_name": "Mark Coldwell", + "author_inst": "Novacyt Group" + }, + { + "author_name": "Helen Chen", + "author_inst": "Novacyt Group" + }, + { + "author_name": "Lee Koh", + "author_inst": "Novacyt Group" + }, + { + "author_name": "Daryl Borley", + "author_inst": "Novacyt Group" + }, + { + "author_name": "Paul Oladimeji", + "author_inst": "Novacyt Group" + }, + { + "author_name": "Stephen Kidd", + "author_inst": "Novacyt Group" + }, + { + "author_name": "Joanne Martin", + "author_inst": "Queen Mary University of London" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.07.21256803", "rel_title": "Neutralizing response against E484K variant after original SARS-CoV-2 infection", @@ -751592,125 +753539,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.11.443286", - "rel_title": "Preclinical evaluation of a SARS-CoV-2 mRNA vaccine PTX-COVID19-B", - "rel_date": "2021-05-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.11.443286", - "rel_abs": "Safe and effective vaccines are needed to end the COVID-19 pandemic caused by SARS-CoV-2. Here we report the preclinical development of a lipid nanoparticle (LNP) formulated SARS-CoV-2 mRNA vaccine, PTX-COVID19-B. PTX-COVID19-B was chosen among three candidates after the initial mouse vaccination results showed that it elicited the strongest neutralizing antibody response against SARS-CoV-2. Further tests in mice and hamsters indicated that PTX-COVID19-B induced robust humoral and cellular immune responses and completely protected the vaccinated animals from SARS-CoV-2 infection in the lung. Studies in hamsters also showed that PTX-COVID19-B protected the upper respiratory tract from SARS-CoV-2 infection. Mouse immune sera elicited by PTX-COVID19-B vaccination were able to neutralize SARS-CoV-2 variants of concern (VOCs), including the B.1.1.7, B.1.351 and P.1 lineages. No adverse effects were induced by PTX-COVID19-B in both mice and hamsters. These preclinical results indicate that PTX-COVID19-B is safe and effective. Based on these results, PTX-COVID19-B was authorized by Health Canada to enter clinical trials in December 2020 with a phase 1 clinical trial ongoing (ClinicalTrials.gov number: NCT04765436).\n\nOne Sentence SummaryPTX-COVID19-B is a SARS-CoV-2 mRNA vaccine that is highly immunogenic, safe, and effective in preventing SARS-CoV-2 infection in mice and hamsters and is currently being evaluated in human clinical trials.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Jun Liu", - "author_inst": "University of Toronto" - }, - { - "author_name": "Patrick Budylowski", - "author_inst": "University of Toronto" - }, - { - "author_name": "Reuben Samson", - "author_inst": "University of Toronto" - }, - { - "author_name": "Bryan D Griffin", - "author_inst": "Sunnybrook Research Institute" - }, - { - "author_name": "Giorgi Babuadze", - "author_inst": "Sunnybrook Research Institute" - }, - { - "author_name": "Bhavisha Rathod", - "author_inst": "Mount Sinai Hospital" - }, - { - "author_name": "Karen Colwill", - "author_inst": "Mount Sinai Hospital" - }, - { - "author_name": "Jumai A Abioye", - "author_inst": "Providence Therapeutics Holdings Inc." - }, - { - "author_name": "Jordan A Schwartz", - "author_inst": "Providence Therapeutics Holdings Inc." - }, - { - "author_name": "Ryan Law", - "author_inst": "University of Toronto" - }, - { - "author_name": "Lily Yip", - "author_inst": "Sunnybrook Research Institute" - }, - { - "author_name": "Sang Kyun Ahn", - "author_inst": "University of Toronto" - }, - { - "author_name": "Serena Chau", - "author_inst": "University of Toronto" - }, - { - "author_name": "Maedeh Naghibosadat", - "author_inst": "Sunnybrook Research Institute" - }, - { - "author_name": "Yuko Arita", - "author_inst": "Providence Therapeutics Holding Inc." - }, - { - "author_name": "Queenie Hu", - "author_inst": "Mount Sinai Hospital" - }, - { - "author_name": "Feng Yun Yue", - "author_inst": "University of Toronto" - }, - { - "author_name": "Arinjay Banerjee", - "author_inst": "University of Saskatchewan" - }, - { - "author_name": "Karen Mossman", - "author_inst": "McMaster University" - }, - { - "author_name": "Samira Mubareka", - "author_inst": "University of Toronto" - }, - { - "author_name": "Robert A Kozak", - "author_inst": "Sunnybrook Research Institute" - }, - { - "author_name": "Michael S Pollanen", - "author_inst": "University of Toronto" - }, - { - "author_name": "Natalia Martin Orozco", - "author_inst": "Providence Therpeutics Holdings Inc." - }, - { - "author_name": "Anne-Claude Gingras", - "author_inst": "University of Toronto" - }, - { - "author_name": "Eric G Marcusson", - "author_inst": "Providence Therapeutics Holdings Inc." - }, - { - "author_name": "Mario A Ostrowski", - "author_inst": "University of Toronto" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.05.11.443609", "rel_title": "Early cross-coronavirus reactive signatures of protective humoral immunity against COVID-19", @@ -752778,6 +754606,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, + { + "rel_doi": "10.1101/2021.05.06.21256289", + "rel_title": "The performance of the SARS-CoV-2 RT-PCR test as a tool for detecting SARS-CoV-2 infection in the population. A survey of routine laboratory RT-PCR test results from the region of Muenster, Germany", + "rel_date": "2021-05-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.06.21256289", + "rel_abs": "ObjectivesTo evaluate the population-based performance of the SARS-CoV-2 RT-PCR test as a tool for detecting SARS-CoV-2 infection during the pandemic in 2020.\n\nMethodsWe analysed SARS-CoV-2 RT-PCR results of 162,457 people living in Munster, Germany screened at nursing homes, testing sites, at schools, regional hospitals, and by general practitioners. All PCRs were done with the same cobas SARS-CoV-2 RT-PCR system (Roche Diagnostics). We stratified positive RT-PCR results by cycle threshold (Ct) values, periods of the national test strategy, age, sex, and symptoms.\n\nResultsAmong 162,457 individuals, 4164 (2.6%) had a positive RT-PCR test result, defined as Ct<40. Depending on the national test strategy, higher positive rates were associated with testing predominantly symptomatic people. Children (0-9 years) and older adults (70+ years). Only 40.6% of test positives showed low Ct values < 25 (potentially infectious). The percentage of Ct values below 25 was lower among children (0-9), adolescents (10-19), and among the elderly (70+ years).\n\nConclusionsRT-PCR testing as a tool for mass screening should not be used alone as a base for pandemic decision making including measures such as quarantine, isolation, and lockdown.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Andreas Stang", + "author_inst": "University Hospital of Essen" + }, + { + "author_name": "Johannes Robers", + "author_inst": "MVZ Labor Muenster Hafenweg GmbH" + }, + { + "author_name": "Birte Schonert", + "author_inst": "MVZ Labor Muenster Hafenweg GmbH" + }, + { + "author_name": "Karl-Heinz Joeckel", + "author_inst": "Institute of Medical Informatics, Biometry and Epidemiology, UniversityHospital of Essen" + }, + { + "author_name": "Angela Spelsberg", + "author_inst": "Tumorzentrum Aachen e.V." + }, + { + "author_name": "Ulrich Keil", + "author_inst": "Institute of Epidemiology and Social Medicine, University of Muenster" + }, + { + "author_name": "Paul Cullen", + "author_inst": "MVZ Labor Muenster Hafenweg GmbH" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.07.21249238", "rel_title": "multiSero: open multiplex-ELISA platform for analyzing antibody responses to SARS-CoV-2 infection", @@ -754494,49 +756365,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.11.21256930", - "rel_title": "Clinicopathological features and outcome of COVID-19- early experiences from three covid hospitals, Chittagong, Bangladesh", - "rel_date": "2021-05-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.11.21256930", - "rel_abs": "IntroductionCOVID 19 is an unknown virus affecting mankind creating a deadly experience to all. It is true for Bangladesh also. So the objectives of the present study is to find the clinicopathological features and outcome of COVID patients admitted in three COVID dedicated hospitals of Chittagong, Bnagladesh.\n\nMethodsThis was an observational study where a total of 209 patients admitted in three COVID dedicated hospital were recruited. Clinicopathological data were recorded and patients were under observation till discharge and thus outcome were recorded. Prior consent was taken from the patients and ethical clearance was also taken. Data was compiled and analyzed by SPSS-20.\n\nResultsAmong 209 patients most of them were male 139(66.5%) and male to female ratio was 1.98:1. Age group distribution revealed more were aggregated in age group 41-50 years 36(17.2%), 51-60 years 54(25.8%) and 61-70 years 57(27.3%). Among all 92(44%) patients were RT-PCR positive and 117(56%) were probable cases. Fever was present in 195(93.3%) cases, cough in 180(86.1%), respiratory distress in 105(50.2%) anosmia in 123(58.8%), aguesea in 112 (53.58%) and lethargy was present in 143(68.42%). Chest X-ray findings revealed 73(34.9%) had bilateral patchy opacities, 20(9.6%) had unilateral opacities 65(31.1%) had consolidations, 6(2.9%) had ground glass opacities and 2(1.0%) had pleural effusion. Supplemental O2 was given in 173(82.8%) patients, Favipiravir in 59(28.2%), Remdisivir in 111(53.1%), Methylprednisolone in 87(41.6%), Dexamethasone in 93(44.5%), Antibiotics in 204(97.60%), Toccilizumab in 34(16.3%), plasma in 18(8.6%) and LMWH in 200(95.7%) patients. Regarding outcome of the COVID patients admitted, 85(92.4%) patients improved, 6(6.5%) died who were RT-PCR positive and 107(91.15%) improved, 9(7.7%) died who were probable cases. Total death rate was 7.1%.\n\nConclusionPresent study findings were some early activities among COVID patients in the years 2020. Male were more affected and middle age group people were the most victims.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Rajat Sanker Roy Biswas", - "author_inst": "CMOSHMC" - }, - { - "author_name": "Jishu Dev Nath", - "author_inst": "CMOSHMC" - }, - { - "author_name": "Pranab Kumar Barua", - "author_inst": "BITID" - }, - { - "author_name": "Safatuj Jahan", - "author_inst": "CMOSHMC" - }, - { - "author_name": "Mohammed Saiful Islam", - "author_inst": "CMOSHMC" - }, - { - "author_name": "Kazi Forhad Ahmed", - "author_inst": "CMOSHMC" - }, - { - "author_name": "Md Rejaul Karim", - "author_inst": "Rangamati Medical College" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.11.21256719", "rel_title": "Incidence and Epidemiological study of COVID-19 in Nagpur urban region (India) using Molecular testing", @@ -755312,6 +757140,53 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.05.04.21256650", + "rel_title": "Importance of E484K and N501Y mutations in SARS-CoV-2 for genomic surveillance: rapid detection by restriction enzyme analysis", + "rel_date": "2021-05-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.04.21256650", + "rel_abs": "IntroductionVariants of Concern of SARS-CoV-2 (VOCs), the new coronavirus responsible for COVID-19, have emerged in several countries. Two mutations in the gene coding for the Spike protein of the viral genome are particularly important and associated with some of these variants: E484K and N501Y. Restriction enzyme analysis is proposed as a rapid method to detect these two mutations.\n\nMethodologyA search on GISAID was performed in April 2021 to detect the frequency of these two mutations in the sequence available and their association with other lineages. A small amplicon from the Spike gene was digested with two enzymes: HpyAV, which allows detecting E484K mutation, and MseI, for detecting the N501Y one.\n\nResultsThe mutations E484K and N501Y, associated with VOCs, have emerged in several other lineages, particularly E484K. A 100% correlation was observed with sequencing results.\n\nConclusionsThe proposed methodology, which allows screening a great number of samples, will probably help to provide more information on the prevalence and epidemiology of these mutations worldwide, to select the candidates for whole-genome sequencing.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Rossana C Jaspe", + "author_inst": "IVIC" + }, + { + "author_name": "Yoneira Sulbaran", + "author_inst": "IVIC" + }, + { + "author_name": "Carmen L Loureiro", + "author_inst": "IVIC" + }, + { + "author_name": "Pierina D Angelo", + "author_inst": "INHRR" + }, + { + "author_name": "Lieska Rodriguez", + "author_inst": "INHRR" + }, + { + "author_name": "Domingo J Garzaro", + "author_inst": "IVIC" + }, + { + "author_name": "Hector R Rangel", + "author_inst": "IVIC" + }, + { + "author_name": "Flor H Pujol", + "author_inst": "IVIC" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.07.21256539", "rel_title": "Immune profile of children with post-acute sequelae of SARS-CoV-2 infection (Long Covid)", @@ -756244,133 +758119,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.05.21256690", - "rel_title": "A new SARS-CoV-2 variant poorly detected by RT-PCR on nasopharyngeal samples, with high lethality", - "rel_date": "2021-05-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.05.21256690", - "rel_abs": "BackgroundIn early January 2021, an outbreak of nosocomial cases of COVID-19 emerged in Western France, with RT-PCR tests repeatedly negative on nasopharyngeal samples but positive on lower respiratory tract samples. Whole genome sequencing (WGS) revealed a new variant, currently defining a novel SARS-CoV-2 lineage: B.1.616. In March, WHO classified this variant as under investigation (VUI). We analyzed the characteristics and outcomes of COVID-19 cases related to this new variant.\n\nMethodsClinical, virological, and radiological data were retrospectively collected from medical charts in the two hospitals involved. We enrolled patients with at least one of the following: i) positive SARS-CoV-2 RT-PCR on a respiratory sample; ii) seroconversion with anti-SARS-CoV-2 IgG/IgM; iii) suggestive symptoms and typical features of COVID-19 on chest CT scan. Cases were categorized as either: i) B.1.616; ii) variant of concern (VOC); iii) unknown.\n\nFindingsFrom January 1st to March 24th, 2021, 114 patients fulfilled the inclusion criteria: B.1.616 (n=34), VOC (n=32), and unknown (n=48). B.1.616-related cases were older than VOC-related cases (81 years [73-88], vs 73 years [67-82], P<0.05) and their first RT-PCR tests were less often positive (5/34, 15% vs 31/32, 97%, P<0.05). The B.1.616 variant was independently associated with severe disease (multivariable Cox model HR 4.2 [1.3- 13.5], P=0.018), and increased lethality (logrank test P=0.01): 28-day mortality 15/34 (44%) with B.1.616, vs. 5/32 (16%) for VOC, P=0.036.\n\nInterpretationWe report a nosocomial outbreak of COVID-19 cases related to a new variant, B.1.616, poorly detected by RT-PCR on nasopharyngeal samples, with high lethality.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSAmong the numerous SARS-CoV-2 variants described worldwide, only 3 are currently classified as Variant of Concern (VOC) by the WHO, since they are associated with either an increased risk in transmissibility, severity, or significant reduction in neutralization by antibodies: B.1.1.7, B.1.351 and P.1 (Pango lineage nomenclature). With the ongoing circulation of SARS-CoV-2 in many places worldwide, the emergence of new variants may reduce the efficacy of vaccines and jeopardize our prospects to control the pandemic. In early January 2021, an outbreak of cases highly suggestive of COVID-19 despite negative RT-PCR tests on repeated nasopharyngeal (NP) samples was reported in Western France, leading to several nosocomial clusters. Whole-genome sequencing (WGS) from lower respiratory tract samples identified a new lineage of SARS-CoV-2 virus, classified as B1.616. Consequently, the French public health agency (Sante publique France) and the WHO classified B.1.616 as variant under investigation (VUI).\n\nAdded value of this studyOur observational study, conducted from January 1st to March 24th 2021 in the B.1.616 identified area, provides the first clinical and virological description of B.1.616-associated COVID-19. The 34 cases had clinical, biological and radiological findings in line with classical features of COVID-19, while RT-PCR tests on nasopharyngeal (NP) samples failed to detect SARS-CoV-2 in most patients. Indeed, this gold-standard test was positive in only 15% of the first tests in B.1.616-related COVID-19 patients. Of note, the diagnostic performance of RT-PCR tests was satisfactory on lower respiratory tract samples, suggesting that failure to detect B.1.616 on NP samples would be due to a viral load below the limit of detection in the upper respiratory tract, rather than to genomic mismatches between routine RT-PCR targets and this variant. In our cohort, B.1.616 was independently associated with worse clinical outcome, with high 28-day mortality (44%).\n\nImplications of all the available evidenceDiagnosis of B.1.616-related COVID-19 cases should not rely on RT-PCR tests on NP samples. In the epidemic area, strict infection control measures must be maintained as long as COVID-19 diagnosis is not ruled out, in order to limit nosocomial clusters and case fatality. Further studies are needed to confirm and investigate the association between genomic characteristics of B.1.616, and i) poor detection by RT-PCR tests on NP samples; ii) prognosis.", - "rel_num_authors": 28, - "rel_authors": [ - { - "author_name": "Pierre FILLATRE", - "author_inst": "Centre Hospitalier Yves Le Foll" - }, - { - "author_name": "Marie Jose DUFOUR", - "author_inst": "Centre Hospitalier Pierre-le-Damany" - }, - { - "author_name": "Sylvie BEHILLIL", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Remi VATAN", - "author_inst": "Centre Hospitalier Pierre-le-Damany" - }, - { - "author_name": "Pascale REUSSE", - "author_inst": "Centre Hospitalier Pierre-le-Damany" - }, - { - "author_name": "Alice GABELLEC", - "author_inst": "Centre Hospitalier Pierre-le-Damany" - }, - { - "author_name": "Nicolas VELMANS", - "author_inst": "Centre Hospitalier Pierre-le-Damany" - }, - { - "author_name": "Catherine MONTAGNE", - "author_inst": "Centre Hospitalier Pierre-le-Damany" - }, - { - "author_name": "Sophie GEFFROY", - "author_inst": "Centre Hospitalier Pierre-le-Damany" - }, - { - "author_name": "Edith DROUMAGUET", - "author_inst": "Centre Hospitalier Pierre-le-Damany" - }, - { - "author_name": "Veronique MEROUR", - "author_inst": "Centre Hospitalier Pierre-le-Damany" - }, - { - "author_name": "Vincent Enouf", - "author_inst": "Insitut Pasteur" - }, - { - "author_name": "Rodolphe BUZELE", - "author_inst": "CH de Saint-Brieuc" - }, - { - "author_name": "Marion VALENCE", - "author_inst": "CH de Saint-Brieuc" - }, - { - "author_name": "Elena GUILLOTEL", - "author_inst": "CH de Saint-Brieuc" - }, - { - "author_name": "Bertrand GAGNIERE", - "author_inst": "Sante publique France" - }, - { - "author_name": "Artem BAIDALUK", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Anna ZHUKOVA", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Mathieu TOURDJMAN", - "author_inst": "Sante publique France" - }, - { - "author_name": "Vincent THIBAULT", - "author_inst": "CHU Rennes" - }, - { - "author_name": "Claire GROLHIER", - "author_inst": "CHU Rennes" - }, - { - "author_name": "Charlotte PRONIER", - "author_inst": "CHU Rennes" - }, - { - "author_name": "Xavier LESCURE", - "author_inst": "CHU Bichat" - }, - { - "author_name": "Etienne SIMON-LORIERE", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Dominique COSTAGLIOLA", - "author_inst": "Institut Pierre Louis d Epidemiologie et de Sante Publique" - }, - { - "author_name": "Sylvie VAN DER WERF", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Pierre TATTEVIN", - "author_inst": "CHU Rennes" - }, - { - "author_name": "Nicolas MASSART", - "author_inst": "CH de Saint Brieuc" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.06.21256706", "rel_title": "Saudi Arabian SARS-CoV-2 genomes implicate a mutant Nucleocapsid protein in modulating host interactions and increased viral load in COVID-19 patients", @@ -757402,6 +759150,29 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.05.09.443331", + "rel_title": "SARS-CoV-2 ferritin nanoparticle vaccines elicit broad SARS coronavirus immunogenicity", + "rel_date": "2021-05-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.09.443331", + "rel_abs": "The need for SARS-CoV-2 next-generation vaccines has been highlighted by the rise of variants of concern (VoC) and the long-term threat of other coronaviruses. Here, we designed and characterized four categories of engineered nanoparticle immunogens that recapitulate the structural and antigenic properties of prefusion Spike (S), S1 and RBD. These immunogens induced robust S-binding, ACE2-inhibition, and authentic and pseudovirus neutralizing antibodies against SARS-CoV-2 in mice. A Spike-ferritin nanoparticle (SpFN) vaccine elicited neutralizing titers more than 20-fold higher than convalescent donor serum, following a single immunization, while RBD-Ferritin nanoparticle (RFN) immunogens elicited similar responses after two immunizations. Passive transfer of IgG purified from SpFN- or RFN-immunized mice protected K18-hACE2 transgenic mice from a lethal SARS-CoV-2 virus challenge. Furthermore, SpFN- and RFN-immunization elicited ACE2 blocking activity and neutralizing ID50 antibody titers >2,000 against SARS-CoV-1, along with high magnitude neutralizing titers against major VoC. These results provide design strategies for pan-coronavirus vaccine development.\n\nHIGHLIGHTSO_LIIterative structure-based design of four Spike-domain Ferritin nanoparticle classes of immunogens\nC_LIO_LISpFN-ALFQ and RFN-ALFQ immunization elicits potent neutralizing activity against SARS-CoV-2, variants of concern, and SARS-CoV-1\nC_LIO_LIPassively transferred IgG from immunized C57BL/6 mice protects K18-hACE2 mice from lethal SARS-CoV-2 challenge\nC_LI", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "M. Gordon Joyce", + "author_inst": "WRAIR" + }, + { + "author_name": "Kayvon Modjarrad", + "author_inst": "Walter Reed Army Institute of Research" + } + ], + "version": "1", + "license": "", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.05.10.443474", "rel_title": "Binding of SARS-CoV-2 fusion peptide to host membranes", @@ -758658,169 +760429,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.05.21256681", - "rel_title": "A Prenylated dsRNA Sensor Protects Against Severe COVID-19 and is Absent in Horseshoe Bats", - "rel_date": "2021-05-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.05.21256681", - "rel_abs": "Cell autonomous antiviral defenses can inhibit the replication of viruses and reduce transmission and disease severity. To better understand the antiviral response to SARS-CoV-2, we used interferon-stimulated gene (ISG) expression screening to reveal that OAS1, through RNase L, potently inhibits SARS-CoV-2. We show that while some people can express a prenylated OAS1 variant, that is membrane-associated and blocks SARS-CoV-2 infection, other people express a cytosolic, nonprenylated OAS1 variant which does not detect SARS-CoV-2 (determined by the splice-acceptor SNP Rs10774671). Alleles encoding nonprenylated OAS1 predominate except in people of African descent. Importantly, in hospitalized patients, expression of prenylated OAS1 was associated with protection from severe COVID-19, suggesting this antiviral defense is a major component of a protective antiviral response. Remarkably, approximately 55 million years ago, retrotransposition ablated the OAS1 prenylation signal in horseshoe bats (the presumed source of SARS-CoV-2). Thus, SARS-CoV-2 never had to adapt to evade this defense. As prenylated OAS1 is widespread in animals, the billions of people that lack a prenylated OAS1 could make humans particularly vulnerable to the spillover of coronaviruses from horseshoe bats.", - "rel_num_authors": 37, - "rel_authors": [ - { - "author_name": "Arthur Wickenhagen", - "author_inst": "MRC University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, University of Glasgow, UK" - }, - { - "author_name": "Elena Sugrue", - "author_inst": "MRC University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, University of Glasgow, UK" - }, - { - "author_name": "Spyros Lytras", - "author_inst": "MRC University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, University of Glasgow, UK" - }, - { - "author_name": "Srikeerthana Kuchi", - "author_inst": "MRC University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, University of Glasgow, UK" - }, - { - "author_name": "Matthew L Turnbull", - "author_inst": "MRC University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, University of Glasgow, UK" - }, - { - "author_name": "Colin Loney", - "author_inst": "MRC University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, University of Glasgow, UK" - }, - { - "author_name": "Vanessa Herder", - "author_inst": "MRC University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, University of Glasgow, UK" - }, - { - "author_name": "Jay Allan", - "author_inst": "MRC University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, University of Glasgow, UK" - }, - { - "author_name": "Innes Jarmson", - "author_inst": "MRC University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, University of Glasgow, UK" - }, - { - "author_name": "Natalia Cameron-Ruiz", - "author_inst": "MRC University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, University of Glasgow, UK" - }, - { - "author_name": "Margus Varjak", - "author_inst": "MRC University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, University of Glasgow, UK" - }, - { - "author_name": "Rute M Pinto", - "author_inst": "MRC University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, University of Glasgow, UK" - }, - { - "author_name": "Douglas G Stewart", - "author_inst": "MRC University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, University of Glasgow, UK" - }, - { - "author_name": "Simon Swingler", - "author_inst": "MRC University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, University of Glasgow, UK" - }, - { - "author_name": "Marko Noerenberg", - "author_inst": "MRC University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, University of Glasgow, UK" - }, - { - "author_name": "Edward J D Greenwood", - "author_inst": "Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cam" - }, - { - "author_name": "Thomas W M Crozier", - "author_inst": "Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cam" - }, - { - "author_name": "Quan Gu", - "author_inst": "MRC University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, University of Glasgow, UK" - }, - { - "author_name": "Sara Clohisey", - "author_inst": "Roslin Institute, University of Edinburgh, United Kingdom" - }, - { - "author_name": "Bo Wang", - "author_inst": "Roslin Institute, University of Edinburgh, United Kingdom" - }, - { - "author_name": "Fabio Trindade Maranhao Costa", - "author_inst": "Laboratory of Tropical Diseases Prof. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University o" - }, - { - "author_name": "Monique Freire Santana", - "author_inst": "Department of Education and Research, Oncology Control Centre of Amazonas State FCECON, Manaus, AM, Brazil; Tropical Medicine Foundation Dr. Heitor Vieira Doura" - }, - { - "author_name": "Luiz Carlos de Lima Ferreira", - "author_inst": "Department of Pathology and Forensic Medicine, Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, AM, Brazil" - }, - { - "author_name": "- ISARIC4C-Investigators", - "author_inst": "" - }, - { - "author_name": "Joao Luiz Da Silva Filho", - "author_inst": "Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, UK" - }, - { - "author_name": "Matthias Marti", - "author_inst": "Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, UK" - }, - { - "author_name": "Richard J Stanton", - "author_inst": "Division of Infection & Immunity, Cardiff University, Cardiff, United Kingdom" - }, - { - "author_name": "Eddie C Y Wang", - "author_inst": "Division of Infection & Immunity, Cardiff University, Cardiff, United Kingdom" - }, - { - "author_name": "Alfredo Castello-Palomares", - "author_inst": "MRC University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, University of Glasgow, UK" - }, - { - "author_name": "Antonia Ho", - "author_inst": "MRC University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, University of Glasgow, UK" - }, - { - "author_name": "Kenneth Baillie", - "author_inst": "Roslin Institute, University of Edinburgh, United Kingdom" - }, - { - "author_name": "Ruth F Jarrett", - "author_inst": "MRC University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, University of Glasgow, UK" - }, - { - "author_name": "David L Robertson", - "author_inst": "MRC University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, University of Glasgow, UK" - }, - { - "author_name": "Massimo Palmarini", - "author_inst": "MRC University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, University of Glasgow, UK" - }, - { - "author_name": "Paul J Lehner", - "author_inst": "Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cam" - }, - { - "author_name": "Suzannah J Rihn", - "author_inst": "MRC University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, University of Glasgow, UK" - }, - { - "author_name": "Sam J Wilson", - "author_inst": "MRC University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, University of Glasgow, UK" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.06.21256407", "rel_title": "Cumulative incidence of SARS-CoV-2 infections among adults in Georgia, USA, August-December 2020", @@ -759780,6 +761388,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.06.21256629", + "rel_title": "Development and validation of cost-effective one-step multiplex RT-PCR assay for detecting the SARS-CoV-2 infection using SYBR Green melting curve analysis", + "rel_date": "2021-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.06.21256629", + "rel_abs": "TaqMan probe-based expensive commercial real-time (RT) PCR kits are being used in COVID-19 diagnosis. The unprecedented scale of SARS-CoV-2 infections has urgently needed to meet the challenge of testing more persons at a reasonable cost. This study developed a rapid, simple, and cost-effective alternative diagnostic method based on melting curve analysis of SYBR green multiplex assay with a host-specific internal control. A total of 90 randomly selected samples were used for comparing the assay with an available commercial kit to analyse the variation and validity of this in-house developed method. Our customized designed primers specifically detected the virus as similar to commercial kit manufactured by Sansure Biotech Inc. We optimized separately the N, E, S, and RdRp genes by SYBR Green RT-PCR method based on melting curve analysis. Afterwards, a multiplex COVID-19 diagnosis method targeting N and E genes of the virus along with the {beta}-actin gene of the host as an internal control has been established. The total run-time of our proposed method was less than 90 minutes. The cost of each sample processing was less than $2. Overall, this one-step and one-tube method can revolutionize the COVID-19 diagnosis in developing countries.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Shovon Lal Sarkar", + "author_inst": "Jashore University of Science and Technology" + }, + { + "author_name": "A. S. M. Rubayet Ul Alam", + "author_inst": "Jashore University of Science and Technology" + }, + { + "author_name": "Prosanto Kumar Das", + "author_inst": "Jashore University of Science and Technology" + }, + { + "author_name": "Md. Hasan Ali Pramanik", + "author_inst": "Jashore University of Science and Technology" + }, + { + "author_name": "Hassan M. Al-Emran", + "author_inst": "Jashore University of Science and Technology" + }, + { + "author_name": "Iqbal Kabir Jahid", + "author_inst": "Jashore University of Science and Technology" + }, + { + "author_name": "Md. Anwar Hossain", + "author_inst": "Jessore University of Science and Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.04.21256637", "rel_title": "Travel-driven emergence and spread of SARS-CoV-2 lineage B.1.620 with multiple VOC-like mutations and deletions in Europe", @@ -760676,65 +762327,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.05.05.21256598", - "rel_title": "How can risk of COVID-19 transmission be minimised in domiciliary care for older people: development, parameterisation and initial results of a simple mathematical model", - "rel_date": "2021-05-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.05.21256598", - "rel_abs": "This paper proposes and analyses a stochastic model for the spread of an infectious disease that is transmitted between clients and care workers in the UK domiciliary care setting. Interactions between clients and care workers are modelled using specially generated networks, with network parameters reflecting realistic patterns of care needs and visit allocation. These networks are then used to simulate and SEIR-type epidemic dynamics with different numbers of infectious and recovery stages. The results indicate that with the same overall capacity provided by care workers, the minimum peak proportion of infection, and the smallest overall size of infection are achieved for the highest proportion of overlap between visit allocation, i.e. when care workers have the highest chances of being allocated a visit to the same client they have visited before. An intuitive explanation of this is that while providing the required care coverage, maximising overlap in visit allocation reduces the possibility of an infectious care worker inadvertently spreading the infection to other clients. The model is quite generic and can be adapted to any particular directly transmitted infectious disease, such as, more recently, COVID-19, provided accurate estimates of disease parameters can be obtained from real data.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Istvan Kiss", - "author_inst": "University of Sussex" - }, - { - "author_name": "Konstantin Blyuss", - "author_inst": "University of Sussex" - }, - { - "author_name": "Yuliya Kyrychko", - "author_inst": "University of Sussex" - }, - { - "author_name": "Jo Middleton", - "author_inst": "University of Oxford" - }, - { - "author_name": "Daniel Roland", - "author_inst": "University of Kent" - }, - { - "author_name": "Lavinia Bertini", - "author_inst": "University of Sussex" - }, - { - "author_name": "Leanne Bogen-Johnston", - "author_inst": "University of Sussex" - }, - { - "author_name": "Wendy Wood", - "author_inst": "University of Brighton" - }, - { - "author_name": "Rebecca Sharp", - "author_inst": "NHS" - }, - { - "author_name": "Julien Forder", - "author_inst": "University of Kent" - }, - { - "author_name": "Jackie A Cassell", - "author_inst": "Brighton and Sussex Medical School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.05.06.21256587", "rel_title": "Short-term effects of BNT162b2 mRNA COVID-19 vaccination on physiological measures: a prospective study", @@ -761766,6 +763358,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2021.05.05.21256285", + "rel_title": "Thermal Camera detection of High Temperature for mass COVID Screening", + "rel_date": "2021-05-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.05.21256285", + "rel_abs": "The COVID-19 [SARS-COV-2] pandemic has had a devastating global impact, with both the human and socio economic costs being severe. One result of the COVID-19 pandemic is the emergence of an urgent requirement for effective techniques and technologies for screening individuals showing symptoms of infection in a non-invasive and non-contact way. Systems that exploit thermal imaging technology to screen individuals show promise to satisfy the desired criteria, including offering a non-contact, non-invasive method of temperature measurement. Furthermore, the potential for mass and passive screening makes thermal imaging systems an attractive technology where current standard of care methods are not practical.\n\nCritically, any fever screening solution must be capable of accurate temperature measurement and subsequent prediction of core temperature. This is essential to ensure a high sensitivity in identifying fever while maintaining a low rate of false positives. This paper discusses the results and analysis of a clinical trial undertaken by Thales UK Ltd and the Queen Elizabeth University Teaching Hospital in Glasgow to assess the accuracy and operation of the High Temperature Detection (HTD) system developed by Thales UK Ltd when used in a clinical setting.\n\nResults of this single centre prospective observational cohort study show that the measured laboratory accuracy of the Thales HTD system (RMSE=0.1{degrees}C) is comparable to the accuracy when used in a clinical setting (RMSE = 0.15{degrees}C) when measuring a calibrated blackbody source at typical skin temperature. For measurement of forehead skin temperature, the system produced results commensurate with close contact measurement methods (R = 0.86, Mean error=0.05{degrees}C).. Compared to measured tympanic temperatures, measurement of the forehead skin temperature by the HTD system showed a moderate correlation (R = 0.43),), which is stronger than close contact IR forehead thermometers (R = 0.20,0.35) An improved correlation was observed between the maximum facial temperature measured by the HTD system and measured tympanic temperatures (R = 0.53), which is significantly stronger than the close contact methods. A linear predictive model for tympanic temperature based on the measured maximum facial temperatures resulted in a root mean square error (RMSE = 0.50{degrees}C) that is marginally larger than what is expected as a compound of errors in the measuring devices (RMSE=0.45{degrees}C).\n\nThe study demonstrates that the HTD could be applied in the clinical and non-clinical setting as a screening mechanism to detect citizens with raised temperature. This approach would enable high volume surveillance and identification of individuals that contribute to further spread of COVID-19. Deployment of the HTD system could be implemented as part of a screening tool to support measures to enhance public safety and confidence in areas of high throughput, such as airports, shopping centres or places of work.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Richard S Maguire", + "author_inst": "Thales UK Ltd" + }, + { + "author_name": "Matt Hogg", + "author_inst": "Thales UK Ltd" + }, + { + "author_name": "Iain D Carrie", + "author_inst": "Thales UK Ltd" + }, + { + "author_name": "Maria Blaney", + "author_inst": "Queen Elizabeth University Hospital Glasgow" + }, + { + "author_name": "Antonin Couturier", + "author_inst": "Thales UK Ltd" + }, + { + "author_name": "Lucy Longbottom", + "author_inst": "Queen Elizabeth University Hospital Glasgow" + }, + { + "author_name": "Jack Thomson", + "author_inst": "Queen Elizabeth University Hospital Glasgow" + }, + { + "author_name": "Nicola Baxter", + "author_inst": "Queen Elizabeth University Hospital Glasgow" + }, + { + "author_name": "Aimee Thompson", + "author_inst": "Queen Elizabeth University Hospital Glasgow" + }, + { + "author_name": "Craig Warren", + "author_inst": "Queen Elizabeth University Hospital Glasgow" + }, + { + "author_name": "David J Lowe", + "author_inst": "Queen Elizabeth University Hospital Glasgow" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2021.05.05.21254713", "rel_title": "Multi-site Evaluation of SARS-CoV-2 Spike Mutation Detection Using a Multiplex Real-time RT-PCR Assay", @@ -762998,117 +764649,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.04.21256382", - "rel_title": "Longitudinal SARS-CoV-2 infection study at Ulm University", - "rel_date": "2021-05-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.04.21256382", - "rel_abs": "In light of the COVID-19 pandemic, universities around the world were challenged by the difficult decision whether classes could be held face-to-face in the winter semester 20/21. The gross anatomy course is considered an essential practical element of medical school. In order to protect the participants and teaching staff and to gain more knowledge about SARS-CoV-2 infections among students during a semester with face-to-face teaching a longitudinal test study was conducted. Medical students from the first three years of medical school were also invited. Out of a total of almost 1,000 swabs, only two active asymptomatic infections were detected at the start of the semester, none during the semester. At semester start, approximately 6% of the students had antibodies. At the end of the semester, only nine seroconversions after infection in 671 individuals occurred. This was surprisingly low because a massive second wave of infections hit Germany during the same period. The conclusion therefore is that face-to-face teaching under these measures was not infection-promoting even with high incidence rates in the overall population with the SARS-CoV-2 variants present at that time period. Moreover, the results are indicative of a preventive effect of hygiene concepts together with repetitive testings before and during a semester.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Michael Schoen", - "author_inst": "Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany" - }, - { - "author_name": "Clemens Lindenau", - "author_inst": "Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany" - }, - { - "author_name": "Anja Boeckers", - "author_inst": "Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany" - }, - { - "author_name": "Claire-Marie Altrock", - "author_inst": "Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany" - }, - { - "author_name": "David A. C. Messerer", - "author_inst": "Department of Anesthesiology and Intensive Care Medicine, Ulm University Hospital, Ulm, Germany & Institute of Clinical and Experimental Trauma Immunology, Ulm " - }, - { - "author_name": "Lydia Krys", - "author_inst": "Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany & Institute of Forensic Medicine, University Hospital Ulm, Ulm, Germany" - }, - { - "author_name": "Anastasia Nosanova", - "author_inst": "Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany" - }, - { - "author_name": "Nicole Lang", - "author_inst": "Center for Clinical Studies, University Hospital Ulm, Ulm, Germany" - }, - { - "author_name": "Andrea Reny", - "author_inst": "Center for Clinical Studies, University Hospital Ulm, Ulm, Germany" - }, - { - "author_name": "Joris Kroschel", - "author_inst": "Central Department for Clinical Chemistry, University Hospital Ulm, Ulm, Germany" - }, - { - "author_name": "Alexandra Beil", - "author_inst": "Central Department for Clinical Chemistry, University Hospital Ulm, Ulm, Germany" - }, - { - "author_name": "Elke Pensel", - "author_inst": "Clinical Transfusion Medicine and Immunogenetics, University Hospital Ulm, Ulm, Germany" - }, - { - "author_name": "Claudia Grab", - "author_inst": "Faculty of Medicine, Ulm University, Ulm, Germany" - }, - { - "author_name": "Benjamin Mayer", - "author_inst": "Institute of Epidemiology and Medical Biometry, Ulm University, Ulm, Germany" - }, - { - "author_name": "Ulrich Fassnacht", - "author_inst": "Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany" - }, - { - "author_name": "Jan Philipp Delling", - "author_inst": "Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany" - }, - { - "author_name": "Magdalena Engelmann", - "author_inst": "Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany" - }, - { - "author_name": "Astrid Horneffer", - "author_inst": "Faculty of Medicine, Ulm University, Ulm, Germany" - }, - { - "author_name": "Maria Zernickel", - "author_inst": "Clinic of Pediatrics and Adolescent Medicine, Ulm University Hospital, Ulm, Germany" - }, - { - "author_name": "Klaus-Michael Debatin", - "author_inst": "Clinic of Pediatrics and Adolescent Medicine, Ulm University Hospital, Ulm, Germany" - }, - { - "author_name": "Jan Muench", - "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany" - }, - { - "author_name": "Frank Kirchhoff", - "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany" - }, - { - "author_name": "Thomas Wirth", - "author_inst": "Faculty of Medicine, Ulm University, Ulm, Germany & Institute of Physiological Chemistry, Ulm University, Ulm, Germany" - }, - { - "author_name": "Tobias M. Boeckers", - "author_inst": "Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany & Faculty of Medicine, Ulm University, Ulm, Germany" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.04.21256590", "rel_title": "Covid-19 and the South Asian Countries: factors ruling the pandemic", @@ -764076,6 +765616,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.05.03.21256525", + "rel_title": "Outbreaks of Covid-19 Variants in Prisons: A Mathematical Modeling Analysis of Vaccination and Re-Opening Policies", + "rel_date": "2021-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.03.21256525", + "rel_abs": "BackgroundResidents of correctional facilities have experienced disproportionately higher rates of SARS-CoV-2 infection and Covid-19-related mortality. To protect against outbreaks, many prisons and jails imposed heavy restrictions on in-person activities, which are now beginning to lift. Uncertainty surrounds the safety of these moves.\n\nMethods and FindingsWe obtained system-wide resident-day level data for the California state prison system, the nations third largest. We used the data to develop a transmission-dynamic stochastic microsimulation model that projects the impact of various policy scenarios on risks of SARS-CoV-2 infections and related hospitalization among residents after an initial infection is introduced to a prison. The policy scenarios vary according to levels of vaccine coverage, baseline immunity, resumption of activities, and use of non-pharmaceutical interventions (e.g., masking, physical distancing). The analyses were conducted across 5 types of prisons that differed in their residential layouts, security levels, and resident demographics.\n\nIf a viral variant is introduced into a prison that has resumed pre-2020 contact levels, has moderate vaccine coverage, and has no baseline immunity, 23-74% of residents are expected to be infected over 200 days. High vaccination coverage coupled with use of non-pharmaceutical measures reduces cumulative infections to 2-54% of residents. In prisons consisting mostly of dormitory housing, even with high vaccine coverage and non-pharmaceutical interventions, resumption of in-person activities is associated with substantial risk, unless there is high baseline immunity (e.g., [≥]50%) from prior outbreaks. In prisons consisting mostly of cell housing, <10% of residents are expected to become infected, even with no baseline immunity. However, hospitalization risks are substantial in prisons that house medically vulnerable populations, even for prisons consisting mostly of cells. Risks of large outbreaks are substantially higher if there is continued introduction of infections into a prison. Some findings may not be transportable to other carceral settings, and our assumptions regarding viral variants will not be accurate for all variants.\n\nConclusionsBalancing the benefits of resuming normal in-person activities against the risks of Covid-19 outbreaks is a difficult challenge for correctional systems. The policy choices are not strictly binary. To protect against viral variants, prisons should focus on achieving both high vaccine coverage and maintaining widespread use of non-pharmaceutical interventions. With both in place, some prisons, especially those with lower room occupancy that have already had large outbreaks, could safely resume in-person activities, while continuing testing and measures to protect the medically-vulnerable.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Theresa S Ryckman", + "author_inst": "Stanford University" + }, + { + "author_name": "Elizabeth T Chin", + "author_inst": "Stanford University" + }, + { + "author_name": "Lea Prince", + "author_inst": "Stanford University" + }, + { + "author_name": "David Leidner", + "author_inst": "No Affiliation" + }, + { + "author_name": "Elizabeth Long", + "author_inst": "Stanford University" + }, + { + "author_name": "David M Studdert", + "author_inst": "Stanford University" + }, + { + "author_name": "Joshua A Salomon", + "author_inst": "Stanford University" + }, + { + "author_name": "Fernando Alarid-Escudero", + "author_inst": "Center for Research and Teaching in Economics (CIDE)" + }, + { + "author_name": "Jason R Andrews", + "author_inst": "Stanford University" + }, + { + "author_name": "Jeremy D Goldhaber-Fiebert", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.03.21256532", "rel_title": "COVID-19 infection and hospitalization according to the burden of chronic noncommunicable diseases in Brazil", @@ -764835,61 +766430,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.05.05.442780", - "rel_title": "Prior aerosol infection with lineage A SARS-CoV-2 variant protects hamsters from disease, but not reinfection with B.1.351 SARS-CoV-2 variant", - "rel_date": "2021-05-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.05.442780", - "rel_abs": "The circulation of SARS-CoV-2 has resulted in the emergence of variants of concern (VOCs). It is currently unclear whether previous infection with SARS-CoV-2 provides protection against reinfection with VOCs. Here, we show that low dose aerosol exposure to hCoV-19/human/USA/WA-CDC-WA1/2020 (WA1, lineage A), resulted in a productive mild infection. In contrast, low dose of SARS-CoV-2 via fomites did not result in productive infection in the majority of exposed hamsters and these animals remained non-seroconverted. After recovery, hamsters were re-exposed to hCoV-19/South African/KRISP-K005325/2020 (VOC B.1.351) via an intranasal challenge. Seroconverted rechallenged animals did not lose weight and shed virus for 3 days. They had little infectious virus and no pathology in the lungs. In contrast, shedding, weight loss and extensive pulmonary pathology caused by B.1.351 replication was observed in the non-seroconverted animals. The rechallenged seroconverted animals did not transmit virus to naive sentinels via direct contact transmission, in contrast to the non-seroconverted animals. Reinfection with B.1.351 triggered an anamnestic response that boosted not only neutralizing titers against lineage A, but also titers against B.1.351. Our results confirm that aerosol exposure is a more efficient infection route than fomite exposure. Furthermore, initial infection with SARS-CoV-2 lineage A does not prevent heterologous reinfection with B.1.351 but prevents disease and onward transmission. These data suggest that previous SARS-CoV-2 exposure induces partial protective immunity. The reinfection generated a broadly neutralizing humoral response capable of effectively neutralizing B.1.351 while maintaining its ability to neutralize the virus to which the initial response was directed against.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Kwe Claude Yinda", - "author_inst": "Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA" - }, - { - "author_name": "Julia Port", - "author_inst": "Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA" - }, - { - "author_name": "Trenton Bushmaker", - "author_inst": "bushmakertj@niaid.nih.gov" - }, - { - "author_name": "Robert Fischer", - "author_inst": "Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA" - }, - { - "author_name": "Jonathan Schulz", - "author_inst": "Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA" - }, - { - "author_name": "Myndi Holbrook", - "author_inst": "Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA" - }, - { - "author_name": "Carl Shaia", - "author_inst": "Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institutes of Health, Hamilton, MT, USA" - }, - { - "author_name": "Emmie de Wit", - "author_inst": "Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA" - }, - { - "author_name": "Neeltje van Doremalen", - "author_inst": "Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA" - }, - { - "author_name": "Vincent Munster", - "author_inst": "Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA" - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.05.05.442725", "rel_title": "1H, 13C and 15N resonance assignment of the SARS-CoV-2 full-length nsp1 protein and its mutants reveals its unique secondary structure features in solution.", @@ -765797,6 +767337,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, + { + "rel_doi": "10.1101/2021.05.03.21255976", + "rel_title": "Preventing COVID-19 Outbreaks Through Surveillance Testing in Healthcare Facilities - A Modelling Study", + "rel_date": "2021-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.03.21255976", + "rel_abs": "Surveillance testing within healthcare facilities provides an opportunity to prevent severe outbreaks of coronavirus disease 2019 (COVID-19). However, the quantitative impact of different available surveillance strategies is not well-understood. Our study adds to the available body of evidence by examining different strategies for their potential to decrease the probability of outbreaks in these facilities. Based on our findings, we propose determinants of successful surveillance measures. To this end, we establish an individual-based model representative of a mental health hospital yielding generalizable results. Attributes and features of this facility were derived from a prototypical hospital, which provides psychiatric, psychosomatic and psychotherapeutic treatment. We estimate the relative reduction of outbreak probability for three test strategies (entry test, once-weekly test and twice-weekly test) relative to a symptom-based baseline strategy. We found that fast diagnostic test results and adequate compliance of the clinic population are mandatory for conducting effective surveillance. The robustness of these results towards uncertainties is demonstrated via comprehensive sensitivity analyses. In summary, we robustly quantified the efficacy of different surveillance scenarios and conclude that active testing in mental health hospitals and similar facilities successfully reduces the number of COVID-19 outbreaks.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Tim Litwin", + "author_inst": "Institute of Medical Biometry and Statistics (IMBI), Medical Center, University of Freiburg" + }, + { + "author_name": "Jens Timmer", + "author_inst": "Institute of Physics, University of Freiburg" + }, + { + "author_name": "Mathias Berger", + "author_inst": "Department of Psychiatry and Psychotherapy, Medical Center, University of Freiburg" + }, + { + "author_name": "Andreas Wahl-Kordon", + "author_inst": "Oberberg Hospital Schwarzwald" + }, + { + "author_name": "Matthias Mueller", + "author_inst": "Oberberg Group, Berlin" + }, + { + "author_name": "Clemens Kreutz", + "author_inst": "Institute of Medical Biometry and Statistics (IMBI), Medical Center, University of Freiburg" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.05.02.21256492", "rel_title": "Changes in work and health of Australians during the COVID-19 pandemic: a longitudinal cohort study", @@ -766785,73 +768364,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, - { - "rel_doi": "10.1101/2021.04.30.21256383", - "rel_title": "COVID-19 vaccine-associated cerebral venous thrombosis in Germany: a descriptive study", - "rel_date": "2021-05-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.30.21256383", - "rel_abs": "ObjectiveReports of cerebral sinus and venous thrombosis (CVT) after ChAdOx1 vaccination against SARS-CoV-2 have raised safety concerns. We aimed to estimate the incidence of CVT within one month from first dose administration and the frequency of vaccine-induced immune thrombotic thrombocytopenia (VITT) as the underlying mechanism after vaccination with BNT162b2, ChAdOx1, and mRNA-1273, in Germany.\n\nMethodsA web-based questionnaire was e-mailed to all Departments of Neurology. We asked to report cases of CVT within one month of a COVID-19 vaccination. Other cerebral events could also be reported. Incidence rates of CVT were calculated by using official statistics of nine German States.\n\nResultsA total of 45 CVT cases were reported. In addition, 9 primary ischemic strokes, 4 primary intracerebral hemorrhages, and 4 other neurological events were recorded. Of the CVT patients, 35 (77.8%) were female, and 36 (80.0%) were below the age of 60 years. Fifty-three events were observed after vaccination with ChAdOx1 (85.5%), 9 after BNT162b2 (14.5%), and none after mRNA-1273 vaccination. After 7,126,434 first vaccine doses, the incidence rate of CVT within one month from first dose administration was 6.5 (95% CI, 4.4-9.2) per 100,000 person-years for all vaccines and 17.9 (11.8-26.1) for ChAdOx1 (after 2,320,535 ChAdOx1 first doses). The adjusted incidence rate ratio was 9.68 (3.46-34.98) for ChAdOx1 compared to mRNA-based vaccines and 3.14 (1.22-10.65) for women compared to non-women. In 26/45 patients with CVT (57.8%), VITT was graded highly probable.\n\nConclusionsGiven an incidence of 0.22-1.75 per 100,000 person-years for CVT in the general population, these findings point towards a higher risk for CVT after ChAdOx1 vaccination, especially for women.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Joerg B. Schulz", - "author_inst": "RWTH Aachen University" - }, - { - "author_name": "Peter Berlit", - "author_inst": "German Society of Neurology" - }, - { - "author_name": "Hans-Christoph Diener", - "author_inst": "Medical Faculty of the University Duisburg-Essen" - }, - { - "author_name": "Christian Gerloff", - "author_inst": "University Hospital Hamburg-Eppendorf" - }, - { - "author_name": "Andreas Greinacher", - "author_inst": "Universitaetsmedizin Greifswald" - }, - { - "author_name": "Christine Klein", - "author_inst": "University of Luebeck" - }, - { - "author_name": "Gabor C. Petzold", - "author_inst": "University Hospital Bonn" - }, - { - "author_name": "Marco Piccininni", - "author_inst": "Charite - Universitaetsmedizin Berlin" - }, - { - "author_name": "Sven Poli", - "author_inst": "University of Tuebingen" - }, - { - "author_name": "Rainer Roehrig", - "author_inst": "RWTH Aachen University" - }, - { - "author_name": "Helmuth Steinmetz", - "author_inst": "University Hospital Frankfurt" - }, - { - "author_name": "Thomas Thiele", - "author_inst": "Universitaetsmedizin Greifswald" - }, - { - "author_name": "Tobias Kurth", - "author_inst": "Charite - Universitaetsmedizin Berlin" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2021.04.30.21256413", "rel_title": "Persistent neuropsychiatric symptoms after COVID-19: a systematic review and meta-analysis.", @@ -767479,6 +768991,85 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.05.04.438781", + "rel_title": "Highly functional Cellular Immunity in SARS-CoV-2 Non-Seroconvertors is associated with immune protection", + "rel_date": "2021-05-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.04.438781", + "rel_abs": "The role of T cells in the control of SARS-CoV-2 infection has been underestimated in favor of neutralizing antibodies. However, cellular immunity is essential for long-term viral control and protection from disease severity. To understand T-cell immunity in the absence of antibody generation we focused on a group of SARS-CoV-2 Non-Seroconvertors (NSC) recovered from infection. We performed an immune comparative analysis of SARS-CoV-2 infected individuals stratified by the absence or presence of seroconversion and disease severity. We report high levels of total naive and low effector CD8+ T cells in NSC. Moreover, polyfunctional Nucleocapsid (NP)-specific CD8+ T-cell responses, as well as reduced levels of T-cell activation monitored by PD-1 and activation-induced markers, were distinctive immunological traits in NSC. Longitudinal data support the stability of the NSC phenotype over three months. Our results implicate highly functional SARS-CoV-2 Spike and NP T-cell responses with low immune activation in protection from disease severity in the absence of seroconversion.\n\nSUMMARYTo understand SARS-CoV-2 specific T-cell immunity in the absence of seroconversion, we characterized immunological features of Non-Seroconvertors recovered from infection. Highly functional specific T-cell responses and low immune activation were determinants of immune protection from severe disease.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Athina Kilpelainen", + "author_inst": "IrsiCaixa AIDS Research Institute, Badalona, Spain, Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain" + }, + { + "author_name": "Esther Jimenez-Moyano", + "author_inst": "IrsiCaixa AIDS Research Institute, Badalona, Spain" + }, + { + "author_name": "Oscar Blanch-Lombarte", + "author_inst": "IrsiCaixa AIDS Research Institute, Badalona, Spain, Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain" + }, + { + "author_name": "Dan Ouchi", + "author_inst": "IrsiCaixa AIDS Research Institute, Badalona, Spain" + }, + { + "author_name": "Ruth Penya", + "author_inst": "IrsiCaixa AIDS Research Institute, Badalona, Spain" + }, + { + "author_name": "Bibiana Quirant-Sanchez", + "author_inst": "Germans Trias i Pujol Research Institute (IGTP). Department of Cell Biology, Physiology, Immunology, Universitat Autonoma de Barcelona, Cerdanyola del Valles, S" + }, + { + "author_name": "Anna Chamorro", + "author_inst": "Lluita contra la SIDA Foundation, Hospital Universitari Germans Trias i Pujol, Badalona, Spain" + }, + { + "author_name": "Eva Martinez-Caceres", + "author_inst": "Germans Trias i Pujol Research Institute (IGTP). Department of Cell Biology, Physiology, Immunology, Universitat Autonoma de Barcelona, Cerdanyola del Valles, S" + }, + { + "author_name": "Roger Paredes", + "author_inst": "IrsiCaixa AIDS Research Institute, Badalona, Spain. Lluita contra la SIDA Foundation, Hospital Universitari Germans Trias i Pujol, Badalona, Spain. Infectious D" + }, + { + "author_name": "Lourdes Mateu", + "author_inst": "Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain. Lluita contra la SIDA Foundation, Hospital Universitari Germans Trias i Pujol, Badalona, Spain" + }, + { + "author_name": "Jorge Carrillo", + "author_inst": "IrsiCaixa AIDS Research Institute, Badalona, Spain" + }, + { + "author_name": "Juli\u00e0 Blanco", + "author_inst": "IrsiCaixa AIDS Research Institute, Badalona, Spain. Germans Trias i Pujol Research Institute (IGTP), Universitat Autonoma de Barcelona, Cerdanyola del Valles, S" + }, + { + "author_name": "Christian Brander", + "author_inst": "IrsiCaixa AIDS Research Institute, Badalona, Spain. ICREA, Pg Lluis Comanys 23, Barcelona, Spain. University of Vic Central University of Catalonia, (UVicUCC), " + }, + { + "author_name": "Marta Massanella", + "author_inst": "IrsiCaixa AIDS Research Institute, Badalona, Spain" + }, + { + "author_name": "Bonaventura Clotet", + "author_inst": "IrsiCaixa AIDS Research Institute, Badalona, Spain" + }, + { + "author_name": "Julia G Prado", + "author_inst": "IrsiCaixa AIDS Research Institute, Badalona, Spain. Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain. Universitat Autonoma de Barcelona, Cerdany" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.05.03.442520", "rel_title": "A novel highly potent inhibitor of TMPRSS2-like proteases blocks SARS-CoV-2 variants of concern and is broadly protective against infection and mortality in mice", @@ -768133,85 +769724,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2021.04.29.21256236", - "rel_title": "POPULATION-BASED SERO-EPIDEMIOLOGICAL STUDY PROTOCOL FOR THE IMPACT OF SMOKING ON SARS-COV-2 INFECTION AND COVID-19 OUTCOMES - THE TROINA STUDY", - "rel_date": "2021-05-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.29.21256236", - "rel_abs": "After the global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), research has highlighted several aspects of the pandemic, focusing on clinical features and risk factors associated with infection and disease severity. However, emerging results on the role of smoking in SARS-CoV-2 infection susceptibility or COVID-19 outcomes are conflicting, and their robustness remains uncertain. In this context, this project aims at quantifying the proportion of SARS-CoV-S antibody seroprevalence, studying the changes in antibody levels over time, and analyzing the association between smoking status and infection using seroprevalence data.\n\nThe added value of this research is that the current smoking status of the population to be studied will be biochemically verified, in order to avoid the bias associated with self-reported smoking status. As such, the results from this survey may provide actionable metric to study the role of smoking in SARS-CoV-2 spread, and therefore implement the most appropriate public health measures to control the pandemic.\n\nThe research design involves a 6-month prospective cohort study with serial sampling of the same individuals. Each participant will be surveyed about their demographics and COVID-19-related information, and blood sampling will be collected upon recruitment and at specified follow-up time points (namely, after 8 and 24 weeks). Blood samples will be screened for the presence of SARS-CoV-2 specific antibodies and serum cotinine.\n\nOverall, we expect to find a higher prevalence of antibodies in individuals at high-risk for viral exposure (i.e., healthcare or other essential workers), according to previous literature, and to refine current estimates on the association between smoking status and SARS-CoV-2/COVID-19. Our results may serve as a reference for future clinical research and the methodology could be exploited in public health sectors and policies.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Riccardo Polosa", - "author_inst": "Institute of Internal Medicine, AOU Policlinico V. Emanuele, Catania, Italy; Department of Clinical and Experimental Medicine, University of Catania, Italy; Cen" - }, - { - "author_name": "V. Tomaselli", - "author_inst": "Center of Excellence for the Acceleration of Harm Reduction (CoEHAR), University of Catania, Italy. Department of Political and Social Sciences, University of C" - }, - { - "author_name": "P. Ferrara", - "author_inst": "Center for Public Health Research, University of Milan Bicocca, Monza, Italy; Value&[minus]based Healthcare Unit, IRCCS MultiMedica, Milan, Italy" - }, - { - "author_name": "A. C. Romeo", - "author_inst": "Oasi Research Institute &[minus] IRCCS, Troina, Italy" - }, - { - "author_name": "S. Rust", - "author_inst": "Center of Excellence for the Acceleration of Harm Reduction (CoEHAR), University of Catania, Italy." - }, - { - "author_name": "D. Saitta", - "author_inst": "Department of Clinical & Experimental Medicine, University of Catania, Italy; Center of Excellence for the Acceleration of Harm Reduction (CoEHAR), University o" - }, - { - "author_name": "F. Caraci", - "author_inst": "Center of Excellence for the Acceleration of Harm Reduction (CoEHAR), University of Catania, Italy; Oasi Research Institute &[minus] IRCCS, Troina, Italy; Depar" - }, - { - "author_name": "C. Romano", - "author_inst": "Oasi Research Institute &[minus] IRCCS, Troina, Italy" - }, - { - "author_name": "M. Thangaraju", - "author_inst": "Bioanalytical Laboratory, Center for Smoking Cessation, Duke University Medical Center, Durham, USA; Department of Psychiatry and Behavioral Sciences, Duke Univ" - }, - { - "author_name": "P. Zuccarello", - "author_inst": "Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia, University of Catania, Italy" - }, - { - "author_name": "J. Rose", - "author_inst": "Bioanalytical Laboratory, Center for Smoking Cessation, Duke University Medical Center, Durham, USA; Department of Psychiatry and Behavioral Sciences, Duke Univ" - }, - { - "author_name": "M. Ferrante", - "author_inst": "Center of Excellence for the Acceleration of Harm Reduction (CoEHAR), University of Catania, Italy; Department of Medical, Surgical Sciences and Advanced Techno" - }, - { - "author_name": "J. Belsey", - "author_inst": "JB Medical Ltd, Sudbury, UK" - }, - { - "author_name": "F. Cibella", - "author_inst": "Center of Excellence for the Acceleration of Harm Reduction (CoEHAR), University of Catania, Italy; National Research Council of Italy, Institute of Biomedicine" - }, - { - "author_name": "E. Interlandi", - "author_inst": "CIDEC Federazione Sanit\u00e0" - }, - { - "author_name": "R. Ferri", - "author_inst": "Oasi Research Institute &[minus] IRCCS, Troina, Italy" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.30.21255934", "rel_title": "Baricitinib plus Standard of Care for Hospitalized Adults with COVID-19", @@ -768947,6 +770459,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hiv aids" }, + { + "rel_doi": "10.1101/2021.04.29.21256354", + "rel_title": "The landscape of circulating platelet aggregates in COVID-19", + "rel_date": "2021-05-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.29.21256354", + "rel_abs": "A characteristic clinical feature of COVID-19 is the frequent incidence of microvascular thrombosis. In fact, COVID-19 autopsy reports have shown widespread thrombotic microangiopathy characterized by extensive diffuse microthrombi within peripheral capillaries and arterioles in lungs, hearts, and other organs, resulting in multiorgan failure. However, the underlying process of COVID-19-associated microvascular thrombosis remains elusive due to the lack of tools to statistically examine platelet aggregation (i.e., the initiation of microthrombus formation) in detail. Here we present a method for massive image-based profiling, temporal monitoring, and big data analysis of circulating platelets and platelet aggregates in the blood of COVID-19 patients at single-cell resolution, to provide previously unattainable insights into the disease. In fact, our analysis of the image data from 110 hospitalized patients shows the anomalous presence of excessive platelet aggregates in nearly 90% of all COVID-19 patients. Furthermore, results indicate strong links between the concentration of platelet aggregates and the severity, mortality, and respiratory condition of patients with COVID-19. Finally, high-dimensional analysis based on deep learning shows that the disease behaves as systemic thrombosis.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Yuqi Zhou", + "author_inst": "University of Tokyo" + }, + { + "author_name": "Masako Nishikawa", + "author_inst": "University of Tokyo" + }, + { + "author_name": "Hiroshi Kanno", + "author_inst": "University of Tokyo" + }, + { + "author_name": "Tinghui Xiao", + "author_inst": "University of Tokyo" + }, + { + "author_name": "Takuma Suzuki", + "author_inst": "University of Tokyo" + }, + { + "author_name": "Yuma Ibayashi", + "author_inst": "University of Tokyo" + }, + { + "author_name": "Jeffrey Harmon", + "author_inst": "University of Tokyo" + }, + { + "author_name": "Shigekazu Takizawa", + "author_inst": "University of Tokyo" + }, + { + "author_name": "Kotaro Hiramatsu", + "author_inst": "University of Tokyo" + }, + { + "author_name": "Nao Nitta", + "author_inst": "CYBO" + }, + { + "author_name": "Risako Kameyama", + "author_inst": "University of Tokyo" + }, + { + "author_name": "Walker Peterson", + "author_inst": "University of Tokyo" + }, + { + "author_name": "Jun Takiguchi", + "author_inst": "University of Tokyo" + }, + { + "author_name": "Mohammad Shifat-E-Rabbi", + "author_inst": "University of Virginia" + }, + { + "author_name": "Yan Zhuang", + "author_inst": "University of Virginia" + }, + { + "author_name": "Xuwang Yin", + "author_inst": "University of Virginia" + }, + { + "author_name": "Abu Rubaiyat", + "author_inst": "University of Virginia" + }, + { + "author_name": "Yunjie Deng", + "author_inst": "University of Tokyo" + }, + { + "author_name": "Hongqian Zhang", + "author_inst": "University of Tokyo" + }, + { + "author_name": "Shgeki Miyata", + "author_inst": "Japanese Red Cross Society" + }, + { + "author_name": "Gustavo Rhode", + "author_inst": "University of Virginia" + }, + { + "author_name": "Wataru Iwasaki", + "author_inst": "University of Tokyo" + }, + { + "author_name": "Yutaka Yatomi", + "author_inst": "University of Tokyo" + }, + { + "author_name": "Keisuke Goda", + "author_inst": "University of Tokyo" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.02.21255857", "rel_title": "Detection of SARS-CoV-2 infection in gargle, spit and sputum specimens", @@ -769971,57 +771594,6 @@ "type": "new results", "category": "neuroscience" }, - { - "rel_doi": "10.1101/2021.05.02.442358", - "rel_title": "Vitamin C inhibits SARS coronavirus-2 main protease essential for viral replication", - "rel_date": "2021-05-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.02.442358", - "rel_abs": "There is an urgent need for anti-viral agents that treat and/or prevent Covid-19 caused by SARS-Coronavirus (CoV-2) infections. The replication of the SARS CoV-2 is dependent on the activity of two cysteine proteases, a papain-like protease, PL-pro, and the 3C-like protease known as main protease Mpro or 3CLpro. The shortest and the safest path to clinical use is the repurposing of drugs with binding affinity to PLpro or 3CLpro that have an established safety profile in humans. Several studies have reported crystal structures of SARS-CoV-2 main protease in complex with FDA approved drugs such as those used in treatment of hepatitis C. Here, we report the crystal structure of 3CLpro in complex Vitamin C (L-ascorbate) bound to the proteins active site at 2.5 [A]ngstrom resolution. The crystal structure of the Vitamin C 3CLpro complex may aid future studies on the effect of Vitamin C not only on the coronavirus main protease but on related proteases of other infectious viruses.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Tek Narsingh Malla", - "author_inst": "University of Wisconsin Milwaukee" - }, - { - "author_name": "Suraj Pandey", - "author_inst": "University of Wisconsin Milwaukee" - }, - { - "author_name": "Luis Aldama", - "author_inst": "Northeastern Illinois University" - }, - { - "author_name": "Dennis Feliz", - "author_inst": "Northeastern Illinois University" - }, - { - "author_name": "Moraima Noda", - "author_inst": "Northeastern Illinois University" - }, - { - "author_name": "Ishwor Poudyal", - "author_inst": "University of Wisconsin Milwaukee" - }, - { - "author_name": "George N. Phillips Jr.", - "author_inst": "Rice University" - }, - { - "author_name": "Emina A. Stojkovic", - "author_inst": "Northeastern Illinois University" - }, - { - "author_name": "Marius Schmidt", - "author_inst": "University of Wisconsin Milwaukee" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.04.28.21256277", "rel_title": "Serum Neurofilament Light is Elevated in COVID-19 Positive Adults in the ICU and is Associated with Co-Morbid Cardiovascular Disease, Neurological Complications, and Acuity of Illness", @@ -770933,6 +772505,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2021.04.29.21256322", + "rel_title": "The impact of vaccination on the spread patterns of the COVID epidemic", + "rel_date": "2021-05-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.29.21256322", + "rel_abs": "A modified model of the epidemic under conditions of mass vaccination was developed. A comparison of the model results with statistical observations in Israel shows good agreement.\n\nModel calculations are performed on the efficacy of limiting the development of an epidemic by both lockdown and vaccination. Mass vaccination of the population is the most radical method of limiting the growth of the epidemic. The introduction of a lockdown cannot completely prevent the development of an epidemic. The likelihood of the emergence of new strains of the virus is assessed. Without vaccination, the probability of more than two new virus strains per year affecting the epidemic growth process is found to be about 60%. A controlled calculation was made of the effect of the timing of changes in lockdown conditions during the vaccination period on the development of the epidemic. It was particularly shown that the cancellation of the lockdown together with the start of vaccination did not reduce the maximum number of new infections. A controlling calculation was made of the effects of gradually cancelling lockdown. On the basis of these calculations, it is possible to assess the development of the epidemic in different variants of partial lockdown cancellation.\n\nThree dimensionless complexes, made up of the intensities of transmission, vaccination and lockdown restrictions, are found to determine the epidemics development.\n\nThe intensity of the coronavirus epidemic depends on climatic characteristics, in particular air temperature and the UV index. A relationship is given to estimate the influence of these factors on infection growth.\n\nThe way forward for further development of the model is outlined. The immediate goal of modifying the model is to use it for each age group in the population and to find out the links between vaccination rates and the psychological state of the population, i.e. peoples readiness for mass vaccination.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Denis Below", + "author_inst": "University of Potsdam" + }, + { + "author_name": "Felix Mairanowski", + "author_inst": "Husmann Rus" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.04.29.21256307", "rel_title": "Modelling digital and manual contact tracing for COVID-19. Are low uptakes and missed contacts deal-breakers?", @@ -771741,45 +773336,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2021.04.27.21256187", - "rel_title": "Estimating the early impact of immunization against COVID-19 on deaths among elderly people in Brazil: analyses of secondary data on vaccine coverage and mortality.", - "rel_date": "2021-04-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.27.21256187", - "rel_abs": "BackgroundVaccination against COVID-19 in Brazil started in January 2021, with health workers and the elderly as the priority groups. We assessed whether there was an impact of vaccinations on the mortality of elderly individuals in a context of wide transmission of the SARS-CoV-2 gamma (P.1) variant.\n\nMethodsBy May 27, 2021, 147238,414 COVID-19 deaths had been reported to the Brazilian Mortality Information System. Denominators for mortality rates were calculated by correcting population estimates for all-cause deaths reported in 2020. Proportionate mortality at ages 70-79 and 80+ years relative to deaths at all ages were calculated for deaths due to COVID-19 and to other causes, as were COVID-19 mortality rate ratios relative to individuals aged 0-69 years. Vaccine coverage data were obtained from the Ministry of Health. All results were tabulated by epidemiological weeks 1-19, 2021.\n\nFindingsThe proportion of all COVID-19 deaths at ages 80+ years was over 25% in weeks 1-6 and declined rapidly to 12.4% in week 19, whereas proportionate COVID-19 mortality for individuals aged 70-79 years started to decline by week 15. Trends in proportionate mortality due to other causes remained stable. Mortality rates were over 13 times higher in the 80+ years age group compared to that of 0-69 year olds up to week 6, and declined to 5.0 times in week 19. Vaccination coverage (first dose) of 90% was reached by week 9 for individuals aged 80+ years and by week 13 for those aged 70-79 years. Coronavac accounted for 65.4% and AstraZeneca for 29.8% of all doses administered in weeks 1-4, compared to 36.5% and 53.3% in weeks 15-19, respectively.\n\nInterpretationRapid scaling up of vaccination coverage among elderly Brazilians was associated with important declines in relative mortality compared to younger individuals, in a setting where the gamma variant predominates. Had mortality rates among the elderly remained proportionate to what was observed up to week 6, an estimated additional 43,802 COVID-related deaths would have been expected up to week 19.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Cesar G Victora", - "author_inst": "Universidade Federal de Pelotas" - }, - { - "author_name": "Marcia C. Castro", - "author_inst": "Harvard TH Chan School of Public Health" - }, - { - "author_name": "Susie Gurzenda", - "author_inst": "Harvard T. H. Chan School of Public Health" - }, - { - "author_name": "Arnaldo Medeiros", - "author_inst": "Ministry of Health, Brazil" - }, - { - "author_name": "Giovanny VA Franca", - "author_inst": "Ministry of Health, Brazil" - }, - { - "author_name": "Aluisio JD Barros", - "author_inst": "Universidade Federal de Pelotas, Brazil" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.27.21256222", "rel_title": "COVID-19 Outcomes and Sequencing of SARS-CoV-2 isolated from Veterans in New England", @@ -772313,6 +773869,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.29.21255961", + "rel_title": "Wastewater-based estimation of the effective reproductive number of SARS-CoV-2", + "rel_date": "2021-04-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.29.21255961", + "rel_abs": "BackgroundThe effective reproductive number, Re, is a critical indicator to monitor disease dynamics, inform regional and national policies, and estimate the effectiveness of interventions. It describes the average number of new infections caused by a single infectious person through time. To date, Re estimates are based on clinical data such as observed cases, hospitalizations, and/or deaths. These estimates are temporarily biased when clinical testing or reporting strategies change.\n\nObjectivesWe show that the dynamics of SARS-CoV-2 RNA in wastewater can be used to estimate Re in near real-time, independent of clinical data and without the associated biases.\n\nMethodsWe collected longitudinal measurements of SARS-CoV-2 RNA in wastewater in Zurich, CH, and San Jose (CA), USA. We combined this data with information on the temporal dynamics of shedding (the shedding load distribution) to estimate a time series proportional to the daily COVID-19 infection incidence. We estimated a wastewater-based Re from this incidence.\n\nResultsThe method to estimate Re from wastewater works robustly on data from two different countries and two wastewater matrices. The resulting estimates are as similar to the Re estimates from case report data as Re estimates based on observed cases, hospitalizations, and deaths are among each other. We further provide details on the effect of sampling frequency and the shedding load distribution on the ability to infer Re.\n\nDiscussionTo our knowledge, this is the first time Re has been estimated from wastewater. This method provides a low cost, rapid, and independent way to inform SARS-CoV-2 monitoring during the ongoing pandemic and is applicable to future wastewater-based epidemiology targeting other pathogens.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Jana S Huisman", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Jeremie Scire", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Lea Caduff", + "author_inst": "Eawag, Swiss Federal Institute of Aquatic Science and Technology" + }, + { + "author_name": "Xavier Fernandez-Cassi", + "author_inst": "Ecole Polytechnique Federale de Lausanne" + }, + { + "author_name": "Pravin Ganesanandamoorthy", + "author_inst": "Eawag, Swiss Federal Institute of Aquatic Science and Technology" + }, + { + "author_name": "Anina Kull", + "author_inst": "Eawag, Swiss Federal Institute of Aquatic Science and Technology" + }, + { + "author_name": "Andreas Scheidegger", + "author_inst": "Eawag, Swiss Federal Institute of Aquatic Science and Technology" + }, + { + "author_name": "Elyse Stachler", + "author_inst": "Eawag, Swiss Federal Institute of Aquatic Science and Technology" + }, + { + "author_name": "Alexandria B Boehm", + "author_inst": "Stanford" + }, + { + "author_name": "Bridgette Hughes", + "author_inst": "Verily Life Sciences" + }, + { + "author_name": "Alisha Knudson", + "author_inst": "Verily Life Sciences" + }, + { + "author_name": "Aaron Topol", + "author_inst": "Verily Life Sciences" + }, + { + "author_name": "Krista R Wigginton", + "author_inst": "University of Michigan" + }, + { + "author_name": "Marlene K Wolfe", + "author_inst": "Stanford" + }, + { + "author_name": "Tamar Kohn", + "author_inst": "Ecole Polytechnique Federale de Lausanne" + }, + { + "author_name": "Christoph Ort", + "author_inst": "Eawag, Swiss Federal Institute of Aquatic Science and Technology" + }, + { + "author_name": "Tanja Stadler", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Timothy R Julian", + "author_inst": "Eawag, Swiss Federal Institute of Aquatic Science and Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.04.29.21256186", "rel_title": "COVID-19 Vaccine Acceptance Among Healthcare Workers in a United States Medical Center", @@ -773325,89 +774968,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.26.21256016", - "rel_title": "Rapidly increasing SARS-CoV-2 seroprevalence and limited clinical disease in three Malian communities: a prospective cohort study", - "rel_date": "2021-04-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.26.21256016", - "rel_abs": "BackgroundThe extent of SARS-CoV-2 exposure and transmission in Mali and the surrounding region is not well understood, although infection has been confirmed in nearly 14,000 symptomatic individuals and their contacts since the first case in March 2020. We aimed to estimate the cumulative incidence of SARS-CoV-2 in three Malian communities, and understand factors associated with infection.\n\nMethodsBetween 27 July 2020 and 29 January 2021, we collected blood samples along with demographic, social, medical and self-reported symptoms information from residents aged 6 months and older in three study communities at two study visits. SARS-CoV-2 antibodies were measured using a highly specific two-antigen ELISA optimized for use in Mali. We calculated cumulative adjusted seroprevalence for each site and evaluated factors associated with serostatus at each visit by univariate and multivariate analysis.\n\nFindingsOverall, 94.8% (2533/2672) of participants completed both study visits. A total of 50.3% (1343/2672) of participants were male, and 31.3% (837/2672) were aged <10 years, 27.6% (737/2672) were aged 10-17 years, and 41.1% (1098/2572) were aged [≥]18 years. The cumulative SARS-CoV-2 exposure rate was 58.5% (95% CI: 47.5 to 69.4). This varied between sites and was 73.4% (95% CI: 59.2 to 87.5) in the urban community of Sotuba, 53.2% (95% CI: 42.8 to 63.6) in the rural town of Bancoumana, and 37.1% (95% CI: 29.6 to 44.5) in the rural village of Doneguebougou. This equates to an infection rate of approximately 1% of the population every three days in the study communities between visits. Increased age and study site were associated with serostatus at both study visits. There was minimal difference in reported symptoms based on serostatus.\n\nInterpretationThe true extent of SARS-CoV-2 exposure in Mali is greater than previously reported and now approaches hypothetical herd immunity in urban areas. The epidemiology of the pandemic in the region may be primarily subclinical and within background illness rates. In this setting, ongoing surveillance and augmentation of diagnostics to characterize locally circulating variants will be critical to implement effective mitigation strategies like vaccines.\n\nFundingThis project was funded by the Intramural Research Program of the National Institute of Allergy and Infectious Diseases, National Institute of Biomedical Imaging and Bioengineering, and National Cancer Institute.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Issaka Sagara", - "author_inst": "MRTC/USTTB" - }, - { - "author_name": "John Woodford", - "author_inst": "NIAID" - }, - { - "author_name": "Mamady Kone", - "author_inst": "MRTC/USTTB" - }, - { - "author_name": "Mahamadoun Hamady Assadou", - "author_inst": "MRTC/USTTB" - }, - { - "author_name": "Abdoulaye Katile", - "author_inst": "MRTC/USTTB" - }, - { - "author_name": "Oumar Attaher", - "author_inst": "MRTC/USTTB" - }, - { - "author_name": "Amatigue Zeguime", - "author_inst": "MRTC/USTTB" - }, - { - "author_name": "M'Bouye Doucoure", - "author_inst": "MRTC/USTTB" - }, - { - "author_name": "Emily Higbee", - "author_inst": "LMIV, NIAID, NIH" - }, - { - "author_name": "Jacquelyn Lane", - "author_inst": "LMIV, NIAID, NIH" - }, - { - "author_name": "Justin Doritchamou", - "author_inst": "LMIV, NIAID, NIH" - }, - { - "author_name": "Irfan Zaidi", - "author_inst": "LMIV, NIAID, NIH" - }, - { - "author_name": "Dominic Esposito", - "author_inst": "FNLCR, NIH" - }, - { - "author_name": "Jennifer Kwan", - "author_inst": "LCIM, NIAID, NIH" - }, - { - "author_name": "Kaitlyn Sadtler", - "author_inst": "NIBIB, NIH" - }, - { - "author_name": "Alassane Dicko", - "author_inst": "MRTC/USTTB" - }, - { - "author_name": "Patrick Duffy", - "author_inst": "LMIV, NIAID, NIH" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.27.21256163", "rel_title": "Estimating local outbreak risks and the effects of non-pharmaceutical interventions in age-structured populations: SARS-CoV-2 as a case study", @@ -774211,6 +775771,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.27.21256018", + "rel_title": "Clinical manifestations of hospitalized COVID-19 patients in Bangladesh: a 14-day observational study", + "rel_date": "2021-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.27.21256018", + "rel_abs": "ObjectivesSevere acute respiratory coronavirus-2 (SARS-CoV-2) is currently a significant public health concern and causing a pandemic in the world. Despite of immense attention to the coronavirus disease-2019 (COVID-19), very little attention has been given to the kinetics of disease progression in infected patients. Therefore, in this study, we present a 14-day clinical observation of hospital-admitted COVID-19 patients.\n\nMethodsAfter recording the demography of 42 COVID-19 patients on day 1, we observed the clinical progression for 14 days by investigating the hematological and biochemical responses of patients blood and serum, respectively.\n\nResultsApproximately 62% of the hospital-admitted COVID-19 patients presented cough, followed by fever (approximately 52%). The top comorbidities of these patients were hypertension (30%) and diabetes mellitus (19%). The average blood hemoglobin level was slightly low among the patients in early days of infection and went up to the normal level on the latter days. A substantial increase in the level of ALT/SGPT (up to 106 units/L; SEM: 12.64) and AST/SGOT (up to 64.35 units/L; SEM: 5.013) in COVID-19 patients was observed, which may suggest that infection with CoV-2019 is associated with the functionality of other organs of COVID-19 patients.\n\nConclusionThis 14-day observational study may help clinicians to decide the choice of treatment of COVID-19 patients.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Modhusudon Shaha", + "author_inst": "Monash University" + }, + { + "author_name": "Md. Azizul Islam", + "author_inst": "Bangladesh Army Medical Corps, Dhaka Cantonment, Dhaka, Bangladesh" + }, + { + "author_name": "Faizul Huq", + "author_inst": "Department of Medicine, Combined Military Hospital, Dhaka Cantonment, Dhaka, Bangladesh" + }, + { + "author_name": "Bithi Roy", + "author_inst": "Department of Agronomy, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh" + }, + { + "author_name": "Ashraful Kabir", + "author_inst": "Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton-3800, Victoria, Australia" + }, + { + "author_name": "Md Salimullah", + "author_inst": "National Institute of Biotechnology, Ganakbari, Savar, Dhaka-1349, Bangladesh" + }, + { + "author_name": "Mamun Al Mahtab", + "author_inst": "Department of Hepatology, Bangabandhu Sheikh Mujib Medical University Hospital, Dhaka, Bangladesh" + }, + { + "author_name": "Sheikh Mohammad Fazle Akbar", + "author_inst": "Ehime University School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.26.21256118", "rel_title": "Anti-SARS-CoV-2 antibody levels are concordant across multiple platforms but are not fully predictive of sterilizing immunity", @@ -775307,41 +776914,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.04.26.21256109", - "rel_title": "COVID-19 vaccine willingness and cannabis use histories", - "rel_date": "2021-04-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.26.21256109", - "rel_abs": "BackgroundCannabis use is associated with problematic health-behaviors such as excessive alcohol and tobacco use, and sedentary behavior. Here, we examined the association between cannabis use history and an especially topical health-behavior, willingness to receive a COVID-19 vaccine.\n\nMethodsCOVID-19 vaccine willingness was surveyed in a subset of participants from the Tulsa 1000 Study, which is a longitudinal study of psychiatric treatment-seeking and healthy control participants. We identified 45 participants who completed a COVID-19 vaccine questionnaire and reported more than 10 lifetime cannabis uses. Those participants were compared to a group of 45 individuals with very light (<10) cannabis use histories who were propensity score-matched on age, sex, income, and race. Two-group t-tests and Bayes factor analysis on vaccine willingness were conducted between groups. Exploratory correlation analyses were conducted on vaccine willingness and lifetime cannabis use levels within the cannabis group only.\n\nResultsVaccine willingness did not differ between the two groups (t88=0.33, p=.74; BF01=4.3). However, a negative correlation was identified within the cannabis group, such that higher lifetime cannabis use histories correlated with less willingness to receive a vaccine (rho43= -.33, p=.03).\n\nConclusionsAlthough vaccine willingness did not differ between the two matched groups, preliminary evidence suggests that heavy lifetime cannabis use might indicate a reluctance to engage in health-promoting behaviors like receiving a COVID-19 vaccine.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Philip A. Spechler", - "author_inst": "Laureate Institute for Brain Research" - }, - { - "author_name": "Jennifer L. Stewart", - "author_inst": "Laureate Institute for Brain Research" - }, - { - "author_name": "Rayus Kuplicki", - "author_inst": "Laureate Institute for Brain Research" - }, - { - "author_name": "- the Tulsa 1000 Investigators", - "author_inst": "" - }, - { - "author_name": "Martin P. Paulus", - "author_inst": "Laureate Institute for Brain Research" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.04.26.21256087", "rel_title": "The initial impact of a national BNT162b2 mRNA COVID-19 vaccine rollout", @@ -776173,6 +777745,25 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2021.04.28.441840", + "rel_title": "Regulation of Lysosome-Associated Membrane Protein 3 (LAMP3) in Lung Epithelial Cells by Coronaviruses (SARS-CoV-1/2) and Type I Interferon Signaling", + "rel_date": "2021-04-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.28.441840", + "rel_abs": "Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection is a major risk factor for mortality and morbidity in critical care hospitals around the world. Lung epithelial type II cells play a major role in several physiological processes, including recognition and clearance of respiratory viruses as well as repair of lung injury in response to environmental toxicants. Gene expression profiling of lung epithelial type II-specific genes led to the identification of lysosomal-associated membrane protein 3 (LAMP3). Intracellular locations of LAMP3 include plasma membrane, endosomes, and lysosomes. These intracellular organelles are involved in vesicular transport and facilitate viral entry and release of the viral RNA into the host cell cytoplasm. In this study, regulation of LAMP3 expression in human lung epithelial cells by several respiratory viruses and type I interferon signaling was investigated. Coronaviruses including SARS-CoV-1 and SARS-CoV-2 significantly induced LAMP3 expression in lung epithelial cells within 24 hours after infection that required the presence of ACE2 viral entry receptor. Time-course experiments revealed that the induced expression of LAMP3 by SARS-CoV-2 was correlated with the induced expression of interferon-beta1 (IFNB1) and signal transducers and activator of transcription 1 (STAT1) mRNA levels. LAMP3 was also induced by direct IFN-beta treatment or by infection with influenza virus lacking the non-structural protein1(NS1) in NHBE bronchial epithelial cells. LAMP3 expression was induced in human lung epithelial cells by several respiratory viruses, including respiratory syncytial virus (RSV) and the human parainfluenza virus 3 (HPIV3). Location in lysosomes and endosomes as well as induction by respiratory viruses and type I Interferon suggests that LAMP3 may have an important role in inter-organellar regulation of innate immunity and a potential target for therapeutic modulation in health and disease. Furthermore, bioinformatics revealed that a subset of lung type II cell genes were differentially regulated in the lungs of COVID-19 patients.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Ramana Chilakamarti", + "author_inst": "Dartmouth-Hitchcock Medical Center, Dartmouth Med School, Lebanon, New Hampshire" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.04.28.441474", "rel_title": "Nucleic acid delivery of immune-focused SARS-CoV-2 nanoparticles drive rapid and potent immunogenicity capable of single-dose protection", @@ -777221,41 +778812,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.04.19.21255763", - "rel_title": "COVID-Nets: Deep CNN Architectures for Detecting COVID-19 Using Chest CT Scans", - "rel_date": "2021-04-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.19.21255763", - "rel_abs": "This paper introduces two novel deep convolutional neural network (CNN) architectures for automated detection of COVID-19. The first model, CovidResNet, is inspired by the deep residual network (ResNet) architecture. The second model, CovidDenseNet, exploits the power of densely connected convolutional networks (DenseNet). The proposed networks are designed to provide fast and accurate diagnosis of COVID-19 using computed tomography (CT) images for the multi-class and binary classification tasks. The architectures are utilized in a first experimental study on the SARS-CoV-2 CT-scan dataset, which contains 4173 CT images for 210 subjects structured in a subject-wise manner for three different classes. First, we train and test the networks to differentiate COVID-19, non-COVID-19 viral infections, and healthy. Second, we train and test the networks on binary classification with three different scenarios: COVID-19 vs. healthy, COVID-19 vs. other non-COVID-19 viral pneumonia, and non-COVID-19 viral pneumonia vs. healthy. Our proposed models achieve up to 93.96% accuracy, 99.13% precision, 94% sensitivity, 97.73% specificity, and a 95.80% F1-score for binary classification, and up to 83.89% accuracy, 80.36% precision, 82% sensitivity, 92% specificity, and a 81% F1-score for the three-class classification tasks. The experimental results reveal the validity and effectiveness of the proposed networks in automated COVID-19 detection. The proposed models also outperform the baseline ResNet and DenseNet architectures while being more efficient.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Hammam Alshazly", - "author_inst": "University of Luebeck" - }, - { - "author_name": "Christoph Linse", - "author_inst": "University of Luebeck" - }, - { - "author_name": "Mohamed Abdalla", - "author_inst": "King Khalid University" - }, - { - "author_name": "Erhardt Barth", - "author_inst": "University of Luebeck" - }, - { - "author_name": "Thomas Martinetz", - "author_inst": "University of Luebeck" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2021.04.21.21255862", "rel_title": "A Generalizable Data Assembly Algorithm for Infectious Disease Outbreaks", @@ -777954,6 +779510,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.04.23.21253857", + "rel_title": "The Barrier to Vaccination Is Not Vaccine Hesitancy: Patterns of COVID-19 Vaccine Acceptance over the Course of the Pandemic in 23 Countries", + "rel_date": "2021-04-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.23.21253857", + "rel_abs": "BackgroundAt present, evidence is inconclusive regarding what factors influence vaccine intent, and whether there are widespread disparities across populations and time. The current study provides new insights regarding vaccine intent and potential differences across 23 countries and over time.\n\nMethodsOur data come from a unique longitudinal survey that contains responses from Facebook users (N=1,425,172) from the 23 countries from four continents collected in 18 waves from July 2020 through March 2021.\n\nResultsWe find that vaccine intent varies significantly across countries and over time. Across countries, there are notable disparities in intent to vaccinate. Regarding time, intent has recently reached an all-time high. Our data demonstrates that intent to vaccinate has increased as countries have deployed vaccines on larger scales with undecidedness declining. However, there are some countries where vaccine intent is stagnant and in one country - Egypt - where it seems to have declined.\n\nInterpretationsLarge numbers of citizens across the world are willing to get vaccinated. In the vast majority of countries in our sample, these were high enough to reach more conservative levels of herd immunity1 if combined with numbers of persons already infected. As such, the main barrier to vaccination is not vaccine hesitancy, but the shortage of vaccines. This sends a clear message to politicians who need to work on a quick and fair distribution of vaccine; and to scientists who need to focus their attention on understanding remaining pockets of vaccine skepticism or undecidedness and on factors that explain actual vaccine behavior, rather than intent.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Ammina Kothari", + "author_inst": "Rochester Institute of Technology" + }, + { + "author_name": "Gerit Pfuhl", + "author_inst": "UiT The Arctic University of Norway" + }, + { + "author_name": "David Schieferdecker", + "author_inst": "Free University Berlin" + }, + { + "author_name": "Casey Taggart Harris", + "author_inst": "University of Arkansas" + }, + { + "author_name": "Caitlin Tidwell", + "author_inst": "University of Arkansas" + }, + { + "author_name": "Kevin M. Fitzpatrick", + "author_inst": "University of Arkansas" + }, + { + "author_name": "Stephanie Godleski", + "author_inst": "Rochester Institute of Technology" + }, + { + "author_name": "Saurabh Sanjay", + "author_inst": "Rochester Institute of Technology" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.04.26.441498", "rel_title": "Mechanical control of innate immune responses against viral infection revealed in a human Lung Alveolus Chip", @@ -778830,33 +780433,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.04.20.21255830", - "rel_title": "Miami-Dade: A Case Study of Domestic Violence Arrests During the COVID-19 Pandemic", - "rel_date": "2021-04-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.20.21255830", - "rel_abs": "The global health crisis that started early in 2020 has triggered a surge of interest in the effect (if any) of COVID-19 on patterns of domestic violence.1 The first systematic review and meta-analysis examining domestic violence during the pandemic revealed quite a lot of diversity in the approaches used to measure potential effects. Drawing on the time series forecasting literature, this brief report contributes to the growing body of evidence around the issue of domestic violence during the pandemic. Arrest data from Miami-Dade County (US) are leveraged along with a robust approach towards model identification, which is used to generate a suitably accurate forecast against which the observed pandemic period domestic violence data can be compared. The pattern uncovered for Miami-Dade County was similar what was found in other U.S. cities that during the pandemic experienced spikes (+95 CI) in the level of domestic violence arrests that were greater than expected. Interestingly these spikes appeared shortly after dips (-95 CI) in observed arrests fell below the expected level.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Justin Kurland", - "author_inst": "University of Southern Mississippi" - }, - { - "author_name": "Alex R. Piquero", - "author_inst": "University of Miami; Monash University" - }, - { - "author_name": "Nicole Leeper Piquero", - "author_inst": "University of Miami" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.04.24.21256053", "rel_title": "How the COVID-19 pandemic is shaping research in Africa: inequalities in scholarly output and collaborations and new opportunities for scientific leadership", @@ -779688,6 +781264,77 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.04.24.441228", + "rel_title": "A synthetic peptide CTL vaccine targeting nucleocapsid confers protection from SARS-CoV-2 challenge in rhesus macaques", + "rel_date": "2021-04-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.24.441228", + "rel_abs": "BackgroundPersistent transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has given rise to a COVID-19 pandemic. Several vaccines, evoking protective spike antibody responses, conceived in 2020, are being deployed in mass public health vaccination programs. Recent data suggests, however, that as sequence variation in the spike genome accumulates, some vaccines may lose efficacy.\n\nMethodsUsing a macaque model of SARS-CoV-2 infection, we tested the efficacy of a peptide-based vaccine targeting MHC Class I epitopes on the SARS-CoV-2 nucleocapsid protein. We administered biodegradable microspheres with synthetic peptides and adjuvants to rhesus macaques. Unvaccinated control and vaccinated macaques were challenged with 1 x 108 TCID50 units of SARS-CoV-2, followed by assessment of clinical symptoms, viral load, chest radiographs, sampling of peripheral blood and bronchoalveolar lavage (BAL) fluid for downstream analysis.\n\nResultsVaccinated animals were free of pneumonia-like infiltrates characteristic of SARS-CoV-2 infection and presented with lower viral loads relative to controls. Gene expression in cells collected from BAL samples of vaccinated macaques revealed a unique signature associated with enhanced development of adaptive immune responses relative to control macaques.\n\nConclusionsWe demonstrate that a room temperature stable peptide vaccine based on known immunogenic HLA Class I bound CTL epitopes from the nucleocapsid protein can provide protection against SARS-CoV-2 infection in non-human primates.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC=\"FIGDIR/small/441228v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (35K):\norg.highwire.dtl.DTLVardef@c0730aorg.highwire.dtl.DTLVardef@c0bff7org.highwire.dtl.DTLVardef@7b1ea6org.highwire.dtl.DTLVardef@11950a5_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Paul Harris", + "author_inst": "Columbia University" + }, + { + "author_name": "Trevor Brasel", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Christopher Massey", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "CV Herst", + "author_inst": "Flow Pharma" + }, + { + "author_name": "Scott Burkholz", + "author_inst": "Flow Pharma" + }, + { + "author_name": "Peter Lloyd", + "author_inst": "Flow Pharma" + }, + { + "author_name": "Tikoes Blankenberg", + "author_inst": "Dignity Health Mercy Medical Center" + }, + { + "author_name": "Thomas Bey", + "author_inst": "Dignity Health Mercy Medical Center" + }, + { + "author_name": "Richard Carback", + "author_inst": "Flow Pharma" + }, + { + "author_name": "Thomas Hodge", + "author_inst": "Flow Pharma" + }, + { + "author_name": "Serban Ciotlos", + "author_inst": "Flow Pharma" + }, + { + "author_name": "Lu Wang", + "author_inst": "Flow Pharma" + }, + { + "author_name": "Jason Edward Comer", + "author_inst": "UTMB" + }, + { + "author_name": "Reid M. Rubsamen", + "author_inst": "Flow Pharma" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.04.23.441195", "rel_title": "Broad cross-reactivity across sarbecoviruses exhibited by a subset of COVID-19 donor-derived neutralizing antibodies", @@ -780616,53 +782263,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.04.23.21255998", - "rel_title": "Knowledge and Impact of COVID-19 on Middle-Aged and Older People living with HIV in Lima, Peru", - "rel_date": "2021-04-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.23.21255998", - "rel_abs": "COVID-19 has had an unprecedented worldwide impact, and Peru has had one of the highest COVID-19 case rates despite implementation of an early strict nationwide quarantine. Repercussions on Perus healthcare system may impact vulnerable populations, particularly people with HIV (PWH). We explored the knowledge of COVID-19 and the socioeconomic and health impact of the pandemic among middle-aged and older PWH. A cross-sectional telephone survey was administered to 156 PWH age [≥]40 years receiving care in one of two large HIV clinics in Lima, Peru. The majority of PWH (age 52{+/-}7.7 years, 41% female, 65% completed secondary school or less) were knowledgeable regarding COVID-19 symptoms and prevention methods. Nearly half of those employed prior to the pandemic reported job loss. Female sex (unadjusted prevalence ratio [PR] 1.85 [95%CI 1.27-2.69]), low educational level (PR 1.62 [1.06-2.48]) and informal work (PR 1.58 [1.06-2.36]) were risk factors for unemployment but not in adjusted models. Increased anxiety was reported in 64% and stress in 77%. COVID-19 has had a substantial socioeconomic and mental health impact on PWH living in Lima, Peru, particularly those with lower educational levels and informal workers. Efforts are needed to ensure continued medical care and socioeconomic support of PWH in Peru.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Monica Maria Diaz", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Diego M Cabrera", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Marcela Gil-Zacarias", - "author_inst": "Universidad Peruana Cayetano Heredia Facultad de Medicina" - }, - { - "author_name": "Valeria Ramirez", - "author_inst": "Universidad Peruana Cayetano Heredia Facultad de Medicina" - }, - { - "author_name": "Manuel Saavedra", - "author_inst": "Universidad Peruana Cayetano Heredia Facultad de Medicina" - }, - { - "author_name": "Cesar Carcamo", - "author_inst": "Universidad Peruana Cayetano Heredia Facultad de Salud Publica y Administracion" - }, - { - "author_name": "Evelyn Hsieh", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Patricia J Garcia", - "author_inst": "Universidad Peruana Cayetano Heredia Facultad de Salud Publica y Administracion" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "hiv aids" - }, { "rel_doi": "10.1101/2021.04.23.21256014", "rel_title": "Risk factors associated with severe outcomes of COVID-19: An updated rapid review to inform national guidance on vaccine prioritization in Canada", @@ -781482,6 +783082,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2021.04.25.21255897", + "rel_title": "Contrasting epidemiology and population genetics of COVID-19 infections defined with 74 polymorphic loci in SARS-CoV-2 genomes sampled globally.", + "rel_date": "2021-04-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.25.21255897", + "rel_abs": "SARS-CoV-2, the coronavirus causing COVID-19, has infected and killed several millions of people worldwide. Since the first COVID-19 outbreak in December 2019, SARS-CoV-2 has evolved with a few genetic variants associated with higher infectivity. We aimed to identify polymorphic loci in SARS-CoV-2 that can be used to define and monitor the viral epidemiology and population genetics in different geographical regions. Between December 2019 and September 2020, we sampled 5,959 SARS-CoV-2 genomes. More than 80% of the genomes sampled in Africa, Asia, Europe, North America, Oceania and South America were reportedly isolated from clinical infections in older patients, [≥] 20 years. We used the first indexed genome (NC_045512.2) as a reference and constructed multilocus genotypes (MLGs) for each sampled genome based on amino acids detected at 74 polymorphic loci located in ORF1ab, ORF3a, ORF8, matrix (M), nucleocapsid (N) and spike (S) genes. Eight of the 74 loci were informative in estimating the risk of carrying infections with mutant alleles among different age groups, gender and geographical regions. Four mutant alleles - ORF1ab L4715, S G614, and N K203 and R204 reached 90% prevalence globally, coinciding with peaks in transmission but not COVID-19 severity, from March to August 2020. During this period, the MLG genetic diversity was moderate in Asia, Oceania and North America; in contrast to Africa, Europe and South America, where lower genetic diversity and absence of linkage disequilibrium indicated clonal SARS-CoV-2 transmission. Despite close relatedness to Asian MLGs, MLGs in the global population were genetically differentiated by geographic region, suggesting structure in SARS-CoV-2 populations. Our findings demonstrate the utility of the 74 loci as a genetic tool to study and monitor SARS-CoV-2 transmission dynamics and evolution, which can inform future control interventions.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Felicia Chan", + "author_inst": "Central Clinical School, Monash University, Melbourne, Australia.The Macfarlane Burnet Institute for Medical Research" + }, + { + "author_name": "Ricardo Ataide", + "author_inst": "Department of Medicine, University of Melbourne, Australia. Walter and Eliza Hall Institute, Melbourne, Australia" + }, + { + "author_name": "Jack S Richards", + "author_inst": "The Macfarlane Burnet Institute for Medical Research. Department of Medicine, University of Melbourne, Australia. Departmet of Infectious Diseases, Monash Unive" + }, + { + "author_name": "Charles Akugbey Narh", + "author_inst": "The Macfarlane Burnet Institute for Medical Research. Department of Medicine, University of Melbourne, Australia. Departmet of Infectious Diseases, Monash Unive" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.25.21256085", "rel_title": "Developing RT-LAMP Assays for Detection of SARS-CoV-2 in Saliva", @@ -782242,41 +783873,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2021.04.23.21255879", - "rel_title": "A systematic review on Multisystem Inflammatory Syndrome in Children (MIS-C) with COVID-19: Development of a scoring system for clinical diagnosis", - "rel_date": "2021-04-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.23.21255879", - "rel_abs": "BackgroundThere is growing evidence of Multisystem Inflammatory Syndrome in Children (MIS-C) resembling Kawasaki disease in children infected with SARS-CoV-2. The review was undertaken to evaluate the case definition, the spectrum of clinical presentations and current management practices in children with COVID-19 presenting with or without MIS-C.\n\nMethodsThe individual patient data from 119 studies accounting for 333 children were analyzed. We devised a scoring system as per WHO criteria to classify the patients as MIS-C or without MIS-C. A score of 3 was given for the presence of fever (>24h) and a score of 1 for lab-confirmed diagnosis of SARS-CoV-2. Additionally, a score of 1 was given for a) rash or conjunctivitis or muco-cutaneous inflammation signs, b) hypotension or shock, c) diarrhea, vomiting or abdominal pain, d) features of myocardial dysfunction as determined by abnormal eco-cardiography or elevated Troponin or N-terminal pro B-type Natriuretic Peptide (NT-proBNP), e) evidence of coagulopathy as evidenced by elevated levels of prothrombin time PT, partial thromboplastin time PTT or D-dimer, f) laboratory evidence of inflammation as determined by elevated erythrocyte sedimentation rate (ESR) or C-reactive protein (CRP) or procalcitonin. A negative score of (-3) was given when there was a diagnosis of sepsis, staphylococcal or streptococcal shock syndrome. Based on these criteria, a minimum score of 6 was essential to classify the child as MIS-C.\n\nResultsBased on this score, 18% (52/289) of cases were identified to be MIS-C. A greater proportion of children with MIS-C had cardiac involvement (MIS-C 80% vs Non-MIS-C 20%) and gastrointestinal involvement (MIS-C 71% vs Non-MIS-C 12%). Lymphopenia was commonly reported in MIS-C (MIS-C 54.2% vs Non-MIS-C 29.7%). In addition to routine inflammatory markers, significantly greater proportion of children with MIS-C had elevated Ferritin, LDH, Fibrinogen and IL-6. Children with MIS-C were less likely to have respiratory symptoms like cough (MIS-C 25% vs Non-MIS-C 75%) and rhinorrhea (MIS-C 4% vs Non-MIS-C 22.8%). A greater proportion of children with MIS-C required intensive care and aggressive treatment; and mortality rates were also higher in MIS-C group (MIS-C 10% vs Non-MIS-C 1%).\n\nConclusionThe children with COVID-19 having cardiac and/or gastrointestinal involvement are more likely to develop MIS-C. The children with MIS-C have higher mortality rates. The scoring system developed herein will aid clinicians in patient diagnosis and timely management.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Dr.Suchitra Vishwambhar Surve", - "author_inst": "ICMR-National Institute for research in reproductive Health" - }, - { - "author_name": "Ms. Shaini Joseph", - "author_inst": "ICMR- National Institute for Research in Reproductive Health" - }, - { - "author_name": "Dr. Rahul K Gajbhiye", - "author_inst": "ICMR- National Institute for Research in Reproductive Health" - }, - { - "author_name": "Smita D Mahale", - "author_inst": "ICMR- National Institute for Research in Reproductive Health" - }, - { - "author_name": "Dr. Deepak N Modi", - "author_inst": "ICMR-National Institute for Research in Reproductive Heath" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2021.04.21.21255852", "rel_title": "Epidemiology of COVID-19 and effect of public health interventions, Chennai, India, March - October 2020", @@ -782900,6 +784496,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nutrition" }, + { + "rel_doi": "10.1101/2021.04.21.21255881", + "rel_title": "Associations of SARS-CoV-2 serum IgG with occupation and demographics of military personnel", + "rel_date": "2021-04-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.21.21255881", + "rel_abs": "BackgroundCountries across the globe have mobilized their armed forces in response to COVID-19, placing them at increased risk for viral exposure. Humoral responses to SARS-CoV-2 among military personnel serve as biomarkers of infection and provide a basis for disease surveillance and recognition of work-related risk factors.\n\nMethodsEnzyme-linked immunosorbent assays (ELISA) were used to measure SARS-CoV-2 spike antigen-specific IgG in serum obtained from N=995 US National Guard soldiers between April-June 2020. Occupational information, e.g. military operating specialty (MOS) codes, and demographic data were obtained via questionnaire. Plaque assays with live SARS-CoV-2 were used to assess serum neutralizing capacity for limited subjects (N=12).\n\nResultsThe SARS-CoV-2 IgG seropositivity rate among the study population was 10.3% and significantly associated with occupation and demographics. Odds ratios were highest for those working in MOS 2T-Transportation (3.6; 95% CI 0.7-18) and 92F-Fuel specialist/ground and aircraft (6.8; 95% CI 1.5-30), as well as black race (2.2; 95% CI 1.2-4.1), household size [≥]6 (2.5; 95% CI 1.3-4.6) and known COVID-19 exposure (2.0; 95% CI 1.2-3.3). Seropositivity tracked along major interstate highways and clustered near the international airport and the New York City border. SARS-CoV-2 spike IgG+ serum exhibited low to moderate SARS-CoV-2 neutralizing capacity with IC50s ranging from 1:15 to 1:280. In limited follow-up testing SARS-CoV-2 serum IgG levels remained elevated up to 7 months.\n\nConclusionsThe data highlight increased SARS-CoV-2 seroprevalence among National Guard vs. the local civilian population in association with transportation-related occupations and specific demographics.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Joseph Zell", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Carolina Lucas", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Jon Klein", + "author_inst": "Yale University" + }, + { + "author_name": "Akiko Iwasaki", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Martin Slade", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Jian Liu", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Adam V Wisnewski", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Carrie Redlich", + "author_inst": "Yale University School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2021.04.21.21255878", "rel_title": "Addressing racial/ethnic disparities in the COVID-19 vaccination campaign", @@ -783876,73 +785519,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.04.23.441101", - "rel_title": "Neutralization of variant under investigation B.1.617 with sera of BBV152 vaccinees", - "rel_date": "2021-04-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.23.441101", - "rel_abs": "The drastic rise in the number of cases in Maharashtra, India has created a matter of concern for public health experts. Twelve isolates of VUI lineage B.1.617 were propagated in VeroCCL81 cells and characterized. Convalescent sera of the COVID-19 cases and recipients of BBV152 (Covaxin) were able to neutralize VUI B.1.617.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Pragya Yadav", - "author_inst": "ICMR-National Institute of Virology" - }, - { - "author_name": "Gajanan N Sapkal", - "author_inst": "ICMR-National Institute of Virology" - }, - { - "author_name": "Priya Abraham", - "author_inst": "Indian Council of Medical Research-National Institute of Virology" - }, - { - "author_name": "Raches Ella", - "author_inst": "Bharat Biotech International Limited, Genome Valley, Hyderabad, Telangana, India Pin-500 078" - }, - { - "author_name": "Gururaj Deshpande", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India, Pin-411021" - }, - { - "author_name": "Deepak Y Patil", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India, Pin-411021" - }, - { - "author_name": "Dimpal Nyayanit", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India, Pin-411021" - }, - { - "author_name": "Nivedita Gupta", - "author_inst": "Indian Council of Medical Research, V. Ramalingaswami Bhawan, P.O. Box No. 4911, Ansari Nagar, New Delhi, India Pin-110029" - }, - { - "author_name": "Rima R Sahay", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India, Pin-411021" - }, - { - "author_name": "Anita M Shete", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India, Pin-411021" - }, - { - "author_name": "Samiran Panda", - "author_inst": "Indian Council of Medical Research, V. Ramalingaswami Bhawan, P.O. Box No. 4911, Ansari Nagar, New Delhi, India Pin-110029" - }, - { - "author_name": "Balram Bhargava", - "author_inst": "Indian Council of Medical Research, V. Ramalingaswami Bhawan, P.O. Box No. 4911, Ansari Nagar, New Delhi, India Pin-110029" - }, - { - "author_name": "V Krishna Mohan", - "author_inst": "Bharat Biotech International Limited, Genome Valley, Hyderabad, Telangana, India Pin-500 078" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.04.23.440619", "rel_title": "Topical TMPRSS2 inhibition prevents SARS-CoV-2 infection in differentiated primary human airway cells", @@ -784914,6 +786490,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.04.20.21255780", + "rel_title": "Frequency of neurological manifestations in COVID-19: a systematic review and meta-analysis of 350 studies", + "rel_date": "2021-04-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.20.21255780", + "rel_abs": "ObjectiveTo summarize the frequency of neurological manifestations reported in COVID-19 patients and investigate the association of these manifestations with disease severity and mortality.\n\nDesignSystematic review and meta-analysis\n\nEligibility criteriaStudies enrolling consecutive COVID-19 patients (probable or confirmed) presenting with neurological manifestations.\n\nData sourcesPubMed, Medline, Cochrane library, clinicaltrials.gov and EMBASE from 31st December 2019 to 15th December 2020.\n\nData extraction and analysisTwo authors independently screened titles and abstracts retrieved by literature search. Risk of bias was examined using Joanna Briggs Institute (JBI) scale. A random-effects meta-analysis was performed, and pooled prevalence and 95% Confidence Intervals (CI) were calculated for neurological manifestations. Odds ratio (OR) and 95%CI were calculated to determine the association of neurological manifestations with disease severity and mortality. Presence of heterogeneity was assessed using I-square, meta-regression, and subgroup analyses. Statistical analyses were conducted in R version 3.6.2.\n\nResultsOf 2,455 citations, 350 studies were included in this review, providing data on 145,634 COVID-19 patients, 89% of whom were hospitalized. Forty-one neurological manifestations (24 symptoms and 17 diagnoses) were identified. Pooled prevalence of the most common neurological symptoms included: fatigue (32%), myalgia (20%), taste impairment (21%), smell impairment (19%) and headache (13%). A low risk of bias was observed in 85% of studies; studies with higher risk of bias yielded higher prevalence estimates. Stroke was the most common neurological diagnosis (pooled prevalence-2%). In COVID-19 patients aged >60, the pooled prevalence of acute confusion/delirium was 34% and the presence of any neurological manifestations in this age group was associated with mortality (OR 1.80; 95%CI 1.11 to 2.91).\n\nConclusionsUp to one-third of COVID-19 patients analysed in this review experienced at least one neurological manifestation. One in 50 patients experienced stroke. In those over 60, more than one-third had acute confusion/delirium; the presence of neurological manifestations in this group was associated with near doubling of mortality. Results must be interpreted keeping in view the limitations of observational studies and associated bias.\n\nSystematic review registrationPROSPERO CRD42020181867.\n\nWhat is already known on this topicThe frequency of neurological manifestations including fatigue, myalgia, taste and smell impairments, headache and dizziness in COVID-19 patients has been reported in a few systematic reviews and meta-analyses. However, considerable heterogeneity has been observed in terms of methodological quality of the studies, severity of the disease, mean age and hospitalization status of the patients. The evidence regarding the frequency of neurological diagnoses including stroke, encephalitis, Guillain Barre syndrome (GBS) is also limited to case reports and case series and no data exists thus far on the pooled prevalence estimates for neurological diagnoses in COVID-19 patients.\n\nWhat this study addsTo the best of the authors knowledge, this is the largest systematic review and meta-analysis to date (including 350 studies with data on 145,634 cases) summarizing the evidence on the frequency of the full spectrum of neurological manifestations in COVID-19 patients in the overall, young and elderly populations. For the first time, our review reports the pooled prevalence of stroke in COVID-19 patients. Risk of bias, old age and disease severity were potential determinants of the frequency and nature of neurological manifestations as well as its association with mortality. Our review also highlights the need to develop reporting standards for studies describing the frequency of clinical features. Moreover, we note that this will be the first systematic review and meta-analysis on this subject to include studies reported in all languages.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Shubham Misra", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Kavitha Kolappa", + "author_inst": "World Health Organization, Brain Health Unit" + }, + { + "author_name": "Manya Prasad", + "author_inst": "Institute of Liver and Biliary Sciences, New Delhi" + }, + { + "author_name": "Divya Radhakrishnan", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Kiran T Thakur", + "author_inst": "Columbia University Irving Medical Center-New York Presbyterian Hospital, New York" + }, + { + "author_name": "Tom Solomon", + "author_inst": "University of Liverpool, Liverpool" + }, + { + "author_name": "Benedict Daniel Michael", + "author_inst": "University of Liverpool, Liverpool" + }, + { + "author_name": "Andrea Sylvia Winkler", + "author_inst": "Technical University of Munich, Germany" + }, + { + "author_name": "Ettore Beghi", + "author_inst": "Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan" + }, + { + "author_name": "Alla Guekht", + "author_inst": "Pirogov Russian National Research Medical University, Moscow" + }, + { + "author_name": "Carlos A A Pardo", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Greta Karen Wood", + "author_inst": "University of Liverpool, Liverpool" + }, + { + "author_name": "Sherry Hsiang-Yi Chou", + "author_inst": "University of Pittsburgh School of Medicine, Pittsburgh PA" + }, + { + "author_name": "Ericka L Fink", + "author_inst": "UPMC Children's Hospital of Pittsburgh, Pittsburgh PA" + }, + { + "author_name": "Erich Schmutzhard", + "author_inst": "Medical University Innsbruck, Austria" + }, + { + "author_name": "Amir Kheradmand", + "author_inst": "The Johns Hopkins Hospital" + }, + { + "author_name": "Fan Kee Hoo", + "author_inst": "University Putra Malaysia" + }, + { + "author_name": "Amit Kumar", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Animesh Das", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Achal K Srivastava", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Ayush Agarwal", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Tarun Dua", + "author_inst": "World Health Organization, Brain Health Unit" + }, + { + "author_name": "Kameshwar Prasad", + "author_inst": "Rajendra Institute of Medical Sciences, Ranchi" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2021.04.21.21255832", "rel_title": "Shut Down Schools, Knock Down the Virus? Causal Inference on the School Closures' Effect on the Spread of COVID-19", @@ -785822,33 +787505,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "endocrinology" }, - { - "rel_doi": "10.1101/2021.04.14.21255385", - "rel_title": "Evolution of case fatality rates in the second wave of coronavirus in England: effects of false positives, a Variant of Concern and vaccination.", - "rel_date": "2021-04-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.14.21255385", - "rel_abs": "1ObjectiveTo track the statistical case fatality rate (CFR) in the second wave of the UK coronavirus outbreak, and to understand its variations over time.\n\nDesignPublicly available UK government data and clinical evidence on the time between first positive PCR test and death are used to determine the relationships between reported cases and deaths, according to age groups and across regions in England.\n\nMain Outcome MeasuresEstimates of case fatality rates and their variations over time.\n\nResultsThroughout October and November 2020, deaths in England can be broadly understood in terms of CFRs which are approximately constant over time. The same CFRs prove a poor predictor of deaths when applied back to September, when prevalence of the virus was comparatively low, suggesting that the potential effect of false positive tests needs to be taken into account. Similarly, increasing CFRs are needed to match cases to deaths when projecting the model forwards into December. The growth of the S gene dropout VOC in December occurs too late to explain this increase in CFR alone, but at 33% increased mortality, it can explain the peak in deaths in January. Seasonal effects could be in part responsible for the early December increase in CFR, and if so, the estimate of increased mortality would be reduced. There is also evidence that the prevalence of B.1.1.7 may have been slower amongst older age groups, and if this is a factor, then 33% could be an underestimate of mortality. From the second half of January, the CFRs for older age groups show a marked decline. Since the fraction of the VOC has not decreased, this decline is likely to be the result of the rollout of vaccination. However, due to the rapidly decreasing nature of the raw cases, any imprecisions in the time-to-death distribution are magnified in this time period, rendering estimates of vaccinations effect less precise.\n\nConclusionsThe relationship between cases and deaths, even when controlling for age, is not static through the second wave of coronavirus in England. An apparently anomalous low case-fatality ratio in September can be accounted for by a 0.4% false-positive fraction. The rapid growth in CFR in December can be understood in part in terms of a more deadly new variant B.1.1.7, while a decline in January correlates with vaccine roll-out, suggesting that vaccine reduce the severity of infection, as well as the risk.\n\nSummary BoxO_ST_ABSWhat is already known on this topicC_ST_ABSThe case fatality rate (CFR) is a useful measure which enables one to estimate future deaths based on current infections. In England, there was a surge in Covid-19 CFR around the beginning of December.\n\nWhat the study addsUsing it, we monitor the case-fatality rate across time, region and age group from publicly available case data. This quantity is related to the lethality of the virus. It shows a sharp increase in December 2020, which parallels the spread of the B.1.1.7 variant. The January peak in actual deaths matches that predicted by cases if B.1.1.7 is about 33% more deadly; this estimate would be lower if there is a seasonal effect on deaths, and higher if at the peak the variant was less pervasive amongst older age groups. A steady drop in CFR from January suggests that vaccination not only reduces transmission but also the risk of serious illness among those infected. It is notable that these conclusions are reached with publicly available data independent of clinical studies.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "James A Ackland", - "author_inst": "Department of Psychology, University of Cambridge" - }, - { - "author_name": "Graeme J Ackland", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "David J Wallace", - "author_inst": "ICMS Edinburgh" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.04.19.21255745", "rel_title": "Strategies for COVID-19 vaccination under a shortage scenario: a geo-stochastic modelling approach.", @@ -786588,6 +788244,105 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.04.22.21255637", + "rel_title": "Evaluation of a novel, rapid antigen detection test for the diagnosis of SARS-CoV-2", + "rel_date": "2021-04-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.22.21255637", + "rel_abs": "BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus disease 2019 (COVID-19) is currently finally determined in laboratory settings by real-time reverse-transcription polymerase-chain-reaction (rt-PCR). However, simple testing with immediately available results are crucial to gain control over COVID-19. The aim was to evaluate such a point-of-care antigen rapid test (AG-rt) device in its performance compared to laboratory-based rt-PCR testing in COVID-19 suspected, symptomatic patients.\n\nMethodsFor this prospective study, two specimens each of 541 symptomatic female (54.7%) and male (45.3%) patients aged between 18 and 95 years tested at five emergency departments (ED, n=296) and four primary healthcare centres (PHC, n=245), were compared, using AG-rt (positive/negative/invalid) and rt-PCR (positive/negative and cycle threshold, Ct) to diagnose SARS-CoV-2. Diagnostic accuracy, sensitivity, specificity, positive predictive values (PPV), negative predictive value (NPV), and likelihood ratios (LR+/-) of the AG-rt were assessed.\n\nResultsDifferences between ED and PHC were detected regarding gender, age, symptoms, disease prevalence, and diagnostic performance. Overall, 174 (32.2%) were tested positive on AG-rt and 213 (39.4%) on rt-PCR. AG correctly classified 91.7% of all rt-PCR positive cases with a sensitivity of 80.3%, specificity of 99.1%, PPV of 98.3, NPV of 88.6%, LR(+) of 87.8, and LR(-) of 0.20. The highest sensitivities and specificities of AG-rt were detected in PHC (sensitivity: 84.4%, specificity: 100.0%), when using Ct of 30 as cut-off (sensitivity: 92.5%, specificity: 97.8%), and when symptom onset was within the first three days (sensitivity: 82.9%, specificity: 99.6%).\n\nConclusionsThe highest sensitivity was detected with a high viral load. Our findings suggest that AG-rt are comparable to rt-PCR to diagnose SARS-CoV-2 in COVID-19 suspected symptomatic patients presenting both at emergency departments and primary health care centres.\n\nSUMMARYThe rapid SARS-Cov-2 antigen test (SARS-CoV-2 Rapid Antigen Test (Roche Diagnostics), was compared in symptomatic patients with PCR testing both in emergency departments and primary health care centres. It showed an overall sensitivity of 80.3% and specificity of 99.1%; these were higher with lower PCR cycle threshold numbers and with a shorter onset of symptoms.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Rainer Thell", + "author_inst": "Emergency Dep., Klinik Donaustadt" + }, + { + "author_name": "Verena Kallab", + "author_inst": "Emergency Dep., Klinik Donaustadt" + }, + { + "author_name": "Wolfgang Weinhappel", + "author_inst": "Medizinmariahilf" + }, + { + "author_name": "Wolfgang Mueckstein", + "author_inst": "Medizinmariahilf" + }, + { + "author_name": "Lukas Heschl", + "author_inst": "Landarztpraxis Oed" + }, + { + "author_name": "Martina Heschl", + "author_inst": "Landarztpraxis Oed" + }, + { + "author_name": "Stefan Korsatko", + "author_inst": "Ordination Medius" + }, + { + "author_name": "Franz Toedling", + "author_inst": "Ordination Toedling" + }, + { + "author_name": "Amelie Blaschke", + "author_inst": "Emergency Dep., Klinik Donaustadt Vienna" + }, + { + "author_name": "Theresa Herzog", + "author_inst": "Emergency Dep., Klinik Donaustadt Vienna" + }, + { + "author_name": "Anna Klicpera", + "author_inst": "Emergency Dep., Klinik Donaustadt Vienna" + }, + { + "author_name": "Clara Koeller", + "author_inst": "Emergency Dep., Klinik Hietzing Vienna" + }, + { + "author_name": "Moritz Haugk", + "author_inst": "Emergency Dep., Klinik Hietzing Vienna" + }, + { + "author_name": "Anna Kreil", + "author_inst": "Emergency Dep., Klinik Landstrasse Vienna" + }, + { + "author_name": "Alexander Spiel", + "author_inst": "Emergency Dep., Klinik Ottakring Vienna" + }, + { + "author_name": "Philipp Kreuzer", + "author_inst": "Emergency Dep., University Clinic Graz" + }, + { + "author_name": "Robert Krause", + "author_inst": "Dep. of Infectiology, University Clinic Graz" + }, + { + "author_name": "Christian Sebesta", + "author_inst": "Dep. of Internal Med. 2, Klinik Donaustadt" + }, + { + "author_name": "Stefan Winkler", + "author_inst": "Dep. of Infectiology, Med. University Vienna" + }, + { + "author_name": "Brenda Laky", + "author_inst": "Aurrom, Medical University of Vienna" + }, + { + "author_name": "Marton Szell", + "author_inst": "Emergency Department, Klinik Donaustadt Vienna" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.22.21255133", "rel_title": "Verification of the Abbott Alinity m Resp-4-Plex Assay for detection of SARS-CoV-2, influenza A/B, and respiratory syncytial virus", @@ -787499,273 +789254,6 @@ "type": "new results", "category": "systems biology" }, - { - "rel_doi": "10.1101/2021.04.20.440647", - "rel_title": "Immune Correlates of Protection by mRNA-1273 Immunization against SARS-CoV-2 Infection in Nonhuman Primates", - "rel_date": "2021-04-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.20.440647", - "rel_abs": "Immune correlates of protection can be used as surrogate endpoints for vaccine efficacy. The nonhuman primate (NHP) model of SARS-CoV-2 infection replicates key features of human infection and may be used to define immune correlates of protection following vaccination. Here, NHP received either no vaccine or doses ranging from 0.3 - 100 g of mRNA-1273, a mRNA vaccine encoding the prefusion-stabilized SARS-CoV-2 spike (S-2P) protein encapsulated in a lipid nanoparticle. mRNA-1273 vaccination elicited robust circulating and mucosal antibody responses in a dose-dependent manner. Viral replication was significantly reduced in bronchoalveolar lavages and nasal swabs following SARS-CoV-2 challenge in vaccinated animals and was most strongly correlated with levels of anti-S antibody binding and neutralizing activity. Consistent with antibodies being a correlate of protection, passive transfer of vaccine-induced IgG to naive hamsters was sufficient to mediate protection. Taken together, these data show that mRNA-1273 vaccine-induced humoral immune responses are a mechanistic correlate of protection against SARS-CoV-2 infection in NHP.\n\nOne-Sentence SummarymRNA-1273 vaccine-induced antibody responses are a mechanistic correlate of protection against SARS-CoV-2 infection in NHP.", - "rel_num_authors": 63, - "rel_authors": [ - { - "author_name": "Kizzmekia S. Corbett", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of Ameri" - }, - { - "author_name": "Martha C. Nason", - "author_inst": "Biostatistics Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health; Bethesda, Ma" - }, - { - "author_name": "Britta Flach", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of Ameri" - }, - { - "author_name": "Matthew Gagne", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of Ameri" - }, - { - "author_name": "Timothy S. Johnston", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of Ameri" - }, - { - "author_name": "Shruti N. Shah", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of Ameri" - }, - { - "author_name": "Venkata Vishwanadh Edara", - "author_inst": "Emory University" - }, - { - "author_name": "Katharine Floyd", - "author_inst": "Emory University" - }, - { - "author_name": "Lilin Lai", - "author_inst": "Emory University" - }, - { - "author_name": "Charlene McDanal", - "author_inst": "Department of Surgery, Duke University Medical Center, Durham, North Carolina, 27708; United States of America." - }, - { - "author_name": "Joseph R. Francica", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of Ameri" - }, - { - "author_name": "Barbara Flynn", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of Ameri" - }, - { - "author_name": "Kai Wu", - "author_inst": "Moderna Inc., Cambridge, MA, 02139; United States of America" - }, - { - "author_name": "Angela Choi", - "author_inst": "Moderna Inc., Cambridge, MA, 02139; United States of America" - }, - { - "author_name": "Matthew Koch", - "author_inst": "Moderna Inc., Cambridge, MA, 02139; United States of America" - }, - { - "author_name": "Olubukola M. Abiona", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of Ameri" - }, - { - "author_name": "Anne P. Werner", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of Ameri" - }, - { - "author_name": "Gabriela S. Alvarado", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of Ameri" - }, - { - "author_name": "Shayne F. Andrew", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of Ameri" - }, - { - "author_name": "Mitzi M. Donaldson", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of Ameri" - }, - { - "author_name": "Jonathan Fintzi", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of Ameri" - }, - { - "author_name": "Dillon R. Flebbe", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of Ameri" - }, - { - "author_name": "Evan Lamb", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of Ameri" - }, - { - "author_name": "Amy T. Noe", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of Ameri" - }, - { - "author_name": "Saule T. Nurmukhambetova", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of Ameri" - }, - { - "author_name": "Samantha J. Provost", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of Ameri" - }, - { - "author_name": "Anthony Cook", - "author_inst": "Bioqual, Inc.; Rockville, Maryland, 20850; United States of America" - }, - { - "author_name": "Alan Dodson", - "author_inst": "Bioqual, Inc.; Rockville, Maryland, 20850; United States of America" - }, - { - "author_name": "Andrew Faudree", - "author_inst": "Bioqual, Inc.; Rockville, Maryland, 20850; United States of America" - }, - { - "author_name": "Jack Greenhouse", - "author_inst": "Bioqual, Inc.; Rockville, Maryland, 20850; United States of America" - }, - { - "author_name": "Swagata Kar", - "author_inst": "Bioqual, Inc.; Rockville, Maryland, 20850; United States of America" - }, - { - "author_name": "Laurent Pessaint", - "author_inst": "Bioqual, Inc.; Rockville, Maryland, 20850; United States of America" - }, - { - "author_name": "Maciel Porto", - "author_inst": "Bioqual, Inc.; Rockville, Maryland, 20850; United States of America" - }, - { - "author_name": "Katelyn Steingrebe", - "author_inst": "Bioqual, Inc.; Rockville, Maryland, 20850; United States of America" - }, - { - "author_name": "Daniel Valentin", - "author_inst": "Bioqual, Inc.; Rockville, Maryland, 20850; United States of America" - }, - { - "author_name": "Serge Zouantcha", - "author_inst": "Bioqual, Inc.; Rockville, Maryland, 20850; United States of America" - }, - { - "author_name": "Kevin W. Bock", - "author_inst": "Infectious Disease Pathogenesis Section; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United" - }, - { - "author_name": "Mahnaz Minai", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Bianca M. Nagata", - "author_inst": "Infectious Disease Pathogenesis Section; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United" - }, - { - "author_name": "Juan I. Moliva", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of Ameri" - }, - { - "author_name": "Renee van de Wetering", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of Ameri" - }, - { - "author_name": "Seyhan Boyoglu-Barnum", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of Ameri" - }, - { - "author_name": "Kwanyee Leung", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of Ameri" - }, - { - "author_name": "Wei Shi", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of Ameri" - }, - { - "author_name": "Eun Sung Yang", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of Ameri" - }, - { - "author_name": "Yi Zhang", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of Ameri" - }, - { - "author_name": "John-Paul Todd", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of Ameri" - }, - { - "author_name": "Lingshu Wang", - "author_inst": "VRC/NIAID/NIH" - }, - { - "author_name": "Hanne Andersen", - "author_inst": "Bioqual, Inc.; Rockville, Maryland, 20850; United States of America" - }, - { - "author_name": "Kathryn E. Foulds", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of Ameri" - }, - { - "author_name": "Darin K. Edwards", - "author_inst": "Moderna Inc" - }, - { - "author_name": "John R. K Mascola", - "author_inst": "Vaccine Research Center, NIAID, NIH" - }, - { - "author_name": "Ian N. Moore", - "author_inst": "Infectious Disease Pathogenesis Section; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United" - }, - { - "author_name": "Mark G. Lewis", - "author_inst": "Bioqual, Inc.; Rockville, Maryland, 20850; United States of America" - }, - { - "author_name": "Andrea Carfi", - "author_inst": "Moderna Inc., Cambridge, MA, 02139; United States of America" - }, - { - "author_name": "David Montefiori", - "author_inst": "Duke University" - }, - { - "author_name": "Mehul S. Suthar", - "author_inst": "Emory University" - }, - { - "author_name": "Adrian McDermott", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of Ameri" - }, - { - "author_name": "Nancy J. Sullivan", - "author_inst": "VRC, NIH" - }, - { - "author_name": "Mario Roederer", - "author_inst": "Vaccine Research Center" - }, - { - "author_name": "Daniel C. Douek", - "author_inst": "NIH Vaccine Research Center" - }, - { - "author_name": "Barney S. Graham", - "author_inst": "Vaccine Research Center, NIAID, NIH" - }, - { - "author_name": "Robert A. Seder", - "author_inst": "NIH" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.04.17.21255668", "rel_title": "Higher COVID-19 Vaccination Rates among Unemployed in the United States: State Level Study in the First 100 days of Vaccine Initiation", @@ -788389,6 +789877,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.14.21255399", + "rel_title": "Choosing the right tool for the job: A comprehensive assessment of serological assays for SARS-CoV-2 as surrogates for authentic virus neutralization", + "rel_date": "2021-04-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.14.21255399", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in late 2019 and has since caused a global pandemic resulting in millions of cases and deaths1-4. Diagnostic tools and serological assays are critical for controlling the outbreak5-7, especially assays designed to quantitate neutralizing antibody levels, considered the best correlate of protection8-11. As vaccines become increasingly available12, it is important to identify reliable methods for measuring neutralizing antibody responses that correlate with authentic virus neutralization but can be performed outside of biosafety level 3 (BSL3) laboratories. While many neutralizing assays using pseudotyped virus have been developed, there have been few studies comparing the different assays to each other as surrogates for authentic virus neutralization9,10,13,14. Here we characterized three enzyme-linked immunosorbent assays (ELISAs) and three pseudotyped VSV virus neutralization assays and assessed their concordance with authentic virus neutralization. The most accurate assays for predicting authentic virus neutralization were luciferase and secreted embryonic alkaline phosphatase (SEAP) expressing pseudotyped virus neutralizations, followed by GFP expressing pseudotyped virus neutralization, and then the ELISAs.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Nicholas Wohlgemuth", + "author_inst": "St Jude Children's Research Hospital" + }, + { + "author_name": "Kendall Whitt", + "author_inst": "University of Tennessee Health Science Center" + }, + { + "author_name": "Sean Cherry", + "author_inst": "St. Jude Children's Research Hospital" + }, + { + "author_name": "Ericka Kirkpatrick Roubidoux", + "author_inst": "St Jude Children's Research Hospital" + }, + { + "author_name": "Chun-Yang Lin", + "author_inst": "St Jude Children's Research Hospital" + }, + { + "author_name": "Kim J Allison", + "author_inst": "St Jude Children's Research Hospital" + }, + { + "author_name": "Ashleigh Gowen", + "author_inst": "St Jude Children's Research Hospital" + }, + { + "author_name": "Pamela Freiden", + "author_inst": "St Jude Children's Research Hospital" + }, + { + "author_name": "E. Kaitlynn Allen", + "author_inst": "St Jude Children's Research Hospital" + }, + { + "author_name": "- St. Jude Investigative Team", + "author_inst": "-" + }, + { + "author_name": "Aditya H Gaur", + "author_inst": "St Jude Children's Research Hospital" + }, + { + "author_name": "Jeremie H Estepp", + "author_inst": "St Jude Children's Research Hospital" + }, + { + "author_name": "Li Tang", + "author_inst": "St Jude Children's Research Hospital" + }, + { + "author_name": "Tomi Mori", + "author_inst": "St Jude Children's Research Hospital" + }, + { + "author_name": "Diego R Hijano", + "author_inst": "St Jude Children's Research Hospital" + }, + { + "author_name": "Maureen A McGargill", + "author_inst": "St Jude Children's Research Hospital" + }, + { + "author_name": "Florian Krammer", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Michael A Whitt", + "author_inst": "University of Tennessee Health Science Center" + }, + { + "author_name": "Joshua Wolf", + "author_inst": "St Jude Children's Research Hospital" + }, + { + "author_name": "Paul G Thomas", + "author_inst": "St. Jude Children's Research Hospital" + }, + { + "author_name": "Stacey Schultz-Cherry", + "author_inst": "St. Jude Children's Research Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.13.21255442", "rel_title": "Gender differences in the determinants of willingness to get the COVID-19 vaccine among the working-age population in Japan", @@ -789365,37 +790952,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "ophthalmology" }, - { - "rel_doi": "10.1101/2021.04.16.21255636", - "rel_title": "Estimating the effect of mobility on SARS-CoV-2 transmission during the first and second wave of the COVID-19 epidemic in Switzerland: a population-based study", - "rel_date": "2021-04-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.16.21255636", - "rel_abs": "The effect of mobility and its value for surveillance in different waves of the COVID-19 epidemic is still unclear. In this study, we compared the role of mobility during the first and second epidemic wave in Switzerland by analysing the link between daily travel distances and the effective reproduction number Rt of SARS-CoV-2. Here we used aggregated mobile phone data from a representative panel survey of the Swiss population to measure human mobility. We estimated the effects of reductions in daily travel distance on Rt via a regression model. We compared mobility effects between the first wave (March 2-April 7, 2020) and the second wave (October 1-December 10, 2020) across mode of transport, travel purpose, sociodemographic subgroup and movement radius. We found that human mobility was associated with the effective reproduction number of SARS-CoV-2 during both the first and second epidemic wave in Switzerland. The estimated relative effects of mobility were similar in both waves for all modes of transport, travel purposes, and sociodemographic subgroups but differed by movement radius. Moreover, smaller mobility reductions in the second wave translated into smaller overall reductions of Rt. Mobility data from mobile phones have a continued potential to support real-time surveillance of COVID-19 during epidemic waves.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Adrian Lison", - "author_inst": "ETH Zurich" - }, - { - "author_name": "Joel Persson", - "author_inst": "ETH Zurich" - }, - { - "author_name": "Nicolas Banholzer", - "author_inst": "ETH Zurich" - }, - { - "author_name": "Stefan Feuerriegel", - "author_inst": "ETH Zurich" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2021.04.15.21255255", "rel_title": "The impact of COVID-19 pandemic on AMI and Stroke mortality in Lombardy: Evidence from the epicenter of the pandemic", @@ -790199,6 +791755,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.04.15.21255558", + "rel_title": "Vaccines, social measures and Covid19 - A European evidence-based analysis", + "rel_date": "2021-04-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.15.21255558", + "rel_abs": "BackgroundA fully quantitative picture of national effectiveness in controlling the spread of the Covid19 virus should consider the percentage of a population vaccinated in relation to the percentage of a population as active cases.\n\nMethodsPublicly available data from 27 European countries on nine dates in 2021. Data were (i) initial Covid19 vaccinations and (ii) Covid19 active cases, both as percentages of a countrys population. Dividing (i) by (ii) yielded a new metric, the V ratio, which can increase as (i) increase or as (ii) decreases or both. I correlated the change in V ratio with the change in R statistic in the 27 counties and nine dates.\n\nResultsMean European V ratio increased from January 11 2021 onwards; inverse correlation was found between V ratio and R statistic (p<0.001, r2=0.15, df=234). Initial threshold V ratio of 10-15 resulted in an R statistic of 1.0 or lower; this threshold increased to 30-40 with further vaccinations. Variation between countries in the V ratio increased with time.\n\nConclusionThis quantitative assessment and use of a summary data-derived threshold index showed the integrated effectiveness of vaccinations and social measures for European countries for Covid19. It established a threshold range for an R value of 1 and calculation of the number of vaccinations needed in Europe to reduce the infectivity of the virus to unity. Results can be used to quantify the relation between transmission following vaccination and social measures to control the spread of Covid19.\n\nSummary box What is already known in the epidemiology of the Covid19 pandemic in Europe countries is time- and country-based estimates of the R statistic as a measure of infectivity, the percentages of vaccinated persons to reduce infectivity and the number of active cases amenable to social measures. What is not known is how these three parameters interact.\n\nWhat does this study add? This study adds by invention an index (V) of percentage vaccinated population divided by percentage active cases. It then examines the corresponding V index in relation to the R statistic. It derives a range threshold V ratio for an R statistic of unity and extends this to suggest the total number of vaccines needed in Europe.\n\nPolicy implicationsThese results will allow policy judgements to be made on the basis of measured evidence, and not just models, of the means to reduce the Covid19 pandemic in Europe. The R statistic captures the development of the pandemic; the V ratio measures the integrated and quantified measures to reduce it. Further development of the analysis could assist in calculating the relative effectiveness of vaccination and social measures linked to a range of values of the V ratio. It can also be used as an alarm call to identify states which, even given 100% vaccination, may not reduce their R statistic below unity.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "John R Porter", + "author_inst": "University of Copenhagen" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.04.14.21255500", "rel_title": "Modelling COVID-19 evolution in Italy with an augmented SIRD model using open data", @@ -791091,81 +792666,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.15.21255300", - "rel_title": "A Feasibility Trial to Evaluate the Composite Efficacy of Inhaled Nitric Oxide in the Treatment of Covid 19 Pneumonia : Impact on Viral Load and Clinical Outcomes", - "rel_date": "2021-04-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.15.21255300", - "rel_abs": "BackgroundHypoxic patients with Covid 19 pneumonia are at high risk of adverse outcomes. Inhaled Nitric Oxide (iNO) inhibits viral entry and replication of SARS-CoV2 and in vivo proof of its antiviral actions is unavailable to date. This feasibility study was conducted to test the antiviral effects of iNO and to describe clinical outcomes.\n\nTrial design and MethodsThe phase II open label, randomised controlled feasibility trial(ISRCTN 16806663) conducted at a South Indian tertiary care referral centre, recruited COVID-19 pneumonia patients with hypoxic respiratory failure and allocated them into iNO cases and control groups(1:1). iNO was administered as pulses for 30 minutes for three consecutive days at 12-hour intervals in cases, in addition to standard of care received by the control group. The primary outcome was decline in viral load, as defined by a surrogate change in the RT-PCR cycle threshold. The co-primary clinical outcome was time to improvement of >2 points on the WHO Ordinal Scale(WOS).\n\nResultsAmong the 29 patients enrolled, 14 iNO cases and 11 controls completed the study protocol. Longitudinal analysis revealed a significant difference in the decline (p <0.002, N= 23) in viral load among the iNO cases compared to controls. The proportion of patients achieving 2-point improvement in the WOS within 14 days of randomisation was significantly higher in the iNO cases (n=11, 79%), as compared to the controls (n=4, 36%) (p=0.05).\n\nConclusionsOur study demonstrated significant improvement in virological and clinical outcomes among patients with adjunct iNO therapy and no adverse effects were reported.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Merlin Moni", - "author_inst": "Amrita Institute of Medical Science" - }, - { - "author_name": "Thushara Madathil", - "author_inst": "Amrita Institute of Medical Sciences" - }, - { - "author_name": "Dipu Sathyapalan", - "author_inst": "Amrita Institute of Medical Science" - }, - { - "author_name": "Veena Menon", - "author_inst": "Amrita Institute of Medical Science" - }, - { - "author_name": "Georg Gutjahr", - "author_inst": "Amrita Institute of Medical Science" - }, - { - "author_name": "Fabia Edathadathil", - "author_inst": "Amrita Institute of Medical Science" - }, - { - "author_name": "Deepthi Sureshkumar", - "author_inst": "Amrita Institute of Medical Science" - }, - { - "author_name": "Preetha Prasanna", - "author_inst": "Amrita Institute of Medical Science" - }, - { - "author_name": "Soumya Jose", - "author_inst": "Amrita Institute of Medical Science" - }, - { - "author_name": "Roshni Jerome", - "author_inst": "Amrita Institute of Medical Science" - }, - { - "author_name": "Ajai Krishnan", - "author_inst": "Amrita Institute of Medical Science" - }, - { - "author_name": "Indulekha Pillai", - "author_inst": "Amrita Institute of Medical Science" - }, - { - "author_name": "Geetha Kumar", - "author_inst": "Amrita Institute of Medical Science" - }, - { - "author_name": "Bipin Nair", - "author_inst": "Amrita Institute of Medical Science" - }, - { - "author_name": "Aveek Jayant Jr.", - "author_inst": "Amrita Institute of Medical Sciences and Research Centre" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.18.21255688", "rel_title": "Sensitive on-site detection of SARS-CoV-2 by ID NOW COVID-19", @@ -792177,6 +793677,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.19.21255578", + "rel_title": "Health Belief, Planned Behavior, or Psychological Antecedents: What predicts COVID-19 Vaccine Hesitancy better among the Bangladeshi Adults?", + "rel_date": "2021-04-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.19.21255578", + "rel_abs": "BackgroundThis study aimed to determine the prevalence and investigate the constellations of psychological determinants of the COVID-19 vaccine hesitancy among the Bangladeshi adult population utilizing the health belief model-HBM (perceived susceptibility to and severity of COVID-19, perceived benefits of and barriers to COVID-19 vaccination, and cues to action), the theory of planned behavior-TPB (attitude toward COVId-19 vaccine, subjective norm, perceived behavioral control, and anticipated regret), and the novel 5C psychological antecedents (confidence, constraints, complacency, calculation, and collective responsibility). We compared the predictability of these theoretical frameworks to see which framework explains the highest variance in COVID-19 vaccine hesitancy.\n\nMethodsThis study adopted a cross-sectional research design. We collected data from a nationally representative sample of 1497 respondents through both online and face-to-face interviews. We employed multiple linear regression analysis to assess the predictability of each model of COVID-19 vaccine hesitancy.\n\nResultsWe found a 41.1% prevalence of COVID-19 vaccine hesitancy among our study respondents. After controlling the effects of socio-economic, demographic, and other COVID-19 related covariates, we found that the TPB has the highest predictive power (adjusted R2 =0.43), followed by the 5C psychological antecedents of vaccination (adjusted R2 =0.32) and the HBM (adjusted R2 =0.31) in terms of explaining total variance in the COVID-19 vaccine hesitancy among the adults of Bangladesh.\n\nConclusionsThis study provides evidence that theoretical frameworks like the HBM, the TPB, and the 5C psychological antecedents can be used to explore the psychological determinants of vaccine hesitancy, where the TBP has the highest predictability. Our findings can be used to design targeted interventions to reduce vaccine hesitancy and increase vaccine uptake.\n\nKey QuestionsO_ST_ABSWhat is already known?C_ST_ABS There is a global-level insurgence of COVID-19 vaccine hesitancy, where the majority of studies come from western, educated, industrialized, rich, and democratic (WEIRD) countries.\n To date, an online survey found that the prevalence of COVID-19 vaccine hesitancy in Bangladesh was 32.5%.\n Few studies from WEIRD countries have adopted the Health Believe Model and/or the Theory of Planned Behavior to explore the predictors of COVID-19 vaccine hesitancy.\n\n\nWhat are the new findings? This study found a 41.1% prevalence of COVID-19 vaccine hesitancy among a nationally representative sample of Bangladesh.\n After controlling the effects of demographic, socio-economic, and other COVID-19 related covariates, we found that the TPB has the highest predictive power, followed by the 5C psychological antecedents and the HBM in terms of explaining total variance in the COVID-19 vaccine hesitancy among the adults of Bangladesh.\n\n\nWhat do the new findings imply? Theoretical frameworks like the HBM, the TPB, and the 5C psychological antecedents can be used to explore the multitude of the psychological determinants of vaccine hesitancy, where the TPB has the highest predictability.\n Findings can be used to design targeted interventions to reduce COVID-19 vaccine hesitancy and increase vaccine demand and uptake.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Mohammad Bellal Hossain", + "author_inst": "Department of Population Sciences, University of Dhaka" + }, + { + "author_name": "Md Zakiul Alam", + "author_inst": "Department of Population Sciences, University of Dhaka" + }, + { + "author_name": "Md Syful Islam", + "author_inst": "Department of Population Science, Jatiya Kabi Kazi Nazrul Islam University" + }, + { + "author_name": "Shafayat Sultan", + "author_inst": "Department of Population Sciences, University of Dhaka" + }, + { + "author_name": "Md Mahir Faysal", + "author_inst": "Department of Population Sciences, University of Dhaka" + }, + { + "author_name": "Sharmin Rima", + "author_inst": "Ovibashi Karmi Unnayan Program (OKUP), Dhaka" + }, + { + "author_name": "Md Anwer Hossain", + "author_inst": "Department of Population Sciences, University of Dhaka" + }, + { + "author_name": "Abdullah Al Mamun", + "author_inst": "Department of Population Sciences, University of Dhaka" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.04.20.21255059", "rel_title": "Infants have lower RT-PCR cycle threshold for SARS-CoV-2 in comparison with older children and adults", @@ -793361,61 +794908,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.04.12.21255346", - "rel_title": "Fraction of COVID-19 hospitalizations and deaths attributable to chronic diseases", - "rel_date": "2021-04-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.12.21255346", - "rel_abs": "AimTo estimate the fraction of hospitalizations and deaths from COVID-19 attributable to chronic diseases due to poor nutrition and smoking in Mexico.\n\nMethodsWe used data from the Mexican surveillance system of COVID-19. We considered six chronic diseases (obesity, COPD, hypertension, diabetes, cardiovascular disease, and chronic kidney disease) to define a multimorbidity variable: no diseases, 1 disease, 2 diseases, or 3 or more diseases. We calibrated the database using bias quantification methods to consider the undiagnosed cases of chronic diseases. To estimate the risks of hospitalization and death due to chronic diseases, we fitted Poisson regression models with robust standard errors, adjusting for possible confounders. Using these risks, we calculated attributable fractions using the population attributable fraction (PAF).\n\nResultsChronic diseases accounted for to 25.4% (24.8%, 26.1%), 28.3% (27.8%, 28.7%) and 15.3% (14.9%,15.7%) of the hospitalizations among adults below 40 years, 40 to 59, and 60 years and older respectively (95% CI). For COVID-19-related deaths, 50.1% (48.6%, 51.5%), 40.5% (39.7%, 41.3%), and 18.7% (18.0%, 19.5%) were attributable to chronic diseases in adults under 40 years, 40 to 59, and 60 years and older, respectively.\n\nConclusionChronic diseases linked to malnutrition and tobacco use contributed to a higher burden of hospitalization and deaths from COVID-19 in Mexico, particularly among younger adults. Medical and structural interventions to curb chronic disease incidence and facilitate disease control are urgently needed.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Francisco Reyes-S\u00e1nchez", - "author_inst": "National Institute of Public Health. Center for Population Health Research" - }, - { - "author_name": "Ana Basto-Abreu", - "author_inst": "National Institute of Public Health. Center for Population Health Research" - }, - { - "author_name": "Rossana Torres-Alvarez", - "author_inst": "National Institute of Public Health. Center for Population Health Research" - }, - { - "author_name": "Francisco Canto-Osorio", - "author_inst": "National Institute of Public Health. Center for Population Health Research" - }, - { - "author_name": "Romina Gonz\u00e1lez-Morales", - "author_inst": "National Institute of Public Health. Population Health Research Center" - }, - { - "author_name": "Dwight Dyer", - "author_inst": "Ministry of Health, General Direction of Health Information" - }, - { - "author_name": "Ruy L\u00f3pez Ridaura", - "author_inst": "Ministry of Health, National Center for Preventive Programs and Disease Control" - }, - { - "author_name": "Christian Arturo Zaragoza Jim\u00e9nez", - "author_inst": "Ministry of Health, Director of Epidemiological Information" - }, - { - "author_name": "Juan A. Rivera", - "author_inst": "National Institute of Public Health. General Director" - }, - { - "author_name": "Tonatiuh Barrientos-Guti\u00e9rrez", - "author_inst": "National Institute of Public Health. Population Health Research Center" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.04.19.440086", "rel_title": "Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 specific mechanisms and vulnerabilities", @@ -794255,6 +795747,25 @@ "type": "new results", "category": "synthetic biology" }, + { + "rel_doi": "10.1101/2021.04.18.440358", + "rel_title": "Network controllability enrichment analysis reveals that SARS-CoV-2 infection tends to target indispensable nodes of a directed human protein-protein interaction network", + "rel_date": "2021-04-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.18.440358", + "rel_abs": "The COVID-19 disease has been a global threat caused by the new coronavirus species, SARS-CoV-2, since early 2020 with an urgent need for therapeutic interventions. In order to provide insight into human proteins targeted by SARS-CoV-2, here we study a directed human protein-protein interaction network (dhPPIN) based on our previous work on network controllability of virus targets. We previously showed that human proteins targeted by viruses tend to be those whose removal in a dhPPIN requires more control of the network dynamics, which were classified as indispensable nodes. In this study we introduce a more comprehensive rank-based enrichment analysis of our previous dhPPIN for SARS-CoV-2 infection and show that SARS-CoV-2 also tends to target indispensable nodes in the dhPPIN using multiple proteomics datasets, supporting validity and generality of controllability analysis of viral infection in humans. Also, we find differential controllability among SARS-CoV-2, SARS-CoV-1, and MERS-CoV from a comparative proteomics study. Moreover, we show functional significance of indispensable nodes by analyzing heterogeneous datasets from a genome-wide CRISPR screening study, a time-course phosphoproteomics study, and a genome-wide association study. Specifically, we identify SARS-CoV-2 ORF3A as most frequently interacting with indispensable proteins in the dhPPIN, which are enriched in TGF-beta signaling and tend to be sources nodes and interact with each other. Finally, we built an integrated network model of ORF3A-interacting indispensable proteins with multiple functional supports to provide hypotheses for experimental validation as well as therapeutic opportunities. Therefore, a sub-network of indispensable proteins targeted by SARS-CoV-2 could serve as a prioritized network of drug targets and a basis for further functional and mechanistic studies from a network controllability perspective.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Ho-Joon Lee", + "author_inst": "Yale University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "systems biology" + }, { "rel_doi": "10.1101/2021.04.14.21255104", "rel_title": "Mortality reduction in ICU-admitted COVID-19 patients in Suriname after treatment with convalescent plasma acquired via gravity filtration", @@ -795311,45 +796822,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.16.21255130", - "rel_title": "Expanding access to SARS-CoV-2 IgG and IgM serologic testing using fingerstick whole blood, plasma, and rapid lateral flow assays", - "rel_date": "2021-04-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.16.21255130", - "rel_abs": "Serologic testing for SARS-CoV-2 antibodies can be used to confirm diagnosis, estimate seroprevalence, screen convalescent plasma donors, and assess vaccine efficacy. Several logistical and infrastructure challenges limit access to SARS-CoV-2 serologic testing. Dried blood spot (DBS) samples have been used for serology testing of various diseases in resource-limited settings. We examined the use of DBS samples and capillary blood (fingerstick) plasma collected in Microtainer tubes for SARS-CoV-2 testing with the automated Abbott ARCHITECT SARS-CoV-2 IgG (List 6R86) and IgM assays and use of venous whole blood with a prototype PANBIO rapid point-of-care lateral flow SARS-CoV-2 IgG assay. The ARCHITECT SARS-CoV-2 IgG assay was initially optimized for use with DBS, venous and capillary plasma, and venous whole blood collected from patients with symptoms and PCR-confirmed COVID-19 and negative asymptomatic controls. Assay linearity and reproducibility was confirmed with 3 contrived DBS samples, with sample stability and signal recovery after 14 days at room temperature. ARCHITECT SARS-CoV-2 IgG and IgM assay results showed high concordance between fingerstick DBS and venous DBS samples, and between fingerstick DBS and venous whole blood samples (n=61). Discordant results were seen in 3 participants (2 IgG, 1 IgM) who were in the process of seroreversion at the time of sample collection and had results near the assay cutoff. Use of fingerstick plasma collected in Microtainer tubes (n=109) showed 100% concordant results (R2=0.997) with matched patient venous plasma on the ARCHITECT SARS-CoV-2 IgG assay. High concordance of assay results (92.9% positive, 100% negative) was also observed for the PANBIO SARS-CoV-2 IgG assay compared to the ARCHITECT SARS-CoV-2 IgG assay run with matched venous plasma (n=61). Fingerstick DBS and plasma samples are easy and inexpensive to collect and, along with the use of rapid point-of-care testing platforms, will expand access to SARS-CoV-2 serology testing, particularly in resource-limited areas.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Mark C Anderson", - "author_inst": "Abbott Laboratories" - }, - { - "author_name": "Vera Holzmayer", - "author_inst": "Abbott Laboratories" - }, - { - "author_name": "Ana Vallari", - "author_inst": "Abbott Laboratories" - }, - { - "author_name": "Russell Taylor", - "author_inst": "Abbott Laboratories" - }, - { - "author_name": "James Moy", - "author_inst": "Rush University Medical Center" - }, - { - "author_name": "Gavin Cloherty", - "author_inst": "Abbott Laboratories" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.16.21255638", "rel_title": "Enumerating asymptomatic COVID-19 cases and estimating SARS-CoV-2 fecal shedding rates via wastewater-based epidemiology", @@ -796073,6 +797545,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.09.21255206", + "rel_title": "High prevalence of SARS-CoV-2 B.1.1.7 (UK variant) and the novel B.1.525 lineage in Oyo State, Nigeria", + "rel_date": "2021-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.09.21255206", + "rel_abs": "The emergence of new SARS-CoV-2 variants with enhanced transmissibility or decreased susceptibility to immune responses is a major threat to global efforts to end the coronavirus disease 2019 (COVID-19) pandemic. Disparities in viral genomic surveillance capabilities and efforts have resulted in gaps in our understanding of the viral population dynamics across the globe. Nigeria, despite having the largest population of any nation in Africa, has had relatively little SARS-CoV-2 sequence data made publicly available. Here we report the whole-genome sequences of 74 SARS-CoV-2 isolates collected from individuals in Oyo State, Nigeria in January 2021. Most isolates belonged to either the B.1.1.7 Alpha \"variant of concern\" or the B.1.525 Eta lineage, which is currently considered a \"variant of interest\" containing multiple spike protein mutations previously associated with enhanced transmissibility and possible immune escape. Nigeria has the highest reported frequency of the B.1.525 lineage globally with phylogenetic characteristics consistent with a recent monophyletic origin and rapid expansion. Spike protein from the B.1.525 lineage displayed both increased infectivity and decreased neutralization by convalescent sera compared to Spike proteins from other clades. These results, along with indications that the virus is outpacing the B.1.1.7 lineage in Nigeria, suggest that the B.1.525 lineage represents another \"variant of concern\" and further underline the importance of genomic surveillance in undersampled regions across the globe.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Egon A Ozer", + "author_inst": "Northwestern University" + }, + { + "author_name": "Lacy M Simons", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Olubusuyi M Adewumi", + "author_inst": "University of Ibadan" + }, + { + "author_name": "Adeola A Fowotade", + "author_inst": "University of Ibadan" + }, + { + "author_name": "Ewean C Omoruyi", + "author_inst": "University of Ibadan" + }, + { + "author_name": "Johnson A Adeniji", + "author_inst": "University of Ibadan" + }, + { + "author_name": "Taylor J Dean", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Janet Zayas", + "author_inst": "Department of Microbial Pathogens and Immunity, Rush University Medical Center" + }, + { + "author_name": "Pavan P Bhimalli", + "author_inst": "Department of Microbial Pathogens and Immunity, Rush University Medical Center" + }, + { + "author_name": "Michelle K Ash", + "author_inst": "Department of Microbial Pathogens and Immunity, Rush University Medical Center" + }, + { + "author_name": "Adam Godzik", + "author_inst": "University of California Riverside School of Medicine, Biosciences Division" + }, + { + "author_name": "Jeffrey R Schneider", + "author_inst": "Department of Microbial Pathogens and Immunity, Rush University Medical Center" + }, + { + "author_name": "Joao I Mamede", + "author_inst": "Department of Microbial Pathogens and Immunity, Rush University Medical Center" + }, + { + "author_name": "Babafemi O Taiwo", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Judd F. Hultquist", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Ramon Lorenzo-Redondo", + "author_inst": "Northwestern University Feinberg School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.10.21255250", "rel_title": "Standardized and optimized preservation, extraction and quantification techniques for detection of fecal SARS-CoV-2 RNA", @@ -796957,45 +798508,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2021.04.14.21255434", - "rel_title": "Comorbidity Risk Factors Contributing to COVID-19 Related Deaths in Florida, March 1, 2020-January 16, 2021", - "rel_date": "2021-04-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.14.21255434", - "rel_abs": "ObjectivesTo assess the association of specific comorbid conditions to COVID-19 deaths in Florida among decedents 16 to 64 years of age.\n\nMethodsThis report uses Florida vital statistics death data over the period of March 1, 2020 through January 16, 2021, to estimate the effects of comorbid conditions on COVID-19 mortality for decedents 16 to 64 years of age. All cases of COVID-19 death occurring in Florida, regardless of resident status, were evaluated. The comorbidities, or contributing causes of death, identified in this report include Down syndrome, asthma, diabetes, pulmonary fibrosis, obesity, dementia, immunodeficiency, kidney disease, chronic obstructive pulmonary disease, hypertension, heart disease, and chronic liver disease and cirrhosis. The study uses a binary logistic regression to examine the relationship between COVID-19 and non-COVID-19 death and contributing causes of death based on information in the death record. Odds ratios were calculated as a residual of the logistic regression.\n\nResultsAmong COVID-19 deaths, Down syndrome was 15.26 times more likely to be a contributing cause of death compared to non-COVID-19 deaths followed by asthma (OR 7.74), diabetes (OR 6.11), pulmonary fibrosis (OR 5.13), obesity (OR 4.66), dementia (OR 4.51), immunodeficiency (OR 2.49), and kidney disease (OR 2.13). Chronic liver disease and cirrhosis (OR 0.95) and cancer (OR 0.79) had lower odds of being a contributing cause of death.\n\nConclusionsHeart disease, chronic liver disease and cirrhosis, and cancer were not risk factors for death from COVID-19 among decedents. Additional studies are needed to elucidate associations between race/ethnicity, socioeconomic status, and behavioral factors.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Ursula K Weiss", - "author_inst": "Florida Department of Health" - }, - { - "author_name": "Jason D Maynard", - "author_inst": "Florida Department of Health" - }, - { - "author_name": "Katherine McDaniel", - "author_inst": "Florida Department of Health" - }, - { - "author_name": "Alyssa Cohen", - "author_inst": "Florida Department of Health" - }, - { - "author_name": "Marie Bailey", - "author_inst": "Florida Department of Health" - }, - { - "author_name": "Scott A Rivkees", - "author_inst": "Florida Department of Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.14.21255499", "rel_title": "Seroprevalence of anti-SARS-CoV-2 antibodies among school and daycare children and personnel: Protocol for a cohort study in Montreal, Canada", @@ -797867,6 +799379,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.16.21255412", + "rel_title": "Humoral and cellular immune responses against SARS-CoV-2 variants and human coronaviruses after single BNT162b2 vaccination.", + "rel_date": "2021-04-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.16.21255412", + "rel_abs": "Vaccine-induced neutralizing antibodies are key in combating the COVID-19 pandemic. However, delays of boost immunization due to limited availability of vaccines may leave individuals vulnerable to infection and disease for prolonged periods. The emergence of SARS-CoV-2 variants of concern (VOC), B.1.1.7 (United Kingdom), B.1.351 (South Africa) and P.1 (Brazil), may reinforce this issue with the latter two being able to evade control by antibodies. We assessed humoral and T cell responses against SARS-CoV-2 WT and VOC and endemic human coronaviruses (hCoV) that were induced after single and double vaccination with BNT162b2. Despite readily detectable IgG against the receptor-binding domain (RBD) of the SARS-CoV-2 S protein at day 14 after a single vaccination, inhibition of SARS-CoV-2 S-driven host cell entry was weak and particularly low for the B.1.351 variant. Frequencies of SARS-CoV-2 specific T cells were low in many vaccinees after application of a single dose and influenced by immunity against endemic hCoV. The second vaccination significantly boosted T cell frequencies reactive for WT, B.1.1.7 and B.1.351 variants. These results call into question whether neutralizing antibodies significantly contribute to protection against COVID-19 upon single vaccination and suggest that cellular immunity is central for the early defenses against COVID-19.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Metodi Stankov", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Anne Cossmann", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Agnes Bonifacius", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Alexandra Jablonka", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Gema Morillas Ramos", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Nina Goedecke", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Anna Zychlinsky Scharff", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Christine Happle", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Anna-Lena Boeck", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Anh Thu Tran", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Isabell Pink", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Marius M Hoeper", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Rainer Blasczyk", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Martin Winkler", + "author_inst": "University of Goettingen Medical Center" + }, + { + "author_name": "Inga Nehlmeier", + "author_inst": "German Primate Center, Goettingen" + }, + { + "author_name": "Amy Kempf", + "author_inst": "German Primate Center, Goettingen" + }, + { + "author_name": "Heike Hofmann-Winkler", + "author_inst": "German Primate Center, Goettingen" + }, + { + "author_name": "Markus Hoffmann", + "author_inst": "German Primate Center, Goettingen" + }, + { + "author_name": "Britta Eiz-Vesper", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Stefan Poehlmann", + "author_inst": "German Primate Center, Goettingen" + }, + { + "author_name": "Georg Behrens", + "author_inst": "Hannover Medical School" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.16.440215", "rel_title": "SARS-CoV-2 spike protein expressing epithelial cells promotes senescence associated secretory phenotype in endothelial cells and increased inflammatory response", @@ -798703,37 +800314,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.04.12.21255325", - "rel_title": "Quarantine, relaxation and mutation explaining the CoViD-19 epidemic in Sao Paulo State (Brazil)", - "rel_date": "2021-04-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.12.21255325", - "rel_abs": "BackgroundThe continuous SARS-CoV-2 transmission in several countries could contribute to the mutations appearance. The circulation of more virulent variants may increase the number of severe CoViD-19 needing hospital care and fatalities hugely.\n\nMethodsThe partial quarantine in Sao Paulo State and further relaxation associated with the mutations are explained by a mathematical model based on the CoViD-19 natural history encompassing the age-dependent fatality. The model parameters were fitted considering the observed data from Sao Paulo State.\n\nResultsThe partial quarantine was explained by the less virulent SARS-CoV-2 transmission, but the relaxation alone could not explain the epidemic observed in Sao Paulo State. However, more virulent variants plus the transmission among isolated individuals explained the increased CoViD-19 fatalities.\n\nConclusionsThe model described the CoViD-19 epidemic in Sao Paulo State by considering the partial quarantine, relaxation and mutations. The model provided a potential epidemiological scenario in the absence of mass vaccination.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Hyun Mo Yang", - "author_inst": "Unicamp" - }, - { - "author_name": "Luis Pedro Pedro Lombardi Junior", - "author_inst": "State University of Campinas" - }, - { - "author_name": "Fabio Fernandes Morato Castro", - "author_inst": "General Hospital of the Medicine School of University of S\u00e3o Paulo" - }, - { - "author_name": "Ariana Campos Yang", - "author_inst": "General Hospital of the Medicine School of University of S\u00e3o Paulo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.04.12.21255297", "rel_title": "Breakpoint modelling of temporal associations between non-pharmaceutical interventions and the incidence of symptomatic COVID-19 in the Republic of Ireland", @@ -799513,6 +801093,57 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.04.14.439928", + "rel_title": "Evaluation of the SARS-CoV-2 inactivation efficacy associated with buffers from three kits used on high-throughput RNA extraction platforms", + "rel_date": "2021-04-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.14.439928", + "rel_abs": "Rapid and demonstrable inactivation of SARS-CoV-2 is crucial to ensure operator safety during high-throughput testing of clinical samples. The inactivation efficacy of SARS-CoV-2 was evaluated using commercially available lysis buffers from three viral RNA extraction kits used on two high-throughput (96-well) RNA extraction platforms (Qiagen QiaCube HT and the ThermoFisher Kingfisher Flex) in combination with thermal treatment. Buffer volumes and sample ratios were chosen for their optimised suitability for RNA extraction rather than inactivation efficacy and tested against a representative sample type; SARS-CoV-2 spiked into viral transport medium (VTM). A lysis buffer from the MagMax Pathogen RNA/DNA kit (ThermoFisher), used on the Kingfisher Flex, which included guanidinium isothiocycnate (GITC), a detergent, and isopropanol demonstrated a minimum inactivation efficacy of 1 x 105 TCID50/ml. An alternative lysis buffer from the MagMax Viral/Pathogen Nucleic Acid kit (Thermofisher) also used on the Kingfisher Flex and the lysis buffer from QIAamp 96 Virus QIAcube HT Kit (Qiagen) used on the QiaCube HT (both of which contained GITC and a detergent) reduced titres by 1 x 104 TCID50/ml but did not completely inactivate the virus. Heat treatment alone (15 minutes, 68 {degrees}C) did not completely inactivate the virus, demonstrating a reduction of 1 x 103 TCID50/ml. When inactivation methods included both heat treatment and addition of lysis buffer, all methods were shown to completely inactivate SARS-CoV-2 inactivation against the viral titres tested. Results are discussed in the context of the operation of a high-throughput diagnostic laboratory.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Ruth E Thom", + "author_inst": "Defence Science and Technology Laboratory, Porton Down, Salisbury, SP4 IJQ, UK" + }, + { + "author_name": "Lin Eastaugh", + "author_inst": "Dstl" + }, + { + "author_name": "David Ulaeto", + "author_inst": "Dstl" + }, + { + "author_name": "James S Findlay", + "author_inst": "Defence Science and Technology Laboratory, Porton Down" + }, + { + "author_name": "Sophie Smither", + "author_inst": "Dstl" + }, + { + "author_name": "Amanda Phelps", + "author_inst": "Dstl" + }, + { + "author_name": "Helen Stapleton PhD", + "author_inst": "Datl" + }, + { + "author_name": "Karleigh A Hamblin", + "author_inst": "Defence Science and Technology Laboratory" + }, + { + "author_name": "Simon A Weller", + "author_inst": "Defence Science and Technology Laboratory, Porton Down" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.04.15.440035", "rel_title": "Scalable, methanol-free manufacturing of the SARS-CoV-2 receptor binding domain in engineered Komagataella phaffii", @@ -800597,65 +802228,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.04.14.439891", - "rel_title": "An mRNA SARS-CoV-2 vaccine employing a novel delivery vehicle with a TLR-9 agonist induces neutralizing antibodies and T cell memory", - "rel_date": "2021-04-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.14.439891", - "rel_abs": "The SARS-CoV-2 pandemic has necessitated the rapid development of prophylactic vaccines. Two mRNA vaccines have been approved for emergency use by the FDA and have demonstrated extraordinary effectiveness. The success of these mRNA vaccines establishes the speed of development and therapeutic potential of mRNA. These authorized vaccines encode full-length versions of the SARS-CoV-2 spike protein. They are formulated with Lipid Nanoparticle (LNP) delivery vehicles that have inherent immunostimulatory properties. Different vaccination strategies and alternative mRNA delivery vehicles would be desirable to ensure flexibility of future generations of SARS-CoV-2 vaccines and the development of mRNA vaccines in general.\n\nHere, we report on the development of an alternative mRNA vaccine approach using a delivery vehicle called Charge-Altering Releasable Transporters (CARTs). Using these inherently nonimmunogenic vehicles we can tailor the vaccine immunogenicity by inclusion of co-formulated adjuvants such as oligodeoxynucleotides with CpG motifs (CpG-ODN). Mice vaccinated with the mRNA-CART vaccine developed therapeutically relevant levels of RBD-specific neutralizing antibodies in both the circulation and in the lung bronchial fluids. In addition, vaccination elicited strong and long lasting RBD-specific TH1 T cell responses including CD4+ and CD8+ T cell memory.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Ole Haabeth", - "author_inst": "Stanford University" - }, - { - "author_name": "Julian Lohmeyer", - "author_inst": "Stanford University" - }, - { - "author_name": "Adrienne Sallets", - "author_inst": "Stanford University" - }, - { - "author_name": "Timothy Blake", - "author_inst": "Stanford University" - }, - { - "author_name": "Idit Sagiv-Barfi", - "author_inst": "Stanford University" - }, - { - "author_name": "Debra Czerwinski", - "author_inst": "Stanford University" - }, - { - "author_name": "Blaine McCarthy", - "author_inst": "Stanford University" - }, - { - "author_name": "Abigail E. Powell", - "author_inst": "Stanford University" - }, - { - "author_name": "Paul A Wender", - "author_inst": "Stanford University" - }, - { - "author_name": "Robert M. Waymouth", - "author_inst": "Stanford University" - }, - { - "author_name": "Ronald Levy", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.04.11.21254776", "rel_title": "You're just there, alone in your room with your thoughts: A qualitative study about the impact of lockdown among young people during the COVID-19 pandemic", @@ -801419,6 +802991,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.14.439840", + "rel_title": "Pattern Detection in Multiple Genome Sequences with Applications: The Case of All SARS-CoV-2 Complete Variants", + "rel_date": "2021-04-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.14.439840", + "rel_abs": "Pattern detection and string matching are fundamental problems in computer science and the accelerated expansion of bioinformatics and computational biology have made them a core topic for both disciplines. The SARS-CoV-2 pandemic has made such problems more demanding with hundreds or thousands of new genome variants discovered every week, because of constant mutations, and the need for fast and accurate analyses. Medicines and, mostly, vaccines must be altered to adapt and efficiently address mutations. The need of computational tools for genomic analysis, such as sequence alignment, is very important, although, in most cases the resources and computational power needed is vast. The presented data structures and algorithms, specifically built for text mining and pattern detection, can help to address efficiently several bioinformatics problems. With a single execution of advanced algorithms, with limited space and time complexity, it is possible to acquire knowledge on all repeated patterns that exist in multiple genome sequences and this information can be used for further meta analyses. The potentials of the presented solutions are demonstrated with the analysis of more than 55,000 SARS-CoV-2 genome sequences (collected on March 10, 2021) and the detection of all repeated patterns with length up to 60 nucleotides in these sequences, something practically impossible with other algorithms due to its complexity. These results can be used to help provide answers to questions such as all variants common patterns, sequence alignment, palindromes and tandem repeats detection, genome comparisons, etc.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Konstantinos Xylogiannopoulos", + "author_inst": "University of Calgary" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.04.14.439844", "rel_title": "The SARS-CoV-2 mRNA-1273 vaccine elicits more RBD-focused neutralization, but with broader antibody binding within the RBD", @@ -802227,57 +803818,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.04.09.21255199", - "rel_title": "Post-acute COVID-19 sequelae in cases managed in the community or hospital in the UK: a population based study", - "rel_date": "2021-04-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.09.21255199", - "rel_abs": "ObjectiveTo compare post-COVID-19 sequelae between hospitalised and non-hospitalised individuals\n\nDesignPopulation-based cohort study\n\nSetting1,383 general practices in England contributing to Clinical Practice Research Database Aurum\n\nParticipants46,687 COVID-19 cases diagnosed between 1st August to 17th October 2020 (45.4% male; mean age 40), either hospitalised within two weeks of diagnosis or non-hospitalised, and followed-up for a maximum of three months.\n\nMain outcome measuresEvent rates of new symptoms, diseases, prescriptions and healthcare utilisation in hospitalised and non-hospitalised individuals, with between-group comparison using Cox regression. Outcomes compared at 6 and 12 months prior to index date, equating to first UK wave and pre-pandemic. Non-hospitalised group outcomes stratified by age and sex.\n\nResults45,272 of 46,687 people were non-hospitalised; 1,415 hospitalised. Hospitalised patients had higher rates of 13/26 symptoms and 11/19 diseases post-COVID-19 than the community group, received more prescriptions and utilised more healthcare. The largest differences were noted for rates per 100,000 person-weeks [95%CI] of breathlessness: 536 [432 to 663] v. 85 [77 to 93]; joint pain: 295 [221 to 392] v. 168 [158 to 179]; diabetes: 303 [225 to 416] v. 36 [32 to 42], hypertension: 244 [178 to 344] v. 47 [41 to 53]. Although low, rates of chest tightness, tinnitus and lung fibrosis were higher in the community group. 4.2% (1882/45,272) of the community group had a post-acute burden, most frequently reporting anxiety, breathlessness, chest pain and fatigue. In those non-hospitalised, age and sex differences existed in outcome rates. Healthcare utilisation in the community group increased 28.5% post-COVID-19 relative to pre-pandemic.\n\nConclusionsPost-COVID-19 sequelae differ between hospitalised and non-hospitalised individuals, with age and sex-specific differences in those non-hospitalised. Most COVID-19 cases managed in the community do not report ongoing issues to healthcare professionals. Post-COVID-19 follow-up and management strategies need to be tailored to specific groups.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Hannah R Whittaker", - "author_inst": "Imperial College London" - }, - { - "author_name": "Claudia Gulea", - "author_inst": "Imperial College London" - }, - { - "author_name": "Ardita Koteci", - "author_inst": "Imperial College London" - }, - { - "author_name": "Constantinos Kallis", - "author_inst": "Imperial College London" - }, - { - "author_name": "Ann D Morgan", - "author_inst": "Imperial College London" - }, - { - "author_name": "Chukwuma Iwundu", - "author_inst": "Imperial College London" - }, - { - "author_name": "Mark Weeks", - "author_inst": "Imperial College London" - }, - { - "author_name": "Rikisha Gupta", - "author_inst": "Imperial College London" - }, - { - "author_name": "Jennifer K Quint", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.04.12.21255369", "rel_title": "The risk factors of COVID-19 in a longitudinal population-based study", @@ -803145,6 +804685,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2021.04.13.439681", + "rel_title": "Epitope classification and RBD binding properties of neutralizing antibodies against SARS-CoV-2 variants of concern", + "rel_date": "2021-04-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.13.439681", + "rel_abs": "Severe acute respiratory syndrome coronavirus-2 (SAR-CoV-2) causes coronavirus disease 2019 (COVID19) that is responsible for short and long-term disease, as well as death, in susceptible hosts. The receptor binding domain (RBD) of the SARS-CoV-2 Spike (S) protein binds to cell surface angiotensin converting enzyme type-II (ACE2) to initiate viral attachment and ultimately viral pathogenesis. The SARS-CoV-2 S RBD is a major target of neutralizing antibodies (NAbs) that block RBD - ACE2 interactions. In this report, NAb-RBD binding epitopes in the protein databank were classified as C1, C1D, C2, C3, or C4, using a RBD binding profile (BP), based on NAb-specific RBD buried surface area and used to predict the binding epitopes of a series of uncharacterized NAbs. Naturally occurring SARS-CoV-2 RBD sequence variation was also quantified to predict NAb binding sensitivities to the RBD-variants. NAb and ACE2 binding studies confirmed the NAb classifications and determined whether the RBD variants enhanced ACE2 binding to promote viral infectivity, and/or disrupted NAb binding to evade the host immune response. Of 9 single RBD mutants evaluated, K417T, E484K, and N501Y disrupted binding of 65% of the NAbs evaluated, consistent with the assignment of the SARS-CoV-2 P.1 Japan/Brazil strain as a variant of concern (VoC). RBD variants E484K and N501Y exhibited ACE2 binding equivalent to a Wuhan-1 reference SARS-CoV-2 RBD. While slightly less disruptive to NAb binding, L452R enhanced ACE2 binding affinity. Thus, the L452R mutant, associated with the SARS-CoV-2 California VoC (B.1.427/B.1.429-California), has evolved to enhance ACE2 binding, while simultaneously disrupting C1 and C2 NAb classes. The analysis also identified a non-overlapping antibody pair (1213H7 and 1215D1) that bound to all SARS-CoV-2 RBD variants evaluated, representing an excellent therapeutic option for treatment of SARS-CoV-2 WT and VoC strains.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Ashlesha Deshpande", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Bethany D. Harris", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Luis Martinez-Sobrido", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "James J. Kobie", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Mark R Walter", + "author_inst": "University of Alabama at Birmingham" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.04.13.439482", "rel_title": "Variant SARS-CoV-2 mRNA vaccines confer broad neutralization as primary or booster series in mice", @@ -804221,57 +805796,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.02.21254642", - "rel_title": "Detection of SARS-CoV-2 specific IgA in the human milk of COVID-19 vaccinated, lactating health care workers", - "rel_date": "2021-04-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.02.21254642", - "rel_abs": "ImportanceIn 2019, a deadly virus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for COVID-19, emerged. In December 2020, two mRNA-based COVID-19 vaccines were approved for use in the United States (US) which provide immunity to those receiving the vaccine. Maternally derived antibodies are a key element of infants immunity. Certain vaccines given to pregnant and lactating mothers provide immunity to infants through transmission across the placenta, umbilical cord (IgG) and human milk (IgA). Human milk produced by mothers with a history of COVID-19 infection contains SARS-CoV-2 IgA and IgG.\n\nObjectiveTo determine whether SARS-CoV-2 specific immunoglobulins are found in human milk after the COVID-19 vaccination, and to characterize the types of immunoglobulins present.\n\nDesign, setting, and participantsThis is a prospective observational study conducted at Shands Hospital, University of Florida from December 2020 to March 2021. Twenty-two lactating healthcare workers who received the SARS-CoV-2 mRNA vaccine (Pfizer/BioNtech or Moderna) made up the sample group. Plasma and human milk were collected at three-time points (pre-vaccination, post-first vaccine dose, and post-second vaccine dose). SARS-CoV-2 specific IgA and IgG in human milk and in plasma were measured by ELISA. Maternal demographics was compiled.\n\nExposuresPfizer/BioNtech or Moderna vaccination.\n\nMain outcome and measureLevels of SARS-CoV-2 IgA and IgG in human milk and plasma.\n\nResultsWe found significant secretion of SARS-CoV-2 specific IgA and IgG in human milk and plasma after SARS-CoV-2 vaccination.\n\nConclusions and relevanceOur results show that the mRNA-based COVID-19 vaccines induce SARS-CoV-2 specific IgA and IgG secretion in human milk. Further studies are needed to determine the duration of this immune response, its capacity to neutralize the COVID-19 virus, the transfer of passive immunity to breastfeeding infants, and the potential therapeutic use of human milk IgA to combat SARS-CoV-2 infections and COVID-19.\n\nKEY POINTSO_ST_ABSQuestionC_ST_ABSIs there SARS-CoV-2 specific IgA in the human milk of lactating women after COVID-19 vaccination?\n\nFindingsIn this prospective observational study that included 22 lactating women, we found SARS-CoV-2 specific IgA in the human milk in response to the COVID-19 vaccination series. There is statistically significant secretion of SARS-CoV-2 IgA in human milk after mRNA COVID-19 vaccination series completion (p < 0.0001).\n\nMeaningNewborn immunologic defense is present but immature. SARS-CoV-2 IgA secreted in the human milk could potentially provide COVID-19 protection to nursing infants. These results could guide a strategy for SARS-CoV-2 vaccination among lactating women.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Vivian Valcarce", - "author_inst": "University of Florida" - }, - { - "author_name": "Lauren S Stafford", - "author_inst": "University of Florida" - }, - { - "author_name": "Josef Neu", - "author_inst": "University of Florida" - }, - { - "author_name": "Nicole Cacho", - "author_inst": "University of Florida" - }, - { - "author_name": "Leslie Parkier", - "author_inst": "University of Florida" - }, - { - "author_name": "Martina Mueller", - "author_inst": "Medical University of South Carolina" - }, - { - "author_name": "David Burchfield", - "author_inst": "University of Florida" - }, - { - "author_name": "Nan Li", - "author_inst": "university of Florida" - }, - { - "author_name": "Joseph Larkin III", - "author_inst": "University of Florida" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.10.21254672", "rel_title": "Inhaled budesonide for COVID-19 in people at higher risk of adverse outcomes in the community: interim analyses from the PRINCIPLE trial", @@ -804887,6 +806411,45 @@ "type": "confirmatory results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.04.11.438530", + "rel_title": "Undergraduate student interest in healthcare career in the context of COVID-19 pandemic", + "rel_date": "2021-04-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.11.438530", + "rel_abs": "ObjectivesThe healthcare profession has been long considered an excellent career choice. Pre-medical experience is documented to be important in shaping future medical landscape. In the wake of the pandemic, there has been intense media spotlight on the healthcare profession and change in academic environment, necessitating analyses of student experience. This project aims to assess change in undergraduate student interest in healthcare career using cross-sectional survey study.\n\nMethodsThe project was approved by our Institutional Review Board. Voluntary survey collected data on demographics, socioeconomics, media exposure, academic environment, and change in interest in a healthcare profession. Survey was distributed through the university undergraduate pre-health listserv. Total of 297 responses were obtained. Descriptive statistics including Fishers exact test were applied in the analysis.\n\nResultsMajority of the respondents were Asians (54.9%), second generation immigrants (52.2%), and female (73.4%). Large proportion of the respondents were negatively affected by the pandemic, with losing a job or internship personally (42.1%) or a family member or a friend (62.6%). Students had mixed response to online learning environment, with 27.3% of students noting no change, 40.4% students noting increased difficulty, and 32.3% students noting decreased difficulty of classes. During the pandemic, 47.5% of students noted increased interest in pursuing healthcare career. The change in interest in healthcare career was not associated with xdemographics, economic hardship, or online learning environment.\n\nDiscussionDespite the challenges of COVID-19 pandemic, students showed strong interest in pursuing healthcare careers.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Stephanie Y Jo", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Jingxin Li", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Ananya Dewan", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Yu-Chia Cheng", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Haoxiang Hou", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Ronnie A Sebro", + "author_inst": "University of Pennsylvania" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "scientific communication and education" + }, { "rel_doi": "10.1101/2021.04.08.21254922", "rel_title": "Development of a tool to prioritize the monitoring of COVID-19 patients by public health teams", @@ -806035,41 +807598,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2021.04.08.21254861", - "rel_title": "Reflections of COVID-19 cases on the wastewater loading of SARS-CoV-2 RNA: A case of three major cities of Gujarat, India", - "rel_date": "2021-04-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.08.21254861", - "rel_abs": "The scientific community has widely supported wastewater monitoring of SARS-CoV-2 due to the early and prolonged excretion of coronavirus in the faecal matter. In the present study, eighteen influent wastewater samples from different wastewater treatment plants and pumping stations (5 samples from Vadodara city, 4 from Gandhinagar, and nine from Ahmedabad city) were collected and analyzed for the occurrence of SARS-CoV-2 RNA in Gujarat province, India. The results showed the highest SARS-CoV-2 genome concentration in Vadodara (3078 copies/ L), followed by Ahmedabad (2968 copies/ L) and Gandhinagar (354 copies/ L). The comparison of genome concentration more or less corresponded to the number of confirmed and active cases in all three cities. The study confirms the potential of the Surveillance of Wastewater for Early Epidemic Prediction (SWEEP) that can be used at a large scale around the globe for better dealing with the pandemic situation.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=132 SRC=\"FIGDIR/small/21254861v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (39K):\norg.highwire.dtl.DTLVardef@142ae8aorg.highwire.dtl.DTLVardef@d10157org.highwire.dtl.DTLVardef@1af0dbdorg.highwire.dtl.DTLVardef@1af1b23_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Vaibhav Srivastava", - "author_inst": "Indian Institute of Technology Gandhinagar" - }, - { - "author_name": "Shilangi Gupta", - "author_inst": "Indian Institute of Technology Gandhinagar" - }, - { - "author_name": "Arbind Patel", - "author_inst": "Indian Institute of Technology Gandhinagar" - }, - { - "author_name": "Madhvi Joshi", - "author_inst": "GBRC" - }, - { - "author_name": "Manish Kumar", - "author_inst": "Indian Institute of Technology Gandhinagar" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.04.08.439059", "rel_title": "Exploring zebrafish larvae as a COVID-19 model: probable SARS-COV-2 replication in the swim bladder", @@ -806929,6 +808457,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.08.21255055", + "rel_title": "Direct and indirect effectiveness of mRNA vaccination against SARS-CoV-2 infection in long-term care facilities in Spain", + "rel_date": "2021-04-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.08.21255055", + "rel_abs": "ObjectivesTo estimate indirect and total (direct plus indirect) effects of COVID-19 vaccination in residents in long-term care facilities (LTCF).\n\nDesignRegistries-based cohort study including all residents in LTCF [≥]65 years offered vaccination between 27 December 2020 and 10 March 2021. Risk of SARS-CoV-2 infection following vaccination was compared with the risk in the same individuals in a period before vaccination. Risk in non-vaccinated was also compared to a period before the vaccination programme to estimate indirect protection. Standardized cumulative risk was computed adjusted by previous documented infection (before the start of follow-up) and daily-varying SARS-CoV-2 incidence and reproductive number.\n\nParticipants573,533 records of 299,209 individuals in the National vaccination registry were selected; 99.0% had [≥]1 vaccine-dose, 99.8% was Pfizer/BioNTech (BNT162b2). Residents mean age was 85.9, 70.9% were females. A previous SARS-CoV-2 infection was found in around 25% and 13% of participants, respectively, at the time of vaccine offer and in the reference period.\n\nMain outcome measuresDocumented SARS-CoV-2 infection identified in the National COVID-19 laboratory registry.\n\nResultsTotal VE was 57.2% (95% Confidence Interval: 56.1%-58.3%), and was highest [≥]28 days after the first vaccine-dose (proxy of [≥]7 days after the second dose) and for individuals naive to SARS-CoV-2 [81.8% (81.0%-82.7%)] compared to those with previous infection [56.8% (47.1%-67.7%)]. Vaccination prevented up to 9.6 (9.3-9.9) cases per 10.000 vaccinated per day; 11.6 (11.3-11.9) if naive vs. 0.8 (0.5-1.0) if previous infection. Indirect protection in the non-vaccinated could only be estimated for naive individuals, at 81.4% (73.3%-90.3%) and up to 12.8 (9.4-16.2) infections prevented per 10.000 indirectly protected per day.\n\nConclusionsOur results confirm the effectiveness of mRNA vaccination in institutionalized elderly population, endorse the policy of universal vaccination in this setting, including in people with previous infection, and suggest that even non-vaccinated individuals benefit from indirect protection.\n\nKey messagesO_LICOIVD-19 vaccination reduced the risk of documented SARS-CoV-2 infection in institutionalized elderly by 57.2% (56.1% to 58.3%), which increased to 81.2% (80.2% to 82%) for the fully vaccinated.\nC_LIO_LIIn individuals naive to SARS-CoV-2 vaccination reduced the risk by up to 81.8% and averted up to 11.6 cases per 10,000 vaccinated persons per day.\nC_LIO_LIThose with previous infection also benefited from a risk reduction of 57%, which translated in less than 1 infection averted per 10,000 vaccinated persons per day.\nC_LIO_LINon-vaccinated individuals living in facilities where the majority (residents and staff) had been vaccinated showed a risk reduction similar to those actually vaccinated.\nC_LI", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Susana Monge", + "author_inst": "Centre for the Coordination of Health Alerts and Emergencies. Ministry of Health, Spain" + }, + { + "author_name": "Carmen Olmedo", + "author_inst": "Vaccines division. Ministry of Health, Spain" + }, + { + "author_name": "Belen Alejos", + "author_inst": "Independent Collaborator" + }, + { + "author_name": "Marife Lapena", + "author_inst": "Data analytics department, General Directorate of Digital Health and National Health Service Information Systems, Ministry of Health." + }, + { + "author_name": "Maria Jose Sierra", + "author_inst": "Centre for the Coordination of Alerts and Health Emergencies, General Directorate of Public Health, Ministry of Health." + }, + { + "author_name": "Aurora Limia", + "author_inst": "Vaccines division, General Directorate of Public Health, Ministry of Health." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.07.21255094", "rel_title": "Modelling the impact of extending dose intervals for COVID-19 vaccines in Canada", @@ -807861,41 +809428,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.04.06.21254988", - "rel_title": "Neighbourhood characteristics associated with the geographic variation in laboratory confirmed COVID-19 in Ontario, Canada: a multilevel analysis", - "rel_date": "2021-04-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.06.21254988", - "rel_abs": "PurposeThere is limited information on the role of individual- and neighbourhood-level characteristics in explaining the geographic variation in the novel coronavirus 2019 (COVID-19) between regions. This study quantified the magnitude of the variation in COVID-19 rates between neighbourhoods in Ontario, Canada, and examined the extent to which neighbourhood-level differences are explained by census-based neighbourhood measures, after adjusting for individual-level covariates (i.e., age, sex, and chronic conditions).\n\nMethodsWe conducted a multilevel population-based study of individuals nested within neighbourhoods. COVID-19 laboratory testing data were obtained from a centralized laboratory database and linked to health-administrative data. The median rate ratio and the variance partition coefficient were used to quantify the magnitude of the neighbourhood-level characteristics on the variation of COVID-19 rates.\n\nResultsThe unadjusted median rate ratio for the between-neighbourhood variation in COVID-19 was 2.22. In the fully adjusted regression models, the individual- and neighbourhood-level covariates accounted for about 44% of the variation in COVID-19 between neighbourhoods, with 43% attributable to neighbourhood-level census-based characteristics.\n\nConclusionNeighbourhood-level characteristics could explain almost half of the observed geographic variation in COVID-19. Understanding how neighbourhood-level characteristics influence COVID-19 rates can support jurisdictions in creating effective and equitable intervention strategies.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Tristan Watson", - "author_inst": "University of Toronto" - }, - { - "author_name": "Jeffrey C Kwong", - "author_inst": "ICES" - }, - { - "author_name": "Kathy Kornas", - "author_inst": "University of Toronto" - }, - { - "author_name": "Sharmistha Mishra", - "author_inst": "University of Toronto" - }, - { - "author_name": "Laura C Rosella", - "author_inst": "University of Toronto" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.04.07.21255072", "rel_title": "Behavioural responses to Covid-19 health certification: A rapid review", @@ -808487,6 +810019,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.04.07.21254497", + "rel_title": "Characterising contact in disease outbreaks via a network model of spatial-temporal proximity", + "rel_date": "2021-04-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.07.21254497", + "rel_abs": "Contact tracing is a key tool in epidemiology to identify and control outbreaks of infectious diseases. Existing contact tracing methodologies produce contact maps of individuals based on a binary definition of contact which can be hampered by missing data and indirect contacts. Here, we present a Spatial-temporal Epidemiological Proximity (StEP) model to recover contact maps in disease outbreaks based on movement data. The StEP model accounts for imperfect data by considering probabilistic contacts between individuals based on spatial-temporal proximity of their movement trajectories, creating a robust movement network despite possible missing data and unseen transmission routes. Using real-world data we showcase the potential of StEP for contact tracing with outbreaks of multidrug-resistant bacteria and COVID-19 in a large hospital group in London, UK. In addition to the core structure of contacts that can be recovered using traditional methods of contact tracing, the StEP model reveals missing contacts that connect seemingly separate outbreaks. Comparison with genomic data further confirmed that these recovered contacts indeed improve characterisation of disease transmission and so highlights how the StEP framework can inform effective strategies of infection control and prevention.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Ashleigh C Myall", + "author_inst": "Imperial College London" + }, + { + "author_name": "Robert L Peach", + "author_inst": "Imperial College London" + }, + { + "author_name": "Yu Wan", + "author_inst": "Imperial College London" + }, + { + "author_name": "Siddharth Mookerjee", + "author_inst": "Imperial College NHS Trust" + }, + { + "author_name": "Elita Jauneikaite", + "author_inst": "Imperial College London" + }, + { + "author_name": "Frankie Bolt", + "author_inst": "Imperial College London" + }, + { + "author_name": "James Richard Price", + "author_inst": "Imperial College London" + }, + { + "author_name": "Frances Davies", + "author_inst": "Imperial College NHS Trust" + }, + { + "author_name": "Andrea Yeong Wiesse", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Alison Holmes", + "author_inst": "Imperial College London" + }, + { + "author_name": "Mauricio Barahona", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.04.06.21253465", "rel_title": "Social, demographic and behavioural determinants of SARS-CoV-2 infection: A case-control study carried out during mass community testing of asymptomatic individuals in South Wales, December 2020", @@ -809675,93 +811266,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2021.04.07.438812", - "rel_title": "Identifying SARS-CoV-2 Antiviral Compounds by Screening for Small Molecule Inhibitors of Nsp14/nsp10 Exoribonuclease", - "rel_date": "2021-04-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.07.438812", - "rel_abs": "SARS-CoV-2 is a coronavirus that emerged in 2019 and rapidly spread across the world causing a deadly pandemic with tremendous social and economic costs. Healthcare systems worldwide are under great pressure, and there is urgent need for effective antiviral treatments. The only currently approved antiviral treatment for COVID-19 is remdesivir, an inhibitor of viral genome replication. SARS-CoV-2 proliferation relies on the enzymatic activities of the non-structural proteins (nsp), which makes them interesting targets for the development of new antiviral treatments. With the aim to identify novel SARS-CoV-2 antivirals, we have purified the exoribonuclease/methyltransferase (nsp14) and its cofactor (nsp10) and developed biochemical assays compatible with high-throughput approaches to screen for exoribonuclease inhibitors. We have screened a library of over 5000 commercial compounds and identified patulin and aurintricarboxylic acid (ATA) as inhibitors of nsp14 exoribonuclease in vitro. We found that patulin and ATA inhibit replication of SARS-CoV-2 in a VERO E6 cell-culture model. These two new antiviral compounds will be valuable tools for further coronavirus research as well as potentially contributing to new therapeutic opportunities for COVID-19.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Clovis Basier", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Souradeep Basu", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Rupert Beale", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Agustina P Bertolin", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Berta Canal", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Joseph F Curran", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Tom D Deegan", - "author_inst": "The University of Dundee" - }, - { - "author_name": "John FX Diffley", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Lucy S Drury", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Ryo Fujisawa", - "author_inst": "The University of Dundee" - }, - { - "author_name": "Michael Howell", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Karim Labib", - "author_inst": "The University of Dundee" - }, - { - "author_name": "Allison W McClure", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Jennifer Milligan", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Rachel Ulferts", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Florian Weissmann", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Mary Wu", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Jingkun Zeng", - "author_inst": "The Francis Crick Institute" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.04.07.438810", "rel_title": "Identification of SARS-CoV-2 Antiviral Compounds by Screening for Small Molecule Inhibitors of the nsp14 RNA Cap Methyltransferase", @@ -810845,6 +812349,101 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2021.04.08.438904", + "rel_title": "The impact of viral mutations on recognition by SARS-CoV-2 specific T-cells", + "rel_date": "2021-04-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.08.438904", + "rel_abs": "We identify amino acid variants within dominant SARS-CoV-2 T-cell epitopes by interrogating global sequence data. Several variants within nucleocapsid and ORF3a epitopes have arisen independently in multiple lineages and result in loss of recognition by epitope-specific T-cells assessed by IFN-{gamma} and cytotoxic killing assays. These data demonstrate the potential for T-cell evasion and highlight the need for ongoing surveillance for variants capable of escaping T-cell as well as humoral immunity.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Thushan I de Silva", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Guihai Liu", + "author_inst": "University of Oxford" + }, + { + "author_name": "Benjamin B Lindsey", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Danning Dong", + "author_inst": "University of Oxford" + }, + { + "author_name": "Dhruv Shah", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Alexander J Mentzer", + "author_inst": "University of Oxford" + }, + { + "author_name": "Adrienn Angyal", + "author_inst": "The University of Sheffield Medical School" + }, + { + "author_name": "Rebecca Brown", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Matthew D Parker", + "author_inst": "The University of Sheffield" + }, + { + "author_name": "Zixi Yin", + "author_inst": "Weatherall Institute of Molecular Medicine" + }, + { + "author_name": "Xuan Yao", + "author_inst": "University of Oxford" + }, + { + "author_name": "Lance Turtle", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Susanna Dunachie", + "author_inst": "University of Oxford" + }, + { + "author_name": "- COVID-19 Genomics UK (COG-UK) Consortium", + "author_inst": "-" + }, + { + "author_name": "Mala K Maini", + "author_inst": "University College London" + }, + { + "author_name": "Graham Ogg", + "author_inst": "University of Oxford" + }, + { + "author_name": "Julian Charles Knight", + "author_inst": "Oxford University" + }, + { + "author_name": "Yanchun Peng", + "author_inst": "University of Oxford" + }, + { + "author_name": "Sarah L Rowland-Jones", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Tao Dong", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.04.07.21255081", "rel_title": "Effectiveness of CoronaVac in the setting of high SARS-CoV-2 P.1 variant transmission in Brazil: A test-negative case-control study", @@ -811825,93 +813424,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.04.06.21254728", - "rel_title": "Social and Clinical Determinants of COVID-19 Outcomes: Modeling Real-World Data from a Pandemic Epicenter", - "rel_date": "2021-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.06.21254728", - "rel_abs": "IMPORTANCEAs the United States continues to accumulate COVID-19 cases and deaths, and disparities persist, defining the impact of risk factors for poor outcomes across patient groups is imperative.\n\nOBJECTIVEOur objective is to use real-world healthcare data to quantify the impact of demographic, clinical, and social determinants associated with adverse COVID-19 outcomes, to identify high-risk scenarios and dynamics of risk among racial and ethnic groups.\n\nDESIGNA retrospective cohort of COVID-19 patients diagnosed between March 1 and August 20, 2020. Fully adjusted logistical regression models for hospitalization, severe disease and mortality outcomes across 1-the entire cohort and 2-within self-reported race/ethnicity groups.\n\nSETTINGThree sites of the NewYork-Presbyterian health care system serving all boroughs of New York City. Data was obtained through automated data abstraction from electronic medical records.\n\nPARTICIPANTSDuring the study timeframe, 110,498 individuals were tested for SARS-CoV-2 in the NewYork-Presbyterian health care system; 11,930 patients were confirmed for COVID-19 by RT-PCR or covid-19 clinical diagnosis.\n\nMAIN OUTCOMES AND MEASURESThe predictors of interest were patient race/ethnicity, and covariates included demographics, comorbidities, and census tract neighborhood socio-economic status. The outcomes of interest were COVID-19 hospitalization, severe disease, and death.\n\nRESULTSOf confirmed COVID-19 patients, 4,895 were hospitalized, 1,070 developed severe disease and 1,654 suffered COVID-19 related death. Clinical factors had stronger impacts than social determinants and several showed race-group specificities, which varied among outcomes. The most significant factors in our all-patients models included: age over 80 (OR=5.78, p= 2.29x10-24) and hypertension (OR=1.89, p=1.26x10-10) having the highest impact on hospitalization, while Type 2 Diabetes was associated with all three outcomes (hospitalization: OR=1.48, p=1.39x10-04; severe disease: OR=1.46, p=4.47x10-09; mortality: OR=1.27, p=0.001). In race-specific models, COPD increased risk of hospitalization only in Non-Hispanics (NH)-Whites (OR=2.70, p=0.009). Obesity (BMI 30+) showed race-specific risk with severe disease NH-Whites (OR=1.48, p=0.038) and NH-Blacks (OR=1.77, p=0.025). For mortality, Cancer was the only risk factor in Hispanics (OR=1.97, p=0.043), and heart failure was only a risk in NH-Asians (OR=2.62, p=0.001).\n\nCONCLUSIONS AND RELEVANCEComorbidities were more influential on COVID-19 outcomes than social determinants, suggesting clinical factors are more predictive of adverse trajectory than social factors.\n\nKEY POINTSO_ST_ABSQUESTIONC_ST_ABSWhat is the impact of patient self-reported race, ethnicity, socioeconomic status, and clinical profile on COVID-19 hospitalizations, severity, and mortality?\n\nFINDINGSIn patients diagnosed with COVID-19, being over 50 years of age, having type 2 diabetes and hypertension were the most important risk factors for hospitalization and severe outcomes regardless of patient race or socioeconomic status.\n\nMEANINGIn this large sample pf patients diagnosed with COVID-19 in New York City, we found that clinical comorbidity, more so than social determinants of health, was associated with important patient outcomes.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Jyothi Manohar", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Sajjad Abedian", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Rachel Martini", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Scott Kulm", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Kaylee Ho", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Paul Christos", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Mirella Salvatore", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Thomas R Campion", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Julianne Imperato-McGinley", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Said Ibrahim", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Teresa H Evering", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Erica Phillips", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Rulla Tamimi", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Vivian Bea", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Onyinye Balogun", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Andrea Sboner", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Olivier Elemento", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Melissa Boneta Davis", - "author_inst": "Weill Cornell Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.04.01.21254815", "rel_title": "Monitoring the opioid epidemic via social media discussions", @@ -812743,6 +814255,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.05.21254934", + "rel_title": "Levels of produced antibodies after vaccination with mRNA vaccine; effect of previous infection with SARS-CoV-2", + "rel_date": "2021-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.05.21254934", + "rel_abs": "The aim of this study was to estimate the immunogenic effect of mRNA vaccine against SARS-CoV-2. This study included 510 participants who received mRNA vaccine. The measurement of anti-Covid-19 antibodies was performed using the Abbott SARS-CoV-2 IgG quantitative assay (Abbott). Overall, mean title of anti-Spike antibodies was 19319.2{+/-}1787.5 AU/ml. Vaccination induced a robust immunogenic response in previous infected with SARS-CoV-2 compared. Additionally, individuals that were asymptomatic after vaccination produced lower levels of antibodies compared to feverish individuals. In conclusion, remarkable high level of anti-Spike Covid-19 antibodies was found after vaccination.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Theocharis Konstantinidis", + "author_inst": "Democritus University of Thrace" + }, + { + "author_name": "Stavroula Zisaki", + "author_inst": "Blood Transfusion Center, University General Hospital of Alexandroupolis Dragana Campus, 68100 Alexandroupolis, Greece" + }, + { + "author_name": "Ioannis Mitroulis", + "author_inst": "Democritus University of Thrace" + }, + { + "author_name": "Eleni Konstantinidou", + "author_inst": "Blood Transfusion Center, General Hospital of Drama" + }, + { + "author_name": "Eftychia G Kontekaki", + "author_inst": "Blood Transfusion Center, University General Hospital of Alexandroupolis Dragana Campus, 68100 Alexandroupolis, Greece" + }, + { + "author_name": "Gioulia Romanidou", + "author_inst": "Nephrology Department, General Hospital Sismanogleio Komotini" + }, + { + "author_name": "Alexandros Karvelas", + "author_inst": "Laboratory of Microbiology, Democritus University of Thrace, University General Hospital of Alexandroupolis Dragana Campus, 68100 Alexandroupolis, Greece" + }, + { + "author_name": "Ioanna Nanousi", + "author_inst": "Blood Transfusion Center, University General Hospital of Alexandroupolis Dragana Campus, 68100 Alexandroupolis, Greece" + }, + { + "author_name": "Leonidas Lazidis", + "author_inst": "Blood Transfusion Center, University General Hospital of Alexandroupolis Dragana Campus, 68100 Alexandroupolis, Greece" + }, + { + "author_name": "Dimitrios Cassimos", + "author_inst": "Pediatric Department, Democritus University of Thrace, Alexandroupolis" + }, + { + "author_name": "Christina Tsigalou", + "author_inst": "Democritus University of Thrace" + }, + { + "author_name": "George Martinis", + "author_inst": "Blood Transfusion Center, University General Hospital of Alexandroupolis Dragana Campus, 68100 Alexandroupolis, Greece" + }, + { + "author_name": "Maria Panopoulou", + "author_inst": "Democritus University of Thrace" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.05.21254712", "rel_title": "Evaluation of the performance of SARS-CoV-2 antibody assays for the longitudinal population-based study of COVID-19 spread in St. Petersburg, Russia", @@ -813679,57 +815258,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, - { - "rel_doi": "10.1101/2021.04.03.21254866", - "rel_title": "Understanding how Victoria, Australia gained control of its second COVID-19 wave", - "rel_date": "2021-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.03.21254866", - "rel_abs": "Victoria has been Australias hardest hit state by the COVID-19 pandemic, but was successful in reversing its second wave of infections through aggressive policy interventions. The clear reversal in the epidemic trajectory combined with information on the timing and geographical scope of policy interventions offers the opportunity to estimate the relative contribution of each change. We developed a compartmental model of the COVID-19 epidemic in Victoria that incorporated age and geographical structure, and calibrated it to data on case notifications, deaths and health service needs according to the administrative divisions of Victorias healthcare, termed clusters. We achieved a good fit to epidemiological indicators, at both the state level and for individual clusters, through a combination of time-varying processes that included changes to case detection rates, population mobility, school closures, seasonal forcing, physical distancing and use of face coverings. Estimates of the risk of hospitalisation and death among persons with disease that were needed to achieve this close fit were markedly higher than international estimates, likely reflecting the concentration of the epidemic in groups at particular risk of adverse outcomes, such as residential facilities. Otherwise, most fitted parameters were consistent with the existing literature on COVID-19 epidemiology and outcomes. We estimated a significant effect for each of the calibrated time-varying processes on reducing the risk of transmission per contact, with broad estimates of the reduction in transmission risk attributable to seasonal forcing (27.8%, 95% credible interval [95%CI] 9.26-44.7% for mid-summer compared to mid-winter), but narrower estimates for the individual-level effect of physical distancing of 12.5% (95%CI 5.69-27.9%) and of face coverings of 39.1% (95%CI 31.3-45.8%). That the multi-factorial public health interventions and mobility restrictions led to the dramatic reversal in the epidemic trajectory is supported by our model results, with the mandatory face coverings likely to have been particularly important.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "James M Trauer", - "author_inst": "Monash University" - }, - { - "author_name": "Michael J Lydeamore", - "author_inst": "Monash University" - }, - { - "author_name": "Gregory W Dalton", - "author_inst": "Department of Health, Victoria" - }, - { - "author_name": "David V Pilcher", - "author_inst": "Monash University" - }, - { - "author_name": "Michael T Meehan", - "author_inst": "James Cook University" - }, - { - "author_name": "Emma S McBryde", - "author_inst": "James Cook University" - }, - { - "author_name": "Allen C Cheng", - "author_inst": "Monash University" - }, - { - "author_name": "Brett Sutton", - "author_inst": "Department of Health, Victoria" - }, - { - "author_name": "Romain Ragonnet", - "author_inst": "Monash University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.04.03.21254748", "rel_title": "CERC-002, a human anti-LIGHT mAb reduces respiratory failure and death in hospitalized COVID-19 ARDS patients", @@ -814557,6 +816085,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.06.21254612", + "rel_title": "Making sense of non-randomized comparative treatment studies in times of Covid-19: A case study of tocilizumab", + "rel_date": "2021-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.06.21254612", + "rel_abs": "BACKGROUNDTocilizumab (TCZ) is an interleukin-6 inhibitor and the second established effective drug for the treatment of hospitalized patients with Covid-19. In this study, we sought to validate the recent positive findings from the randomised clinical trial RECOVERY and to evaluate the challenges in the analysis and interpretation of non-randomized comparative effectiveness studies in Covid-19.\n\nMETHODSWe performed a retrospective cohort study using an openly available database of hospitalised Covid-19 patients in Spain. The primary outcome was all-cause in-hospital mortality at 28 days. We used multivariable Fine and Gray competing risk models which adjusted for both fixed and time-variant confounders to investigate the effect of TCZ on the primary outcome.\n\nRESULTSWe analysed 2547 patients hospitalised with Covid-19 between 1st January and 28th June 2020. Patients in the TCZ group tended to have more severe Covid-19 at admission, as measured by biomarkers of disease severity including CRP, D-dimer and LDH. At 28 days, 91 out of 440 TCZ patients had died compared to 267 out of 2107 patients in the control group. In multivariable analysis, there was no evidence of an association between TCZ and the primary outcome (adjusted hazard ratio 1.20, 95% CI 0.86 to 1.64, P=0.26).\n\nCONCLUSIONSOur observational study failed to find a benefit of TCZ on all-cause in-hospital mortality in Covid-19 patients compared with randomized trials, highlighting the impact that unmeasured confounding and other sources of bias can have in a retrospective observational setting. For future observational studies, we recommend prospective data collection to ensure all variables have the necessary quality, completeness and timing for reliable treatment evaluation.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Ruth R C Owen", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Nawab Qizilbash", + "author_inst": "Oxon Epidemiology" + }, + { + "author_name": "Sara Velazquez Diaz", + "author_inst": "Fundacion de Investigacion HM Hospitales" + }, + { + "author_name": "Jose Maria Castellano Vazquez", + "author_inst": "Fundacion de Investigacion HM Hospitales" + }, + { + "author_name": "Stuart J Pocock", + "author_inst": "London School of Hygiene and Tropical Medicine" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.06.21254014", "rel_title": "COVID-19 vaccine hesitancy among individuals with cancer, autoimmune diseases, and other serious comorbid conditions", @@ -815485,33 +817048,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.31.21254646", - "rel_title": "Timing is everything: the relationship between COVID outcomes and the date at which mask mandates are relaxed", - "rel_date": "2021-04-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.31.21254646", - "rel_abs": "ImportanceSeveral states including Texas and Mississippi have lifted their mask mandates, sparking concerns that this policy change could lead to a surge in cases and hospitalizations.\n\nObjectiveTo estimate the increase in incidence, hospitalizations, and deaths in Texas and Mississippi following the removal of mask mandates, and to evaluate the relative reduction of these outcomes if policy change is delayed by 90 days.\n\nDesign, Setting, and ParticipantsThis study uses an age-stratified compartmental model parameterized to incidence data in Texas and Mississippi to simulate increased transmission following policy change in March or June 2021, and to estimate the resulting number of incidence, hospitalizations, and deaths.\n\nMain Outcomes and MeasuresThe increase in incidence, hospitalizations, and deaths if mask mandates are lifted on March 14 compared to lifting on June 12.\n\nResultsIf transmission is increased by 67% when mask mandates are lifted, we projected 11.39 (CrI: 11.22 - 11.55) million infections, 170,909 (CrI: 167,454 - 174,379) hospitalizations, and 5647 (5511 - 5804) deaths (Figure 1) in Texas from March 14 through the end of 2021. Delaying NPI lift until June reduces the average number of infections, hospitalizations, and deaths by 36%, 65%, and 62%, respectively. Proportionate differences were similar for the state of Mississippi. Peak hospitalization rates would be reduced by 79% and 63% in Texas and Mississippi, respectively.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC=\"FIGDIR/small/21254646v1_fig1.gif\" ALT=\"Figure 1\">\nView larger version (32K):\norg.highwire.dtl.DTLVardef@49cbbforg.highwire.dtl.DTLVardef@df7928org.highwire.dtl.DTLVardef@18b5885org.highwire.dtl.DTLVardef@160b6d1_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1:C_FLOATNO Cumulative number of infections, hospitalizations, and deaths for (A) Texas and (B) Mississippi through 2021 if NPI were lifted on March 14 (red) or June 12 (blue).\n\nC_FIG Conclusions and RelevanceRemoval of mask mandates in March 2021 is premature. Delaying this policy change until June 2021, when a larger fraction of the population has been vaccinated, will avert more than half of the expected COVID-19 hospitalizations and deaths, and avoid an otherwise likely strain on healthcare capacity.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Affan Shoukat", - "author_inst": "Center for Infectious Disease Modeling and Analysis (CIDMA), Yale School of Public Health, New Haven, Connecticut, USA" - }, - { - "author_name": "Alison P. Galvani", - "author_inst": "Center for Infectious Disease Modeling and Analysis (CIDMA), Yale School of Public Health, New Haven, Connecticut, USA" - }, - { - "author_name": "Meagan C. Fitzpatrick", - "author_inst": "Center for Vaccine Development and Global Health, University of Maryland School of Medicine, 685 W Baltimore St, Baltimore, MD 21201, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.31.21254115", "rel_title": "Genomic epidemiology of SARS-CoV-2 in Russia reveals recurring cross-border transmission throughout 2020", @@ -816391,6 +817927,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2021.04.01.21254681", + "rel_title": "The association of ABO blood group with the asymptomatic COVID-19 cases in India", + "rel_date": "2021-04-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.01.21254681", + "rel_abs": "The COVID-19 pandemic has resulted several waves of infection in many countries worldwide. The large variations in case fatality ratio among different geographical regions suggests that the human susceptibility against this virus varies substantially. Several studies from different parts of the world showed a significant association of ABO blood group and COVID-19 susceptibility. It was shown that individuals with blood group O are at the lower risk of coronavirus infection. To establish the association of ABO blood group in SARS-CoV-2 susceptibility, we for the first time analysed SARS-CoV-2 neutralising antibodies as well as blood groups among 509 random individuals from three major districts of Eastern Uttar Pradesh region of India.. Interestingly, we found neutralising antibodies in significantly higher percentage of people with blood group AB (0.36) followed by B (0.31), A (0.22) and lowest in people with blood group O (0.11). This indicates that people with blood group AB are at comparatively higher risk of infection than other blood groups. Further, in line to previous reports we too observed that people with blood group O have significantly decreased risk of SARS-CoV-2 infection. Thus, among the asymptomatic SARS-CoV-2 infected individuals with blood group AB has highest, whilst blood group O has lowest risk of infection.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Prajjval Pratap Singh", + "author_inst": "Cytogenetics Laboratory Department of Zoology, Banaras Hindu University, India" + }, + { + "author_name": "Abhishek K Srivastava", + "author_inst": "Mohd. Hasan P. G. College, Jaunpur, India" + }, + { + "author_name": "Sudhir K Upadhyay", + "author_inst": "Department of Environmental Science, Veer Bahadur Singh Purvanchal University, Jaunpur, India" + }, + { + "author_name": "Ashish Singh", + "author_inst": "Genome Foundation Rural Centre Kalavari, Jaunpur, India, 222131" + }, + { + "author_name": "Pranav Gupta", + "author_inst": "Independent researcher" + }, + { + "author_name": "Sanjeev Maurya", + "author_inst": "Genome Foundation Rural Centre Kalavari, Jaunpur, India, 222131" + }, + { + "author_name": "Shashank Upadhyay", + "author_inst": "Invertis University, Bareilly, Uttar Pradesh, India" + }, + { + "author_name": "Rudra K Pandey", + "author_inst": "Cytogenetics Laboratory Department of Zoology, Banaras Hindu University, India" + }, + { + "author_name": "Anshika Shrivastava", + "author_inst": "Cytogenetics Laboratory Department of Zoology, Banaras Hindu University, India" + }, + { + "author_name": "Priya Dev", + "author_inst": "Department of Neurology, Institute of Medical Science, Banaras Hindu University, India" + }, + { + "author_name": "Vanya Singh", + "author_inst": "Cytogenetics Laboratory Department of Zoology, Banaras Hindu University, India" + }, + { + "author_name": "Rahul Mishra", + "author_inst": "Cytogenetics Laboratory Department of Zoology, Banaras Hindu University, India" + }, + { + "author_name": "Manoj K Shukla", + "author_inst": "Department of Medicinal Chemistry, Institute of Medical Science, Banaras Hindu University, India" + }, + { + "author_name": "Govind Chaubey", + "author_inst": "District Institute Of Education & Training, Sarnath, Varanasi, 221007" + }, + { + "author_name": "Pradeep Kumar", + "author_inst": "Department of Biotechnology, Veer Bahadur Singh Purvanchal University, Jaunpur, India" + }, + { + "author_name": "Vandana Rai", + "author_inst": "Department of Biotechnology, Veer Bahadur Singh Purvanchal University, Jaunpur, India" + }, + { + "author_name": "Yamini B Tripathy", + "author_inst": "Department of Medicinal Chemistry, Institute of Medical Science, Banaras Hindu University, India" + }, + { + "author_name": "Abhishek Pathak", + "author_inst": "Department of Neurology, Institute of Medical Science, Banaras Hindu University, India" + }, + { + "author_name": "Vijaya N Mishra", + "author_inst": "Department of Neurology, Institute of Medical Science, Banaras Hindu University, India" + }, + { + "author_name": "Chandana Basu Mallick", + "author_inst": "Centre for Genetic Disorders, Banaras Hindu University, India" + }, + { + "author_name": "Panjak Shrivastava", + "author_inst": "DNA Fingerprinting Unit, State Forensic Science Laboratory, Department of Home (Police), Government of MP, Sagar, India" + }, + { + "author_name": "Gyaneshwer Chaubey", + "author_inst": "Cytogenetics Laboratory Department of Zoology, Banaras Hindu University, India" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.03.31.21254695", "rel_title": "A BIBLIOMETRIC ANALYSIS OF RHEUMATOLOGY AND COVID-19 RESEARCHES", @@ -817311,57 +818950,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2021.04.05.438524", - "rel_title": "Antibody response to SARS-CoV-2 mRNA vaccines in pregnant women and their neonates", - "rel_date": "2021-04-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.05.438524", - "rel_abs": "Pregnant women were excluded from initial clinical trials for COVID-19 vaccines1-2, thus the immunologic response to vaccination in pregnancy and the transplacental transfer of maternal antibodies are just beginning to be studied4-5.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Malavika Prabhu", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Elisabeth A Murphy", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Ashley C Sukhu", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Jim Yee", - "author_inst": "New York Presbyterian Weill Cornell Medicine" - }, - { - "author_name": "Sunidhi Singh", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Dorothy Eng", - "author_inst": "New York Presbyterian Weill Cornell Medicine" - }, - { - "author_name": "Zhen Zhao", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Laura E Riley", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Yawei Jenny Yang", - "author_inst": "Weill Cornell Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.03.29.21253914", "rel_title": "Clinical Evidence for Improved Outcomes with Histamine Antagonists and Aspirin in 22,560 COVID-19 Patients", @@ -818309,6 +819897,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.31.21254472", + "rel_title": "T-cell responses as a correlate of COVID-19 vaccination. A pilot study in Health Care Workers.", + "rel_date": "2021-04-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.31.21254472", + "rel_abs": "BackgroundIt is crucial to assess the levels of protection generated by natural infection or SARS-CoV-2 vaccines, mainly in individuals professionally exposed and in vulnerable groups. Measuring T-cell responses may complement antibody tests currently in use as correlates of protection. Our aim was to assess the feasibility of a validated assay of T-cell responses.\n\nMethodsTwenty health-care-workers (HCW) were included. Antibody test to SARS-CoV-2 N and S-proteins in parallel with a commercially available whole-blood-interferon-gamma-release-assay (IGRA) to S-peptides and two detection methods, CLIA and ELISA were determined.\n\nResultsIGRA test detected T-cell responses in naturally exposed and vaccinated HCW already after first vaccination dose. The correlation by the two detection methods was very high (R>0.8) and sensitivity and specificity ranged between 100 and 86% and 100-73% respectively. Even though there was a very high concordance between specific antibody levels and the IGRA assay in the ability to detect immune response to SARS-CoV-2, there was a relatively low quantitative correlation. In the small group primed by natural infection, one vaccine dose was sufficient to reach immune response plateau. IGRA was positive in one, with Ig(S) antibody negative vaccinated immunosuppressed HCW illustrating another advantage of the IGRA-test.\n\nConclusionWhole-blood-IGRA-tests amenable to automation and constitutes a promising additional tool for measuring the state of the immune response to SARS-CoV-2; they are applicable to large number of samples and may become a valuable correlate of protection to COVID-19, particularly for vulnerable groups at risk of being re-exposed to infection, as are health-care-workers.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Monica Martinez-Gallo", + "author_inst": "Immunology Division, Hospital Universitari Vall d,Hebron (HUVH), Vall d,Hebron Research Institute (VHIR), Department of Cell Biology, Physiology and Barcelona," + }, + { + "author_name": "Juliana Esperalba-Ezquerra", + "author_inst": "Microbiology Division, Hospital Universitari Vall d,Hebron (HUVH). Microbiology and Genetics Department, Universitat Autonoma de Barcelona (UAB). Barcelona. Spa" + }, + { + "author_name": "Ricardo Pujol-Borrell", + "author_inst": "Immunology Division, Hospital Universitari Vall d,Hebron (HUVH), Vall d,Hebron Research Institute (VHIR), Department of Cell Biology, Physiology and Barcelona," + }, + { + "author_name": "Victor Sanda", + "author_inst": "Immunology Division, Hospital Universitari Vall d,Hebron (HUVH), Jeffrey Model Foundation Excellence Center. Barcelona, Catalonia, Spain" + }, + { + "author_name": "Iria Arrese-Munoz", + "author_inst": "Immunology Division, Hospital Universitari Vall d,Hebron (HUVH), Vall d,Hebron Research Institute (VHIR), Department of Cell Biology, Physiology and Barcelona," + }, + { + "author_name": "Candela Fernandez-Naval", + "author_inst": "Microbiology Department, Vall d,Hebron Research Institute (VHIR), Barcelona, Spain. Universitat Autonoma de Barcelona (UAB), Barcelona, Spain." + }, + { + "author_name": "Andres Anton-Pagarolas", + "author_inst": "Microbiology Division, Hospital Universitari Vall d,Hebron (HUVH). Microbiology and Genetics Department, Universitat Autonoma de Barcelona (UAB). Barcelona. Spa" + }, + { + "author_name": "Victoria Cardona", + "author_inst": "Allergy Section, Internal Medicine Department. Hospital Universitari Vall d,Hebron (HUVH). ARADyAL research network ISCIII. Spain. VHIR. Medicine Department, Un" + }, + { + "author_name": "Moises Labrador-Horrillo", + "author_inst": "Allergy Section, Internal Medicine Department. Hospital Universitari Vall d,Hebron (HUVH). ARADyAL research network ISCIII. Spain. VHIR. Medicine Department, Un" + }, + { + "author_name": "Tomas Pumarola-Sune", + "author_inst": "Microbiology Division, Hospital Universitari Vall d,Hebron (HUVH). Microbiology and Genetics Department, Universitat Autonoma de Barcelona (UAB). Barcelona. Spa" + }, + { + "author_name": "Manuel Hernandez-Gonzalez", + "author_inst": "Immunology Division, Hospital Universitari Vall d,Hebron (HUVH), Vall d,Hebron Research Institute (VHIR), Department of Cell Biology, Physiology and Barcelona," + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2021.04.03.21254847", "rel_title": "Equity Impacts of Dollar Store Vaccine Distribution", @@ -819277,45 +820924,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.29.21254542", - "rel_title": "Situation of COVID-19 in Brazil: An analysis via growth models as implemented in the ModInterv system for monitoring the pandemic", - "rel_date": "2021-04-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.29.21254542", - "rel_abs": "In this work we analyze the cumulative curves of deaths attributed to COVID-19 in the 26 Brazilian States and the Federal District up until August 21, 2020. Mathematical growth models implemented by the application ModInterv COVID-19, which can be accessed via internet browser or via a mobile app, were used to investigate at which stage the epidemic is in each of the Brazilian federal units. The analysis revealed that almost all states in the Northern and Northeastern regions were already in the saturation phase, meaning that the epidemic was relatively under control, whereas in all Southern states and in most states in the Midwest the epidemic was still accelerating or showed only a slight deceleration. The Southeastern region presented a great diversity of epidemic stages, with each state being found at a different stage, ranging from acceleration to saturation. It is argued that understanding this heterogeneous geographical distribution of the epidemic is relevant for public health authorities, as it may help in devising more effective strategies against the COVID-19 pandemic in a continental country like Brazil.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Giovani L. Vasconcelos", - "author_inst": "Universidade Federal do Parana" - }, - { - "author_name": "Gerson C. Duarte-Filho", - "author_inst": "Universidade Federal de Sergipe" - }, - { - "author_name": "Arthur A. Brum", - "author_inst": "Universidade Federal de Pernambuco" - }, - { - "author_name": "Raydonal Ospina", - "author_inst": "Universidade Federal de Pernambuco" - }, - { - "author_name": "Francisco . A. G Almeida", - "author_inst": "Universidade Federal de Sergipe" - }, - { - "author_name": "Antonio M. S. Macedo", - "author_inst": "Universidade Federal de Pernambuco" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.26.21254425", "rel_title": "Comparison of post-COVID depression and major depressive disorder", @@ -820123,6 +821731,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.30.21254333", + "rel_title": "Factors associated with nonessential workplace attendance during the Covid-19 pandemic in the UK in early 2021: evidence from cross-sectional surveys", + "rel_date": "2021-04-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.30.21254333", + "rel_abs": "Background and aimsWorking from home where possible is important in reducing spread of Covid-19. In early 2021, a quarter of people in England who believed they could work entirely from home reported attending their workplace. To inform interventions to reduce this, this study examined associated factors.\n\nMethodsData from the ongoing CORSAIR survey series of nationally representative samples of people in the UK aged 16+ years in January-February 2021 were used. The study sample was 1422 respondents who reported that they could work completely from home. The outcome measure was self-reported workplace attendance at least once during the preceding week. Factors of interest were analysed in three blocks: 1) sociodemographic variables, 2) variables relating to respondents circumstances, and 3) psychological variables.\n\nResults26.8% (95%CI=24.5%-29.1%) of respondents reported having attended their workplace at least once in the preceding week. Sociodemographic variables and living circumstances significantly independently predicted non-essential workplace attendance: male gender (OR=1.85,95%CI=1.33-2.58), dependent children in the household (OR=1.65,95%CI=1.17-2.32), financial hardship (OR=1.14,95%CI=1.08-1.21), socio-economic grade C2DE (OR=1.74, 95%CI=1.19-2.53), working in sectors such as health or social care (OR=4.18, 95%CI=2.56-6.81), education and childcare (OR=2.45, 95%CI=1.45-4.14) and key public service (OR=3.78, 95%CI=1.83-7.81), and having been vaccinated (OR=2.08,95%CI=1.33-3.24).\n\nConclusionsNon-essential workplace attendance in the UK in early 2021 during the Covid-19 pandemic was significantly independently associated with a range of sociodemographic variables and personal circumstances. Having been vaccinated, financial hardship, socio-economic grade C2DE, having a dependent child at home, working in certain key sectors were associated with higher likelihood of workplace attendance.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Susan Michie", + "author_inst": "University College London, Centre for Behaviour Change" + }, + { + "author_name": "Henry WW Potts", + "author_inst": "University College London, Institute of Health Informatics" + }, + { + "author_name": "Robert West", + "author_inst": "University College London, Department of Behavioural Science and Health" + }, + { + "author_name": "Richard Amlot", + "author_inst": "Kings College London, Department of Psychological Medicine" + }, + { + "author_name": "Louise E Smith", + "author_inst": "Kings College London, Department of Psychological Medicine" + }, + { + "author_name": "Nicola T Fear", + "author_inst": "Kings College London, Department of Psychological Medicine" + }, + { + "author_name": "G James Rubin", + "author_inst": "Kings College London, Department of Psychological Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.03.30.21254564", "rel_title": "Smoking modulates different secretory subpopulations expressing SARS-CoV-2 entry genes in the nasal and bronchial airways", @@ -821075,53 +822726,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, - { - "rel_doi": "10.1101/2021.03.31.21254680", - "rel_title": "Accessibility, inclusivity, and implementation of COVID-19 clinical management guidelines early in the pandemic: a global survey", - "rel_date": "2021-04-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.31.21254680", - "rel_abs": "BackgroundWith a rapidly changing evidence base, high-quality clinical management guidelines (CMGs) are key tools for aiding clinical decision making and increasing access to best available evidence-based care. A rapid review of COVID-19 CMGs found that most lacked methodological rigour, overlooked many at-risk populations, and had variations in treatment recommendations. Furthermore, social science literature highlights the complexity of implementing guidelines in local contexts where they were not developed and the resulting potential to compound health inequities. The aim of this study was to evaluate access to, inclusivity of, and implementation of Covid-19 CMGs in different settings.\n\nMethodsA cross-sectional survey of clinicians worldwide from 15 June to 20 July 2020, to explore access to and implementation of Covid-19 CMGs and treatment and supportive care recommendations provided. Data on accessibility, inclusivity, and implementation of CMGs. were analyzed by geographic location.\n\nResultsSeventy-six clinicians, from 27 countries responded, 82% from high-income countries, 17% from low-middle income countries. Most respondents reported access to Covid-19 CMG and confidence in implementation of these. However, many respondents, particularly from LMICs reported barriers to implementation, including limited access to treatments and equipment. Only 20% of respondents reported having access to CMGs covering care for children, 25% for pregnant women and 50% for older adults (>65 years). Themes emerging were for CMGs to include recommendations for different at-risk populations, and settings, include supportive care guidance, be readily updated as evidence emerges, and CMG implementation supported by training, and access to treatments recommended.\n\nConclusionOur findings highlight important gaps in Covid-19 CMG development and implementation challenges during a pandemic, particularly affecting different at-risk populations and lower resourced settings. The findings highlight a need for a new, harmonized evidence-based, that is inclusive and adaptable for different context, incorporating implementation support, to improve access in evidence-based care recommendations during an emergency.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Caitlin Pilbeam", - "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford" - }, - { - "author_name": "Deobrah Malden", - "author_inst": "Nuffield Department of Population Health, University of Oxford" - }, - { - "author_name": "Katherine Newell", - "author_inst": "Nuffield Department of Population Health, University of Oxford" - }, - { - "author_name": "Andrew Dagens", - "author_inst": "International Severe Acute Respiratory and Emerging Infection Consortium (ISARIC) Global Support Centre, Centre for Tropical Medicine and Global Health, Nuffiel" - }, - { - "author_name": "Kalynn Kennon", - "author_inst": "Infectious Diseases Data Observatory (IDDO), Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford" - }, - { - "author_name": "Melina Michelen", - "author_inst": "International Severe Acute Respiratory and Emerging Infection Consortium (ISARIC) Global Support Centre, Centre for Tropical Medicine and Global Health, Nuffiel" - }, - { - "author_name": "Nina Gobat", - "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford" - }, - { - "author_name": "Louise Sigfrid", - "author_inst": "International Severe Acute Respiratory and Emerging Infection Consortium (ISARIC) Global Support Centre, Centre for Tropical Medicine and Global Health, Univer" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.31.21254494", "rel_title": "Interim Report: Safety And Immunogenicity Of An Inactivated Vaccine Against Sars-Cov-2 In Healthy Chilean Adults In A Phase 3 Clinical Trial", @@ -822345,6 +823949,77 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.04.01.438089", + "rel_title": "Placental expression of ACE2 and TMPRSS2 in maternal SARS-CoV-2 infection: are placental defenses mediated by fetal sex?", + "rel_date": "2021-04-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.01.438089", + "rel_abs": "BackgroundSex differences in vulnerability to and severity of SARS-CoV-2 infection have been described in non-pregnant populations. ACE2 and TMPRSS2, host molecules required for viral entry, are regulated by sex steroids and expressed in the placenta. We sought to investigate whether placental ACE2 and TMPRSS2 expression vary by fetal sex and in the presence of maternal SARS-CoV-2 infection.\n\nMethodsPlacental ACE2 and TMPRSS2 were quantified in 68 pregnant individuals (38 SARS-CoV-2 positive, 30 SARS-CoV-2 negative) delivering at Mass General Brigham from April to June 2020. Maternal SARS-CoV-2 status was determined by nasopharyngeal RT-PCR. Placental SARS-CoV-2 viral load was quantified. RTqPCR was performed to quantify expression of ACE2 and TMPRSS2 relative to the reference gene YWHAZ. Western blots were performed on placental homogenates to quantify protein levels. The impact of fetal sex and SARS-CoV-2 exposure on ACE2 and TMPRSS2 expression was analyzed by 2-way ANOVA.\n\nResultsSARS-CoV-2 virus was undetectable in all placentas. Maternal SARS-CoV-2 infection impacted TMPRSS2 placental gene and protein expression in a sexually dimorphic fashion (2-way ANOVA interaction p-value: 0.002). We observed no impact of fetal sex or maternal SARS-CoV-2 status on placental ACE2 gene or protein expression. Placental TMPRSS2 expression was significantly correlated with ACE2 expression in males (Spearmans {rho}=0.54, p=0.02) but not females ({rho}=0.23, p=0.34) exposed to maternal SARS-CoV-2.\n\nConclusionsSex differences in placental TMPRSS2 but not ACE2 were observed in the setting of maternal SARS-CoV-2 infection. These findings may have implications for offspring vulnerability to placental infection and vertical transmission.These findings may have implications for offspring vulnerability to placental infection and vertical transmission.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Lydia L Shook", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Evan A Bordt", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Marie-Charlotte Meinsohn", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "David Pepin", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Rose M De Guzman", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Sara Brigada", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Laura J Yockey", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Kaitlyn E James", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Mackenzie W Sullivan", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Lisa M Bebell", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Drucilla J Roberts", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Anjali J Kaimal", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Danny Schust", + "author_inst": "University of Missouri School of Medicine" + }, + { + "author_name": "Andrea G Edlow", + "author_inst": "Massachusetts General Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "developmental biology" + }, { "rel_doi": "10.1101/2021.04.01.438120", "rel_title": "Analysis of glycosylation and disulfide bonding of wild-type SARS-CoV-2 spike glycoprotein", @@ -823277,93 +824952,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.30.21254655", - "rel_title": "COVID-19 vaccine impact on rates of SARS-CoV-2 cases and post vaccination strain sequences among healthcare workers at an urban academic medical center: a prospective cohort study", - "rel_date": "2021-03-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.30.21254655", - "rel_abs": "BackgroundCOVID-19 vaccine trials and post-implementation data suggest vaccination decreases SARS-CoV-2 infections.\n\nObjectiveEstimate COVID-19 vaccinations impact on SARS-CoV-2 case rates and viral diversity among healthcare workers (HCW) during a high community prevalence period.\n\nDesign, Setting, ParticipantsA prospective cohort study from Boston Medical Center (BMC)s HCW vaccination program, where staff received two doses of BNT162b2 or mRNA-1273.\n\nMeasurementsPCR-confirmed SARS-CoV-2 cases among HCWs from December 09, 2020 to February 23, 2021. Weekly SARS-CoV-2 rates per 100,000 person-day overall and by time from first injection (1-14 and >14 days) were compared with surrounding community rates. Viral genome sequences from SARS CoV-2 positive samples.\n\nResultsSARS-CoV-2 cases occurred in 1.4% (96/7109) of HCWs given at least a first dose and 0.3% (17/5913) of HCWs given both vaccine doses. Adjusted SARS-CoV-2 infection rate ratios were 0.73 (95% CI 0.53-1.00) 1-14 days and 0.18 (0.10-0.32) >14 days from first dose. HCW SARS-CoV-2 cases >14 days from initial dose compared to within 14 days were more often older (46 versus 38 years, p=0.007), Latinx (10% versus 8%, p=0.03), and asymptomatic (48% versus 11%, p=0.0002). SARS-CoV-2 rates among HCWs fell below those of the surrounding community, with a 18% versus 11% weekly decrease respectively (p=0.14). Comparison of 48 SARS-CoV-2 genomes sequenced from post-first dose cases did not indicate selection pressure towards known spike-antibody escape mutations.\n\nLimitationsUnable to adjust for infection risk outside of the workplace. Lack follow up on symptoms post SARS-CoV-2 diagnosis. Small number of vaccinated HCW cases.\n\nConclusionOur results indicate a positive impact of COVID-19 vaccines on SARS-CoV-2 case rates. Post-vaccination isolates did not show unusual genetic diversity or selection for mutations of concern.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Tara C Bouton", - "author_inst": "Section of Infectious Diseases, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA" - }, - { - "author_name": "Sara Lodi", - "author_inst": "Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA" - }, - { - "author_name": "Jacquelyn Turcinovic", - "author_inst": "3National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA" - }, - { - "author_name": "Sarah E Weber", - "author_inst": "Section of Infectious Diseases, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA" - }, - { - "author_name": "Emily Quinn", - "author_inst": "Biostatistics and Epidemiology Data Analytics Center, Boston University School of Public Health, Boston, MA, USA" - }, - { - "author_name": "Cathy Korn", - "author_inst": "Department of Infection Control, Boston Medical Center, Boston, MA, USA" - }, - { - "author_name": "Jacqueline Steiner", - "author_inst": "Department of Infection Control, Boston Medical Center, Boston, MA, USA" - }, - { - "author_name": "Elissa M Schechter-Perkins", - "author_inst": "Department of Emergency Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA" - }, - { - "author_name": "Elizabeth Duffy", - "author_inst": "Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA" - }, - { - "author_name": "Elizabeth J. Ragan", - "author_inst": "Section of Infectious Diseases, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA" - }, - { - "author_name": "Bradford P. Taylor", - "author_inst": "Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA" - }, - { - "author_name": "Beau Schaeffer", - "author_inst": "Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA" - }, - { - "author_name": "Nancy Miller", - "author_inst": "Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA" - }, - { - "author_name": "Ravin Davidoff", - "author_inst": "Boston Medical Center and Boston University School of Medicine, Boston, MA, USA" - }, - { - "author_name": "William P. Hanage", - "author_inst": "Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA" - }, - { - "author_name": "John Connor", - "author_inst": "National Emerging Infectious Diseases Laboratories and Department of Microbiology, Boston University School of Medicine, Boston, MA, USA" - }, - { - "author_name": "Cassandra Pierre", - "author_inst": "Section of Infectious Diseases, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA" - }, - { - "author_name": "Karen R Jacobson", - "author_inst": "Section of Infectious Diseases, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.29.21254566", "rel_title": "Saliva as a Reliable Sample for COVID-19 Diagnosis in Paediatric Patients", @@ -823935,6 +825523,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.29.21254557", + "rel_title": "Second wave mortality among patients hospitalised for COVID-19 in Sweden: a nationwide observational cohort study", + "rel_date": "2021-03-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.29.21254557", + "rel_abs": "BackgroundDuring the first pandemic wave, a substantial decline in mortality was seen among hospitalised COVID-19 patients. We aimed to study if the decreased mortality continued during the second wave, using data compiled by the Swedish National Board of Health and Welfare.\n\nMethodRetrospective nationwide observational study of all patients hospitalised in Sweden between March 1st and December 31st, 2020, with SARS-CoV-2 RNA positivity 14 days before to 5 days after admission and a discharge code for COVID-19. Outcome was 60-day all-cause mortality. Poisson regression was used to estimate the relative risk (RR) for death by month of admission, adjusting for age, sex, socio-economic data, comorbidity, care dependency, and country of birth.\n\nFindingsA total of 32 452 patients were included. December had the highest number of admissions/month (n=8253) followed by April (n=6430). The 60-day crude mortality decreased from 24{middle dot}7% (95% CI, 23{middle dot}0%-26{middle dot}5%) for March to 10{middle dot}4% (95% CI, 8{middle dot}9%-12{middle dot}1%) for July-September (as reported previously), later increased to 19{middle dot}9% (95% CI, 19{middle dot}1-20{middle dot}8) for December. RR for 60-day death for December (reference) was higher than those for June to November (RR ranging from 0{middle dot}74 to 0{middle dot}89; 95% CI <1 for all months). SARS-CoV-2 variants of concern were only sporadically found in Sweden before January 2021.\n\nInterpretationThe decreased mortality of hospitalised COVID-19 patients after the first wave turned and increased during the second wave. Focused research is urgent to describe if this increase was caused by a high load of patients, management and treatment, viral properties, or other factors.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSDuring the first pandemic wave, a substantial decline in mortality was seen among hospitalised COVID-19 patients in many countries. As the reason for this decline has not been clarified, no one could foresee how mortality would change during forthcoming waves.\n\nAdded valueThis retrospective nationwide study of all patients hospitalised for COVID-19 in Sweden from March to December 2020 showed that the gradual decrease in mortality seen in the first pandemic wave was followed by an increased crude and adjusted 60-day all-cause mortality during the second wave. This increase in mortality occurred although the standard-of-care recommendations for hospitalised COVID-19 patients did not change in Sweden during the second half of 2020.\n\nImplications of all the available evidenceWhile improved standard-of-care was believed to be an important factor for the decrease in mortality during the first pandemic wave, the increasing mortality during the second wave has no apparent explanation. As the currently known virus variants of concern occurred only sporadically in Sweden before January 2021, they were most likely not involved. Focused research is urgent to describe if this increase in mortality was caused by a high load of patients, management and treatment factors, viral properties, or other circumstances", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Kristoffer Stralin", + "author_inst": "Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden, Department of Medicine, Huddinge, Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "Erik Wahlstrom", + "author_inst": "National Board of Health and Welfare, Sweden" + }, + { + "author_name": "Sten Walther", + "author_inst": "Swedish Intensive Care Registry, Varmland County Council, Karlstad, Sweden, Department of Cardiothoracic and Vascular Surgery, Heart Centre, Linkoping Universit" + }, + { + "author_name": "Anna M Bennet-Bark", + "author_inst": "National Board of Health and Welfare, Sweden" + }, + { + "author_name": "Mona Heurgren", + "author_inst": "National Board of Health and Welfare, Sweden" + }, + { + "author_name": "Thomas Linden", + "author_inst": "National Board of Health and Welfare, Sweden" + }, + { + "author_name": "Johanna Holm", + "author_inst": "National Board of Health and Welfare, Sweden" + }, + { + "author_name": "Hakan Hanberger", + "author_inst": "Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linkoping University, Linkoping" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.29.21254579", "rel_title": "Clustering of patient comorbidities within electronic medical records enables high-precision COVID-19 mortality prediction", @@ -824815,29 +826450,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.03.31.437815", - "rel_title": "Differential mutational profile of SARS-CoV-2 proteins across deceased and asymptomatic patients", - "rel_date": "2021-03-31", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.31.437815", - "rel_abs": "The SARS-CoV-2 infection spread at an alarming rate with many places showed multiple peaks in incidence. Present study involves a total of 332 SARS-CoV-2 sequences from 114 Asymptomatic and 218 Deceased patients from twenty-one different countries. The mining of mutations was done using the GISAID CoVSurver (www.gisaid.org/epiflu-applications/covsurver-mutations-app) with the reference sequence hCoV-19/Wuhan/WIV04/2019 present in NCBI with Accession number NC-045512.2. The impact of the mutations on SARS-CoV-2 proteins mutation was predicted using PredictSNP1(loschmidt.chemi.muni.cz/predictsnp1) which is a meta-server integrating six predictor tools: SIFT, PhD-SNP, PolyPhen-1, PolyPhen-2, MAPP and SNAP. The iStable integrated server (predictor.nchu.edu.tw/iStable) was used to predict shifts in the protein stability due to mutations. A total of 372 variants were observed in the 332 SARS-CoV-2 sequences with several variants incident in multiple patients accounting for a total of 1596 incidences. Asymptomatic and Deceased specific mutants constituted 32% and 62% of the repertoire respectively indicating their exclusivity. However, the most prevalent mutations were those present in both. Though some parts of the genome are more variable than others but there was clear difference between incidence and prevalence. NSP3 with 68 variants had total occurrence of only 105 whereas Spike protein had 346 occurrences with just 66 variants. For Deleterious variants, NSP3 had the highest incidence of 25 followed by NSP2 (16), ORF3a (14) and N (14). Spike protein had just 7 Deleterious variants out of 66. Deceased patients have more Deleterious than Neutral variants as compared to the symptomatic ones. Further, it appears that the Deleterious variants which decrease protein stability are more significant in pathogenicity of SARS-CoV-2.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Rezwanuzzaman Laskar", - "author_inst": "Aliah University" - }, - { - "author_name": "Safdar Ali", - "author_inst": "Aliah University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.03.31.437666", "rel_title": "Emerging SARS-CoV-2 mutation hotspots associated with clinical outcomes", @@ -825625,6 +827237,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.30.437647", + "rel_title": "A recombinant receptor-binding domain in trimeric form generates completely protective immunity against SARS-CoV-2 infection in nonhuman primates", + "rel_date": "2021-03-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.30.437647", + "rel_abs": "Safe and effective vaccination is critical to combatting the COVID-19 pandemic. Here, we developed a trimeric SARS-CoV-2 receptor-binding domain (RBD) subunit vaccine candidate that simulates the natural structure of the spike (S) trimer glycoprotein. Immunization with RBD-trimer induced robust humoral and cellular immune responses and a high level of neutralizing antibodies that were maintained for at least 4 months. Moreover, the antibodies that were produced in response to the vaccine effectively neutralized the SARS-CoV-2 501Y.V2 variant. Of note, when the titers of the antibodies dropped to a sufficiently low level, only one boost quickly activated the anamnestic immune response, resulting in complete protection against the SARS-CoV-2 challenge in rhesus macaques without typical histopathological changes or viral replication in the lungs and other respiratory tissues. Our results indicated that immunization with SARS-CoV-2 RBD-trimer could raise long-term and broad immunity protection in nonhuman primates, thereby offering an optimal vaccination strategy against COVID-19.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Limin Yang", + "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early Warning (CASCIRE), CAS-TWAS Cen" + }, + { + "author_name": "Deyu Tian", + "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early Warning (CASCIRE), CAS-TWAS Cen" + }, + { + "author_name": "Jian-bao Han", + "author_inst": "Kunming National High-Level Biosafety Research Center for Nonhuman Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of" + }, + { + "author_name": "Wenhui Fan", + "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early Warning (CASCIRE), CAS-TWAS Cen" + }, + { + "author_name": "Yuan Zhang", + "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early Warning (CASCIRE), CAS-TWAS Cen" + }, + { + "author_name": "Yunlong Li", + "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early Warning (CASCIRE), CAS-TWAS Cen" + }, + { + "author_name": "Wenqiang Sun", + "author_inst": "University of Chinese Academy of Sciences, Beijing 101408, China" + }, + { + "author_name": "Yanqiu Wei", + "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early Warning (CASCIRE), CAS-TWAS Cen" + }, + { + "author_name": "Xiaodong Tian", + "author_inst": "University of Chinese Academy of Sciences, Beijing 101408, China" + }, + { + "author_name": "Dan-dan Yu", + "author_inst": "Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunm" + }, + { + "author_name": "Xiao-li Feng", + "author_inst": "Kunming National High-Level Biosafety Research Center for Nonhuman Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of" + }, + { + "author_name": "Gong Cheng", + "author_inst": "Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China" + }, + { + "author_name": "Yong-tang Zheng", + "author_inst": "Kunming National High-Level Biosafety Research Center for Nonhuman Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of" + }, + { + "author_name": "Yuhai Bi", + "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early Warning (CASCIRE), CAS-TWAS Cen" + }, + { + "author_name": "Wenjun Liu", + "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early Warning (CASCIRE), CAS-TWAS Cen" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.03.30.437704", "rel_title": "Sequence analysis of SARS-CoV-2 in nasopharyngeal samples from patients with COVID-19 illustrates population variation and diverse phenotypes, placing the in vitro growth properties of B.1.1.7 and B.1.351 lineage viruses in context.", @@ -826581,101 +828268,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.28.21254404", - "rel_title": "Quantitative detection of SARS-CoV-2 B.1.1.7 variant in wastewater by allele-specific RT-qPCR", - "rel_date": "2021-03-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.28.21254404", - "rel_abs": "Wastewater-based epidemiology (WBE) has emerged as a critical public health tool in tracking the SARS-CoV-2 epidemic. Monitoring SARS-CoV-2 variants of concern in wastewater has to-date relied on genomic sequencing, which lacks sensitivity necessary to detect low variant abundances in diluted and mixed wastewater samples. Here, we develop and present an open-source method based on allele specific RT-qPCR (AS RT-qPCR) that detects and quantifies the B.1.1.7 variant, targeting spike protein mutations at three independent genomic loci highly predictive of B.1.1.7 (HV69/70del, Y144del, and A570D). Our assays can reliably detect and quantify low levels of B.1.1.7 with low cross-reactivity, and at variant proportions between 0.1% and 1% in a background of mixed SARS-CoV-2. Applying our method to wastewater samples from the United States, we track B.1.1.7 occurrence over time in 19 communities. AS RT-qPCR results align with clinical trends, and summation of B.1.1.7 and wild-type sequences quantified by our assays strongly correlate with SARS-CoV-2 levels indicated by the US CDC N1/N2 assay. This work paves the path for rapid inexpensive surveillance of B.1.1.7 and other SARS-CoV-2 variants in wastewater.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Wei Lin Lee PhD", - "author_inst": "Singapore-MIT Alliance for Research and Technology" - }, - { - "author_name": "Kyle A McElroy PhD", - "author_inst": "Biobot Analytics, Inc" - }, - { - "author_name": "Federica Armas PhD", - "author_inst": "Singapore-MIT Alliance for Research and Technology" - }, - { - "author_name": "Maxim Imakaev PhD", - "author_inst": "Biobot Analytics, Inc" - }, - { - "author_name": "Xiaoqiong Gu PhD", - "author_inst": "Singapore-MIT Alliance for Research and Technology" - }, - { - "author_name": "Claire Duvallet PhD", - "author_inst": "Biobot Analytics, Inc" - }, - { - "author_name": "Franciscus Chandra", - "author_inst": "Singapore-MIT Alliance for Research and Technology" - }, - { - "author_name": "Hongjie Chen PhD", - "author_inst": "Singapore-MIT Alliance for Research and Technology" - }, - { - "author_name": "Mats Leifels PhD", - "author_inst": "Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore" - }, - { - "author_name": "Samuel Mendola", - "author_inst": "Biobot Analytics, Inc" - }, - { - "author_name": "Roisin Floyd-O Sullivan", - "author_inst": "Biobot Analytics, Inc" - }, - { - "author_name": "Morgan M Powell", - "author_inst": "Biobot Analytics, Inc" - }, - { - "author_name": "Shane T Wilson", - "author_inst": "Biobot Analytics, Inc" - }, - { - "author_name": "Fuqing Wu", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Amy Xiao", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Katya Moniz PhD", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Mariana Matus PhD", - "author_inst": "Biobot Analytics, Inc" - }, - { - "author_name": "Newsha Ghaeli", - "author_inst": "Biobot Analytics, Inc" - }, - { - "author_name": "Janelle Thompson PhD", - "author_inst": "Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore" - }, - { - "author_name": "Eric J Alm PhD", - "author_inst": "Massachusetts Institute of Technology" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.27.21254452", "rel_title": "Risk factors for developing COVID-19: a population-based longitudinal study (COVIDENCE UK)", @@ -827603,6 +829195,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.26.21254394", + "rel_title": "SARS-CoV-2 infection risk among unvaccinated is negatively associated with community-level vaccination rates", + "rel_date": "2021-03-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.26.21254394", + "rel_abs": "Mass vaccination has the potential to curb the current COVID-19 pandemic by protecting vaccinees from the disease and possibly lowering the chance of transmission to unvaccinated individuals. The high effectiveness of the widely-administered BNT162b vaccine in preventing not only the disease but also infection suggests a potential for a population-level effect, critical for disease eradication. However, this putative effect is difficult to observe, especially in light of highly fluctuating spatio-temporal epidemic dynamics. Here, analyzing vaccination records and test results collected during a rapid vaccine rollout for a large population from 223 geographically defined communities, we find that the rates of vaccination in each community are highly correlated with a later decline in infections among a cohort of under 16 years old which are unvaccinated. These results provide observational evidence that vaccination not only protects individual vaccinees but also provides cross-protection to unvaccinated individuals in the community.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Oren Milman", + "author_inst": "Technion - Israel Institute of Technology" + }, + { + "author_name": "Idan Yelin", + "author_inst": "Technion-Israel Institute of Technology" + }, + { + "author_name": "Noga Aharony", + "author_inst": "Technion - Israel Institute of Technology" + }, + { + "author_name": "Rachel Katz", + "author_inst": "Maccabi Healthcare Services" + }, + { + "author_name": "Esma Herzel", + "author_inst": "Maccabi Healthcare Services" + }, + { + "author_name": "Amir Ben-Tov", + "author_inst": "Maccabi Healthcare Services" + }, + { + "author_name": "Jacob Kuint", + "author_inst": "Maccabi Healthcare Services" + }, + { + "author_name": "Sivan Gazit", + "author_inst": "Maccabi Healthcare Services" + }, + { + "author_name": "Gabriel Chodick", + "author_inst": "Maccabi Healthcare Services" + }, + { + "author_name": "Tal Patalon", + "author_inst": "Maccabi Healthcare Services" + }, + { + "author_name": "Roy Kishony", + "author_inst": "Technion - Israel Institute of Technology" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.28.437426", "rel_title": "COVID-19 dominant D614G mutation in the SARS-CoV-2 spike protein desensitizes its temperature-dependent denaturation", @@ -828371,41 +830022,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.25.21254281", - "rel_title": "The new SARS-CoV-2 variant and reinfection in the resurgence of COVID-19 outbreaks in Manaus, Brazil", - "rel_date": "2021-03-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.25.21254281", - "rel_abs": "Manaus, a city of 2.2 million population, the capital of Amazonas state of Brazil was hit badly by two waves of COVID-19 with more than 10,000 severe acute respiratory syndrome deaths by the end of February 2021. It was estimated that the first wave infected over three quarters of the population in Manaus based on routine blood donor data, and the second wave was largely due to reinfection with a new variant named P1 strain. In this work, we revisit these claims, and discuss biological constraints. In particular, we model the two waves with a two-strain model without a significant proportion of reinfections.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Daihai He", - "author_inst": "Hong Kong Polytechnic University" - }, - { - "author_name": "Guihong Fan", - "author_inst": "Columbus State University" - }, - { - "author_name": "Xueying Wang", - "author_inst": "Washington State University" - }, - { - "author_name": "Yingke Li", - "author_inst": "Xinjiang Agriculture University" - }, - { - "author_name": "Zhihang Peng", - "author_inst": "Nanjing Medical University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.25.21254289", "rel_title": "On the association between SARS-COV-2 variants and COVID-19 mortality during the second wave of the pandemic in Europe", @@ -829197,6 +830813,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.20.21253835", + "rel_title": "A small number of early introductions seeded widespread transmission of SARS-CoV-2 in Quebec, Canada", + "rel_date": "2021-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.20.21253835", + "rel_abs": "Using genomic epidemiology, we investigated the arrival of SARS-CoV-2 to Quebec, the Canadian province most impacted by COVID-19, with >280,000 positive cases and >10,000 deaths in a population of 8.5 million as of March 1st, 2021. We report 2,921 high-quality SARS-CoV-2 genomes in the context of >12,000 publicly available genomes sampled globally over the first pandemic wave (up to June 1st, 2020). By combining phylogenetic and phylodynamic analyses with epidemiological data, we quantify the number of introduction events into Quebec, identify their origins, and characterize the spatio-temporal spread of the virus. Conservatively, we estimated at least 500 independent introduction events, the majority of which happened from spring break until two weeks after the Canadian border closed for non-essential travel. Subsequent mass repatriations did not generate large transmission lineages (>50 cases), likely due to mandatory quarantine measures in place at the time. Consistent with common spring break and snowbird destinations, most of the introductions were inferred to have originated from Europe via the Americas. Fewer than 100 viral introductions arrived during spring break, of which 5-10 led to the largest transmission lineages of the first wave (accounting for 36-58% of all sequenced infections). These successful viral transmission lineages dispersed widely across the province, consistent with founder effects and superspreading dynamics. Transmission lineage size was greatly reduced after March 11th, when a quarantine order for returning travelers was enacted. While this suggests the effectiveness of early public health measures, the biggest transmission lineages had already been ignited prior to this order. Combined, our results reinforce how, in the absence of tight travel restrictions or quarantine measures, fewer than 100 viral introductions in a week can ensure the establishment of extended transmission chains.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Carmen L\u00eda Murall", + "author_inst": "McGill University" + }, + { + "author_name": "Eric Fournier", + "author_inst": "Laboratoire de Sant\u00e9 Publique du Qu\u00e9bec" + }, + { + "author_name": "Jose Hector Galvez", + "author_inst": "McGill University" + }, + { + "author_name": "Arnaud N'Guessan", + "author_inst": "University of Montreal" + }, + { + "author_name": "Sarah J Reiling", + "author_inst": "McGill University" + }, + { + "author_name": "Pierre-Olivier Quirion", + "author_inst": "McGill University" + }, + { + "author_name": "Sana Naderi", + "author_inst": "McGill University" + }, + { + "author_name": "Anne-Marie Roy", + "author_inst": "McGill University" + }, + { + "author_name": "Shu-Huang Chen", + "author_inst": "McGill University" + }, + { + "author_name": "Paul Stretenowich", + "author_inst": "McGill University" + }, + { + "author_name": "Mathieu Bourgey", + "author_inst": "McGill University" + }, + { + "author_name": "David Bujold", + "author_inst": "McGill University" + }, + { + "author_name": "Romain Gregoire", + "author_inst": "McGill University" + }, + { + "author_name": "Pierre Lepage", + "author_inst": "McGill University" + }, + { + "author_name": "Janick St-Cyr", + "author_inst": "McGill University" + }, + { + "author_name": "Patrick Willet", + "author_inst": "McGill University" + }, + { + "author_name": "R\u00e9jean Dion", + "author_inst": "Laboratoire de Sant\u00e9 Publique du Qu\u00e9bec" + }, + { + "author_name": "Hugues Charest", + "author_inst": "Laboratoire de Sant\u00e9 Publique du Qu\u00e9bec" + }, + { + "author_name": "Gregory Mark Lathrop", + "author_inst": "McGill University" + }, + { + "author_name": "Michel Roger", + "author_inst": "Laboratoire de Sant\u00e9 Publique du Qu\u00e9bec" + }, + { + "author_name": "Guillaume Bourque", + "author_inst": "McGill University" + }, + { + "author_name": "Jiannis Ragoussis", + "author_inst": "McGill University" + }, + { + "author_name": "B. Jesse Shapiro", + "author_inst": "McGill University" + }, + { + "author_name": "Sandrine Moreira", + "author_inst": "Laboratoire de Sant\u00e9 Publique du Qu\u00e9bec" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.20.21254035", "rel_title": "SARS-CoV-2 Acquisition and Immune Pathogenesis Among School-Aged Learners in Four K-12 Schools", @@ -830421,77 +832148,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.22.21254093", - "rel_title": "Racial/ethnic disparities in sleep in mothers and infants during the Covid-19 pandemic", - "rel_date": "2021-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.22.21254093", - "rel_abs": "Study ObjectivesTo quantify the association between race/ethnicity and maternal and infant self-reported sleep health at 4 months, exploring the role of maternal depression, stress and symptoms of trauma related to the COVID-19 pandemic as potential mediators.\n\nMethodsParticipants were recruited as part of the COVID-19 Mother Baby Outcomes (COMBO) cohort at Columbia University (N=71 non-Hispanic White, N=14 African American (AA), N=113 Hispanic, N=40 other/declined). Data on infant sleep were collected at 4 months postpartum. A subset of 149 women also completed questionnaires assessing maternal mental health and sleep. Multivariable regressions were used to separately estimate associations of race/ethnicity and mental health with multiple sleep domains for infants and mothers adjusting for individual-level covariates.\n\nResultsCompared to non-Hispanic White, Hispanic infants slept less at night ({beta}=- 101.7{+/-}17.6, p<0.0001) and AA and Hispanic infants went to bed later (respectively {beta} =1.9{+/-}0.6, p<0.0001, {beta}=1.7{+/-}0.3, p<0.0001). Hispanic mothers were less likely to perceive infant sleep as a problem ({beta}=1.0{+/-}0.3, p=0.006). Compared to non-Hispanic White mothers, Hispanic mothers reported worse maternal sleep latency ({beta}=1.2{+/-}0.4, p=0.002), and efficiency ({beta}=0.8{+/-}0.4, p=0.03), but better subjective sleep quality ({beta}=-0.7{+/-}0.4, p=0.05), and less daytime dysfunction ({beta}=-0.8{+/-}0.4, p=0.04). Maternal mental health scores were statistically significant predictors of multiple domains of maternal sleep but did not mediate the association between race/ethnicity and sleep.\n\nConclusionsRacial/ethnic disparities in maternal and infant sleep are observable at 4 months post-partum. Maternal stress, depression and symptoms of trauma related to the COVID-19 pandemic did not mediate these associations.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Maristella Lucchini", - "author_inst": "Division of Developmental Neuroscience, Psychiatry Department, Columbia University Irving Medical Center, New York, NY USA" - }, - { - "author_name": "Margaret Kyle", - "author_inst": "Division of Developmental Neuroscience, Psychiatry Department, Columbia University Irving Medical Center, New York, NY USA" - }, - { - "author_name": "Nicol\u00f3 Pini", - "author_inst": "Division of Developmental Neuroscience, Psychiatry Department, Columbia University Irving Medical Center, New York, NY USA" - }, - { - "author_name": "Ayesha Sania", - "author_inst": "Division of Developmental Neuroscience, Psychiatry Department, Columbia University Irving Medical Center, New York, NY USA" - }, - { - "author_name": "Vanessa Babineau", - "author_inst": "Division of Developmental Neuroscience, Psychiatry Department, Columbia University Irving Medical Center, New York, NY USA" - }, - { - "author_name": "Morgan R. Firestein", - "author_inst": "Division of Developmental Neuroscience, Psychiatry Department, Columbia University Irving Medical Center, New York, NY USA" - }, - { - "author_name": "Cristina R Fern\u00e1ndez", - "author_inst": "Division of Child and Adolescent Health, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY USA" - }, - { - "author_name": "Lauren C Shuffrey", - "author_inst": "Division of Developmental Neuroscience, Psychiatry Department, Columbia University Irving Medical Center, New York, NY USA" - }, - { - "author_name": "Jennifer R Barbosa", - "author_inst": "Division of Developmental Neuroscience, Psychiatry Department, Columbia University Irving Medical Center, New York, NY USA" - }, - { - "author_name": "Cynthia Rodriguez", - "author_inst": "New York State Psychiatric Institute, New York, NY" - }, - { - "author_name": "William P Fifer", - "author_inst": "Division of Developmental Neuroscience, Psychiatry Department, Columbia University Irving Medical Center, New York, NY USA" - }, - { - "author_name": "Carmela Alc\u00e1tara", - "author_inst": "School of Social Work, Columbia University, New York, NY USA" - }, - { - "author_name": "Catherine Monk", - "author_inst": "Division of Developmental Neuroscience, Psychiatry Department, Columbia University Irving Medical Center, New York, NY USA" - }, - { - "author_name": "Dani Dumitriu", - "author_inst": "Division of Child and Adolescent Health, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2021.03.22.21254130", "rel_title": "Trends, patterns and psychological influences on COVID-19 vaccination intention: findings from a large prospective community cohort study in England and Wales (Virus Watch)", @@ -831351,6 +833007,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.22.21254140", + "rel_title": "Feasibility and effectiveness of daily temperature screening to detect COVID-19 in a large public university setting", + "rel_date": "2021-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.22.21254140", + "rel_abs": "BackgroundMany persons with active SARS-CoV-2 infection experience mild or no symptoms, presenting barriers to COVID-19 prevention. Regular temperature screening is nonetheless used in some settings, including University campuses, to reduce transmission potential. We evaluated the potential impact of this strategy using a prospective University-affiliated cohort.\n\nMethodsBetween June and August 2020, 2,912 participants were enrolled and tested for SARS-CoV-2 by PCR at least once (median: 3, range: 1-9). Participants reported temperature and symptoms daily via electronic survey using a previously owned or study-provided thermometer. We assessed feasibility and acceptability of daily temperature monitoring, calculated sensitivity and specificity of various fever-based strategies for restricting campus access to reduce transmission, and estimated the association between measured temperature and SARS-CoV-2 test positivity using a longitudinal binomial mixed model.\n\nResultsMost participants (70.2%) did not initially have a thermometer for taking their temperature daily. Across 5481 total person months, the average daily completion rate of temperature values was 61.6% (IQR: 41.8%-86.2%). Sensitivity for SARS-CoV-2 ranged from 0% (95%CI 0-9.7%) to 40.5% (95%CI 25.6-56.7%) across all strategies for self-report of possible COVID-19 symptoms on day of specimen collection, with corresponding specificity of 99.9% (95%CI 99.8-100%) to 95.3% (95%CI 94.7-95.9%). An increase of 0.1{degrees}F in individual mean body temperature on the same day as specimen collection was associated with 1.11 increased odds of SARS-CoV-2 positivity (95%CI 1.06-1.17).\n\nConclusionsDaily temperature monitoring was feasible and acceptable; however, the majority of potentially infectious individuals were not detected by temperature monitoring, suggesting that temperature screening is insufficient as a primary means of detection to reduce transmission of SARS-CoV-2.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Shelley N Facente", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Lauren A. Hunter", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Laura J. Packel", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Yi Li", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Anna Harte", + "author_inst": "University Health Services, University of California Berkeley" + }, + { + "author_name": "Guy Nicolette", + "author_inst": "University Health Services, University of California Berkeley" + }, + { + "author_name": "Shana McDevitt", + "author_inst": "Innovative Genomics Institute, University of California Berkeley" + }, + { + "author_name": "Maya Petersen", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Arthur L. Reingold", + "author_inst": "University of California, Berkeley" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.22.21254125", "rel_title": "Testing and Vaccination to Reduce the Impact of COVID-19 in Nursing Homes: An Agent-Based Approach", @@ -832327,65 +834034,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.23.21253520", - "rel_title": "Optimizing SARS-CoV-2 Variant of Concern Screening: Experience from British Columbia, Canada, Early 2021", - "rel_date": "2021-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.23.21253520", - "rel_abs": "Comprehensive and timely testing is required for SARS-CoV-2 variant of concern (VoC) screening. Whole genome sequencing (WGS) provides the broadest means to detect circulating VoCs, but requires longer turnaround time than targeted molecular testing by quantitative polymerase chain reaction (qPCR). We demonstrated the feasibility of a combined testing approach for VoC prevalence assessment in British Columbia, and showed high concordance between qPCR testing and WGS. This directly informed wider VoC screening strategy implementation, and public health efforts.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Catherine A Hogan", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Hind Sbihi", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Agatha Jassem", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Natalie Prystajecky", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "John R Tyson", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Tracy D Lee", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Frankie Tsang", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Loretta Janz", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Corrinne Ng", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Marc G Romney", - "author_inst": "St. Paul's Hospital" - }, - { - "author_name": "Linda Hoang", - "author_inst": "BC Centre for Disease Control" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.23.21254172", "rel_title": "Shielding of Viruses such as SARS-CoV-2 from Ultraviolet Radiation in Particles Generated by Sneezing or Coughing: Numerical Simulations of Survival Fractions", @@ -832973,6 +834621,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.25.21254344", + "rel_title": "Wastewater monitoring outperforms case numbers as a tool to track COVID-19 incidence dynamics when test positivity rates are high", + "rel_date": "2021-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.25.21254344", + "rel_abs": "Wastewater-based epidemiology (WBE) has been shown to coincide with, or anticipate, confirmed COVID-19 case numbers. During periods with high test positivity rates, however, case numbers may be underreported, whereas wastewater does not suffer from this limitation. Here we investigated how the dynamics of new COVID-19 infections estimated based on wastewater monitoring or confirmed cases compare to true COVID-19 incidence dynamics. We focused on the first pandemic wave in Switzerland (February to April, 2020), when test positivity ranged up to 26%. SARS-CoV-2 RNA loads were determined 2-4 times per week in three Swiss wastewater treatment plants (Lugano, Lausanne and Zurich). Wastewater and case data were combined with a shedding load distribution and an infection-to-case confirmation delay distribution, respectively, to estimate incidence dynamics. Finally, the estimates were compared to reference incidence dynamics determined by a validated compartmental model. Incidence dynamics estimated based on wastewater data were found to better track the timing and shape of the reference infection peak compared to estimates based on confirmed cases. In contrast, case confirmations provided a better estimate of the subsequent decline in infections. Under a regime of high-test positivity rates, WBE thus provides critical information that is complementary to clinical data to monitor the pandemic trajectory.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Xavier Fernandez-Cassi", + "author_inst": "EPFL" + }, + { + "author_name": "Andreas Scheidegger", + "author_inst": "Eawag" + }, + { + "author_name": "Carola Baenziger", + "author_inst": "Eawag" + }, + { + "author_name": "Federica Cariti", + "author_inst": "EPFL" + }, + { + "author_name": "Alex Tunas Corzon", + "author_inst": "EPFL" + }, + { + "author_name": "Pravin Ganesanandamoorthy", + "author_inst": "Eawag" + }, + { + "author_name": "Joseph Chadi Lemaitre", + "author_inst": "EPFL" + }, + { + "author_name": "Christoph Ort", + "author_inst": "Eawag" + }, + { + "author_name": "Timothy R Julian", + "author_inst": "Eawag" + }, + { + "author_name": "Tamar Kohn", + "author_inst": "EPFL" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.24.21254227", "rel_title": "COVID-19 Vaccination Prioritization Based on Cardiovascular Risk Factors and Number-Needed-to-Vaccinate to Prevent Death", @@ -833841,33 +835544,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.25.21254356", - "rel_title": "Molecular beacons allow specific RT-LAMP detection of B.1.1.7 variant SARS-CoV-2", - "rel_date": "2021-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.25.21254356", - "rel_abs": "Over the course of the COVID-19 pandemic, several SARS-CoV-2 genetic variants of concern have appeared and spread throughout the world. Detection and identification of these variants is important to understanding and controlling their rapid spread. Current detection methods for a particularly concerning variant, B.1.1.7, require expensive qPCR machines and depend on the absence of a signal rather than a positive indicator of variant presence. Here we report an assay using a pair of molecular beacons paired with reverse transcription loop mediated amplification to allow isothermal amplification from saliva to specifically detect B.1.1.7 and other variants which contain a characteristic deletion in the gene encoding the viral spike protein. This assay is specific, affordable and allows multiplexing with other SARS-CoV-2 LAMP primer sets.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Scott Sherrill-Mix", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Gregory D Van Duyne", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Frederic D Bushman", - "author_inst": "University of Pennsylvania" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.23.21253873", "rel_title": "Estimated Deaths, Intensive Care Admissions and Hospitalizations Averted in Canada during the COVID-19 Pandemic", @@ -834563,6 +836239,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.26.21254385", + "rel_title": "On discrete time epidemic models in Kermack-McKendrick form", + "rel_date": "2021-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.26.21254385", + "rel_abs": "Surprisingly, the discrete-time version of the general 1927 Kermack-McKendrick epidemic model has, to our knowledge, not been formulated in the literature, and we rectify this omission here. The discrete time version is as general and flexible as its continuous-time counterpart, and contains numerous compartmental models as special cases. In contrast to the continuous time version, the discrete time version of the model is very easy to implement computationally, and thus promises to become a powerful tool for exploring control scenarios for specific infectious diseases. To demonstrate the potential, we investigate numerically how the incidence-peak size depends on model ingredients. We find that, with the same reproduction number and initial speed of epidemic spread, compartmental models systematically predict lower peak sizes than models that use a fixed duration for the latent and infectious periods.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Odo Diekmann", + "author_inst": "Utrecht University" + }, + { + "author_name": "Hans G. Othmer", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Robert Planque", + "author_inst": "Vrije Universiteit Amsterdam" + }, + { + "author_name": "Martin CJ Bootsma", + "author_inst": "Utrecht University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.25.21254315", "rel_title": "Characterizing the incidence of adverse events of special interest for COVID-19 vaccines across eight countries: a multinational network cohort study", @@ -835471,37 +837178,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.03.25.21254310", - "rel_title": "Is the vitamin D status of patients with COVID-19 associated with reduced mortality?", - "rel_date": "2021-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.25.21254310", - "rel_abs": "ObjectiveA systematic review with meta-analysis was performed to assess a possible association between plasma vitamin D levels and mortality in patients with COVID - 19.\n\nMethodsPubMed, EMBASE, and Cochrane Library databases were searched. Studies involving COVID-19 patients that reported an association between plasma vitamin D levels and COVID-19 mortality published until February 5, 2020, were included. The risk ratio (RR) and confidence interval (CI) were pooled using a fixed-effects or random-effects model.\n\nResultsA total of 11 studies that measured plasma vitamin D levels at admission were included in the meta-analysis, ten cohorts and one case-controls. Low plasma vitamin D levels (25(OH)D) in patients with COVID-19 were not associated with mortality (RR=1.35, 95%CI 0.84-1.86). Subgroup analysis by vitamin D cut-off (<20 or 25 ng/ml and <10 or 12 ng/ml) showed were not associated with mortality. When the RR in mortality analysis was calculated included four studies that did not perform adjusted analysis for confounding factors, the result was 1.43 (95% CI 1.18-1.69), suggesting that confounders may have led many observational studies to incorrectly estimate the association between vitamin D status and mortality in COVID-19 patients.\n\nConclusionDeficient vitamin D levels were not associated with a higher mortality rate in patients with COVID-19. Randomized clinical trials are needed to assess this association.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Paulo R Bignardi", - "author_inst": "Pontifical Catholic University of Parana - Londrina - Brazil" - }, - { - "author_name": "Paula Andrade Castello", - "author_inst": "Pontifical Catholic University of Parana - Londrina - Brazil" - }, - { - "author_name": "Bruno Matos Aquino", - "author_inst": "Pontifical Catholic University of Parana - Londrina - Brazil" - }, - { - "author_name": "Vinicius Daher Alvares Delfino", - "author_inst": "State University of Londrina - Parana - Brazil" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.24.21253587", "rel_title": "Genetic epidemiology of SARS-CoV-2 transmission in renal dialysis units - a high risk community-hospital interface", @@ -836349,6 +838025,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2021.03.19.21253675", + "rel_title": "System-wide hematopoietic and immune signaling aberrations in COVID-19 revealed by deep proteome and phosphoproteome analysis", + "rel_date": "2021-03-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21253675", + "rel_abs": "The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has become a global crisis. To gain systems-level insights into its pathogenesis, we compared the blood proteome and phosphoproteome of ICU patients with or without SARS-CoV-2 infection, and healthy control subjects by quantitative mass spectrometry. We find that COVID-19 is marked with hyperactive T cell and B cell signaling, compromised innate immune response, and dysregulated inflammation, coagulation, metabolism, RNA splicing, transcription and translation pathways. SARS-CoV-2 infection causes global reprogramming of the kinome and kinase-substrate network, resulting in defective antiviral defense via the CK2-OPN-IL-12/IFN-/{beta} axis, lymphocyte cell death via aberrant JAK/STAT signaling, and inactivation of innate immune cells via inhibitory SIRPA, SIGLEC and SLAM family receptor signaling. Our work identifies CK2, SYK, JAK3, TYK2 and IL-12 as potential targets for immunomodulatory treatment of severe COVID-19 and provides a valuable approach and resource for deciphering the mechanism of pathogen-host interactions.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Tomonori Kaneko", + "author_inst": "Western University" + }, + { + "author_name": "Sally Esmail", + "author_inst": "Western University" + }, + { + "author_name": "Courtney Voss", + "author_inst": "Western University" + }, + { + "author_name": "Claudio M Martin", + "author_inst": "Western University" + }, + { + "author_name": "Marat Slessarev", + "author_inst": "Western University" + }, + { + "author_name": "Owen Hovey", + "author_inst": "Western University" + }, + { + "author_name": "Xuguang Liu", + "author_inst": "Western University" + }, + { + "author_name": "Mingliang Ye", + "author_inst": "Dalian Institute of Chemical Physics" + }, + { + "author_name": "Sung Kim", + "author_inst": "Western University" + }, + { + "author_name": "Douglas Fraser", + "author_inst": "Western University" + }, + { + "author_name": "Shawn SC Li", + "author_inst": "Western University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.20.21253990", "rel_title": "Changes in live births, preterm birth, low birth weight, and cesarean deliveries in the United States during the SARS-CoV-2 pandemic", @@ -837460,101 +839195,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.03.19.21253680", - "rel_title": "Population homogeneity for the antibody response to COVID-19 Comirnaty vaccine is only reached after the second dose", - "rel_date": "2021-03-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21253680", - "rel_abs": "While mRNA vaccines authorized for emergency use are administrated worldwide in an effort to contain the COVID19 crisis, little is known about the heterogeneity of the immune response they induce. Here, we report the first 6 weeks of a longitudinal study that quantifies the humoral immune response to BNT162b2 mRNA COVID-19 (Pfizer/BioNTech, Comirnaty) in 1245 health care providers, the Lx1000HCW-PZF cohort. We reveal a striking inter-individual variation 3 weeks after the 1st dose administration that only in part related to age and sex. While population homogeneity in robust IgG responses was reached upon 2nd dose administration, IgM and IgA levels remain low and heterogenous. Our findings of isotypic and heterogenous antibody responses to Comirnaty highlight the need for evaluating the efficacy of COVID-19 mRNA vaccine in preventing infection aside disease, and - contrary to what has been proposed - advocate for the interval between the two doses not to be extended.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Joao F Viana", - "author_inst": "Centro Hospitalar de Lisboa Ocidental" - }, - { - "author_name": "Marie-Louise Bergman", - "author_inst": "Instituto Gulbenkian de Ciencia" - }, - { - "author_name": "Ligia A Gon\u00e7alves", - "author_inst": "Instituto Gulbenkian de Ciencia" - }, - { - "author_name": "Nadia Duarte", - "author_inst": "Instituto Gulbenkian de Ciencia" - }, - { - "author_name": "Teresa Penha Coutinho", - "author_inst": "Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal" - }, - { - "author_name": "Patricia C Borges", - "author_inst": "Instituto Gulbenkian de Ciencia" - }, - { - "author_name": "Christian Diwo", - "author_inst": "Instituto Gulbenkian de Ciencia" - }, - { - "author_name": "Rute Castro", - "author_inst": "Instituto de Biologia Experimental e Tecnologica" - }, - { - "author_name": "Paula Matoso", - "author_inst": "Instituto Gulbenkian de Ciencia" - }, - { - "author_name": "Vanessa Malheiro", - "author_inst": "Instituto Gulbenkian de Ciencia" - }, - { - "author_name": "Ana Brennand", - "author_inst": "Instituto Gulbenkian de Ciencia" - }, - { - "author_name": "Lindsay Kosack", - "author_inst": "Instituto Gulbenkian de Ciencia" - }, - { - "author_name": "Onome Akpogheneta", - "author_inst": "Instituto Gulbenkian de Ciencia" - }, - { - "author_name": "Joao M Figueira", - "author_inst": "Centro Hospitalar de Lisboa Ocidental" - }, - { - "author_name": "Concei\u00e7ao Cardoso", - "author_inst": "Centro Hospitalar de Lisboa Ocidental" - }, - { - "author_name": "Ana M Casaca", - "author_inst": "Centro Hospitalar de Lisboa Ocidental" - }, - { - "author_name": "Paula M Alves", - "author_inst": "Instituto de Biologia Experimental e Tecnologica" - }, - { - "author_name": "Telmo Nunes", - "author_inst": "Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portuga" - }, - { - "author_name": "Carlos Penha-Gon\u00e7alves", - "author_inst": "Instituto Gulbenkian de Ciencia" - }, - { - "author_name": "Jocelyne Demengeot", - "author_inst": "Instituto Gulbenkian de Ciencia" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.19.21253620", "rel_title": "SARS-CoV-2 genome sequencing from COVID-19 in Ecuadorian patients: a whole country analysis.", @@ -838250,6 +839890,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.19.21253922", + "rel_title": "Recalibrating SARS-CoV-2 antigen rapid lateral flow test relative sensitivity from validation studies to absolute sensitivity for detecting individuals with live virus", + "rel_date": "2021-03-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21253922", + "rel_abs": "Testing for SARS-CoV-2 internationally has focused on COVID-19 diagnosis among symptomatic individuals using reverse transcriptase polymerase chain reaction (PCR) tests. Recently, however, SARS-CoV-2 antigen rapid lateral flow tests (LFT) have been rolled out in several countries for testing asymptomatic individuals in public health programmes. Validation studies for LFT have been largely cross-sectional, reporting sensitivity, specificity and predictive values of LFT relative to PCR. However, because PCR detects genetic material left behind for a long period when the individual is no longer infectious, these statistics can under-represent sensitivity of LFT for detecting infectious individuals, especially when sampling asymptomatic populations. LFTs (intended to detect individuals with live virus) validated against PCR (intended to diagnose infection) are not reporting against a gold standard of equivalent measurements. Instead, these validation studies have reported relative performance statistics that need recalibrating to the purpose for which LFT is being used. We present an approach to this recalibration.\n\nWe derive a formula for recalibrating relative performance statistics from LFT vs PCR validation studies to give likely absolute sensitivity of LFT for detecting individuals with live virus. We show the differences between widely reported apparent sensitivities of LFT and its absolute sensitivity as a test of presence of live virus. After accounting for within-individual viral kinetics and epidemic dynamics within asymptomatic populations we show that a highly performant test of live virus should show a LFT-to-PCR relative sensitivity of less than 50% in conventional validation studies, which after re-calibration would be an absolute sensitivity of more than 80%.\n\nFurther studies are needed to ascertain the absolute sensitivity of LFT as a test of infectiousness in COVID-19 responses. These studies should include sampling for viral cultures and longitudinal series of LFT and PCR, ideally in cohorts sampled from both contacts of cases and the general population.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Irene Petersen", + "author_inst": "UCL" + }, + { + "author_name": "Alexander Crozier", + "author_inst": "UCL" + }, + { + "author_name": "Iain Buchan", + "author_inst": "Liverpool University" + }, + { + "author_name": "Michael J Mina", + "author_inst": "Harvard School of Public Health" + }, + { + "author_name": "Jonathan W Bartlett", + "author_inst": "University of Bath" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.16.21253662", "rel_title": "WiFi mobility models for COVID-19 enable less burdensome and more localized interventions for university campuses", @@ -839218,65 +840893,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.03.24.435771", - "rel_title": "3D visualization of SARS-CoV-2 infection and receptor distribution in Syrian hamster lung lobes display distinct spatial arrangements", - "rel_date": "2021-03-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.24.435771", - "rel_abs": "SARS-CoV-2 attaches to angiotensin-converting enzyme 2 (ACE2) to gain entry into cells after which the spike protein is cleaved by the transmembrane serine protease 2 (TMPRRS2) to facilitate viral-host membrane fusion. ACE2 and TMPRRS2 expression profiles have been analyzed at the genomic, transcriptomic, and single-cell RNAseq level, however, biologically relevant protein receptor organization in whole tissues is still poorly understood. To describe the organ-level architecture of receptor expression, related to the ability of ACE2 and TMPRRS2 to mediate infectivity, we performed a volumetric analysis of whole Syrian hamster lung lobes. Lung tissue of infected and control animals were stained using antibodies against ACE2 and TMPRRS2, combined with fluorescent spike protein and SARS-CoV-2 nucleoprotein staining. This was followed by light-sheet microscopy imaging to visualize expression patterns. The data demonstrates that infection is restricted to sites with both ACE2 and TMPRRS2, the latter is expressed in the primary and secondary bronchi whereas ACE2 is predominantly observed in the terminal bronchioles and alveoli. Conversely, infection completely overlaps at these sites where ACE2 and TMPRSS2 co-localize.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=154 SRC=\"FIGDIR/small/435771v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (60K):\norg.highwire.dtl.DTLVardef@150fc65org.highwire.dtl.DTLVardef@1ea6a56org.highwire.dtl.DTLVardef@eb3c43org.highwire.dtl.DTLVardef@1c1877e_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Ilhan Tomris", - "author_inst": "Utrecht University" - }, - { - "author_name": "Kim M Bouwman", - "author_inst": "Utrecht University" - }, - { - "author_name": "Youri Adolfs", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Danny Noack", - "author_inst": "Erasmus Medical Center" - }, - { - "author_name": "Roosmarijn van der Woude", - "author_inst": "Utrecht University" - }, - { - "author_name": "Sander Herfst", - "author_inst": "ErasmusMC" - }, - { - "author_name": "Geert-Jan Boons", - "author_inst": "University of Georgia" - }, - { - "author_name": "Bart Haagmans", - "author_inst": "Erasmus Medical Center" - }, - { - "author_name": "R. Jeroen Pasterkamp", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Barry Rockx", - "author_inst": "Erasmus University Medical Center" - }, - { - "author_name": "Robert Paul de Vries", - "author_inst": "Utrecht Institute for Pharmaceutical Sciences, Utrecht University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.03.23.436686", "rel_title": "Untangling the cell immune response dynamic for severe and critical cases of SARS-CoV-2 infection", @@ -839949,6 +841565,20 @@ "type": "PUBLISHAHEADOFPRINT", "category": "surgery" }, + { + "rel_doi": "10.1101/2021.03.23.21254170", + "rel_title": "What Explains the Socioeconomic Status-Health Gradient? Evidence from Workplace COVID-19 Infections", + "rel_date": "2021-03-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.23.21254170", + "rel_abs": "This paper studies the contribution of the workplace to the SES-health gradient. Our analysis is based on a unique dataset that tracks various health outcomes and workplace risks among healthcare workers during the first four months of the coronavirus 2019 (COVID-19) pandemic. The setting provides an exceptional opportunity to test for work-related disparities in health, while controlling for confounding determinants of the SES-health gradient. We find that low-SES nurses were systematically more likely to contract COVID-19 as a result of workplace exposure. These differentials existed in all healthcare institutions, but were particularly large in non-hospital settings. In contrast, we find no relationship between SES and non work-related infection rates. The differences in workplace infection rates are substantially larger than those implied by standard task-based indices of transmission risk, and cannot be attributable to easily identifiable metrics of workplace risk. Together, our results show how subtle differences in work conditions or job duties can substantially contribute to the SES-health gradient.", + "rel_num_authors": 0, + "rel_authors": null, + "version": "1", + "license": "", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2021.03.20.21253397", "rel_title": "Incidence of and factors associated with SARS-CoV-2 infection among people living with HIV in Southern Spain", @@ -840755,125 +842385,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.18.21253778", - "rel_title": "Alpha-1 blockers and susceptibility to COVID-19 in benign prostate hyperplasia patients : an international cohort study", - "rel_date": "2021-03-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.18.21253778", - "rel_abs": "Alpha-1 blockers, often used to treat benign prostate hyperplasia (BPH), have been hypothesized to prevent COVID-19 complications by minimising cytokine storms release. We conducted a prevalent-user active-comparator cohort study to assess association between alpha-1 blocker use and risks of three COVID-19 outcomes: diagnosis, hospitalization, and hospitalization requiring intensive services. Our study included 2.6 and 0.46 million users of alpha-1 blockers and of alternative BPH therapy during the period between November 2019 and January 2020, found in electronic health records from Spain (SIDIAP) and the United States (Department of Veterans Affairs, Columbia University Irving Medical Center, IQVIA OpenClaims, Optum DOD, Optum EHR). We estimated hazard ratios using state-of-the-art techniques to minimize potential confounding, including large-scale propensity score matching/stratification and negative control calibration. We found no differential risk for any of COVID-19 outcome, pointing to the need for further research on potential COVID-19 therapies.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Akihiko Nishimura", - "author_inst": "Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA" - }, - { - "author_name": "Junqing Xie", - "author_inst": "Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Oxford University, Oxford, UK" - }, - { - "author_name": "Kristin Kostka", - "author_inst": "Real World Solutions, IQVIA, Cambridge, MA, USA .\tThe OHDSI Center at The Roux Institute, Northeastern University, Portland, ME, USA" - }, - { - "author_name": "Talita Duarte-Salles", - "author_inst": "Fundaci\u00f3 Institut Universitari per a la recerca a l'Atenci\u00f3 Prim\u00e1ria de Salut Jordi Gol i Gurina, (IDIAPJGol), Barcelona, Spain" - }, - { - "author_name": "Sergio Fernandez Bertolin", - "author_inst": "Fundaci\u00f3 Institut Universitari per a la recerca a \u013aAtenci\u00f3 Prim\u00e1ria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain" - }, - { - "author_name": "Maria Aragon", - "author_inst": "Fundaci\u00f3 Institut Universitari per a la recerca a \u013aAtenci\u00f3Prim\u00e1ria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain" - }, - { - "author_name": "Clair Blacketer", - "author_inst": "Observational Health Data Analytics, Janssen Research and Development, Titusville, NJ, USA" - }, - { - "author_name": "Azza Shoaibi", - "author_inst": "Observational Health Data Analytics, Janssen Research and Development, Titusville, NJ, USA" - }, - { - "author_name": "Scott L Duvall", - "author_inst": "VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT, USA. Department of Internal Medicine, University of Utah " - }, - { - "author_name": "Kristine E. Lynch", - "author_inst": "VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT, USA . Department of Internal Medicine, University of Utah" - }, - { - "author_name": "Michael E. Matheny", - "author_inst": "Tennessee Valley Healthcare System, Veterans Affairs Medical Center, Nashville, TN, USA . Department of Biomedical Informatics, Vanderbilt University Medical Ce" - }, - { - "author_name": "Thomas Falconer", - "author_inst": "Department of Biomedical Informatics, Columbia University, New York, USA" - }, - { - "author_name": "Daniel R Morales", - "author_inst": "Division of Population Health and Genomics, University of Dundee, UK . Department of Public Health, University of Southern Denmark, Denmark" - }, - { - "author_name": "Mitchell M Conover", - "author_inst": "Observational Health Data Analytics, Janssen Research and Development, Titusville, NJ, USA" - }, - { - "author_name": "Seng Chan You", - "author_inst": "Department of Preventive Medicine and Public Health, Yonsei University College of Medicine, Seoul, Korea" - }, - { - "author_name": "Nicole Pratt", - "author_inst": "Quality Use of Medicines and Pharmacy Research Centre, Clinical and Health Sciences, University of South Australia, Adelaide, Australia" - }, - { - "author_name": "James Weaver", - "author_inst": "Observational Health Data Analytics, Janssen Research and Development, Titusville, NJ, USA" - }, - { - "author_name": "Anthony G. Sena", - "author_inst": "Observational Health Data Analytics, Janssen Research and Development, Titusville, NJ, USA . Department of Medical Informatics, Erasmus University Medical Cente" - }, - { - "author_name": "Martijn J Schuemie", - "author_inst": "Observational Health Data Analytics, Janssen Research and Development, Titusville, NJ, USA. Department of Biostatistics, UCLA Fielding School of Public Health, " - }, - { - "author_name": "Jenna Reps", - "author_inst": "Observational Health Data Analytics, Janssen Research and Development, Titusville, NJ, USA" - }, - { - "author_name": "Christian Reich", - "author_inst": "Real World Solutions, IQVIA, Cambridge, MA, USA" - }, - { - "author_name": "Peter R Rijnbeek", - "author_inst": "Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands" - }, - { - "author_name": "Patrick B Ryan", - "author_inst": "Observational Health Data Analytics, Janssen Research and Development, Titusville, NJ, USA" - }, - { - "author_name": "George Hripcsak", - "author_inst": "Department of Biomedical Informatics, Columbia University, New York, USA" - }, - { - "author_name": "DANIEL PRIETO-ALHAMBRA", - "author_inst": "Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Oxford University, Oxford, UK" - }, - { - "author_name": "Marc A Suchard", - "author_inst": "Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA. Department of Computational Med" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.16.21253634", "rel_title": "Pre-pandemic Cognitive Function and COVID-19 Vaccine Hesitancy: Prospective Cohort Study", @@ -841813,6 +843324,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.03.15.21253549", + "rel_title": "Impact of Clinical and Genomic Factors on SARS-CoV2 Disease Severity", + "rel_date": "2021-03-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.15.21253549", + "rel_abs": "The SARS-CoV2 virus behind the COVID-19 pandemic is manifesting itself in different ways among infected people. While many are experiencing mild flue-like symptoms or are even remaining asymptomatic after infection, the virus has also led to serious complications, overloading ICUs while claiming more than 2.6 million lives world-wide. In this work, we apply AI methods to better understand factors that drive the severity of the disease. From the UK BioBank dataset we analyzed both clinical and genomic data of patients infected by this virus. Leveraging positive-unlabeled machine learning algorithms coupled with RubricOE, a state-of-the-art genomic analysis framework for genomic feature extraction, we propose severity prediction algorithms with high F1 score. Furthermore, we extracted insights on clinical and genomic factors driving the severity prediction. We also report on how these factors have evolved during the pandemic w.r.t. significant events such as the emergence of the B.1.1.7 SARS-CoV2 virus strain.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Sanjoy Dey", + "author_inst": "IBM Research" + }, + { + "author_name": "Aritra Bose", + "author_inst": "IBM Research" + }, + { + "author_name": "Prithwish Chakraborty", + "author_inst": "IBM Research" + }, + { + "author_name": "Mohamed Ghalwash", + "author_inst": "IBM Research" + }, + { + "author_name": "Aldo Guzman Saenz", + "author_inst": "IBM Research" + }, + { + "author_name": "Filipp Ultro", + "author_inst": "IBM Research" + }, + { + "author_name": "Kenney NG", + "author_inst": "IBM Research" + }, + { + "author_name": "Jianying Hu", + "author_inst": "IBM Research" + }, + { + "author_name": "Laxmi Parida", + "author_inst": "IBM Research" + }, + { + "author_name": "Daby Sow", + "author_inst": "IBM Research" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2021.03.16.21253371", "rel_title": "Axes of Prognosis: Identifying Subtypes of COVID-19 Outcomes", @@ -842805,81 +844371,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.20.21252680", - "rel_title": "Age-related changes in the upper respiratory microbiome are associated with SARS-CoV-2 susceptibility and illness severity", - "rel_date": "2021-03-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.20.21252680", - "rel_abs": "Children are less susceptible to SARS-CoV-2 and typically have milder illness courses than adults. We studied the nasopharyngeal microbiomes of 274 children, adolescents, and young adults with SARS-CoV-2 exposure using 16S rRNA gene sequencing. We find that higher abundances of Corynebacterium species are associated with SARS-CoV-2 infection and SARS-CoV-2-associated respiratory symptoms, while higher abundances of Dolosigranulum pigrum are present in SARS-CoV-2-infected individuals without respiratory symptoms. We also demonstrate that the abundances of these bacteria are strongly, and independently, associated with age, suggesting that the nasopharyngeal microbiome may be a potentially modifiable mechanism by which age influences SARS-CoV-2 susceptibility and severity.\n\nSummaryEvaluation of nasopharyngeal microbiome profiles in children, adolescents, and young adults with a SARS-CoV-2-infected close contact identified specific bacterial species that vary in abundance with age and are associated with SARS-CoV-2 susceptibility and the presence of SARS-CoV-2-associated respiratory symptoms.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Jillian H. Hurst", - "author_inst": "Duke University" - }, - { - "author_name": "Alexander W. McCumber", - "author_inst": "Duke University" - }, - { - "author_name": "Jhoanna N. Aquino", - "author_inst": "Duke University" - }, - { - "author_name": "Javier Rodriguez", - "author_inst": "Duke University" - }, - { - "author_name": "Sarah M. Heston", - "author_inst": "Duke University" - }, - { - "author_name": "Debra J. Lugo", - "author_inst": "Duke University" - }, - { - "author_name": "Alexandre T. Rotta", - "author_inst": "Duke University" - }, - { - "author_name": "Nicholas A. Turner", - "author_inst": "Duke University" - }, - { - "author_name": "Trevor S. Pfeiffer", - "author_inst": "Duke University" - }, - { - "author_name": "Thaddeus C. Gurley", - "author_inst": "Duke University" - }, - { - "author_name": "M. Anthony Moody", - "author_inst": "Duke University" - }, - { - "author_name": "Thomas N. Denny", - "author_inst": "Duke University" - }, - { - "author_name": "John F Rawls", - "author_inst": "Duke University" - }, - { - "author_name": "Christopher W. Woods", - "author_inst": "Duke University School of Medicine" - }, - { - "author_name": "Matthew S. Kelly", - "author_inst": "Duke University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.22.436379", "rel_title": "Antidepressant and antipsychotic drugs reduce viral infection by SARS-CoV-2 and fluoxetine show antiviral activity against the novel variants in vitro", @@ -843899,6 +845390,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.22.436405", + "rel_title": "Recurrence quantification analysis of heart rate variability is a COVID-safe alternative to gas analysis in the detection of metabolic thresholds", + "rel_date": "2021-03-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.22.436405", + "rel_abs": "The first aim of the study was to verify if in individuals with different physical fitness levels the Recurrence Quantification Analysis (RQA) of Heart Rate Variability (HRV) time series could be an alternative to Gas Exchange (GE) analysis in the determination of metabolic thresholds. The second aim was to investigate the validity of the RQA method compared to the GE method in thresholds detection. The two metabolic thresholds were estimated in thirty young individuals during Cardiopulmonary Exercise Testing on a cycle-ergometer and HR, VO2 and Workload were measured by the two different methods (RQA and GE methods). RM ANOVA was used to assess main effects of methods and methods-by-groups interaction effects for HR, VO2 and Workload at the aerobic (AerT) and the anaerobic (AnT) thresholds. Validity of the RQA at both thresholds was assessed for HR, VO2 and Workload by Ordinary Least Products (OLP) regression analysis, Typical Percentage Errors (TE), Intraclass Correlation Coefficients (ICC) and the Bland Altman plots. No methods-by-groups interaction effects were detected for HR, VO2 and Workload at the AerT and the AnT. The OLP regression analysis showed that at both thresholds RQA and GE methods had very strong correlations (r >0.8) in all variables (HR, VO2 and Workload). Slope and intercept values always included the 1 and the 0, respectively. At the AerT the TE ranged from 4.02% to 10.47% (HR and Workload, respectively) and in all variables ICC values were excellent ([≥]0.85). At the AnT the TE ranged from 2.61% to 6.64% (HR and Workload, respectively) and in all variables ICC values were excellent ([≥]0.89). Our results suggest that the RQA of HRV time series is a COVID-safe approach for the determination of metabolic thresholds in individuals with different physical fitness levels, therefore, it can be used as a valid method for threshold detection alternative to gas analysis.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Giovanna Zimatore", + "author_inst": "Universit\u00e0 degli Studi eCampus: Universita degli Studi eCampus" + }, + { + "author_name": "MariaChiara Gallotta", + "author_inst": "Sapienza University of Rome: Universita degli Studi di Roma La Sapienza" + }, + { + "author_name": "Valerio Bonavolnt\u00e0", + "author_inst": "University of Bari: Universita degli Studi di Bari Aldo Moro" + }, + { + "author_name": "Matteo Campanella", + "author_inst": "eCampus University: Universita degli Studi eCampus" + }, + { + "author_name": "Marco De Spirito", + "author_inst": "Fondazione Policlinico Universitario Agostino Gemelli IRCCS" + }, + { + "author_name": "Laura Guidetti", + "author_inst": "University Niccolo Cusano: Universita degli Studi Niccolo Cusano" + }, + { + "author_name": "Carlo Baldari", + "author_inst": "eCampus University: Universita degli Studi eCampus" + } + ], + "version": "1", + "license": "cc_by", + "type": "confirmatory results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.03.19.21253997", "rel_title": "The Impact of Early or Late Lockdowns on the Spread of COVID-19 in US Counties", @@ -844835,53 +846369,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hiv aids" }, - { - "rel_doi": "10.1101/2021.03.19.21253947", - "rel_title": "Developing machine learning models for predicting intensive care unit resource use during the COVID-19 pandemic", - "rel_date": "2021-03-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21253947", - "rel_abs": "ImportanceThe COVID-19 pandemic has put massive strains on hospitals, and tools to guide hospital planners in resource allocation during the ebbs and flows of the pandemic are urgently needed.\n\nObjectiveWe investigate whether Machine Learning (ML) can be used for predictions of intensive care requirements 5 and 10 days into the future.\n\nDesignRetrospective design where health Records from 34,012 SARS-CoV-2 positive patients was extracted. Random Forest (RF) models were trained to predict risk of ICU admission and use of mechanical ventilation after n days (n = 5, 10).\n\nSettingTwo Danish regions, encompassing approx. 2.5 million citizens.\n\nParticipantsAll patients from the bi-regional area with a registered positive SARS-CoV-2 test from March 2020 to January 2021.\n\nMain outcomesPrediction of future 5- and 10-day requirements of ICU admission and ventilator use. Mortality was also predicted.\n\nResultsModels predicted 5-day risk of ICU admission with an area under the receiver operator characteristic curve (ROC-AUC) of 0.986 and 5-day risk of use of ventilation with an ROC-AUC of 0.995. The corresponding 5-day forecasting models predicted the needed ICU capacity with a coefficient of determination (R2) of 0.930 and use of ventilation with an R2 of 0.934. Performance was comparable but slightly reduced for 10-day forecasting models.\n\nConclusionsRandom Forest-based modelling can be used for accurate 5- and 10-day forecasting predictions of ICU resource requirements.\n\nFundingThe study was funded by grants from the Novo Nordisk Foundation to MS (#NNF20SA0062879 and #NNF19OC0055183) and MN (#NNF20SA0062879).\n\nThe foundation took no part in project design, data handling and manuscript preparation.\n\nKEY POINTSO_ST_ABSQuestionC_ST_ABSCan machine learning models (ML) be used for predicting hospital and intensive care unit (ICU) resource requirements, and thus assist in logistics crisis management during the COVID-19 pandemic?\n\nFindingsRetrospective study of the resource use of 34.012 COVID-19 patients during the first and second COVID-19 wave in Denmark. ML models were trained for the purpose of predicting the number of patients needing ICU admission and ventilators 5 and 10 day after their first positive SARS-CoV-2 test. The study demonstrates that ML models can accurately predict intensive care admission requirements with 5-day area under the receiver operator characteristic curve (ROC-AUC) of 0.986 and need for ventilator support with a ROC-AUC of 0.995. 10-day predictions were comparable.\n\nMeaningThe study demonstrates that ML modelled could be a useful tool for hospital planners during crisis management, including the current COVID-19 pandemic.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Stephan Slot Lorenzen", - "author_inst": "University of Copenhagen, Dep. of Computer Science" - }, - { - "author_name": "Mads Nielsen", - "author_inst": "University of Copenhagen, Dep. of Computer Science" - }, - { - "author_name": "Espen Jimenez-Solem", - "author_inst": "Copenhagen Univ. Hospital, Bispebjerg" - }, - { - "author_name": "Tonny Studsgaard Petersen", - "author_inst": "Copenhagen Univ. Hospital, Bispebjerg" - }, - { - "author_name": "Anders Perner", - "author_inst": "Copenhagen Univ. Hospital, Rigshospitalet" - }, - { - "author_name": "Hans-Christian Thorsen-Meyer", - "author_inst": "Copenhagen Univ. Hospital, Rigshospitalet" - }, - { - "author_name": "Christian Igel", - "author_inst": "Univ. of Copenhagen, Dep. of Computer Science" - }, - { - "author_name": "Martin Sillesen", - "author_inst": "Copenhagen Univ. Hospital, Rigshospitalet" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.19.21253920", "rel_title": "Reduced BNT162b2 mRNA vaccine response in SARS-CoV-2-naive nursing home residents", @@ -845809,6 +847296,77 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.03.22.436468", + "rel_title": "Characterisation of B.1.1.7 and Pangolin coronavirus spike provides insights on the evolutionary trajectory of SARS-CoV-2", + "rel_date": "2021-03-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.22.436468", + "rel_abs": "The recent emergence of SARS-CoV-2 variants with increased transmission, pathogenesis and immune resistance has jeopardised the global response to the COVID-19 pandemic. Determining the fundamental biology of viral variants and understanding their evolutionary trajectories will guide current mitigation measures, future genetic surveillance and vaccination strategies. Here we examine virus entry by the B.1.1.7 lineage, commonly referred to as the UK/Kent variant. Pseudovirus infection of model cell lines demonstrate that B.1.1.7 entry is enhanced relative to the Wuhan-Hu-1 reference strain, particularly under low expression of receptor ACE2. Moreover, the entry characteristics of B.1.1.7 were distinct from that of its predecessor strain containing the D614G mutation. These data suggest evolutionary tuning of spike protein function. Additionally, we found that amino acid deletions within the N-terminal domain (NTD) of spike were important for efficient entry by B.1.1.7. The NTD is a hotspot of diversity across sarbecoviruses, therefore, we further investigated this region by examining the entry of closely related CoVs. Surprisingly, Pangolin CoV spike entry was 50-100 fold enhanced relative to SARS-CoV-2; suggesting there may be evolutionary pathways by which SARS-CoV-2 may further optimise entry. Swapping the NTD between Pangolin CoV and SARS-CoV-2 demonstrates that changes in this region alone have the capacity to enhance virus entry. Thus, the NTD plays a hitherto unrecognised role in modulating spike activity, warranting further investigation and surveillance of NTD mutations.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Samuel J Dicken", + "author_inst": "University College London" + }, + { + "author_name": "Matthew J Murray", + "author_inst": "University College London" + }, + { + "author_name": "Lucy G Thorne", + "author_inst": "University College London" + }, + { + "author_name": "Ann-Kathrin Reuschl", + "author_inst": "University College London" + }, + { + "author_name": "Calum Forrest", + "author_inst": "University College London" + }, + { + "author_name": "Maaroothen Ganeshalingham", + "author_inst": "University College London" + }, + { + "author_name": "Luke Muir", + "author_inst": "University College London" + }, + { + "author_name": "Mphatso D Kalemera", + "author_inst": "University College London" + }, + { + "author_name": "Machaela Palor", + "author_inst": "University College London" + }, + { + "author_name": "Laura E McCoy", + "author_inst": "University College London" + }, + { + "author_name": "Clare Jolly", + "author_inst": "University College London" + }, + { + "author_name": "Greg J Towers", + "author_inst": "University College London" + }, + { + "author_name": "Matthew Reeves", + "author_inst": "University College London" + }, + { + "author_name": "Joe Grove", + "author_inst": "University College London" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.03.22.436427", "rel_title": "Replicative fitness SARS-CoV-2 20I/501Y.V1 variant in a human reconstituted bronchial epithelium", @@ -847045,29 +848603,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.19.21253957", - "rel_title": "Comparing the efficacy of anti-infectious drugs for the treatment of mild to severe COVID-19 patients: a protocol for a systematic review and network meta-analysis of randomized clinical trials", - "rel_date": "2021-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21253957", - "rel_abs": "BackgroundCOVID-19 is a viral infection spreading at a great speed and has quickly caused an extensive burden to individuals, families, countries, and the world. No intervention has yet been proven highly effective for the treatment of COVID-19. Different drugs were being evaluated and reported through randomized clinical trials, and more are currently under trial. This review aimed to compare the efficacy of anti-infectious drugs with a comparator of the standard of care or placebo in patients with COVID-19.\n\nMethods and analysisTwo independent review authors will extract data and assess a risk of bias using RoB2. Randomized controlled trials (RCT) that evaluate single and/or combined antiviral drugs recommended by WHO latest guideline for the treatment of COVID-19 will be included. We will search for Pub Med, the Cochrane Center for Clinical Trial database (CENTRAL), clinicaltrials.gov, etc. databases for articles published in the English language between December 2019 to April 2021. We will follow the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols (PRISMA-P) involving Network Meta-analysis guidelines for the design and reporting of the results. The primary endpoints will be time to clinical recovery and time to RNA negativity. The certainty of evidence will be evaluated using the GRADE extension of NMA. Data analysis will be performed using the frequentist NMA approach with netmeta package implemented in R.\n\nEthics and disseminationThere are no ethical considerations associated with this study as we will use publicly available data from previously published studies. We plan to publish results in open access peer-reviewed journals.\n\nPROSPERO registration numberID=CRD42021230919.\n\nStrengths and limitations of this studyO_LIThis will be the first systematic review and network meta-analysis to assess the efficacy specific to anti-infectious drugs category for for mild to severe patients of COVID-19.\nC_LIO_LIIts compliance with the Preferred Reporting Items for Systematic Review and Meta-Analysis for Protocols (PRISMA-P) involving network meta-analysis(NMA) will ensure the quality of reporting.\nC_LIO_LIDoing both pairwise meta-analysis and network meta-analysis (NMA) can comprehensively analyse direct and indirect comparison results of different anti-infectious drugs for COVID 19 will give more reliable conclusions aswell as the rank of those drugs.\nC_LIO_LIThere is risk of heterogeneity and inconsistency, given the different anti-infectious drugs that will be included; however, we try to control intransitivity by carefully identifying the eligibility criteria depending on PICOS strategy and assess inconsistency using local as well as global approaches.\nC_LIO_LIThe limitation of this study is it will not explore the economic benefits of these drugs.\nC_LI", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Dejene Tolossa Debela", - "author_inst": "Addis Ababa University" - }, - { - "author_name": "Kidist Digamo Heraro", - "author_inst": "Addis Ababa University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.18.21253898", "rel_title": "First wastewater surveillance-based city zonation for effective COVID-19 pandemic preparedness powered by early warning: A study of Ahmedabad, India", @@ -847931,6 +849466,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, + { + "rel_doi": "10.1101/2021.03.17.21253834", + "rel_title": "Pulmonary Fibrosis after COVID-19 is Associated with Severity of Illness and Blood Leukocyte Telomere Length", + "rel_date": "2021-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.17.21253834", + "rel_abs": "The risk factors for development of fibrotic interstitial lung abnormalities (ILA) after severe COVID-19 are incompletely described and the extent to which CT findings correlate with symptoms and physical function after hospitalization remain unclear. At 4 months after hospitalization, fibrotic ILA was more common in those who underwent mechanical ventilation (72%) than in those who did not (20%). We demonstrate that severity of initial illness, duration of mechanical ventilation, lactate dehydrogenase on admission, and leukocyte telomere length are independent risk factors for fibrotic ILA. These fibrotic changes correlate with lung function, cough and measures of frailty, but not with dyspnea.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Claire F. McGroder", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "David Zhang", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Mohammad A Choudhury", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Mary M. Salvatore", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Belinda M. D'Souza", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Eric A. Hoffman", + "author_inst": "University of Iowa Carver College of Medicine" + }, + { + "author_name": "Ying Wei", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Matthew R Baldwin", + "author_inst": "Columbia University Vagelos College of Physicians and Surgeons" + }, + { + "author_name": "Christine Kim Garcia", + "author_inst": "Columbia University Medical Center" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2021.03.20.21254005", "rel_title": "Alternative splicing of OAS1 alters the risk for severe COVID-19", @@ -849323,33 +850909,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.17.21253800", - "rel_title": "Investigation of the ventilation situation in a lecture room of building 033 at the Universita\u0308t der Bundeswehr Mu\u0308nchen", - "rel_date": "2021-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.17.21253800", - "rel_abs": "The SARS-CoV-2 pandemic is limiting both the private and public lives of many people around the world. It is now considered certain that SARS-CoV-2 is transmitted via droplets, smear infection, and aerosol particles. While simple masks, spacing, and hand hygiene significantly reduce the risk of infection via the first two routes mentioned, the risk from aerosol particles remains. These small particles move with the air in the room and spread unhindered throughout it. To reduce the risk of infection from viruses present in aerosol particles, the following options exist. First, good respiratory masks can be worn to reduce the viral load in the inhaled air. Another option is to make the viruses harmless (e.g., by UV light). A third option is to reduce the viral load in the room by bringing in virus-free air and moving contaminated air out or cleaning the air in the room. To investigate how well virus load reduction via ventilation works in a real lecture room, measurements were carried out at the Universitat der Bundeswehr Munchen (University of the Federal Armed Forces Munich). The lecture room holds a maximum of approx. 90 people and has a ventilation system as well as 2 windows that can be opened. In the absence of a ventilation system in a comparable room, the effectiveness of a room air cleaner was also investigated.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Christian J. K\u00e4hler", - "author_inst": "Universit\u00e4t der Bundeswehr M\u00fcnchen, Institute of Fluid Mechanics and Aerodynamics" - }, - { - "author_name": "Thomas Fuchs", - "author_inst": "Universit\u00e4t der Bundeswehr M\u00fcnchen, Institute of Fluid Mechanics and Aerodynamics" - }, - { - "author_name": "Rainer Hain", - "author_inst": "Universit\u00e4t der Bundeswehr M\u00fcnchen, Institute of Fluid Mechanics and Aerodynamics" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.19.21253893", "rel_title": "Return to normal: COVID-19 vaccination under mitigation measures", @@ -850029,6 +851588,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "surgery" }, + { + "rel_doi": "10.1101/2021.03.16.21253708", + "rel_title": "Homophily in risk and behavior complicate understanding the COVID-19 epidemic curve", + "rel_date": "2021-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.16.21253708", + "rel_abs": "New COVID-19 diagnoses have dropped faster than expected in the United States. Interpretations of the decrease have focused on changing factors (e.g. mask-wearing, vaccines, etc.), but predictive models largely ignore heterogeneity in behaviorally-driven exposure risks among distinct groups. We present a simplified compartmental model with differential mixing in two behaviorally distinct groups. We show how homophily in behavior, risk, and exposure can lead to early peaks and rapid declines that critically do not signal the end of the outbreak. Instead, higher exposure risk groups may more rapidly exhaust available susceptibles while the lower risk group are still in a (slower) growth phase of their outbreak curve. This simplified model demonstrates that complex incidence curves, such as those currently seen in the US, can be generated without changes to fundamental drivers of disease dynamics. Correct interpretation of incidence curves will be critical for policy decisions to effectively manage the pandemic.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Nina H Fefferman", + "author_inst": "University of Tennessee" + }, + { + "author_name": "Matthew J Silk", + "author_inst": "University of Tennessee, Knoxville" + }, + { + "author_name": "Dana K Pasquale", + "author_inst": "Duke University" + }, + { + "author_name": "James Moody", + "author_inst": "Duke University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.10.21253291", "rel_title": "Monitoring the propagation of SARS CoV2 variants by tracking identified mutation in wastewater using specific RT-qPCR", @@ -850929,45 +852519,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.15.21253588", - "rel_title": "A combined strategy to detect plasma samples reliably with high anti-SARS-CoV-2 neutralizing antibody titers in routine laboratories", - "rel_date": "2021-03-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.15.21253588", - "rel_abs": "The determination of anti-SARS-CoV-2 neutralizing antibodies (NAbs) is of interest in many respects. High NAb titers, for example, are the most important criterion regarding the effectiveness of convalescent plasma therapy. However, common cell culture-based NAb assays are time-consuming and feasible only in special laboratories. Our data reveal the suitability of a novel ELISA-based surrogate virus neutralization test (sVNT) to easily measure the inhibition-capability of NAbs in the plasma of COVID-19 convalescents. We propose a combined strategy to detect plasma samples with high NAb titers ([≥] 1:160) reliably and to, simultaneously, reduce the risk of erroneously identifying low-titer specimens. For this approach, results of the sVNT assay are compared to and combined with those acquired from the Euroimmun anti-SARS-CoV-2 IgG assay. Both assays are appropriate for high-throughput screening in standard BSL-2 laboratories. Our measurements further show a long-lasting humoral immunity of at least 11 months after symptom onset.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Bastian Fischer", - "author_inst": "Institute for Laboratory and Transfusion Medicine, Heart and Diabetes Centre NRW" - }, - { - "author_name": "Christoph Lichtenberg", - "author_inst": "Institute for Laboratory and Transfusion Medicine, Heart and Diabetes Centre NRW" - }, - { - "author_name": "Lisa Mueller", - "author_inst": "Institute of Virology, University Hospital Duesseldorf" - }, - { - "author_name": "Joerg Timm", - "author_inst": "Institute of Virology, University Hospital Duesseldorf" - }, - { - "author_name": "Johannes Fischer", - "author_inst": "Institute for Transplantation Diagnostics and Cellular Therapeutics, University Hospital Duesseldorf" - }, - { - "author_name": "Cornelius Knabbe", - "author_inst": "Institute for Laboratory and Transfusion Medicine, Heart and Diabetes Centre NRW" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.18.436001", "rel_title": "Dendritic cell deficiencies persist seven months after SARS-CoV-2 infection", @@ -851883,6 +853434,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.18.436013", + "rel_title": "The B1.351 and P.1 variants extend SARS-CoV-2 host range to mice", + "rel_date": "2021-03-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.18.436013", + "rel_abs": "Receptor recognition is a major determinant of viral host range, infectivity and pathogenesis. Emergences have been associated with serendipitous events of adaptation upon encounters with novel hosts, and the high mutation rate of RNA viruses may explain their frequent host shifts. SARS-CoV-2 extensive circulation in humans results in the emergence of variants, including variants of concern (VOCs) with diverse mutations notably in the spike, and increased transmissibility or immune escape. Here we show that, unlike the initial and Delta variants, the three VOCs bearing the N501Y mutation can infect common laboratory mice. Contact transmission occurred from infected to naive mice through two passages. This host range expansion likely results from an increased binding of the spike to the mouse ACE2. Together with the observed contact transmission, it raises the possibility of wild rodent secondary reservoirs enabling the emergence of new variants.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Xavier Montagutelli", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Matthieu Prot", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Laurine Levillayer", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Eduard Baquero Salazar", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Gregory Jouvion", + "author_inst": "Ecole Nationale Veterinaire" + }, + { + "author_name": "Laurine Conquet", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Maxima Beretta", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Flora Donati", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Melanie Albert", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Fabiana Gambaro", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Sylvie Behillil", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Vincent Enouf", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Dominique Rousset", + "author_inst": "Institut Pasteur de la Guyane" + }, + { + "author_name": "Jean Jaubert", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Sylvie van der Werf", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Hugo Mouquet", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Felix Rey", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Etienne Simon-Loriere", + "author_inst": "Institut Pasteur" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.03.15.21253570", "rel_title": "Evaluation of RNA extraction free method for detection of SARS-COV-2 in salivary samples for mass screening for COVID-19", @@ -852787,41 +854425,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.03.15.21253668", - "rel_title": "A Longitudinal Analysis of COVID-19 Lockdown Stringency on Sleep and Resting Heart Rate Measures across 20 Countries", - "rel_date": "2021-03-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.15.21253668", - "rel_abs": "Lockdowns imposed to stem the spread of COVID-19 massively disrupted the daily routines of many worldwide, but studies to date are mostly confined to observations within a limited number of countries, based on subjective reports and survey from specific time periods during the pandemic. We investigated associations between lockdown stringency and objective sleep and resting-heart rate measures in 113,000 users of a consumer sleep tracker across 20 countries from Jan-Jul 2020. With stricter lockdown measures, midsleep times were universally delayed, particularly on weekdays, while midsleep variability and resting heart rate declined. These shifts (midsleep: +0.09 to +0.58 hours; midsleep variability: -0.12 to -0.26 hours; resting heart rate: -0.35 to -2.08 bpm) correlated with the severity of lockdown across different countries and highlight the graded influence of mobility restriction and social isolation on human physiology.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Ju Lynn Ong", - "author_inst": "National University of Singapore" - }, - { - "author_name": "TeYang Lau", - "author_inst": "National University of Singapore" - }, - { - "author_name": "Mari Karsikas", - "author_inst": "Oura Health" - }, - { - "author_name": "Hannu Kinnunen", - "author_inst": "Oura Health" - }, - { - "author_name": "Michael W.L. Chee", - "author_inst": "National University of Singapore" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.03.15.21253637", "rel_title": "COVID-19 and Cognitive Impairment: Severity, Evolution, and Functional Impact during Inpatient Rehabilitation", @@ -853541,6 +855144,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.15.21253267", + "rel_title": "Can we predict antibody responses in SARS-CoV-2? A cohort analysis.", + "rel_date": "2021-03-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.15.21253267", + "rel_abs": "BackgroundAfter infection with severe acute respiratory syndrome coronavirus (SARS-CoV-2), Immunoglobulin G (IgG) antibodies and virus-specific neutralizing antibodies (nAbs) develop. This study describes antibody responses in a cohort of recovered COVID-19 patients to identify predictors.\n\nMethodsWe recruited patients with confirmed SARS-CoV-2 infection from Heidelberg, Germany. Blood samples were collected three weeks after COVID-19 symptoms ended. Participants with high antibody titers were invited for follow-up visits. IgG titers were measured by the Euroimmun Assay, and nAbs titers in a SARS-CoV-2 infection-based assay.\n\nResults281 participants were enrolled between April and August 2020 with IgG testing, 145 (51.6%) had nAbs, and 35 (12.5%) had follow-up. The median IgG optical density (OD) ratio was 3.1 (Interquartile range (IQR) 1.6-5.1), and 24.1% (35/145) had a nAb titer>1:80. Higher IgG titers were associated with increased age and more severe disease, and higher nAbs were associated with male gender and CT-value of 25-30 on RT-PCR at diagnosis. The median IgG OD ratio on follow-up was 3.7 (IQR 2.9-5.9), a median increase of 0.5 (IQR -0.3-1.7). Six participants with follow-up nAbs all had titers [≤] 1:80.\n\nConclusionsWhile age and disease severity were correlated with IgG responses, predictive factors for nAbs in convalescent patients remain unclear.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Mary Gaeddert", + "author_inst": "Division of Tropical Medicine, Center of Infectious Diseases, Heidelberg University Hospital, Germany" + }, + { + "author_name": "Philip Kitchen", + "author_inst": "Division of Tropical Medicine, Center of Infectious Diseases, Heidelberg University Hospital, Germany" + }, + { + "author_name": "Tobias Broger", + "author_inst": "Division of Tropical Medicine, Center of Infectious Diseases, Heidelberg University Hospital, Germany" + }, + { + "author_name": "Stefen Weber", + "author_inst": "Division of Tropical Medicine, Center of Infectious Diseases, Heidelberg University Hospital, Germany" + }, + { + "author_name": "Ralf Bartenschlager", + "author_inst": "Department of Infectious Diseases, Molecular Virology, Heidelberg University Hospital, Heidelberg, Germany" + }, + { + "author_name": "Anna Plaszczyca", + "author_inst": "Department of Infectious Diseases, Molecular Virology, Heidelberg University Hospital, Heidelberg, Germany" + }, + { + "author_name": "Hans-Georg Kr\u00e4usslich", + "author_inst": "Virology, Center of Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany" + }, + { + "author_name": "Barbara M\u00fcller", + "author_inst": "Virology, Center of Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany" + }, + { + "author_name": "Margarida Souto-Carneiro", + "author_inst": "Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany" + }, + { + "author_name": "Maike Janssen", + "author_inst": "Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany" + }, + { + "author_name": "Carsten M\u00fcller-Tidow", + "author_inst": "Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany" + }, + { + "author_name": "Uta Merle", + "author_inst": "Department of Gastroenterology, Heidelberg University Hospital, Germany" + }, + { + "author_name": "Yannis Herrmann", + "author_inst": "Division of Tropical Medicine, Center of Infectious Diseases, Heidelberg University Hospital, Germany" + }, + { + "author_name": "Lukas Raedeker", + "author_inst": "Division of Tropical Medicine, Center of Infectious Diseases, Heidelberg University Hospital, Germany" + }, + { + "author_name": "Jakob Sebastian", + "author_inst": "Division of Tropical Medicine, Center of Infectious Diseases, Heidelberg University Hospital, Germany" + }, + { + "author_name": "Niall Brindl", + "author_inst": "Division of Tropical Medicine, Center of Infectious Diseases, Heidelberg University Hospital, Germany" + }, + { + "author_name": "Tim Starck", + "author_inst": "Heidelberg Institute of Global Health, Heidelberg University Hospital, Heidelberg, Germany" + }, + { + "author_name": "Claudia M. Denkinger", + "author_inst": "Division of Tropical Medicine, Center of Infectious Diseases, Heidelberg University Hospital, Germany" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.17.21253782", "rel_title": "B.1.1.7 became the dominant variant in Lebanon.", @@ -854525,25 +856215,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.03.16.21253767", - "rel_title": "The Influence of Covid-19 Vaccine on Daily Cases, Hospitalization, and Death Rate in Tennessee: A Case Study in the United States", - "rel_date": "2021-03-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.16.21253767", - "rel_abs": "The COVID-19 outbreak highlights the vulnerability to novel infections, and vaccination remains a foreseeable method to return to normal life. However, infrastructure is inadequate for the whole population to be vaccinated immediately. Therefore, policies have adopted a strategy to vaccinate the elderly and vulnerable population while delaying others. This study uses the Tennessee official statistic from the onset of COVID vaccination (17th of December 2021) to understand how age-specific vaccination strategies reduce daily cases, hospitalization, and death rate. The result shows that vaccination strategy can significantly influence the numbers of patients with COVID-19 in all age groups and lower hospitalization and death rates just in older age groups. The Elderly had a 95% lower death rate from December to March; however, and no change in the death rate in other age groups. The Hospitalization rate was reduced by 80% in this study cohort for people aged 80 or older, while people who were between 50 to 70 had almost the same hospitalization rate. The study indicates that vaccination targeting older age groups is the optimal way to avoid higher transmissions and reduce hospitalization and death rate for older groups.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Ali Roghani", - "author_inst": "University of Utah" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2021.03.16.21253764", "rel_title": "The impact of policy timing on the spread of COVID-19", @@ -855675,6 +857346,141 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2021.03.16.435594", + "rel_title": "Circular RNA Vaccines against SARS-CoV-2 and Emerging Variants", + "rel_date": "2021-03-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.16.435594", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its emerging variants of concern (VOC), such as Delta (B.1.617.2) and Omicron (B.1.1.529), has continued to drive the worldwide pandemic. Therefore, there is a high demand for vaccines with enhanced efficacy, high thermostability, superior design flexibility, and fast manufacturing speed. Here, we report a circular RNA (circRNA) vaccine that encodes the trimeric RBD of SARS-CoV-2 Spike protein. Without the need of nucleotide modification, 5-capping or 3-polyadenylation, circRNA could be rapidly produced via in vitro transcription and is highly thermostable whether stored in naked or lipid-nanoparticle (LNP)-encapsulated format. LNP-encapsulated circRNARBD elicited potent neutralizing antibodies and T cell responses, providing robust protection against Beta (B.1.351) and native viruses in mice and rhesus macaques, respectively. Notably, circRNA vaccine enabled higher and more durable antigen production than 1m{Psi}-modified mRNA vaccine, eliciting a higher proportion of neutralizing antibodies and stronger Th1-biased immune responses. Importantly, we found that circRNARBD-Omicron vaccine induced effective neutralizing antibodies against only Omicron but not Delta variant. By contrast, circRNARBD-Delta could elicit high level of neutralizing antibodies against both Delta and Omicron. Following two doses of either native- or Delta-specific vaccination, circRNARBD-Delta, but not Omicron or Beta vaccines, could effectively boost the neutralizing antibodies against both Delta and Omicron variants. These results suggest that circRNARBD-Delta is a favorable choice for vaccination to provide a broad-spectrum protection against the current variants of concern of SARS-CoV-2.", + "rel_num_authors": 30, + "rel_authors": [ + { + "author_name": "Liang Qu", + "author_inst": "Peking University" + }, + { + "author_name": "Zongyi Yi", + "author_inst": "Peking University" + }, + { + "author_name": "Yong Shen", + "author_inst": "Peking Universtiy" + }, + { + "author_name": "Liangru Lin", + "author_inst": "Peking University" + }, + { + "author_name": "Feng Chen", + "author_inst": "Peking University" + }, + { + "author_name": "Yiyuan Xu", + "author_inst": "Peking University" + }, + { + "author_name": "Zeguang Wu", + "author_inst": "Peking University" + }, + { + "author_name": "Huixian Tang", + "author_inst": "Peking University" + }, + { + "author_name": "Xiaoxue Zhang", + "author_inst": "Peking University" + }, + { + "author_name": "Feng Tian", + "author_inst": "Peking University" + }, + { + "author_name": "Chunhui Wang", + "author_inst": "Peking University" + }, + { + "author_name": "Xia Xiao", + "author_inst": "Chinese Academy of Medical Sciences & Peking Union Medical College" + }, + { + "author_name": "Xiaojing Dong", + "author_inst": "Chinese Academy of Medical Sciences & Peking Union Medical College" + }, + { + "author_name": "Li Guo", + "author_inst": "Chinese Academy of Medical Sciences & Peking Union Medical College" + }, + { + "author_name": "Shuaiyao Lu", + "author_inst": "Chinese Academy of Medical Sciences and Peking Union Medical College" + }, + { + "author_name": "Chengyun Yang", + "author_inst": "Chinese Academy of Medical Sciences and Peking Union Medical College" + }, + { + "author_name": "Cong Tang", + "author_inst": "Chinese Academy of Medical Sciences and Peking Union Medical College" + }, + { + "author_name": "Yun Yang", + "author_inst": "Chinese Academy of Medical Sciences and Peking Union Medical College" + }, + { + "author_name": "Wenhai Yu", + "author_inst": "Chinese Academy of Medical Sciences and Peking Union Medical College" + }, + { + "author_name": "Junbin Wang", + "author_inst": "Chinese Academy of Medical Sciences and Peking Union Medical College" + }, + { + "author_name": "Yanan Zhou", + "author_inst": "Chinese Academy of Medical Sciences and Peking Union Medical College" + }, + { + "author_name": "Qing Huang", + "author_inst": "Chinese Academy of Medical Sciences and Peking Union Medical College" + }, + { + "author_name": "Ayijiang Yisimayi", + "author_inst": "Peking University" + }, + { + "author_name": "Yunlong Cao", + "author_inst": "Peking University" + }, + { + "author_name": "Youchun Wang", + "author_inst": "National Institutes for Food and Drug Control" + }, + { + "author_name": "Zhuo Zhou", + "author_inst": "Peking University" + }, + { + "author_name": "Xiaozhong Peng", + "author_inst": "Chinese Academy of Medical Sciences and Peking Union Medical College" + }, + { + "author_name": "Jianwei Wang", + "author_inst": "Chinese Academy of Medical Sciences & Peking Union Medical College" + }, + { + "author_name": "Xiaoliang Sunney Xie", + "author_inst": "Peking University" + }, + { + "author_name": "Wensheng Wei", + "author_inst": "Peking University" + } + ], + "version": "1", + "license": "", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.03.15.435497", "rel_title": "Killed whole genome-reduced bacteria surface-expressed coronavirus fusion peptide vaccines protect against disease in a porcine model", @@ -856815,49 +858621,6 @@ "type": "new results", "category": "systems biology" }, - { - "rel_doi": "10.1101/2021.03.14.435180", - "rel_title": "Differential gene expression by RNA-Seq in Sigma-2 Receptor/TMEM97 knockout cells reveals its role in complement activation and SARS-CoV-2 viral uptake", - "rel_date": "2021-03-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.14.435180", - "rel_abs": "Our lab has recently shown that the Sigma-2 Receptor/Transmembrane Protein 97 (sigma-2R/TMEM97) interacts with the low-density lipoprotein receptor (LDLR) and facilitates the enhanced uptake of various ligands including lipoproteins and intrinsically disordered proteins. TMEM97 has been recently been shown to interact with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral proteins, highlighting its potential involvement with viral entry into the cell. We hypothesized that sigma-2R/TMEM97 may play a role in facilitating viral uptake, and with the regulation of inflammatory and thrombotic pathways that are involved with viral infection. In this study, we identified the top differentially expressed genes upon the knockout of sigma-2R/TMEM97, and analyzed the genes involved with the inflammatory and thrombotic cascades, effects that are observed in patients infected with SARS-CoV-2. We found that the ablation of sigma-2R/TMEM97 resulted in an increase in Complement Component 4 Binding Protein (C4BP) proteins, at both the translational and transcriptional levels. We also showed that sigma-2R/TMEM97 interacts with the cellular receptor for SARS-CoV-2, the human angiotensin-converting enzyme 2 (ACE2) receptor, forming a protein complex, and that disruption of this complex results in the inhibition of viral uptake. The results of this study suggest that sigma-2R/TMEM97 may be a novel therapeutic target to inhibit SARS-CoV-2 viral uptake, as well as to decrease inflammatory and thrombotic effects through the modulation of the complement cascade.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Aladdin Riad", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Yann Aubert", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Chenbo Zeng", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Thomas J. A. Graham", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "E. James Petersson", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Brian C. Capell", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Robert H. Mach", - "author_inst": "University of Pennsylvania" - } - ], - "version": "1", - "license": "", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2021.03.15.435326", "rel_title": "Structure, Mechanism and Crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase", @@ -858125,6 +859888,53 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.03.12.21253495", + "rel_title": "All Models Are Useful: Bayesian Ensembling for Robust High Resolution COVID-19 Forecasting", + "rel_date": "2021-03-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.12.21253495", + "rel_abs": "Timely, high-resolution forecasts of infectious disease incidence are useful for policy makers in deciding intervention measures and estimating healthcare resource burden. In this paper, we consider the task of forecasting COVID-19 confirmed cases at the county level for the United States. Although multiple methods have been explored for this task, their performance has varied across space and time due to noisy data and the inherent dynamic nature of the pandemic. We present a forecasting pipeline which incorporates probabilistic forecasts from multiple statistical, machine learning and mechanistic methods through a Bayesian ensembling scheme, and has been operational for nearly 6 months serving local, state and federal policymakers in the United States. While showing that the Bayesian ensemble is at least as good as the individual methods, we also show that each individual method contributes significantly for different spatial regions and time points. We compare our models performance with other similar models being integrated into CDC-initiated COVID-19 Forecast Hub, and show better performance at longer forecast horizons. Finally, we also describe how such forecasts are used to increase lead time for training mechanistic scenario projections. Our work demonstrates that such a real-time high resolution forecasting pipeline can be developed by integrating multiple methods within a performance-based ensemble to support pandemic response.\n\nACM Reference FormatAniruddha Adiga, Lijing Wang, Benjamin Hurt, Akhil Peddireddy, Przemys-law Porebski,, Srinivasan Venkatramanan, Bryan Lewis, Madhav Marathe. 2021. All Models Are Useful: Bayesian Ensembling for Robust High Resolution COVID-19 Forecasting. In Proceedings of ACM Conference (Conference17). ACM, New York, NY, USA, 9 pages. https://doi.org/10.1145/nnnnnnn.nnnnnnn", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Aniruddha Adiga", + "author_inst": "University of Virginia" + }, + { + "author_name": "Lijing Wang", + "author_inst": "University of Virginia" + }, + { + "author_name": "Benjamin Hurt", + "author_inst": "University of Virginia" + }, + { + "author_name": "Akhil Sai Peddireddy", + "author_inst": "University of Virginia" + }, + { + "author_name": "Przemyslaw Porebski", + "author_inst": "University of Virginia" + }, + { + "author_name": "Srinivasan Venkatramanan", + "author_inst": "University of Virginia" + }, + { + "author_name": "Bryan Lewis", + "author_inst": "University of Virginia" + }, + { + "author_name": "Madhav Marathe", + "author_inst": "University of Virginia" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.12.21253481", "rel_title": "Modeling the use of SARS-CoV-2 vaccination to safely relax non-pharmaceutical interventions", @@ -859145,53 +860955,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "endocrinology" }, - { - "rel_doi": "10.1101/2021.02.26.21252327", - "rel_title": "Interventions to control nosocomial transmission of SARS-CoV-2: a modelling study", - "rel_date": "2021-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.26.21252327", - "rel_abs": "BackgroundEmergence of more transmissible SARS-CoV-2 variants requires more efficient control measures to limit nosocomial transmission and maintain healthcare capacities during pandemic waves. Yet, the relative importance of different strategies is unknown.\n\nMethodsWe developed an agent-based model and compared the impact of personal protective equipment (PPE), screening of healthcare workers (HCWs), contact tracing of symptomatic HCWs, and restricting HCWs from working in multiple units (HCW cohorting) on nosocomial SARS-CoV-2 transmission. The model was fit on hospital data from the first wave in the Netherlands (February until August 2020) and assumed that HCWs used 90% effective PPE in COVID-19 wards and self-isolated at home for seven days immediately upon symptom onset. Intervention effects on the effective reproduction number (RE), HCW absenteeism and the proportion of infected individuals among tested individuals (positivity rate) were estimated for a more transmissible variant.\n\nResultsIntroduction of a variant with 56% higher transmissibility increased - all other variables kept constant - RE from 0.4 to 0.65 (+63%) and nosocomial transmissions by 303%, mainly because of more transmissions caused by pre-symptomatic patients and HCWs. Compared to baseline, PPE use in all hospital wards (assuming 90% effectiveness) reduced RE by 85% and absenteeism by 57%. Screening HCWs every three days with perfect test sensitivity reduced RE by 67%, yielding a maximum test positivity rate of 5%. Screening HCWs every three or seven days assuming time-varying test sensitivities reduced RE by 9% and 3%, respectively. Contact tracing reduced RE by at least 32% and achieved higher test positivity rates than screening interventions. HCW cohorting reduced RE by 5%. Sensitivity analyses for 50% and 70% effectiveness of PPE use did not change interpretation.\n\nConclusionsIn response to the emergence of more transmissible SARS-CoV-2 variants, PPE use in all hospital wards might still be most effective in preventing nosocomial transmission. Regular screening and contact tracing of HCWs are also effective interventions, but critically depend on the sensitivity of the diagnostic test used.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Thi Mui Pham", - "author_inst": "Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht" - }, - { - "author_name": "Hannan Tahir", - "author_inst": "Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht" - }, - { - "author_name": "Janneke HHM van de Wijgert", - "author_inst": "Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht; Institute of Infection, Veterinary, and Ecological Sciences, University o" - }, - { - "author_name": "Bastiaan Van der Roest", - "author_inst": "Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht" - }, - { - "author_name": "Pauline Ellerbroek", - "author_inst": "Department of Internal Medicine, University Medical Center Utrecht" - }, - { - "author_name": "Marc JM Bonten", - "author_inst": "Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht; Department of Medical Microbiology, University Medical Center Utrecht" - }, - { - "author_name": "Martin CJ Bootsma", - "author_inst": "Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht; Mathematical Institute, Utrecht University" - }, - { - "author_name": "Mirjam E Kretzschmar", - "author_inst": "Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.07.21252875", "rel_title": "Age-dependent impact of the major common genetic risk factor for COVID-19 on severity and mortality", @@ -860015,6 +861778,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.08.21252979", + "rel_title": "Changes in eating habits and lifestyles in Peruvian population during social isolation by the COVID-19 pandemic", + "rel_date": "2021-03-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.08.21252979", + "rel_abs": "BackgroundThe COVID-19 pandemic caused that some governments have implemented house confinement measures with probable consequences on lifestyle, particularly affecting eating habits, physical activity, sleep quality, and mental health.\n\nObjectivesThe aim of this study was to assess the frequency of lifestyles, physical activity and sleep characteristics, as well as changes in eating habits in the Peruvian population during COVID-19 pandemic.\n\nMethodsA Cross-sectional descriptive study was performed. We analyzed adults from Peru between July to August 2020 based on an online self-administered questionnaire divided into sociodemographic, anthropometrics and COVID-19 diagnostic reported, lifestyle habits and frequency of consumption of foods.\n\nFindingsDuring confinement by COVID-19, 1176 participants were studied, 39% were student, 37.5% were workers and 46% were assert not to work. The population asserted gain weight (1 to 3 Kg) and 35.7% were overweight. The lifestyles habits showed that 54.8% affirmed to doing physical activity and a large proportion (37.2%) asserted sleep less. The Peruvian population presented a main feeding patter of breakfast (95.7%), lunch (97.5%), dinner (89.1%) and brunch (44.9%). Likewise, feeding habits before and during COVID-19 pandemic showed that vegetables (OR:1.56, CI95% 1.21 - 200), fruit (OR: 1.42, CI95% 1.10 - 1.81), legumes (OR:1.67, CI95% 1.23 - 2.28) and eggs (OR: 2.00, CI95% 1.52 - 2.65) presented significantly consumption increase during social isolation, while bakery products (OR: 0.74, CI95% 0.56 - 0.97), meat, snack, refreshment and fast-food decrease consumption. Other food no significant differences were presented.\n\nConclusionThis study in a Peruvian population showed an important frequency of overweight and sleep disorders. There was a slight increase in physical activity despite the social isolation measures and an increase in health eating habits, nevertheless a majority reported gaining weight.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Salomon Huancahuire-Vega", + "author_inst": "Universidad Peruana Union (UPeU)" + }, + { + "author_name": "Edda E. Newball-Noriega", + "author_inst": "Universidad Peruana Union (UPeU)" + }, + { + "author_name": "Ricardo Rojas-Humpire", + "author_inst": "Universidad Peruana Union (UPeU)" + }, + { + "author_name": "Jacksaint Saintila", + "author_inst": "Universidad Peruana Union (UPeU)" + }, + { + "author_name": "Mery Rodriguez Vasquez", + "author_inst": "Universidad Peruana Union (UPeU)" + }, + { + "author_name": "Percy Ruiz-Mamani", + "author_inst": "Universidad Privada San Juan Bautista" + }, + { + "author_name": "Wilter Morales-Garcia", + "author_inst": "Universidad Peruana Union (UPeU)" + }, + { + "author_name": "Michael White", + "author_inst": "Universidad Peruana Union (UPeU)" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.03.08.21253009", "rel_title": "Seroprevalence of anti-SARS-CoV-2 IgG antibodies in Juba, South Sudan: a population-based study", @@ -861007,149 +862817,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.10.21252749", - "rel_title": "Therapeutic Anticoagulation in Critically Ill Patients with Covid-19-Preliminary Report", - "rel_date": "2021-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.10.21252749", - "rel_abs": "BackgroundThrombosis may contribute to morbidity and mortality in Covid-19. We hypothesized that therapeutic anticoagulation would improve outcomes in critically ill patients with Covid-19.\n\nMethodsWe conducted an open-label, adaptive, multiplatform, randomized, clinical trial. Patients with severe Covid-19, defined as the requirement for organ support with high flow nasal cannula, non-invasive ventilation, invasive ventilation, vasopressors, or inotropes, were randomized to receive therapeutic anticoagulation with heparin or pharmacological thromboprophylaxis as per local usual care. The primary outcome was an ordinal scale combining in-hospital mortality (assigned -1) and days free of organ support to day 21.\n\nResultsTherapeutic anticoagulation met the pre-defined criteria for futility in patients with severe Covid-19. The primary outcome was available for 1,074 participants (529 randomized to therapeutic anticoagulation and 545 randomized to usual care pharmacological thromboprophylaxis). Median organ support-free days were 3 days (interquartile range -1, 16) in patients assigned to therapeutic anticoagulation and 5 days (interquartile range -1, 16) in patients assigned to usual care pharmacological thromboprophylaxis (adjusted odds ratio 0.87, 95% credible interval (CrI) 0.70-1.08, posterior probability of futility [odds ratio<1.2] 99.8%). Hospital survival was comparable between groups (64.3% vs. 65.3%, adjusted odds ratio 0.88, 95% CrI 0.67-1.16). Major bleeding occurred in 3.1% of patients assigned to therapeutic anticoagulation and 2.4% of patients assigned to usual care pharmacological thromboprophylaxis.\n\nConclusionsIn patients with severe Covid-19, therapeutic anticoagulation did not improve hospital survival or days free of organ support compared to usual care pharmacological thromboprophylaxis.\n\nTrial registration numbers NCT02735707, NCT04505774, NCT04359277, NCT04372589", - "rel_num_authors": 32, - "rel_authors": [ - { - "author_name": "Ewan C Goligher", - "author_inst": "University of Toronto, Toronto, Canada; University Health Network, Toronto, Canada" - }, - { - "author_name": "Charlotte Ann Bradbury", - "author_inst": "University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, United Kingdom" - }, - { - "author_name": "Bryan J McVerry", - "author_inst": "University of Pittsburgh, Pittsburgh, United States" - }, - { - "author_name": "Patrick R Lawler", - "author_inst": "University of Toronto, Toronto, Canada; Peter Munk Cardiac Centre at University Health Network, Toronto, Canada" - }, - { - "author_name": "Jeffrey S Berger", - "author_inst": "NYU Grossman School of Medicine, New York City, United States" - }, - { - "author_name": "Michelle N Gong", - "author_inst": "Montefiore Medical Center, Bronx, United States; Albert Einstein College of Medicine, Bronx, United States" - }, - { - "author_name": "Marc Carrier", - "author_inst": "Ottawa Hospital Research Institute, Ottawa, Canada; Institut du Savoir Montfort, Ottawa, Canada" - }, - { - "author_name": "Harmony R Reynolds", - "author_inst": "NYU Grossman School of Medicine, New York City, United States" - }, - { - "author_name": "Anand Kumar", - "author_inst": "University of Manitoba, Winnipeg, Canada" - }, - { - "author_name": "Alexis F Turgeon", - "author_inst": "Universite Laval, Quebec City, Canada;" - }, - { - "author_name": "Lucy Z Kornblith", - "author_inst": "Zuckerberg San Francisco General Hospital/University of California, San Francisco, United States" - }, - { - "author_name": "Susan R Kahn", - "author_inst": "McGill University, Montreal, Canada" - }, - { - "author_name": "John C Marshall", - "author_inst": "St. Michael's Hospital Unity Health, Toronto, Canada" - }, - { - "author_name": "Keri S Kim", - "author_inst": "University of Illinois, Chicago, United States" - }, - { - "author_name": "Brett L Houston", - "author_inst": "University of Manitoba, Winnipeg, Canada; CancerCare Manitoba, Winnipeg, Canada" - }, - { - "author_name": "Lennie P. G. Derde", - "author_inst": "University Medical Center Utrecht, Utrecht, The Netherlands" - }, - { - "author_name": "Mary Cushman", - "author_inst": "Larner College of Medicine at the University of Vermont, Burlington, United States" - }, - { - "author_name": "Tobias Tritschler", - "author_inst": "Inselspital, Bern University Hospital, Bern, Switzerland" - }, - { - "author_name": "Derek C Angus", - "author_inst": "University of Pittsburgh, Pittsburgh, United States" - }, - { - "author_name": "Lucas C Godoy", - "author_inst": "University of Toronto, Toronto, Canada; Peter Munk Cardiac Centre at University Health Network, Toronto, Canada" - }, - { - "author_name": "Zoe McQuilten", - "author_inst": "Monash University, Melbourne, Australia" - }, - { - "author_name": "Bridget-Anne Kirwan", - "author_inst": "SOCAR Research SA, Nyon, Switzerland; London School of Hygeine and Tropical Medicine, London, UK" - }, - { - "author_name": "Michael E Farkouh", - "author_inst": "University of Toronto, Toronto, Canada; University Health Network, Toronto, Canada" - }, - { - "author_name": "Maria M Brooks", - "author_inst": "University of Pittsburgh, Pittsburgh, United States" - }, - { - "author_name": "Roger J Lewis", - "author_inst": "Berry Consultants, Austin, United States; Harbor-UCLA Medical Center, Torrance, United States" - }, - { - "author_name": "Anthony Gordon", - "author_inst": "Imperial College London, London, United Kingdom; Imperial College Healthcare NHS Trust, St. Mary's Hospital, London, United Kingdom" - }, - { - "author_name": "Scott Berry", - "author_inst": "Berry Consultants, Austin, United States" - }, - { - "author_name": "Colin J McArthur", - "author_inst": "Australian and New Zealand Intensive Care Research Centre, Monash University, Melbourne, Australia; Auckland City Hospital, Auckland, New Zealand; NHS Blood and" - }, - { - "author_name": "Matthew D Neal", - "author_inst": "University of Pittsburgh, Pittsburgh, United States; UPMC, Pittsburgh, United States" - }, - { - "author_name": "Judith S Hochman", - "author_inst": "NYU Grossman School of Medicine, New York City, United States" - }, - { - "author_name": "Steven A Webb", - "author_inst": "Australian and New Zealand Intensive Care Research Centre, Monash University, Melbourne, Australia; St John of God Hospital, Subiaco, Australia" - }, - { - "author_name": "Ryan Zarychanski", - "author_inst": "University of Manitoba, Winnipeg, Canada; CancerCare Manitoba, Winnipeg, Canada" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2021.03.10.21253251", "rel_title": "Model Based Estimation of the SARS-CoV-2 Immunization Level in Austria and Consequences for Herd Immunity Effects", @@ -861933,6 +863600,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.10.21253235", + "rel_title": "Wastewater Surveillance of SARS-CoV-2 across 40 U.S. states", + "rel_date": "2021-03-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.10.21253235", + "rel_abs": "Wastewater-based disease surveillance is a promising approach for monitoring community outbreaks. Here we describe a nationwide campaign to monitor SARS-CoV-2 in the wastewater of 159 counties in 40 U.S. states, covering 13% of the U.S. population from February 18 to June 2, 2020. Out of 1,751 total samples analyzed, 846 samples were positive for SARS-CoV-2 RNA, with overall viral concentrations declining from April to May. Wastewater viral titers were consistent with, and appeared to precede, clinical COVID-19 surveillance indicators, including daily new cases. Wastewater surveillance had a high detection rate (>80%) of SARS-CoV-2 when the daily incidence exceeded 13 per 100,000 people. Detection rates were positively associated with wastewater treatment plant catchment size. To our knowledge, this work represents the largest-scale wastewater-based SARS-CoV-2 monitoring campaign to date, encompassing a wide diversity of wastewater treatment facilities and geographic locations. Our findings demonstrate that a national wastewater-based approach to disease surveillance may be feasible and effective.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Fuqing Wu", + "author_inst": "Department of Biological Engineering, Massachusetts Institute of Technology" + }, + { + "author_name": "Amy Xiao", + "author_inst": "Department of Biological Engineering, Massachusetts Institute of Technology" + }, + { + "author_name": "Jianbo Zhang", + "author_inst": "Department of Biological Engineering, Massachusetts Institute of Technology" + }, + { + "author_name": "Katya Moniz", + "author_inst": "Department of Biological Engineering, Massachusetts Institute of Technology" + }, + { + "author_name": "Noriko Endo", + "author_inst": "Biobot Analytics, Inc., Cambridge, MA" + }, + { + "author_name": "Federica Armas:", + "author_inst": "Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore" + }, + { + "author_name": "Mary Bushman", + "author_inst": "Harvard T.H. Chan School of Public Health, Harvard University" + }, + { + "author_name": "Peter R Chai", + "author_inst": "Division of Medical Toxicology, Department of Emergency Medicine, Brigham and Women's Hospital, Harvard Medical School" + }, + { + "author_name": "Claire Duvallet", + "author_inst": "Biobot Analytics, Inc., Cambridge, MA" + }, + { + "author_name": "Timothy B Erickson", + "author_inst": "Division of Medical Toxicology, Department of Emergency Medicine, Brigham and Women's Hospital, Harvard Medical School" + }, + { + "author_name": "Katelyn Foppe", + "author_inst": "Biobot Analytics, Inc., Cambridge, MA" + }, + { + "author_name": "Newsha Ghaeli", + "author_inst": "Biobot Analytics, Inc., Cambridge, MA" + }, + { + "author_name": "Xiaoqiong Gu", + "author_inst": "Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore" + }, + { + "author_name": "William P Hanage", + "author_inst": "Harvard T.H. Chan School of Public Health, Harvard University" + }, + { + "author_name": "Katherine H Huang", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Wei Lin Lee", + "author_inst": "Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore" + }, + { + "author_name": "Mariana Matus", + "author_inst": "Biobot Analytics, Inc., Cambridge, MA" + }, + { + "author_name": "Kyle A McElroy", + "author_inst": "Biobot Analytics, Inc., Cambridge, MA" + }, + { + "author_name": "Steven F Rhode", + "author_inst": "Massachusetts Water Resources Authority, Boston" + }, + { + "author_name": "Stefan Wuertz", + "author_inst": "Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University" + }, + { + "author_name": "Janelle Thompson", + "author_inst": "Singapore Centre for Environmental Life Sciences Engineering; Asian School of the Environment, Nanyang Technological University" + }, + { + "author_name": "Eric J Alm", + "author_inst": "Department of Biological Engineering; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.10.21252001", "rel_title": "The BioNTech / Pfizer vaccine BNT162b2 induces class-switched SARS-CoV-2-specific plasma cells and potential memory B cells as well as IgG and IgA serum and IgG saliva antibodies upon the first immunization", @@ -862713,29 +864483,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.10.21253346", - "rel_title": "Acceptance and intake of COVID-19 vaccines among older Germans", - "rel_date": "2021-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.10.21253346", - "rel_abs": "The main aim of this study was to investigate the various factors influencing COVID-19 vaccination acceptance and actual intake among older Germans aged over 75 years old (N = 1037). We found that the intention to get vaccinated or intake of the COVID-19 vaccine were positively related to the perceptions of becoming infected, perceptions of the severity of the potential long-term effects, the vaccines efficacy, and the benefits of vaccination. Meanwhile, the intention to get the vaccine or vaccine intake were decreased by perceptions of the negative side-effects and the general impediments to vaccination.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Marta Malesza", - "author_inst": "University of Economics and Human Sciences in Warsaw" - }, - { - "author_name": "Erich Wittmann", - "author_inst": "German Research Center for Environmental Health, Munich, Germany" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.03.11.21253189", "rel_title": "Risk, clinical course and outcome of ischemic stroke in patients hospitalized with COVID-19: a multicenter cohort study", @@ -863487,6 +865234,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.11.21253309", + "rel_title": "Day Camp in the Time of COVID-19: What Went Right?", + "rel_date": "2021-03-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.11.21253309", + "rel_abs": "ObjectiveTo evaluate whether a successful camp experience can be achieved with implementation of COVID-19 education, screening and hygiene protocols, and designated cohorts during the summer of 2020.\n\nStudy DesignA survey study of summer day camp directors in the metro-New York area was conducted in September, 2020. The survey inquired about camper demographics, COVID-10 related policies, and the number of COVID-19 cases and exposures at each camp.\n\nResultsResponses were received from 77% (23/30) of camp directors at the completion of the 2020 summer. There were 8,480 camper children and 3,698 staff across the 23 camps surveyed. A variety of precautions were taken to limit COVID-19 incidence among campers and staff, most often including COVID-19 screening at entry, cohorting campers, maximizing outdoor activities, mandating mask use when indoors, and frequent hand sanitizing. Six staff and one camper tested positive for COVID-19. There was no secondary spread within the staff or campers in any of the camps.\n\nConclusionCamps successfully stayed open in the summer of 2020. The low level of COVID-19 in the community was critical to the initial success of camp opening. Policies that were consistent and maintained among the camps helped prevent further spread.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Sharon Nachman", + "author_inst": "Stony Brook Children's Hospital" + }, + { + "author_name": "Gabrielle Brauner", + "author_inst": "Stony Brook Children's Hospital" + }, + { + "author_name": "Aviva Beleck", + "author_inst": "Stony Brook Children's Hospital" + }, + { + "author_name": "Andrew S Handel", + "author_inst": "Stony Brook Children's Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2021.03.11.21253350", "rel_title": "Oxygen provision to severely ill COVID-19 patients at the peak of the 2020 pandemic in a Swedish district hospital: medical records-based cohort study", @@ -864519,37 +866297,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.11.21253361", - "rel_title": "Mean Vitamin D levels in 19 European Countries & COVID-19 Mortality over 10 months", - "rel_date": "2021-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.11.21253361", - "rel_abs": "ObjectivesReports early in the epidemic linking low mean national Vitamin D level with increased COVID-19 death, and until recently little research on the impact of Vitamin D deficiency on severity of COVID-19, led to this update of the initial report studying mortality up to the end of January 2021.\n\nDesign and SettingCoronavirus pandemic data for 19 European countries were downloaded from Our World in Data, which was last updated on January 24, 2021. Data from March 21, 2020 to January 22, 2021 were included in the statistical analysis. Vitamin-D (25)-HD mean data were collected by literature review. Poisson mixed-effect model was used to model the data.\n\nResultsEuropean countries with Vitamin-D (25)-HD mean less than or equal to 50 have higher COVID-19 death rates as compared with European countries with Vitamin-D (25)-HD mean greater than 50, relative risk of 2.155 (95% CI: 1.068 - 4.347, p-value = 0.032). A statistically significant negative moderate Spearman rank correlation was observed between Vitamin-D (25)-HD mean and the number of COVID-19 deaths for each 14-day period during the COVID-19 pandemic time period.\n\nConclusionsThe observation of the significantly lower COVID-19 mortality rates in countries with lowest annual sun exposure but highest mean Vitamin-D (25)-HD levels provides support for the use of food fortification. The need to consider re-configuring vaccine strategy due to emergence of large number of COVID-19 variants provides an opportunity to undertake such therapeutic randomized control trials.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Amar Ahmad", - "author_inst": "New York University" - }, - { - "author_name": "Christian Heumann", - "author_inst": "Ludwig-Maximilians-Universitat Munchen" - }, - { - "author_name": "Raghib Ali", - "author_inst": "New York University" - }, - { - "author_name": "Tim Oliver", - "author_inst": "Barts Cancer Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.11.21253301", "rel_title": "Quantifying Contact Patterns in Response to COVID-19 Public Health Measures in Canada", @@ -865145,6 +866892,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.12.21253444", + "rel_title": "COVID-19 vaccine hesitancy among undergraduate medical students: results from a nationwide survey in India", + "rel_date": "2021-03-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.12.21253444", + "rel_abs": "COVID-19 vaccine was launched in India on 16 January 2021, prioritizing health care workers which included medical students. We aimed to assess vaccine hesitancy and factors related to it among undergraduate medical students in India. An online questionnaire was filled by 1068 medical students across 22 states and union territories of India from 2 February - 7 March 2021. Vaccine hesitancy was found among 10.6%. Concern regarding vaccine safety and efficacy, hurried testing of vaccines prior to launch and lack of trust in government agencies predicted COVID-19 vaccine hesitancy. Risk perception regarding contracting COVID-19 vaccine reduced COVID-19 vaccine hesitancy as well as hesitation in participating in COVID-19 vaccine trials. Choosing between the two available vaccines (Covishield and Covaxin) was considered important by medical students both for themselves and their future patients. Covishield was preferred to Covaxin by students. Majority of those willing to take the COVID-19 vaccine felt that it was important for them to resume their clinical posting, face-to-face classes and get their personal life back on track. Around three-fourths medical students viewed that COVID-19 vaccine should be made mandatory for both health care workers and international travellers. Prior adult vaccination didnt have an effect upon COVID-19 vaccine hesitancy. Targeted awareness campaigns, regulatory oversight of vaccine trials and public release of safety and efficacy data and trust building activities could further reduce COVID-19 vaccine hesitancy among medical students.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Jyoti Jain", + "author_inst": "All India Institute of Medical Sciences (AIIMS), Jodhpur" + }, + { + "author_name": "Suman Saurabh", + "author_inst": "All India Institute of Medical Sciences (AIIMS), Jodhpur" + }, + { + "author_name": "Akhil Dhanesh Goel", + "author_inst": "All India Institute of Medical Sciences (AIIMS), Jodhpur" + }, + { + "author_name": "Manoj Kumar Gupta", + "author_inst": "All India Institute of Medical Sciences (AIIMS), Jodhpur" + }, + { + "author_name": "Pankaj Bhardwaj", + "author_inst": "All India Institute of Medical Sciences (AIIMS), Jodhpur" + }, + { + "author_name": "Pankaja Ravi Raghav", + "author_inst": "All India Institute of Medical Sciences (AIIMS), Jodhpur" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.12.21253454", "rel_title": "Modelling, prediction and design of national COVID-19 lockdowns by stringency and duration", @@ -866024,57 +867810,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2021.03.09.21253206", - "rel_title": "Proteome-wide Mendelian randomization identifies causal links between blood proteins and severe COVID-19", - "rel_date": "2021-03-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.09.21253206", - "rel_abs": "The COVID-19 pandemic death toll now surpasses two million individuals and there is a need for early identification of individuals at increased risk of mortality. Host genetic variation partially drives the immune and biochemical responses to COVID-19 that lead to risk of mortality. We identify and prioritise blood proteins and biomarkers that may indicate increased risk for severe COVID-19, via a proteome Mendelian randomization approach by collecting genome-wide association study (GWAS) summary statistics for >4,000 blood proteins. After multiple testing correction, troponin I3, cardiac type (TNNI3) had the strongest effect (odds ratio (O.R.) of 6.86 per standard deviation increase in protein level), with proteinase 3 (PRTN3) (O.R.=2.48), major histocompatibility complex, class II, DQ alpha 2 (HLA-DQA2) (O.R.=2.29), the C4A-C4B heterodimer (O.R.=1.76) and low-density lipoprotein receptor-related protein associated protein 1 (LRPAP1) (O.R.=1.73) also being associated with higher odds of severe COVID-19. Conversely, major histocompatibility complex class I polypeptide-related sequence A (MHC1A) (O.R.=0.6) and natural cytotoxicity triggering receptor 3 (NCR3) (O.R.=0.46) were associated with lower odds. These proteins are involved in heart muscle contraction, natural killer and antigen presenting cells, and the major histocompatibility complex. Based on these findings, it may be possible to better predict which patients may develop severe COVID-19 and to design better treatments targeting the implicated mechanisms.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Alish B. Palmos", - "author_inst": "King's College London" - }, - { - "author_name": "Vincent Millischer", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "David K. Menon", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Timothy R. Nicholson", - "author_inst": "King's College London" - }, - { - "author_name": "Leonie Taams", - "author_inst": "King's College London" - }, - { - "author_name": "Benedict Michael", - "author_inst": "University of Liverpool" - }, - { - "author_name": "- COVID Clinical Neuroscience Study Consortium", - "author_inst": "" - }, - { - "author_name": "Christopher Huebel", - "author_inst": "King's College London" - }, - { - "author_name": "Gerome Breen", - "author_inst": "King's College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2021.03.08.21253157", "rel_title": "Functional Antibodies in COVID-19 Convalescent Plasma", @@ -866873,6 +868608,33 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.03.09.21253179", + "rel_title": "Prediction of COVID-19 mortality among hospitalized patients in Sudan", + "rel_date": "2021-03-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.09.21253179", + "rel_abs": "BackgroundCOVID-19 was primarily reported in China. The mortality rate across countries had ranged from 1% up to more than 10% and it is underestimated in some countries. Advanced age is the most frequently reported factor associated to mortality. Other factors were the presence of comorbidities such as diabetes mellitus, hypertension and obesity. Several models for mortality prediction had been developed to assist in improving the prognosis. The aim of our study was to assess the factors related to mortality among COVID-19 patients and develop a prediction model based on these factors.\n\nMethodsA retrospective cohort study assessed the factors related to the mortality among COVID-19 patients who attended Imperial Hospital isolation centre on November-December, 2020, Khartoum, Sudan. Statistical tests performed were chi-square test, odds ratio and regression to develop the prediction model. Tests were considered statistically significant when p < 0.05.\n\nResults105 patients were studied. 29% of the patients were deceased, while, 71% were discharged alive. A statistically significant association was found between the age and severity with regards to mortality rate (p=0.034, 0.018 respectively). The model equation for mortality prediction: Mortality = -14.724+ (1.387* Age) + (-0.323* Gender) + (1.814* Admission) + (0.193* Ischemic Heart Disease) + (-0.369* Fever) + (1.595* Cough) + (1.953* Complications) + (0.149* Duration of hospitalization) + (0.999* Enoxaparin dose).\n\nConclusionsAge, admission ward, cough and enoxaparin dose were statistically significant predictors for COVID-19 mortality (p= 0.014, 0.011, 0.015, 0.006 respectively).", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ghada Omer Hamad Abd El-Raheem", + "author_inst": "Imperial Hospital" + }, + { + "author_name": "Maysoun Ahmed Awad Yousif", + "author_inst": "Imperial Hospital" + }, + { + "author_name": "Doaa Salih Ibrahim Mohamed", + "author_inst": "Imperial Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.03.08.21253110", "rel_title": "Incidence of SARS-CoV-2 infection according to baseline antibody status in staff and residents of 100 Long Term Care Facilities (VIVALDI study)", @@ -868025,205 +869787,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.03.09.434529", - "rel_title": "Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19", - "rel_date": "2021-03-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.09.434529", - "rel_abs": "Type I interferon (IFN-I) neutralizing autoantibodies have been found in some critical COVID-19 patients; however, their prevalence and longitudinal dynamics across the disease severity scale, and functional effects on circulating leukocytes remain unknown. Here, in 284 COVID-19 patients, we found IFN-I autoantibodies in 19% of critical, 6% of severe and none of the moderate cases. Longitudinal profiling of over 600,000 peripheral blood mononuclear cells using multiplexed single-cell epitope and transcriptome sequencing from 54 COVID-19 patients, 15 non-COVID-19 patients and 11 non-hospitalized healthy controls, revealed a lack of IFN-I stimulated gene (ISG-I) response in myeloid cells from critical cases, including those producing anti-IFN-I autoantibodies. Moreover, surface protein analysis showed an inverse correlation of the inhibitory receptor LAIR-1 with ISG-I expression response early in the disease course. This aberrant ISG-I response in critical patients with and without IFN-I autoantibodies, supports a unifying model for disease pathogenesis involving ISG-I suppression via convergent mechanisms.", - "rel_num_authors": 46, - "rel_authors": [ - { - "author_name": "Monique G.P. van der Wijst", - "author_inst": "Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherland; Institute of Human Genetics, University of Cali" - }, - { - "author_name": "Sara E. Vazquez", - "author_inst": "Medical Scientist Training Program, University of California. San Francisco, CA, USA; Tetrad Graduate Program, University of California, San Francisco, CA, USA;" - }, - { - "author_name": "George C. Hartoularos", - "author_inst": "Institute of Human Genetics, University of California, San Francisco, CA, USA; Division of Rheumatology, Department of Medicine, University of California, San F" - }, - { - "author_name": "Paul Bastard", - "author_inst": "Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; University of Paris, Imagine" - }, - { - "author_name": "Tianna Grant", - "author_inst": "Institute of Human Genetics, University of California, San Francisco, CA, USA; Division of Rheumatology, Department of Medicine, University of California, San F" - }, - { - "author_name": "Raymund Bueno", - "author_inst": "Institute of Human Genetics, University of California, San Francisco, CA, USA; Division of Rheumatology, Department of Medicine, University of California, San F" - }, - { - "author_name": "David S. Lee", - "author_inst": "Institute of Human Genetics, University of California, San Francisco, CA, USA; Division of Rheumatology, Department of Medicine, University of California, San F" - }, - { - "author_name": "John R. Greenland", - "author_inst": "Department of Medicine, San Francisco VA Health Care System, University of California, San Francisco, CA, USA." - }, - { - "author_name": "Yang Sun", - "author_inst": "Institute of Human Genetics, University of California, San Francisco, CA, USA; Division of Rheumatology, Department of Medicine, University of California, San F" - }, - { - "author_name": "Richard Perez", - "author_inst": "Institute of Human Genetics, University of California, San Francisco, CA, USA; School of Medicine, University of California, San Francisco, San Francisco, Calif" - }, - { - "author_name": "Anton Ogorodnikov", - "author_inst": "Institute of Human Genetics, University of California, San Francisco, CA, USA; Division of Rheumatology, Department of Medicine, University of California, San F" - }, - { - "author_name": "Alyssa Ward", - "author_inst": "Institute of Human Genetics, University of California, San Francisco, CA, USA; Division of Rheumatology, Department of Medicine, University of California, San F" - }, - { - "author_name": "Sabrina A. Mann", - "author_inst": "Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA." - }, - { - "author_name": "Kara L. Lynch", - "author_inst": "Zuckerberg San Francisco General, San Francisco, CA, USA." - }, - { - "author_name": "Cassandra Yun", - "author_inst": "Zuckerberg San Francisco General, San Francisco, CA, USA." - }, - { - "author_name": "Diane V. Havlir", - "author_inst": "Division of HIV, Infectious Disease and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA." - }, - { - "author_name": "Gabriel Chamie", - "author_inst": "Division of HIV, Infectious Disease and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA." - }, - { - "author_name": "Carina Marquez", - "author_inst": "Division of HIV, Infectious Disease and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA." - }, - { - "author_name": "Bryan Greenhouse", - "author_inst": "Division of HIV, Infectious Disease and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA." - }, - { - "author_name": "Michail S. Lionakis", - "author_inst": "Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Ins" - }, - { - "author_name": "Philip J. Norris", - "author_inst": "Zuckerberg San Francisco General, San Francisco, CA, USA; Department of Laboratory Medicine, University of California, San Francisco, CA, USA; Vitalant Research" - }, - { - "author_name": "Larry J. Dumont", - "author_inst": "Vitalant Research Institute, Denver, CO, USA; University of Colorado School of Medicine, Aurora, CO, USA; Geisel School of Medicine at Dartmouth, Lebanon, NH, U" - }, - { - "author_name": "Kathleen Kelly", - "author_inst": "Vitalant Research Institute, Denver, CO, USA." - }, - { - "author_name": "Peng Zhang", - "author_inst": "St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA." - }, - { - "author_name": "Qian Zhang", - "author_inst": "St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA." - }, - { - "author_name": "Adrian Gervais", - "author_inst": "University of Paris, Imagine Institute, Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller Univer" - }, - { - "author_name": "Tom Le Voyer", - "author_inst": "University of Paris, Imagine Institute, Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller Univer" - }, - { - "author_name": "Alexander Whatley", - "author_inst": "Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA." - }, - { - "author_name": "Yichen Si", - "author_inst": "Department of Biostaticstics, University of Michigan." - }, - { - "author_name": "Ashley Byrne", - "author_inst": "Chan Zuckerberg Biohub, San Francisco, CA, USA." - }, - { - "author_name": "Alexis J. Combes", - "author_inst": "ImmunoX Initiative, University of California, San Francisco, CA, USA; Department of Pathology, University of California, San Francisco, CA, USA; UCSF CoLabs, Un" - }, - { - "author_name": "Arjun Arkal", - "author_inst": "ImmunoX Initiative, University of California, San Francisco, CA, USA; Department of Pathology, University of California, San Francisco, CA, USA; UCSF CoLabs, Un" - }, - { - "author_name": "Yun S. Song", - "author_inst": "Chan Zuckerberg Biohub, San Francisco, CA, USA; Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA; Departm" - }, - { - "author_name": "Gabriela K. Fragiadakis", - "author_inst": "Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA; ImmunoX Initiative, University of California, San Fr" - }, - { - "author_name": "- UCSF COMET consortium", - "author_inst": "-" - }, - { - "author_name": "Kirsten Kangelaris", - "author_inst": "Division of Infectious Disease, Department of Medicine, University of California, San Francisco, CA, USA." - }, - { - "author_name": "Carolyn S. Calfee", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine and the Cardiovascular Research Institute, University of California, San Francisco, CA," - }, - { - "author_name": "David J. Erle", - "author_inst": "Institute of Human Genetics, University of California, San Francisco, CA, USA; ImmunoX Initiative, University of California, San Francisco, CA, USA; Zuckerberg " - }, - { - "author_name": "Carolyn Hendrickson", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine and the Cardiovascular Research Institute, University of California, San Francisco, CA," - }, - { - "author_name": "Matthew F. Krummel", - "author_inst": "ImmunoX Initiative, University of California, San Francisco, CA, USA; Department of Pathology, University of California, San Francisco, CA, USA." - }, - { - "author_name": "Prescott G. Woodruff", - "author_inst": "ImmunoX Initiative, University of California, San Francisco, CA, USA; Division of Pulmonary and Critical Care Medicine, Department of Medicine and the Cardiovas" - }, - { - "author_name": "Charles R. Langelier", - "author_inst": "Division of Infectious Disease, Department of Medicine, University of California, San Francisco, CA, USA." - }, - { - "author_name": "Jean-Laurent Casanova", - "author_inst": "Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; University of Paris, Imagine" - }, - { - "author_name": "Joseph L. Derisi", - "author_inst": "Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA." - }, - { - "author_name": "Mark S. Anderson", - "author_inst": "Diabetes Center, University of California, San Francisco, CA, USA; Endocrine Division, Department of Medicine, University of California, San Francisco, CA, USA." - }, - { - "author_name": "Chun J. Ye", - "author_inst": "Institute of Human Genetics, University of California, San Francisco, CA, USA; Division of Rheumatology, Department of Medicine, University of California, San F" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.03.10.434447", "rel_title": "Naturally-acquired immunity in Syrian Golden Hamsters provides protection from re-exposure to emerging heterosubtypic SARS-CoV-2 variants B.1.1.7 and B.1.351", @@ -869599,6 +871162,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.05.21252541", + "rel_title": "Early estimates of SARS-CoV-2 B.1.1.7 variant emergence in a university setting", + "rel_date": "2021-03-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.05.21252541", + "rel_abs": "Recent identification of the highly transmissible novel SARS-CoV-2 variant in the United Kingdom (B.1.1.7) has raised concerns for renewed pandemic surges worldwide 1,2. B.1.1.7 was first identified in the US on December 29, 2020 and may become dominant by March 2021 3. However, the regional prevalence of B.1.1.7 is largely unknown because of limited molecular surveillance for SARS-CoV-2 4. Quantitative PCR data from a surveillance testing program on a large university campus with roughly 30,000 students provides local situational awareness at a pivotal moment in the COVID-19 pandemic.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Kaitlyn E Johnson", + "author_inst": "The University of Texas at Austin, Austin" + }, + { + "author_name": "Spencer Woody", + "author_inst": "The University of Texas at Austin" + }, + { + "author_name": "Michael Lachmann", + "author_inst": "Santa Fe Institute" + }, + { + "author_name": "Spencer J Fox", + "author_inst": "The University of Texas at Austin" + }, + { + "author_name": "Jessica Klima", + "author_inst": "The University of Texas at Austin" + }, + { + "author_name": "Terrance S Hines", + "author_inst": "The University of Texas at Austin" + }, + { + "author_name": "Lauren Ancel Meyers", + "author_inst": "The University of Texas at Austin" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.07.21253080", "rel_title": "COVID-19 vaccine distrust in Colombian university students: Frequency and associated variables", @@ -870691,81 +872297,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.03.09.434371", - "rel_title": "Quantitative proteomics of hamster lung tissues infected with SARS-CoV-2 reveal host-factors having implication in the disease pathogenesis and severity", - "rel_date": "2021-03-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.09.434371", - "rel_abs": "Syrian golden hamsters (Mesocricetus auratus) infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) manifests lung pathology that resembles human COVID-19 patients. In this study, efforts were made to check the infectivity of a local SARS-CoV-2 isolate in hamster model and evaluate the differential expression of lung proteins during acute infection and convalescence. The findings of this study confirm the infectivity of this isolate in vivo. Analysis of clinical parameters and tissue samples shows a similar type of pathophysiological manifestation of SARS-CoV-2 infection as reported earlier in COVID-19 patients and hamsters infected with other isolates. The lung-associated pathological changes were very prominent on the 4th day post-infection (dpi), mostly resolved by 14dpi. Here, we carried out quantitative proteomic analysis of the lung tissues from SARS-CoV-2-infected hamsters at day 4 and day 14 post infection. This resulted in the identification of 1,585 differentially expressed proteins of which 68 proteins were significantly altered among both the infected groups. Pathway analysis revealed complement and coagulation cascade, platelet activation, ferroptosis and focal adhesion as the top enriched pathways. In addition, we also identified altered expression of two pulmonary surfactant-associated proteins (Sftpd and Sftpb), known for their protective role in lung function. Together, these findings will aid in the identification of candidate biomarkers and understanding the mechanism(s) involved in SARS-CoV-2 pathogenesis.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=143 HEIGHT=200 SRC=\"FIGDIR/small/434371v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (31K):\norg.highwire.dtl.DTLVardef@1930556org.highwire.dtl.DTLVardef@14376d6org.highwire.dtl.DTLVardef@2f064eorg.highwire.dtl.DTLVardef@1472572_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Voddu Suresh", - "author_inst": "Institute of Life Sciences, Bhubaneswar" - }, - { - "author_name": "Varshasnata Mohanty", - "author_inst": "Institute of Life Sciences, Bhubaneswar" - }, - { - "author_name": "Kiran Avula", - "author_inst": "Institute of Life Sciences, Bhubaneswar" - }, - { - "author_name": "Arup Ghosh", - "author_inst": "Institute of Life Sciences, Bhubaneswar" - }, - { - "author_name": "Bharti Singh", - "author_inst": "Institute of Life Sciences, Bhubaneswar" - }, - { - "author_name": "R Rajendra Kumar Reddy", - "author_inst": "Institute of Life Sciences, Bhubaneswar" - }, - { - "author_name": "Amol Ratnakar Suryawanshi", - "author_inst": "Institute of Life Sciences, Bhubaneswar" - }, - { - "author_name": "Sunil Raghav", - "author_inst": "Institute of Life Sciences, Bhubaneswar" - }, - { - "author_name": "Soma Chattopadhyay", - "author_inst": "Institute of Life Sciences, Bhubaneswar" - }, - { - "author_name": "Punit Prasad", - "author_inst": "Institute of Life Sciences, Bhubaneswar" - }, - { - "author_name": "Rajeeb Kumar Swain", - "author_inst": "Institute of Life Sciences, Bhubaneswar" - }, - { - "author_name": "Rupesh Dash", - "author_inst": "Institute of Life Sciences, Bhubaneswar" - }, - { - "author_name": "Ajay Parida", - "author_inst": "Institute of Life Sciences, BHubaneswar" - }, - { - "author_name": "Gulam Hussain Syed", - "author_inst": "Institute of Life Sciences, Bhubaneswar" - }, - { - "author_name": "Shantibhusan Senapati", - "author_inst": "Institute of Life Sciences, Bhubaneswar" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.03.09.434359", "rel_title": "In vitro rapid inactivation of SARS-CoV-2 by visible light photocatalysis using boron-doped bismuth oxybromide", @@ -871745,6 +873276,133 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.03.07.434227", + "rel_title": "Development of potency, breadth and resilience to viral escape mutations in SARS-CoV-2 neutralizing antibodies", + "rel_date": "2021-03-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.07.434227", + "rel_abs": "Antibodies elicited in response to infection undergo somatic mutation in germinal centers that can result in higher affinity for the cognate antigen. To determine the effects of somatic mutation on the properties of SARS-CoV-2 spike receptor-binding domain (RBD)-specific antibodies, we analyzed six independent antibody lineages. As well as increased neutralization potency, antibody evolution changed pathways for acquisition of resistance and, in some cases, restricted the range of neutralization escape options. For some antibodies, maturation apparently imposed a requirement for multiple spike mutations to enable escape. For certain antibody lineages, maturation enabled neutralization of circulating SARS-CoV-2 variants of concern and heterologous sarbecoviruses. Antibody-antigen structures revealed that these properties resulted from substitutions that allowed additional variability at the interface with the RBD. These findings suggest that increasing antibody diversity through prolonged or repeated antigen exposure may improve protection against diversifying SARS-CoV-2 populations, and perhaps against other pandemic threat coronaviruses.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Frauke Muecksch", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Yiska Weisblum", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Christopher Barnes", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Fabian Schmidt", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Dennis Schaefer-Babajew", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Julio Lorenzi", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Andrew Flyak", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Andrew DeLaitsch", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Kathryn Huey-Tubman", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Shurong Hou", + "author_inst": "Unversity Of Massachussets Medical School" + }, + { + "author_name": "Celia Schiffer", + "author_inst": "Unversity Of Massachussets Medical School" + }, + { + "author_name": "Christian Gaebler", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Zijun Wang", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Justin Da Silva", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Daniel Poston", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Shlomo Finkin", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Alice Cho", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Melissa Cipolla", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Thiago Oliveira", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Katrina Millard", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Victor Ramos", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Anna Gazumyan", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Magdalena Rutkowska", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Marina Caskey", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Michel Nussenzweig", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Pamela Bjorkman", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Theodora Hatziioannou", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Paul Bieniasz", + "author_inst": "The Rockefeller University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.03.05.434168", "rel_title": "Deletion disrupts a conserved antibody epitope in a SARS-CoV-2 variant of concern", @@ -872781,77 +874439,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.03.01.21252653", - "rel_title": "Recommendations for COVID-19 Vaccination in People with Rheumatic Disease: Developed by the Singapore Chapter of Rheumatologists", - "rel_date": "2021-03-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.01.21252653", - "rel_abs": "AimPeople with rheumatic diseases (PRD) remain vulnerable in the era of the COVID-19 pandemic. We formulated recommendations to meet the urgent need for a consensus for vaccination against SARS-CoV-2 in PRD.\n\nMethodsSystematic literature reviews were performed to evaluate (1) outcomes in PRD with COVID-19; (2) efficacy, immunogenicity and safety of COVID-19 vaccination; and (3) published guidelines/recommendations for non-live, non-COVID-19 vaccinations in PRD. Recommendations were formulated based on the evidence and expert opinion according to the Grading of Recommendations Assessment, Development and Evaluation methodology.\n\nResultsThe consensus comprises two overarching principles and seven recommendations. Vaccination against SARS-CoV-2 in PRD should be aligned with prevailing national policy and should be individualized through shared decision between the healthcare provider and patient. We strongly recommended that eligible PRD and household contacts be vaccinated against SARS-CoV-2. We conditionally recommended that the COVID-19 vaccine be administered during quiescent disease if possible. Immunomodulatory drugs, other than rituximab, can be continued alongside vaccination. We conditionally recommended that the COVID-19 vaccine be administered prior to commencing rituximab if possible. For patients on rituximab, the vaccine should be administered a minimum of 6 months after the last dose and/or 4 weeks prior to the next dose of rituximab. Post-vaccination antibody titres against SARS-CoV-2 need not be measured. Any of the approved COVID-19 vaccines may be used, with no particular preference.\n\nConclusionThese recommendations provide guidance for COVID-19 vaccination in PRD. Most recommendations in this consensus are conditional, reflecting a lack of evidence or low-level evidence. (words 247)", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Amelia Santosa", - "author_inst": "Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore" - }, - { - "author_name": "Chuanhui Xu", - "author_inst": "Department of Rheumatology, Allergy and Immunology, Tan Tock Seng Hospital, Singapore" - }, - { - "author_name": "Thaschawee Arkachaisri", - "author_inst": "Rheumatology and Immunology Service, Department of Paediatric Subspecialties, KK Women's and Children's Hospital, Singapore" - }, - { - "author_name": "Kok Ooi Kong", - "author_inst": "Department of Rheumatology, Allergy and Immunology, Tan Tock Seng Hospital, Singapore" - }, - { - "author_name": "Aisha Lateef", - "author_inst": "Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore" - }, - { - "author_name": "Tau Hong Lee", - "author_inst": "National Centre for Infectious Diseases, Singapore" - }, - { - "author_name": "Keng Hong Leong", - "author_inst": "Leong Keng Hong Arthritis and Medical Clinic, Singapore" - }, - { - "author_name": "Andrea HL Low", - "author_inst": "Department of Rheumatology & Immunology, Singapore General Hospital, Singapore" - }, - { - "author_name": "Melonie K Sriranganathan", - "author_inst": "Department of Medicine, Changi General Hospital, Singapore" - }, - { - "author_name": "Teck Choon Tan", - "author_inst": "Division of Rheumatology, Department of Medicine, Khoo Teck Puat Hospital, Singapore" - }, - { - "author_name": "Gim Gee Teng", - "author_inst": "Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore" - }, - { - "author_name": "Bernard Y Thong", - "author_inst": "Department of Rheumatology, Allergy and Immunology, Tan Tock Seng Hospital, Singapore" - }, - { - "author_name": "Warren Fong", - "author_inst": "Department of Rheumatology & Immunology, Singapore General Hospital, Singapore" - }, - { - "author_name": "Manjari Lahiri", - "author_inst": "Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "rheumatology" - }, { "rel_doi": "10.1101/2021.03.04.21252893", "rel_title": "Measuring the exposure of Black, Asian and other ethnic groups to Covid-infected neighbourhoods in English towns and cities", @@ -873463,6 +875050,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.04.21252931", + "rel_title": "A common TMPRSS2 variant protects against severe COVID-19", + "rel_date": "2021-03-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.04.21252931", + "rel_abs": "Infection with SARS-CoV-2 has a wide range of clinical presentations, from asymptomatic to life-threatening. Old age is the strongest factor associated with increased COVID19-related mortality, followed by sex and pre-existing conditions. The importance of genetic and immunological factors on COVID19 outcome is also starting to emerge, as demonstrated by population studies and the discovery of damaging variants in genes controlling type I IFN immunity and of autoantibodies that neutralize type I IFNs. The human protein transmembrane protease serine type 2 (TMPRSS2) plays a key role in SARS-CoV-2 infection, as it is required to activate the virus spike protein, facilitating entry into target cells. We focused on the only common TMPRSS2 non-synonymous variant predicted to be damaging (rs12329760), which has a minor allele frequency of [~]25% in the population. In a large population of SARS-CoV-2 positive patients, we show that this variant is associated with a reduced likelihood of developing severe COVID19 (OR 0.87, 95%CI:0.79-0.97, p=0.01). This association was stronger in homozygous individuals when compared to the general population (OR 0.65, 95%CI:0.50-0.84, p=1.3x10-3). We demonstrate in vitro that this variant, which causes the amino acid substitution valine to methionine, impacts the catalytic activity of TMPRSS2 and is less able to support SARS-CoV-2 spike-mediated entry into cells.\n\nTMPRSS2 rs12329760 is a common variant associated with a significantly decreased risk of severe COVID19. Further studies are needed to assess the expression of the TMPRSS2 across different age groups. Moreover, our results identify TMPRSS2 as a promising drug target, with a potential role for camostat mesilate, a drug approved for the treatment of chronic pancreatitis and postoperative reflux esophagitis, in the treatment of COVID19. Clinical trials are needed to confirm this.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Alessia David", + "author_inst": "Centre for Integrative System Biology and Bioinformatics, Imperial College London, London" + }, + { + "author_name": "Nicholas Parkinson", + "author_inst": "Roslin Institute, University of Edinburgh" + }, + { + "author_name": "Thomas P Peacock", + "author_inst": "Department of Infectious Diseases, Imperial College London" + }, + { + "author_name": "Erola Pairo-Castineira", + "author_inst": "Roslin Institute, University of Edinburgh" + }, + { + "author_name": "Tarun Khanna", + "author_inst": "Centre for Integrative System Biology and Bioinformatics, Imperial College London" + }, + { + "author_name": "Aurelie Cobat", + "author_inst": "Laboratory of Human Genetics of Infectious Diseases, INSERM" + }, + { + "author_name": "Albert Tenesa", + "author_inst": "Roslin Institute, University of Edinburgh" + }, + { + "author_name": "Vanessa Sancho-Shimizu", + "author_inst": "Department of Paediatric Infectious Diseases & Virology, Imperial College London" + }, + { + "author_name": "- GenOMICC Investigators, ISARIC4C Investigators", + "author_inst": "" + }, + { + "author_name": "Jean-Laurent Casanova", + "author_inst": "St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University" + }, + { + "author_name": "Laurent Abel", + "author_inst": "Laboratory of Human Genetics of Infectious Diseases, INSERM" + }, + { + "author_name": "Wendy S Barclay", + "author_inst": "Department of Infectious Diseases, Imperial College London" + }, + { + "author_name": "J Kenneth Baillie", + "author_inst": "Roslin Institute, University of Edinburgh" + }, + { + "author_name": "Michael J.E. Sternberg", + "author_inst": "Centre for Integrative System Biology and Bioinformatics, Imperial College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2021.03.04.21252903", "rel_title": "Impact of remdesivir on 28 day mortality in hospitalized patients with COVID-19: February 2021 Meta-analysis", @@ -874543,29 +876201,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.05.21252962", - "rel_title": "Decisive Conditions for Strategic Vaccination against SARS-CoV-2", - "rel_date": "2021-03-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.05.21252962", - "rel_abs": "While vaccines against SARS-CoV-2 are being administered, in most countries it may still take months until their supply can meet demand. The majority of available vaccines elicits strong immune responses when administered as prime-boost regimens. Since the immunological response to the first (\"prime\") injection may provide already a substantial reduction in infectiousness and protection against severe disease, it may be more effective--under certain immunological and epidemiological conditions--to vaccinate as many people as possible with only one shot, instead of administering a person a second (\"boost\") shot. Such a vaccination campaign may help to more effectively slow down the spread of SARS-CoV-2, reduce hospitalizations, and reduce fatalities, which is our objective. Yet, the conditions which make single-dose vaccination favorable over prime-boost administrations are not well understood. By combining epidemiological modeling, random sampling techniques, and decision tree learning, we find that single-dose vaccination is robustly favored over prime-boost vaccination campaigns, even for low single-dose efficacies. For realistic scenarios and assumptions for SARS-CoV-2, recent data on new variants included, we show that the difference between prime-boost and single-shot waning rates is the only discriminative threshold, falling in the narrow range of 0.01-0.02 day-1 below which single-dose vaccination should be considered.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Lucas B\u00f6ttcher", - "author_inst": "Dept. of Computational Medicine, University of California, Los Angeles, CA 90095-1766, United States of America" - }, - { - "author_name": "Jan Nagler", - "author_inst": "Deep Dynamics Group, Centre for Human and Machine Intelligence, Frankfurt School of Finance & Management, Frankfurt, Germany" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.04.21252939", "rel_title": "Adjusting COVID-19 seroprevalence survey results to account for test sensitivity and specificity", @@ -875309,6 +876944,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.05.21253019", + "rel_title": "Elevated mortality among people experiencing homelessness with COVID-19", + "rel_date": "2021-03-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.05.21253019", + "rel_abs": "We reviewed publicly available data from major U.S. health jurisdictions to compare case fatality rates in people experiencing homelessness (PEH) to the general population. Case fatality among PEH was 1.3 times (95% CI 1.1, 1.5) that of the general population, suggesting that PEH should be prioritized for vaccination.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Kathryn M Leifheit", + "author_inst": "UCLA Fielding School of Public Health, Department of Health Policy and Management" + }, + { + "author_name": "Lelia H Chaisson", + "author_inst": "University of Illinois at Chicago, Department of Medicine, Division of Infectious Diseases" + }, + { + "author_name": "Jesus A Medina", + "author_inst": "UCLA David Geffen School of Medicine" + }, + { + "author_name": "Rafik Wahbi", + "author_inst": "UCLA Fielding School of Public Health, Department of Community Health Sciences" + }, + { + "author_name": "Chelsea L Shover", + "author_inst": "UCLA David Geffen School of Medicine, Department of Medicine, Division of General Internal Medicine and Health Services Research" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.05.21252998", "rel_title": "COVID-19 mRNA vaccine is not detected in human milk", @@ -876225,93 +877895,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2021.03.06.433708", - "rel_title": "SARS-CoV-2 surveillance in Norway rats (Rattus norvergicus) from Antwerp sewer system, Belgium", - "rel_date": "2021-03-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.06.433708", - "rel_abs": "BackgroundSARS-CoV-2 human-to-animal transmission can lead to the establishment of novel reservoirs and the evolution of new variants with the potential to start new outbreaks in humans.\n\nAimWe tested Norway rats inhabiting the sewer system of Antwerp, Belgium, for the presence of SARS-CoV-2 following a local COVID-19 epidemic peak. In addition, we discuss the use and interpretation of SARS-CoV-2 serological tests on non-human samples.\n\nMethodsBetween November and December 2020, Norway rat oral swabs, feces and tissues from the sewer system of Antwerp were collected to be tested by RT-qPCR for the presence of SARS-CoV-2. Serum samples were screened for the presence of anti-SARS-CoV-2 IgG antibodies using a Luminex microsphere immunoassay (MIA). Samples considered positive were then checked for neutralizing antibodies using a conventional viral neutralization test (cVNT).\n\nResultsThe serum of 35 rats was tested by MIA showing 3 potentially positive sera that were later shown to be negative by cVNT. All tissue samples of 39 rats analyzed tested negative for SARS-CoV-2 RNA.\n\nConclusionThis is the first study that evaluates SARS-CoV-2 infection in urban rats. We can conclude that the sample of 39 rats had never been infected with SARS-CoV-2. We show that diagnostic serology tests can give misleading results when applied on non-human samples. SARS-CoV-2 monitoring activities should continue due to the emergence of new variants prone to infect Muridae rodents.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Valeria Carolina Colombo", - "author_inst": "Evolutionary Ecology Group, University of Antwerp" - }, - { - "author_name": "Vincent Sluydts", - "author_inst": "Evolutionary Ecology Group, University of Antwerp" - }, - { - "author_name": "Joachim Marien", - "author_inst": "Evolutionary Ecology Group, University of Antwerp" - }, - { - "author_name": "Bram Vanden Broecke", - "author_inst": "Evolutionary Ecology Group, University of Antwerp" - }, - { - "author_name": "Natalie Van Houtte", - "author_inst": "Evolutionary Ecology Group, University of Antwerp" - }, - { - "author_name": "Wannes Leirs", - "author_inst": "Evolutionary Ecology Group, University of Antwerp" - }, - { - "author_name": "Lotte Jacobs", - "author_inst": "Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium" - }, - { - "author_name": "Arne Iserbyt", - "author_inst": "Evolutionary Ecology Group, University of Antwerp" - }, - { - "author_name": "Marine Hubert", - "author_inst": "Evolutionary Ecology Group, University of Antwerp" - }, - { - "author_name": "Leo Heyndrickx", - "author_inst": "Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine" - }, - { - "author_name": "Hanne Goris", - "author_inst": "Evolutionary Ecology Group, University of Antwerp" - }, - { - "author_name": "Peter Delputte", - "author_inst": "Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp" - }, - { - "author_name": "Naomi De Roeck", - "author_inst": "Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp" - }, - { - "author_name": "Joris Elst", - "author_inst": "Evolutionary Ecology Group, University of Antwerp" - }, - { - "author_name": "Robbert Boudewijns", - "author_inst": "KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Virology and Chemotherapy, Molecular Vaccinology and Vaccine Discovery, KU" - }, - { - "author_name": "Kevin Arien", - "author_inst": "Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine" - }, - { - "author_name": "Herwig Leirs", - "author_inst": "Evolutionary Ecology Group, University of Antwerp" - }, - { - "author_name": "Sophie Gryseels", - "author_inst": "Evolutionary Ecology Group, University of Antwerp" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "ecology" - }, { "rel_doi": "10.1101/2021.03.05.434150", "rel_title": "Long-read sequencing of SARS-CoV-2 reveals novel transcripts and a diverse complex transcriptome landscape.", @@ -877451,6 +879034,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.01.21252250", + "rel_title": "Just 2% of SARS-CoV-2-positive individuals carry 90% of the virus circulating in communities", + "rel_date": "2021-03-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.01.21252250", + "rel_abs": "We analyze data from the Fall 2020 pandemic response efforts at the University of Colorado Boulder (USA), where more than 72,500 saliva samples were tested for SARS-CoV-2 using quantitative RT-PCR. All samples were collected from individuals who reported no symptoms associated with COVID-19 on the day of collection. From these, 1,405 positive cases were identified. The distribution of viral loads within these asymptomatic individuals was indistinguishable from what has been previously reported in symptomatic individuals. Regardless of symptomatic status, approximately 50% of individuals who test positive for SARS-CoV-2 seem to be in non-infectious phases of the disease, based on having low viral loads in a range from which live virus has rarely been isolated. We find that, at any given time, just 2% of individuals carry 90% of the virions circulating within communities, serving as viral \"super-carriers\" and possibly also super-spreaders.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Qing Yang", + "author_inst": "University of Colorado Boulder, Boulder, Colorado, 80303, USA" + }, + { + "author_name": "Tassa K Saldi", + "author_inst": "University of Colorado Boulder, Boulder, Colorado, 80303, USA" + }, + { + "author_name": "Erika Lasda", + "author_inst": "University of Colorado Boulder, Boulder, Colorado, 80303, USA" + }, + { + "author_name": "Carolyn J Decker", + "author_inst": "University of Colorado Boulder, Boulder, Colorado, 80303, USA" + }, + { + "author_name": "Camille L Paige", + "author_inst": "University of Colorado Boulder, Boulder, Colorado, 80303, USA" + }, + { + "author_name": "Denise G Muhlrad", + "author_inst": "University of Colorado Boulder, Boulder, Colorado, 80303, USA" + }, + { + "author_name": "Patrick K Gonzales", + "author_inst": "University of Colorado Boulder, Boulder, Colorado, 80303, USA" + }, + { + "author_name": "Morgan R Fink", + "author_inst": "University of Colorado Boulder, Boulder, Colorado, 80303, USA" + }, + { + "author_name": "Kimngan L Tat", + "author_inst": "University of Colorado Boulder, Boulder, Colorado, 80303, USA" + }, + { + "author_name": "Cole R Hager", + "author_inst": "University of Colorado Boulder, Boulder, Colorado, 80303, USA" + }, + { + "author_name": "Jack C Davis", + "author_inst": "University of Colorado Boulder, Boulder, Colorado, 80303, USA" + }, + { + "author_name": "Christopher D Ozeroff", + "author_inst": "University of Colorado Boulder, Boulder, Colorado, 80303, USA" + }, + { + "author_name": "Nicholas R Meyerson", + "author_inst": "University of Colorado Boulder, Boulder, Colorado, 80303, USA" + }, + { + "author_name": "Stephen K Clark", + "author_inst": "University of Colorado Boulder, Boulder, Colorado, 80303, USA" + }, + { + "author_name": "Will T Fattor", + "author_inst": "University of Colorado Boulder, Boulder, Colorado, 80303, USA" + }, + { + "author_name": "Alison R Gilchrist", + "author_inst": "University of Colorado Boulder, Boulder, Colorado, 80303, USA" + }, + { + "author_name": "Arturo Barbachano-Guerrero", + "author_inst": "University of Colorado Boulder, Boulder, Colorado, 80303, USA" + }, + { + "author_name": "Emma R Worden-Sapper", + "author_inst": "University of Colorado Boulder, Boulder, Colorado, 80303, USA" + }, + { + "author_name": "Sharon S Wu", + "author_inst": "University of Colorado Boulder, Boulder, Colorado, 80303, USA" + }, + { + "author_name": "Gloria R Brisson", + "author_inst": "University of Colorado Boulder, Boulder, Colorado, 80303, USA" + }, + { + "author_name": "Matthew B McQueen", + "author_inst": "University of Colorado Boulder, Boulder, Colorado, 80303, USA" + }, + { + "author_name": "Robin D Dowell", + "author_inst": "University of Colorado Boulder, Boulder, Colorado, 80303, USA" + }, + { + "author_name": "Leslie A Leinwand", + "author_inst": "University of Colorado Boulder, Boulder, Colorado, 80303, USA" + }, + { + "author_name": "Roy R Parker", + "author_inst": "University of Colorado Boulder, Boulder, Colorado, 80303, USA" + }, + { + "author_name": "Sara Sawyer", + "author_inst": "University of Colorado Boulder" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.25.20134866", "rel_title": "Clinical course and risk factors for in-hospital mortality of 205 patients with SARS-CoV-2 pneumonia in Como, Lombardy Region, Italy", @@ -878255,37 +879953,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2021.03.02.21252269", - "rel_title": "An Explainable Artificial Intelligence based Prospective Framework for COVID-19 Risk Prediction", - "rel_date": "2021-03-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.02.21252269", - "rel_abs": "Given the spread of COVID-19 to vast geographical regions and populations, it is not feasible to undergo or recommend the RT-PCR based tests to all individuals with flu-like symptoms. The reach of RT-PCR based testing is still limited due to the high cost of the test and huge population in few countries. Thus, alternative methods for COVID-19 infection risk prediction can be useful. We built an explainable artificial intelligence (AI) based integrated web-based prospective framework for COVID-19 risk prediction. We employed a two-step procedure for the non-clinical prediction of COVID19 infection risk. In the first step we assess the initial risk of COVID19 infection based on carefully selected parameters associated with COVID-19 positive symptoms from recent research. Generally, X-ray scans are cheaper and easily available in most government and private health centres. Therefore, based on the outcome of the computed initial risk in first step, we further provide an optional prediction using the chest X-ray scans in the second step of our proposed AI based prospective framework. Since there is a bottleneck to undergo an expensive RT-PCR based confirmatory test in economically backward nations, this is a crucial part of our explainable AI based prospective framework. The initial risk assessment outcome is analysed in combination with the advanced deep learning-based analysis of chest X-ray scans to provide an accurate prediction of COVID-19 infection risk. This prospective web-based AI framework can be employed in limited resource settings after clinical validation in future. The cost and time associated with the adoption of this prospective AI based prospective framework will be minimal and hence it will be beneficial to majority of the population living in low-income settings such as small towns and rural areas that have limited access to advanced healthcare facilities.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Vishal Sharma", - "author_inst": "BML Munjal University, Gurugram, Haryana, India" - }, - { - "author_name": "Piyush \u00a0", - "author_inst": "BML Munjal University, Gurugram, Haryana, India" - }, - { - "author_name": "Samarth Chhatwal", - "author_inst": "BML Munjal University, Gurugram, Haryana, India" - }, - { - "author_name": "Bipin Singh", - "author_inst": "BML Munjal University, Gurugram, Haryana, India" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2021.03.02.21252430", "rel_title": "Evaluation of accuracy, exclusivity, limit-of-detection and ease-of-use of LumiraDx\u2122 - Antigen-detecting point-of-care device for SARS-CoV-2", @@ -879137,6 +880804,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.23.21252268", + "rel_title": "The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape", + "rel_date": "2021-03-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.23.21252268", + "rel_abs": "The emergence and rapid rise in prevalence of three independent SARS-CoV-2 \"501Y lineages, B.1.1.7, B.1.351 and P.1, in the last three months of 2020 prompted renewed concerns about the evolutionary capacity of SARS-CoV-2 to adapt to both rising population immunity, and public health interventions such as vaccines and social distancing. Viruses giving rise to the different 501Y lineages have, presumably under intense natural selection following a shift in host environment, independently acquired multiple unique and convergent mutations. As a consequence, all have gained epidemiological and immunological properties that will likely complicate the control of COVID-19. Here, by examining patterns of mutations that arose in SARS-CoV-2 genomes during the pandemic we find evidence of a major change in the selective forces acting on various SARS-CoV-2 genes and gene segments (such as S, nsp2 and nsp6), that likely coincided with the emergence of the 501Y lineages. In addition to involving continuing sequence diversification, we find evidence that a significant portion of the ongoing adaptive evolution of the 501Y lineages also involves further convergence between the lineages. Our findings highlight the importance of monitoring how members of these known 501Y lineages, and others still undiscovered, are convergently evolving similar strategies to ensure their persistence in the face of mounting infection and vaccine induced host immune recognition.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Darren P Martin", + "author_inst": "Institute of Infectious Diseases and Molecular Medicine, Division Of Computational Biology, Department of Integrative Biomedical Sciences, University of Cape To" + }, + { + "author_name": "Steven Weaver", + "author_inst": "Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Pennsylvania, USA" + }, + { + "author_name": "Houryiah Tegally", + "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South" + }, + { + "author_name": "Emmanuel James San", + "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South" + }, + { + "author_name": "Stephen D Shank", + "author_inst": "Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Pennsylvania, USA" + }, + { + "author_name": "Eduan Wilkinson", + "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South" + }, + { + "author_name": "Jennifer Giandhari", + "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South" + }, + { + "author_name": "Sureshnee Naidoo", + "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South" + }, + { + "author_name": "Yeshnee Pillay", + "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South" + }, + { + "author_name": "Lavanya Singh", + "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South" + }, + { + "author_name": "Richard J Lessells", + "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South " + }, + { + "author_name": "- NGS-SA Consortium", + "author_inst": "-" + }, + { + "author_name": "- COVID-19 Genomics UK (COG-UK) Consortium", + "author_inst": "-" + }, + { + "author_name": "Ravindra K Gupta", + "author_inst": "Clinical Microbiology, University of Cambridge, Cambridge, UK; Africa Health Research Institute, KwaZulu-Natal, South Africa" + }, + { + "author_name": "Joel O Wertheim", + "author_inst": "Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA" + }, + { + "author_name": "Anton Nekturenko", + "author_inst": "Department of Biochemistry and Molecular Biology, The Pennsylvania State University, Pennsylvania, USA" + }, + { + "author_name": "Ben Murrell", + "author_inst": "Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "Gordon W Harkins", + "author_inst": "South African Medical Research Council Capacity Development Unit, South African National Bioinformatics Institute, University of the Western cape, Bellville, So" + }, + { + "author_name": "Philippe Lemey", + "author_inst": "Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium" + }, + { + "author_name": "Oscar MacLean", + "author_inst": "MRC-University of Glasgow Centre for Virus Research, Scotland, UK" + }, + { + "author_name": "David L Robertson", + "author_inst": "MRC-University of Glasgow Centre for Virus Research, Scotland, UK" + }, + { + "author_name": "Tulio de Oliveira", + "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory South Africa; Department of Global Health, University of Washington, Sea" + }, + { + "author_name": "Sergei L Kosakovsky Pond", + "author_inst": "Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Pennsylvania, USA" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.25.21252234", "rel_title": "SWIFT: A Deep Learning Approach to Prediction of Hypoxemic Events in Critically-Ill Patients Using SpO2 Waveform Prediction", @@ -880117,113 +881891,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.03.04.433852", - "rel_title": "Optimization of an LNP-mRNA vaccine candidate targeting SARS-CoV-2 receptor-binding domain", - "rel_date": "2021-03-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.04.433852", - "rel_abs": "In 2020, two mRNA-based vaccines, encoding the full length of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein, have been introduced for control of the coronavirus disease (COVID-19) pandemic1,2. However, reactogenicity, such as fever, caused by innate immune responses to the vaccine formulation remains to be improved. Here, we optimized a lipid nanoparticle (LNP)-based mRNA vaccine candidate, encoding the SARS-CoV-2 spike protein receptor-binding domain (LNP-mRNA-RBD), which showed improved immunogenicity by removing reactogenic materials from the vaccine formulation and protective potential against SARS-CoV-2 infection in cynomolgus macaques. LNP-mRNA-RBD induced robust antigen-specific B cells and follicular helper T cells in the BALB/c strain but not in the C57BL/6 strain; the two strains have contrasting abilities to induce type I interferon production by dendritic cells. Removal of reactogenic materials from original synthesized mRNA by HPLC reduced type I interferon (IFN) production by dendritic cells, which improved immunogenicity. Immunization of cynomolgus macaques with an LNP encapsulating HPLC-purified mRNA induced robust anti-RBD IgG in the plasma and in various mucosal areas, including airways, thereby conferring protection against SARS-CoV-2 infection. Therefore, fine-tuning the balance between the immunogenic and reactogenic activity of mRNA-based vaccine formulations may offer safer and more efficacious outcomes.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Kouji Kobiyama", - "author_inst": "Division of Vaccine Science, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo" - }, - { - "author_name": "Masaki Imai", - "author_inst": "Division of Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo" - }, - { - "author_name": "Nao Jounai", - "author_inst": "Biologics Division, Vaccine Research Laboratories, Daichi Sankyo Co., Ltd." - }, - { - "author_name": "Misako Nakayama", - "author_inst": "Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science" - }, - { - "author_name": "Kou Hioki", - "author_inst": "Division of Vaccine Science, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo" - }, - { - "author_name": "Kiyoko Iwatsuki-Horimoto", - "author_inst": "Division of Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo" - }, - { - "author_name": "Seiya Yamayoshi", - "author_inst": "Division of Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo" - }, - { - "author_name": "Jun Tsuchida", - "author_inst": "Division of Vaccine Science, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo" - }, - { - "author_name": "Takako Niwa", - "author_inst": "Biologics Division, Modality Research Laboratories, Daichi Sankyo Co., Ltd." - }, - { - "author_name": "Takashi Suzuki", - "author_inst": "Biologics Division, Modality Research Laboratories, Daichi Sankyo Co., Ltd." - }, - { - "author_name": "Mutsumi Ito", - "author_inst": "Division of Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo" - }, - { - "author_name": "Shinya Yamada", - "author_inst": "Division of Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo" - }, - { - "author_name": "Tokiko Watanabe", - "author_inst": "Division of Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo" - }, - { - "author_name": "Maki Kiso", - "author_inst": "Division of Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo" - }, - { - "author_name": "Hideo Negishi", - "author_inst": "Division of Vaccine Science, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo" - }, - { - "author_name": "Burcu Temizoz", - "author_inst": "Division of Vaccine Science, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo" - }, - { - "author_name": "Hirohito Ishigaki", - "author_inst": "Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science" - }, - { - "author_name": "Yoshinori Kitagawa", - "author_inst": "Division of Microbiology and Infectious Diseases, Department of Pathology, Shiga University of Medical Science" - }, - { - "author_name": "Cong Thanh Nguyen", - "author_inst": "Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science" - }, - { - "author_name": "Yasushi Itoh", - "author_inst": "Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science" - }, - { - "author_name": "Fumihiko Takeshita", - "author_inst": "Biologics Division, Vaccine Research Laboratories, Daichi Sankyo Co., Ltd." - }, - { - "author_name": "Yoshihiro Kawaoka", - "author_inst": "Division of Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo" - }, - { - "author_name": "Ken J Ishii", - "author_inst": "Division of Vaccine Science, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.03.04.433887", "rel_title": "SARS-CoV-2 variant with higher affinity to ACE2 shows reduced sera neutralization susceptibility", @@ -880911,6 +882578,217 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.02.25.21252477", + "rel_title": "Preliminary Efficacy of the NVX-CoV2373 Covid-19 Vaccine Against the B.1.351 Variant", + "rel_date": "2021-03-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.25.21252477", + "rel_abs": "BackgroundThe emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants threatens progress toward control of the Covid-19 pandemic. Evaluation of Covid-19 vaccine efficacy against SARS-CoV-2 variants is urgently needed to inform vaccine development and use.\n\nMethodsIn this phase 2a/b, multicenter, randomized, observer-blinded, placebo-controlled trial in South Africa, healthy human immunodeficiency virus (HIV)-negative adults (18 to 84 years) or medically stable people living with HIV (PLWH) (18 to 84 years) were randomized in a 1:1 ratio to receive two doses, administered 21 days apart, of either NVX-CoV2373 nanoparticle vaccine (5 {micro}g recombinant spike protein with 50 {micro}g Matrix-M1 adjuvant) or placebo. The primary endpoints were safety and vaccine efficacy [≥]7 days following the second dose against laboratory-confirmed symptomatic Covid-19 in previously SARS-CoV-2 uninfected participants.\n\nResultsA total of 4387 participants were randomized and dosed at least once, 2199 with NVX-CoV2373 and 2188 with placebo. Approximately 30% of participants were seropositive at baseline. Among 2684 baseline seronegative participants (94% HIV-negative; 6% PLWH), there were 15 and 29 predominantly mild to moderate Covid-19 cases in NVX-CoV2373 and placebo recipients, respectively; vaccine efficacy was 49.4% (95% confidence interval [CI]: 6.1 to 72.8). Efficacy in HIV-negative participants was 60.1% (95% CI: 19.9 to 80.1), and did not differ by baseline serostatus. Of the primary endpoint cases with available whole genome sequencing, 38 (92.7%) of 41 were the B.1.351 variant. Post-hoc vaccine efficacy against B.1.351 was 51.0% (95% CI: - 0.6 to 76.2) in HIV-negative participants. Among placebo recipients, the incidence of symptomatic Covid-19 was similar in baseline seronegative vs baseline seropositive participants during the first 2 months of follow-up (5.3% vs 5.2%). Preliminary local and systemic reactogenicity were primarily mild to moderate and transient, and higher with NVX-CoV2373; serious adverse events were rare in both groups.\n\nConclusionsThe NVX-CoV2373 vaccine was efficacious in preventing Covid-19, which was predominantly mild to moderate and due to the B.1.351 variant, while evidence of prior infection with the presumptive original SARS-CoV-2 did not confer protection against probable B.1.351 disease. (Funded by Novavax, The Bill and Melinda Gates Foundation, and the Coalition for Epidemic Preparedness Innovations; ClinicalTrials.gov number, NCT04533399)", + "rel_num_authors": 49, + "rel_authors": [ + { + "author_name": "Vivek Shinde", + "author_inst": "Novavax" + }, + { + "author_name": "Sutika Bhikha", + "author_inst": "Vaccines and Infectious Diseases Analytics Research Unit (VIDA); University of the Witwatersrand Johannesburg" + }, + { + "author_name": "Zaheer Hossain", + "author_inst": "Josha Research Center, South Africa" + }, + { + "author_name": "Moherndran Archary", + "author_inst": "Enhancing Care Foundation; University of KwaZulu Natal" + }, + { + "author_name": "Qasim Bhorat", + "author_inst": "Soweto Clinical Trials Centre" + }, + { + "author_name": "Lee Fairlie", + "author_inst": "Maternal and Child Health at Wits RHI" + }, + { + "author_name": "Umesh Lalloo", + "author_inst": "Enhancing Care Foundation" + }, + { + "author_name": "Mduduzi Lawrance Sandile Masilela", + "author_inst": "Setshaba Research Centre" + }, + { + "author_name": "Dhayendre Moodley", + "author_inst": "CAPRISA Umlazi CRS" + }, + { + "author_name": "Sherika Hanley", + "author_inst": "CAPRISA Umlazi CRS" + }, + { + "author_name": "Leon Fouche", + "author_inst": "Clinical Research Physician / LCRI" + }, + { + "author_name": "Cheryl Louw", + "author_inst": "Madibeng Centre for Research, Brits and Department of Family Medicine, School of Health Sciences, University of Pretoria, Pretoria" + }, + { + "author_name": "Michele Tameris", + "author_inst": "South African TB Vaccine Initiative, University of Cape Town, Cape Town, South Africa" + }, + { + "author_name": "Nishanta Singh", + "author_inst": "South African Medical Research Council (SAMRC), HIV Prevention Research Unit (HPRU)" + }, + { + "author_name": "Ameena Goga", + "author_inst": "South African Medical Research Council (SAMRC), HIV Prevention Research Unit (HPRU)" + }, + { + "author_name": "Keertan Dheda", + "author_inst": "Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute" + }, + { + "author_name": "Coert Grobbelaar", + "author_inst": "University of Pretoria., Aurum Pretoria CRS (The Aurum Institute)" + }, + { + "author_name": "Gertruida Kruger", + "author_inst": "MERC Research Middlesburg, South Africa" + }, + { + "author_name": "Nazira Carrim-Ganey", + "author_inst": "PEERMED Clinical Trial Centre, Kempton Park, South Africa" + }, + { + "author_name": "Vicky Baillie", + "author_inst": "Vaccines and Infectious Diseases Analytics Research Unit (VIDA); University of the Witwatersrand Johannesburg" + }, + { + "author_name": "Tulio de Oliveira", + "author_inst": "University of KwaZulu-Natal" + }, + { + "author_name": "Anthonet Lombard Koen", + "author_inst": "South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, J" + }, + { + "author_name": "Jonah J Lombaard", + "author_inst": "Josha Research Center" + }, + { + "author_name": "Rosie Mngqibisa", + "author_inst": "Enhancing Care Foundation; University of KwaZulu Natal" + }, + { + "author_name": "As'ad Ebrahim Bhorat", + "author_inst": "Soweto Clinical Trials Centre" + }, + { + "author_name": "Gabriella Benade", + "author_inst": "Maternal and Child Health at Wits RHI" + }, + { + "author_name": "Natasha Lalloo", + "author_inst": "Enhancing Care Foundation" + }, + { + "author_name": "Annah Pitsi", + "author_inst": "8Setshaba Research Centre, Tshwane, South Africa" + }, + { + "author_name": "Pieter-Louis Vollgraaff", + "author_inst": "Limpopo Clinical Research Initiative" + }, + { + "author_name": "Angelique Luabeya", + "author_inst": "South African TB Vaccine Initiative, University of Cape Town, Cape Town, South Africa" + }, + { + "author_name": "Aliasgar Esmail", + "author_inst": "Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute" + }, + { + "author_name": "Friedrich G. Petrick", + "author_inst": "MERC Research, Middlesburg, South Africa" + }, + { + "author_name": "Aylin Oommen Jose", + "author_inst": "Vaccines and Infectious Diseases Analytics Research Unit (VIDA); University of the Witwatersrand Johannesburg" + }, + { + "author_name": "Sharne Foulkes", + "author_inst": "Josha Research Center" + }, + { + "author_name": "Khatija Ahmed", + "author_inst": "Setshaba Research Centre" + }, + { + "author_name": "Asha Thombrayil", + "author_inst": "Vaccines and Infectious Diseases Analytics Research Unit (VIDA); University of the Witwatersrand Johannesburg" + }, + { + "author_name": "Lou Fries", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Shane Cloney-Clark", + "author_inst": "Novavax,Inc." + }, + { + "author_name": "Mingzhu Zhu", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Chijioke Bennett", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Gary Albert", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Emmanuel Faust", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Joyce Plested", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Andreana Robertson", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Susan Neal", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Iksung Cho", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Gregory M. Glenn", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Filip Dubovsky", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Shabir Madhi", + "author_inst": "University of the Witwatersrand" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.01.21252710", "rel_title": "Public perception of ethical issues related to COVID-19 control measures in Singapore, Hong Kong, and Malaysia: A cross-sectional survey", @@ -881871,53 +883749,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, - { - "rel_doi": "10.1101/2021.03.01.433498", - "rel_title": "Atorvastatin effectively inhibits late replicative cycle steps of SARS-CoV-2 in vitro", - "rel_date": "2021-03-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.01.433498", - "rel_abs": "IntroductionSARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) has caused a pandemic of historic proportions and continues to spread worldwide. Currently, there is no effective therapy against this virus. This article evaluated the in vitro antiviral effect of Atorvastatin against SARS-CoV-2 and also identified the interaction affinity between Atorvastatin and three SARS-CoV-2 proteins, using in silico structure-based molecular docking approach.\n\nMaterials and methodsThe antiviral activity of Atorvastatin against SARS-CoV-2 was evaluated by three different treatment strategies using a clinical isolate of SARS-CoV-2. The interaction of Atorvastatin with Spike, RNA-dependent RNA polymerase (RdRp) and 3C-like protease (3CLpro) was evaluated by molecular docking.\n\nResultsAtorvastatin showed anti-SARS-CoV-2 activity of 79%, 54.8%, 22.6% and 25% at 31.2, 15.6, 7.9, and 3.9 {micro}M, respectively, by pre-post-treatment strategy. In addition, atorvastatin demonstrated an antiviral effect of 26.9% at 31.2 {micro}M by pre-infection treatment. This compound also inhibited SARS-CoV-2 in 66.9%, 75%, 27.9% and 29.2% at concentrations of 31.2, 15.6, 7.9, and 3.9 {micro}M, respectively, by post-infection treatment. The interaction of atorvastatin with SARS-CoV-2 Spike, RdRp and 3CL protease yielded a binding affinity of -8.5 Kcal/mol, -6.2 Kcal/mol, and -7.5 Kcal/mol, respectively.\n\nConclusionOur study demonstrated the in vitro anti-SARS-CoV-2 activity of Atorvastatin, mainly against the late steps of the viral replicative cycle. A favorable binding affinity with viral proteins by bioinformatics methods was also shown. Due to its low cost, availability, well-established safety and tolerability, and the extensive clinical experience of atorvastatin, it could prove valuable in reducing morbidity and mortality from COVID-19.\n\nImportanceThe COVID-19 pandemic constitutes the largest global public health crisis in a century, with enormous health and socioeconomic challenges. Therefore, it is necessary to search for specific antivirals against its causative agent (SARS-CoV-2). In this sense, the use of existing drugs may represent a useful treatment option in terms of safety, cost-effectiveness, and timeliness. Atorvastatin is widely used to prevent cardiovascular events. This compound modulates the synthesis of cholesterol, a molecule necessary in different stages of the viral replicative cycle. Our study demonstrated the antiviral potential of atorvastatin against SARS-CoV-2, using an in vitro model. Furthermore, the ability of Atorvastatin to directly interfere with three viral targets (Spike, RdRp and 3CL protease) was demonstrated by bioinformatic methods. This compound is a well-studied, low-cost, and generally well-tolerated drug, so it could be a promising antiviral for the treatment of COVID-19.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Maria Isabel Zapata-Cardona", - "author_inst": "Universidad de Antioquia" - }, - { - "author_name": "Lizdany Fl\u00f3rez-\u00c1lvarez", - "author_inst": "Universidad de Antioquia" - }, - { - "author_name": "Wildeman Zapata-Builes", - "author_inst": "Universidad Cooperativa de Colombia" - }, - { - "author_name": "Ariadna Guerra-Sandoval", - "author_inst": "Universidad del Tolima" - }, - { - "author_name": "Carlos Guerra-Almonacid", - "author_inst": "Universidad del Tolima" - }, - { - "author_name": "Jaime Hincapi\u00e9-Garc\u00eda", - "author_inst": "Universidad de Antioquia" - }, - { - "author_name": "Maria Teresa Rugeles", - "author_inst": "Universidad de Antioquia" - }, - { - "author_name": "Juan Carlos Hern\u00e1ndez", - "author_inst": "Universidad Cooperativa de Colombia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.03.01.21252705", "rel_title": "Estimation of secondary household attack rates for emergent SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in San Francisco", @@ -882909,6 +884740,121 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.03.03.432690", + "rel_title": "Dissecting CD8+ T cell pathology of severe SARS-CoV-2 infection by single-cell epitope mapping", + "rel_date": "2021-03-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.03.432690", + "rel_abs": "The current COVID-19 pandemic represents a global challenge. A better understanding of the immune response against SARS-CoV-2 is key to unveil the differences in disease severity and to develop future vaccines targeting novel SARS-CoV-2 variants. Feature barcode technology combined with CITE-seq antibodies and DNA-barcoded peptide-MHC I Dextramer reagents enabled us to identify relevant SARS-CoV-2-derived epitopes and compare epitope-specific CD8+ T cell populations between mild and severe COVID-19. We identified a strong CD8+ T cell response against an S protein-derived epitope. CD8+ effector cells in severe COVID-19 displayed hyperactivation, T cell exhaustion and were missing characteristics of long-lived memory T cells. We identify A*0101 WTAGAAAYY as an immunogenic CD8+ T cell epitope with the ability to drive clonal expansion. We provide an in-depth characterization of the CD8+ T cell-mediated response to SARS-CoV-2 infection which will be relevant for the development of molecular and targeted therapies and potential adjustments of vaccination strategies.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Felix Schreibing", + "author_inst": "Institute of Experimental Medicine and Systems Biology, University Hospital RWTH Aachen, Germany" + }, + { + "author_name": "Monica Hannani", + "author_inst": "Institute of Experimental Medicine and Systems Biology, University Hospital RWTH Aachen, Germany" + }, + { + "author_name": "Fabio Ticconi", + "author_inst": "Institute for Computational Genomics, University Hospital RWTH Aachen" + }, + { + "author_name": "Eleanor Fewings", + "author_inst": "Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany" + }, + { + "author_name": "James Shiniti Nagai", + "author_inst": "Uniklinik RWTH University Aachen" + }, + { + "author_name": "Matthias Begemann", + "author_inst": "Institute of Human Genetics, Medical Faculty, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Christoph Kuppe", + "author_inst": "Institute of Experimental Medicine and Systems Biology" + }, + { + "author_name": "Ingo Kurth", + "author_inst": "RWTH Aachen, University Hospital" + }, + { + "author_name": "Jennifer Kranz", + "author_inst": "Department of Urology and Paediatric Urology, St Antonius Hospital, Eschweiler, Germany" + }, + { + "author_name": "Dario Frank", + "author_inst": "Department of Medicine, St Antonius Hospital, Eschweiler, Germany" + }, + { + "author_name": "Teresa M Anslinger", + "author_inst": "Department of Renal and Hypertensive Disorders, Rheumatological and Immunological Diseases (Medical Clinic II), University Hospital RWTH Aachen" + }, + { + "author_name": "Patrick Ziegler", + "author_inst": "Institute for Occupational, Social and Environmental Medicine, University Hospital RWTH Aachen" + }, + { + "author_name": "Thomas Kraus", + "author_inst": "Institute for Occupational, Social and Environmental Medicine, University Hospital RWTH Aachen" + }, + { + "author_name": "J\u00fcrgen Enczmann", + "author_inst": "Institute for Transplantation Diagnostics and Cell Therapeutics, University Hospital D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Vera Balz", + "author_inst": "Institute for Transplantation Diagnostics and Cell Therapeutics, University Hospital D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Frank Windhofer", + "author_inst": "Institute for Transplantation Diagnostics and Cell Therapeutics, University Hospital D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Paul Balfanz", + "author_inst": "Department of Cardiology, Angiology and Intensive Care Medicine, University Hospital RWTH Aachen" + }, + { + "author_name": "Christian Kurts", + "author_inst": "Institute of Experimental Immunology, University of Bonn, Germany" + }, + { + "author_name": "Gernot Marx", + "author_inst": "Department of Intensive and Intermediate Care, University Hospital RWTH Aachen" + }, + { + "author_name": "Nikolaus Marx", + "author_inst": "Department of Cardiology, Angiology and Intensive Care Medicine, University Hospital RWTH Aachen" + }, + { + "author_name": "Michael Dreher", + "author_inst": "Department of Pneumology and Intensive Care Medicine, University Hospital RWTH Aachen" + }, + { + "author_name": "Rebekka K Schneider", + "author_inst": "Department of Cell Biology, RWTH Aachen University" + }, + { + "author_name": "Julio Saez-Rodriguez", + "author_inst": "Heidelberg University" + }, + { + "author_name": "Ivan Gesteira Costa Filho", + "author_inst": "RWTH Aachen University Hospital" + }, + { + "author_name": "Rafael Kramann", + "author_inst": "RWTH Aachen University Hospital" + } + ], + "version": "1", + "license": "", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.03.03.433699", "rel_title": "Comparative analysis of codon usage patterns in SARS-CoV-2, its mutants and other respiratory viruses", @@ -884101,81 +886047,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.26.21252227", - "rel_title": "Sequence Analysis of 20,453 SARS-CoV-2 Genomes from the Houston Metropolitan Area Identifies the Emergence and Widespread Distribution of Multiple Isolates of All Major Variants of Concern", - "rel_date": "2021-03-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.26.21252227", - "rel_abs": "[Abstract]Since the beginning of the SARS-CoV-2 pandemic, there has been international concern about the emergence of virus variants with mutations that increase transmissibility, enhance escape from the human immune response, or otherwise alter biologically important phenotypes. In late 2020, several \"variants of concern\" emerged globally, including the UK variant (B.1.1.7), South Africa variant (B.1.351), Brazil variants (P.1 and P.2), and two related California \"variants of interest\" (B.1.429 and B.1.427). These variants are believed to have enhanced transmissibility capacity. For the South Africa and Brazil variants, there is evidence that mutations in spike protein permit it to escape from some vaccines and therapeutic monoclonal antibodies. Based on our extensive genome sequencing program involving 20,453 virus specimens from COVID-19 patients dating from March 2020, we report identification of all important SARS-CoV-2 variants among Houston Methodist Hospital patients residing in the greater metropolitan area. Although these variants are currently at relatively low frequency in the population, they are geographically widespread. Houston is the first city in the United States to have all variants documented by genome sequencing. As vaccine deployment accelerates worldwide, increased genomic surveillance of SARS-CoV-2 is essential to understanding the presence and frequency of consequential variants and their patterns and trajectory of dissemination. This information is critical for medical and public health efforts to effectively address and mitigate this global crisis.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Scott Wesley Long", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Randall J Olsen", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Paul A. Christensen", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Sishir Subedi", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Robert Olson", - "author_inst": "Argonne National Laboratory" - }, - { - "author_name": "James J Davis", - "author_inst": "Argonne National Laboratory" - }, - { - "author_name": "Matthew Ojeda Saavedra", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Prasanti Yerramilli", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Layne Pruitt", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Kristina Reppond", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Madison N Shyer", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Jessica E Cambric", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Ilya J. Finkelstein", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Jimmy Gollihar", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "James Musser", - "author_inst": "Houston Methodist Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pathology" - }, { "rel_doi": "10.1101/2021.02.27.21251952", "rel_title": "The prevalence, incidence and risk factors of mental health problems and mental health services use before and 9 months after the COVID-19 outbreak among the general Dutch population. A 3-wave prospective study.", @@ -884879,6 +886750,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.01.21251633", + "rel_title": "Distinct systemic and mucosal immune responses to SARS-CoV-2", + "rel_date": "2021-03-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.01.21251633", + "rel_abs": "Coordinated local mucosal and systemic immune responses following SARS-CoV-2 infection protect against COVID-19 pathologies or fail leading to severe clinical outcomes. To understand this process, we performed an integrated analysis of SARS-CoV-2 spike-specific antibodies, cytokines, viral load and 16S bacterial communities in paired nasopharyngeal swabs and plasma samples from a cohort of clinically distinct COVID-19 patients during acute infection. Plasma viral load was associated with systemic inflammatory cytokines that were elevated in severe COVID-19, and also with spike-specific neutralizing antibodies. In contrast, nasopharyngeal viral load correlated with SARS-CoV-2 humoral responses but inversely with interferon responses, the latter associating with protective microbial communities. Potential pathogenic microrganisms, often implicated in secondary respiratory infections, were associated with mucosal inflammation and elevated in severe COVID-19. Our results demonstrate distinct tissue compartmentalization of SARS-CoV-2 immune responses and highlight a role for the nasopharyngeal microbiome in regulating local and systemic immunity that determines COVID-19 clinical outcomes.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Nikaia Smith", + "author_inst": "Translational Immunology Lab, Department of Immunology, Institut Pasteur, F-75015, Paris" + }, + { + "author_name": "Pedro Goncalves", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Bruno Charbit", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Ludivine Grzelak", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Maxime Beretta", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Cyril Planchais", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Timothee Bruel", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Vincent Rouilly", + "author_inst": "DATACTIX" + }, + { + "author_name": "Vincent Bondet", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "jerome hadjadj", + "author_inst": "Institut Imagine" + }, + { + "author_name": "Nader Yatim", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Helene Pere", + "author_inst": "APHP" + }, + { + "author_name": "Sarah Merkling", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Solen Kerneis", + "author_inst": "Assistance Publique-Hopitaux de Paris, hopital Cochin, Department of Infectious diseases" + }, + { + "author_name": "Frederic Rieux-Leucat", + "author_inst": "Institut Imagine" + }, + { + "author_name": "Benjamin Terrier", + "author_inst": "AP-HP" + }, + { + "author_name": "Olivier Schwartz", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Hugo Mouquet", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Darragh Duffy", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "James Di Santo", + "author_inst": "Institut Pasteur" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.28.21252536", "rel_title": "COVID-19 Related Chemosensory Changes in Individuals with Self-Reported Obesity", @@ -885919,53 +887885,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.02.25.21252404", - "rel_title": "COVID-19 International Border Surveillance Cohort Study at Toronto's Pearson Airport", - "rel_date": "2021-03-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.25.21252404", - "rel_abs": "ObjectivesThe primary objective was to estimate the positivity rate of air travelers coming to Toronto, Canada in September and October, 2020, at arrival, day 7 and day 14. Secondary objectives were to estimate degree of risk based on country of origin; to assess knowledge and attitudes towards COVID-19 control measures; and subjective well-being during the quarantine period.\n\nDesignProspective cohort of arriving international travelers.\n\nSettingToronto Pearson Airport Terminal 1, Toronto, Canada.\n\nParticipantsPassengers arriving on international flights. Inclusion criteria were those aged 18 or older who had a final destination within 100 km of the airport; spoke English or French; and provided consent. Excluded were those taking a connecting flight; who had no internet access; who exhibited symptoms of COVID-19 on arrival; or who were exempted from quarantine.\n\nMain outcome measuresPositive for SARS-CoV-2 virus on RT-PCR with self-administered nasal-oral swab, and general well-being using the WHO-5 index.\n\nResultsOf 16,361 passengers enrolled, 248 (1{middle dot}5%, 95% CI 1.3%,1.5%) tested positive. Of these, 167 (67%) were identified on arrival, 67 (27%) on day 7, and 14 (6%) on day 14. The positivity rate increased from 1% in September to 2% in October. Average well-being score declined from 19.8 (out of a maximum of 25) to 15.5 between arrival and day 7 (p<0.001).\n\nConclusionsA single arrival test will pick up two-thirds of individuals who will become positive, with most of the rest detected on the second test at day 7. These results support strategies identified through mathematical models that a reduced quarantine combined with testing can be as effective as a 14 day quarantine.\n\nArticle SummaryO_ST_ABSStrengths and limitations of this studyC_ST_ABSO_LIDecisions regarding border restrictions have been based on trial and error and mathematical models with limited empirical data to support such decision-making.\nC_LIO_LIThis study assessed the prevalence of SARS-CoV-2 in a cohort of international travellers at arrival, day 7 and 14 of quarantine.\nC_LIO_LIIt is limited to one airport and there is the potential from bias due to non-participation and loss to follow-up.\nC_LIO_LISelf-collected nasal-oral swabs were used which facilitated participation but may have reduced sensitivity.\nC_LI", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Vivek Goel", - "author_inst": "University of Toronto" - }, - { - "author_name": "David Bulir", - "author_inst": "McMaster University" - }, - { - "author_name": "Eric De Prophetis", - "author_inst": "University of Toronto" - }, - { - "author_name": "Munaza Jamil", - "author_inst": "McMaster Health Labs" - }, - { - "author_name": "Laura Rosella", - "author_inst": "University of Toronto" - }, - { - "author_name": "Dominik Mertz", - "author_inst": "McMaster University" - }, - { - "author_name": "Cheryl Regehr", - "author_inst": "University of Toronto" - }, - { - "author_name": "Marek Smieja", - "author_inst": "McMaster University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.02.28.21252616", "rel_title": "The negative consequences of failing to communicate uncertainties during a pandemic:The case of COVID-19 vaccines", @@ -886773,6 +888692,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.02.27.21252572", + "rel_title": "Estimating the burden of post-COVID-19 syndrome in a population-based cohort study of SARS-CoV-2 infected individuals: Implications for healthcare service planning", + "rel_date": "2021-03-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.27.21252572", + "rel_abs": "BackgroundLonger-term consequences after SARS-CoV-2 infection are becoming an important burden to societies and healthcare systems. Data on post-COVID-19 syndrome in the general population are required for the timely planning of healthcare services and resources. The objective of this study was to assess the prevalence of impaired health status and physical and mental health symptoms among individuals at least six months after SARS-CoV-2 infection, and to characterize their healthcare utilization.\n\nMethodsThis population-based prospective cohort study (Zurich SARS-CoV-2 Cohort) enrolled 431 adults from the general population with polymerase chain reaction-confirmed SARS-CoV-2 infection reported to health authorities between 27 February 2020 and 05 August 2020 in the Canton of Zurich, Switzerland. We evaluated the proportion of individuals reporting not to have fully recovered since SARS-CoV-2 infection, and the proportion reporting fatigue (Fatigue Assessment Scale), dyspnea (mMRC dyspnea scale) or depression (DASS-21) at six to eight months after diagnosis. Furthermore, the proportion of individuals with at least one healthcare contact after their acute illness was evaluated. Multivariable logistic regression models were used to assess factors associated with these main outcomes.\n\nResultsSymptoms were present in 385 (89%) participants at diagnosis and 81 (19%) were initially hospitalized. At six to eight months, 111 (26%) reported not having fully recovered. 233 (55%) participants reported symptoms of fatigue, 96 (25%) had at least grade 1 dyspnea, and 111 (26%) had DASS-21 scores indicating symptoms of depression. 170 (40%) participants reported at least one general practitioner visit related to COVID-19 after acute illness, and 10% (8/81) of initially hospitalized individuals were rehospitalized. Individuals that have not fully recovered or suffer from fatigue, dyspnea or depression were more likely to have further healthcare contacts. However, a third of individuals (37/111) that have not fully recovered did not seek further care.\n\nConclusionsIn this population-based study, a relevant proportion of participants suffered from longer-term consequences after SARS-CoV-2 infection. With millions infected across the world, our findings emphasize the need for the timely planning of resources and patient-centered services for post-COVID-19 care.\n\nRegistrationISRCTN14990068", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Dominik Menges", + "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich" + }, + { + "author_name": "Tala Ballouz", + "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich" + }, + { + "author_name": "Alexia Anagnostopoulos", + "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich" + }, + { + "author_name": "Helene E Aschmann", + "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich" + }, + { + "author_name": "Anja Domenghino", + "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich" + }, + { + "author_name": "Jan S Fehr", + "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich" + }, + { + "author_name": "Milo A Puhan", + "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.02.27.21252535", "rel_title": "Modeling infection dynamics and mitigation strategies to support K-6 in-person instruction during the COVID-19 pandemic", @@ -887809,53 +889771,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2021.02.28.433291", - "rel_title": "Structural O-Glycoform Heterogeneity of the SARS-CoV-2 Spike Protein Receptor-Binding Domain Revealed by Native Top-Down Mass Spectrometry", - "rel_date": "2021-03-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.28.433291", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) utilizes an extensively glycosylated surface spike (S) protein to mediate host cell entry and the S protein glycosylation is strongly implicated in altering viral binding/function and infectivity. However, the structures and relative abundance of the new O-glycans found on the S protein regional-binding domain (S-RBD) remain cryptic because of the challenges in intact glycoform analysis. Here, we report the complete structural characterization of intact O-glycan proteoforms using native top-down mass spectrometry (MS). By combining trapped ion mobility spectrometry (TIMS), which can separate the protein conformers of S-RBD and analyze their gas phase structural variants, with ultrahigh-resolution Fourier transform ion cyclotron resonance (FTICR) MS analysis, the O-glycoforms of the S-RBD are comprehensively characterized, so that seven O-glycoforms and their relative molecular abundance are structurally elucidated for the first time. These findings demonstrate that native top-down MS can provide a high-resolution proteoform-resolved mapping of diverse O-glycoforms of the S glycoprotein, which lays a strong molecular foundation to uncover the functional roles of their O-glycans. This proteoform-resolved approach can be applied to reveal the structural O-glycoform heterogeneity of emergent SARS-CoV-2 S-RBD variants, as well as other O-glycoproteins in general.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "David S Roberts", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Morgan W Mann", - "author_inst": "University of Wisconsin-Madison School of Medicine and Public Health" - }, - { - "author_name": "Jake A Melby", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Eli J Larson", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Yanlong Zhu", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Allan R Brasier", - "author_inst": "University of Wisconsin-Madison School of Medicine and Public Health" - }, - { - "author_name": "Song Jin", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Ying Ge", - "author_inst": "University of Wisconsin-Madison" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.03.01.433404", "rel_title": "CD47 as a potential biomarker for the early diagnosis of severe COVID-19", @@ -888423,6 +890338,153 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.02.24.21252396", + "rel_title": "Genetics of symptom remission in outpatients with COVID-19", + "rel_date": "2021-03-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.24.21252396", + "rel_abs": "We conducted a genome-wide association study of time to remission of COVID-19 symptoms in 1723 outpatients with at least one risk factor for disease severity from the COLCORONA clinical trial. We found a significant association at 5p13.3 (rs1173773; P = 4.94 x 10-8) near the natriuretic peptide receptor 3 gene (NPR3). By day 15 of the study, 44%, 54% and 59% of participants with 0, 1, or 2 copies of the effect allele respectively, had symptom remission. In 851 participants not treated with colchicine (placebo), there was a significant association at 9q33.1 (rs62575331; P = 2.95 x 10-8) in interaction with colchicine (P = 1.19 x 10-5) without impact on risk of hospitalisations, highlighting a possibly shared mechanistic pathway. By day 15 of the study, 46%, 62% and 64% of those with 0, 1, or 2 copies of the effect allele respectively, had symptom remission. The findings need to be replicated and could contribute to the biological understanding of COVID-19 symptom remission.", + "rel_num_authors": 33, + "rel_authors": [ + { + "author_name": "Marie-Pierre Dube", + "author_inst": "Montreal Heart Institute, Montreal, Canada" + }, + { + "author_name": "Audrey Lemacon", + "author_inst": "Montreal Heart Institute, Montreal, Canada" + }, + { + "author_name": "Amina Barhdadi", + "author_inst": "Montreal Heart Institute, Montreal, Canada" + }, + { + "author_name": "Louis-Philippe Lemieux Perreault", + "author_inst": "Montreal Heart Institute, Montreal, Canada" + }, + { + "author_name": "Essaid Oussaid", + "author_inst": "Montreal Heart Institute, Montreal, Canada" + }, + { + "author_name": "Geraldine Asselin", + "author_inst": "Montreal Heart Institute, Montreal, Canada" + }, + { + "author_name": "Sylvie Provost", + "author_inst": "Montreal Heart Institute, Montreal, Canada" + }, + { + "author_name": "Maxine Sun", + "author_inst": "Montreal Heart Institute, Montreal, Canada" + }, + { + "author_name": "Johanna Sandoval", + "author_inst": "Montreal Heart Institute, Montreal, Canada" + }, + { + "author_name": "Marc-Andre Legault", + "author_inst": "Montreal Heart Institute, Montreal, Canada" + }, + { + "author_name": "Ian Mongrain", + "author_inst": "Universite de Montreal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada" + }, + { + "author_name": "Anick Dubois", + "author_inst": "Montreal Heart Institute, Montreal, Canada" + }, + { + "author_name": "Diane Valois", + "author_inst": "Universite de Montreal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada" + }, + { + "author_name": "Emma Dedelis", + "author_inst": "Universite de Montreal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada" + }, + { + "author_name": "Jennifer Lousky", + "author_inst": "Universite de Montreal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada" + }, + { + "author_name": "Julie Choi", + "author_inst": "Universite de Montreal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada" + }, + { + "author_name": "Elisabeth Goulet", + "author_inst": "Montreal Heart Institute, Montreal, Canada" + }, + { + "author_name": "Christiane Savard", + "author_inst": "Montreal Heart Institute, Montreal, Canada" + }, + { + "author_name": "Lea-Mei Chicoine", + "author_inst": "Montreal Heart Institute, Montreal, Canada" + }, + { + "author_name": "Marieve Cossette", + "author_inst": "Montreal Health Innovations Coordinating Centre, Montreal, Canada" + }, + { + "author_name": "Malorie Chabot-Blanchet", + "author_inst": "Montreal Health Innovations Coordinating Centre, Montreal, Canada" + }, + { + "author_name": "Marie-Claude Guertin", + "author_inst": "Montreal Health Innovations Coordinating Centre, Montreal, Canada" + }, + { + "author_name": "Simon de Denus", + "author_inst": "Montreal Heart Institute, Montreal, Canada" + }, + { + "author_name": "Nadia Bouabdallaoui", + "author_inst": "Montreal Heart Institute, Montreal, Canada" + }, + { + "author_name": "Richard Marchand", + "author_inst": "Montreal Heart Institute, Montreal, Canada" + }, + { + "author_name": "Zohar Bassevitch", + "author_inst": "Montreal Health Innovations Coordinating Centre, Montreal, Canada" + }, + { + "author_name": "Anna Nozza", + "author_inst": "Montreal Health Innovations Coordinating Centre, Montreal, Canada" + }, + { + "author_name": "Daniel Gaudet", + "author_inst": "Ecogene-21 and Department of Medicine, Universite de Montreal, Chicoutimi, Canada" + }, + { + "author_name": "Philippe L L'Allier", + "author_inst": "Montreal Heart Institute, Montreal, Canada" + }, + { + "author_name": "Julie Hussin", + "author_inst": "Montreal Heart Institute, Montreal, Canada" + }, + { + "author_name": "Guy Boivin", + "author_inst": "Centre Hospitalier de l'Universite Laval, Quebec city, Canada" + }, + { + "author_name": "David Busseuil", + "author_inst": "Montreal Heart Institute, Montreal, Canada" + }, + { + "author_name": "Jean-Claude Tardif", + "author_inst": "Montreal Heart Institute, Montreal, Canada" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.25.21252410", "rel_title": "Consistency of performance of adverse outcome prediction models for hospitalized COVID-19 patients", @@ -889239,77 +891301,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.26.21252510", - "rel_title": "Screening for SARS-CoV-2 infections in daycare facilities for children in a large city in Germany", - "rel_date": "2021-03-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.26.21252510", - "rel_abs": "BackgroundThe role of pre-school children as a source and distributor of SARS-CoV-2 infections is still unclear. Daycare facilities that care particularly for young children with limited hygiene measures may contribute to the infection dynamics during the pandemic. The aim of this study was to implement and evaluate a voluntary SARS-CoV-2 screening program in daycare facilities.\n\nMethodsThe study was conducted over a period of 4 weeks, from June 10th to July 7th 2020. The aim was to screen a representative group of 5000 individuals (children and staff at a ratio 3:1) attending daycare facilities in Dusseldorf, North Rhine-Westphalia. Tests were performed twice per week with oral rinsing water as sample material for the detection of SARS-CoV-2-RNA by molecular pool testing.\n\nResultsA total number of 5210 participants (75.9% children and 24.1% staff) from 115 day care centers participated in the study. Of a total of 34,068 returned samples (81.7%) during the study period, only one SARS-CoV-2 infection of a child was detected in the study cohort with one likely secondary infection within the daycare facility. Of note, during the study phase, no increase of SARS- CoV-2 infections was observed in daycare center compared to the overall incidence in Dusseldorf.\n\nConclusionsA voluntary screening program for SARS-CoV-2 infections could successfully be implemented in daycare facilities. Although the low overall incidence during the study period precludes firm conclusions, there was no evidence for increased transmission in children attending daycare facilities compared to the general population of Dusseldorf.\n\nSummarySARS-CoV-2 screening programs in daycare facilities may help to detect asymptomatic infections at an early stage and thereby support containment. Here, a large screening study was evaluated suggesting similar infection rates in daycare facilities compared to the general population.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Nadine Luebke", - "author_inst": "Institute of virology" - }, - { - "author_name": "Anna-Kathrin Schupp", - "author_inst": "Institute for virology" - }, - { - "author_name": "Renate Bredahl", - "author_inst": "Public Health Authority of Duesseldorf" - }, - { - "author_name": "Ursula Kraus", - "author_inst": "Youth Welfare Service of Duesseldorf" - }, - { - "author_name": "Sandra Hauka", - "author_inst": "institute of virology" - }, - { - "author_name": "Marcel Andree", - "author_inst": "institute of virology" - }, - { - "author_name": "Lutz Ehlkes", - "author_inst": "Public Health Authority of Duesseldorf" - }, - { - "author_name": "Thomas Klein", - "author_inst": "Youth Welfare Service of Duesseldorf" - }, - { - "author_name": "Alexandra Graupner", - "author_inst": "institute of virology" - }, - { - "author_name": "Johannes Horn", - "author_inst": "Youth Welfare Service of Duesseldorf" - }, - { - "author_name": "Ralph Brinks", - "author_inst": "Medizinische Biometrie und Epidemiologie, University Witten-Herdecke" - }, - { - "author_name": "Klaus Goebels", - "author_inst": "Public Health Authority of Duesseldorf" - }, - { - "author_name": "Ortwin Adams", - "author_inst": "Institute of virology" - }, - { - "author_name": "Joerg Timm", - "author_inst": "Institute of virology; University hospital Duesseldorf" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.25.21252470", "rel_title": "A Multilayer Model for Early Detection of COVID-19", @@ -889925,6 +891916,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.02.25.432957", + "rel_title": "GUIdeStaR (G-quadruplex, Uorf, IRES, Small RNA, Repeats), bioinformatics tool for gene characterization- case study: development of attribute selection and classification methods based on GuideStar for studying human transcription factor genes mediated by SARS-COV-2 small ncRNA", + "rel_date": "2021-02-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.25.432957", + "rel_abs": "GUIdEStaR integrates existing databases of various types of G-quadruplex, upstream Open Reading Frame (uORF), Internal Ribosome Entry Site (IRES), methylation to RNA and histone protein, small RNA, and repeats. GUIdEStaR consists of approx. 40,000 genes and 320,000 transcripts. An mRNA transcript is divided into 5 regions (5UTR, 3UTR, exon, intron, and biological region) where each region contains presence-absence data of 169 different types of elements. Recently, artificial intelligence (AI) based analysis of sequencing data has been gaining popularity in the area of bioinformatics. GUIdEStaR generates datasets that can be used as inputs to AI methods. At the GUIdEStaR homepage, users submit gene symbols by clicking a \"Send\" button, and shortly result files in CSV format are available for download at the result website. Users have an option to send the result files to their email addresses. Additionally, the entire database and the example Java codes are also freely available for download. Here, we demonstrate the database usage with three neural network classification studies-1) small RNA study for classifying transcription factor (TF) genes into either one of TF mediated by small RNA originated from SARS-CoV-2 or by human microRNA (miRNA), 2) cell membrane receptor study for classifying receptor genes as either with virus interaction or without one, and 3) nonsense mediated mRNA decay (NMD) study for classifying cell membrane and nuclear receptors as either NMD target or non-target. GUIdEStaR is available for access to the easy-to-use web-based database at www.guidestar.kr and for download at https://sourceforge.net/projects/guidestar.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Jee Eun Kang", + "author_inst": "Korea University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.02.20.21251598", "rel_title": "A statewide analysis of SARS-CoV-2 transmission in New York", @@ -890993,69 +893003,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.23.21252325", - "rel_title": "Scalable Epidemiological Workflows to Support COVID-19 Planning and Response", - "rel_date": "2021-02-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.23.21252325", - "rel_abs": "The COVID-19 global outbreak represents the most significant epidemic event since the 1918 influenza pandemic. Simulations have played a crucial role in supporting COVID-19 planning and response efforts. Developing scalable workflows to provide policymakers quick responses to important questions pertaining to logistics, resource allocation, epidemic forecasts and intervention analysis remains a challenging computational problem. In this work, we present scalable high performance computing-enabled workflows for COVID-19 pandemic planning and response. The scalability of our methodology allows us to run fine-grained simulations daily, and to generate county-level forecasts and other counter-factual analysis for each of the 50 states (and DC), 3140 counties across the USA. Our workflows use a hybrid cloud/cluster system utilizing a combination of local and remote cluster computing facilities, and using over 20,000 CPU cores running for 6-9 hours every day to meet this objective. Our state (Virginia), state hospital network, our university, the DOD and the CDC use our models to guide their COVID-19 planning and response efforts. We began executing these pipelines March 25, 2020, and have delivered and briefed weekly updates to these stakeholders for over 30 weeks without interruption.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Dustin Machi", - "author_inst": "Biocomplexity Institute and Initiative, University of Virginia" - }, - { - "author_name": "Parantapa Bhattacharya", - "author_inst": "Biocomplexity Institute and Initiative, University of Virginia" - }, - { - "author_name": "Stefan Hoops", - "author_inst": "Biocomplexity Institute and Initiative, University of Virginia" - }, - { - "author_name": "Jiangzhuo Chen", - "author_inst": "Biocomplexity Institute and Initiative, University of Virginia" - }, - { - "author_name": "Henning Mortveit", - "author_inst": "Biocomplexity Institute and Initiative, University of Virginia; Department of Engineering Systems and Environment, University of Virginia" - }, - { - "author_name": "Srinivasan Venkatramanan", - "author_inst": "Biocomplexity Institute and Initiative, University of Virginia" - }, - { - "author_name": "Bryan Lewis", - "author_inst": "Biocomplexity Institute and Initiative, University of Virginia" - }, - { - "author_name": "Mandy Wilson", - "author_inst": "Biocomplexity Institute and Initiative, University of Virginia" - }, - { - "author_name": "Arindam Fadikar", - "author_inst": "Argonne National Laboratory" - }, - { - "author_name": "Tom Maiden", - "author_inst": "Pittsburgh Supercomputing Center" - }, - { - "author_name": "Christopher L. Barrett", - "author_inst": "Biocomplexity Institute and Initiative, University of Virginia; Department of Computer Science, University of Virginia" - }, - { - "author_name": "Madhav V. Marathe", - "author_inst": "Biocomplexity Institute and Initiative, University of Virginia; Department of Computer Science, University of Virginia" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.24.21252331", "rel_title": "Knowledge, Attitude, and Practices towards SARS-COV-2 Infection in the United Arab Emirates Population: a Cross-sectional Survey-based Study", @@ -892027,6 +893974,205 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.25.432969", + "rel_title": "Antibodies with potent and broad neutralizing activity against antigenically diverse and highly transmissible SARS-CoV-2 variants", + "rel_date": "2021-02-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.25.432969", + "rel_abs": "The emergence of highly transmissible SARS-CoV-2 variants of concern (VOC) that are resistant to therapeutic antibodies highlights the need for continuing discovery of broadly reactive antibodies. We identify four receptor-binding domain targeting antibodies from three early-outbreak convalescent donors with potent neutralizing activity against 12 variants including the B.1.1.7 and B.1.351 VOCs. Two of them are ultrapotent, with sub-nanomolar neutralization titers (IC50 <0.0006 to 0.0102 g/mL; IC80 < 0.0006 to 0.0251 g/mL). We define the structural and functional determinants of binding for all four VOC-targeting antibodies, and show that combinations of two antibodies decrease the in vitro generation of escape mutants, suggesting potential means to mitigate resistance development. These results define the basis of therapeutic cocktails against VOCs and suggest that targeted boosting of existing immunity may increase vaccine breadth against VOCs.\n\nOne Sentence SummaryUltrapotent antibodies from convalescent donors neutralize and mitigate resistance of SARS-CoV-2 variants of concern.", + "rel_num_authors": 46, + "rel_authors": [ + { + "author_name": "Lingshu Wang", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Tongqing Zhou", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Yi Zhang", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Eun Sung Yang", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Chaim A. Schramm", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Wei Shi", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Amarendra Pegu", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Olamide K. Oloninyi", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Amy Ransier", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Samuel Darko", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Sandeep R. Narpala", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Christian Hatcher", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "David R. Martinez", + "author_inst": "The University of North Carolina at Chapel Hill" + }, + { + "author_name": "Yaroslav Tsybovsky", + "author_inst": "Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "Emily Phung", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Olubukola M. Abiona", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Evan M. Cale", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Lauren A. Chang", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Kizzmekia S. Corbett", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Anthony T. DiPiazza", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Ingelise J. Gordon", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Kwanyee Leung", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Tracy Liu", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Rosemarie D. Mason", + "author_inst": "Vaccine Research Center, NIAID, NIH" + }, + { + "author_name": "Alexandra Nazzari", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Laura Novik", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Adam S. Olia", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Tyler Stephens", + "author_inst": "Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "Christopher D. Stringham", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Chloe Adrienna Talana", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "I-Ting Teng", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Danielle Wagner", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Alicia T. Widge", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Baoshan Zhang", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Mario Roederer", + "author_inst": "Vaccine Research Center" + }, + { + "author_name": "Julie E. Ledgerwood", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Tracy J. Ruckwardt", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Martin R. Gaudinski", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Ralph S. Baric", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Barney S. Graham", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Adrian B. McDermott", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Daniel C. Douek", + "author_inst": "NIH Vaccine Research Center" + }, + { + "author_name": "Peter D. Kwong", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "John R. Mascola", + "author_inst": "Vaccine Research Center, NIAID, NIH" + }, + { + "author_name": "Nancy J. Sullivan", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "John Misasi", + "author_inst": "National Institutes of Health" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.02.25.432893", "rel_title": "Graphene oxide/silver nanoparticle ink formulations rapidly inhibit influenza A virus and OC43 coronavirus infection in vitro", @@ -892711,33 +894857,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.02.25.432821", - "rel_title": "Transposable elements as sensors of SARS-CoV-2 infection", - "rel_date": "2021-02-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.25.432821", - "rel_abs": "Transposable element (TE) transcription is induced in response to viral infections. TE induction triggers a robust and durable interferon (IFN) response, providing a host defense mechanism. Still, the connection between SARS-CoV-2 IFN response and TEs remains largely unknown. Here, we analyzed TE expression changes in response to SARS-CoV-2 infection in different human cellular models. We find that compared to other viruses, which cause global upregulation of TEs, SARS-CoV-2 infection results in a significantly milder TE response in both primary lung epithelial cells and in iPSC-derived lung alveolar type 2 cells. TE activation precedes, and correlates with, the induction of IFN-related genes, suggesting that the limited activation of TEs following SARS-CoV-2 infection may be the reason for the weak IFN response. Diminished TE activation was not observed in lung cancer cell lines with very high viral load. Moreover, we identify two variables which explain most of the observed diverseness in immune responses: basal expression levels of TEs in the pre-infected cells, and the viral load. Finally, analyzing the SARS-CoV-2 interactome, as well as the epigenetic landscape around the TEs that are activated following infection, we identify SARS-CoV-2 interacting proteins, which may regulate chromatin structure and TE transcription in response to a high viral load. This work provides a functional explanation for SARS-CoV-2s success in its fight against the host immune system, and suggests that TEs could be used as sensors and serve as potential drug targets for COVID-19.\n\nKey points O_LIUnlike other viruses, SARS-CoV-2 invokes a weak and inefficient transposable element (TE) response\nC_LIO_LITE induction precedes and predicts IFN response\nC_LIO_LIBasal TE expression and viral load explain immune responses\nC_LIO_LIDistinct chromatin and enhancer binding factors occupancy on TEs induced by SARS-CoV-2\nC_LI", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Matan Sorek", - "author_inst": "The Hebrew University of Jerusalem" - }, - { - "author_name": "Eran Meshorer", - "author_inst": "The Hebrew University of Jerusalem" - }, - { - "author_name": "Sharon Schlesinger", - "author_inst": "the Hebrew University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.02.25.432136", "rel_title": "Comparison of the pathogenicity and virus shedding of SARS CoV-2 VOC 202012/01 and D614G variant in hamster model", @@ -893877,6 +895996,93 @@ "type": "new results", "category": "scientific communication and education" }, + { + "rel_doi": "10.1101/2021.02.25.432837", + "rel_title": "Stratified Random Sampling Methodology for Observing Community Mask Use within Indoor Settings: Results from Louisville, Kentucky during the COVID-19 Pandemic", + "rel_date": "2021-02-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.25.432837", + "rel_abs": "Wearing a facial mask can limit COVID-19 transmission. Measurements of communities mask use behavior have mostly relied on self-report. This studys objective was to devise a method for measuring the prevalence of mask-wearing and proper mask use in indoor public areas without relying on self-report. A stratified random sample of retail trade stores (public areas) in Louisville, Kentucky, USA, was selected and targeted for observation by trained surveyors during December 14-20, 2020. The stratification allowed for investigating mask use behavior by city district, retail trade group, and public area size. The average mask use prevalence among observed visitors of the 382 visited public areas was 96%, while the average prevalence of proper use was 86%. In 17% of the public areas, at least one unmasked visitor was among the observed visitors; in 48%, at least one improperly masked visitor was observed. The average mask use among staff was 92%, but unmasked staff were observed in fewer public areas, as an unmasked staff member was observed in 11% of the visited public areas. The average prevalence of proper make use among staff was 87%, similar to the average among visitors. However, the percentage of public areas where at least one improperly masked staff was observed was 33. Significant disparities in mask use and its proper use were observed among both visitors and staff by public area size, retail trade type, and geographical area. Observing unmasked and incorrectly masked visitors was more common in small (less than 1500 square feet) public areas than larger ones, also in food and grocery stores than other retail stores. Also, the majority of the observed unmasked persons were male and middle age adults.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "SEYED M. KARIMI", + "author_inst": "University of Louisville School of Public Health and Information Sciences" + }, + { + "author_name": "Sonali S Salunkhe", + "author_inst": "University of Louisville School of Public Health and Information Sciences" + }, + { + "author_name": "Kelsey B White", + "author_inst": "University of Louisville School of Public Health and Information Sciences" + }, + { + "author_name": "Bert M. Little", + "author_inst": "University of Louisville School of Public Health and Information Sciences" + }, + { + "author_name": "W. Paul M. McKinney", + "author_inst": "University of Louisville School of Public Health and Information Sciences" + }, + { + "author_name": "Riten M. Mitra", + "author_inst": "University of Louisville School of Public Health and Information Sciences" + }, + { + "author_name": "YuTing M. Chen", + "author_inst": "Louisville Metro Health Department: Louisville Metro Public Health and Wellness" + }, + { + "author_name": "Emily R Adkins", + "author_inst": "University of Louisville School of Public Health and Information Sciences" + }, + { + "author_name": "Julia A. Barclay", + "author_inst": "University of Louisville School of Public Health and Information Sciences" + }, + { + "author_name": "Emmanuel M. Ezekekwu", + "author_inst": "University of Louisville School of Public Health and Information Sciences" + }, + { + "author_name": "Caleb X. He", + "author_inst": "University of Louisville College of Arts and Sciences" + }, + { + "author_name": "Dylan M Hurst", + "author_inst": "University of Louisville College of Arts and Sciences" + }, + { + "author_name": "Martha M M. Popescu", + "author_inst": "University of Louisville College of Arts and Sciences" + }, + { + "author_name": "Devin N. Swinney", + "author_inst": "University of Louisville School of Public Health and Information Sciences" + }, + { + "author_name": "David A. Johnson", + "author_inst": "University of Louisville School of Public Health and Information Sciences" + }, + { + "author_name": "Rebecca M. Hollenbach", + "author_inst": "Louisville Metro Public Health and Wellness" + }, + { + "author_name": "Sarah M. Moyer", + "author_inst": "Louisville Metro Public Health and Wellness" + }, + { + "author_name": "Natalie R DuPre", + "author_inst": "University of Louisville School of Public Health and Information Sciences" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "scientific communication and education" + }, { "rel_doi": "10.1101/2021.02.23.21252276", "rel_title": "Inequalities in the decline and recovery of pathological cancer diagnoses during the first six months of the COVID-19 pandemic: a population-based study", @@ -894765,73 +896971,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.02.23.432418", - "rel_title": "The nonstructural protein 5 of coronaviruses antagonizes GSDMD-mediated pyroptosis by cleaving and inactivating its pore-forming p30 fragment", - "rel_date": "2021-02-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.23.432418", - "rel_abs": "Coronaviruses (CoV) are a family of RNA viruses that typically cause respiratory, enteric and hepatic diseases in animals and humans. Here, we used porcine epidemic diarrhea virus (PEDV) as a model of coronaviruses (CoVs) to illustrate the reciprocal regulation between CoVs infection and pyroptosis. For the first time, we clarified the molecular mechanism of porcine Gasdermin D (pGSDMD)-mediated pyroptosis and demonstrated that amino acids T239 and F240 within pGSDMD-p30 are critical for pyroptosis. Furthermore, 3C-like protease Nsp5 from SARS-CoV-2, MERS-CoV, PDCoV and PEDV can cleave human/porcine GSDMD at the Q193-G194 junction upstream of the caspase-1 cleavage site to produce two fragments which fail to trigger pyroptosis or inhibit viral replication. Thus, we provide clear evidence that coronoviruses may utilize viral Nsp5-GSDMD pathway to help their host cells escaping from pyroptosis, protecting the replication of the virus during the initial period, which suggest an important strategy for coronoviruses infection and sustain.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Fushan Shi", - "author_inst": "Zhejiang University" - }, - { - "author_name": "Qian Lv", - "author_inst": "Zhejiang University" - }, - { - "author_name": "Tingjun Wang", - "author_inst": "Zhejiang University" - }, - { - "author_name": "Jidong Xu", - "author_inst": "Zhejiang University" - }, - { - "author_name": "Wei Xu", - "author_inst": "Zhejiang University" - }, - { - "author_name": "Yuhua Shi", - "author_inst": "Zhejiang University" - }, - { - "author_name": "Xinyu Fu", - "author_inst": "Zhejiang University" - }, - { - "author_name": "Tianming Yang", - "author_inst": "Zhejiang University" - }, - { - "author_name": "Yang Yang", - "author_inst": "Zhejiang A&F University" - }, - { - "author_name": "Lenan Zhuang", - "author_inst": "Zhejiang University" - }, - { - "author_name": "Weihuan Fang", - "author_inst": "Zhejiang University" - }, - { - "author_name": "Jinyan Gu", - "author_inst": "Zhejiang University" - }, - { - "author_name": "Xiaoliang Li", - "author_inst": "Zhejiang University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.02.24.432490", "rel_title": "Targeted Drug Repurposing Against the SARS-CoV-2 E Channel Identifies Blockers With in vitro Antiviral Activity", @@ -895707,6 +897846,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.18.21252037", + "rel_title": "Efficacy and safety of Ivermectin and Hydroxychloroquine in patients with severe COVID-19. A randomized controlled trial", + "rel_date": "2021-02-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.18.21252037", + "rel_abs": "BackgroundIn the search for active drugs against COVID-19, the indications of many have been redirected. Ivermectin and Hydroxychloroquine are drugs that inhibit viral replication in vitro and that have been used in several medical centers.\n\nObjectivesThis clinical trial analyzes the efficacy of Ivermectin and Hydroxychloroquine in patients with moderate COVID-19 and in need of hospitalization.\n\nMethodsThis a controlled, clinical, randomized, double-blind trial that included patients with COVID-19-induced pneumonia and hospitalization criteria, but no severe respiratory failure. Patients were randomized to one of three groups: Group1-hydroxychloroquine, 400 mg every 12 hours on the first day and subsequently, 200 mg every 12 hours for 4 days, Group 2-ivermectin, 12 mg or 18 mg, according to patient weight and, Group 3-placebo. At inclusion, blood samples for arterial blood gases and biochemical markers associated with a poor prognosis were obtained. The primary outcome was established as the duration of hospitalization until discharge due to patient improvement, the total duration of hospitalization, and the safety outcomes were either respiratory deterioration or death.\n\nResultsDuring the month of August, the admission of patients requiring hospitalization mostly encompassed cases with severe respiratory failure, so we ended the recruitment process and analyzed the data that was available at the time. One hundred and six (106) patients with an average age of 53 yrs. ({+/-}16.9) were included, with a greater proportion of males (n=66, 62.2 %). Seventy-two percent (72%) (n= 76) had an associated comorbidity. Ninety percent (90 %) of patients were discharged due to improvement (n=96). The average duration of hospitalization was 6 days (IQR, 3 - 10). No difference in hospitalization duration was found between the treatment groups (Group1: 7 vs Group 2: 6 vs Group 3: 5, p=0.43) nor in respiratory deterioration or death (Group 1: 18 % vs Group 2: 22.2 % vs Group 3: 24.3 %, p =0.83).\n\nConclusionsIn non-critical hospitalized patients with COVID-19 pneumonia, neither ivermectin nor hydroxychloroquine decreases the number of in-hospital days, respiratory deterioration, or deaths.\n\nClinicalTrials identifier NCT04391127", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Jose Lenin Beltran-Gonzalez", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Mario Gonzalez-Gamez", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Emmanuel-Antonio Mendoza-Enciso", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Ramiro Josue Esparza-Maldonado", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Daniel Hernanez-Palacios", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Samuel Duenas-Campos", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Itzel Ovalle-Robles", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Mariana Jocelyn Macias-Guzman", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Andrea Lucia Garcia Diaz", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Cesar Mauricio Gutierrez Pena", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Lucila Martinez-Medina", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Victor Manuel Monroy Colin", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Jose Manuel Arreola Arreola Guerra", + "author_inst": "Centenario Hospital Miguel Hidalgo" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.19.21252080", "rel_title": "In search for the SARS-CoV-2 protection correlate: A head-to-head comparison of two quantitative S1 assays in a group of pre-characterized oligo-/asymptomatic patients", @@ -896607,45 +898813,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2021.02.22.21251757", - "rel_title": "Analyzing Socioeconomic Factors and Health Disparity of COVID-19 Spatiotemporal Spread Patterns at Neighborhood Levels in San Diego County", - "rel_date": "2021-02-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.22.21251757", - "rel_abs": "This study analyzed spatiotemporal spread patterns of COVID-19 confirmed cases at the zip code level in the County of San Diego and compared them to neighborhood social and economic factors. We used correlation analysis, regression models, and geographic weighted regression to identify important factors and spatial patterns. We broke down the temporal confirmed case patterns into four stages from 1 April 2020 to 31 December 2020. The COVID-19 outbreak hotspots in San Diego County are South Bay, El Cajon, Escondido, and rural areas. The spatial patterns among different stages may represent fundamental health disparity issues in neighborhoods. We also identified important variables with strong positive or negative correlations in these categories: ethnic groups, languages, economics, and education. The highest association variables were Pop5andOlderSpanish (Spanish-speaking) in Stage 4 (0.79) and Pop25OlderLess9grade (Less than 9th grade education) in Stage 4 (0.79). We also observed a clear pattern that regions with more well-educated people have negative associations with COVID-19. Additionally, our OLS regression models suggested that more affluent populations have a negative relationship with COVID-19 cases. Therefore, the COVID-19 outbreak is not only a medical disease but a social inequality and health disparity problem.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Ming-Hsiang Tsou", - "author_inst": "San Diego State University" - }, - { - "author_name": "Jian Xu", - "author_inst": "San Diego State University" - }, - { - "author_name": "Chii-Dean Lin", - "author_inst": "San Diego State University" - }, - { - "author_name": "Morgan Daniels", - "author_inst": "San Diego State University" - }, - { - "author_name": "Eunjeong Ko", - "author_inst": "San Diego State University" - }, - { - "author_name": "Joseph Gibbons", - "author_inst": "San Diego State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2021.02.22.21252150", "rel_title": "Seven-month kinetics of SARS-CoV-2 antibodies and protective role of pre-existing antibodies to seasonal human coronaviruses on COVID-19", @@ -897561,6 +899728,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.02.22.21252216", + "rel_title": "The early dynamics of the SARS-CoV-2 epidemic in Portugal", + "rel_date": "2021-02-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.22.21252216", + "rel_abs": "BackgroundGenomic surveillance of SARS-CoV-2 in Portugal was rapidly implemented by the National Institute of Health in the early stages of the COVID-19 epidemic, in collaboration with more than 50 laboratories distributed nationwide. This unprecedented collaborative effort culminated in the generation of 1275 SARS-CoV-2 genome sequences, which represent 15.5% of all confirmed cases in March 2020, making Portugal one of the countries generating the highest volumes of SARS-CoV-2 genomic data during early COVID-19 pandemic.\n\nMethodsWe reconstructed and characterized the spatio-temporal dynamics of SARS-CoV-2 introductions and early dissemination in Portugal using recent phylodynamic models that allow integration of individual-based travel history, in order to obtain a more realistic reconstruction of the viral dynamics.\n\nResultsWe detected at least 277 independent SARS-CoV-2 introductions, mostly from European countries (namely the United Kingdom, Spain, France, Italy and Switzerland), which was broadly consistent with the available travel history data, as well as with the countries with most frequent connectivity and/or with the highest number of Portuguese immigrants. Although most introductions were estimated to have occurred during the last week of February and the first week of March 2020, it is likely that SARS-CoV-2 was silently circulating in Portugal several weeks before the first confirmed local cases on March 2, 2020.\n\nDiscussion and ConclusionWhile the implemented preventive and early control measures seem to have been successful in mitigating community transmission from most independent introductions, our results suggest that their earlier implementation could have largely minimized the number of introductions and subsequent virus expansion. Here we lay the foundation for genomic epidemiology of SARS-CoV-2 in Portugal, and highlight the need for systematic, continuous and geographically-representative genomic surveillance to guide national and international public health authorities toward the characterization and control of SARS-CoV-2 circulating diversity.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Vitor Borges", + "author_inst": "National Institute of Health Dr. Ricardo Jorge, Portugal" + }, + { + "author_name": "Joana Isidro", + "author_inst": "National Institute of Health Dr. Ricardo Jorge, Portugal" + }, + { + "author_name": "Nidia S Trovao", + "author_inst": "Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA" + }, + { + "author_name": "Silvia Duarte", + "author_inst": "National Institute of Health Dr. Ricardo Jorge, Portugal" + }, + { + "author_name": "Helena Cortes-Martins", + "author_inst": "National Institute of Health Dr. Ricardo Jorge, Portugal" + }, + { + "author_name": "Hugo Martiniano", + "author_inst": "National Institute of Health Dr. Ricardo Jorge, Portugal" + }, + { + "author_name": "Isabel Gordo", + "author_inst": "Instituto Gulbenkian de Ciencia (IGC), Oeiras, Portugal" + }, + { + "author_name": "Ricardo Leite", + "author_inst": "Instituto Gulbenkian de Ciencia (IGC), Oeiras, Portugal" + }, + { + "author_name": "Luis Vieira", + "author_inst": "National Institute of Health Dr. Ricardo Jorge, Portugal" + }, + { + "author_name": "- Portuguese network for SARS-CoV-2 genomics (Consortium)", + "author_inst": "" + }, + { + "author_name": "Raquel Guiomar", + "author_inst": "National Institute of Health Dr. Ricardo Jorge, Portugal" + }, + { + "author_name": "Joao Paulo Gomes", + "author_inst": "National Institute of Health Dr. Ricardo Jorge, Portugal" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.02.19.21251949", "rel_title": "Temporal and geographical variation of COVID-19 in-hospital fatality rate in Brazil", @@ -898569,137 +900799,6 @@ "type": "new results", "category": "neuroscience" }, - { - "rel_doi": "10.1101/2021.02.22.432177", - "rel_title": "Increased complement activation is a distinctive feature of severe SARS-CoV-2 infection.", - "rel_date": "2021-02-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.22.432177", - "rel_abs": "Complement activation has been implicated in the pathogenesis of severe SARS-CoV-2 infection. However, it remains to be determined whether increased complement activation is a broad indicator of critical illness (and thus, no different in COVID-19). It is also unclear which pathways are contributing to complement activation in COVID-19, and, if complement activation is associated with certain features of severe SARS-CoV-2 infection, such as endothelial injury and hypercoagulability. To address these questions, we investigated complement activation in the plasma from patients with COVID-19 prospectively enrolled at two tertiary care centers. We compared our patients to two non-COVID cohorts: (a) patients hospitalized with influenza, and (b) patients admitted to the intensive care unit (ICU) with acute respiratory failure requiring invasive mechanical ventilation (IMV). We demonstrate that circulating markers of complement activation (i.e., sC5b-9) are elevated in patients with COVID-19 compared to those with influenza and to patients with non-COVID-19 respiratory failure. Further, the results facilitate distinguishing those who are at higher risk of worse outcomes such as requiring ICU admission, or IMV. Moreover, the results indicate enhanced activation of the alternative complement pathway is most prevalent in patients with severe COVID-19 and is associated with markers of endothelial injury (i.e., Ang2) as well as hypercoagulability (i.e., thrombomodulin and von Willebrand factor). Our findings identify complement activation to be a distinctive feature of COVID-19, and provide specific targets that may be utilized for risk prognostication, drug discovery and personalized clinical trials.\n\nSUMMMARYComplement has been implicated in COVID-19. However, whether this is distinctive of COVID-19 remains unanswered. Ma et al report increased complement activation in COVID-19 compared to influenza and non-COVID respiratory failure, and demonstrate alternative pathway activation as a key marker of multiorgan failure and death.", - "rel_num_authors": 29, - "rel_authors": [ - { - "author_name": "Lina Ma", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Sanjaya K Sahu", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Marlene Cano", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Vasanthan Kuppuswamy", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Jamal Bajwa", - "author_inst": "Marian University" - }, - { - "author_name": "Alexander B Pine", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Matthew M Meizlish", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "George Goshua", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "C Hong Chang", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Hanming Zhang", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Christina Price", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Parveen Bahel", - "author_inst": "Yale New Haven Health System" - }, - { - "author_name": "Henry M Rinder", - "author_inst": "Yale New Haven Health System" - }, - { - "author_name": "Tingting Lei", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Aaron Day", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Daniel Reynolds", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Xiaobo Wu", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Rebecca Schriefer", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Adriana M Rauseo", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Charles W Goss", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Rachel M Presti", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Alfred H Kim", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Andrew E Gelman", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Charles S Dela Cruz", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Alfred I Lee", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Phillip A Mudd", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Hyung J Chun", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "John P Atkinson", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Hrishikesh S Kulkarni", - "author_inst": "Washington University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.02.22.432407", "rel_title": "At the Intersection Between SARS-CoV-2, Macrophages and the Adaptive Immune Response: A Key Role for Antibody-Dependent Pathogenesis But Not Enhancement of Infection in COVID-19", @@ -899555,6 +901654,49 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2021.02.22.432373", + "rel_title": "Structural Basis for SARS-CoV-2 Envelope Protein in Recognition of Human Cell Junction Protein PALS1", + "rel_date": "2021-02-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.22.432373", + "rel_abs": "The COVID-19 pandemic caused by the SARS-CoV-2 virus has created a global health and economic emergency. SARS-CoV-2 viruses hijack human proteins to promote their spread and virulence including the interactions involving the viral envelope (E) protein and human proteins. To understand the structural basis for SARS-CoV-2 viral-host recognition, we used cryo-electron microscopy to determine a structure for the human cell junction protein PALS1 and SARS-CoV-2 E protein complex. The structure shows that the E protein C-terminal DLLV motif recognizes a pocket formed exclusively by hydrophobic residues from the PDZ and SH3 domains in PALS1. Our structural analysis provides an explanation for the observation that the viral E protein recruits PALS1 from lung epithelial cell junctions resulting in vascular leakage, lung damage, viral spread, and virulence. In addition, our structure provides novel targets for peptide- and small-molecule inhibitors that could block the PALS1-E interactions to reduce the E-mediated damage to vascular structures.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Jin Chai", + "author_inst": "Brookhaven National Laboratory" + }, + { + "author_name": "Yuanheng Cai", + "author_inst": "Stony Brook University" + }, + { + "author_name": "Changxu Pang", + "author_inst": "Brookhaven National Laboratory" + }, + { + "author_name": "Liguo Wang", + "author_inst": "Brookhaven National Laboratory" + }, + { + "author_name": "Sean McSweeney", + "author_inst": "Brookhaven National Laboratory" + }, + { + "author_name": "John Shanklin", + "author_inst": "Brookhaven National Laboratory" + }, + { + "author_name": "Qun Liu", + "author_inst": "Brookhaven National Laboratory" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2021.02.22.432379", "rel_title": "Using mixed-effects modeling to estimate decay kinetics of response to SARS-CoV-2 infection", @@ -900499,97 +902641,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.17.21251933", - "rel_title": "Targeting the Coronavirus Nucleocapsid Protein through GSK-3 Inhibition", - "rel_date": "2021-02-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.17.21251933", - "rel_abs": "The coronaviruses responsible for severe acute respiratory syndrome (SARS-CoV), COVID-19 (SARS-CoV-2), Middle East respiratory syndrome (MERS-CoV), and other coronavirus infections express a nucleocapsid protein (N) that is essential for viral replication, transcription, and virion assembly. Phosphorylation of N from SARS-CoV by glycogen synthase kinase 3 (GSK-3) is required for its function and inhibition of GSK-3 with lithium impairs N phosphorylation, viral transcription, and replication. Here we report that the SARS-CoV-2 N protein contains GSK-3 consensus sequences and that this motif is conserved in diverse coronaviruses, raising the possibility that SARS-CoV-2 may be sensitive to GSK-3 inhibitors including lithium. We conducted a retrospective analysis of lithium use in patients from three major health systems who were PCR tested for SARS-CoV-2. We found that patients taking lithium have a significantly reduced risk of COVID-19 (odds ratio = 0.51 [0.35 - 0.74], p = 0.005). We also show that the SARS-CoV-2 N protein is phosphorylated by GSK-3. Knockout of GSK3A and GSK3B demonstrates that GSK-3 is essential for N phosphorylation. Alternative GSK-3 inhibitors block N phosphorylation and impair replication in SARS-CoV-2 infected lung epithelial cells in a cell-type dependent manner. Targeting GSK-3 may therefore provide a new approach to treat COVID-19 and future coronavirus outbreaks.\n\nSignificanceCOVID-19 is taking a major toll on personal health, healthcare systems, and the global economy. With three betacoronavirus epidemics in less than 20 years, there is an urgent need for therapies to combat new and existing coronavirus outbreaks. Our analysis of clinical data from over 300,000 patients in three major health systems demonstrates a 50% reduced risk of COVID-19 in patients taking lithium, a direct inhibitor of glycogen synthase kinase-3 (GSK-3). We further show that GSK-3 is essential for phosphorylation of the SARS-CoV-2 nucleocapsid protein and that GSK-3 inhibition blocks SARS-CoV-2 infection in human lung epithelial cells. These findings suggest an antiviral strategy for COVID-19 and new coronaviruses that may arise in the future.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Xiaolei Liu", - "author_inst": "Perelman School of Medicine at the University of Pennsylvania" - }, - { - "author_name": "Anurag Verma", - "author_inst": "Perelman School of Medicine at the University of Pennsylvania" - }, - { - "author_name": "Gustavo Garcia", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Holly Ramage", - "author_inst": "Perelman School of Medicine at the University of Pennsylvania" - }, - { - "author_name": "Rebecca L Myers", - "author_inst": "Perelman School of Medicine at the University of Pennsylvania" - }, - { - "author_name": "Anastasia Lucas", - "author_inst": "Perelman School of Medicine at the University of Pennsylvania" - }, - { - "author_name": "Jake J Michaelson", - "author_inst": "University of Iowa" - }, - { - "author_name": "William Coryell", - "author_inst": "Carver College of Medicine, University of Iowa" - }, - { - "author_name": "Arvind Kumar", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Alexander W Charney", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Marcelo G. Kazanietz", - "author_inst": "Perelman School of Medicine at the University of Pennsylvania" - }, - { - "author_name": "Daniel J. Rader", - "author_inst": "Perelman School of Medicine at the University of Pennsylvania" - }, - { - "author_name": "Marylyn D. Ritchie", - "author_inst": "Perelman School of Medicine at the University of Pennsylvania" - }, - { - "author_name": "Wade H. Berrettini", - "author_inst": "Perelman School of Medicine at the University of Pennsylvania" - }, - { - "author_name": "David C Schultz", - "author_inst": "Perelman School of Medicine at the University of Pennsylvania" - }, - { - "author_name": "Sara Cherry", - "author_inst": "Perelman School of Medicine at the University of Pennsylvania" - }, - { - "author_name": "Robert Damoiseaux", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Vaithilingaraja Arumugaswami", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Peter S. Klein", - "author_inst": "Perelman School of Medicine at the University of Pennsylvania" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.17.21251905", "rel_title": "Methodological Approach for Wastewater Based Epidemiological Studies for SARS-CoV-2", @@ -901221,6 +903272,53 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2021.02.22.432207", + "rel_title": "Targeting CoV-2 Spike RBD and ACE-2 Interaction with Flavonoids of Anatolian Propolis by in silico and in vitro Studies in terms of possible COVID-19 therapeutics", + "rel_date": "2021-02-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.22.432207", + "rel_abs": "Propolis is a multi-functional bee product with a rich in polyphenols. In this study, the inhibition effect of Anatolian propolis against SARS coronavirus-2 (SARS CoV-2) was investigated as in vitro and in silico. Raw and commercial of propolis samples were used in the study and it was found that both of were rich in caffeic acid, p-coumaric acid, ferulic acid, t-cinnamic acid, hesperetin, chrysin, pinocembrin and caffeic acid phenethyl ester (CAPE) by HPLC-UV analysis. The ethanolic propolis extracts (EPE) were used in the screening ELISA test against the spike S1 protein (SARS Cov-2): ACE-2 inhibition KIT for in vitro study. Binding energy constants of these polyphenols to the CoV-2 Spike S1 RBD and ACE-2proteinwere calculated separately as molecular docking study using AutoDock 4.2 molecular docking software. In addition, pharmacokinetics and drug-likeness properties of these eight polyphenols were calculated according to the SwissADME tool. Binding energy constant of pinocembrin was the highest for both of the receptors, followed by chrysin, CAPE and hesperetin. In silico ADME behavior of the eight polyphenols were found potential ability to work effectively as novel drugs. The findings of both studies showed that propolis has a high inhibitory potential against Covid-19 virus. However, further studies are needed.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Halil Ibrahim Guler", + "author_inst": "Karadeniz Technical University, Faculty of Science, Department of Molecular Biology and Genetics, 61080 Trabzon, TURKEY" + }, + { + "author_name": "Fulya Ay Sal", + "author_inst": "Karadeniz Technical University, Faculty of Science, Department of Biology, 61080 Trabzon, TURKEY" + }, + { + "author_name": "Zehra Can", + "author_inst": "School of Applied Sciences, Bayburt University, Bayburt, TURKEY" + }, + { + "author_name": "Yakup Kara", + "author_inst": "Karadeniz Technical University, Department of Chemistry, Trabzon, TURKEY" + }, + { + "author_name": "Oktay Yildiz", + "author_inst": "Karadeniz Technical University, Faculty of Pharmacy, Basic Pharmaceutical Sciences, Department of Biochemistry, 61080 Trabzon, TURKEY" + }, + { + "author_name": "Ali Osman Belduz", + "author_inst": "Karadeniz Technical University, Faculty of Science, Department of Biology, 61080 Trabzon, TURKEY" + }, + { + "author_name": "Sabriye Canakci", + "author_inst": "Karadeniz Technical University, Faculty of Science, Department of Biology, 61080 Trabzon, TURKEY" + }, + { + "author_name": "Sevgi Kolayli", + "author_inst": "Karadeniz Technical University, Department of Chemistry, Trabzon, TURKEY" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2021.02.20.431855", "rel_title": "A cannabinoid receptor agonist shows anti-inflammatory and survival properties in human SARS-CoV-2-infected iPSC-derived cardiomyocytes", @@ -902105,49 +904203,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.02.18.21251986", - "rel_title": "Reported COVID-19 Incidence in Wisconsin High School Athletes During Fall 2020", - "rel_date": "2021-02-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.18.21251986", - "rel_abs": "IntroductionThe purpose of this study was to describe the reported incidence of COVID-19 in Wisconsin high school athletes in September 2020, and to investigate the relationship of COVID-19 incidence with sport and face mask use.\n\nMethodsSurveys were sent to athletic directors of all Wisconsin high schools regarding sports during September 2020. The association between reported case rates in athletes in each county and the county general population were evaluated with a weighted linear model. Multivariable negative binomial regression models evaluated the associations between COVID-19 incidence and sport type and face mask use by players, adjusting for the county COVID-19 incidence for each school.\n\nResults207 schools that had reinitiated sport reported 270 COVID-19 cases among 30,074 players, for case and incidence rates of 809 cases per 100,000 players and 32.6 cases per 100,000 player-days, respectively. The case rates for athletes in each county were positively correlated with the case rates for the countys general population ({beta} =1.14{+/-}0.20, r=0.60, p<0.001). One hundred fifteen (55%) of cases were attributed to household contact, 85 (41%) to contact outside sport or school, 5 (2.4%) to school contact, and 1 (0.5%) to sport contact. No difference was identified between team and individual sports (incidence rate ratio (IRR)=1.03 [95% CI=0.49-2.2], p=0.93) or between non-contact and contact sports (IRR=0.53 [0.23-1.3], p=0.14), although the difference between outdoor and indoor sports approached statistical significance (IRR=0.52 [0.26-1.1], p=0.07). 84% of schools required face masks while playing. For those sports with >50 participating schools, there were no significant associations between COVID-19 incidence and face mask use in cross country (IRR=0.71 [0.2-2.2], p=0.52), football (IRR=1.6 [0.6-5.1], p=0.404), boys soccer (IRR=2.3 [0.5-17], p=0.31), or girls volleyball (IRR=1.4 [0.3-6.6], p=0.64).\n\nConclusionsIncidence of reported COVID-19 among athletes was related to background county incidence and most cases were attributed to household and community contact. Although not statistically significant, reported COVID-19 incidence may be lower in outdoor sports. Face mask use did not have a significant benefit, which may be due to relatively low rates of COVID-19 and the small number of schools that did not report using face masks.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Phillip Sasser", - "author_inst": "University of Wisconsin School of Medicine and Public Health, Department of Pediatrics" - }, - { - "author_name": "Timothy McGuine", - "author_inst": "University of Wisconsin School of Medicine and Public Health, Department of Orthopedics and Rehabilitation" - }, - { - "author_name": "Kristin Haraldsdottir", - "author_inst": "University of Wisconsin School of Medicine and Public Health, Department of Orthopedics" - }, - { - "author_name": "Kevin Biese", - "author_inst": "University of Wisconsin - Madison" - }, - { - "author_name": "Leslie Goodavish", - "author_inst": "University of Wisconsin School of Medicine and Public Health, Department of Orthopedics and Rehabilitation" - }, - { - "author_name": "Bethany Stevens", - "author_inst": "University of Wisconsin - Madison" - }, - { - "author_name": "Andrew Watson", - "author_inst": "University of Wisconsin School of Medicine and Public Health, Department of Orthopedics and Rehabilitation" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "sports medicine" - }, { "rel_doi": "10.1101/2021.02.17.21251928", "rel_title": "Mortality after surgery with SARS-CoV-2 infection in England: A population-wide epidemiological study", @@ -902827,6 +904882,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.17.431704", + "rel_title": "Host-virus chimeric events in SARS-CoV2 infected cells are infrequent and artifactual", + "rel_date": "2021-02-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.17.431704", + "rel_abs": "Pathogenic mechanisms underlying severe SARS-CoV2 infection remain largely unelucidated. High throughput sequencing technologies that capture genome and transcriptome information are key approaches to gain detailed mechanistic insights from infected cells. These techniques readily detect both pathogen and host-derived sequences, providing a means of studying host-pathogen interactions. Recent studies have reported the presence of host-virus chimeric (HVC) RNA in RNA-seq data from SARS-CoV2 infected cells and interpreted these findings as evidence of viral integration in the human genome as a potential pathogenic mechanism. Since SARS-CoV2 is a positive sense RNA virus that replicates in the cytoplasm it does not have a nuclear phase in its life cycle, it is biologically unlikely to be in a location where splicing events could result in genome integration. Here, we investigated the biological authenticity of HVC events. In contrast to true biological events such as mRNA splicing and genome rearrangement events, which generate reproducible chimeric sequencing fragments across different biological isolates, we found that HVC events across >100 RNA-seq libraries from patients with COVID-19 and infected cell lines, were highly irreproducible. RNA-seq library preparation is inherently error-prone due to random template switching during reverse transcription of RNA to cDNA. By counting chimeric events observed when constructing an RNA-seq library from human RNA and spike-in RNA from an unrelated species, such as fruit-fly, we estimated that ~1% of RNA-seq reads are artifactually chimeric. In SARS-CoV2 RNA-seq we found that the frequency of HVC events was, in fact, not greater than this background \"noise\". Finally, we developed a novel experimental approach to enrich SARS-CoV2 sequences from bulk RNA of infected cells. This method enriched viral sequences but did not enrich for HVC events, suggesting that the majority of HVC events are, in all likelihood, artifacts of library construction. In conclusion, our findings indicate that HVC events observed in RNA-sequencing libraries from SARS-CoV2 infected cells are extremely rare and are likely artifacts arising from either random template switching of reverse-transcriptase and/or sequence alignment errors. Therefore, the observed HVC events do not support SARS-CoV2 fusion to cellular genes and/or integration into human genomes.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Bingyu Yan", + "author_inst": "Purdue University" + }, + { + "author_name": "Srishti Chakravorty", + "author_inst": "Purdue University" + }, + { + "author_name": "Carmen Mirabelli", + "author_inst": "University of Michigan" + }, + { + "author_name": "Luopin Wang", + "author_inst": "Purdue University" + }, + { + "author_name": "Jorge L. Trujillo-Ochoa", + "author_inst": "NIH" + }, + { + "author_name": "Daniel Chauss", + "author_inst": "NIH" + }, + { + "author_name": "Dhaneshwar Kumar", + "author_inst": "NIH, Purdue" + }, + { + "author_name": "Michail S. Lionakis", + "author_inst": "NIH" + }, + { + "author_name": "Matthew R. Olson", + "author_inst": "Purdue University" + }, + { + "author_name": "Christiane E Wobus", + "author_inst": "University of Michigan" + }, + { + "author_name": "Ben Afzali", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Majid Kazemian", + "author_inst": "University of Illinois" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.02.09.21250937", "rel_title": "Increased hazard of mortality in cases compatible with SARS-CoV-2 variant of concern 202012/1 - a matched cohort study", @@ -903591,97 +905709,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2021.02.16.21251535", - "rel_title": "Densely sampled viral trajectories suggest longer duration of acute infection with B.1.1.7 variant relative to non-B.1.1.7 SARS-CoV-2", - "rel_date": "2021-02-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.16.21251535", - "rel_abs": "BackgroundThe alpha and delta SARS-CoV-2 variants have been responsible for major recent waves of COVID-19 despite increasing vaccination rates. The reasons for the increased transmissibility of these variants and for the reduced transmissibility of vaccine breakthrough infections are unclear.\n\nMethodsWe quantified the course of viral proliferation and clearance for 173 individuals with acute SARS-CoV-2 infections using longitudinal quantitative RT-PCR tests conducted using anterior nares/oropharyngeal samples (n = 199,941) as part of the National Basketball Associations (NBA) occupational health program between November 28th, 2020, and August 11th, 2021. We measured the duration of viral proliferation and clearance and the peak viral concentration separately for individuals infected with alpha, delta, and non-variants of interest/variants of concern (non-VOI/VOC), and for vaccinated and unvaccinated individuals.\n\nResultsThe mean viral trajectories of alpha and delta infections resembled those of non-VOI/VOC infections. Vaccine breakthrough infections exhibited similar proliferation dynamics as infections in unvaccinated individuals (mean peak Ct: 20.5, 95% credible interval [19.0, 21.0] vs. 20.7 [19.8, 20.2], and mean proliferation time 3.2 days [2.5, 4.0] vs. 3.5 days [3.0, 4.0]); however, vaccinated individuals exhibited faster clearance (mean clearance time: 5.5 days [4.6, 6.6] vs. 7.5 days [6.8, 8.2]).\n\nConclusionsAlpha, delta, and non-VOI/VOC infections feature similar viral trajectories. Acute infections in vaccinated and unvaccinated people feature similar proliferation and peak Ct, but vaccinated individuals cleared the infection more quickly. Viral concentrations do not fully explain the differences in infectiousness between SARS-CoV-2 variants, and mitigation measures are needed to limit transmission from vaccinated individuals.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Stephen M Kissler", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Joseph R Fauver", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Christina Mack", - "author_inst": "IQVIA" - }, - { - "author_name": "Caroline Tai", - "author_inst": "IQVIA" - }, - { - "author_name": "Mallery Breban", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Anne E. Watkins", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Radhika Samant", - "author_inst": "IQVIA" - }, - { - "author_name": "Deverick Anderson", - "author_inst": "Duke Center for Antimicrobial Stewardship and Infection Prevention" - }, - { - "author_name": "Jessica Metti", - "author_inst": "TEMPUS" - }, - { - "author_name": "Gaurav Khullar", - "author_inst": "TEMPUS" - }, - { - "author_name": "Rachel Baits", - "author_inst": "TEMPUS" - }, - { - "author_name": "Matthew MacKay", - "author_inst": "TEMPUS" - }, - { - "author_name": "Daisy Salgado", - "author_inst": "TEMPUS" - }, - { - "author_name": "Tim Baker", - "author_inst": "TEMPUS" - }, - { - "author_name": "Joel T. Dudley", - "author_inst": "TEMPUS" - }, - { - "author_name": "Christopher E. Mason", - "author_inst": "TEMPUS" - }, - { - "author_name": "David Ho", - "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons" - }, - { - "author_name": "Nathan D Grubaugh", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Yonatan Grad", - "author_inst": "Harvard T. H. Chan School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.16.21251853", "rel_title": "Mortality in COVID-19 amongst women on Hormone Replacement Therapy or Combined Oral Contraception: A cohort study", @@ -904253,6 +906280,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2021.02.18.21251932", + "rel_title": "Antimicrobial use in COVID-19 patients in the first phase of the SARS-CoV-2 pandemic: Rapid review and evidence synthesis", + "rel_date": "2021-02-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.18.21251932", + "rel_abs": "BackgroundAs the numbers of people with COVID-19 continue to increase globally, concerns have been raised regarding the widespread use of antibiotics for the treatment of COVID-19 patients and its consequences for antimicrobial resistance during the pandemic and beyond. The scale and determinants of antibiotic use in the early phase of the pandemic, and whether antibiotic prescribing is beneficial to treatment effectiveness in COVID-19 patients, are still unknown. Unwarranted treatment of this viral infection with antibiotics may exacerbate the problem of antibiotic resistance, while antibiotic resistance may render presumptive treatment of secondary infections in COVID-19 patients ineffective.\n\nMethodsThis rapid review was undertaken to identify studies reporting antimicrobial use in the treatment of hospitalised COVID-19 patients. The review was conducted to comply with PRISMA guidelines for Scoping Reviews (http://www.prisma-statement.org/Extensions/ScopingReviews) and the protocol was registered with the Open Science Framework (OSF): http://osf.io/vp6t5. The following databases: Web of Science, EMBASE, PubMed, CNKI & VIP were searched to identify the relevant studies from 1 Dec 2019 up to 15 June 2020; no limits were set on the language or the country where studies were conducted. The search terms used were: ((\"Covid-19\" or \"SARS-CoV-2\" or \"Coronavirus disease 2019\" or \"severe acute respiratory syndrome coronavirus-2\") and ((\"antibiotic prescribing\" or \"antibiotic use\" or \"antibiotic*\") or \"antimicrobial *\" or \"antimicrobial therapy\" or \"antimicrobial resistance\" or \"antimicrobial stewardship\")). A total of 1216 records were identified through database searching and 118 clinical studies met the inclusion criteria and were taken into data extraction. A bespoke data extraction form was developed and validated through two independent, duplicate extraction of data from five Records. As all the included studies were descriptive in nature, we conducted descriptive synthesis of data and reported pooled estimates such as mean, percentage and frequency. We created a series of scenarios to capture the range of rationales for antibiotic prescribing presented in the included studies.\n\nResultsOur results show that during the early phase of the pandemic, 8501 out of 10 329 COVID-19 patients (82{middle dot}3%) were prescribed antibiotics; antibiotics were prescribed for COVID-19 patients regardless of reported severity, with a similar mean antibiotic prescribing rate between patients with severe or critical illness (75{middle dot}4%) and patients with mild or moderate illness (75{middle dot}1%). The top five frequently prescribed antibiotics for hospitalised COVID-19 patients were azithromycin (28{middle dot}0 % of studies), ceftriaxone (17{middle dot}8%), moxifloxacin (14{middle dot}4%), meropenem (14{middle dot}4%) and piperacillin/tazobactam (12{middle dot}7%). The proportion of patients prescribed antibiotics without clinical justification was 51{middle dot}5% vs 41{middle dot}9 % for patients with mild or moderate illness and those with severe or critical illness respectively. Comparison of patients who were provided antibiotics with a clinical justification with those who were given antibiotics without clinical justification showed lower mortality rates (9{middle dot}5% vs 13{middle dot}1%), higher discharge rates (80{middle dot}9% vs 69{middle dot}3%) and shorter length of hospital of stay (9{middle dot}3 days vs 12{middle dot}2 days). Only 9{middle dot}7% of patients in our included studies were reported to have secondary infections.\n\nConclusionsAntibiotics were prescribed indiscriminately for hospitalised COVID-19 patients regardless of severity of illness during the early phase of the pandemic. COVID-19 related concerns and lack of knowledge drove a large proportion of antibiotic use without specific clinical justification. Although we are still in the midst of the pandemic, the goals of antimicrobial stewardship should remain unchanged for the treatment of COVID-19 patients.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Wenjuan Cong", + "author_inst": "University of Bristol" + }, + { + "author_name": "Narayan Poudel", + "author_inst": "University of Leicester" + }, + { + "author_name": "Nour Alhusein", + "author_inst": "University of Bristol" + }, + { + "author_name": "Hexing Wang", + "author_inst": "Fudan University" + }, + { + "author_name": "Guiqing Yao", + "author_inst": "University of Leicester" + }, + { + "author_name": "Helen Lambert", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.02.16.21251802", "rel_title": "Knowledge, attitudes and perceptions towards COVID-19 vaccinations: a cross-sectional community survey in Bangladesh", @@ -905241,77 +907307,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.17.21251942", - "rel_title": "SARS-CoV-2 Seroprevalence in a University Community: A Longitudinal Study of the Impact of Student Return to Campus on Infection Risk Among Community Members", - "rel_date": "2021-02-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.17.21251942", - "rel_abs": "BackgroundReturning university students represent large-scale, transient demographic shifts and a potential source of transmission to adjacent communities during the COVID-19 pandemic.\n\nMethodsIn this prospective longitudinal cohort study, we tested for IgG antibodies against SARS-CoV-2 in a non-random cohort of residents living in Centre County prior to the Fall 2020 term at the Pennsylvania State University and following the conclusion of the Fall 2020 term. We also report the seroprevalence in a non-random cohort of students collected at the end of the Fall 2020 term.\n\nResultsOf 1313 community participants, 42 (3.2%) were positive for SARS-CoV-2 IgG antibodies at their first visit between 07 August and 02 October 2020. Of 684 student participants who returned to campus for fall instruction, 208 (30.4%) were positive for SARS-CoV-2 antibodies between 26 October and 21 December. 96 (7.3%) community participants returned a positive IgG antibody result by 19 February. Only contact with known SARS-CoV-2-positive individuals and attendance at small gatherings (20-50 individuals) were significant predictors of detecting IgG antibodies among returning students (aOR, 95% CI: 3.1, 2.07-4.64; 1.52, 1.03-2.24; respectively).\n\nConclusionsDespite high seroprevalence observed within the student population, seroprevalence in a longitudinal cohort of community residents was low and stable from before student arrival for the Fall 2020 term to after student departure. The study implies that heterogeneity in SARS-CoV-2 transmission can occur in geographically coincident populations.\n\nAuthors summaryDespite high seroprevalence observed within the student population, seroprevalence in a longitudinal cohort of community residents remained low and stable from before student arrival for the Fall term to after their departure, implying limited transmission between these subpopulations.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Callum Arnold", - "author_inst": "Department of Biology, Pennsylvania State University, University Park, PA, USA, 16802; Center for Infectious Disease Dynamics, Pennsylvania State University, Un" - }, - { - "author_name": "Sreenidhi Srinivasan", - "author_inst": "Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA, 16802; Huck Institutes of the Life Sciences, Pennsylvania Stat" - }, - { - "author_name": "Sophie Rodriguez", - "author_inst": "Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA 16802" - }, - { - "author_name": "Natalie Rydzak", - "author_inst": "Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA 16802" - }, - { - "author_name": "Catherine M Herzog", - "author_inst": "Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA, 16802; Huck Institutes of the Life Sciences, Pennsylvania Stat" - }, - { - "author_name": "Abhinay Gontu", - "author_inst": "Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA 16802" - }, - { - "author_name": "Nita Bharti", - "author_inst": "Department of Biology, Pennsylvania State University, University Park, PA, USA, 16802; Center for Infectious Disease Dynamics, Pennsylvania State University, Un" - }, - { - "author_name": "Meg Small", - "author_inst": "College of Health and Human Development, Pennsylvania State University, University Park, PA, USA 16802; Social Science Research Institute, Pennsylvania State Un" - }, - { - "author_name": "Connie J Rogers", - "author_inst": "Department of Nutritional Sciences, Pennsylvania State University, University Park, PA, USA 16802" - }, - { - "author_name": "Margeaux M Schade", - "author_inst": "College of Health and Human Development, Pennsylvania State University, University Park, PA, USA 16802" - }, - { - "author_name": "Suresh V Kuchipudi", - "author_inst": "Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA 16802; Department of Veterinary and Biomedical Sciences, Pennsyl" - }, - { - "author_name": "Vivek Kapur", - "author_inst": "Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA 16802 ; Huck Institutes of the Life Sciences, Pennsylvania State" - }, - { - "author_name": "Read Andrew", - "author_inst": "Department of Biology, Pennsylvania State University, University Park, PA, USA 16802; Center for Infectious Disease Dynamics, Pennsylvania State University, Uni" - }, - { - "author_name": "Matthew J Ferrari", - "author_inst": "Department of Biology, Pennsylvania State University, University Park, PA, USA 16802; Center for Infectious Disease Dynamics, Pennsylvania State University, Uni" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.17.21251812", "rel_title": "Changes in the rate of cardiometabolic and pulmonary events during the COVID-19 pandemic", @@ -906035,6 +908030,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.02.18.431897", + "rel_title": "Decreased neutralization of SARS-CoV-2 global variants by therapeutic anti-spike protein monoclonal antibodies", + "rel_date": "2021-02-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.18.431897", + "rel_abs": "Monoclonal antibodies against the SARS-CoV-2 spike protein, notably, those developed by Regeneron Pharmaceuticals and Eli Lilly and Company have proven to provide protection against severe COVID-19. The emergence of SARS-CoV-2 variants with heavily mutated spike proteins raises the concern that the therapy could become less effective if any of the mutations disrupt epitopes engaged by the antibodies. In this study, we tested monoclonal antibodies REGN10933 and REGN10987 that are used in combination, for their ability to neutralize SARS-CoV-2 variants B.1.1.7, B.1.351, mink cluster 5 and COH.20G/677H. We report that REGN10987 maintains most of its neutralization activity against viruses with B.1.1.7, B.1.351 and mink cluster 5 spike proteins but that REGN10933 has lost activity against B.1.351 and mink cluster 5. The failure of REGN10933 to neutralize B.1.351 is caused by the K417N and E484K mutations in the receptor binding domain; the failure to neutralize the mink cluster 5 spike protein is caused by the Y453F mutation. The REGN10933 and REGN10987 combination was 9.1-fold less potent on B.1.351 and 16.2-fold less potent on mink cluster 5, raising concerns of reduced efficacy in the treatment of patients infected with variant viruses. The results suggest that there is a need to develop additional monoclonal antibodies that are not affected by the current spike protein mutations.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Takuya Tada", + "author_inst": "Department of Microbiology, NYU Grossman School of Medicine" + }, + { + "author_name": "Belinda M Dcosta", + "author_inst": "Department of Microbiology, NYU Grossman School of Medicine" + }, + { + "author_name": "Hao Zhou", + "author_inst": "Department of Microbiology, NYU Grossman School of Medicine" + }, + { + "author_name": "Ada Vaill", + "author_inst": "Biohaven Pharmaceuticals, Inc." + }, + { + "author_name": "Wes Kazmierski", + "author_inst": "Biohaven Pharmaceuticals, Inc." + }, + { + "author_name": "Nathaniel R Landau", + "author_inst": "Department of Microbiology, NYU Grossman School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.02.18.431844", "rel_title": "Predicting the zoonotic capacity of mammal species for SARS-CoV-2", @@ -907151,81 +909185,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.14.21251704", - "rel_title": "Circulating SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity", - "rel_date": "2021-02-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.14.21251704", - "rel_abs": "Vaccination elicits immune responses capable of potently neutralizing SARS-CoV-2. However, ongoing surveillance has revealed the emergence of variants harboring mutations in spike, the main target of neutralizing antibodies. To understand the impact of globally circulating variants, we evaluated the neutralization potency of 48 sera from BNT162b2 and mRNA-1273 vaccine recipients against pseudoviruses bearing spike proteins derived from 10 strains of SARS-CoV-2. While multiple strains exhibited vaccine-induced cross-neutralization comparable to wild-type pseudovirus, 5 strains harboring receptor-binding domain mutations, including K417N/T, E484K, and N501Y, were highly resistant to neutralization. Cross-neutralization of B.1.351 variants was weak and comparable to SARS-CoV and bat-derived WIV1-CoV, suggesting that a relatively small number of mutations can mediate potent escape from vaccine responses. While the clinical impact of neutralization resistance remains uncertain, these results highlight the potential for variants to escape from neutralizing humoral immunity and emphasize the need to develop broadly protective interventions against the evolving pandemic.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Wilfredo F. Garcia-Beltran", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Evan C. Lam", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard" - }, - { - "author_name": "Kerri St. Denis", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard" - }, - { - "author_name": "Adam D. Nitido", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard" - }, - { - "author_name": "Zeidy H. Garcia", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard" - }, - { - "author_name": "Blake M. Hauser", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard" - }, - { - "author_name": "Jared Feldman", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard" - }, - { - "author_name": "Maia N. Pavlovic", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "David J. Gregory", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Mark C. Poznansky", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Alex Sigal", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "Aaron G. Schmidt", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard" - }, - { - "author_name": "A. John Iafrate", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Vivek Naranbhai", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Alejandro B. Balazs", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.15.21251727", "rel_title": "Artificial Intelligence Applications for COVID-19 in Intensive Care and Emergency Settings: A Systematic Review", @@ -907869,6 +909828,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.02.17.21249755", + "rel_title": "Accuracy of Smartphone Integrated Pulse Oximetry Meets Full FDA Clearance Standards for Clinical Use.", + "rel_date": "2021-02-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.17.21249755", + "rel_abs": "BackgroundPulse oximetry is used as an assessment tool to gauge the severity of COVID-19 infection and identify patients at risk of poor outcomes. 1,2,3,4 The pandemic highlights the need for accurate pulse oximetry, particularly at home, as infection rates increase in multiple global regions including the UK, USA and South Africa 5. Over 100 million Samsung smartphones containing dedicated biosensors (Maxim Integrated Inc, San Jose, CA) and preloaded Apps to perform pulse oximetry, are in use globally. We performed detailed in human hypoxia testing on the Samsung S9 smartphone to determine if this integrated hardware meets full FDA/ISO requirements for clinical pulse oximetry.\n\nMethodsThe accuracy of integrated pulse oximetry in the Samsung 9 smartphone during stable arterial oxygen saturations (SaO2) between 70% and 100% was evaluated in 12 healthy subjects. Inspired oxygen, nitrogen, and carbon dioxide partial pressures were monitored and adjusted via a partial rebreathing circuit to achieve stable target SaO2 plateaus between 70% and 100%. Arterial blood samples were taken at each plateau and saturation measured on each blood sample using ABL-90FLEX blood gas analyzer. Bias, calculated from smartphone readings minus the corresponding arterial blood sample, was reported as root mean square deviation (RMSD).\n\nFindingsThe RMSD of the over 257 data points based on blood sample analysis obtained from 12 human volunteers tested was 2.6%.\n\nInterpretationEvaluation of the smartphone pulse oximeter performance is within requirements of <3.5% RMSD blood oxygen saturation (SpO2) value for FDA/ISO clearance for clinical pulse oximetry. This is the first report of smartphone derived pulse oximetry measurements that meet full FDA/ISO accuracy certification requirements. Both Samsung S9 and S10 contain the same integrated pulse oximeter, thus over 100 million smartphones in current global circulation could be used to obtain clinically accurate spot SpO2 measurements to support at home assessment of COVID-19 patients.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Sara H Browne", + "author_inst": "Division of Infectious Diseases and Global Public Health, University of California San Diego, La Jolla, CA, USA" + }, + { + "author_name": "Mike Bernstein", + "author_inst": "Physio Monitor, LLC, San Ramon, CA, USA" + }, + { + "author_name": "Philip E. Bickler", + "author_inst": "Department of Anesthesia, University of California San Francisco, San Francisco, CA, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2021.02.15.21251766", "rel_title": "Moderators of changes in smoking, drinking, and quitting behaviour associated with the first Covid-19 lockdown in England", @@ -908789,85 +910775,6 @@ "type": "new results", "category": "genetics" }, - { - "rel_doi": "10.1101/2021.02.17.431630", - "rel_title": "A measles-vectored COVID-19 vaccine induces long-term immunity and protection from SARS-CoV-2 challenge in mice", - "rel_date": "2021-02-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.17.431630", - "rel_abs": "In light of the expanding SARS-CoV-2 pandemic, developing efficient vaccines that can provide sufficient coverage for the world population is a global health priority. The measles virus (MV)-vectored vaccine is an attractive candidate given the measles vaccines extensive safety history, well-established manufacturing process, and induction of strong, long-lasting immunity. We developed an MV-based SARS-CoV-2 vaccine using either the full-length spike (S) or S2 subunit as the antigen. While the S2 antigen failed to induce neutralizing antibodies, the prefusion-stabilized, full-length S (MV-ATU2-SF-2P-dER) construct proved to be an attractive vaccine candidate, eliciting strong Th1-dominant T-cell and neutralizing antibody responses against the S antigen while minimizing reactivity to the vector itself. Neutralizing antibody titers remained high three months after homologous prime-boost immunization, and infectious virus was undetectable in all animals after challenge with a mouse-adapted SARS-CoV-2 virus.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Phanramphoei Namprachan Frantz", - "author_inst": "Institut Pasteur, National Center for Genetic Engineering and Biotechnology" - }, - { - "author_name": "Aleksandr Barinov", - "author_inst": "Institut Pasteur, Viroxis" - }, - { - "author_name": "Claude Ruffi\u00e9", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Chantal Combredet", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Val\u00e9rie Najburg", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Samaporn Teeravechyan", - "author_inst": "National Center for Genetic Engineering and Biotechnology" - }, - { - "author_name": "Anan Jongkaewwattana", - "author_inst": "National Center for Genetic Engineering and Biotechnology" - }, - { - "author_name": "Matthieu Prot", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Laurine Conquet", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Xavier Montagutelli", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Priyanka Fernandes", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "H\u00e9l\u00e8ne Strick-Marchand", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "James Di Santo", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Etienne Simon-Loriere", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Christiane Gerke", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Fr\u00e9d\u00e9ric Tangy", - "author_inst": "Institut Pasteur" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.02.13.431090", "rel_title": "A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation", @@ -909758,6 +911665,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2021.02.12.21251626", + "rel_title": "An alternative approach for bioanalytical assay development for wastewater-based epidemiology of SARS-CoV-2", + "rel_date": "2021-02-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.12.21251626", + "rel_abs": "Wastewater-based epidemiology could be applied to track down SARS-CoV-2 outbreaks at high spatio-temporal resolution and could potentially be used as an early-warning for emergence of SARS-CoV-2 circulation in the general population. Epidemiological surveillance of SARS-CoV-2 could play a role in monitoring the spread of the virus in the population and controlling possible outbreaks. However, sensitive sample preparation and detection methods are necessary to detect trace levels of SARS-CoV-2 RNA in influent wastewater (IWW).\n\nUnlike predecessors, method development of a SARS-CoV-2 RNA concentration and detection procedure was performed with IWW samples with high viral SARS-CoV-2 loads (in combination with seeding IWW with a surrogate coronavirus). This is of importance since the SARS-CoV-2 genome in IWW might have already been subject to in-sewer degradation into smaller genome fragments or might be present in a different form (e.g. cell debris,...). Centricon Plus-70 (100 kDa) centrifugal filter devices resulted in the lowest and most reproducible Ct-values for SARS-CoV-2 RNA. Lowering pore sizes did not improve our limit of detection and quantification. Real-time polymerase chain reaction (qPCR) was employed for the amplification of the N1, N2, N3 and E_Sarbeco-gene.\n\nThis is one of the first studies to apply digital polymerase chain reaction (dPCR) for the detection of SARS-CoV-2 RNA in IWW. Interestingly, qPCR results were comparable with dPCR results suggesting that qPCR is a valid method. In this study, dPCR was also used as a proxy to assess the precision of qPCR. In this light, dPCR showed high variability at low concentration levels (100 copies/{micro}L), indicating that variability in bioanalytical assays for SARS-CoV-2 RNA might be substantial.\n\nOn average, the N2-gene showed high in-sample stability in IWW for 10 days of storage at 4 {degrees}C. Between-sample variability was substantial due to the low native concentrations in IWW. Additionally, the E-gene proved to be less stable compared to the N2-gene and showed higher variability. Freezing the IWW samples resulted in a 10-fold decay of loads of the N2- and E-gene in IWW.\n\nAlthough WBE can already aid in filling some knowledge gaps in the epidemiological surveillance of SARS-CoV-2, future WBE studies should aim to further validate and standardize bioanalytical assays, especially with regards to methodological limitations.\n\nHighlightsO_LIDevelopment of an analytical procedure for detection of SARS-CoV-2 RNA in wastewater\nC_LIO_LIExtraction recovery was evaluated in influent wastewater\nC_LIO_LIPrecision measured with dPCR used as a proxy for qPCR\nC_LIO_LIqPCR of the N2 gene fragment showed high in-sample stability of SARS-CoV-2 on average\nC_LI", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Tim Boogaerts", + "author_inst": "Toxicological Centre, University of Antwerp" + }, + { + "author_name": "Lotte Jacobs", + "author_inst": "Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp" + }, + { + "author_name": "Naomi De Roeck", + "author_inst": "Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp" + }, + { + "author_name": "Siel Van den Bogaert", + "author_inst": "Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp" + }, + { + "author_name": "Bert Aertgeerts", + "author_inst": "Academic Centre for General Practice, KU Leuven" + }, + { + "author_name": "Lies Lahousse", + "author_inst": "Department of Bioanalysis, Ghent University" + }, + { + "author_name": "Alexander L.N. van Nuijs", + "author_inst": "Toxicological Centre, University of Antwerp" + }, + { + "author_name": "Peter Delputte", + "author_inst": "Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.02.10.21251507", "rel_title": "Responsive caregiving, opportunities for early learning, and children's safety and security during COVID-19: A rapid review", @@ -910746,69 +912700,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2021.02.16.431021", - "rel_title": "N-Terminal finger stabilizes the reversible feline drug GC376 in SARS-CoV-2 Mpro", - "rel_date": "2021-02-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.16.431021", - "rel_abs": "The main protease (Mpro, also known as 3CL protease) of SARS-CoV-2 is a high priority drug target in the development of antivirals to combat COVID-19 infections. A feline coronavirus antiviral drug, GC376, has been shown to be effective in inhibiting the SARS-CoV-2 main protease and live virus growth. As this drug moves into clinical trials, further characterization of GC376 with the main protease of coronaviruses is required to gain insight into the drugs properties, such as reversibility and broad specificity. Reversibility is an important factor for therapeutic proteolytic inhibitors to prevent toxicity due to off-target effects. Here we demonstrate that GC376 has nanomolar Ki values with the Mpro from both SARS-CoV-2 and SARS-CoV strains. Restoring enzymatic activity after inhibition by GC376 demonstrates reversible binding with both proteases. In addition, the stability and thermodynamic parameters of both proteases were studied to shed light on physical chemical properties of these viral enzymes, revealing higher stability for SARS-CoV-2 Mpro. The comparison of a new X-ray crystal structure of Mpro from SARS-CoV complexed with GC376 reveals similar molecular mechanism of inhibition compared to SARS-CoV-2 Mpro, and gives insight into the broad specificity properties of this drug. In both structures, we observe domain swapping of the N-termini in the dimer of the Mpro, which facilitates coordination of the drugs P1 position. These results validate that GC376 is a drug with an off-rate suitable for clinical trials.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Elena Arutyunova", - "author_inst": "University of Alberta" - }, - { - "author_name": "Muhammad Bashir Khan", - "author_inst": "University of Alberta" - }, - { - "author_name": "Conrad Fischer", - "author_inst": "University of Alberta" - }, - { - "author_name": "Jimmy Lu", - "author_inst": "University of Alberta" - }, - { - "author_name": "Tess Lamer", - "author_inst": "University of Alberta" - }, - { - "author_name": "Wayne Vuong", - "author_inst": "University of Alberta" - }, - { - "author_name": "Marco J van Belkum", - "author_inst": "University of Alberta" - }, - { - "author_name": "Ryan T McKay", - "author_inst": "University of Alberta" - }, - { - "author_name": "D. Lorne Tyrrell", - "author_inst": "University of Alberta" - }, - { - "author_name": "John C Vederas", - "author_inst": "University of Alberta" - }, - { - "author_name": "Howard S Young", - "author_inst": "University of Alberta" - }, - { - "author_name": "M Joanne Lemieux", - "author_inst": "University of Alberta" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.02.14.431177", "rel_title": "Endothelial cells elicit a pro-inflammatory response to SARS-COV-2 without productive viral infection", @@ -911395,6 +913286,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.14.21251708", + "rel_title": "Impact of January 2021 social distancing measures on SARS-CoV-2 B.1.1.7 circulation in France", + "rel_date": "2021-02-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.14.21251708", + "rel_abs": "Facing B.1.1.7 variant, social distancing was strengthened in France in January 2021. Using a 2-strain mathematical model calibrated on genomic surveillance, we estimated that curfew measures allowed hospitalizations to plateau, by decreasing transmission of the historical strain while B.1.1.7 continued to grow. School holidays appear to have further slowed down progression in February. Without progressively strengthened social distancing, a rapid surge of hospitalizations is expected, despite the foreseen increase in vaccination rhythm.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Laura Di Domenico", + "author_inst": "INSERM, Sorbonne Universite" + }, + { + "author_name": "Giulia Pullano", + "author_inst": "INSERM, Sorbonne Universite" + }, + { + "author_name": "Chiara E. Sabbatini", + "author_inst": "INSERM, Sorbonne Universite" + }, + { + "author_name": "Daniel L\u00e9vy-Bruhl", + "author_inst": "Sante publique France" + }, + { + "author_name": "Vittoria Colizza", + "author_inst": "INSERM" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.13.21251681", "rel_title": "Biological attributes of age and gender variations in Indian COVID-19 cases: A retrospective data analysis", @@ -912335,61 +914261,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2021.02.09.21251387", - "rel_title": "Associations between movement behaviors and emotional changes in toddlers and preschoolers during early stages of the COVID-19 pandemic in Chile", - "rel_date": "2021-02-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.09.21251387", - "rel_abs": "BackgroundThere is limited evidence about emotional and behavioral responses in toddlers and preschoolers during the coronavirus disease (COVID-19) pandemic, particularly in Latin America.\n\nObjectiveTo assess associations between changes in movement behaviors (physical activity, screen time and sleeping) and emotional changes in toddlers and preschoolers during early stages of the pandemic in Chile.\n\nMethodsA cross-sectional study conducted from March 30th to April 27th, 2020. Main caregivers of 1-to 5-year-old children living in Chile answered an online survey that included questions about sociodemographic characteristics, changes in the childs emotions and behaviors, movement behaviors and caregivers stress during the pandemic. Multiple linear regressions were used to assess the association between different factors and emotional changes in toddlers and preschoolers.\n\nResultsIn total, 1727 caregivers provided complete data on emotional changes for children aged 2.9{+/-}1.36 years old, 47.9% girls. A large proportion of toddlers and preschoolers in Chile experienced emotional and behavioral changes. Most caregivers reported that children were more affectionate (78.9%), more restless (65.1%), and more frustrated (54.1%) compared with pre-pandemic times. Apart from changes in movement behaviors, factors such as child age, caregivers age and stress, and residential area (urban/rural) were consistently associated with changes in emotions and behaviors.\n\nConclusionThe pandemic substantially affected the emotions and behaviors of toddlers and preschoolers in Chile. Mental health promotion programs should consider multilevel approaches in which the promotion of movement behaviors and support for caregivers should be essential pieces for future responses.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Nicolas Aguilar-Farias", - "author_inst": "Department of Physical Education, Sports and Recreation, Universidad de La Frontera, Chile. UFRO Activate Research Group, Universidad de La Frontera, Chile." - }, - { - "author_name": "Marcelo Toledo-Vargas", - "author_inst": "Department of Physical Education, Sports and Recreation, Universidad de La Frontera, Chile. UFRO Activate Research Group, Universidad de La Frontera, Chile." - }, - { - "author_name": "Sebastian Miranda-Marquez", - "author_inst": "Department of Physical Education, Sports and Recreation, Universidad de La Frontera, Chile. UFRO Activate Research Group, Universidad de La Frontera, Chile." - }, - { - "author_name": "Andrea Cortinez-O'Ryan", - "author_inst": "Department of Physical Education, Sports and Recreation, Universidad de La Frontera, Chile. UFRO Activate Research Group, Universidad de La Frontera, Chile." - }, - { - "author_name": "Pia Martino-Fuentealba", - "author_inst": "Department of Physical Education, Sports and Recreation, Universidad de La Frontera, Chile. UFRO Activate Research Group, Universidad de La Frontera, Chile." - }, - { - "author_name": "Carlos Cristi-Montero", - "author_inst": "IRyS Group, Physical Education School, Pontificia Universidad Catolica de Valparaiso, Valparaiso, Chile." - }, - { - "author_name": "Fernando Rodriguez-Rodriguez", - "author_inst": "IRyS Group, Physical Education School, Pontificia Universidad Catolica de Valparaiso, Valparaiso, Chile." - }, - { - "author_name": "Paula Guarda-Saavedra", - "author_inst": "Department of Physical Education, Sports and Recreation, Universidad de La Frontera, Chile. UFRO Activate Research Group, Universidad de La Frontera, Chile." - }, - { - "author_name": "Borja del Pozo Cruz", - "author_inst": "Centre for Active and Healthy Ageing, Department of Sports Science and Clinical Biomechanics, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmar" - }, - { - "author_name": "Anthony D Okely", - "author_inst": "School of Health & Society and Early Start, Faculty of Arts, Social Sciences and Humanities, University of Wollongong, Australia and Illawarra Health & Medical " - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2021.02.10.21251467", "rel_title": "How has the COVID-19 pandemic impacted on smoking and nicotine dependence among people with severe mental ill health? Analysis of linked data from a UK Closing the Gap Cohort", @@ -913109,6 +914980,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2021.02.09.21250884", + "rel_title": "CLINICAL PERFORMANCE OF THE CALL SCORE FOR THE PREDICTION OF ADMISSION TO ICU AND DEATH IN HOSPITALIZED PATIENTS WITH COVID-19 PNEUMONIA IN A REFERENCE HOSPITAL IN PERU", + "rel_date": "2021-02-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.09.21250884", + "rel_abs": "ObjectiveDetermine the CALL SCOREs diagnostic accuracy for the prediction of ICU admission and death in patients hospitalized for COVID-19 pneumonia in a reference hospital in Peru.\n\nMethodsWe performed an analytical cross-sectional observational study. We included patients with COVID-19 pneumonia treated at the \"Dos de Mayo\" National Hospital. Patients over 18 years old with a diagnosis confirmed by rapid or molecular testing were included. Those with an incomplete, illegible, or missing medical history and/or bacterial or fungal pneumonia were excluded. Data were extracted from medical records. The primary outcomes were mortality and admission to the ICU. The Call Score was calculated for each patient (4 to 13 points) and classified into three risk groups. Summary measures were presented for qualitative and quantitative variables. The area under the model curve and the operational characteristics (sensitivity, specificity) were calculated for the best cut-off point.\n\nResultsThe Call Score reported an area under the curve of 0.59 (IC95%: 0.3 to 0.07), p = 0.43 for predicting death. However, for a cut-off point of 5.5, a sensitivity of 87%and a specificity of 65%were obtained. The area under the curve for ICU admission was 0.67 (95%CI: 0.3 to 0.07), p = 0.43; the 5.5 cut-off point showed a sensitivity of 82%and a specificity of 51%.\n\nConclusionsThe Call Score shows a low performance for predicting mortality and admission to the ICU in Peruvian patients.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Rafael Pichardo-Rodriguez", + "author_inst": "Hospital Dos de Mayo./ Universidad Ricardo Palma." + }, + { + "author_name": "Marcos Saavedra-Velasco", + "author_inst": "Hospital Dos de Mayo." + }, + { + "author_name": "Willy Pena-Oscuvilca", + "author_inst": "Hospital Dos de Mayo" + }, + { + "author_name": "Jhonnathan Ascarza-Saldana", + "author_inst": "Hospital Nacional Edgardo Rebagliati" + }, + { + "author_name": "Cesar Enrique Sanchez Alvarez", + "author_inst": "Hospital Dos de Mayo" + }, + { + "author_name": "Gino Patron", + "author_inst": "Hospital Nacional Dos de Mayo" + }, + { + "author_name": "Oscar Ruiz-Franco", + "author_inst": "Universidad Nacional Mayor de San Marcos" + }, + { + "author_name": "Jhony A. De La Cruz-Vargas", + "author_inst": "Universidad Ricardo Palma." + }, + { + "author_name": "Herney Andres Garcia Perdomo", + "author_inst": "Universidad del Valle, Cali, Colombia" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2021.02.10.21251527", "rel_title": "Outcomes of COVID-19 among Patients with End Stage Renal Disease on Remdesivir", @@ -913989,57 +915911,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.09.21251421", - "rel_title": "Anti-SARS-CoV-2 seropositivity among medical students in Copenhagen", - "rel_date": "2021-02-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.09.21251421", - "rel_abs": "Background Healthcare workers are at a higher risk of getting infected with SARS-CoV-2 than the general population. However, detailed knowledge about medical students and exposure to SARS-CoV-2 is lacking. Thus, we measured the prevalence of SARS-CoV-2 antibodies in a cohort of Danish medical students.\r\n\r\nMethods We invited all medical students at the University of Copenhagen (UCPH) to participate. A venous blood sample was drawn along with completing a self-report questionnaire. Blood samples were analyzed for total antibodies to SARS-CoV-2 and related to symptomatology, social behaviour, and work-life. Seropositive samples were screened for IgM, IgG, and IgA antibodies.\r\n\r\nResults Between October 19th and 26th 1,120 students participated in questionnaire, of these 1,096 were included in the study. Of all included 379 (34.58%) of the participants were seropositive. The risk of seropositivity was significantly increased for participants attending two parties at UCPH, on February the 29th and March 6th 2020 (OR 5.96 (95% CI 4.34-8.24, p<0.001). Further, 461 students (42.06%) worked with COVID-19 patients, which was significantly associated with risk of seropositivity (OR 1.38, 95% CI 1.03-1.85, p=0.033). The symptom most substantially associated with seropositivity was loss of smell and/or taste (n=183 of all, 31.35%) with an OR of 24.48 (95% CI 15.49-40.60, p<0.001).\r\n\r\nConclusion Medical students have the highest reported seropositivity in the Danish healthcare system. The risk of SARS-CoV-2 transmission amongst the students appear to be partly related to working with COVID-19 infected patients, but to a greater extent, their social behaviour.\r\n\r\nMainpoints Medical students have the highest reported seropositivity in the Danish healthcare system. The risk of SARS-CoV-2 transmission amongst the students appear to be partly related to working with COVID-19 infected patients, but to a greater extent, their social behaviour.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Johannes R. Madsen", - "author_inst": "Herlev Hospital" - }, - { - "author_name": "Jacob P.S. Nielsen", - "author_inst": "Herlev Hospital" - }, - { - "author_name": "Kamille Fogh", - "author_inst": "Herlev Hospital" - }, - { - "author_name": "Cecilie B. Hansen", - "author_inst": "Rigshospitalet" - }, - { - "author_name": "Pernille B. Nielsen", - "author_inst": "Herlev Hospital" - }, - { - "author_name": "Theis Lange", - "author_inst": "University of Copenhagen" - }, - { - "author_name": "Rasmus B. Hasselbalch", - "author_inst": "Herlev Hospital" - }, - { - "author_name": "Peter Garred", - "author_inst": "Rigshospitalet" - }, - { - "author_name": "Kasper Iversen", - "author_inst": "Herlev Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.08.21251362", "rel_title": "SARS-CoV-2 re-infection risk in Austria", @@ -914958,6 +916829,32 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.02.08.21251366", + "rel_title": "Survey of symptoms following COVID-19 vaccination in India", + "rel_date": "2021-02-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.08.21251366", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Rajeev Jayadevan", + "author_inst": "Sunrise Hospital" + }, + { + "author_name": "Ramesh Srinivasa Shenoy", + "author_inst": "Indian Medical Association" + }, + { + "author_name": "Anithadevi TS", + "author_inst": "Little Flower Institute of Medical Science and Research Angamaly, Kerala, India" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.02.09.21251052", "rel_title": "Emerging SARS-CoV-2 Lineages in Middle Eastern Jordan with Increasing Mutations Near Antibody Recognition Sites", @@ -915838,28 +917735,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.10.21251502", - "rel_title": "Screening plans for SARS-CoV-2 based on sampling and rotation: an example in the school setting", - "rel_date": "2021-02-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.10.21251502", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Michela Baccini", - "author_inst": "Department of Statistics, Computer Science, Applications, University of Florence, Florence, Italy" - }, - { - "author_name": "Giulia Cereda", - "author_inst": "Department of Statistics, Computer Science, Applications, University of Florence, Florence, Italy" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.10.21251508", "rel_title": "Screening for SARS-CoV-2 by RT-PCR: saliva or nasopharyngeal swab? Systematic review and meta-analysis", @@ -916909,6 +918784,53 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.02.08.21250086", + "rel_title": "Clinical Validation of Automated and Rapid mariPOC SARS-CoV-2 Antigen Test", + "rel_date": "2021-02-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.08.21250086", + "rel_abs": "Novel SARS coronavirus causing COVID-19 was recognized in late 2019. Diagnostics was quickly ramped up worldwide based on the detection of viral RNA. Based on the scientific knowledge for pre-existing coronaviruses, it was expected that the RNA of this novel coronavirus will be detected from symptomatic and at significant rates also from asymptomatic individuals due to persistence of non-infectious RNA. To increase the efficacy of diagnostics, surveillance, screening and pandemic control, rapid methods, such as antigen tests, are needed for decentralized testing and to assess infectiousness. The objective was to validate the analytical and clinical performance, and usability of a novel automated mariPOC SARS-CoV-2 test, which is based on the detection of structural viral proteins using sophisticated optical laser technology. Clinical performance of the test was evaluated against qRT-PCR with nasopharyngeal swab specimens collected from patients suspected of acute SARS-CoV-2 infection. Sensitivity of the mariPOC test was 100.0% (13/13) directly from swab specimens and 84.4% (38/45) from swab specimens in undefined transport mediums. Specificity of the test was 100.0% (201/201). The tests limit of detection was 2.7 TCID50/test and had no cross-reactions with the tested respiratory microbes. Our study shows that the mariPOC can detect infectious individuals already in 20 minutes with clinical sensitivity close to qRT-PCR. The test targets conserved epitopes of SARS-CoV-2 nucleoprotein, making it robust against strain variations. The new test is a promising and versatile tool for syndromic testing of symptomatic cases and for high capacity infection control screening.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Juha M Koskinen", + "author_inst": "ArcDia International Ltd" + }, + { + "author_name": "Petri Antikainen", + "author_inst": "ArcDia International Ltd" + }, + { + "author_name": "Kristina Hotakainen", + "author_inst": "Mehil\u00e4inen Oy" + }, + { + "author_name": "Anu Haveri", + "author_inst": "Finnish Institute for Health and Welfare" + }, + { + "author_name": "Niina Ikonen", + "author_inst": "Finnish Institute for Health and Welfare" + }, + { + "author_name": "Carita Savolainen-Kopra", + "author_inst": "Finnish Institute for Health and Welfare" + }, + { + "author_name": "Kati Sundstr\u00f6m", + "author_inst": "SataDiag, Pori, Finland" + }, + { + "author_name": "Janne O Koskinen", + "author_inst": "ArcDia International Ltd" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.08.21251393", "rel_title": "A SARS-CoV-2 lineage A variant (A.23.1) with altered spike has emerged and is dominating the current Uganda epidemic", @@ -917973,117 +919895,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, - { - "rel_doi": "10.1101/2021.02.08.21250641", - "rel_title": "Genomic surveillance of SARS-CoV-2 in the Bronx enables clinical and epidemiological inference", - "rel_date": "2021-02-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.08.21250641", - "rel_abs": "The Bronx was an early epicenter of the COVID-19 pandemic in the USA. We conducted temporal genomic surveillance of SARS-CoV-2 genomes across the Bronx from March-October 2020. Although the local structure of SARS-CoV-2 lineages mirrored those of New York City and New York State, temporal sampling revealed a dynamic and changing landscape of SARS-CoV-2 genomic diversity. Mapping the trajectories of variants, we found that while some became endemic to the Bronx, other, novel variants rose in prevalence in the late summer/early fall. Geographically resolved genomes enabled us to distinguish between cases of reinfection and persistent infection in two pediatric patients. We propose that limited, targeted, temporal genomic surveillance has clinical and epidemiological utility in managing the ongoing COVID pandemic.\n\nOne sentence summaryTemporally and geographically resolved sequencing of SARS-CoV-2 genotypes enabled surveillance of novel genotypes, identification of endemic viral variants, and clinical inferences, in the first wave of the COVID-19 pandemic in the Bronx.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "J. Maximilian Fels", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Saad Khan", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Ryan Forster", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Karin A Skalina", - "author_inst": "Montefiore Medical Center/Albert Einstein College of Medicine" - }, - { - "author_name": "Surksha Sirichand", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Amy S Fox", - "author_inst": "Montefiore Medical Center/Albert Einstein College of Medicine" - }, - { - "author_name": "Aviv Bergman", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "William B Mitchell", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Lucia R Wolgast", - "author_inst": "Montefiore Medical Center/Albert Einstein College of Medicine" - }, - { - "author_name": "Wendy A Szymczak", - "author_inst": "Montefiore Medical Center/Albert Einstein College of Medicine" - }, - { - "author_name": "Robert H Bortz III", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "M Eugenia Dieterle", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Catalina Florez", - "author_inst": "Albert Einstein College of Medicine and United States Military Academy at West Point" - }, - { - "author_name": "Denise Haslwanter", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Rohit K Jangra", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Ethan Laudermilch", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Ariel S Wirchnianski", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Jason Barnhill", - "author_inst": "United States Military Academy at West Point" - }, - { - "author_name": "David L Goldman", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Hnin Khine", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "D. Yitzchak Goldstein", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Johanna P Daily", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Kartik Chandran", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Libusha Kelly", - "author_inst": "Albert Einstein College of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.08.21251316", "rel_title": "Associations of DMT therapies with COVID-19 severity in multiple sclerosis", @@ -918935,6 +920746,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.02.02.429458", + "rel_title": "Naive human B cells can neutralize SARS-CoV-2 through recognition of its receptor binding domain", + "rel_date": "2021-02-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.02.429458", + "rel_abs": "Exposure to a pathogen elicits an adaptive immune response aimed to control and eradicate. Interrogating the abundance and specificity of the naive B cell repertoire contributes to understanding how to potentially elicit protective responses. Here, we isolated naive B cells from 8 seronegative human donors targeting the SARS-CoV-2 receptor-binding domain (RBD). Single B cell analysis showed diverse gene usage with no restricted complementarity determining region lengths. We show that recombinant antibodies engage SARS-CoV-2 RBD, circulating variants, and pre-emergent coronaviruses. Representative antibodies signal in a B cell activation assay and can be affinity matured through directed evolution. Structural analysis of a naive antibody in complex with spike shows a conserved mode of recognition shared with infection-induced antibodies. Lastly, both naive and affinity-matured antibodies can neutralize SARS-CoV-2. Understanding the naive repertoire may inform potential responses recognizing variants or emerging coronaviruses enabling the development of pan-coronavirus vaccines aimed at engaging germline responses.\n\nOne Sentence SummaryIsolation of antibody germline precursors targeting the receptor binding domain of coronaviruses.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Jared Feldman", + "author_inst": "Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA" + }, + { + "author_name": "Julia Bals", + "author_inst": "Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA" + }, + { + "author_name": "Clara Altomare", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029" + }, + { + "author_name": "Kerri St. Denis", + "author_inst": "Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA" + }, + { + "author_name": "Evan C. Lam", + "author_inst": "Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA" + }, + { + "author_name": "Blake M. Hauser", + "author_inst": "Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA" + }, + { + "author_name": "Larance Ronsard", + "author_inst": "Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA" + }, + { + "author_name": "Maya Sangesland", + "author_inst": "Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA" + }, + { + "author_name": "Thalia Bracamonte Moreno", + "author_inst": "Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA" + }, + { + "author_name": "Vintus Okonkwo", + "author_inst": "Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA" + }, + { + "author_name": "Nathania Hartojo", + "author_inst": "Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA" + }, + { + "author_name": "Alejandro B. Balazs", + "author_inst": "Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA" + }, + { + "author_name": "Goran Bajic", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029" + }, + { + "author_name": "Daniel Lingwood", + "author_inst": "Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA" + }, + { + "author_name": "Aaron G. Schmidt", + "author_inst": "Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.02.09.430547", "rel_title": "SARS-CoV-2 infection models using in vivo and in vitro hACE2-lentivirus transduction", @@ -919915,77 +921801,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.07.21251212", - "rel_title": "Influence of sex on disease severity in children with COVID-19 and Multisystem Inflammatory Syndrome in Latin America", - "rel_date": "2021-02-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.07.21251212", - "rel_abs": "Data from adult studies how that COVID-19 is more severe in men than women. However, no data are available for the pediatric population. For this reason, we performed this study aiming to understand if sex influenced disease severity and outcomes in a large cohort of latin-american children with COVID-19 and Multisystem Inflammatory Syndrome (MIS-C). We found that a higher percentage of male children developed MIS-C (8.9% vs 5% in females) and died (1.2% and 0.4% in females), although on multivariate adjusted analyses the only statistically significant difference was found in need of hospitalization, with females less frequently admitted compared with boys (25.6% vs 35.4%). This data are preliminary and need further independent studies to better assess the role of sex.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Martin Brizuela", - "author_inst": "Pediatric Infectious Disease, Hospital isidoro Iriarte, Quilmes, Buenos Aires, Argentina" - }, - { - "author_name": "Jacopo Lenzi", - "author_inst": "Department of Biomedical and Neuromotor Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy" - }, - { - "author_name": "Rolando Ulloa Gutierrez", - "author_inst": "Infectious Disease Department. Hospital Nacional de Ninos \"Dr. Carlos Saenz Herrera\", CCSS, San Jose, Costa Rica." - }, - { - "author_name": "Omar Yassef", - "author_inst": "Departamento de Docencia e Investigacion, Instituto Latinoamericano de Ecografia en Medicina (ILEM), Ciudad de Mexico, Mexico" - }, - { - "author_name": "Jrge Alberto Rios Aida", - "author_inst": "CLINICA JAS MEDICA, Lima, Peru" - }, - { - "author_name": "Olguita del Aguila", - "author_inst": "Unidad de Infectologia Pediatrica del Hospital Nacional Edgardo Rebagliati Martins-Lima-Peru." - }, - { - "author_name": "Erick arteaga", - "author_inst": "Hospital General Regional 200 IMSS, Mexico" - }, - { - "author_name": "Francisco Campos", - "author_inst": "Hospital Madre Nino San Bartolome, Lima, Peru" - }, - { - "author_name": "Fadia Uribe", - "author_inst": "Hospital Madre Nino San Bartolome, Lima, Peru" - }, - { - "author_name": "Andrea Parra", - "author_inst": "Hospital Pablo Tobon Uribe Medellin, Colombia" - }, - { - "author_name": "Lina Betancur", - "author_inst": "Fundacion Neumologica Colombiana,Bogota, Colombia" - }, - { - "author_name": "Jessica Gomez-Vargas", - "author_inst": "Pediatric Emergency Department, Hospital Nacional de Ninos \"Dr. Carlos Saenz Herrera\", CCSS, San Jose, Costa Rica." - }, - { - "author_name": "Adriana Yock", - "author_inst": "Pediatric Emergency Department, Hospital Nacional de Ninos \"Dr. Carlos Saenz Herrera\", CCSS, San Jose, Costa Rica." - }, - { - "author_name": "danilo buonsenso", - "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2021.02.07.21250695", "rel_title": "Impact on Mental Health of students due to restriction caused by COVID-19 pandemic: Cross-sectional study", @@ -920729,6 +922544,37 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2021.02.09.430519", + "rel_title": "Transformations, Comparisons, and Analysis of Down to Up Protomer States of Variants of the SARS-CoV-2 Prefusion Spike Protein Including the UK Variant B.1.1.7", + "rel_date": "2021-02-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.09.430519", + "rel_abs": "Monitoring and strategic response to variants in SARS-CoV-2 represents a considerable challenge in the current pandemic, as well as potentially future viral outbreaks of similar magnitude. In particular mutations and deletions involving the virions prefusion Spike protein have significant potential impact on vaccines and therapeutics that utilize this key structural viral protein in their mitigation strategies. In this study, we have demonstrated how dominant energetic landscape mappings (\"glue points\") coupled with sequence alignment information can potentially identify or flag key residue mutations and deletions associated with variants. Surprisingly, we also found excellent homology of stabilizing residue glue points across the lineage of {beta} coronavirus Spike proteins, and we have termed this as \"sequence homologous glue points\". In general, these flagged residue mutations and/or deletions are then computationally studied in detail using all-atom biocomputational molecular dynamics over approximately one microsecond in order to ascertain structural and energetic changes in the Spike protein associated variants. Specifically, we examined both a theoretically-based triple mutant and the so-called UK or B.1.1.7 variant. For the theoretical triple mutant, we demonstrated through Alanine mutations, which help \"unglue\" key residue-residue interactions, that these three key stabilizing residues could cause the transition of Down to Up protomer states, where the Up protomer state allows binding of the prefusion Spike protein to hACE2 host cell receptors, whereas the Down state is believed inaccessible. Thus, we are able to demonstrate the importance of glue point residue identification in the overall stability of the prefusion Spike protein. For the B.1.1.7 variant, we demonstrated the critical importance of D614G and N5017 on the structure and binding, respectively, of the Spike protein. Notably, we had previously identified D614 as a key glue point in the inter-protomer stabilization of the Spike protein prior to the emergence of its mutation. The mutant D614G is a structure breaking Glycine mutation demonstrating a relatively more distal Down state RBD and a more stable conformation in general. In addition, we demonstrate that the mutation N501Y may significantly increase the Spike protein binding to hACE2 cell receptors through its interaction with Y41 of hACE2 forming a potentially strong hydrophobic residue binding pair. We note that these two key mutations, D614G and N501Y, are also found in the so-called South African (SA; B.1.351) variant of SARS-CoV-2. Future studies along these lines are, therefore, aimed at mapping glue points to residue mutations and deletions of associated prefusion Spike protein variants in order to help identify and analyze possible \"variants of interest\" and optimize efforts aimed at the mitigation of this current and future virions.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Michael H Peters", + "author_inst": "Virginia Commonwealth University" + }, + { + "author_name": "Oscar Basidas", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Daniel Kokron", + "author_inst": "NASA Ames Research Center" + }, + { + "author_name": "Christopher E. Henze", + "author_inst": "NASA Ames Research Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.02.08.430344", "rel_title": "Energetic and structural features of SARS-CoV-2 N-protein co-assemblies with nucleic acids", @@ -921693,41 +923539,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.02.04.21251155", - "rel_title": "Impact of school closures on the health and well-being of primary school children in Wales UK; a routine data linkage study using the HAPPEN survey (2018-2020).", - "rel_date": "2021-02-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.04.21251155", - "rel_abs": "IntroductionIn response to the COVID-19 pandemic, school closures were implemented across the United Kingdom. This study aimed to explore the impact of school closures on childrens health by comparing health and wellbeing outcomes collected during school closures (April - June 2020) with data from the same period in 2019 and 2018.\n\nMethodsData were collected online via the HAPPEN At Home survey, which captured the typical health behaviours of children aged 8 - 11 years between April - June 2020. These data were compared with data in 2018 and 2019 also collected between April-June, from HAPPEN. Free school meal (FSM) status was used as a proxy for socio-economic deprivation. Analyses were repeated stratifying by FSM.\n\nResultsComparing responses between April - June in 2020 (n=1068), 2019 (n=1150) and 2018 (n=475), there were improvements in physical activity levels, sleep time, happiness and general wellbeing for children during school closures compared to previous years. However, children on FSM ate less fruit and vegetables (21% (95%CI (5.7% to 37%)) and had lower self-assessed school competence compared to 2019. Compared to those not on FSM they also spent less time doing physical activity (13.03% (95%CI: 3.3% to 21.7%) and consumed more takeaways (16.3% (95%CI: 2%-30%)) during school closures.\n\nConclusionThis study suggests that schools play an important role in reducing inequalities in physical health. The physical health (e.g. physical activity and diet) of children eligible for FSM may be impacted by prolonged school closures.\n\nWhat is already known on this subject?In response to the COVID-19 pandemic, by mid-March 2020, 138 countries had implemented national school closures to reduce the number of social contacts between pupils, therefore interrupting the transmission of COVID-19 as part of pandemic plans. UNESCO warned that the global scale and speed of the educational disruption would be unparalleled. There is an ongoing debate with regard to the effectiveness of schools closures on transmission rates, but the fact schools are closed for a long period of time could have detrimental impacts on pupils physical and mental health.\n\nThis study provides evidence of any differences in the health and wellbeing of children prior to and during the COVID-19 enforced lockdown and school closures between March and June 2020. These findings could have a significant impact for the future and support schools to better understand their pupils physical, psychological, emotional and social health. It also contributes to a significant literature gap regarding the impact of school closures on school-aged children.\n\nWhat this study adds?Improvements in physical activity levels, sleep time, happiness and general wellbeing were observed in general for children during school closures compared to previous years. However, children on FSM reported eating less fruit and vegetables and had lower self-assessed school competence compared to 2019. Compared to those not on FSM they also spent less time doing physical activity and consumed more takeaways during school closures. These trends are not evident among children not on FSM. All children reported improvements in wellbeing during lockdown especially on the happiness with family measure.\n\nOverall, findings suggest schools help to reduce inequalities in physical health for socio-economically deprived children. During school closures children from deprived backgrounds are likely to have poorer physical health (e.g. less time spent doing physical activities and poorer diet) and this is not observed in children who are not in receipt of FSM. This research suggests that school closures will result in widening health inequalities and when schools return measures will need to be in place to readdress the widened gap in physical health.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Michaela James", - "author_inst": "Swansea University" - }, - { - "author_name": "Emily Marchant", - "author_inst": "Swansea University" - }, - { - "author_name": "Margaret A Defeyter", - "author_inst": "Northumbria University" - }, - { - "author_name": "Jayne V Woodside", - "author_inst": "Queen's University Belfast" - }, - { - "author_name": "Sinead Brophy", - "author_inst": "Swansea University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.02.04.21251181", "rel_title": "Enhancing Food Security for Families Vulnerable to COVID-19", @@ -922347,6 +924158,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.02.05.21251157", + "rel_title": "How effective was Newfoundland & Labrador's travel ban to prevent the spread of COVID-19? An agent-based analysis", + "rel_date": "2021-02-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.05.21251157", + "rel_abs": "BackgroundTo prevent the spread of COVID-19 in Newfoundland & Labrador (NL), NL implemented a wide travel ban in May 2020. We estimate the effectiveness of this travel ban using a customized agent-based simulation (ABS).\n\nMethodsWe built an individual-level ABS to simulate the movements and behaviors of every member of the NL population, including arriving and departing travellers. The model considers individual properties (spatial location, age, comorbidities) and movements between environments, as well as age-based disease transmission with pre-symptomatic, symptomatic, and asymptomatic transmission rates. We examine low, medium, and high travel volume, traveller infection rates, and traveller quarantine compliance rates to determine the effect of travellers on COVID spread, and the ability of contact tracing to contain outbreaks.\n\nResultsInfected travellers increased COVID cases by 2-52x (8-96x) times and peak hospitalizations by 2-49x (8-94x), with (without) contact tracing. Although contact tracing was highly effective at reducing spread, it was insufficient to stop outbreaks caused by travellers in even the best-case scenario, and the likelihood of exceeding contact tracing capacity was a concern in most scenarios. Quarantine compliance had only a small impact on COVID spread; travel volume and infection rate drove spread.\n\nInterpretationNLs travel ban was likely a critically important intervention to prevent COVID spread. Even a small number of infected travellers can play a significant role in introducing new chains of transmission, resulting in exponential community spread and significant increases in hospitalizations, while outpacing contact tracing capabilities. With the presence of more transmissible variants, e.g., the UK variant, prevention of imported cases is even more critical.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Dionne M Aleman", + "author_inst": "University of Toronto" + }, + { + "author_name": "Benjamin Z Tham", + "author_inst": "University of Toronto" + }, + { + "author_name": "Sean J Wagner", + "author_inst": "IBM Canada" + }, + { + "author_name": "Justin Semelhago", + "author_inst": "University of Toronto" + }, + { + "author_name": "Asghar Mohammadi", + "author_inst": "Memorial University" + }, + { + "author_name": "Paul Price", + "author_inst": "Memorial University" + }, + { + "author_name": "Randy Giffen", + "author_inst": "IBM Canada" + }, + { + "author_name": "Proton Rahman", + "author_inst": "Memorial University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.02.05.21251231", "rel_title": "Design and Estimation for the Population Prevalence of Infectious Diseases", @@ -923619,57 +925477,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.07.21251297", - "rel_title": "The changing characteristics of COVID-19 presentations: A regional comparison of SARS-CoV-2 hospitalised patients during the first and second wave.", - "rel_date": "2021-02-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.07.21251297", - "rel_abs": "BackgroundThis study assesses COVID-19 hospitalised patient demography and outcomes during wave 1 and wave 2, prior to new variants of the virus.\n\nMethodsAll patients with a positive SARS-CoV-2 swab between 10th March 2020 and 5th July 2020 (wave 1) and 1st September 2020 and 16th November 2020 (wave 2) admitted to University Hospitals Birmingham NHS Foundation Trust were included (n=4856), followed for 28 days.\n\nResultsWave 2 patients were younger, more ethnically diverse, had less co-morbidities and disease presentation was milder on presentation. After matching for these factors, mortality was reduced, but without differences in intensive care admissions.\n\nConclusionPrior to new SARS-CoV-2 variants, outcomes for hospitalised patients with COVID-19 were improving but with similar intensive care needs.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Catherine Atkin", - "author_inst": "Acute Medicine, Birmingham Acute Care Research Group, Institute of Inflammation and Ageing, University of Birmingham" - }, - { - "author_name": "Vicky Kamwa", - "author_inst": "Acute Medicine, Birmingham Acute Care Research Group, Institute of Inflammation and Ageing, University of Birmingham" - }, - { - "author_name": "Vinay Reddy-Kolanu", - "author_inst": "Acute Medicine, University Hospitals Birmingham NHS Foundation Trust" - }, - { - "author_name": "Dhruv Parekh", - "author_inst": "A. Intensive Care Medicine, University Hospitals Birmingham NHS Foundation Trust, Edgbaston, Birmingham, B15 2GW, UK. B. Birmingham Acute Care Research Grou" - }, - { - "author_name": "Felicity Evison", - "author_inst": "Research Analytics Department of Health Informatics, University Hospitals Birmingham NHS Foundation Trust" - }, - { - "author_name": "Peter Nightingale", - "author_inst": "NIHR Clinical Research Facility Statistician, University Hospitals Birmingham NHS Foundation Trust" - }, - { - "author_name": "Suzy Gallier", - "author_inst": "PIONEER Technical Director, Lead for Research Analytics Department of Health Informatics, University Hospitals Birmingham NHS Foundation Trust" - }, - { - "author_name": "Simon Ball", - "author_inst": "A. Chief Medical Officer, University Hospitals Birmingham NHS Foundation Trust B. HDR-UK Midlands Site and Better Care Programme, University Hospitals Birmingh" - }, - { - "author_name": "Elizabeth Sapey", - "author_inst": "A. Director of PIONEER: Health Data Research UK (HDRUK) Health Data Research Hub for Acute Care B. Birmingham Acute Care Research Group, Institute of Inflammat" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.06.21251266", "rel_title": "Assessment & mitigation of O2 therapy driven spread of COVID-19", @@ -924597,6 +926404,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.05.430003", + "rel_title": "Neutralization of viruses with European, South African, and United States SARS-CoV-2 variant spike proteins by convalescent sera and BNT162b2 mRNA vaccine-elicited antibodies", + "rel_date": "2021-02-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.05.430003", + "rel_abs": "The increasing prevalence of SARS-CoV-2 variants with mutations in the spike protein has raised concerns that recovered individuals may not be protected from reinfection and that current vaccines will become less effective. The B.1.1.7 isolate identified in the United Kingdom and B.1.351 isolate identified in the Republic of South Africa encode spike proteins with multiple mutations in the S1 and S2 subunits. In addition, variants have been identified in Columbus, Ohio (COH.20G/677H), Europe (20A.EU2) and in domesticated minks. Analysis by antibody neutralization of pseudotyped viruses showed that convalescent sera from patients infected prior to the emergence of the variant viruses neutralized viruses with the B.1.1.7, B.1.351, COH.20G/677H Columbus Ohio, 20A.EU2 Europe and mink cluster 5 spike proteins with only a minor decrease in titer compared to that of the earlier D614G spike protein. Serum specimens from individuals vaccinated with the BNT162b2 mRNA vaccine neutralized D614G virus with titers that were on average 7-fold greater than convalescent sera. Vaccine elicited antibodies neutralized virus with the B.1.1.7 spike protein with titers similar to D614G virus and neutralized virus with the B.1.351 spike with, on average, a 3-fold reduction in titer (1:500), a titer that was still higher than the average titer with which convalescent sera neutralized D614G (1:139). The reduction in titer was attributable to the E484K mutation in the RBD. The B.1.1.7 and B.1.351 viruses were not more infectious than D614G on ACE2.293T cells in vitro but N501Y, an ACE2 contacting residue present in the B.1.1.7, B.1.351 and COH.20G/677H spike proteins caused higher affinity binding to ACE2, likely contributing to their increased transmissibility. These findings suggest that antibodies elicited by primary infection and by the BNT162b2 mRNA vaccine are likely to maintain protective efficacy against B.1.1.7 and most other variants but that the partial resistance of virus with the B.1.351 spike protein could render some individuals less well protected, supporting a rationale for the development of modified vaccines containing E484K.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Takuya Tada", + "author_inst": "Department of Microbiology, NYU Grossman School of Medicine" + }, + { + "author_name": "Belinda M Dcosta", + "author_inst": "Department of Microbiology, NYU Grossman School of Medicine" + }, + { + "author_name": "Marie Samanovic-Golden", + "author_inst": "NYU Langone Vaccine Center and Department of Medicine, NYU Grossman School of Medicine" + }, + { + "author_name": "Ramin S Herati", + "author_inst": "NYU Langone Vaccine Center and Department of Medicine, NYU Grossman School of Medicine" + }, + { + "author_name": "Amber Cornelius", + "author_inst": "NYU Langone Vaccine Center and Department of Medicine, NYU Grossman School of Medicine" + }, + { + "author_name": "Mark J Mulligan", + "author_inst": "NYU Langone Vaccine Center and Department of Medicine, NYU Grossman School of Medicine" + }, + { + "author_name": "Nathaniel R Landau", + "author_inst": "Department of Microbiology, NYU Grossman School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.02.07.429299", "rel_title": "A human antibody with blocking activity to RBD proteins of multiple SARS-CoV-2 variants including B.1.351 showed potent prophylactic and therapeutic efficacy against SARS-CoV-2 in rhesus macaques", @@ -925573,61 +927423,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2021.02.02.21250840", - "rel_title": "Efficacy of Ivermectin in COVID-19 Patients with Mild to Moderate Disease", - "rel_date": "2021-02-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.02.21250840", - "rel_abs": "ObjectiveTo evaluate the efficacy of ivermectin (IVM) as an addition to the standard of care (SOC) treatment in COVID-19 patients with mild and moderate disease\n\nMaterials and MethodsA randomized clinical trial (Trial registration # NCT04392713) was carried out at Combined Military Hospital Lahore from March 15, 2020, to June 15, 2020. Eighty-six patients with reverse transcriptase-polymerase chain reaction (RT-PCR) proven SARS-CoV-2 infection completed the trial protocol. Patients were stratified via the lottery method into two groups. Group A was administered standard of care (SOC) treatment as per existing hospital guidelines whereas group B was given ivermectin (single dose of 12 milligrams) along with SOC treatment. PCR was repeated at 72 hours, 7th day, and at 14th day of admission for both the groups and the point at which the PCR became negative was noted. Complete blood counts, liver function tests and renal function tests were done at recruitment, 7th day, and 14th day. The primary outcome was the viral clearance, measured as days to achieve PCR negativity. The secondary outcome was the development of any adverse side effects pertinent to ivermectin or derangement in baseline laboratory parameters.\n\nResultsIn group A, 36 (80%) participants were males, and 9 (20%) were females, whereas in group B, 37 (90.2%) were males and 4 (9.8%) were females. Mean age was 39.0{+/-} 12.6 and 42.2 {+/-} 12.0 years for groups A and B, respectively (p= 0.394). There was early viral clearance in group B as compared to group A (p=0.001). No adverse reaction or derangements in laboratory parameters was noted in the intervention arm during the trial period.\n\nConclusionIn the intervention arm, early viral clearance was observed and no side effects were documented. Therefore ivermectin is a potential addition to the standard care of treatment in COVID-19 patients.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Syed Karamat Hussain Shah Bukhari", - "author_inst": "CMH Lahore Medical College & Institute of Dentistry" - }, - { - "author_name": "Asma Asghar", - "author_inst": "CMH Lahore Medical College & Institute of Dentistry" - }, - { - "author_name": "Najma Perveen", - "author_inst": "CMH Lahore Medical College & Institute of Dentistry" - }, - { - "author_name": "Arshad Hayat", - "author_inst": "CMH Lahore Medical College & Institute of Dentistry" - }, - { - "author_name": "Sermad Ahmad Mangat", - "author_inst": "CMH Lahore Medical College & Institute of Dentistry" - }, - { - "author_name": "Kamil Rehman Butt", - "author_inst": "CMH Lahore Medical College & Institute of Dentistry" - }, - { - "author_name": "Mohammad Abdullah", - "author_inst": "CMH Lahore Medical College & Institute of Dentistry" - }, - { - "author_name": "Tehreem Fatima", - "author_inst": "CMH Lahore Medical College & Institute of Dentistry" - }, - { - "author_name": "Ahmad Mustafa", - "author_inst": "CMH Lahore Medical College & Institute of Dentistry" - }, - { - "author_name": "Talal Cheema", - "author_inst": "CMH Lahore Medical College & Institute of Dentistry" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.05.21250953", "rel_title": "Convalescent Plasma and Improved Survival in Patients with Hematologic Malignancies and COVID-19", @@ -926367,6 +928162,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.03.21250928", + "rel_title": "Increased SAR-CoV-2 shedding associated with reduced disease severity despite continually emerging genetic variants", + "rel_date": "2021-02-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.03.21250928", + "rel_abs": "Since the first report of SARS-CoV-2 in December 2019, genetic variants have continued to emerge, complicating strategies for mitigating the disease burden of COVID-19. Positive SARS-CoV-2 nasopharyngeal swabs (n=8,735) were collected from Missouri, USA, from March-October 2020, and viral genomes (n=178) were sequenced. Hospitalization status and length of stay were extracted from medical charts of 1,335 patients and integrated with emerging genetic variants and viral shedding analyses for assessment of clinical impacts. Multiple introductions of SARS-CoV-2 into Missouri, primarily from Australia, Europe, and domestic states, were observed. Four local lineages rapidly emerged and spread across urban and rural regions in Missouri. While the majority of Missouri viruses harbored Spike-D614G mutations, a large number of unreported mutations were identified among Missouri viruses, including seven in the RNA-dependent RNA polymerase complex and Spike protein that were positively selected. A 15.6-fold increase in viral RNA levels in swab samples occurred from March to May and remained elevated. Accounting for other comorbidities, individuals test-positive for COVID-19 with high viral loads were less likely to be hospitalized (odds ratio=0.39, 95% confidence interval [CI]=0.20, 0.77) and had shorter hospital stays (hazard ratio=0.34, p=0.003) than those with low viral loads. Overall, the first eight months of the pandemic in Missouri saw multiple locally acquired mutants emerge and dominate in urban and rural locations. Although we were unable to find associations between specific variants and greater disease severity, Missouri COVID-positive individuals that presented with increased viral shedding had less severe disease by several measures.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Cynthia Y Tang", + "author_inst": "University of Missouri" + }, + { + "author_name": "Yang Wang", + "author_inst": "University of Missouri" + }, + { + "author_name": "Cheng Gao", + "author_inst": "University of Missouri" + }, + { + "author_name": "David R Smith", + "author_inst": "Mississippi State University" + }, + { + "author_name": "Jane A McElroy", + "author_inst": "University of Missouri" + }, + { + "author_name": "Tao Li", + "author_inst": "Walter Reed Army Institute of Research" + }, + { + "author_name": "Karen Segovia", + "author_inst": "University of Missouri" + }, + { + "author_name": "Tricia Haynes", + "author_inst": "University of Missouri" + }, + { + "author_name": "Richard Hammer", + "author_inst": "University of Missouri" + }, + { + "author_name": "Christopher Sampson", + "author_inst": "University of Missouri" + }, + { + "author_name": "Detlef Ritter", + "author_inst": "University of Missouri" + }, + { + "author_name": "Christopher Schulze", + "author_inst": "CoxHealth" + }, + { + "author_name": "Robin Trotman", + "author_inst": "CoxHealth" + }, + { + "author_name": "Grace M Lidl", + "author_inst": "Walter Reed Army Institute of Research" + }, + { + "author_name": "Richard Webby", + "author_inst": "St. Jude Children's Research Hospital" + }, + { + "author_name": "Jun Hang", + "author_inst": "Walter Reed Army Institute of Research" + }, + { + "author_name": "Xiu-Feng Wan", + "author_inst": "University of Missouri" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.03.21251078", "rel_title": "Antibody responses boosted in seropositive healthcare workers after single dose of SARS-CoV-2 mRNA vaccine", @@ -927279,33 +929157,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.03.21251057", - "rel_title": "Field performance evaluation of the PanBio rapid SARS-CoV-2 antigen assay in an epidemic driven by 501Y.v2 (lineage B.1.351) in the Eastern Cape, South Africa", - "rel_date": "2021-02-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.03.21251057", - "rel_abs": "BackgroundSouth Africa was the African country most severely affected by the SARS-CoV-2 pandemic during 2020, experiencing 2 waves of infection. During the first wave, diagnostics were largely based on reverse transcription-linked PCR (RT-PCR). The Abbott PanBio antigen test was deployed during the 2nd wave which was driven by emergence of the 501Y.v2 variant. At the time of evaluation in mid-November 2020, 501Y.v2 was the dominant circulating virus in Nelson Mandela Bay, in the Eastern Cape Province.\n\nMethodsA prospective diagnostic evaluation study was undertaken, during a period of high community transmission, to evaluate the field performance of the PanBio antigen RTD. Testing was conducted at mobile community testing centres on 677 ambulant patients seeking SARS-CoV-2 testing. RT-PCR was performed on the original naso-pharyngeal antigen swabs to evaluate test performance.\n\nResultsOf 146 RT-PCR positive individuals, 101 were RTD positive in the clinic. The antigen RTD had an overall sensitivity of 69.2% (95%CI 61.4, 75.8) and specificity of 99.0% (95%CI 98.8, 99.3) in this clinical context. Sensitivity was strongly dependent on the amount of virus in clinical samples, as reflected by the PCR cycle threshold (CT) value, with 100% detection in samples where the CT was <20, 96% with CT between 20-25, 89% with CT between 26-30 and 64% when CT was 31-35.\n\nConclusionsThe assay reliably detected 501Y.v2 infections in ambulatory ill patients. Assay sensitivity was >90% in patients with high viral loads who are expected to be most infectious. Negative and positive predictive values were also >90%.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Oluwakemi Laguda Akingba", - "author_inst": "Walter Sisulu University" - }, - { - "author_name": "Kaitlin Sprong", - "author_inst": "Walter Sisulu University" - }, - { - "author_name": "Diana Ruth Hardie", - "author_inst": "University of Cape Town" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pathology" - }, { "rel_doi": "10.1101/2021.02.03.21250579", "rel_title": "Newborn antibodies to SARS-CoV-2 detected in cord blood after maternal vaccination", @@ -929273,6 +931124,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.02.02.21250984", + "rel_title": "Point-of-care evaluation of a rapid antigen test (CLINITEST Rapid COVID-19 Antigen Test) for diagnosis of SARS-CoV-2 infection in symptomatic and asymptomatic individuals", + "rel_date": "2021-02-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.02.21250984", + "rel_abs": "Rapid antigen assays (RAD) based on lateral flow immunochromatography (LFIC) technology have emerged as a valuable tool for the control of COVID-19 pandemic. Manufacturer{square}independent, real{square}world evaluation of these assays is crucial given the considerable heterogeneity reported in their clinical and analytical performances. Here, we report for the first time on the point-of-care performance of the CLINITEST(R) Rapid COVID-19 Antigen Test (Siemens, Healthineers, Erlangen, Germany) to detect SARS-CoV-2 infection in presumptive COVID-19 cases or asymptomatic close contacts of COVID-19 patients. When compared to RT-PCR, the overall sensitivity of the assay was 80.2 (95% CI, 70.9-87.1) for symptomatic patients sampled (nasopharyngeal specimens) within five days after the onset of symptoms and 60% (95% CI, 40.7-76.6%) for asymptomatic participants. The overall specificity was 100% in both population groups.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Ignacio Torres", + "author_inst": "Microbiology Service, Hospital Clinico Universitario, INCLIVA Research Institute, Valencia, Spain." + }, + { + "author_name": "Sandrine Poujois", + "author_inst": "Microbiology Service, Hospital Clinico Universitario, INCLIVA Research Institute, Valencia, Spain." + }, + { + "author_name": "Eliseo Albert", + "author_inst": "Microbiology Service, Hospital Clinico Universitario, INCLIVA Research Institute, Valencia, Spain." + }, + { + "author_name": "Gabriella Alvarez", + "author_inst": "Microbiology Service, Hospital Clinico Universitario, INCLIVA Research Institute, Valencia, Spain." + }, + { + "author_name": "Javier Colomina", + "author_inst": "Microbiology Service, Hospital Clinico Universitario, INCLIVA Research Institute, Valencia, Spain." + }, + { + "author_name": "David Navarro", + "author_inst": "Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.01.21250946", "rel_title": "Usability of saliva collection devices for SARS-CoV-2 diagnostics", @@ -930041,29 +931931,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.01.31.21250872", - "rel_title": "Returning to a normal life via COVID-19 vaccines in the USA: a large-scale agent-based simulation study", - "rel_date": "2021-02-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.31.21250872", - "rel_abs": "BackgroundIn 2020, COVID-19 has claimed more than 300,000 deaths in the US alone. While non-pharmaceutical interventions were implemented by federal and state governments in the USA, these efforts have failed to contain the virus. Following the FDA approval of two COVID-19 vaccines, however, the hope for the return to normalcy is renewed. This hope rests on an unprecedented nation-wide vaccine campaign, which faces many logistical challenges and is also contingent on several factors whose values are currently unknown.\n\nObjectiveWe study the effectiveness of a nation-wide vaccine campaign in response to different vaccine efficacies, the willingness of the population to be vaccinated, and the daily vaccine capacity under two different federal plans. To characterize the possible outcomes most accurately, we also account for the interactions between non-pharmaceutical interventions and vaccines, through six scenarios that capture a range of possible impact from non-pharmaceutical interventions.\n\nMethodsWe use large-scale cloud-based agent-based simulations by implementing the vaccination campaign using Covasim, an open-source ABM for COVID-19 that has been used in several peer-reviewed studies and accounts for individual heterogeneity as well as a multiplicity of contact networks. Several modifications to the parameters and simulation logic were made to better align the model with current evidence. We chose six non-pharmaceutical intervention scenarios and applied the vaccination intervention following both the plan proposed by Operation Warp Speed (former Trump administration) and the plan of one million vaccines per day, proposed by the Biden administration. We accounted for unknowns in vaccine efficacies and levels of population compliance by varying both parameters. For each experiment, the cumulative infection growth is fitted to a logistic growth model, and the carrying capacities and the growth rates are recorded.\n\nResultsFor both vaccination plans and all non-pharmaceutical intervention scenarios, the presence of the vaccine intervention considerably lowers the total number of infections when life returns to normal, even when the population compliance to vaccines is as low at 20%. We noted an unintended consequence: given the vaccine availability estimates under both federal plans and the focus on vaccinating individuals by age categories, a significant reduction in non-pharmaceutical interventions results in a counterintuitive situation in which higher vaccine compliance then leads to more total infections.\n\nConclusionsAlthough potent, vaccines alone cannot effectively end the pandemic given the current availability estimates and the adopted vaccination strategy. Non-pharmaceutical interventions need to continue and be enforced to ensure high compliance, so that the rate of immunity established by vaccination outpaces that induced by infections.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Junjiang Li", - "author_inst": "Miami University" - }, - { - "author_name": "Philippe Giabbanelli", - "author_inst": "Miami University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.02.01.21250904", "rel_title": "Limited specificity of SARS-CoV-2 antigen-detecting rapid diagnostic tests at low temperatures", @@ -931131,6 +932998,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.01.21250905", + "rel_title": "COVID-19 among bartenders and waiters before and after pub lockdown", + "rel_date": "2021-02-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.01.21250905", + "rel_abs": "AimTo study how different bans on serving alcohol in Norwegian bars and restaurants were related to the detection of SARS-CoV-2 in bartenders and waiters.\n\nMethodsIn 24,276 bartenders and waiters and 1,287,970 persons with other occupations (mean [SD] age 41.7 [12.8] years and 51.7% men), we examined the weekly rates of workers tested and detected with SARS-CoV-2, one to five weeks before and one to five weeks after implementation of different degrees of bans on serving alcohol in pubs and restaurants, across 56 Norwegian municipalities with: 1) full blanket ban, 2) partial ban with hourly restrictions (e.g. from 10 pm), or 3) no ban, adjusted for age, sex and testing behavior.\n\nResultsIn municipalities introducing full ban, COVID-19 among bartenders and waiters had been reduced by 65% by three weeks (from 3.4 [95%CI=2.5-4.3] to 1.2 [95%CI=0.7-1.7] per 1000), i.e. to the same levels as that for persons with other occupations (1.8 [95%CI=1.7-1.9] vs 1.2 [95%CI=1.1-1.3] per 1000). Similarly, in municipalities introducing partial ban, COVID-19 among bartenders and waiters had been reduced by 68% by three weeks (from 2.5 [95%CI=1.4-3.6] to 0.8 [95%CI=0.0-1.5] per 1000). However, there was more uncertainty to the estimated reduction for partial bans.\n\nConclusionMunicipalities with higher levels of confirmed COVID-19 among bartenders and waiters implemented stricter bans on serving of alcohol than other municipalities. Contraction of COVID-19 among bartenders and waiters declined similarly in municipalities with full and partial bans.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Fredrik Methi", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Kjetil Telle", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Karin Magnusson", + "author_inst": "Norwegian Institute of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.01.21250769", "rel_title": "Sarilumab treatment of hospitalised patients with severe or critical COVID-19: a multinational, randomised, adaptive, phase 3, double-blind, placebo-controlled trial", @@ -932159,85 +934053,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, - { - "rel_doi": "10.1101/2021.02.02.21251020", - "rel_title": "SEVERE COVID-19 IS MARKED BY DYSREGULATED SERUM LEVELS OF CARBOXYPEPTIDASE A3 AND SEROTONIN", - "rel_date": "2021-02-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.02.21251020", - "rel_abs": "The immune response plays a critical role in the pathophysiology of SARS-CoV-2 infection ranging from protection to tissue damage. This is observed in the development of acute respiratory distress syndrome when elevated levels of inflammatory cytokines are detected. Several cells of the immune response are implied in this dysregulated immune response including innate immune cells and T and B cell lymphocytes. Mast cells are abundant resident cells of the respiratory tract, able to rapidly release different inflammatory mediators following stimulation. Recently, mast cells have been associated with tissue damage during viral infections, but little is known about their role in SARS-CoV-2 infection. In this study we examined the profile of mast cell activation markers in the serum of COVID-19 patients. We noticed that SARS-CoV-2 infected patients showed increased carboxypeptidase A3 (CPA3), and decreased serotonin levels in their serum. CPA3 levels correlated with C-reactive protein, the number of circulating neutrophils and quick SOFA. CPA3 in serum was a good biomarker for identifying severe COVID-19 patients, while serotonin was a good predictor of SARS-CoV-2 infection. In summary, our results show that serum CPA3 and serotonin levels are relevant biomarkers during SARS-CoV-2 infection, suggesting that mast cells are relevant players in the inflammatory response in COVID-19, might represent targets for therapeutic intervention.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Rodolfo Soria-Castro", - "author_inst": "Departamento de Inmunologia, Escuela Nacional de Ciencias Biologicas, Instituto Politecnico Nacional, ENCB-IPN. Mexico City, Mexico." - }, - { - "author_name": "Yatsiri G. Meneses-Preza", - "author_inst": "Departamento de Inmunologia, Escuela Nacional de Ciencias Biologicas, Instituto Politecnico Nacional, ENCB-IPN. Mexico City, Mexico." - }, - { - "author_name": "Gloria M. Rodriguez-Lopez", - "author_inst": "Departamento de Inmunologia, Escuela Nacional de Ciencias Biologicas, Instituto Politecnico Nacional, ENCB-IPN. Mexico City, Mexico." - }, - { - "author_name": "Sandra Romero-Ramirez", - "author_inst": "Red de Apoyo a la Investigacion, Universidad Nacional Autonoma de Mexico e Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico city, Mex" - }, - { - "author_name": "Victor A. Sosa-Hernandez", - "author_inst": "Red de Apoyo a la Investigacion, Universidad Nacional Autonoma de Mexico e Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico city, Mex" - }, - { - "author_name": "Rodrigo Cervantes-Diaz", - "author_inst": "Red de Apoyo a la Investigacion, Universidad Nacional Autonoma de Mexico e Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico city, Mex" - }, - { - "author_name": "Alfredo Perez-Fragoso", - "author_inst": "Red de Apoyo a la Investigacion, Universidad Nacional Autonoma de Mexico e Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico city, Mex" - }, - { - "author_name": "Jose J Torres-Ruiz", - "author_inst": "Departamento de Atencion Institucional Continua y Urgencias, Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico" - }, - { - "author_name": "Diana Gomez-Martin", - "author_inst": "Departamento de Inmunologia y Reumatologia, Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico" - }, - { - "author_name": "Marcia Campillo-Navarro", - "author_inst": "Research Coordination, Centro Medico Nacional 20 de Noviembre, ISSSTE, Mexico City, Mexico" - }, - { - "author_name": "Violeta D. Alvarez-Jimenez", - "author_inst": "Lab. de Biologia Molecular y Bioseguridad Nivel 3. Centro Medico Naval-SEMAR, Mexico city, Mexico" - }, - { - "author_name": "Sonia M. Perez-Tapia", - "author_inst": "Unidad de Desarrollo e Investigacion en Bioprocesos (UDIBI), Escuela Nacional de Ciencias Biologicas, Instituto Politecnico Nacional, ENCB-IPN. Mexico City, Mex" - }, - { - "author_name": "Alma D. Chavez-Blanco", - "author_inst": "Division de Ciencia Basica, Instituto Nacional de Cancerologia (INCan). Mexico City, Mexico" - }, - { - "author_name": "Sergio Estrada-Parra", - "author_inst": "Departamento de Inmunologia, Escuela Nacional de Ciencias Biologicas, Instituto Politecnico Nacional, ENCB-IPN. Mexico City, Mexico" - }, - { - "author_name": "Jose L. Maravillas-Montero", - "author_inst": "Red de Apoyo a la Investigacion, Universidad Nacional Autonoma de Mexico e Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico city, Mex" - }, - { - "author_name": "Rommel Chacon-Salinas", - "author_inst": "Instituto Politecnico Nacional (IPN)" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.02.21250960", "rel_title": "Colchicine use in patients with COVID-19: a systematic review and meta-analysis", @@ -932885,6 +934700,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2021.02.02.21251017", + "rel_title": "Home Food Procurement Impacts Food Security and Diet Quality during COVID-19", + "rel_date": "2021-02-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.02.21251017", + "rel_abs": "BackgroundHome food procurement (HFP) (i.e. gardening, fishing, foraging, hunting, backyard livestock and canning) have historically been important ways that people obtain food. Recently, some HFP activities have grown (e.g. gardening), while other activities (e.g. hunting) have become less common in the United States. Anecdotally, COVID-19 has sparked an increase in HFP evidenced by increased hunting licenses and shortages in seeds and canning supplies. HFP may have positive benefits for food security and diet quality, though research beyond gardening is especially limited in high-income countries.\n\nMethodsWe examine HFP activities before and since the COVID-19 pandemic, and their relationship to food security and dietary quality using multivariable logit models and matching analysis with a statewide representative survey (n=600) of residents of Vermont, United States.\n\nResultsWe find 29% of respondent households classified as food insecure since COVID-19, and more prevalence among those experiencing a negative job change since COVID-19, households earning less than $50,000 annually, Hispanic and multi-race respondents. Forty-two percent of respondents engaged in HFP activities; the majority of those gardened, and more than half pursued HFP activities more intensely than before the pandemic. HFP was more common among food insecure households, who were more likely to fish, forage, hunt and have backyard livestock. Respondents who were food insecure, Black, Indigenous, People of Color and/or Hispanic, those with a negative job disruption, and larger households all had greater odds of increased intensity of HFP since COVID-19. HFP were significantly associated with eating greater amounts of fruits and vegetables, especially if gardening and canning, while respondents hunting or having backyard livestock were significantly more likely to have higher red meat intake.\n\nConclusionOverall, these results suggest that HFP activities have increased since the start of the COVID-19 pandemic, and may be an important safety net for food insecure households, and provide diet quality impacts. Long-term, HFP activities may have important food security and diet quality impacts, as well as conservation implications, which should be more thoroughly explored. Regardless, the increased interest and intensity of HFP demonstrates multiple opportunities for educational and outreach efforts.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Meredith T. Niles", + "author_inst": "University of Vermont" + }, + { + "author_name": "Kristen Brassard Wirkkala", + "author_inst": "University of Vermont" + }, + { + "author_name": "Emily H. Belarmino", + "author_inst": "University of Vermont" + }, + { + "author_name": "Farryl Bertmann", + "author_inst": "University of Vermont" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "nutrition" + }, { "rel_doi": "10.1101/2021.01.31.21250867", "rel_title": "Standard and anomalous second waves in the COVID-19 pandemic", @@ -934153,157 +935999,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.02.03.429540", - "rel_title": "Variation in predicted COVID-19 risk among lemurs and lorises", - "rel_date": "2021-02-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.03.429540", - "rel_abs": "The novel coronavirus SARS-CoV-2, which in humans leads to the disease COVID-19, has caused global disruption and more than 1.5 million fatalities since it first emerged in late 2019. As we write, infection rates are currently at their highest point globally and are rising extremely rapidly in some areas due to more infectious variants. The primary viral target is the cellular receptor angiotensin-converting enzyme-2 (ACE2). Recent sequence analyses of the ACE2 gene predicts that many nonhuman primates are also likely to be highly susceptible to infection. However, the anticipated risk is not equal across the Order. Furthermore, some taxonomic groups show high ACE2 amino acid conservation, while others exhibit high variability at this locus. As an example of the latter, analyses of strepsirrhine primate ACE2 sequences to date indicate large variation among lemurs and lorises compared to other primate clades despite low sampling effort. Here, we report ACE2 gene and protein sequences for 71 individual strepsirrhines, spanning 51 species and 19 genera. Our study reinforces previous results and finds additional variability in other strepsirrhine species, and suggests several clades of lemurs have high potential susceptibility to SARS-CoV-2 infection. Troublingly, some species, including the rare and Endangered aye-aye (Daubentonia madagascariensis), as well as those in the genera Avahi and Propithecus, may be at high risk. Given that lemurs are endemic to Madagascar and among the primates at highest risk of extinction globally, further understanding of the potential threat of COVID-19 to their health should be a conservation priority. All feasible actions should be taken to limit their exposure to SARS-CoV-2.", - "rel_num_authors": 34, - "rel_authors": [ - { - "author_name": "Amanda D Melin", - "author_inst": "Department of Anthropology and Archaeology, University of Calgary, Canada; Department of Anthropology and Archaeology, University of Calgary, Canada; Alberta Ch" - }, - { - "author_name": "Joseph D Orkin", - "author_inst": "Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain" - }, - { - "author_name": "Mareike C Janiak", - "author_inst": "School of Science, Engineering & Environment, University of Salford, United Kingdom" - }, - { - "author_name": "Alejandro Valenzuela", - "author_inst": "Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain" - }, - { - "author_name": "Lukas FK Kuderna", - "author_inst": "Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain" - }, - { - "author_name": "Frank Marrone III", - "author_inst": "Department of Chemistry, New York University, United States" - }, - { - "author_name": "Hasinala Ramangason", - "author_inst": "Department of Anthropology and Archaeology, University of Calgary, Canada" - }, - { - "author_name": "Julie E Horvath", - "author_inst": "Genomics and Microbiology Research Laboratory, North Carolina Museum of Natural Sciences, Raleigh, NC, USA; Department of Biological and Biomedical Sciences, No" - }, - { - "author_name": "Christian Roos", - "author_inst": "Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany" - }, - { - "author_name": "Andrew C Kitchener", - "author_inst": "Department of Natural Sciences, National Museums Scotland and School of Geosciences, University of Edinburgh, Edinburgh, United Kingdom" - }, - { - "author_name": "Chiea Chuen Khor", - "author_inst": "Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore; Singapore Eye Research Institute, Singapore National Eye Centre, Singapor" - }, - { - "author_name": "Weng Khong Lim", - "author_inst": "SingHealth Duke-NUS Institute of Precision Medicine, Singapore Health Services, Singapore; SingHealth Duke-NUS Genomic Medicine Centre, Singapore Health Service" - }, - { - "author_name": "Jessica GH Lee", - "author_inst": "Department of Conservation, Research and Veterinary Services, Wildlife Reserves Singapore, Singapore" - }, - { - "author_name": "Patrick Tan", - "author_inst": "Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore; SingHealth Duke-NUS Institute of Precision Medicine, Singapore Health Ser" - }, - { - "author_name": "Govindhaswamy Umapathy", - "author_inst": "CSIR-Laboratory for the Conservation of Endangered Species, Centre for Cellular and Molecular Biology, Hyderabad, India" - }, - { - "author_name": "Muthuswamy Raveendran", - "author_inst": "Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States" - }, - { - "author_name": "R. Alan Harris", - "author_inst": "Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States" - }, - { - "author_name": "Ivo Gut", - "author_inst": "Universitat Pompeu Fabra (UPF), Barcelona, Spain." - }, - { - "author_name": "Marta Gut", - "author_inst": "Universitat Pompeu Fabra (UPF), Barcelona, Spain." - }, - { - "author_name": "Esther Lizano", - "author_inst": "Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain" - }, - { - "author_name": "Tilo Nadler", - "author_inst": "Cuc Phuong Commune, Nho Quan District, Ninh Binh Province, Vietnam" - }, - { - "author_name": "Dietmar Zinner", - "author_inst": "Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Goettingen , Germany; Leibniz Science Campus Primate Cognition, Go" - }, - { - "author_name": "Steig E Johnson", - "author_inst": "Department of Anthropology and Archaeology, University of Calgary, Canada" - }, - { - "author_name": "Erich D Jarvis", - "author_inst": "The Vertebrate Genomes Lab, The Rockefeller University, New York, United States; Laboratory of Neurogenetics of Language, The Rockefeller University, New York, " - }, - { - "author_name": "Olivier Fedrigo", - "author_inst": "The Vertebrate Genomes Lab, The Rockefeller University, New York, United States; Howard Hughes Medical Institute, Chevy Chase, Maryland, United States" - }, - { - "author_name": "Dongdong Wu", - "author_inst": "State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Kunming Natural History Muse" - }, - { - "author_name": "Guojie Zhang", - "author_inst": "Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark; China National Genebank, B" - }, - { - "author_name": "Kyle Kai-How Farh", - "author_inst": "Artificial Intelligence Lab, Illumina Inc, San Diego, CA, USA" - }, - { - "author_name": "Jeffrey Rogers", - "author_inst": "Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States" - }, - { - "author_name": "Tomas Marques-Bonet", - "author_inst": "Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain; Catalan Institution of Res" - }, - { - "author_name": "Arcadi Navarro", - "author_inst": "Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain; Catalan Institution of Res" - }, - { - "author_name": "David Juan", - "author_inst": "Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain" - }, - { - "author_name": "Paramjit S Arora", - "author_inst": "Department of Chemistry, New York University, United States" - }, - { - "author_name": "James P Higham", - "author_inst": "Department of Anthropology, New York University, United States; New York Consortium in Evolutionary Primatology, New York, United States" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genetics" - }, { "rel_doi": "10.1101/2021.02.03.429536", "rel_title": "Exaggerated cytokine production in human peripheral blood mononuclear cells by recombinant SARS-CoV-2 spike glycoprotein S1 and its inhibition by dexamethasone", @@ -934963,6 +936658,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, + { + "rel_doi": "10.1101/2021.01.30.21250785", + "rel_title": "Genetic determination of regional connectivity in modelling the spread of COVID-19 outbreak for improved mitigation strategies", + "rel_date": "2021-02-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.30.21250785", + "rel_abs": "Covid-19 has resulted in the death of more than 1,500,000 individuals. Due to the pandemics severity, thousands of genomes have been sequenced and publicly stored with extensive records, an unprecedented amount of data for an outbreak in a single year. Simultaneously, prediction models offered region-specific and often contradicting results, while states or countries implemented mitigation strategies with little information on success, precision, or agreement with neighboring regions. Even though viral transmissions have been already documented in a historical and geographical context, few studies aimed to model geographic and temporal flow from viral sequence information. Here, using a case study of 7 states, we model the flow of the Covid-19 outbreak with respect to phylogenetic information, viral migration, inter- and intra- regional connectivity, epidemiologic and demographic characteristics. By assessing regional connectivity from genomic variants, we can significantly improve predictions in modeling the viral spread and intensity.\n\nContrary to previous results, our study shows that the vast majority of the first outbreak can be traced to very few lineages, despite the existence of multiple worldwide transmissions. Moreover, our results show that while the distance from hotspots is initially important, connectivity becomes increasingly significant as the virus establishes itself. Similarly, isolated local strategies-such as relying on herd immunity-can negatively impact neighboring states. Our work suggests that we can achieve more efficient unified mitigation strategies with selective interventions.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Leonidas Salichos", + "author_inst": "New York Institute of Technology" + }, + { + "author_name": "Jonathan Warrell", + "author_inst": "Yale University" + }, + { + "author_name": "Hannah Cevasco", + "author_inst": "Yale University" + }, + { + "author_name": "Alvin Chung", + "author_inst": "Yale University" + }, + { + "author_name": "Mark Gerstein", + "author_inst": "Yale university" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2021.01.31.21250868", "rel_title": "Molecular epidemiology of SARS-CoV-2 in Greece reveals low rates of onward virus transmission after lifting of travel restrictions based on risk assessment during summer 2020", @@ -935967,93 +937697,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2021.02.01.428871", - "rel_title": "Nanotraps for the containment and clearance of SARS-CoV-2", - "rel_date": "2021-02-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.01.428871", - "rel_abs": "SARS-CoV-2 enters host cells through its viral spike protein binding to angiotensin-converting enzyme 2 (ACE2) receptors on the host cells. Here we show functionalized nanoparticles, termed \"Nanotraps\", completely inhibited SARS-CoV-2 infection by blocking the interaction between the spike protein of SARS-CoV-2 and the ACE2 of host cells. The liposomal-based Nanotrap surfaces were functionalized with either recombinant ACE2 proteins or anti-SARS-CoV-2 neutralizing antibodies and phagocytosis-specific phosphatidylserines. The Nanotraps effectively captured SARS-CoV-2 and completely blocked SARS-CoV-2 infection to ACE2-expressing human cell lines and primary lung cells; the phosphatidylserine triggered subsequent phagocytosis of the virus-bound, biodegradable Nanotraps by macrophages, leading to the clearance of pseudotyped and authentic virus in vitro. Furthermore, the Nanotraps demonstrated excellent biosafety profile in vitro and in vivo. Finally, the Nanotraps inhibited pseudotyped SARS-CoV-2 infection in live human lungs in an ex vivo lung perfusion system. In summary, Nanotraps represent a new nanomedicine for the inhibition of SARS-CoV-2 infection.\n\nHighlightsO_LINanotraps block interaction between SARS-CoV-2 spike protein and host ACE2 receptors\nC_LIO_LINanotraps trigger macrophages to engulf and clear virus without becoming infected\nC_LIO_LINanotraps showed excellent biosafety profiles in vitro and in vivo\nC_LIO_LINanotraps blocked infection to living human lungs in ex vivo lung perfusion system\nC_LI\n\nProgress and PotentialTo address the global challenge of creating treatments for SARS-CoV-2 infection, we devised a nanomedicine termed \"Nanotraps\" that can completely capture and eliminate the SARS-CoV-2 virus. The Nanotraps integrate protein engineering, immunology, and nanotechnology and are effective, biocompatible, safe, stable, feasible for mass production. The Nanotraps have the potential to be formulated into a nasal spray or inhaler for easy administration and direct delivery to the respiratory system, or as an oral or ocular liquid, or subcutaneous, intramuscular or intravenous injection to target different sites of SARS-CoV-2 exposure, thus offering flexibility in administration and treatment. More broadly, the highly versatile Nanotrap platform could be further developed into new vaccines and therapeutics against a broad range of diseases in infection, autoimmunity and cancer, by incorporating with different small molecule drugs, RNA, DNA, peptides, recombinant proteins, and antibodies.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Min Chen", - "author_inst": "University of Chicago" - }, - { - "author_name": "Jillian Rosenberg", - "author_inst": "University of Chicago" - }, - { - "author_name": "Xiaolei Cai", - "author_inst": "University of Chicago" - }, - { - "author_name": "Andy Chao Hsuan Lee", - "author_inst": "University of Chicago" - }, - { - "author_name": "Jiuyun Shi", - "author_inst": "University of Chicago" - }, - { - "author_name": "Mindy Nguyen", - "author_inst": "University of Chicago" - }, - { - "author_name": "Thirushan Wignakumar", - "author_inst": "University of Chicago" - }, - { - "author_name": "Vikranth Mirle", - "author_inst": "University of Chicago" - }, - { - "author_name": "Arianna Joy Edobor", - "author_inst": "University of Chicago" - }, - { - "author_name": "John Fung", - "author_inst": "University of Chicago" - }, - { - "author_name": "Jessica Scott Donington", - "author_inst": "University of Chicago" - }, - { - "author_name": "Kumaran Shanmugarajah", - "author_inst": "University of Chicago" - }, - { - "author_name": "Eugene B. Chang", - "author_inst": "Univeristy of Chicago" - }, - { - "author_name": "Glenn Randall", - "author_inst": "University of Chicago" - }, - { - "author_name": "Pablo Penaloza-MacMaster", - "author_inst": "Northwestern University" - }, - { - "author_name": "Bozhi Tian", - "author_inst": "University of Chicago" - }, - { - "author_name": "Maria Lucia Madariaga", - "author_inst": "University of Chicago" - }, - { - "author_name": "Jun Huang", - "author_inst": "University of Chicago" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2021.02.01.429219", "rel_title": "Enhanced immunogenicity of a synthetic DNA vaccine expressing consensus SARS-CoV-2 Spike protein using needle-free immunization", @@ -936621,6 +938264,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.28.21249932", + "rel_title": "Administration of tocilizumab to patients with high concentrations of IL-6 in the course of COVID-19 is associated with a better prognosis", + "rel_date": "2021-02-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.28.21249932", + "rel_abs": "BackgroundDespite the direct viral activity, the pathogenesis of coronavirus disease 2019 (COVID-19) includes an overproduction of cytokines including interleukin 6 (IL-6). Therefore tocilizumab (TCZ), a monoclonal antibody against IL-6 receptors, became considered as a possible therapeutic option.\n\nMethodsPatients were selected from the SARSTer national database, which included 2332 individuals with COVID-19 and the current study included 825 adult patients with moderate to severe course. The retrospective analysis was performed in 170 patients treated with TCZ and 655 without this medication or any other anti-cytokine therapy. The end-points of treatment effectiveness were a rate of death, need for mechanical ventilation, and clinical improvement.\n\nResultsPatients treated with TCZ were balanced compared to non-TCZ regarding gender, age, BMI, and prevalence of coexisting conditions. The reduced death rate was demonstrated in patients treated with TCZ and baseline IL-6 >100 pg/ml (hazard ratio [HR]: 0.27, 95% confidence interval [CI]:0.10-0.78), or those needing oxygen supplementations who worsened within 7 days of hospitalization (HR: 0.38, 95% CI:0.16-0.88). The best effectiveness of TCZ was achieved in patients with a combination of baseline IL-6>100 pg/ml and either SpO2[≤]90% (HR for death, mechanical ventilation, and clinical improvement after 21 or 28 days: 0.07, 0.14, 5.53, 5.18 respectively) or requiring oxygen supplementation (HR for death and clinical improvement after 21 or 28 days, 0.18, 2.66, 2.85 respectively).\n\nConclusionsTocilizumab administered for COVID-19 in patients with a baseline concentration of IL-6>100 pg/ml is associated with reduced mortality and faster clinical improvement, particularly if there is a need for oxygen supplementation due to SpO2[≤]90%.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Robert Flisiak", + "author_inst": "Medical University of Bialystok, Poland" + }, + { + "author_name": "Jerzy Jaroszewicz", + "author_inst": "Medical University of Silesia, Poland" + }, + { + "author_name": "Magdalena Rogalska", + "author_inst": "Medical University of Bialystok, Poland" + }, + { + "author_name": "Tadeusz Lapinski", + "author_inst": "Medical University of Bialystok, Poland" + }, + { + "author_name": "Aleksandra Berkan-Kawinska", + "author_inst": "Medical University of Lodz, Poland" + }, + { + "author_name": "Beata Bolewska", + "author_inst": "University of Medical Sciences, Poznan, Poland" + }, + { + "author_name": "Magdalena Tudrujek-Zdunek", + "author_inst": "Medical University of Lublin, Poland" + }, + { + "author_name": "Dorota Kozielewicz", + "author_inst": "Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Poland" + }, + { + "author_name": "Marta Rorat", + "author_inst": "Wroclaw Medical University, Poland and Gromkowski Regional Specialist Hospital in Wroclaw, Poland" + }, + { + "author_name": "Piotr Leszczynski", + "author_inst": "University of Medical Sciences, Poznan, Poland" + }, + { + "author_name": "Krzysztof Klos", + "author_inst": "Military Institute of Medicine, Warsaw, Poland" + }, + { + "author_name": "Justyna Kowalska", + "author_inst": "Medical University of Warsaw, Poland" + }, + { + "author_name": "Pawel Pabjan", + "author_inst": "Jan Kochanowski University, Kielce, Poland" + }, + { + "author_name": "Anna Piekarska", + "author_inst": "Medical University of Lodz, Poland" + }, + { + "author_name": "Iwona Mozer-Lisewska", + "author_inst": "University of Medical Sciences, Poznan, Poland" + }, + { + "author_name": "Krzysztof Tomasiewicz", + "author_inst": "Medical University of Lublin, Poland" + }, + { + "author_name": "Malgorzata Pawlowska", + "author_inst": "Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Poland" + }, + { + "author_name": "Krzysztof Simon", + "author_inst": "Wroclaw Medical University, Poland" + }, + { + "author_name": "Joanna Polanska", + "author_inst": "Silesian University of Technology, Gliwice, Poland" + }, + { + "author_name": "Dorota Zarebska-Michaluk", + "author_inst": "Jan Kochanowski University, Kielce, Poland" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.28.20181040", "rel_title": "Modeling the potential impact of indirect transmission on COVID-19 epidemic", @@ -937593,89 +939331,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.01.29.21250749", - "rel_title": "COVID-19 vaccine uptake among healthcare workers in the fourth country to authorize BNT162b2 during the first month of rollout", - "rel_date": "2021-02-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.29.21250749", - "rel_abs": "BackgroundThe Kingdom of Saudi Arabia (KSA) was the fourth country in the world to authorize the BNT162b2 coronavirus disease 2019 (COVID-19) vaccine, which it rolled out on December 17, 2020 and first targeted at healthcare workers (HCWs). This study assesses vaccine uptake among this group during the first month of its availability.\n\nMethodsA national cross-sectional, pilot-validated, self-administered survey was conducted among HCWs in the KSA between December 27, 2020 and January 3, 2021. The survey included sociodemographic details, previous contact with COVID-19 patients, previous infection with COVID-19, receiving (or registering with the Ministry of Health website to receive) the COVID-19 vaccine, sources of HCWs information on vaccines, awareness of emerging variants of concern, and anxiety level using the 7-item Generalized Anxiety Disorder assessment. A descriptive bivariate analysis and multivariate logistic binary regression analysis were performed. The primary evaluated outcome was vaccine uptake.\n\nResultsOf the 1,058 participants who completed the survey, 704 (66.5%) were female, and 626 (59.2%) were nurses. Of all the respondents, 352 (33.27%) were enrolled to receive or had already received the vaccine, while 706 (66.73%) had not registered. In a bivariate analysis, not enrolling for vaccination was more likely in females than males (78.5% vs. 21.5%, P < 0.001), HCWs between the ages of 20 and 40 years than those > 40 years (70.4% vs. 29.6%, P = 0.005), Saudi HCWs than expatriates (78% vs 22%, P < 0.001), and among HCWs who used social media as a source of information than those who did not (69.8% vs. 38.6%, P < 0.001). In a multivariate analysis, independent factors for not enrolling to receive the vaccine included being female (aOR = 0.287, 95%CI = 0.206-0.401, P < 0.001), being less than 40 years of age (aOR = 1.021, 95%CI = 1.002-1.040, P = 0.032), and using social media as a source of information (aOR = 0.207, 95%CI = 0.132-1.354, P = 0.001). Factors associated with uptake were being a Saudi national (aOR = 1.918, 95%CI = 1.363-2.698, P < 0.001), working in an intensive care unit (aOR = 1.495, 95%CI = 1.083-2.063, P = 0.014), and working at a university hospital (aOR = 1.867, 95%CI = 1.380-2.525, P < 0.001).\n\nConclusionsA low level of vaccine uptake was observed especially in female HCWs, those younger than 40 years old, and those who used social media as their source of vaccine information. This survey provides important information for public health authorities in order to scale up vaccination campaigns targeting these HCWs to increase vaccine enrollment and uptake.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Mazin Barry", - "author_inst": "King Saud University" - }, - { - "author_name": "Mohamad-Hani Temsah", - "author_inst": "King Saud University" - }, - { - "author_name": "Fadi Aljamaan", - "author_inst": "King Saud University" - }, - { - "author_name": "Basema Saddik", - "author_inst": "University of Sharjah" - }, - { - "author_name": "Ayman Al-Eyadhy", - "author_inst": "King Saud University" - }, - { - "author_name": "Shelaweeh Alanazi", - "author_inst": "King Saud University" - }, - { - "author_name": "Nurah Alamro", - "author_inst": "King Saud University" - }, - { - "author_name": "Abdullah Alhuzaimi", - "author_inst": "King Saud University" - }, - { - "author_name": "Ali Alhaboob", - "author_inst": "King Saud University" - }, - { - "author_name": "Fahad Alsohime", - "author_inst": "King Saud University" - }, - { - "author_name": "Ali Alaraj", - "author_inst": "Qassim University" - }, - { - "author_name": "Rabih Halwani", - "author_inst": "University of Sharjah" - }, - { - "author_name": "Amr Jamal", - "author_inst": "King Saud University" - }, - { - "author_name": "Omar Temsah", - "author_inst": "AlFaisal University" - }, - { - "author_name": "Fahad Alzamil", - "author_inst": "King Saud University" - }, - { - "author_name": "Ali Alsomialy", - "author_inst": "King Saud University" - }, - { - "author_name": "Jaffar Al-Tawfiq", - "author_inst": "Johns Hopkins Aramco Healthcare" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.01.29.21250794", "rel_title": "COVID-19 Prevention Beliefs and Practices in College Students", @@ -938387,6 +940042,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.29.21250710", + "rel_title": "Under what circumstances could vaccination offset the harm from a more transmissible variant of SARS-COV-2 in NYC? Trade-offs regarding prioritization and speed of vaccination.", + "rel_date": "2021-02-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.29.21250710", + "rel_abs": "IntroductionNew York City (NYC) was a global epicenter of COVID-19. Vaccines against COVID-19 became available in December 2020 with limited supply, resulting in the need for policies regarding prioritization. The next month, SARS-CoV-2 variants were detected that were more transmissible but still vaccine-susceptible, raising scrutiny of these policies. In particular, prioritization of higher-risk people could prevent more deaths per dose of vaccine administered but could also delay herd immunity if the prioritization introduced bottlenecks that lowered vaccination speed (the number of doses that could be delivered per day). We used mathematical modeling to examine the trade-off between prioritization and the vaccination speed.\n\nMethodsA stochastic, discrete-time susceptible-exposed-infected-recovered (SEIR) model with age- and comorbidity-adjusted COVID-19 outcomes (infections, hospitalizations, and deaths by July 1, 2021) was used to examine the trade-off between vaccination speed and whether or not vaccination was prioritized to individuals age 65+ and \"essential workers,\" defined as including first responders and healthcare, transit, education, and public safety workers. The model was calibrated to COVID-19 hospital admissions, hospital census, ICU census, and deaths in NYC. Vaccination speed was assumed to be 10,000 doses per day starting December 15th, 2020 targeting healthcare workers and nursing home populations, and to subsequently expand at alternative starting times and speeds. We compared COVID-outcomes across alternative expansion starting times (January 15th, January 21st, or February 1st) and speeds (20,000, 30,000, 50,000, 100,000, 150,000, or 200,000 doses per day for the first dose), as well as alternative prioritization options (\"yes\" versus \"no\" prioritization of essential workers and people age 65+). Model projections were produced with and without considering the emergence of a SARS-COV-2 variant with 56% greater transmissibility over January and February, 2021.\n\nResultsIn the absence of a COVID-19 vaccine, the emergence of the more transmissible variant would triple the peak in infections, hospitalizations, and deaths and more than double cumulative infections, hospitalizations, and deaths. To offset the harm from the more transmissible variant would require reaching a vaccination speed of at least 100,000 doses per day by January 15th or 150,000 per day by January 21st. Prioritizing people ages 65+ and essential workers increased the number of lives saved per vaccine dose delivered: with the emergence of a more transmissible variant, 8,000 deaths could be averted by delivering 115,000 doses per day without prioritization or 71,000 doses per day with prioritization. If prioritization were to cause a bottleneck in vaccination speed, more lives would be saved with prioritization only if the bottleneck reduced vaccination speed by less than one-third of the maximum vaccine delivery capacity. These trade-offs between vaccination speed and prioritization were robust over a wide range of delivery capacity.\n\nConclusionsThe emergence of a more transmissible variant of SARS-CoV-2 has the potential to triple the 2021 epidemic peak and more than double the 2021 COVID-19 burden in NYC. Vaccination could only offset the harm of the more transmissible variant if high speed were achieved in mid-to late January. Prioritization of COVID-19 vaccines to higher-risk populations saves more lives only if it does not create an excessive vaccine delivery bottleneck.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Hae-Young Kim", + "author_inst": "New York University Grossman School of Medicine" + }, + { + "author_name": "Anna Bershteyn", + "author_inst": "New York University Grossman School of Medicine" + }, + { + "author_name": "Jessica McGillen", + "author_inst": "New York University Grossman School of Medicine" + }, + { + "author_name": "R. Scott Braithwaite", + "author_inst": "New York University Grossman School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.29.21250759", "rel_title": "Genetically predicted serum vitamin D and COVID-19: a Mendelian randomization study", @@ -939215,53 +940901,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.29.21250771", - "rel_title": "Persistent COVID-19 symptoms minimally impact the development of SARS-CoV-2 specific cellular immunity", - "rel_date": "2021-02-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.29.21250771", - "rel_abs": "SARS-CoV-2 represents an unprecedented public health challenge with many unknowns remaining regarding the factors that impact viral pathogenicity and the development of immunity after infection. While the majority of SARS-CoV-2 infected individuals with mild-to-moderate COVID-19 resolve their infection with few complications, a significant number of individuals experienced prolonged symptoms lasting for weeks after initial diagnosis. Persistent viral infections are commonly accompanied by immunologic dysregulation, especially within the cellular immune compartment. However, it is unclear if persistent mild-to-moderate COVID-19 impacts the development of virus-specific cellular immunity. To this end, we analyzed the development of SARS-CoV-2 specific cellular immunity in convalescent COVID-19 patients who experienced eight days or fewer of COVID-19 symptoms, or symptoms persisting for 18 days or more. We observed that the duration of COVID-19 symptoms minimally impacts the magnitude, antigen specificity, and transcriptional profile of SARS-CoV-2 specific cellular immunity within both the CD4+ and CD8+ T cell compartments. Furthermore, we observed that reactivity against the structural N protein from SARS-CoV-2 in convalescent COVID-19 patients correlates with the amount of reactivity against the seasonal human coronaviruses 229E and NL63. These results provide additional insight into the complex processes that regulate the development of cellular immunity against SARS-CoV-2 and related human coronaviruses.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "HengSheng Fang", - "author_inst": "SUNY Upstate Medical University" - }, - { - "author_name": "Adam D Wegman", - "author_inst": "SUNY Upstate Medical University" - }, - { - "author_name": "Kianna Ripich", - "author_inst": "SUNY Upstate Medical University" - }, - { - "author_name": "Heather Friberg", - "author_inst": "Walter Reed Army Institute of Research" - }, - { - "author_name": "Jeffrey Currier", - "author_inst": "Walter Reed Army Institute of Research" - }, - { - "author_name": "Stephen J Thomas", - "author_inst": "Institute for Global Health and Translational Sciences, State University of New York Upstate Medical University, Syracuse, New York, USA." - }, - { - "author_name": "Timothy P Endy", - "author_inst": "SUNY Upstate Medical University" - }, - { - "author_name": "Adam Waickman", - "author_inst": "SUNY Upstate Medical University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.29.21250766", "rel_title": "Using time use diaries to track changing behavior across successive stages of COVID-19 social restrictions", @@ -939849,6 +941488,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2021.01.28.21250606", + "rel_title": "REACT-1 round 8 final report: high average prevalence with regional heterogeneity of trends in SARS-CoV-2 infection in the community in England during January 2021", + "rel_date": "2021-01-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.28.21250606", + "rel_abs": "In early January 2021, England entered its third national lockdown of the COVID-19 pandemic to reduce numbers of deaths and pressure on healthcare services, while rapidly rolling out vaccination to healthcare workers and those most at risk of severe disease and death. REACT-1 is a survey of SARS-CoV-2 prevalence in the community in England, based on repeated cross-sectional samples of the population. Between 6th and 22nd January 2021, out of 167,642 results, 2,282 were positive giving a weighted national prevalence of infection of 1.57% (95% CI, 1.49%, 1.66%). The R number nationally over this period was estimated at 0.98 (0.92, 1.04). Prevalence remained high throughout, but with suggestion of a decline at the end of the study period. The average national trend masked regional heterogeneity, with robustly decreasing prevalence in one region (South West) and increasing prevalence in another (East Midlands). Overall prevalence at regional level was highest in London at 2.83% (2.53%, 3.16%). Although prevalence nationally was highest in the low-risk 18 to 24 year old group at 2.44% (1.96%, 3.03%), it was also high in those over 65 years who are most at risk, at 0.93% (0.82%, 1.05%). Large household size, living in a deprived neighbourhood, and Black and Asian ethnicity were all associated with higher levels of infections compared to smaller households, less deprived neighbourhoods and other ethnicities. Healthcare and care home workers, and other key workers, were more likely to test positive compared to other workers. If sustained lower prevalence is not achieved rapidly in England, pressure on healthcare services and numbers of COVID-19 deaths will remain unacceptably high.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Steven Riley", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" + }, + { + "author_name": "Oliver Eales", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" + }, + { + "author_name": "Caroline E. Walters", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" + }, + { + "author_name": "Haowei Wang", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" + }, + { + "author_name": "Kylie E. C. Ainslie", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" + }, + { + "author_name": "Christina Atchinson", + "author_inst": "School of Public Health, Imperial College London, UK" + }, + { + "author_name": "Claudio Fronterre", + "author_inst": "CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK" + }, + { + "author_name": "Peter J. Diggle", + "author_inst": "CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK" + }, + { + "author_name": "Deborah Ashby", + "author_inst": "School of Public Health, Imperial College London, UK" + }, + { + "author_name": "Christl A Donnelly", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" + }, + { + "author_name": "Graham Cooke", + "author_inst": "Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic" + }, + { + "author_name": "Wendy Barclay", + "author_inst": "Department of Infectious Disease, Imperial College London, UK" + }, + { + "author_name": "Helen Ward", + "author_inst": "School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear" + }, + { + "author_name": "Ara Darzi", + "author_inst": "Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a" + }, + { + "author_name": "Paul Elliott", + "author_inst": "School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.27.21250570", "rel_title": "Mapping a Pandemic: SARS-CoV-2 Seropositivity in the United States", @@ -941173,69 +942887,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.30.428920", - "rel_title": "Impact of Prior Infection on Protection and Transmission of SARS-CoV-2 in Golden Hamsters", - "rel_date": "2021-01-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.30.428920", - "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused over 100 million confirmed human infections, and 2 million more deaths globally since its emergence in the end of 2019. Several studies have shown that prior infection provided protective immunity against SARS-CoV-2 in non-human primate models. However, the effect of prior infection on blocking SARS-CoV-2 transmission is not clear. Here, we evaluated the impact of prior infection on protection and transmission of the SARS-CoV-2 virus in golden hamsters. Our results showed that prior infection provided protective immunity against SARS-CoV-2 re-challenge, but it was not sterizing immunity. The transmission experiment results showed that SARS-CoV-2 was efficiently transmitted from naive hamsters to prior infected hamsters by direct contact and airborne route, but not by indirect contact. Further, the virus was efficiently transmitted from prior infected hamsters to naive hamsters by direct contact, but not by airborne route and indirect contact. Surprisingly, the virus can be transmitted between prior infected hamsters by direct contact during a short period of early infection. Taken together, our study demonstrated that prior infected hamsters with good immunity can still be naturally re-infected, and the virus can be transmitted between prior infected hamsters and the naive through different transmission routes, implying the potential possibility of human re-infection and the risk of virus transmission between prior infected population and the healthy. Our study will help to calculate the herd immunity threshold more accurately, make more reasonable public health decisions, formulate an optimized population vaccination program, as well as aid the implementation of appropriate public health and social measures to control COVID-19.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Cheng Zhang", - "author_inst": "College of Veterinary Medicine, Hebei Agricultural University" - }, - { - "author_name": "Zhendong Guo", - "author_inst": "Military Veterinary Research Institute" - }, - { - "author_name": "Nan Li", - "author_inst": "Military Veterinary Research Institute" - }, - { - "author_name": "Huan Cui", - "author_inst": "College of Veterinary Medicine, Jilin University" - }, - { - "author_name": "Keyin Meng", - "author_inst": "Military Veterinary Research Institute" - }, - { - "author_name": "Lina Liu", - "author_inst": "Military Veterinary Research Institute" - }, - { - "author_name": "Li Zhao", - "author_inst": "Military Veterinary Research Institute" - }, - { - "author_name": "Shanshan Zhang", - "author_inst": "Military Veterinary Research Institute" - }, - { - "author_name": "Chengfeng Qin", - "author_inst": "Beijing Institute of Microbiology and Epidemiology" - }, - { - "author_name": "Juxiang Liu", - "author_inst": "College of Veterinary Medicine, Hebei Agricultural University" - }, - { - "author_name": "Yuwei Gao", - "author_inst": "Military Veterinary Research Institute" - }, - { - "author_name": "Chunmao Zhang", - "author_inst": "Military Veterinary Research Institute" - } - ], - "version": "1", - "license": "", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.01.22.21249651", "rel_title": "Timing of elective tracheotomy and duration of mechanical ventilation amongst patients admitted to intensive care with severe COVID-19: a multicentre prospective cohort study", @@ -942095,6 +943746,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.01.26.21250558", + "rel_title": "Depression Symptoms during the COVID-19 Pandemic among Well-Educated, Employed Adults with Low Infection Risks", + "rel_date": "2021-01-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.26.21250558", + "rel_abs": "Levels and distributions of depression symptoms 8-10 months after the onset of the COVID-19 pandemic are reported in a population of faculty, staff, and students at Duke University who faced minimal infection and economic disruption due to the pandemic. Almost 5,000 respondents age 18-81 years who completed the 20-item Center for Epidemiological Studies-Depression (CES-D) battery reported high rates of depression symptoms with more than 40% reporting levels that indicate risk of moderate depression and 25% indicating risk of severe depression. There is a very steep age gradient with the highest levels reported by the youngest respondents of whom over 40% are at risk of severe depression. Symptoms are worse among those who report the demands of work often interfere with family responsibilities but these pressures neither explain the high reported rates nor the steep age gradient. Severe depression risks are highest among students. High levels of depression symptoms during the pandemic appear to be persistent and not confined to those at greatest risk of infection or economic insecurity.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Duncan Thomas", + "author_inst": "Duke University" + }, + { + "author_name": "Tyson Brown", + "author_inst": "Duke University" + }, + { + "author_name": "Donald H Taylor Jr.", + "author_inst": "Duke University" + }, + { + "author_name": "Ralph Lawton", + "author_inst": "Duke University" + }, + { + "author_name": "Victoria K Lee", + "author_inst": "Duke University" + }, + { + "author_name": "Menna Mburi", + "author_inst": "Duke University" + }, + { + "author_name": "Michelle Wong", + "author_inst": "Duke University" + }, + { + "author_name": "Rachel Kranton", + "author_inst": "Duke University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.01.27.21249817", "rel_title": "Multinational Prevalence of Neurological Phenotypes in Patients Hospitalized with COVID-19", @@ -942795,113 +944493,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.28.21250680", - "rel_title": "The effect of SARS-CoV-2 variant B.1.1.7 on symptomatology, re-infection and transmissibility", - "rel_date": "2021-01-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.28.21250680", - "rel_abs": "BackgroundSARS-CoV-2 variant B.1.1.7 was first identified in December 2020 in England. It is not known if the new variant presents with variation in symptoms or disease course, if previously infected individuals may become reinfected with the new variant, or how the variants increased transmissibility affects measures to reduce its spread.\n\nMethodsUsing longitudinal symptom reports from 36,920 users of the COVID Symptom Study app testing positive for Covid-19 between 28 September and 27 December 2020, we performed an ecological study to examine the association between the regional proportion of B.1.1.7 and reported symptoms, disease course, rates of reinfection, and transmissibility.\n\nFindingsWe found no evidence for changes in reported symptoms or disease duration associated with B.1.1.7. We found a likely reinfection rate of 0.7% (95% CI 0.6-0.8), but no evidence that this was higher compared to older strains. We found an increase in R(t) by a factor of 1.35 (95% CI 1.02-1.69). Despite this, we found that R(t) fell below 1 during regional and national lockdowns, even in regions with high proportions of B.1.1.7.\n\nInterpretationThe lack of change in symptoms indicates existing testing and surveillance infrastructure do not need to change specifically for the new variant, and the reinfection findings suggest that vaccines are likely to remain effective against the new variant.\n\nFundingZoe Global Limited, Department of Health, Wellcome Trust, EPSRC, NIHR, MRC, Alzheimers Society.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSTo identify existing evidence on SARS-CoV-2 variant B.1.1.7 we searched PubMed and Google Scholar for articles between 1 December 2020 and 1 February 2021 using the keywords Covid-19 AND B.1.1.7, finding 281 results. We did not find any studies that investigated B.1.1.7-associated changes in the symptoms experienced, their severity and duration, but found one study showing B.1.1.7 did not change the ratio of symptomatic to asymptomatic infections. We found six articles describing laboratory-based investigations of the responses of B.1.1.7 to vaccine-induced immunity to B.1.1.7, but no work investigating what this means for natural immunity and the likelihood of reinfection outside of the lab. We found five articles demonstrating the increased transmissibility of B.1.1.7.\n\nAdded value of this studyTo our knowledge, this is the first study to explore changes in symptom type and duration, as well as community reinfection rates, associated with B.1.1.7. The work uses self-reported symptom logs from 36,920 users of the COVID Symptom Study app reporting positive test results between 28 September and 27 December 2020. We find that B.1.1.7 is not associated with changes in the symptoms experienced in Covid-19, nor their duration. Building on existing lab studies, our work suggests that natural immunity developed from previous infection provides similar levels of protection to B.1.1.7. We add to the emerging consensus that B.1.1.7 exhibits increased transmissibility.\n\nImplications of all the available evidenceOur findings suggest that existing criteria for obtaining a Covid-19 test in the community need not change for the rise of B.1.1.7. The fact that immunity developed from infection by wild type variants protects against B.1.1.7 provides an indication that vaccines will remain effective against B.1.1.7. R(t) fell below 1 during the UKs national lockdown, even in regions with high levels of B.1.1.7, but further investigation is required to establish the factors that enabled this, to facilitate countries seeking to control the spread of B.1.1.7.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Mark S Graham", - "author_inst": "King's College London" - }, - { - "author_name": "Carole H Sudre", - "author_inst": "MRC Unit for Lifelong Health and Ageing" - }, - { - "author_name": "Anna May", - "author_inst": "Zoe Global Limited" - }, - { - "author_name": "Michela Antonelli", - "author_inst": "King's College London" - }, - { - "author_name": "Benjamin Murray", - "author_inst": "King's College London" - }, - { - "author_name": "Thomas Varsavsky", - "author_inst": "King's College London" - }, - { - "author_name": "Kerstin Klaser", - "author_inst": "King's College London" - }, - { - "author_name": "Liane Dos Santos Canas", - "author_inst": "King's College London" - }, - { - "author_name": "Erika Molteni", - "author_inst": "King's College London" - }, - { - "author_name": "Marc Modat", - "author_inst": "King's College London" - }, - { - "author_name": "David Alden Drew", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Long Alden Nguyen", - "author_inst": "Massachusetts General Hospital and Harvard Medical School" - }, - { - "author_name": "Lorenzo Polidori", - "author_inst": "Zoe Global Limited" - }, - { - "author_name": "Somesh Selvachandran", - "author_inst": "Zoe Global Limited" - }, - { - "author_name": "Christina Hu", - "author_inst": "Zoe Global Limited" - }, - { - "author_name": "Joan Capdevila Pujol", - "author_inst": "Zoe Global Limited" - }, - { - "author_name": "- The COVID-19 Genomics UK (COG-UK) consortium", - "author_inst": "" - }, - { - "author_name": "Alexander Hammers", - "author_inst": "King's College London" - }, - { - "author_name": "Andrew T Chan", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Jonathan Wolf", - "author_inst": "Zoe Global Limited" - }, - { - "author_name": "Timothy Spector", - "author_inst": "King's College London" - }, - { - "author_name": "Claire Steves", - "author_inst": "King's College London" - }, - { - "author_name": "Sebastien Ourselin", - "author_inst": "King's College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.01.27.21250658", "rel_title": "COVID-19 mortality: positive correlation with cloudiness and sunlight but no correlation with latitude in Europe", @@ -943557,6 +945148,85 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.01.28.428665", + "rel_title": "Heterologous vaccination regimens with self-amplifying RNA and Adenoviral COVID vaccines induce superior immune responses than single dose vaccine regimens in mice", + "rel_date": "2021-01-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.28.428665", + "rel_abs": "Several vaccines have demonstrated efficacy against SARS-CoV-2 mediated disease, yet there is limited data on the immune response induced by heterologous vaccination regimens using alternate vaccine modalities. Here, we present a detailed description of the immune response, in mice, following vaccination with a self-amplifying RNA (saRNA) vaccine and an adenoviral vectored vaccine (ChAdOx1 nCoV-19/AZD1222) against SARS-CoV-2. We demonstrate that antibody responses are higher in two dose heterologous vaccination regimens than single dose regimens. Neutralising titres after heterologous prime-boost were at least comparable or higher than the titres measured after homologous prime boost vaccination with viral vectors. Importantly, the cellular immune response after a heterologous regimen is dominated by cytotoxic T cells and Th1+ CD4 T cells which is superior to the response induced in homologous vaccination regimens in mice. These results underpin the need for clinical trials to investigate the immunogenicity of heterologous regimens with alternate vaccine technologies.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Alexandra J Spencer", + "author_inst": "The Jenner Institute, Nuffield Department of Medicine, University of Oxford, United Kingdom" + }, + { + "author_name": "Paul F McKay", + "author_inst": "Department of Infectious Diseases, Imperial College London, Norfolk Place, London, United Kingdom" + }, + { + "author_name": "Sandra Belij-Rammerstorfer", + "author_inst": "The Jenner Institute, Nuffield Department of Medicine, University of Oxford, United Kingdom" + }, + { + "author_name": "Marta Ulaszewska", + "author_inst": "The Jenner Institute, Nuffield Department of Medicine, University of Oxford, United Kingdom" + }, + { + "author_name": "Cameron D Bissett", + "author_inst": "The Jenner Institute, Nuffield Department of Medicine, University of Oxford, United Kingdom" + }, + { + "author_name": "Kai Hu", + "author_inst": "Department of Infectious Diseases, Imperial College London, Norfolk Place, London, United Kingdom" + }, + { + "author_name": "Karnyart Samnuan", + "author_inst": "Department of Infectious Diseases, Imperial College London, Norfolk Place, London, United Kingdom" + }, + { + "author_name": "Anna K Blakney", + "author_inst": "Imperial College London" + }, + { + "author_name": "Hannah R Sharpe", + "author_inst": "The Jenner Institute, Nuffield Department of Medicine, University of Oxford, United Kingdom" + }, + { + "author_name": "Daniel Wright", + "author_inst": "The Jenner Institute, Nuffield Department of Medicine, University of Oxford, United Kingdom" + }, + { + "author_name": "Ciaran Gilbride", + "author_inst": "The Jenner Institute, Nuffield Department of Medicine, University of Oxford, United Kingdom" + }, + { + "author_name": "Adam Truby", + "author_inst": "The Jenner Institute, Nuffield Department of Medicine, University of Oxford, United Kingdom" + }, + { + "author_name": "Elizabeth R Allen", + "author_inst": "The Jenner Institute, Nuffield Department of Medicine, University of Oxford, United Kingdom" + }, + { + "author_name": "Sarah C Gilbert", + "author_inst": "The Jenner Institute, Nuffield Department of Medicine, University of Oxford, United Kingdom" + }, + { + "author_name": "Robin J Shattock", + "author_inst": "Department of Infectious Diseases, Imperial College London, Norfolk Place, London, United Kingdom" + }, + { + "author_name": "Teresa Lambe", + "author_inst": "The Jenner Institute, Nuffield Department of Medicine, University of Oxford, United Kingdom" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.01.28.428743", "rel_title": "Development of spike receptor-binding domain nanoparticle as a vaccine candidate against SARS-CoV-2 infection in ferrets", @@ -944561,149 +946231,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.01.27.428529", - "rel_title": "Genetic and structural basis for recognition of SARS-CoV-2 spike protein by a two-antibody cocktail", - "rel_date": "2021-01-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.27.428529", - "rel_abs": "The SARS-CoV-2 pandemic has led to an urgent need to understand the molecular basis for immune recognition of SARS-CoV-2 spike (S) glycoprotein antigenic sites. To define the genetic and structural basis for SARS-CoV-2 neutralization, we determined the structures of two human monoclonal antibodies COV2-2196 and COV2-21301, which form the basis of the investigational antibody cocktail AZD7442, in complex with the receptor binding domain (RBD) of SARS-CoV-2. COV2-2196 forms an \"aromatic cage\" at the heavy/light chain interface using germline-encoded residues in complementarity determining regions (CDRs) 2 and 3 of the heavy chain and CDRs 1 and 3 of the light chain. These structural features explain why highly similar antibodies (public clonotypes) have been isolated from multiple individuals1-4. The structure of COV2-2130 reveals that an unusually long LCDR1 and HCDR3 make interactions with the opposite face of the RBD from that of COV2-2196. Using deep mutational scanning and neutralization escape selection experiments, we comprehensively mapped the critical residues of both antibodies and identified positions of concern for possible viral escape. Nonetheless, both COV2-2196 and COV2-2130 showed strong neutralizing activity against SARS-CoV-2 strain with recent variations of concern including E484K, N501Y, and D614G substitutions. These studies reveal germline-encoded antibody features enabling recognition of the RBD and demonstrate the activity of a cocktail like AZD7442 in preventing escape from emerging variant viruses.", - "rel_num_authors": 32, - "rel_authors": [ - { - "author_name": "Jinhui Dong", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Seth Zost", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Allison Greaney", - "author_inst": "University of Washington" - }, - { - "author_name": "Tyler N Starr", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Adam S Dingens", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Elaine C Chen", - "author_inst": "Vanderbilt University" - }, - { - "author_name": "Rita Chen", - "author_inst": "Washington University in St. Louis" - }, - { - "author_name": "Brett Case", - "author_inst": "Washington University in St. Louis" - }, - { - "author_name": "Rachel Sutton", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Pavlo Gilchuk", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Jessica Rodriguez", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Erica Armstrong", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Christopher Gainza", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Rachel Nargi", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Elad Binshtein", - "author_inst": "Vanderbilt University" - }, - { - "author_name": "Xuping Xie", - "author_inst": "The University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Xianwen Zhang", - "author_inst": "The University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Pei-Yong Shi", - "author_inst": "The University of Texas Medical Branch at Galveston" - }, - { - "author_name": "James Logue", - "author_inst": "University of Maryland" - }, - { - "author_name": "Stuart Weston", - "author_inst": "University of Maryland" - }, - { - "author_name": "Marisa McGrath", - "author_inst": "University of Maryland" - }, - { - "author_name": "Matthew Frieman", - "author_inst": "University of Maryland" - }, - { - "author_name": "Tyler Brady", - "author_inst": "AstraZeneca" - }, - { - "author_name": "Kevin Tuffy", - "author_inst": "AstraZeneca" - }, - { - "author_name": "Helen Bright", - "author_inst": "AstraZeneca" - }, - { - "author_name": "Yueh-Ming Loo", - "author_inst": "AstraZeneca" - }, - { - "author_name": "Patrick McvTamney", - "author_inst": "AstraZeneca" - }, - { - "author_name": "Mark Esser", - "author_inst": "AstraZeneca" - }, - { - "author_name": "Robert Carnahan", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Michael Diamond", - "author_inst": "Washington University in St. Louis" - }, - { - "author_name": "Jesse Bloom", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "James E Crowe Jr.", - "author_inst": "Vanderbilt University Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.01.27.428353", "rel_title": "Spike mutations decrease SARS-CoV-2 sensitivity to neutralizing antibodies but not ACE2-Ig in vitro", @@ -945507,6 +947034,149 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.27.428380", + "rel_title": "Low-Dose Ad26.COV2.S Protection Against SARS-CoV-2 Challenge in Rhesus Macaques", + "rel_date": "2021-01-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.27.428380", + "rel_abs": "We previously reported that a single immunization with an adenovirus serotype 26 (Ad26) vector-based vaccine expressing an optimized SARS-CoV-2 spike (Ad26.COV2.S) protected rhesus macaques against SARS-CoV-2 challenge. In this study, we evaluated the immunogenicity and protective efficacy of reduced doses of Ad26.COV2.S. 30 rhesus macaques were immunized once with 1x1011, 5x1010, 1.125x1010, or 2x109 vp Ad26.COV2.S or sham and were challenged with SARS-CoV-2 by the intranasal and intratracheal routes. Vaccine doses as low as 2x109 vp provided robust protection in bronchoalveolar lavage, whereas doses of 1.125x1010 vp were required for protection in nasal swabs. Activated memory B cells as well as binding and neutralizing antibody titers following vaccination correlated with protective efficacy. At suboptimal vaccine doses, viral breakthrough was observed but did not show evidence of virologic, immunologic, histopathologic, or clinical enhancement of disease compared with sham controls. These data demonstrate that a single immunization with a relatively low dose of Ad26.COV2.S effectively protected against SARS-CoV-2 challenge in rhesus macaques. Moreover, our findings show that a higher vaccine dose may be required for protection in the upper respiratory tract compared with the lower respiratory tract.", + "rel_num_authors": 32, + "rel_authors": [ + { + "author_name": "Xuan He", + "author_inst": "Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA" + }, + { + "author_name": "Abishek Chandrashekar", + "author_inst": "Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA" + }, + { + "author_name": "Roland C. Zahn", + "author_inst": "Janssen Vaccines and Prevention BV" + }, + { + "author_name": "Frank Wegmann", + "author_inst": "Janssen Vaccines & Prevention B.V., Leiden, Netherlands" + }, + { + "author_name": "Jingyou Yu", + "author_inst": "Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA" + }, + { + "author_name": "Noe B. Mercado", + "author_inst": "Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA" + }, + { + "author_name": "Katherine McMahan", + "author_inst": "Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA" + }, + { + "author_name": "Amanda J. Martinot", + "author_inst": "Tufts University Cummings School of Veterinary Medicine, North Grafton, MA 01536, USA" + }, + { + "author_name": "Cesar Piedra-Mora", + "author_inst": "Tufts University Cummings School of Veterinary Medicine, North Grafton, MA 01536, USA" + }, + { + "author_name": "Sidney Beecy", + "author_inst": "Tufts University Cummings School of Veterinary Medicine, North Grafton, MA 01536, USA" + }, + { + "author_name": "Sarah Ducat", + "author_inst": "Tufts University Cummings School of Veterinary Medicine, North Grafton, MA 01536, USA" + }, + { + "author_name": "Ronnie Chamanza", + "author_inst": "Non-Clinical Safety Toxicology/Pathology, Janssen Research and Development, Beerse, Belgium" + }, + { + "author_name": "Sietske Rosendahl Huber", + "author_inst": "Janssen Vaccines & Prevention BV, Leiden, Netherlands" + }, + { + "author_name": "Leslie van der Fits", + "author_inst": "Janssen Vaccines & Prevention BV, Leiden, Netherlands" + }, + { + "author_name": "Erica N. Borducchi", + "author_inst": "Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA" + }, + { + "author_name": "Michelle Lifton", + "author_inst": "Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA" + }, + { + "author_name": "Jinyan Liu", + "author_inst": "Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA" + }, + { + "author_name": "Felix Nampanya", + "author_inst": "Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA" + }, + { + "author_name": "Shivani Patel", + "author_inst": "Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA" + }, + { + "author_name": "Lauren Peter", + "author_inst": "Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA" + }, + { + "author_name": "Lisa H. Tostanoski", + "author_inst": "Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA" + }, + { + "author_name": "Laurent Pessaint", + "author_inst": "Bioqual, Rockville, MD 20852, USA" + }, + { + "author_name": "Alex Van Ry", + "author_inst": "Bioqual, Rockville, MD 20852, USA" + }, + { + "author_name": "Brad Finneyfrock", + "author_inst": "Bioqual, Rockville, MD 20852, USA" + }, + { + "author_name": "Jason Velasco", + "author_inst": "Bioqual, Rockville, MD 20852, USA" + }, + { + "author_name": "Elyse Teow", + "author_inst": "Bioqual, Rockville, MD 20852, USA" + }, + { + "author_name": "Renita Brown", + "author_inst": "Bioqual, Rockville, MD 20852, USA" + }, + { + "author_name": "Anthony Cook", + "author_inst": "Bioqual, Rockville, MD 20852, USA" + }, + { + "author_name": "Hanne Andersen", + "author_inst": "Bioqual, Rockville, MD 20852, USA" + }, + { + "author_name": "Mark G. Lewis", + "author_inst": "Bioqual, Rockville, MD 20852, USA" + }, + { + "author_name": "Hanneke Schuitemaker", + "author_inst": "Janssen Vaccines & Prevention BV, Leiden, Netherlands" + }, + { + "author_name": "Dan H. Barouch", + "author_inst": "Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Ragon Institute of MGH, MIT, and " + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.01.27.428428", "rel_title": "Efficacy of GC-376 against SARS-CoV-2 virus infection in the K18 hACE2 transgenic mouse model", @@ -946375,41 +948045,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.22.21250282", - "rel_title": "Model-driven mitigation measures for reopening schools during the COVID-19 pandemic", - "rel_date": "2021-01-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.22.21250282", - "rel_abs": "Reopening schools is an urgent priority as the COVID-19 pandemic drags on. To explore the risks associated with returning to in-person learning and the value of mitigation measures, we developed stochastic, network-based models of SARS-CoV-2 transmission in primary and secondary schools. We find that a number of mitigation measures, alone or in concert, may reduce risk to acceptable levels. Student cohorting, in which students are divided into two separate populations that attend in-person classes on alternating schedules, can reduce both the likelihood and the size of outbreaks. Proactive testing of teachers and staff can help catch introductions early, before they spread widely through the school. In secondary schools, where the students are more susceptible to infection and have different patterns of social interaction, control is more difficult. Especially in these settings, planners should also consider testing students once or twice weekly. Vaccinating teachers and staff protects these individuals and may have a protective effect on students as well. Other mitigations, including mask-wearing, social distancing, and increased ventilation, remain a crucial component of any reopening plan.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Ryan Seamus McGee", - "author_inst": "University of Washington" - }, - { - "author_name": "Julian R. Homburger", - "author_inst": "Color Health" - }, - { - "author_name": "Hannah E. Williams", - "author_inst": "Color Health" - }, - { - "author_name": "Carl T. Bergstrom", - "author_inst": "University of Washington" - }, - { - "author_name": "Alicia Y. Zhou", - "author_inst": "Color Health" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.01.21.21249999", "rel_title": "A 3D CNN Classification Model for Accurate Diagnosis of Coronavirus Disease 2019 using Computed Tomography Images", @@ -947065,6 +948700,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "dentistry and oral medicine" }, + { + "rel_doi": "10.1101/2021.01.23.21250374", + "rel_title": "Analysis of the number of deaths in Brazil between 2003 and 2020 and possible inferences about the COVID-19 pandemic and history of other diseases", + "rel_date": "2021-01-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.23.21250374", + "rel_abs": "This work explores data on the number of deaths in Brazil since the beginning of the historical series of IBGE, 2003, together with data for the period 2015-2020 of the Transparency Portal. The graphs for total deaths, deaths from violence and deaths in hospitals are discussed. The relationship between them leads to conclusions about the real dimension of the effect of COVID-19 in Brazilian society during the year 2020 and its relative importance to other diseases that had a lesser impact. Hypotheses are also made about the number of deaths in future years.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Lilian P Sosman", + "author_inst": "UERJ" + }, + { + "author_name": "Andres Reinaldo Rodriguez Papa", + "author_inst": "Observatorio Nacional" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.22.21250308", "rel_title": "Projected spread of COVID-19's second wave in South Africa under different levels of lockdown", @@ -948041,45 +949699,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, - { - "rel_doi": "10.1101/2021.01.24.21250396", - "rel_title": "Estimates of global SARS-CoV-2 infection exposure, infection morbidity, and infection mortality rates", - "rel_date": "2021-01-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.24.21250396", - "rel_abs": "We aimed to estimate, albeit crudely and provisionally, national, regional, and global proportions of respective populations that have been infected with SARS-CoV-2, and to assess infection morbidity and mortality rates, factoring both documented and undocumented infections. The estimates were generated by applying mathematical models to 159 countries and territories. The percentage of the worlds population that has been infected as of 31 December 2020 was estimated at 12.56% (95% CI: 11.17-14.05%). It was lowest in the Western Pacific Region at 0.66% (95% CI: 0.59-0.75%) and highest in the Americas at 41.92% (95% CI: 37.95-46.09%). The global infection fatality rate was 10.73 (95% CI: 10.21-11.29) per 10,000 infections. Globally per 1,000 infections, the infection acute-care bed hospitalization rate was 19.22 (95% CI: 18.73-19.51), the infection ICU bed hospitalization rate was 4.14 (95% CI: 4.10-4.18), the infection severity rate was 6.27 (95% CI: 6.18-6.37), and the infection criticality rate was 2.26 (95% CI: 2.24-2.28). If left unchecked with no interventions, the pandemic would eventually cause 8.18 million (95% CI: 7.30-9.18) deaths, 163.67 million (95% CI: 148.12-179.51) acute-care hospitalizations, 33.01 million (95% CI: 30.52-35.70) ICU hospitalizations, 50.23 million (95% CI: 46.24-54.67) severe cases, and 17.62 million (95% CI: 16.36-18.97) critical cases. The global population remains far below the herd immunity threshold and at risk of repeated waves of infection. Global epidemiology reveals immense regional variation in infection exposure and morbidity and mortality rates.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Houssein H. Ayoub", - "author_inst": "Qatar University, Doha, Qatar" - }, - { - "author_name": "Ghina R. Mumtaz", - "author_inst": "American University of Beirut, Beirut, Lebanon" - }, - { - "author_name": "Shaheen Seedat", - "author_inst": "Weill Cornell Medicine-Qatar, Doha, Qatar" - }, - { - "author_name": "Monia Makhoul", - "author_inst": "Weill Cornell Medicine-Qatar, Doha, Qatar" - }, - { - "author_name": "Hiam Chemaitelly", - "author_inst": "Weill Cornell Medicine-Qatar, Doha, Qatar" - }, - { - "author_name": "Laith J Abu-Raddad", - "author_inst": "Weill Cornell Medicine-Qatar, Doha, Qatar" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.01.25.21250356", "rel_title": "Trends, regional variation, and clinical characteristics of COVID-19 vaccine recipients: a retrospective cohort study in 23.4 million patients using OpenSAFELY.", @@ -949115,6 +950734,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.26.21250512", + "rel_title": "High infection attack rates of SARS-CoV-2 in Dutch households revealed by dense sampling", + "rel_date": "2021-01-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.26.21250512", + "rel_abs": "BackgroundIndoor environments are considered a main setting for transmission of SARS-CoV-2. Households in particular present a close-contact environment with high probability of transmission between persons of different ages and with different roles in society.\n\nMethodsComplete households with a laboratory-confirmed SARS-CoV-2 positive case in the Netherlands (March-May 2020) were included. At least three home visits were performed during 4-6 week of follow-up, collecting naso- and oropharyngeal swabs, oral fluid, faeces and blood samples for molecular and serological analyses of all household members. Symptoms were recorded from two weeks before the first visit up to the last visit. Secondary attack rates (SAR) were estimated with logistic regression. A transmission model was used to assess transmission routes in the household.\n\nResultsA total of 55 households with 187 household contacts were included. In 17 households no transmission took place, and in 11 households all persons were infected. Estimated SARs were high, ranging from 35% (95%CI: 24%-46%) in children to 51% (95%CI: 39%-63%) in adults. Estimated transmission rates in the household were high, with reduced susceptibility of children compared to adolescents and adults (0.67; 95%CI: 0.40-1.1).\n\nConclusionEstimated SARs were higher than reported in earlier household studies, presumably owing to a dense sampling protocol. Children were shown to be less susceptible than adults, but the estimated SAR in children was still high. Our results reinforce the role of households as main multiplier of SARS-CoV-2 infection in the population.\n\nKey pointsWe analyze data from a SARS-CoV-2 household study and find higher secondary attack rates than reported earlier. We argue that this is due to a dense sampling strategy that includes sampling at multiple time points and of multiple anatomical sites.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Daphne F.M. Reukers", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Michiel van Boven", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Adam Meijer", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Nynke Rots", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Chantal Reusken", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Inge Roof", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Arianne B. van Gageldonk-Lafeber", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Wim van der Hoek", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Susan van den Hof", + "author_inst": "National Institute for Public Health and the Environment" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.24.21250074", "rel_title": "Adaptive immunity to human coronaviruses is widespread but low in magnitude", @@ -949959,53 +951629,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.26.21250475", - "rel_title": "Colder and drier winter conditions are associated with greater SARS-CoV-2 transmission: a regional study of the first epidemic wave in north-west hemisphere countries.", - "rel_date": "2021-01-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.26.21250475", - "rel_abs": "Higher transmissibility of SARS-CoV-2 in cold and dry weather conditions has been hypothesized since the onset of the COVID-19 pandemic but the level of epidemiological evidence remains low.\n\nDuring the first wave of the pandemic, Spain, Italy, France, Portugal, Canada and USA presented an early spread, a heavy COVID-19 burden, and low initial public health response until lockdowns. In a context when testing was limited, we calculated the basic reproduction number (R0) in 63 regions from the growth in regional death counts. After adjusting for population density, early spread of the epidemic, and age structure, temperature and humidity were negatively associated to SARS-CoV-2 transmissibility. A reduction of mean absolute humidity by 1g/m3 was associated with a 0.15-unit increase of R0. Below 10{degrees}C, a temperature reduction of 1{degrees}C was associated with a 0.16-unit increase of R0.\n\nOur results confirm a dependency of SARS-CoV-2 transmissibility to weather conditions in the absence of control measures during the first wave. The transition from summer-to winter-like conditions likely contributed to the intensification of the second wave in north-west hemisphere countries. Adjustments of the levels of social mobility restrictions need to account for increased SARS-CoV-2 transmissibility in winter conditions.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Jordi Landier", - "author_inst": "French National Research Institute for Sustainable Development, UMR SESSTIM" - }, - { - "author_name": "Juliette Paireau", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Stanislas Rebaudet", - "author_inst": "Aix Marseille Univ, UMR SESSTIM & Hopital Europeen Marseille" - }, - { - "author_name": "Eva Legendre", - "author_inst": "Aix Marseille Univ, UMR SESSTIM" - }, - { - "author_name": "Laurent Le Hot", - "author_inst": "Aix Marseille Univ, UMR SESSTIM" - }, - { - "author_name": "Arnaud Fontanet", - "author_inst": "Institut Pasteur, Emerging Diseases Epidemiology Unit" - }, - { - "author_name": "SIMON CAUCHEMEZ", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Jean Gaudart", - "author_inst": "Aix Marseille Univ" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.01.26.428240", "rel_title": "Immunogenic Potential of DNA Vaccine candidate, ZyCoV-D against SARS-CoV-2 in Animal Models", @@ -950809,6 +952432,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.20.21250152", + "rel_title": "High density lipoprotein cholesterol and risk of subsequent COVID-19 hospitalisation: the UK Biobank study", + "rel_date": "2021-01-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.20.21250152", + "rel_abs": "ObjectiveThere is growing evidence of, and biological plausibility for, elevated levels of high-density lipoprotein cholesterol (HDL-C), being related to lower rates of severe infection. Accordingly, we tested whether pre-pandemic HDL-C within the normal range is associated with subsequent COVID-19 hospitalisations and death.\n\nApproachWe analysed data on 317,306 participants from UK Biobank, a prospective cohort study, baseline data for which were collected between 2006 and 2010. Follow-up for COVID-19 was via hospitalisation records and a national mortality registry.\n\nResultsAfter controlling for a series of confounding factors which included health behaviours, inflammatory markers, and socio-economic status, higher levels of HDL-C were related to a lower risk of later hospitalisation for COVID-19. The effect was linear (p-value for trend 0.001) such that a 0.2 mmol/L increase in HDL-C was associated with a corresponding 9% reduction in risk (odds ratio; 95% confidence interval: 0.91; 0.86, 0.96). A very similar pattern of association was apparent when COVID-19 mortality was the outcome of interest (odds ratio per 0.2 mmol/l increase in HDL-C: 0.90; 0.81, 1.00); again, a stepwise effect was evident (p-value for trend 0.03).\n\nConclusionsThese novel results for HDL-C and COVID-19 events warrant testing in other studies.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Camille Lassale", + "author_inst": "Hospital del Mar Research Institute IMIM" + }, + { + "author_name": "Mark Hamer", + "author_inst": "UCL" + }, + { + "author_name": "Alvaro Hernaez", + "author_inst": "August Pi i Sunyer Biomedical Research Institute (IDIBAPS)" + }, + { + "author_name": "Catharine R Gale", + "author_inst": "MRC Lifecourse Epidemiology Unit, University of Southampton, UK" + }, + { + "author_name": "George David Batty", + "author_inst": "University College London" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.19.21250097", "rel_title": "Contact patterns before and during the UK's Autumn 2020 COVID-19 lockdown among university students and staff", @@ -951833,97 +953491,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2021.01.20.21250109", - "rel_title": "Numbers of close contacts of individuals infected with SARS-CoV-2 and their association with government intervention strategies.", - "rel_date": "2021-01-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.20.21250109", - "rel_abs": "BackgroundContact tracing is conducted with the primary purpose of interrupting transmission from individuals who are likely to be infectious to others. Secondary analyses of data on the numbers of close contacts of confirmed cases could also: provide an early signal of increases in contact patterns that might precede larger than expected case numbers; evaluate the impact of government interventions on the number of contacts of confirmed cases; or provide data information on contact rates between age cohorts for the purpose of epidemiological modelling.\n\nMethodsWe analysed data from 140,204 contacts of 39861 cases in Ireland from 1st May to 1st December 2020. Only close contacts were included in the analysis. A close contact was defined as any individual who had had > 15 minutes face-to-face (<2 m) contact with a case; any household contact; or any individual sharing a closed space for longer than 2 hours, in any setting.\n\nResultsThe number of contacts per case was overdispersed, the mean varied considerably over time, and was temporally associated with government interventions. Negative binomial regression models highlighted greater numbers of contacts within specific population demographics, after correcting for temporal associations. Separate segmented regression models of the number of cases over time and the average number of contacts per case indicated that a breakpoint indicating a rapid decrease in the number of contacts per case in October 2020 preceded a breakpoint indicating a reduction in the number of cases by 11 days.\n\nDiscussionThese data were collected for a specific purpose and therefore any inferences must be made with caution. The data are representative of contact rates of cases, and not of the overall population. However, the data may be a more accurate indicator of the likely degree of onward transmission than might be the case if a random sample of the population were taken. Furthermore, since we analysed only the number of close contacts, the total number of contacts per case would have been higher. Nevertheless, this analysis provides useful information for monitoring the impact of government interventions on the number of contacts; for helping pre-empt increases or decreases in case numbers, and for triangulating assumptions regarding the contact mixing rates between different age cohorts for epidemiological modelling.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Conor G McAloon", - "author_inst": "School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland" - }, - { - "author_name": "Patrick Wall", - "author_inst": "School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin 4, Ireland" - }, - { - "author_name": "Francis Butler", - "author_inst": "School of Biosystems and Food Engineering, University College Dublin, Belfield, Dublin 4, Ireland" - }, - { - "author_name": "Mary Codd", - "author_inst": "School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin 4, Ireland" - }, - { - "author_name": "Eamonn Gormley", - "author_inst": "School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland" - }, - { - "author_name": "Cathal Walsh", - "author_inst": "Department of Mathematics and Statistics, University of Limerick, Ireland" - }, - { - "author_name": "Jim Duggan", - "author_inst": "School of Computer Science, National University of Ireland Galway, Galway, Ireland" - }, - { - "author_name": "T Brendan Murphy", - "author_inst": "School of Mathematics and Statistics, University College Dublin, Belfield, Dublin 4, Ireland" - }, - { - "author_name": "Philip Nolan", - "author_inst": "National University of Ireland Maynooth, Kildare, Ireland" - }, - { - "author_name": "Breda Smyth", - "author_inst": "Department of Public Health, Health Service Executive West, Galway" - }, - { - "author_name": "Katie O'Brien", - "author_inst": "Department of Health, Dublin 2, Ireland" - }, - { - "author_name": "Conor Teljeur", - "author_inst": "Health Information and Quality Authority, Georges Court, Dublin 7, Ireland" - }, - { - "author_name": "Martin J Green", - "author_inst": "School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK" - }, - { - "author_name": "Kieran Culhane", - "author_inst": "Central Statistics Office, Ardee road, Rathmines, Dublin, Ireland" - }, - { - "author_name": "Claire Buckley", - "author_inst": "COVID-19 Contact Management Programme, Health Service Executive, Ireland" - }, - { - "author_name": "Jennifer Martin", - "author_inst": "COVID-19 Contact Management Programme, Health Service Executive, Ireland" - }, - { - "author_name": "Sarah Doyle", - "author_inst": "COVID-19 Contact Management Programme, Health Service Executive, Ireland" - }, - { - "author_name": "Ciara Carroll", - "author_inst": "COVID-19 Contact Management Programme, Health Service Executive, Ireland" - }, - { - "author_name": "Simon J More", - "author_inst": "Centre for Veterinary Epidemiology and Risk Analysis, School of Veterinary Medicine, University College Dublin, Belfield, Dublin, Ireland" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.01.24.21250406", "rel_title": "On mobility trends analysis of COVID-19 dissemination in Mexico City", @@ -952895,6 +954462,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.22.21249953", + "rel_title": "Prediction of In-hospital Mortality among Adults with COVID-19 Infection", + "rel_date": "2021-01-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.22.21249953", + "rel_abs": "Prediction of mortality from COVID-19 infection might help triage patients to hospitalization and intensive care. To estimate the risk of inpatient mortality, we analyzed the data of 13,190 adult patients in the New York City Health + Hospitals system admitted for COVID-19 infection from March 1 to June 30, 2020. They had a mean age 58 years, 40% were Latinx, 29% Black, 9% White and 22% of other races/ethnicities and 2,875 died. We used Machine learning (Gradient Boosted Decision Trees; XGBoost) to select predictors of inpatient mortality from demographics, vital signs and lab tests results from initial encounters. XGBoost identified O2 saturation, systolic and diastolic blood pressure, pulse rate, respiratory rate, age, and BUN with an Area Under the Receiver Operating Characteristics Curve = 94%. We applied CART to find cut-points in these variables, logistic regression to calculate odds-ratios for those categories, and assigned points to the categories to develop a score. A score = 0 indicates a 0.8% (95% confidence interval, 0.5 - 1.0%) risk of dying and [≥] 12 points indicates a 98% (97-99%) risk, and other scores have intermediate risks. We translated the models into an online calculator for the probability of mortality with 95% confidence intervals (as pictured):\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=138 HEIGHT=200 SRC=\"FIGDIR/small/21249953v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (31K):\norg.highwire.dtl.DTLVardef@109228forg.highwire.dtl.DTLVardef@bbe826org.highwire.dtl.DTLVardef@8652a9org.highwire.dtl.DTLVardef@9d04b3_HPS_FORMAT_FIGEXP M_FIG C_FIG danielevanslab.shinyapps.io/COVID_mortality/", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Daniel S Evans", + "author_inst": "San Francisco Coordinating Center, California Pacific Medical Center Research Institute, Sutter Health" + }, + { + "author_name": "Kyoung Min Kim", + "author_inst": "Yongin Severence Hospital, Yonsei University College of Medicine" + }, + { + "author_name": "Xiaqing Jiang", + "author_inst": "San Francisco Coordinating Center, California Pacific Medical Center, Sutter Health" + }, + { + "author_name": "Jessica Jacobson", + "author_inst": "New York City Health + Hospitals/Bellevue-NYU Grossman School of Medicine" + }, + { + "author_name": "Warren Browner", + "author_inst": "California Pacific Medical Center" + }, + { + "author_name": "Steven R Cummings", + "author_inst": "San Francisco Coordinating Center, California Pacific Medical Center Research Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.23.21249978", "rel_title": "Do Not Attempt Resuscitation (DNAR) status in people with suspected COVID-19: Secondary analysis of the PRIEST observational cohort study", @@ -953751,77 +955357,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.01.22.427863", - "rel_title": "CD8+ T cell epitope variations suggest a potential antigen presentation deficiency for spike protein of SARS-CoV-2", - "rel_date": "2021-01-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.22.427863", - "rel_abs": "COVID-19 is caused by a newly identified coronavirus, SARS-CoV-2, and has become a pandemic around the world. The illustration of the immune responses against SARS-CoV-2 is urgently needed for understanding the pathogenesis of the disease and its vaccine development. CD8+ T cells are critical for virus clearance and induce long lasting protection in the host. Here we identified specific HLA-A2 restricted T cell epitopes in the spike protein of SARS-CoV-2. Seven epitope peptides (n-Sp1, 2, 6, 7, 11, 13, 14) were confirmed to bind with HLA-A2 and potentially be presented by antigen presenting cells to induce host immune responses. Tetramers containing these peptides could interact with specific CD8+ T cells from convalescent COVID-19 patients, and one dominant epitope (n-Sp1) was defined. In addition, these epitopes could activate and generate epitope-specific T cells in vitro, and those activated T cells showed cytotoxicity to target cells. Meanwhile, all these epitopes exhibited high frequency of variations. Among them, n-Sp1 epitope variation 5L>F significantly decreased the proportion of specific T cell activation; n-Sp1 epitope 8L>V variant showed significantly reduced binding to HLA-A2 and decreased the proportion of n-Sp1-specific CD8+ T cell, which potentially contributes to the immune escape of SAR-CoV-2.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Congling Qiu", - "author_inst": "Affiliated Huaqiao Hospital; Department of Microbiology and Immunology; Institute of Geriatric Immunology; School of Medicine, Jinan University, Guangzhou, Chin" - }, - { - "author_name": "Chanchan Xiao", - "author_inst": "Department of Microbiology and Immunology; Institute of Geriatric Immunology; Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Lab; School of Medicine" - }, - { - "author_name": "Zhigang Wang", - "author_inst": "Affiliated Huaqiao Hospital, School of Medicine, Jinan University, Guangzhou, China" - }, - { - "author_name": "Xiongfei Chen", - "author_inst": "Guangzhou Center for Disease Control and Prevention, Guangzhou, China" - }, - { - "author_name": "Lijuan Gao", - "author_inst": "Department of Microbiology and Immunology; Institute of Geriatric Immunology; Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Lab; School of Medicine" - }, - { - "author_name": "Jieping Den", - "author_inst": "Department of Microbiology and Immunology; Institute of Geriatric Immunology; Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Lab; School of Medicine" - }, - { - "author_name": "Jun Su", - "author_inst": "Affiliated Huaqiao Hospital, School of Medicine, Jinan University, Guangzhou, China" - }, - { - "author_name": "Huanxin Su", - "author_inst": "Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Lab; State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Scien" - }, - { - "author_name": "Evandro Fei Fang", - "author_inst": "Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Lab; Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, L" - }, - { - "author_name": "ZhangJing Zhang", - "author_inst": "School of Chinese Medicine, LKS Faculty of Medicine, the University of Hong Kong, Hong Kong, China" - }, - { - "author_name": "Jikai Zhang", - "author_inst": "Institute of Biologics and Pharmaceuticals Research, Guangzhou, China" - }, - { - "author_name": "Oscar Junhong Luo", - "author_inst": "Department of Systems Biomedical Sciences, School of Medicine, Jinan University, Guangzhou, China" - }, - { - "author_name": "Pengchen Wang", - "author_inst": "Department of Microbiology and Immunology; Institute of Geriatric Immunology; Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Lab; School of Medicine" - }, - { - "author_name": "Guobing Chen", - "author_inst": "Department of Microbiology and Immunology; Institute of Geriatric Immunology; Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Lab; School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.01.16.21249943", "rel_title": "Artificial Intelligence for Emotion-Semantic Trending and People Emotion Detection During COVID-19 Social Isolation", @@ -954509,6 +956044,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2021.01.20.21249656", + "rel_title": "Clinical prediction rule for SARS-CoV-2 infection from 116 U.S. emergency departments", + "rel_date": "2021-01-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.20.21249656", + "rel_abs": "ObjectivesAccurate and reliable criteria to rapidly estimate the probability of infection with the novel coronavirus-2 that causes the severe acute respiratory syndrome (SARS-CoV-2) and associated disease (COVID-19) remain an urgent unmet need, especially in emergency care. The objective was to derive and validate a clinical prediction rule for SARS-CoV-2 infection that uses simple criteria widely available at the point of care.\n\nMethodsData came from the Registry data from the national REgistry of suspected COVID-19 in EmeRgency care (RECOVER network) comprising 116 hospitals from 25 states in the US. Clinical predictors and 30-day outcomes were abstracted from medical records of 19,850 emergency department (ED) patients tested for SARS-CoV-2. The criterion standard for diagnosis of SARS-CoV-2 required a positive molecular test from a swabbed sample or positive antibody testing within 30 days. The prediction rule was derived from a 50% random sample (n=9,925) using unadjusted analysis of 107 candidate variables as a screening step, followed by stepwise forward logistic regression on 72 variables.\n\nResultsMultivariable regression yielded a 13-variable score, which was simplified to 13-point rule: +1 point each for age>50 years, measured temperature>37.5{degrees}C, oxygen saturation<95%, Black race, Hispanic or Latino ethnicity, household contact with known or suspected COVID-19, patient reported history of dry cough, anosmia/dysgeusia, myalgias or fever; and -1 point each for White race, no direct contact with infected person, or smoking. In the validation sample (n=9,975), the score produced an area under the receiver operating character curve of 0.80 (95% CI: 0.79-0.81), and this level of accuracy was retained across patients enrolled from the early spring to summer of 2020. In the simplified rule, a score of zero produced a sensitivity of 95.6% (94.8-96.3%), specificity of 20.0% (19.0-21.0%), likelihood ratio negative of 0.22 (0.19-0.26). Increasing points on the simplified rule predicted higher probability of infection (e.g., >75% probability with +5 or more points).\n\nConclusionCriteria that are available at the point of care can accurately predict the probability of SARS-CoV-2 infection. These criteria could assist with decision about isolation and testing at high throughput checkpoints.\n\nKey pointsO_ST_ABSQuestionC_ST_ABSCan clinical criteria, derived solely from interview and vital signs accurately estimate the probability of infection from the novel coronavirus (SARS-CoV-2) that causes COVID-19?\n\nFindingsFrom derivation sample (n=9,925), we derived a set of 13 clinical criteria that produced an area under the receiver operating characteristic curve of 0.80 (0.79-0.81) in a validation sample (n=9,925). At a score of zero, the simplified version of the criteria produced sensitivity of 95.6% (94.8 to 96.3%), and specificity of 20.0% (19.0 to 21.0%).\n\nMeaningClinical criteria can estimate the probability of SARS-CoV-2 infection.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Jeffrey Kline", + "author_inst": "IUSOM" + }, + { + "author_name": "- RECOVER Network", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "emergency medicine" + }, { "rel_doi": "10.1101/2021.01.16.21249956", "rel_title": "Clinical effectiveness of convalescent plasma in hospitalized patients with COVID-19: a systematic review and meta-analysis", @@ -955173,41 +956731,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.01.21.20228569", - "rel_title": "Improving Fabric Face Masks: Impact of Design Features on the Protection Offered by Fabric Face Masks", - "rel_date": "2021-01-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.21.20228569", - "rel_abs": "ObjectiveWith much of the public around the world depending on fabric face masks to protect themselves and others, it is essential to understand how the protective ability of fabric masks can be enhanced. This study evaluated the protection offered by eighteen fabric masks designs. In addition, it assessed the benefit of including three design features: insert filters, surgical mask underlayers, and nose wires.\n\nMethodsQuantitative fit tests were conducted on different masks and with some additional design features. An array of fabric masks were tested on a single participant to account for variability in face shapes. The effects of insert filters, surgical mask underlayers and nose wires were also assessed.\n\nResultsAs expected, the fabric masks offered low degrees of protection; however, alterations in design showed significant increase in their protective ability. The most effective designs were multi-layered masks that fit tightly to the face and lacked dead space between the user and mask. Also, low air-resistance insert filters and surgical mask underlays provided the greatest increase in protection.\n\nConclusionsOur findings indicate substantial heterogeneity in the protection offered by various fabric face masks. We also note some design features which may enhance the protection these masks offer.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Eugenia O'Kelly", - "author_inst": "Cambridge University" - }, - { - "author_name": "Anmol Arora", - "author_inst": "Cambridge University" - }, - { - "author_name": "Sophia Pirog", - "author_inst": "Northwestern University" - }, - { - "author_name": "James Ward", - "author_inst": "Cambridge University" - }, - { - "author_name": "P John Clarkson", - "author_inst": "University of Cambridge" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.01.21.20202119", "rel_title": "Effects of Diabetes and Blood Glucose on COVID-19 Mortality: A Retrospective Observational Study", @@ -956151,6 +957674,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.21.427579", + "rel_title": "Evidence of ongoing recombination in SARS-CoV-2 through genealogical reconstruction", + "rel_date": "2021-01-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.21.427579", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWThe evolutionary process of genetic recombination has the potential to rapidly change the properties of a viral pathogen, and its presence is a crucial factor to consider in the development of treatments and vaccines. It can also significantly affect the results of phylogenetic analyses and the inference of evolutionary rates. The detection of recombination from samples of sequencing data is a very challenging problem, and is further complicated for SARS-CoV-2 by its relatively slow accumulation of genetic diversity. The extent to which recombination is ongoing for SARS-CoV-2 is not yet resolved. To address this, we use a parsimony-based method to reconstruct possible genealogical histories for samples of SARS-CoV-2 sequences, which enables us to pinpoint specific recombination events that could have generated the data. We propose a statistical framework for disentangling the effects of recurrent mutation from recombination in the history of a sample, and hence provide a way of estimating the probability that ongoing recombination is present. We apply this to samples of sequencing data collected in England and South Africa, and find evidence of ongoing recombination.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Anastasia Ignatieva", + "author_inst": "University of Warwick" + }, + { + "author_name": "Jotun Hein", + "author_inst": "University of Oxford, The Alan Turing Institute" + }, + { + "author_name": "Paul A Jenkins", + "author_inst": "University of Warwick, The Alan Turing Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2021.01.21.427574", "rel_title": "Evolving Insights from SARS-CoV-2 Genome from 200K COVID-19 Patients", @@ -956851,41 +958401,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.15.21249896", - "rel_title": "Estimating Effect-sizes to Infer if COVID-19 transmission rates were low because of Masks, Heat or High because of Air-conditioners, Tests", - "rel_date": "2021-01-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.15.21249896", - "rel_abs": "How does one interpret the observed increase or decrease in COVID-19 case rates? Did the compliance to the non-pharmaceutical interventions, seasonal changes in the temperature influence the transmission rates or are they purely an artefact of the number of tests? To answer these questions, we estimate the effect-sizes from these different factors on the reproduction ratios (Rt) from the different states of the USA during March 9 to August 9. Ideally Rt should be less than 1 to keep the pandemic under control and our model predicts many of these factors contributed significantly to the Rts: Post-lockdown opening of the restaurants and nightclubs contributed 0.04 (CI 0.04-0.04) and 0.11 (CI. 0.11-0.11) to Rt. The mask mandates helped reduce Rt by 0.28 (CI 0.28-0.29)), whereas the testing rates which may have influenced the number of infections observed, did not influence Rt beyond 10,000 daily tests 0.07 (CI -0.57-0.42). In our attempt to understand the role of temperature, the contribution to the Rt was found to increase on both sides of 55 F, which we infer as a reflection of the climatization needs. A further analysis using the cooling and heating needs showed contributions of 0.24 (CI 0.18-0.31) and 0.31 (CI 0.28-0.33) respectively. The work thus illustrates a data-driven approach for estimating the effect-sizes on the graded policies, and the possibility of prioritizing the interventions, if necessary by weighing the economic costs and ease of acceptance with them.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "C. K. Sruthi", - "author_inst": "Jawaharlal Nehru Centre for Advanced Scientific Research" - }, - { - "author_name": "Malay Ranjan Biswal", - "author_inst": "Jawaharlal Nehru Centre for Advanced Scientific Research" - }, - { - "author_name": "Brijesh Saraswat", - "author_inst": "Jawaharlal Nehru Centre for Advanced Scientific Research" - }, - { - "author_name": "Himanshu Joshi", - "author_inst": "Jawaharlal Nehru Centre for Advanced Scientific Research" - }, - { - "author_name": "Meher K Prakash", - "author_inst": "Jawaharlal Nehru Centre for Advanced Scientific Research" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.01.15.21249889", "rel_title": "Development and validation of multivariable prediction models for adverse COVID-19 outcomes in IBD patients", @@ -957409,6 +958924,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.19.21249678", + "rel_title": "The Role of Disease Severity and Demographics in the Clinical Course of COVID-19 Patients Treated with Convalescent Plasma", + "rel_date": "2021-01-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.19.21249678", + "rel_abs": "Treatment of patients with COVID-19 using convalescent plasma from recently recovered patients has been shown to be safe, but the time course of change in clinical status following plasma transfusion in relation to baseline disease severity has not yet been described. We analyzed short, descriptive daily reports of patient status in 7,180 hospitalized recipients of COVID-19 convalescent plasma in the Mayo Clinic Expanded Access Program. We assessed, from the day following transfusion, whether the patient was categorized by his or her physician as better, worse or unchanged compared to the day before, and whether, on the reporting day, the patient received mechanical ventilation, was in the ICU, had died or had been discharged. Most patients improved following transfusion, but clinical improvement was most notable in mild to moderately ill patients. Patients classified as severely ill upon enrollment improved, but not as rapidly, while patients classified as critically ill/end-stage and patients on ventilators showed worsening of disease status even after treatment with convalescent plasma. Patients age 80 and over showed little or no clinical improvement following transfusion. Clinical status at enrollment and age appear to be the primary factors in determining the therapeutic effectiveness of COVID-19 convalescent plasma among hospitalized patients.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Tengfei Ma", + "author_inst": "Michigan State University" + }, + { + "author_name": "Chad C. Wiggins", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Breanna M. Kornatowski", + "author_inst": "Michigan State University" + }, + { + "author_name": "Ra'ed S. Hailat", + "author_inst": "Michigan State University" + }, + { + "author_name": "Andrew C. Clayburn", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Winston Guo", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Patrick W. Johnson", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Jonathon W. Senefeld", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Stephen A. Klassen", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Sarah E. Baker", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Katelyn A. Bruno", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "DeLisa Fairweather", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "R. Scott Wright", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Rickey E. Carter", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Chenxi Li", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Michael J. Joyner", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Nigel Paneth", + "author_inst": "Michigan State University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.17.21249878", "rel_title": "NEWS2 and laboratory predictors correlated with clinical deterioration in hospitalised patients with COVID-19", @@ -958209,53 +959807,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.01.18.21250049", - "rel_title": "Examining the effect of information channel on COVID-19 vaccine acceptance", - "rel_date": "2021-01-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.18.21250049", - "rel_abs": "Hesitancy towards the COVID-19 vaccine remains high among the US population. Now that the vaccine is available to priority populations, it is critical to convince those that are hesitant to take the vaccine. Public health communication about the vaccine as well as misinformation on the vaccine occurs through a variety of different information channels. Some channels of information are more commonly found to spread misinformation. Given the expansive information environment, we sought to characterize the use of different media channels for COVID-19 vaccine information and determine the relationship between information channel and vaccine acceptance. We conducted a convenience sample of vaccine priority groups (N=2,650) between December 13 and 23, 2020 and conducted bivariate chi-squared tests and multivariable multinomial logistic regression analyses to determine the relative impact of channels of information on vaccine acceptance. We found traditional channels of information, especially National TV, National newspapers, and local newspapers increased the relative risk of vaccine acceptance. Individuals who received information from traditional media compared to social media or both traditional and social media were most likely to accept the vaccine. The implications of this study suggest social media channels have a role to play in educating the hesitant to accept the vaccine, while traditional media channels should continue to promote data-driven and informed vaccine content to their viewers.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Rachael Piltch-Loeb", - "author_inst": "Harvard TH Chan School of Public Health" - }, - { - "author_name": "Elena Savoia", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Beth Goldberg", - "author_inst": "Jigsaw, Google LLC" - }, - { - "author_name": "Brian Hughes", - "author_inst": "American University" - }, - { - "author_name": "Tanner Verhey", - "author_inst": "Trust and Safety, Google LLC" - }, - { - "author_name": "Juliette Kayyem", - "author_inst": "Harvard Kennedy School, Harvard University" - }, - { - "author_name": "Cynthia Miller-Idriss", - "author_inst": "American University" - }, - { - "author_name": "Marcia Testa", - "author_inst": "Harvard TH Chan School of Public Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.01.18.21249821", "rel_title": "Improved screening of COVID-19 cases through a Bayesian network symptoms model and psychophysical olfactory test", @@ -959435,6 +960986,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.01.17.21249913", + "rel_title": "Seroprevalence of anti-SARS-CoV-2 antibodies in Iquitos, Loreto, Peru.", + "rel_date": "2021-01-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.17.21249913", + "rel_abs": "BackgroundDetection of SARS-CoV-2 antibodies among people at risk is critical for understanding both the prior transmission of COVID-19 and vulnerability of the population to the continuing transmission and, when done serially, the intensity of ongoing transmission over an interval in a community. In this study, we estimated the seroprevalence of COVID-19 in a representative population-based cohort of Iquitos, one of the regions with the highest mortality rates from COVID-19 in Peru, where a devastating number of cases occurred in March 2020.\n\nMethodsWe conducted a population-based study of transmission tested each participant using the COVID-19 IgG/IgM Rapid Test from Orient Gene Biotech and used survey analysis methods to estimate seroprevalence accounting for the sampling design effect and test performance characteristics. Here we report results from the baseline (13 to 18 July 2020) and the first month of follow-up (13 to 18 August 2020) study.\n\nFindingsWe enrolled a total of 716 participants and estimated seroprevalence of 70.0% (95% CI: 67.0%-73.4%), a test-re-test positivity of 65% (95% CI: 61.0%-68.3%), and an incidence of new exposures of 1.8% (95% CI: 0.9%-3.2%) data that suggest that transmission is ongoing but is occurring at low levels. We observed significant differences in the seroprevalence between age groups, with participants 18 to 29 years of age having lower seroprevalence than children <12 years of age (Prevalence ratio =0.85 [PR]; 95% CI: 0.73 - 0.98), suggesting that children were not refractory to infection in this setting.\n\nInterpretationIquitos demonstrates one of the highest rates of seroprevalence of COVID-19 worldwide. Current data shows a limited case burden in Iquitos for the past seven months and suggests that these levels are sufficient to provide significant but incomplete herd immunity.\n\nFundingDireccion Regional de Salud de Loreto, DIRESA, Loreto, Peru", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Carlos Alvarez-Antonio", + "author_inst": "Direccion Regional de Salud de Loreto, DIRESA, Loreto, Peru" + }, + { + "author_name": "Graciela Meza-Sanchez", + "author_inst": "Direccion Regional de Salud de Loreto, DIRESA, Loreto, Peru & Universidad Nacional de la Amazonia Peruana, Loreto, Peru" + }, + { + "author_name": "Carlos Calampa", + "author_inst": "Direccion Regional de Salud de Loreto, DIRESA, Loreto, Peru & Universidad Nacional de la Amazonia Peruana, Loreto, Peru" + }, + { + "author_name": "Wilma Casanova", + "author_inst": "Universidad Nacional de la Amazonia Peruana, Loreto, Peru" + }, + { + "author_name": "Cristiam Carey", + "author_inst": "Universidad Nacional de la Amazonia Peruana, Loreto, Peru" + }, + { + "author_name": "Freddy Alava", + "author_inst": "Direccion Regional de Salud de Loreto, DIRESA, Loreto, Peru" + }, + { + "author_name": "Hugo Rodriguez-Ferrucci", + "author_inst": "Universidad Nacional de la Amazonia Peruana, Loreto, Peru" + }, + { + "author_name": "Antonio Marty Quispe", + "author_inst": "Centro de Investigacion en Bioingenieria, Universidad de Ingenieria y Tecnologia, Lima, Peru & Universidad Continental, Huancayo, Peru" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.01.19.21250085", "rel_title": "Incidence and Relative Risk of infection with SARS-CoV-2 virus (Covid-19) in European Soccer Players.", @@ -960147,85 +961745,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.19.21250079", - "rel_title": "Head-to-head comparison of direct-input RT-PCR and RT-LAMP against RTqPCR on extracted RNA for rapid SARS-CoV-2 diagnostics", - "rel_date": "2021-01-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.19.21250079", - "rel_abs": "Viral pandemics, such as Covid-19, pose serious threats to human societies. To control the spread of highly contagious viruses such as SARS-CoV-2, effective test-trace-isolate strategies require population-wide, systematic testing. Currently, RT-qPCR on extracted RNA is the only broadly accepted test for SARS-CoV-2 diagnostics, which bears the risk of supply chain bottlenecks, often exaggerated by dependencies on proprietary reagents. Here, we directly compare the performance of gold standard diagnostic RT-qPCR on extracted RNA to direct input RT-PCR, RT-LAMP and bead-LAMP on 384 primary patient samples collected from individuals with suspected Covid-19 infection. With a simple five minute crude sample inactivation step and one hour of total reaction time, we achieve assay sensitivities of 98% (direct RT-PCR), 93% (bead-LAMP) and 82% (RT-LAMP) for clinically relevant samples (diagnostic RT-qPCR Ct <35) and a specificity of >98%. For direct RT-PCR, our data further demonstrate a perfect agreement between real-time and end-point measurements, which allow a simple binary classification similar to the powerful visual readout of colorimetric LAMP assays. Our study provides highly sensitive and specific, easy to implement, rapid and cost-effective alternatives to diagnostic RT-qPCR tests.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Max J Kellner", - "author_inst": "IMP Vienna, IMBA Vienna" - }, - { - "author_name": "Martin Matl", - "author_inst": "IMP Vienna, IMBA Vienna" - }, - { - "author_name": "Julian J Ross", - "author_inst": "IMBA Vienna" - }, - { - "author_name": "Jakob Schnabl", - "author_inst": "IMBA Vienna" - }, - { - "author_name": "Dominik Handler", - "author_inst": "IMBA Vienna" - }, - { - "author_name": "Robert Heinen", - "author_inst": "IMP Vienna, IMBA Vienna" - }, - { - "author_name": "Justine Schaeffer", - "author_inst": "AGES Vienna" - }, - { - "author_name": "Peter Hufnagl", - "author_inst": "AGES Vienna" - }, - { - "author_name": "Alexander Indra", - "author_inst": "AGES Vienna" - }, - { - "author_name": "Marcus Dekens", - "author_inst": "IMP Vienna" - }, - { - "author_name": "Robert Fritsche-Polanz", - "author_inst": "KFJ Vienna; Klinik Favoriten" - }, - { - "author_name": "Manuela Foedinger", - "author_inst": "KFJ Vienna; Klinik Favoriten" - }, - { - "author_name": "Johannes Zuber", - "author_inst": "IMP Vienna" - }, - { - "author_name": "Franz Allerberger", - "author_inst": "AGES Vienna" - }, - { - "author_name": "Andrea Pauli", - "author_inst": "Research Institute of Molecular Pathology (IMP)" - }, - { - "author_name": "Julius Brennecke", - "author_inst": "IMBA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.19.21249592", "rel_title": "The N501Y mutation in SARS-CoV-2 spike leads to morbidity in obese and aged mice and is neutralized by convalescent and post-vaccination human sera", @@ -960933,6 +962452,77 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.01.19.426885", + "rel_title": "Rapid protection from COVID-19 in nonhuman primates vaccinated intramuscularly but not intranasally with a single dose of a recombinant vaccine", + "rel_date": "2021-01-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.19.426885", + "rel_abs": "The ongoing pandemic of Coronavirus disease 2019 (COVID-19) continues to exert a significant burden on health care systems worldwide. With limited treatments available, vaccination remains an effective strategy to counter transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Recent discussions concerning vaccination strategies have focused on identifying vaccine platforms, number of doses, route of administration, and time to reach peak immunity against SARS-CoV-2. Here, we generated a single dose, fast-acting vesicular stomatitis virus-based vaccine derived from the licensed Ebola virus (EBOV) vaccine rVSV-ZEBOV, expressing the SARS-CoV-2 spike protein and the EBOV glycoprotein (VSV-SARS2-EBOV). Rhesus macaques vaccinated intramuscularly (IM) with a single dose of VSV-SARS2-EBOV were protected within 10 days and did not show signs of COVID-19 pneumonia. In contrast, intranasal (IN) vaccination resulted in limited immunogenicity and enhanced COVID-19 pneumonia compared to control animals. While IM and IN vaccination both induced neutralizing antibody titers, only IM vaccination resulted in a significant cellular immune response. RNA sequencing data bolstered these results by revealing robust activation of the innate and adaptive immune transcriptional signatures in the lungs of IM-vaccinated animals only. Overall, the data demonstrates that VSV-SARS2-EBOV is a potent single-dose COVID-19 vaccine candidate that offers rapid protection based on the protective efficacy observed in our study.\n\nOne sentence summaryVSV vaccine protects NHPs from COVID-19 in 10 days", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Wakako Furuyama", + "author_inst": "NIAID/NIH" + }, + { + "author_name": "Kyle Shifflett", + "author_inst": "NIAID/NIH" + }, + { + "author_name": "Amanda N Pinksi", + "author_inst": "University of California-Irvine" + }, + { + "author_name": "Amanda J Griffin", + "author_inst": "NIAID/NIH" + }, + { + "author_name": "Friederike Feldmann", + "author_inst": "NIAID/NIH" + }, + { + "author_name": "Atsushi Okumura", + "author_inst": "NIAID/NIH" + }, + { + "author_name": "Tylisha Gourdine", + "author_inst": "NIAID/NIH" + }, + { + "author_name": "Allen Jankeel", + "author_inst": "University of California" + }, + { + "author_name": "Jamie Lovaglio", + "author_inst": "NIAID/NIH" + }, + { + "author_name": "Patrick W Hanley", + "author_inst": "NIAID/NIH" + }, + { + "author_name": "Tina Thomas", + "author_inst": "NIAID/NIH" + }, + { + "author_name": "Chad S Clancy", + "author_inst": "NIAID/NIH" + }, + { + "author_name": "Ilhem Messaoudi", + "author_inst": "University of California" + }, + { + "author_name": "Andrea Marzi", + "author_inst": "NIAID/NIH" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.01.15.426463", "rel_title": "Native-like SARS-CoV-2 spike glycoprotein expressed by ChAdOx1 nCoV-19/AZD1222 vaccine", @@ -961937,61 +963527,6 @@ "type": "confirmatory results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.01.15.426691", - "rel_title": "SARS-CoV-2 infection reduces Kru\u0308ppel-Like Factor 2 in human lung autopsy", - "rel_date": "2021-01-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.15.426691", - "rel_abs": "Acute respiratory distress syndrome (ARDS) occurred in ~12% of hospitalized COVID-19 patients in a recent New York City cohort. Pulmonary endothelial dysfunction, characterized by increased expression of inflammatory genes and increased monolayer permeability, is a major component of ARDS. Vascular leak results in parenchymal accumulation of leukocytes, protein, and extravascular water, leading to pulmonary edema, ischemia, and activation of coagulation associated with COVID-19. Endothelial inflammation further contributes to uncontrolled cytokine storm in ARDS. We have recently demonstrated that Kruppel-like factor 2 (KLF2), a transcription factor which promotes endothelial quiescence and monolayer integrity, is significantly reduced in experimental models of ARDS. Lung inflammation and high-tidal volume ventilation result in reduced KLF2, leading to pulmonary endothelial dysfunction and acute lung injury. Mechanistically, we found that KLF2 is a potent transcriptional activator of Rap guanine nucleotide exchange factor 3 (RAPGEF3) which orchestrates and maintains vascular integrity. Moreover, KLF2 regulates multiple genome-wide association study (GWAS)-implicated ARDS genes. Whether lung KLF2 is regulated by SARS-CoV-2 infection is unknown. Here we report that endothelial KLF2 is significantly reduced in human lung autopsies from COVID-19 patients, which supports that ARDS due to SARS-CoV-2 is a vascular phenotype possibly attributed to KLF2 down-regulation. We provide additional data demonstrating that KLF2 is down-regulated in SARS-CoV infection in mice.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Tzu-Han Lee", - "author_inst": "University of Chicago" - }, - { - "author_name": "David Wu", - "author_inst": "University of Chicago" - }, - { - "author_name": "Robert Guzy", - "author_inst": "University of Chicago" - }, - { - "author_name": "Nathan Schoettler", - "author_inst": "University of Chicago" - }, - { - "author_name": "Ayodeji Adegunsoye", - "author_inst": "University of Chicago" - }, - { - "author_name": "Jeffrey Mueller", - "author_inst": "University of Chicago" - }, - { - "author_name": "Aliya Hussein", - "author_inst": "University of Chicago" - }, - { - "author_name": "Anne Sperling", - "author_inst": "University of Chicago" - }, - { - "author_name": "Gokhan M Mutlu", - "author_inst": "University of Chicago" - }, - { - "author_name": "Yun Fang", - "author_inst": "University of Chicago" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "pathology" - }, { "rel_doi": "10.1101/2021.01.17.427024", "rel_title": "Tropism of SARS-CoV-2 for Developing Human Cortical Astrocytes", @@ -963743,6 +965278,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.01.13.21249642", + "rel_title": "Do antibody positive healthcare workers have lower SARS-CoV-2 infection rates than antibody negative healthcare workers? Large multi-centre prospective cohort study (the SIREN study), England: June to November 2020", + "rel_date": "2021-01-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.13.21249642", + "rel_abs": "BackgroundThere is an urgent need to better understand whether individuals who have recovered from COVID-19 are protected from future SARS-CoV-2 infection.\n\nMethodsA large multi-centre prospective cohort was recruited from publicly funded hospital staff in the UK. Participants attended regular SARS-CoV-2 PCR and antibody testing (every 2-4 weeks) and completed fortnightly questionnaires on symptoms and exposures. At enrolment, participants were assigned to either the positive cohort (antibody positive or prior PCR/antibody test positive) or negative cohort (antibody negative, not previously known to be PCR/antibody positive). Potential reinfections were clinically reviewed and classified according to case definitions (confirmed, probable, possible (subdivided by symptom-status)) depending on hierarchy of evidence. Individuals in the primary infection were excluded from this analysis if infection was confirmed by antibody only. Reinfection rates in the positive cohort were compared against new PCR positives in the negative cohort using a mixed effective multivariable logistic regression analysis.\n\nFindingsBetween 18 June and 09 November 2020, 44 reinfections (2 probable, 42 possible) were detected in the baseline positive cohort of 6,614 participants, collectively contributing 1,339,078 days of follow-up. This compares with 318 new PCR positive infections and 94 antibody seroconversions in the negative cohort of 14,173 participants, contributing 1,868,646 days of follow-up. The incidence density per 100,000 person days between June and November 2020 was 3.3 reinfections in the positive cohort, compared with 22.4 new PCR confirmed infections in the negative cohort. The adjusted odds ratio was 0.17 for all reinfections (95% CI 0.13-0.24) compared to PCR confirmed primary infections. The median interval between primary infection and reinfection was over 160 days.\n\nInterpretationA prior history of SARS-CoV-2 infection was associated with an 83% lower risk of infection, with median protective effect observed five months following primary infection. This is the minimum likely effect as seroconversions were not included.\n\nFundingDepartment of Health and Social Care and Public Health England, with contributions from the Scottish, Welsh and Northern Irish governments.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Victoria Jane Hall", + "author_inst": "Public Health England" + }, + { + "author_name": "Sarah Foulkes", + "author_inst": "Public Health England" + }, + { + "author_name": "Andre Charlett", + "author_inst": "Public Health England" + }, + { + "author_name": "Ana Atti", + "author_inst": "Public Health England" + }, + { + "author_name": "Edward JM Monk", + "author_inst": "Public Health England" + }, + { + "author_name": "Ruth Simmons", + "author_inst": "Public Health England" + }, + { + "author_name": "Edgar Wellington", + "author_inst": "Public Health England" + }, + { + "author_name": "Michelle J Cole", + "author_inst": "Public Health England" + }, + { + "author_name": "Ayoub Saei", + "author_inst": "Public Health England" + }, + { + "author_name": "Blanche Oguti", + "author_inst": "Public Health England" + }, + { + "author_name": "Katie Munro", + "author_inst": "Public Health England" + }, + { + "author_name": "Sarah Wallace", + "author_inst": "Public Health England" + }, + { + "author_name": "Peter D Kirwan", + "author_inst": "Public Health England" + }, + { + "author_name": "Madhumita Shrotri", + "author_inst": "Public Health England" + }, + { + "author_name": "Amoolya Vusirikala", + "author_inst": "Public Health England" + }, + { + "author_name": "Sakib Rokadiya", + "author_inst": "Public Health England" + }, + { + "author_name": "Meaghan Kall", + "author_inst": "Public Health England" + }, + { + "author_name": "Maria Zambon", + "author_inst": "Public Health England" + }, + { + "author_name": "Mary Ramsay", + "author_inst": "Public Health England" + }, + { + "author_name": "Tim Brooks", + "author_inst": "Public Health England" + }, + { + "author_name": "- SIREN Sudy Group", + "author_inst": "" + }, + { + "author_name": "Colin S Brown", + "author_inst": "Public Health England" + }, + { + "author_name": "Meera A Chand", + "author_inst": "Public Health England" + }, + { + "author_name": "Susan Hopkins", + "author_inst": "Public Health England" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.14.21249829", "rel_title": "Direct Simulation of the CoVid-19 epidemic", @@ -964550,89 +966196,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.14.21249839", - "rel_title": "Innate lymphoid cells and disease tolerance in SARS-CoV-2 infection", - "rel_date": "2021-01-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.14.21249839", - "rel_abs": "Risk of severe COVID-19 increases with age, is greater in males, and is associated with lymphopenia, but not with higher burden of SARS-CoV-2. It is unknown whether effects of age and sex on abundance of specific lymphoid subsets explain these correlations. This study found that the abundance of innate lymphoid cells (ILCs) decreases more than 7-fold over the human lifespan -- T cell subsets decrease less than 2-fold -- and is lower in males than in females. After accounting for effects of age and sex, ILCs, but not T cells, were lower in adults hospitalized with COVID-19, independent of lymphopenia. Among SARS-CoV-2-infected adults, the abundance of ILCs, but not of T cells, correlated inversely with odds and duration of hospitalization, and with severity of inflammation. ILCs were also uniquely decreased in pediatric COVID-19 and the numbers of these cells did not recover during follow-up. In contrast, children with MIS-C had depletion of both ILCs and T cells, and both cell types increased during follow-up. In both pediatric COVID-19 and MIS-C, ILC abundance correlated inversely with inflammation. Blood ILC mRNA and phenotype tracked closely with ILCs from lung. Importantly, blood ILCs produced amphiregulin, a protein implicated in disease tolerance and tissue homeostasis, and the percentage of amphiregulin-producing ILCs was higher in females than in males. These results suggest that, by promoting disease tolerance, homeostatic ILCs decrease morbidity and mortality associated with SARS-CoV-2 infection, and that lower ILC abundance accounts for increased COVID-19 severity with age and in males.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Noah J. Silverstein", - "author_inst": "University of Massachusetts Medical School" - }, - { - "author_name": "Yetao Wang", - "author_inst": "University of Massachusetts Medical School" - }, - { - "author_name": "Zachary Manickas-Hill", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard" - }, - { - "author_name": "Claudia C. Carbone", - "author_inst": "University of Massachusetts Medical School" - }, - { - "author_name": "Ann Dauphin", - "author_inst": "University of Massachusetts Medical School" - }, - { - "author_name": "Brittany P Boribong", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Maggie Loiselle", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Jameson Davis", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Maureen M Leonard", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Leticia Kuri-Cervantes", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Nuala J Meyer", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Michael R Betts", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Jonathan Z. Li", - "author_inst": "Brigham and Women's Hospital, Harvard Medical School" - }, - { - "author_name": "Bruce D. Walker", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard" - }, - { - "author_name": "Xu G. Yu", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard" - }, - { - "author_name": "Lael M Yonker", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Jeremy Luban", - "author_inst": "University of Massachusetts Medical School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.14.21249372", "rel_title": "Detection of SARS-Cov-2 RNA in serum is associated with increased mortality risk in hospitalized COVID-19 patients.", @@ -965336,6 +966899,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, + { + "rel_doi": "10.1101/2021.01.15.21249731", + "rel_title": "SARS-CoV-2 reinfection in a cohort of 43,000 antibody-positive individuals followed for up to 35 weeks", + "rel_date": "2021-01-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.15.21249731", + "rel_abs": "BackgroundReinfection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been documented, raising public health concerns. Risk and incidence rate of SARS-CoV-2 reinfection were assessed in a large cohort of antibody-positive persons in Qatar.\n\nMethodsAll SARS-CoV-2 antibody-positive persons with a PCR-positive swab [≥]14 days after the first-positive antibody test were individually investigated for evidence of reinfection. Viral genome sequencing was conducted for paired viral specimens to confirm reinfection. Incidence of reinfection was compared to incidence of infection in the complement cohort of those antibody-negative.\n\nResultsAmong 43,044 anti-SARS-CoV-2 positive persons who were followed for a median of 16.3 weeks (range: 0-34.6), 314 individuals (0.7%) had at least one PCR positive swab [≥]14 days after the first-positive antibody test. Of these individuals, 129 (41.1%) had supporting epidemiological evidence for reinfection. Reinfection was next investigated using viral genome sequencing. Applying the viral-genome-sequencing confirmation rate, the risk of reinfection was estimated at 0.10% (95% CI: 0.08-0.11%). The incidence rate of reinfection was estimated at 0.66 per 10,000 person-weeks (95% CI: 0.56-0.78). Incidence rate of reinfection versus month of follow-up did not show any evidence of waning of immunity for over seven months of follow-up. Meanwhile, in the complement cohort of 149,923 antibody-negative persons followed for a median of 17.0 weeks (range: 0-45.6), risk of infection was estimated at 2.15% (95% CI: 2.08-2.22%) and incidence rate of infection was estimated at 13.69 per 10,000 person-weeks (95% CI: 13.22-14.14). Efficacy of natural infection against reinfection was estimated at 95.2% (95% CI: 94.1-96.0%). Reinfections were less severe than primary infections. Only one reinfection was severe, two were moderate, and none were critical or fatal. Most reinfections (66.7%) were diagnosed incidentally through random or routine testing, or through contact tracing.\n\nConclusionsReinfection is rare. Natural infection appears to elicit strong protection against reinfection with an efficacy [~]95% for at least seven months.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Laith J Abu-Raddad", + "author_inst": "Weill Cornell Medicine-Qatar, Doha, Qatar" + }, + { + "author_name": "Hiam Chemaitelly", + "author_inst": "Weill Cornell Medicine-Qatar, Doha, Qatar" + }, + { + "author_name": "Peter Coyle", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Joel A Malek", + "author_inst": "Weill Cornell Medicine-Qatar, Doha, Qatar" + }, + { + "author_name": "Ayeda A. Ahmed", + "author_inst": "Weill Cornell Medicine-Qatar, Doha, Qatar" + }, + { + "author_name": "Yasmin A. Mohamoud", + "author_inst": "Weill Cornell Medicine-Qatar, Doha, Qatar" + }, + { + "author_name": "Shameem Younuskunju", + "author_inst": "Weill Cornell Medicine-Qatar, Doha, Qatar" + }, + { + "author_name": "Houssein H. Ayoub", + "author_inst": "Qatar University, Doha, Qatar" + }, + { + "author_name": "Zaina Al Kanaani", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Einas Al Kuwari", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Adeel A Butt", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Andrew Jeremijenko", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Anvar Hassan Kaleeckal", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Ali Nizar Latif", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Riyazuddin Mohammad Shaik", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Hanan F. Abdul Rahim", + "author_inst": "Qatar University, Doha, Qatar" + }, + { + "author_name": "Gheyath K. Nasrallah", + "author_inst": "Qatar University, Doha, Qatar" + }, + { + "author_name": "Hadi M. Yassine", + "author_inst": "Qatar University, Doha, Qatar" + }, + { + "author_name": "Mohamed G. Al Kuwari", + "author_inst": "Primary Health Care Corporation, Doha, Qatar" + }, + { + "author_name": "Hamad Eid Al Romaihi", + "author_inst": "Ministry of Public Health, Doha, Qatar" + }, + { + "author_name": "Mohamed H. Al-Thani", + "author_inst": "Ministry of Public Health, Doha, Qatar" + }, + { + "author_name": "Abdullatif Al Khal", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Roberto Bertollini", + "author_inst": "Ministry of Public Health, Doha, Qatar" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.12.21249654", "rel_title": "From SARS and MERS to COVID-19: a review of the quality and responsiveness of clinical management guidelines in outbreak settings", @@ -966384,233 +968054,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.12.21249672", - "rel_title": "Characteristics and outcomes of 118,155 COVID-19 individuals with a history of cancer in the United States and Spain", - "rel_date": "2021-01-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.12.21249672", - "rel_abs": "PurposeWe aimed to describe the demographics, cancer subtypes, comorbidities and outcomes of patients with a history of cancer with COVID-19 from March to June 2020. Secondly, we compared patients hospitalized with COVID-19 to patients diagnosed with COVID-19 and patients hospitalized with influenza.\n\nMethodsWe conducted a cohort study using eight routinely-collected healthcare databases from Spain and the US, standardized to the Observational Medical Outcome Partnership common data model. Three cohorts of patients with a history of cancer were included: i) diagnosed with COVID-19, ii) hospitalized with COVID-19, and iii) hospitalized with influenza in 2017-2018. Patients were followed from index date to 30 days or death. We reported demographics, cancer subtypes, comorbidities, and 30-day outcomes.\n\nResultsWe included 118,155 patients with a cancer history in the COVID-19 diagnosed and 41,939 in the COVID-19 hospitalized cohorts. The most frequent cancer subtypes were prostate and breast cancer (range: 5-19% and 1-14% in the diagnosed cohort, respectively). Hematological malignancies were also frequent, with non-Hodgkins lymphoma being among the 5 most common cancer subtypes in the diagnosed cohort. Overall, patients were more frequently aged above 65 years and had multiple comorbidities. Occurrence of death ranged from 8% to 14% and from 18% to 26% in the diagnosed and hospitalized COVID-19 cohorts, respectively. Patients hospitalized with influenza (n=242,960) had a similar distribution of cancer subtypes, sex, age and comorbidities but lower occurrence of adverse events.\n\nConclusionPatients with a history of cancer and COVID-19 have advanced age, multiple comorbidities, and a high occurence of COVID-19-related events. Additionaly, hematological malignancies were frequent in these patients.This observational study provides epidemiologic characteristics that can inform clinical care and future etiological studies.", - "rel_num_authors": 53, - "rel_authors": [ - { - "author_name": "Elena Roel Mrs", - "author_inst": "Fundacio Institut Universitari per a la recerca a l'Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain" - }, - { - "author_name": "Andrea Pistillo Mr", - "author_inst": "Fundacio Institut Universitari per a la recerca a l'Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain" - }, - { - "author_name": "Martina Recalde Mrs", - "author_inst": "Fundacio Institut Universitari per a la recerca a l'Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain" - }, - { - "author_name": "Anthony G Sena Mr", - "author_inst": "Janssen Research and Development, Titusville, NJ USA" - }, - { - "author_name": "Sergio Fernandez-Bertolin Mr", - "author_inst": "Fundacio Institut Universitari per a la recerca a l'Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain" - }, - { - "author_name": "Maria Aragon Mrs", - "author_inst": "Fundacio Institut Universitari per a la recerca a l'Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain" - }, - { - "author_name": "Diana Puente Dr", - "author_inst": "Fundacio Institut Universitari per a la recerca a l'Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain" - }, - { - "author_name": "Waheed-Ul-Rahman Ahmed Mr", - "author_inst": "Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Botnar Research Centre, Windmill Road, Oxford, OX3 7LD, U" - }, - { - "author_name": "Heba Alghoul Mr", - "author_inst": "Faculty of Medicine, Islamic University of Gaza, Palestine" - }, - { - "author_name": "Osaid Alser Mr", - "author_inst": "Massachusetts General Hospital, Harvard Medical School, USA" - }, - { - "author_name": "Thamir M Alshammari Dr", - "author_inst": "Medication Safety Research Chair, King Saud University" - }, - { - "author_name": "Carlos Areia Mr", - "author_inst": "Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK" - }, - { - "author_name": "Clair Blacketer Mrs", - "author_inst": "Janssen Research and Development, Titusville, NJ USA" - }, - { - "author_name": "William Carter Mr", - "author_inst": "Data Science to Patient Value Program, Department of Medicine, University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Paula Casajust Mrs", - "author_inst": "Real-World Evidence, Trial Form Support, Barcelona, Spain" - }, - { - "author_name": "Aedin C Culhane Dr", - "author_inst": "Department of Data Science, Dana-Farber Cancer Institute, Boston MA, USA" - }, - { - "author_name": "Dalia Dawoud Dr", - "author_inst": "Faculty of Pharmacy, Cairo University, Cairo, Egypt" - }, - { - "author_name": "Frank DeFalco Mr", - "author_inst": "Janssen Research & Development, Titusville, NJ, USA" - }, - { - "author_name": "Scott L Duvall Dr", - "author_inst": "VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT, USA" - }, - { - "author_name": "Thomas Falconer Mr", - "author_inst": "Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA New York-Presbyterian Hospital, 622 W 168 St, PH20 New " - }, - { - "author_name": "Asieh Golozar Dr", - "author_inst": "Department of Epidemiology, Johns Hopkins School of Public, Baltimore MD, USA" - }, - { - "author_name": "Mengchun Gong Mr", - "author_inst": "HDC Technologies Co. Ltd. Beijing, China" - }, - { - "author_name": "Laura Hester Dr", - "author_inst": "Associate Director, Epidemiology, Janssen Research and Development, LLC." - }, - { - "author_name": "George Hripcsak Mr", - "author_inst": "Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA" - }, - { - "author_name": "Eng Hooi Tan Dr", - "author_inst": "Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, OX3 7LD, UK" - }, - { - "author_name": "Hokyun Jeon Mr", - "author_inst": "Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Gyeonggi do, Republic of Korea" - }, - { - "author_name": "Jitendra Jonnagaddala Dr", - "author_inst": "School of Public Health and Community Medicine, UNSW Sydney" - }, - { - "author_name": "Lana YH Lai Dr", - "author_inst": "School of Medical Sciences, University of Manchester, UK" - }, - { - "author_name": "Kristine E Lynch Dr", - "author_inst": "VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT, USA" - }, - { - "author_name": "Michael E Matheny Mr", - "author_inst": "Tennessee Valley Healthcare System, Veterans Affairs Medical Center, Nashville, TN, USA" - }, - { - "author_name": "Daniel R Morales Dr", - "author_inst": "Division of Population Health and Genomics, University of Dundee, UK" - }, - { - "author_name": "Karthik Natarajan Dr", - "author_inst": "Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA" - }, - { - "author_name": "Fredrik Nyberg Dr", - "author_inst": "School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden" - }, - { - "author_name": "Anna Ostropolets Mrs", - "author_inst": "Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA" - }, - { - "author_name": "Jose D Posada Dr", - "author_inst": "Department of Medicine, School of Medicine, Stanford University, Redwood City, CA USA" - }, - { - "author_name": "Albert Prats-Uribe Mr", - "author_inst": "Centre for Statistics in Medicine, NDORMS, University of Oxford" - }, - { - "author_name": "Christian G Reich Dr", - "author_inst": "Real World Solutions, IQVIA, Cambridge, MA USA" - }, - { - "author_name": "Donna Rivera Mrs", - "author_inst": "Division of Cancer Control and Population Sciences, National Cancer Institute, Rockville, MD" - }, - { - "author_name": "Lisa M Schilling Mrs", - "author_inst": "Department of Medicine, Data Science to Patient Value Program, University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Isabelle Soerjomataram Dr", - "author_inst": "Section of Cancer Surveillance, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008 Lyon, France" - }, - { - "author_name": "Karishma Shah Mrs", - "author_inst": "Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Botnar Research Centre, Windmill Road, Oxford, OX3 7LD, U" - }, - { - "author_name": "Nigam Shah Dr", - "author_inst": "Department of Medicine, School of Medicine, Stanford University, Redwood City, CA USA" - }, - { - "author_name": "Yang Shen Mr", - "author_inst": "HDC Technologies Co. Ltd. Beijing, China" - }, - { - "author_name": "Matthew Spotnitz Mr", - "author_inst": "Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA" - }, - { - "author_name": "Vignesh Subbian Dr", - "author_inst": "College of Engineering, The University of Arizona, Tucson, Arizona, USA" - }, - { - "author_name": "Marc A Suchard Dr", - "author_inst": "Fielding School of Public Health, University of California, Los Angeles" - }, - { - "author_name": "Annalisa Trama Dr", - "author_inst": "Fondazione IRCSS Istituto Nazionale dei Tumori, Milan - Italy" - }, - { - "author_name": "Lin Zhang Dr", - "author_inst": "School of Population Medicine and Public Health, Peking Union Medical College, Chinese Academy of Medical Sciences." - }, - { - "author_name": "Ying Zhang Dr", - "author_inst": "Janssen Research & Development, Titusville, NJ, USA" - }, - { - "author_name": "Patrick Ryan Dr", - "author_inst": "Janssen Research & Development, Titusville, NJ, USA" - }, - { - "author_name": "Daniel Prieto-Alhambra Dr", - "author_inst": "Centre for Statistics in Medicine, NDORMS, University of Oxford" - }, - { - "author_name": "Kristin Kostka Mrs", - "author_inst": "Real World Solutions, IQVIA, Cambridge, MA USA" - }, - { - "author_name": "Talita Duarte-Salles Dr", - "author_inst": "Fundacio Institut Universitari per a la recerca a l'Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.01.11.20248947", "rel_title": "A mixture of essential oils from three Cretan Aromatic Plants (thyme, Greek sage and Cretan dittany, CAPeo) inhibits SASR-CoV-2 proliferation: in vitro evidence and a Proof-of-Concept intervention study in mild ambulatory COVID-19-positive patients", @@ -967150,6 +968593,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.13.21249563", + "rel_title": "COVID-19: Rapid Antigen detection for SARS-CoV-2 by lateral flow assay: a national systematic evaluation for mass-testing", + "rel_date": "2021-01-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.13.21249563", + "rel_abs": "Lateral flow device (LFD) viral antigen immunoassays have been developed around the world as diagnostic tests for SARS-CoV-2 infection. They have been proposed to deliver an infrastructure-light, cost-economical solution giving results within half an hour. Here we report on standardised laboratory evaluations of LFDs, and for those that met the published criteria, field testing in the Falcon-C19 research study and UK pilots (UK COVID-19 testing centres, hospital, schools, armed forces). 4/64 LFDs so far have desirable performance characteristics (Orient Gene, Deepblue, Abbott and Innova SARS-CoV-2 Antigen Rapid Qualitative Test). All these LFDs have a viral antigen detection of >90% at 100,000 RNA copies/ml. 8951 Innova LFD tests were performed with a kit failure rate of 5.6% (502/8951, 95% CI: 5.1-6.1), false positive rate of 0.32% (22/6954, 95% CI: 0.20-0.48). Viral antigen detection/sensitivity across the sampling cohort when performed by laboratory scientists (156/198, 95% CI 72.4-84.3) was 78.8%. Our results suggest LFDs have promising performance characteristics for mass population testing and can be used to identify infectious positive individuals. The Innova LFD shows good viral antigen detection/sensitivity with excellent specificity, although kit failure rates and the impact of training are potential issues. These results support the expanded evaluation of LFDs, and assessment of greater access to testing on COVID-19 transmission.\n\nFundingDepartment of Health and Social Care. University of Oxford. Public Health England Porton Down, Manchester University NHS Foundation Trust, National Institute of Health Research.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "- UK COVID-19 Lateral Flow Oversight Team", + "author_inst": "" + }, + { + "author_name": "Tim Peto", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.14.21249848", "rel_title": "Understanding COVID-19 dynamics and the effects of interventions in the Philippines: A mathematical modelling study", @@ -968394,29 +969860,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.14.21249809", - "rel_title": "Evaluating the effects of re-opening plans on dynamics of COVID-19 in SP", - "rel_date": "2021-01-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.14.21249809", - "rel_abs": "Coronavirus disease 2019 (COVID-19) was declared a pandemic by the World Health Organization in early March 2020. In Brazil, Sao Paulo is the most affected state, comprising about 20% of the countrys cases. With no vaccine available to date, distancing measures have been taken to reduce virus transmission. To reduce the pandemics effect on the economy, the government of Sao Paulo has proposed a plan consisting of five phases of the gradual re-opening of activities. In this context, we have developed a mathematical model to simulate the gradual re-opening plan on the transmission dynamics of COVID-19, in the city of Sao Paulo. The model shows that a precipitous reopening can cause a higher peak of the disease, which may compromise the local health system. Waiting for the reduction in the incidence of infected individuals for at least 15 days to phase transition is the most efficient strategy compared to the fixed-period scenario at each phase of the re-opening plan.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Felipe Alves Rubio", - "author_inst": "University of Campinas" - }, - { - "author_name": "Thomas Nogueira Vilches", - "author_inst": "University of Campinas" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.01.15.21249871", "rel_title": "Impact of COVID-19 on Care-Home Mortality and Life Expectancy in Scotland", @@ -969256,6 +970699,45 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.01.14.426705", + "rel_title": "Mutation rates and selection on synonymous mutations in SARS-CoV-2", + "rel_date": "2021-01-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.14.426705", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWThe COVID-19 pandemic has seen an unprecedented response from the sequencing community. Leveraging the sequence data from more than 140,000 SARS-CoV-2 genomes, we study mutation rates and selective pressures affecting the virus. Understanding the processes and effects of mutation and selection has profound implications for the study of viral evolution, for vaccine design, and for the tracking of viral spread. We highlight and address some common genome sequence analysis pitfalls that can lead to inaccurate inference of mutation rates and selection, such as ignoring skews in the genetic code, not accounting for recurrent mutations, and assuming evolutionary equilibrium. We find that two particular mutation rates, G[->]U and C[->]U, are similarly elevated and considerably higher than all other mutation rates, causing the majority of mutations in the SARS-CoV-2 genome, and are possibly the result of APOBEC and ROS activity. These mutations also tend to occur many times at the same genome positions along the global SARS-CoV-2 phylogeny (i.e., they are very homoplasic). We observe an effect of genomic context on mutation rates, but the effect of the context is overall limited. While previous studies have suggested selection acting to decrease U content at synonymous sites, we bring forward evidence suggesting the opposite.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Nicola De Maio", + "author_inst": "EMBL-EBI" + }, + { + "author_name": "Conor R Walker", + "author_inst": "EMBL-European Bioinformatics Institute" + }, + { + "author_name": "Yatish Turakhia", + "author_inst": "University of California, Santa Cruz" + }, + { + "author_name": "Robert Lanfear", + "author_inst": "Australian National University" + }, + { + "author_name": "Russell Corbett-Detig", + "author_inst": "UC Santa Cruz" + }, + { + "author_name": "Nick Goldman", + "author_inst": "EMBL-European Bioinformatics Institute" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2021.01.14.426695", "rel_title": "SARS-CoV-2 spike protein arrested in the closed state induces potent neutralizing responses", @@ -970388,33 +971870,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.11.21249509", - "rel_title": "Rates and predictors of uptake of formal and informal mental health support during the COVID-19 pandemic: an analysis of 26,740 adults in the UK in lockdown", - "rel_date": "2021-01-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.11.21249509", - "rel_abs": "PurposeThe coronavirus disease 2019 (COVID-19) pandemic has put a great strain on peoples mental health. A growing number of studies have shown worsening mental health measures globally during the pandemic. However, there is a lack of empirical study on how people support their mental health during the COVID-19 pandemic. This study aimed to examine a number of formal and informal mental health supports. Further, it explored factors that might be associated with the use of different types mental health support.\n\nMethodData from 26,740 adults in the UCL COVID -19 Social Study were analysed between 13th April, 2020 and 3rd July, 2020. Data were analysed using logistic and Poisson regression models.\n\nResultsAbout 45% of people reported talking to friends or family members to support their mental health, 43% engaging in self-care activities, 20% taking medication, 9% speaking to mental health professionals, 8% talking to a GP or other health professional, and another 8% using helpline or online services. Gender, education, living status, loneliness, pre-existing mental health conditions, general depression and anxiety, coping and personality were found to be associated with the use of mental health support.\n\nConclusionWhile the negative impacts caused by the COVID-19 pandemic are inevitable, people can play an active role in managing their mental health. Understanding the patterns and predictors of various kinds of mental health support during the pandemic is crucial for future service planning and delivery through recognising potential barriers to mental health care faced by certain groups.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Feifei Bu", - "author_inst": "Department of Behavioral Science and Health, University College London" - }, - { - "author_name": "Hei Wan Mak", - "author_inst": "Department of Behavioral Science and Health, University College London" - }, - { - "author_name": "Daisy Fancourt", - "author_inst": "Department of Behavioral Science and Health, University College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.01.12.21249152", "rel_title": "Predictors of COVID-19 Vaccine Hesitancy: Socio-demographics, Co-Morbidity and Past Racial Discrimination", @@ -971158,6 +972613,57 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.01.13.423947", + "rel_title": "A rapid phenomics workflow for the in vitro identification of antiviral drugs", + "rel_date": "2021-01-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.13.423947", + "rel_abs": "BackgroundThe current COVID-19 pandemic has highlighted the need for new and fast methods to identify novel or repurposed therapeutic drugs. Here we present a method for untargeted phenotypic drug screening of virus-infected cells, combining Cell Painting with antibody-based detection of viral infection in a single assay. We designed an image analysis pipeline for segmentation and classification of virus-infected and non-infected cells, followed by extraction of morphological properties.\n\nResultsWe show that the methodology can successfully capture virus-induced phenotypic signatures of MRC-5 human lung fibroblasts infected with Human coronavirus 229E (CoV-229E). Moreover, we demonstrate that our method can be used in phenotypic drug screening using a panel of nine host- and virus-targeting antivirals. Treatment with effective antiviral compounds reversed the morphological profile of the host cells towards a non-infected state.\n\nConclusionsThe method can be used in drug discovery for morphological profiling of novel antiviral compounds on both infected and non-infected cells.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Jonne Rietdijk", + "author_inst": "Uppsala University" + }, + { + "author_name": "Marianna Tampere", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Aleksandra Pettke", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Polina Georgiev", + "author_inst": "Uppsala University" + }, + { + "author_name": "Maris Lapins", + "author_inst": "Uppsala University" + }, + { + "author_name": "Ulrika Warpman Berglund", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Ola Spjuth", + "author_inst": "Uppsala University" + }, + { + "author_name": "Marjo-Riitta Puumalainen", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Jordi Carreras-Puigvert", + "author_inst": "Uppsala University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2021.01.12.426373", "rel_title": "Phylogenetic analyses of SARS-CoV-2 B.1.1.7 lineage suggest a single origin followed by multiple exportation events versus convergent evolution", @@ -971910,97 +973416,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.05.21249237", - "rel_title": "Enisamium is an inhibitor of the SARS-CoV-2 RNA polymerase and shows improvement of recovery in COVID-19 patients in an interim analysis of a clinical trial", - "rel_date": "2021-01-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.05.21249237", - "rel_abs": "Pandemic SARS-CoV-2 causes a mild to severe respiratory disease called Coronavirus Disease 2019 (COVID-19). Control of SARS-CoV-2 spread will depend on vaccine-induced or naturally acquired protective herd immunity. Until then, antiviral strategies are needed to manage COVID-19, but approved antiviral treatments, such as remdesivir, can only be delivered intravenously. Enisamium (laboratory code FAV00A, trade name Amizon(R)) is an orally active inhibitor of influenza A and B viruses in cell culture and clinically approved in countries of the Commonwealth of Independent States. Here we show that enisamium can inhibit SARS-CoV-2 infections in NHBE and Caco-2 cells. In vitro, the previously identified enisamium metabolite VR17-04 directly inhibits the activity of the SARS-CoV-2 RNA polymerase. Docking and molecular dynamics simulations suggest that VR17-04 prevents GTP and UTP incorporation. To confirm enisamiums antiviral properties, we conducted a double-blind, randomized, placebo-controlled trial in adult, hospitalized COVID-19 patients, which needed medical care either with or without supplementary oxygen. Patients received either enisamium (500 mg per dose) or placebo for 7 days. A pre-planned interim analysis showed in the subgroup of patients needing supplementary oxygen (n = 77) in the enisamium group a mean recovery time of 11.1 days, compared to 13.9 days for the placebo group (log-rank test; p=0.0259). No significant difference was found for all patients (n = 373) or those only needing medical care (n = 296). These results thus suggest that enisamium is an inhibitor of SARS-CoV-2 RNA synthesis and that enisamium treatment shortens the time to recovery for COVID-19 patients needing oxygen.\n\nSignificance statementSARS-CoV-2 is the causative agent of COVID-19. Although vaccines are now becoming available to prevent SARS-CoV-2 spread, the development of antivirals remains necessary for treating current COVID-19 patients and combating future coronavirus outbreaks. Here, we report that enisamium, which can be administered orally, can prevent SARS-CoV-2 replication and that its metabolite VR17-04 can inhibit the SARS-CoV-2 RNA polymerase in vitro. Moreover, we find that COVID-19 patients requiring supplementary oxygen, recover more quickly than patients treated with a placebo. Enisamium may therefore be an accessible treatment for COVID-19 patients.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Olha Holubovska", - "author_inst": "O.O. Bogomolets National Medical University" - }, - { - "author_name": "Denisa Bojkova", - "author_inst": "University Hospital Frankfurt" - }, - { - "author_name": "Stefano Elli", - "author_inst": "Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni" - }, - { - "author_name": "Marco bechtel", - "author_inst": "University Hospital Frankfurt" - }, - { - "author_name": "David Boltz", - "author_inst": "IIT Research institute" - }, - { - "author_name": "Miguel Muzzio", - "author_inst": "IIT Research institute" - }, - { - "author_name": "Xinjian Peng", - "author_inst": "IIT Research institute" - }, - { - "author_name": "Frederico Sala", - "author_inst": "Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni" - }, - { - "author_name": "Cesare Cosentino", - "author_inst": "3Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni" - }, - { - "author_name": "Alla Mironenko", - "author_inst": "L.V. Gromashevsky Institute of Epidemiology and Infectious Diseases of the NAMS of Ukraine" - }, - { - "author_name": "Jens Milde", - "author_inst": "Pharmalog Institut fuer klinische Forschung GmbH" - }, - { - "author_name": "Yuriy Lebed", - "author_inst": "Pharmaxi LLC" - }, - { - "author_name": "Holger Stammer", - "author_inst": "Pharmalog Institut fuer klinische Forschung GmbH" - }, - { - "author_name": "Andrew Goy", - "author_inst": "Farmak Joint Stock Company" - }, - { - "author_name": "Marco Guerrini", - "author_inst": "Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni" - }, - { - "author_name": "Lutz Mueller", - "author_inst": "Dr. Regenold GmbH" - }, - { - "author_name": "Jindrich Cinatl", - "author_inst": "University Hospital Frankfurt" - }, - { - "author_name": "Victor Margitich", - "author_inst": "Farmak Joint Stock Company" - }, - { - "author_name": "Aartjan te Velthuis", - "author_inst": "University of Cambridge" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.04.21249249", "rel_title": "Role of pollution and weather indicators in the COVID-19 outbreak: A brief study on Delhi, India", @@ -972732,6 +974147,53 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.01.12.425991", + "rel_title": "Novel RT-ddPCR assays for determining the transcriptional profile of SARS-CoV-2", + "rel_date": "2021-01-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.12.425991", + "rel_abs": "The exact mechanism of coronavirus replication and transcription is not fully understood; however, a hallmark of coronavirus transcription is the generation of negative-sense RNA intermediates that serve as the templates for the synthesis of positive-sense genomic RNA (gRNA) and an array of subgenomic mRNAs (sgRNAs) encompassing sequences arising from discontinuous transcription.\n\nExisting PCR-based diagnostic assays for SAR-CoV-2 are qualitative or semi-quantitative and do not provide the resolution needed to assess the complex transcription dynamics of SARS-CoV-2 over the course of infection. We developed and validated a novel panel of specially designed SARS-CoV-2 ddPCR-based assays to map the viral transcription profile. Application of these assays to clinically relevant samples will enhance our understanding of SARS-CoV-2 replication and transcription and may also inform the development of improved diagnostic tools and therapeutics.\n\nHighlightsO_LIWe developed a novel panel of 7 quantitative RT-ddPCRs assays for SARS-Cov-2\nC_LIO_LIOur panel targets nongenic and genic regions in genomic and subgenomic RNAs\nC_LIO_LIAll assays detect 1-10 copies and are linear over 3-4 orders of magnitude\nC_LIO_LIAll assays correlated with the clinical Abbott SARS-CoV-2 Viral Load Assay\nC_LIO_LIClinical samples showed higher copy numbers for targets at the 3 end of the genome\nC_LI", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Sushama Telwatte", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Nitasha Kumar", + "author_inst": "San Francisco VA Health Care System" + }, + { + "author_name": "Albert Vallejo-Gracia", + "author_inst": "Gladstone Institutes" + }, + { + "author_name": "G. Renuka Kumar", + "author_inst": "Gladstone Institutes" + }, + { + "author_name": "Chuanyi M Lu", + "author_inst": "San Francisco VA Health Care System" + }, + { + "author_name": "Melanie Ott", + "author_inst": "Gladstone Institutes" + }, + { + "author_name": "Joseph K Wong", + "author_inst": "San Francisco VA Health Care System" + }, + { + "author_name": "Steven A Yukl", + "author_inst": "San Francisco Veteran Affairs Medical Center" + } + ], + "version": "1", + "license": "", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.01.10.20249014", "rel_title": "Cerebrospinal fluid in COVID-19 neurological complications: no cytokine storm or neuroinflammation.", @@ -973724,109 +975186,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2021.01.10.426120", - "rel_title": "Potent SARS-CoV-2 Neutralizing Antibodies Directed Against Spike N-Terminal Domain Target a Single Supersite", - "rel_date": "2021-01-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.10.426120", - "rel_abs": "Numerous antibodies that neutralize SARS-CoV-2 have been identified, and these generally target either the receptor-binding domain (RBD) or the N-terminal domain (NTD) of the viral spike. While RBD-directed antibodies have been extensively studied, far less is known about NTD-directed antibodies. Here we report cryo-EM and crystal structures for seven potent NTD-directed neutralizing antibodies in complex with spike or isolated NTD. These structures defined several antibody classes, with at least one observed in multiple convalescent donors. The structures revealed all seven antibodies to target a common surface, bordered by glycans N17, N74, N122, and N149. This site - formed primarily by a mobile {beta}-hairpin and several flexible loops - was highly electropositive, located at the periphery of the spike, and the largest glycan-free surface of NTD facing away from the viral membrane. Thus, in contrast to neutralizing RBD-directed antibodies that recognize multiple non-overlapping epitopes, potent NTD-directed neutralizing antibodies target a single supersite.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Gabriele Cerutti", - "author_inst": "Columbia University" - }, - { - "author_name": "Yicheng Guo", - "author_inst": "Columbia University" - }, - { - "author_name": "Tongqing Zhou", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Jason Gorman", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Myungjin Lee", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Micah Rapp", - "author_inst": "Columbia University" - }, - { - "author_name": "Eswar R Reddem", - "author_inst": "Columbia University" - }, - { - "author_name": "Jian Yu", - "author_inst": "Columbia University" - }, - { - "author_name": "Fabiana Bahna", - "author_inst": "Columbia University" - }, - { - "author_name": "Jude Bimela", - "author_inst": "Columbia University" - }, - { - "author_name": "Yaoxing Huang", - "author_inst": "Columbia University" - }, - { - "author_name": "Phinikoula S Katsamba", - "author_inst": "Columbia University" - }, - { - "author_name": "Liu Lihong", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Manoj S Nair", - "author_inst": "Columbia University" - }, - { - "author_name": "Reda Rawi", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Adam S Olia", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Pengfei Wang", - "author_inst": "Columbia University Vagelos College of Physicians and Surgeons" - }, - { - "author_name": "Gwo-Yu Chuang", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "David D Ho", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Zizhang Sheng", - "author_inst": "Columbia University" - }, - { - "author_name": "Peter D Kwong", - "author_inst": "Columbia University, National Institutes of Health" - }, - { - "author_name": "Lawrence Shapiro", - "author_inst": "Columbia University, National Institutes of Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.01.08.425965", "rel_title": "Molecular Dynamics Analysis of a Flexible Loop at the Binding Interface of the SARS-CoV-2 Spike Protein Receptor-Binding Domain", @@ -974842,6 +976201,253 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, + { + "rel_doi": "10.1101/2021.01.08.20248149", + "rel_title": "Antiviral drugs in hospitalized patients with COVID-19 - the DisCoVeRy trial", + "rel_date": "2021-01-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.08.20248149", + "rel_abs": "BackgroundLopinavir/ritonavir, lopinavir/ritonavir-interferon (IFN)-{beta}-1a and hydroxychloroquine efficacy for COVID-19 have been evaluated, but detailed evaluation is lacking.\n\nObjectiveTo determine the efficacy of lopinavir/ritonavir, lopinavir/ritonavir-IFN-{beta}-1a, hydroxychloroquine or remdesivir for improving the clinical, virological outcomes in COVID-19 inpatients.\n\nDesignOpen-label, randomized, adaptive, controlled trial.\n\nSettingMulti-center trial with patients from France.\n\nParticipants583 COVID-19 inpatients requiring oxygen and/or ventilatory support\n\nInterventionStandard of care (SoC, control), SoC plus lopinavir/ritonavir (400 mg lopinavir and 100 mg ritonavir every 12h for 14 days), SoC plus lopinavir/ritonavir plus IFN-{beta}-1a (44 g of subcutaneous IFN-{beta}-1a on days 1, 3, and 6), SoC plus hydroxychloroquine (400 mg twice on day 1 then 400 mg once daily for 9 days) or SoC plus remdesivir (200 mg intravenously on day 1 then 100 mg once-daily for hospitalization duration or 10 days).\n\nMeasurementsThe primary outcome was the clinical status at day 15, measured by the WHO 7-point ordinal scale. Secondary outcomes included SARS-CoV-2 quantification in respiratory specimens and safety analyses.\n\nResultsAdjusted Odds Ratio (aOR) for the WHO 7-point ordinal scale were not in favor of investigational treatments: lopinavir/ritonavir versus control, aOR 0.83, 95%CI, 0.55 to 1.26, P=0.39; lopinavir/ritonavir-IFN-{beta}-1a versus control, aOR 0.69, 95%CI, 0.45 to 1.04, P=0.08; hydroxychloroquine versus control, aOR 0.93, 95%CI, 0.62 to 1.41, P=0.75. No significant effect on SARS-CoV-2 RNA clearance in respiratory tract was evidenced. Lopinavir/ritonavir-containing treatments were significantly associated with more SAE.\n\nLimitationsNot a placebo-controlled, no anti-inflammatory agents tested.\n\nConclusionNo improvement of the clinical status at day 15 nor SARS-CoV-2 RNA clearance in respiratory tract specimens by studied drugs. This comforts the recent Solidarity findings.\n\nRegistrationNCT04315948.\n\nFundingPHRC 2020, Dim OneHealth, REACTing", + "rel_num_authors": 58, + "rel_authors": [ + { + "author_name": "Florence ADER", + "author_inst": "CHU Lyon" + }, + { + "author_name": "Nathan PEIFFER-SMADJA", + "author_inst": "CHU Bichat" + }, + { + "author_name": "Julien POISSY", + "author_inst": "CHU Lille" + }, + { + "author_name": "Maude BOUSCAMBERT-DUCHAMP", + "author_inst": "CHU Lyon" + }, + { + "author_name": "Drifa BELHADI", + "author_inst": "CHU Bichat" + }, + { + "author_name": "Alpha DIALLO", + "author_inst": "ANRS" + }, + { + "author_name": "Christelle DELMAS", + "author_inst": "ANRS" + }, + { + "author_name": "Juliette SAILLARD", + "author_inst": "Inserm" + }, + { + "author_name": "Aline DECHANET", + "author_inst": "CHU Bichat" + }, + { + "author_name": "Noemie MERCIER", + "author_inst": "ANRS" + }, + { + "author_name": "Axelle DUPONT", + "author_inst": "CHU Bichat" + }, + { + "author_name": "Toni ALFAIATE", + "author_inst": "CHU Bichat" + }, + { + "author_name": "Francois-Xavier LESCURE", + "author_inst": "CHU Bichat" + }, + { + "author_name": "Francois RAFFI", + "author_inst": "CHU Nantes" + }, + { + "author_name": "Francois GOEHRINGER", + "author_inst": "CHU Nancy" + }, + { + "author_name": "Antoine KIMMOUN", + "author_inst": "CHU Nancy" + }, + { + "author_name": "Stephane JAUREGUIBERRY", + "author_inst": "CHU Bicetre" + }, + { + "author_name": "Jean REIGNIER", + "author_inst": "CHU Nantes" + }, + { + "author_name": "Saad NSEIR", + "author_inst": "CHU Lille" + }, + { + "author_name": "Francois DANION", + "author_inst": "CHU Strasbourg" + }, + { + "author_name": "Raphael CLERE-JEHL", + "author_inst": "CHU Strasbourg" + }, + { + "author_name": "Kevin BOUILLER", + "author_inst": "CHU Besancon" + }, + { + "author_name": "Jean-Christophe NAVELLOU", + "author_inst": "CHU Besancon" + }, + { + "author_name": "Violaine TOLSMA", + "author_inst": "CH Annecy Gennevois" + }, + { + "author_name": "Andre CABIE", + "author_inst": "CHU Fort de France" + }, + { + "author_name": "Clement DUBOST", + "author_inst": "HIA Begin" + }, + { + "author_name": "Johan COURJON", + "author_inst": "CHU Nice" + }, + { + "author_name": "Sylvie LEROY", + "author_inst": "CHU Nice" + }, + { + "author_name": "Joy MOOTIEN", + "author_inst": "CH Mulhouse" + }, + { + "author_name": "Rostane GACI", + "author_inst": "CHR Mets-Thionville" + }, + { + "author_name": "Bruno MOURVILLIER", + "author_inst": "CHU Reims" + }, + { + "author_name": "Emmanuel FAURE", + "author_inst": "CHU Lille" + }, + { + "author_name": "Valerie POURCHER", + "author_inst": "CHU Pitie-Salpetriere" + }, + { + "author_name": "Sebastien GALLIEN", + "author_inst": "CHU Mondor" + }, + { + "author_name": "Odile LAUNAY", + "author_inst": "CHU Cochin" + }, + { + "author_name": "Karine LACOMBE", + "author_inst": "CHU Saint Antoine" + }, + { + "author_name": "Jean-Philippe LANOIX", + "author_inst": "CHU Amiens" + }, + { + "author_name": "Alain MAKINSON", + "author_inst": "CHU Montpellier" + }, + { + "author_name": "Guillaume MARTIN-BLONDEL", + "author_inst": "CHU Toulouse" + }, + { + "author_name": "Lila BOUADMA", + "author_inst": "CHU Bichat" + }, + { + "author_name": "elisabeth BOTELHO-NEVERS", + "author_inst": "CHU Saint Etienne" + }, + { + "author_name": "Amandine GAGNEUX-BRUNON", + "author_inst": "CHU Saint Etienne" + }, + { + "author_name": "Olivier EPAULARD", + "author_inst": "CHU Grenoble" + }, + { + "author_name": "Lionel PIROTH", + "author_inst": "CHU Dijon" + }, + { + "author_name": "Florent WALLET", + "author_inst": "CHU Lyon" + }, + { + "author_name": "Jean-Christophe RICHARD", + "author_inst": "CHU Lyon" + }, + { + "author_name": "Jean REUTER", + "author_inst": "CHU Luxembourg" + }, + { + "author_name": "Therese STAUB", + "author_inst": "CHU Luxembourg" + }, + { + "author_name": "Maya HITES", + "author_inst": "CHU Erasme" + }, + { + "author_name": "Marion NORET", + "author_inst": "CH Annecy Gennevois" + }, + { + "author_name": "Claire ANDREJAK", + "author_inst": "CHU Amiens" + }, + { + "author_name": "Gilles PEYTAVIN", + "author_inst": "CHU Bichat" + }, + { + "author_name": "Bruno LINA", + "author_inst": "CHU Lyon" + }, + { + "author_name": "Dominique COSTAGLIOLA", + "author_inst": "Inserm" + }, + { + "author_name": "Yazdan YAZDANPANAH", + "author_inst": "CHU Bichat" + }, + { + "author_name": "Charles BURDET", + "author_inst": "CHU Bichat" + }, + { + "author_name": "France MENTRE", + "author_inst": "CHU Bichat" + }, + { + "author_name": "- DisCoVeRy study group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.05.21249310", "rel_title": "Ivermectin as a potential treatment for mild to moderate COVID-19: A double blind randomized placebo-controlled trial", @@ -975758,105 +977364,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.30.20248277", - "rel_title": "Utilization of Whole Genome Sequencing to Understand SARS-CoV-2 Transmission Dynamics in Long-Term Care Facilities, Correctional Facilities and Meat Processing Plants in Minnesota, March - June 2020", - "rel_date": "2021-01-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.30.20248277", - "rel_abs": "Congregate settings and high-density workplaces have endured a disproportionate impact from COVID-19. In order to provide further understanding of the transmission patterns of SARS-CoV-2 in these settings, whole genome sequencing (WGS) was performed on samples obtained from 8 selected outbreaks in Minnesota from March - June, 2020. WGS and phylogenetic analysis was conducted on 319 samples, constituting 14.4% of the 2,222 total SARS-CoV-2-positive individuals associated with these outbreaks. Among the sequenced specimens, three LTCFs and both correctional facilities had spread associated with a single genetic sequence. A fourth LTCF had outbreak cases associated with two distinct sequences. In contrast, cases associated with outbreaks in the two meat processing plants represented multiple SARS-CoV-2 sequences. These results suggest that a single introduction of SARS-CoV-2 into a facility can result in a widespread outbreak, and early identification and cohorting of cases, along with continued vigilance with infection prevention and control measures is imperative.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Nicholas B Lehnertz", - "author_inst": "Minnesota Department of Health" - }, - { - "author_name": "Xiong Wang", - "author_inst": "Minnesota Department of Health" - }, - { - "author_name": "Jacob Garfin", - "author_inst": "Minnesota Department of Health" - }, - { - "author_name": "Joanne Taylor", - "author_inst": "Center for Disease Control and Prevention" - }, - { - "author_name": "Jennifer Zipprich", - "author_inst": "Minnesota Department of Health" - }, - { - "author_name": "Brittany VonBank", - "author_inst": "Minnesota Department of Health" - }, - { - "author_name": "Karen Martin", - "author_inst": "Minnesota Department of Health" - }, - { - "author_name": "Dana Eikmeier", - "author_inst": "Minnesota Department of Health" - }, - { - "author_name": "Carlota Medus", - "author_inst": "Minnesota Department of Health" - }, - { - "author_name": "Brooke Wiedinmyer", - "author_inst": "Minnesota Department of Health" - }, - { - "author_name": "Carmen Bernu", - "author_inst": "Minnesota Department of Health" - }, - { - "author_name": "Matthew Plumb", - "author_inst": "Minnesota Department of Health" - }, - { - "author_name": "Kelly Pung", - "author_inst": "Minnesota Department of Health" - }, - { - "author_name": "Margaret A Honein", - "author_inst": "Center for Disease Control and Prevention" - }, - { - "author_name": "Rosalind Carter", - "author_inst": "Center for Disease Control and Prevention" - }, - { - "author_name": "Duncan MacCannell", - "author_inst": "Center for Disease Control and Prevention" - }, - { - "author_name": "Kirk E. Smith", - "author_inst": "Minnesota Department of Health" - }, - { - "author_name": "Kathryn Como-Sabetti", - "author_inst": "Minnesota Department of Health" - }, - { - "author_name": "Kris Ehresmann", - "author_inst": "Minnesota Department of Health" - }, - { - "author_name": "Richard Danila", - "author_inst": "Minnesota Department of Health" - }, - { - "author_name": "Ruth Lynfield", - "author_inst": "Minnesota Department of Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.05.21249190", "rel_title": "Host genome analysis of structural variations by Optical Genome Mapping provides clinically valuable insights into genes implicated in critical immune, viral infection, and viral replication pathways in patients with severe COVID-19.", @@ -976644,6 +978151,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, + { + "rel_doi": "10.1101/2021.01.07.21249366", + "rel_title": "Quarantine fatigue thins fat-tailed coronavirus impacts in U.S. cities by making epidemics inevitable", + "rel_date": "2021-01-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.07.21249366", + "rel_abs": "We use detailed location data to show that contacts between individuals in most U.S. cities and counties are fat tailed, suggesting that the fat tails documented in a small number of superspreading clusters are widespread. We integrate these results into a stochastic compartmental model to show that COVID-19 cases were also fat tailed for many U.S. cities for several weeks in the spring and summer. Due to epidemiological thresholds, fat-tailed cases would have been more prevalent if not for the gradual increase in contact rates throughout the summer that made outbreaks more certain.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Marc N Conte", + "author_inst": "Fordham University" + }, + { + "author_name": "Matthew Gordon", + "author_inst": "Yale University" + }, + { + "author_name": "Charles Sims", + "author_inst": "University of Tennessee, Knoxville" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.06.20248960", "rel_title": "Impact of B.1.1.7 variant mutations on antibody recognition of linear SARS-CoV-2 epitopes", @@ -977543,53 +979077,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.07.425801", - "rel_title": "Fibrinolysis influences SARS-CoV-2 infection in ciliated cells", - "rel_date": "2021-01-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.07.425801", - "rel_abs": "Rapid spread of COVID-19 has caused an unprecedented pandemic worldwide, and an inserted furin site in SARS-CoV-2 spike protein (S) may account for increased transmissibility. Plasmin, and other host proteases, may cleave the furin site of SARS-CoV-2 S protein and {gamma} subunits of epithelial sodium channels ({gamma} ENaC), resulting in an increment in virus infectivity and channel activity. As for the importance of ENaC in the regulation of airway surface and alveolar fluid homeostasis, whether SARS-CoV-2 will share and strengthen the cleavage network with ENaC proteins at the single-cell level is urgently worthy of consideration. To address this issue, we analyzed single-cell RNA sequence (scRNA-seq) datasets, and found the PLAU (encoding urokinase plasminogen activator), SCNN1G ({gamma}ENaC), and ACE2 (SARS-CoV-2 receptor) were co-expressed in alveolar epithelial, basal, club, and ciliated epithelial cells. The relative expression level of PLAU, TMPRSS2, and ACE2 were significantly upregulated in severe COVID-19 patients and SARS-CoV-2 infected cell lines using Seurat and DESeq2 R packages. Moreover, the increments in PLAU, FURIN, TMPRSS2, and ACE2 were predominately observed in different epithelial cells and leukocytes. Accordingly, SARS-CoV-2 may share and strengthen the ENaC fibrinolytic proteases network in ACE2 positive airway and alveolar epithelial cells, which may expedite virus infusion into the susceptible cells and bring about ENaC associated edematous respiratory condition.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Myoung Ryoul Park", - "author_inst": "National Institute of Crop Science Suwon" - }, - { - "author_name": "Chunmei Cai", - "author_inst": "Qingdao Agricultural University" - }, - { - "author_name": "Min-Jung Seo", - "author_inst": "National Institute of Crop Science Suwon" - }, - { - "author_name": "Hong-Tae Yun", - "author_inst": "National Institute of Crop Science Suwon" - }, - { - "author_name": "Soo-Kwon Park", - "author_inst": "National Institute of Crop Science" - }, - { - "author_name": "Man-Soo Choi", - "author_inst": "National Institute of Crop Science" - }, - { - "author_name": "Chang-Hwan Park", - "author_inst": "National Institute of Crop Science Miryang" - }, - { - "author_name": "Jung Kyung Moon", - "author_inst": "National Institute of Agricultural Science" - } - ], - "version": "1", - "license": "", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.01.08.425793", "rel_title": "Vimentin binds to SARS-CoV-2 spike protein and antibodies targeting extracellular vimentin block in vitro uptake of SARS-CoV-2 virus-like particles", @@ -978325,6 +979812,33 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.01.07.425307", + "rel_title": "Stable Interaction Of The UK B.1.1.7 lineage SARS-CoV-2 S1 Spike N501Y Mutant With ACE2 Revealed By Molecular Dynamics Simulation", + "rel_date": "2021-01-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.07.425307", + "rel_abs": "Corona Virus Disease of 2019 (COVID-19) caused by Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) has caused a massive health crisis across the globe, with some genetic variants gaining enhanced infectivity and competitive fitness, and thus significantly aggravating the global health concern. In this regard, the recent SARS-CoV-2 alpha variant, B.1.1.7 lineage, reported from the United Kingdom (UK), is of great significance in that it contains several mutations that increase its infection and transmission rates as evident from clinical reports. Specifically, the N501Y mutation in the SARS-CoV-2 spike S1 receptor binding domain (S1-RBD) has been shown to possess an increased affinity for ACE2, although the basis for this is not entirely clear yet. Here, we dissect the mechanism underlying the increased affinity using molecular dynamics (MD) simulations of the available ACE2-S1-RBD complex structure (6M0J) and show a prolonged and stable interfacial interaction of the N501Y mutant S1-RBD with ACE2 compared to the wild type S1-RBD. Additionally, we find that the N501Y mutant S1-RBD displays altered dynamics that likely aids in its enhanced interaction with ACE2. By elucidating a mechanistic basis for the increased affinity of the N501Y mutant S1-RBD for ACE2, we believe that the results presented here will aid in developing therapeutic strategies against SARS-CoV-2 including designing drugs targeting the ACE2-S1-RBD interaction.\n\nSignificanceThe emergence of the new SARS-CoV-2 lineage in the UK in December 2020 has further aggravated the COVID-19 pandemic due to an increased ability of the variant to infect human hosts, likely due to mutations in the viral S1 spike protein including the N501Y S1-RBD mutation that is located at the interface of S1-RBD and ACE2, the host cell receptor for SARS-CoV-2. Given its location at the interface, N501Y S1-RBD mutation can therefore potentially alter the interfacial interaction. Multiple, all-atom, explicit solvent MD simulations of the ACE2-S1-RBD complex carried here indicated a more stable interaction between the N501Y mutant S1-RBD and ACE2 through stabilizing interfacial interactions of residues at one end of the interface that are either sequentially or physically near the mutation site. These mechanistic details will aid in better understanding the mechanism by which the alpha variant has increased infectivity as well as in designing better therapeutics including ACE2-S1 spike protein inhibitors that will, in turn, help thwarting the current and future pandemic.\n\nHighlightsO_LIN501 in the wild type SARS-CoV-2 S1-RBD forms unsustained hydrogen bonds with residues in the ACE2, namely Y41 and K353\nC_LIO_LIY501 in the N501Y mutant SARS-CoV-2 S1-RBD is not capable of forming substantial hydrogen bonds with ACE2 within the time span of the current simulation\nC_LIO_LIEvidence from analyzing the simulation results suggests that Y501 of S1-RBD could form other types of non-covalent interactions with ACE2, such as van der Waals interactions\nC_LIO_LIN501Y S1-RBD mutation stabilizes the position of interfacial residues neighboring to the mutation site, as well as other non-interfacial residues that are distant from the mutation site\nC_LIO_LIThese altered dynamics results in more stable interaction of S1-RBD with ACE2 which could be the main reason underlying the reported enhanced affinity of S1-RBD in the SARS-CoV-2 alpha variant (UK B.1.1.7 lineage) to ACE2\nC_LI", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Wesam Ahmed", + "author_inst": "College of Health & Life Sciences, Hamad Bin Khalifa University, Doha, Qatar" + }, + { + "author_name": "Angelin M Phillip", + "author_inst": "College of Health & Life Sciences, Hamad Bin Khalifa University, Doha, Qatar" + }, + { + "author_name": "Kabir H Biswas", + "author_inst": "College of Health & Life Sciences, Hamad Bin Khalifa University, Doha, Qatar" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.01.07.425724", "rel_title": "Immunoinformatic based analytics on T-cell epitope from spike protein of SARS-CoV-2 concerning Indian population.", @@ -979285,45 +980799,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.06.21249312", - "rel_title": "Long term impact on lung function of patients with moderate and severe COVID-19. A prospective cohort study", - "rel_date": "2021-01-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.06.21249312", - "rel_abs": "IntroductionA significant number of patients continue to recover from COVID-19; however, little is known about the lung function capacity among survivors. We aim to determine the long-term impact on lung function capacity in patients who have survived moderate or severe COVID-19 disease in a resource-poor setting.\n\nMethods and analysisThis prospective cohort study will include patients aged 15 years and above and have reverse transcriptase-polymerase chain reaction (RT-PCR) positive for COVID 19 (nasopharyngeal or oropharyngeal). Patients with a pre-existing diagnosis of obstructive or interstitial lung disease, lung fibrosis and cancers, connective tissue disorders, autoimmune conditions affecting the lungs, underlying heart disease, history of syncope and refuse to participate will be excluded. Pulmonary function will be assessed using spirometry and diffusion lung capacity for carbon monoxide (DLCO) at three- and six-months interval. A chest X-ray at three and six-month follow-up and CT-chest will be performed if clinically indicated after consultation with the study pulmonologist or Infectious Disease (ID) physician. Echocardiogram (ECHO) to look for pulmonary hypertension at the three months visit and repeated at six months if any abnormality is identified initially. Data analysis will be performed using standard statistical software.\n\nEthics and disseminationThe proposal was reviewed and approved by ethics review committee (ERC) of the institution (ERC reference number 2020-4735-11311). Informed consent will be obtained from each study participant. The results will be disseminated among study participants, institutional, provincial and national level through seminars and presentations. Moreover, the scientific findings will be published in high-impact peer-reviewed medical journals.\n\nStrengths and Limitations of this study- The study has the potential to develop context-specific evidence on the long-term impact on lung function among COVID-19 survivors\n- Findings will play key role in understanding the impact of the disease on vital functions and help devise rehabilitative strategies to best overcome the effects of disease\n- This is a single-center, study recruiting only a limited number of COVID-19 survivors\n- The study participants may loss-to-follow up due to uncertain conditions and disease reemergence", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Sonia Qureshi", - "author_inst": "Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan" - }, - { - "author_name": "Nosheen Nasir", - "author_inst": "Department of Medicine, Aga Khan University, Karachi, Pakistan" - }, - { - "author_name": "Naveed Rashid", - "author_inst": "Department of Medicine, Aga Khan University, Karachi, Pakistan" - }, - { - "author_name": "Naveed Ahmed", - "author_inst": "Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan" - }, - { - "author_name": "Zoya Haq", - "author_inst": "Liaquat National Hospital and Medical College, Karachi, Pakistan" - }, - { - "author_name": "Farah N Qamar", - "author_inst": "Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.05.20249061", "rel_title": "THE INTESTINAL AND ORAL MICROBIOMES ARE ROBUST PREDICTORS OF COVID-19 SEVERITY THE MAIN PREDICTOR OF COVID-19-RELATED FATALITY", @@ -980059,6 +981534,37 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.01.04.425340", + "rel_title": "Natural variants in SARS-CoV-2 S protein pinpoint structural and functional hotspots; implications for prophylaxis strategies", + "rel_date": "2021-01-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.04.425340", + "rel_abs": "In December 2019, a novel coronavirus, termed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified as the cause of pneumonia with severe respiratory distress and outbreaks in Wuhan, China. The rapid and global spread of SARS-CoV-2 resulted in the coronavirus 2019 (COVID-19) pandemic. Earlier during the pandemic, there were limited genetic viral variations. As millions of people became infected, multiple single amino acid substitutions emerged. Many of these substitutions have no consequences. However, some of the new variants show a greater infection rate, more severe disease, and reduced sensitivity to current prophylaxes and treatments. Of particular importance in SARS-CoV-2 transmission are mutations that occur in the Spike (S) protein, the protein on the viral outer envelope that binds to the human angiotensin-converting enzyme receptor (hACE2). Here, we conducted a comprehensive analysis of 441,168 individual virus sequences isolated from humans throughout the world. From the individual sequences, we identified 3,540 unique amino acid substitutions in the S protein. Analysis of these different variants in the S protein pinpointed important functional and structural sites in the protein. This information may guide the development of effective vaccines and therapeutics to help arrest the spread of the COVID-19 pandemic.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Suman Pokhrel", + "author_inst": "Stanford University" + }, + { + "author_name": "Benjamin R Kraemer", + "author_inst": "Stanford University" + }, + { + "author_name": "Scott Burkholz", + "author_inst": "Flow Pharma" + }, + { + "author_name": "Daria Mochly-Rosen", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2021.01.06.425396", "rel_title": "SARS-CoV-2 spike downregulates tetherin to enhance viral spread", @@ -980859,29 +982365,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.04.20248979", - "rel_title": "Reverse Transcriptase Loop Mediated Isothermal Amplification (RT-LAMP) for COVID-19 Diagnosis: A Systematic Review and Meta-Analysis", - "rel_date": "2021-01-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.04.20248979", - "rel_abs": "BackgroundCoronavirus Disease 2019 (COVID-19) has caused a severe outbreak and become a global public health priority. Rapid increment of infection number along with significant deaths have placed the virus as a serious threat to human health. Rapid, reliable, and simple diagnostic methods are critically essential for disease control. While Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) is the current diagnostic gold standard, Reverse Transcriptase Loop-Mediated Isothermal Amplification (RT-LAMP) appears as a compelling alternative diagnostic test due to its more simplicity, shorter time to result, and lower cost. This study examined RT-LAMP application for rapid identification of SARS-CoV-2 infection compared to RT-PCR assay.\n\nMethodsA systematic review and meta-analysis (2020) was conducted in 6 scientific databases following the PRISMA Guideline. Original published studies on human clinical samples in English were included. Articles evaluated sensitivity and specificity of RT-LAMP relative to RT-PCR were considered eligible. Quality assessment of bias and applicability was examined based on QUADAS-2.\n\nResultsA total of 351 studies were found based on the keywords and search queries. 14 eligible case control studies fitted the respective criteria. Quality assessment using QUADAS-2 indicated low risk bias in all included studies. All case studies, comprises 2,112 samples, had the cumulative sensitivity of 95.5% (CI 97.5%=90.8-97.9%) and cumulative specificity of 99.5% (CI 97.5%=97.7-99.9%).\n\nConclusionRT-LAMP assay could be suggested as a reliable alternative COVID-19 diagnostic method with reduced cost and time compared to RT-PCR. RT-LAMP could potentially be utilized during the high-throughput and high-demand critical situations.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Anita Dominique Subali", - "author_inst": "University of Brawijaya, Indonesia" - }, - { - "author_name": "Lowilius Wiyono", - "author_inst": "Universitas Indonesia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.04.21249231", "rel_title": "Modeling COVID-19 outbreaks in United States with distinct testing, lockdown speed and fatigue rates", @@ -981449,6 +982932,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.01.04.21249219", + "rel_title": "The impact of vitamin D supplementation on mortality rate and clinical outcomes of COVID-19 patients: A systematic review and meta-analysis", + "rel_date": "2021-01-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.04.21249219", + "rel_abs": "BackgroundSeveral studies have suggested the positive impact of vitamin D on patients infected with SARS-CoV-2. This systematic review aims to evaluate the effects of vitamin D supplementation on clinical outcomes and mortality rate of COVID-19 patients.\n\nMethodsA comprehensive search was conducted through the databases of PubMed, Scopus, Web of Knowledge, Embase, Ovid, and The Cochrane Library with no limitation in time and language, until December 16, 2020. The results were screened based on their accordance with the subject. Two independent reviewers selected the eligible studies and the outcomes of interest were extracted. Using the Joanna Briggs Institute (JBI) Critical Appraisal Tools for Randomized Controlled Trials (RCTs) and Quasi-Experimental Studies, the remaining results were appraised critically. Statistical analysis was performed using the Comprehensive Meta-Analysis (CMA) software version 2.0.\n\nResultsOf the 2311 results, 1305 duplicated results were removed. After screening the titles, abstracts, and the full-text articles of the remaining records, four studies and 259 patients were enrolled, including 139 patients in vitamin D intervention groups. In three of the studies, the patients survival and mortality rate were evaluated. The pooled analysis of these studies showed a significantly lower mortality rate among the intervention groups (10.56%) compared with the control groups (23.88%) (OR = 0.264, 95% CI = 0.099-0.708, p-value = 0.008). Two of the studies reported the clinical outcomes based on the World Health Organizations Ordinal Scale for Clinical Improvement (OSCI) score for COVID-19, where both of them showed a significant decrease in OSCI score in the vitamin D intervention groups. Additionally, One study reported a lower rate of intensive care unit (ICU) admission, and one study reported a significant decrease in serum levels of Fibrinogen.\n\nConclusionPrescribing vitamin D supplementation to patients with COVID-19 infection seems to decrease the mortality rate, the severity of the disease, and serum levels of the inflammatory markers. Further studies are needed to determine the ideal type, dosage and duration of supplementation.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Leila Nikniaz", + "author_inst": "Tabriz Health Services Management Research Center, Tabriz University of Medical Sciences, Tabriz, Iran" + }, + { + "author_name": "Mohammad Amin Akbarzadeh", + "author_inst": "Research Center for Evidence-Based Medicine, Iranian Evidence-Based Medicine (EBM) Centre, Joanna Briggs Institute Affiliated Group, Tabriz University of Medica" + }, + { + "author_name": "Hossein Hosseinifard", + "author_inst": "Department of Biostatistics, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Mohammad-Salar Hosseini", + "author_inst": "Research Center for Evidence-Based Medicine, Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.30.20249051", "rel_title": "The social experience of participation in a COVID-19 vaccine trial: Subjects' motivations, others' concerns, and insights for vaccine promotion", @@ -982173,181 +983687,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.01.05.422952", - "rel_title": "Immunogenicity of an AAV-based, room-temperature stable, single dose COVID-19 vaccine in mice and non-human primates", - "rel_date": "2021-01-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.05.422952", - "rel_abs": "The SARS-CoV-2 pandemic has affected more than 70 million people worldwide and resulted in over 1.5 million deaths. A broad deployment of effective immunization campaigns to achieve population immunity at global scale will depend on the biological and logistical attributes of the vaccine. Here, two adeno-associated viral (AAV)-based vaccine candidates demonstrate potent immunogenicity in mouse and nonhuman primates following a single injection. Peak neutralizing antibody titers remain sustained at 5 months and are complemented by functional memory T-cells responses. The AAVrh32.33 capsid of the AAVCOVID vaccine is an engineered AAV to which no relevant pre-existing immunity exists in humans. Moreover, the vaccine is stable at room temperature for at least one month and is produced at high yields using established commercial manufacturing processes in the gene therapy industry. Thus, this methodology holds as a very promising single dose, thermostable vaccine platform well-suited to address emerging pathogens on a global scale.", - "rel_num_authors": 40, - "rel_authors": [ - { - "author_name": "Nerea Zabaleta", - "author_inst": "Grousbeck Gene Therapy Center, Mass Eye and Ear and Harvard Medical School" - }, - { - "author_name": "Wenlong Dai", - "author_inst": "Grousbeck Gene Therapy Center, Mass Eye and Ear and Harvard Medical School" - }, - { - "author_name": "Urja Bhatt", - "author_inst": "Grousbeck Gene Therapy Center, Mass Eye and Ear and Harvard Medical School" - }, - { - "author_name": "Jessica A. Chichester", - "author_inst": "Gene Therapy Program, Perelman School of Medicine, University of Pennsylvania" - }, - { - "author_name": "Julio Sanmiguel", - "author_inst": "Grousbeck Gene Therapy Center, Mass Eye and Ear and Harvard Medical School" - }, - { - "author_name": "Reynette Estelien", - "author_inst": "Grousbeck Gene Therapy Center, Mass Eye and Ear and Harvard Medical School" - }, - { - "author_name": "Kristofer T. Michalson", - "author_inst": "Gene Therapy Program, Perelman School of Medicine, University of Pennsylvania" - }, - { - "author_name": "Cheikh Diop", - "author_inst": "Grousbeck Gene Therapy Center, Mass Eye and Ear and Harvard Medical School" - }, - { - "author_name": "Dawid Maciorowski", - "author_inst": "Grousbeck Gene Therapy Center, Mass Eye and Ear and Harvard Medical School" - }, - { - "author_name": "Wenbin Qi", - "author_inst": "Novartis Gene Therapies, San Diego" - }, - { - "author_name": "Elissa Hudspeth", - "author_inst": "Novartis Gene Therapies, North Carolina" - }, - { - "author_name": "Allison Cucalon", - "author_inst": "Grousbeck Gene Therapy Center, Mass Eye and Ear and Harvard Medical School" - }, - { - "author_name": "Cecilia D. Dyer", - "author_inst": "Gene Therapy Program, Perelman School of Medicine, University of Pennsylvania" - }, - { - "author_name": "M. Betina Pampena", - "author_inst": "Gene Therapy Program, Department of Microbiology, Perelman School of Medicine, University of Pennsylvania" - }, - { - "author_name": "James J. Knox", - "author_inst": "Department of Microbiology, Perelman School of Medicine, University of Pennsylvania" - }, - { - "author_name": "Regina C. LaRocque", - "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, Department of Medicine, Harvard Medical School" - }, - { - "author_name": "Richelle C. Charles", - "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, Department of Medicine, Harvard Medical School" - }, - { - "author_name": "Dan Li", - "author_inst": "Grousbeck Gene Therapy Center, Mass Eye and Ear and Harvard Medical School" - }, - { - "author_name": "Maya Kim", - "author_inst": "Grousbeck Gene Therapy Center, Mass Eye and Ear and Harvard Medical School" - }, - { - "author_name": "Abigail Sheridan", - "author_inst": "Grousbeck Gene Therapy Center, Mass Eye and Ear and Harvard Medical School" - }, - { - "author_name": "Nadia Storm", - "author_inst": "Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine" - }, - { - "author_name": "Rebecca I. Johnson", - "author_inst": "Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine" - }, - { - "author_name": "Jared Feldman", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard" - }, - { - "author_name": "Blake M. Hauser", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard" - }, - { - "author_name": "Eric Zinn", - "author_inst": "Grousbeck Gene Therapy Center, Mass Eye and Ear and Harvard Medical School" - }, - { - "author_name": "Aisling Ryan", - "author_inst": "Grousbeck Gene Therapy Center, Mass Eye and Ear and Harvard Medical School" - }, - { - "author_name": "Dione T. Kobayashi", - "author_inst": "Translational Innovation Fund, Mass General Brigham Innovation" - }, - { - "author_name": "Ruchi Chauhan", - "author_inst": "Grousbeck Gene Therapy Center, Mass Eye and Ear and Harvard Medical School" - }, - { - "author_name": "Marion McGlynn", - "author_inst": "Gene Therapy Program, Perelman School of Medicine, University of Pennsylvania" - }, - { - "author_name": "Edward T. Ryan", - "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, Department of Medicine, Harvard Medical School, Department of Immunology and Infectious Disease" - }, - { - "author_name": "Aaron G. Schmidt", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard, Department of Microbiology, Harvard Medical School" - }, - { - "author_name": "Brian Price", - "author_inst": "Albamunity" - }, - { - "author_name": "Anna Honko", - "author_inst": "Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine" - }, - { - "author_name": "Anthony Griffiths", - "author_inst": "Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine" - }, - { - "author_name": "Sam Yaghmour", - "author_inst": "Novartis Gene Therapies, San Diego" - }, - { - "author_name": "Robert Hodge", - "author_inst": "Novartis Gene Therapies, Libertyville, Illinois" - }, - { - "author_name": "Michael R. Betts", - "author_inst": "Gene Therapy Program, Department of Microbiology, Perelman School of Medicine, University of Pennsylvania" - }, - { - "author_name": "Mason W. Freeman", - "author_inst": "Center for Computational & Integrative Biology, Department of Medicine, and Translational Research Center, Massachusetts General Hospital, Harvard Medical Schoo" - }, - { - "author_name": "James M. Wilson", - "author_inst": "Gene Therapy Program, Perelman School of Medicine, University of Pennsylvania" - }, - { - "author_name": "Luk H. Vandenberghe", - "author_inst": "Grousbeck Gene Therapy Center, Mass Eye and Ear and Harvard Medical School" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.01.04.425316", "rel_title": "Molecular Mechanism of the N501Y Mutation for Enhanced Binding between SARS-CoV-2's Spike Protein and Human ACE2 Receptor", @@ -982955,6 +984294,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.12.29.20248977", + "rel_title": "Effects of climate conditions, mobility trends, and countermeasures on the COVID-19 outbreak in Japan", + "rel_date": "2021-01-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.29.20248977", + "rel_abs": "BackgroundBefore Olympic and Paralympic Games in Tokyo, whether an audience shall be allowed or not has been a subject of concern in Japan as of early June, 2021. Object: We evaluated effects of professional baseball games with audiences as an example of the large sports events, on COVID-19 infectiousness.\n\nMethodWe regressed the effective reproduction number R(t) on a dummy variable for professional baseball games with audiences as along with temperature, humidity, mobility, and countermeasures. We examined two study periods: those including and excluding before initiation of the games in 2020.\n\nResultsEstimation results indicate that the period with audiences exhibited significantly lower infectiousness than when audiences were excluded before initiation of the games with audience attendance. However, audiences were found to have a negative but insignificant effect when compared to the period before initiation of the attended games.\n\nDiscussion and ConclusionThis study found no clear evidence indicating that big sports events with audiences raise the COVID-19 infectiousness.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Junko Kurita", + "author_inst": "Tokiwa University, Ibaraki, Japan" + }, + { + "author_name": "Tamie Sugawara", + "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan" + }, + { + "author_name": "Yasushi Ohkusa", + "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.12.29.20248969", "rel_title": "Reliability of Google Trends: Analysis of the Limits and Potential of Web Infoveillance During COVID-19 Pandemic and for Future Research", @@ -983839,41 +985205,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, - { - "rel_doi": "10.1101/2020.12.30.20249052", - "rel_title": "Percentage of reported Covid-19 cases in Colombia: Estimating the true scale of the pandemic", - "rel_date": "2021-01-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.30.20249052", - "rel_abs": "At the outbreak of a virus, data on cases is sparse and commonly severe cases, with a higher probability of a fatal resolution, are detected at a larger rate than mild cases. In addition, in an under-sampling situation, the number of total cases is under-estimated leading to a biased case fatality rate estimation, most likely inflating the virus mortality. In this communication, we present a method to estimate the sub-report in a country that accounts for both the delay time between symptoms onset to death and the countrys demographics. The method is based on the comparison of the corrected case fatality rate (CFR) of the target country with the one of a benchmark country. Using reported data from Instituto Nacional de Salud up to December 28, we utilize our method to provide a comprehensive estimate of the Covid-19 sub-report in Colombia, its regions and some of its cities during 2020.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Nicol\u00e1s Parra-A", - "author_inst": "Universidad Nacional de Colombia" - }, - { - "author_name": "Vladimir Vargas-Calder\u00f3n", - "author_inst": "Universidad Nacional de Colombia" - }, - { - "author_name": "Juan Sebasti\u00e1n Fl\u00f3rez", - "author_inst": "Universidad Nacional de Colombia" - }, - { - "author_name": "Leonel Ardila", - "author_inst": "Universidad Nacional de Colombia" - }, - { - "author_name": "Carlos Viviescas", - "author_inst": "Universidad Nacional de Colombia" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.29.20248953", "rel_title": "Co-circulation of SARS-CoV-2 and Influenza under vaccination scenarios", @@ -984321,6 +985652,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.01.02.21249138", + "rel_title": "Real-World Clinical Performance of the Abbott Panbio with Nasopharyngeal, Throat and Saliva Swabs Among Symptomatic Individuals with COVID-19", + "rel_date": "2021-01-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.02.21249138", + "rel_abs": "BACKGROUNDPoint of Care Testing (POCT) SARS-CoV-2 antigen tests, such as the Abbott Panbio, have great potential to help combat the COVID-19 pandemic. The Panbio is Health Canada approved for the detection of SARS-CoV-2 in symptomatic individuals within the first 7 days of COVID-19 symptom onset(s).\n\nMETHODSSymptomatic adults recently diagnosed with COVID-19 in the community were recruited into the study. Paired nasopharyngeal (NP), throat, and saliva swabs were collected, with one paired swab tested immediately with the Panbio, and the other transported in universal transport media and tested using reverse-transcriptase polymerase chain reaction (RT-PCR). Positive percent agreement (PPA) was calculated. Subsequently, individuals within 7 days of symptom onset who presented to community assessment centres for SARS-CoV-2 testing had Panbio testing completed and paired with RT-PCR results from parallel NP or throat swabs.\n\nRESULTS145 individuals were included in the study. Collection of throat and saliva was stopped early due to poor performance (throat PPA 57.7%, n=61, and saliva PPA 2.6%, n=41). NP swab PPA was 87.7% [n=145, 95% confidence interval 81.0% - 92.7%]. There were 1,641 symptomatic individuals tested by Panbio in community assessment centres, with 268/1641 (16.3%) positive for SARS-CoV-2. There were 37 false negatives, corresponding to a PPA of 86.2% [81.5% - 90.1%].\n\nCONCLUSIONSThe Panbio test reliably detects most cases of SARS-CoV-2 from adults in the POCT community setting presenting within 7 days of symptom onset using nasopharyngeal swabs. Throat and saliva swabs are not reliable specimens for the Panbio.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "William Stokes", + "author_inst": "University of Alberta" + }, + { + "author_name": "Byron Berenger", + "author_inst": "University of Calgary" + }, + { + "author_name": "Danielle Portnoy", + "author_inst": "University of Alberta" + }, + { + "author_name": "Brittney Scott", + "author_inst": "university of Alberta" + }, + { + "author_name": "Jonas Szelewicki", + "author_inst": "University of Alberta" + }, + { + "author_name": "Takshveer Singh", + "author_inst": "University of Calgary" + }, + { + "author_name": "Allison Venner", + "author_inst": "University of Calgary" + }, + { + "author_name": "Leeann Turnbull", + "author_inst": "Alberta Precision Laboratories" + }, + { + "author_name": "Kanti Pabbaraju", + "author_inst": "Alberta Precision Laboratories" + }, + { + "author_name": "Sandy Shokoples", + "author_inst": "Alberta Precision Laboratories" + }, + { + "author_name": "Anita Ah-Ting Wong", + "author_inst": "Alberta Precision Laboratories, Public Health Laboratory" + }, + { + "author_name": "Kara Gill", + "author_inst": "Alberta Precision Laboratories" + }, + { + "author_name": "Tracy Guttridge", + "author_inst": "Alberta Precision Laboratories" + }, + { + "author_name": "Dustin Proctor", + "author_inst": "Alberta Precision Laboratories" + }, + { + "author_name": "Jia Hu", + "author_inst": "University of Calgary" + }, + { + "author_name": "Graham Tipples", + "author_inst": "University of Alberta" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.03.21249157", "rel_title": "Implications in the quantitation of SARS-CoV2 copies in concurrent nasopharyngeal swabs, whole mouth fluid and respiratory droplets", @@ -985105,53 +986515,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.01.03.21249184", - "rel_title": "COVID-19 Vaccine Acceptance Among Health Care Workers in the United States", - "rel_date": "2021-01-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.03.21249184", - "rel_abs": "BackgroundAcceptance of the COVID-19 vaccine will play a major role in combating the pandemic. Healthcare workers (HCWs) are amongst the first group to receive vaccination, so it is important to consider their attitudes about COVID-19 vaccination to better address barriers to widespread vaccination acceptance.\n\nMethodsWe conducted a cross sectional study to assess the attitude of HCWs toward COVID-19 vaccination. Data was collected between October 7th and November 9th, 2020. We received 4080 responses out of which 3479 were complete responses and were included in final analysis.\n\nResults36% of respondents were willing to take the vaccine as soon as it became available while 56% were not sure or would wait to review more data. Vaccine acceptance increased with increasing age, education, and income level. Lower acceptance was noted in females (31%), Black (10%), Latinx (30%) and Conservative/Republican (21%) HCWs, and those working in a rural setting (26%). Direct medical care providers had higher vaccine acceptance (49%). Safety (69%), effectiveness (69%) and speed of development/approval (74%) were noted as the most common concerns regarding COVID-19 vaccination in our survey.\n\nConclusionImmediate acceptance of a COVID-19 vaccine is low, with the majority of HCWs choosing to wait to review more data before deciding on personal vaccination. Overall attitudes toward vaccination were positive but specific concerns regarding COVID-19 vaccine are prevalent. Differences in vaccine acceptance were noted between individual and group characteristics which should be addressed to avoid exacerbating health inequities.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Rahul Shekhar", - "author_inst": "University of New Mexico" - }, - { - "author_name": "Abu Baker Sheikh", - "author_inst": "University of New Mexico" - }, - { - "author_name": "Shubhra Upadhyay", - "author_inst": "University of New Mexico" - }, - { - "author_name": "Mriganka Singh", - "author_inst": "University Hospitals of School of Medicine Case Western University" - }, - { - "author_name": "Saket Kottewar", - "author_inst": "University of Texas Health San Antonio" - }, - { - "author_name": "Hamza Mir", - "author_inst": "University of New Mexico" - }, - { - "author_name": "Eileen Barrett", - "author_inst": "University of New Mexico" - }, - { - "author_name": "Suman Pal", - "author_inst": "University of New Mexico" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.01.02.21249119", "rel_title": "Spatial-temporal relationship between population mobility and COVID-19 outbreaks in South Carolina: A time series forecasting analysis", @@ -985879,6 +987242,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.01.01.20249069", + "rel_title": "Accuracy of the Veterans Health Administration COVID-19 (VACO) Index for predicting short-term mortality among 1,307 Yale New Haven Hospital inpatients and 427,224 Medicare patients", + "rel_date": "2021-01-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.01.20249069", + "rel_abs": "BackgroundThe Veterans Health Administration COVID-19 (VACO) Index incorporates age, sex, and pre-existing comorbidity diagnoses readily available in the electronic health record (EHR) to predict 30-day all-cause mortality in both inpatients and outpatients infected with SARS-CoV-2. We examined the performance of the Index using data from Yale New Haven Hospital (YNHH) and national Medicare data overall, over time, and within important patient subgroups.\n\nMethods and findingsWith measures and weights previously derived and validated in a national Veterans Healthcare Administration (VA) sample, we evaluated the accuracy of the VACO Index for estimating inpatient (YNHH) and both inpatient and outpatient mortality (Medicare) using area under the receiver operating characteristic curve (AUC) and comparisons of predicted versus observed mortality by decile (calibration plots). The VACO Index demonstrated similar discrimination and calibration in both settings, over time, and among important patient subgroups including women, Blacks, Hispanics, Asians, and Native Americans. In sensitivity analyses, we allowed component variables to be re-weighted in the validation datasets and found that weights were largely consistent with those determined in VA data. Supplementing the VACO Index with body mass index and race/ethnicity had no effect on discrimination.\n\nConclusionAmong COVID-19 positive individuals, the VACO Index accurately estimates risk of short-term mortality among a wide variety of patients. While it modestly over-estimates risk in recent intervals, the Index consistently identifies those at greatest relative risk. The VACO Index could identify individuals who should continue practicing social distancing, help determine who should be prioritized for vaccination, and among outpatients who test positive for SARS-CoV-2, indicate who should receive greater clinical attention or monoclonal antibodies.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Joseph T King Jr.", + "author_inst": "VA Connecticut Healthcare System & Yale School of Medicine" + }, + { + "author_name": "James S Yoon", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Zachary M Bredl", + "author_inst": "CareJourney" + }, + { + "author_name": "Joseph P Habboushe", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Graham A Walker", + "author_inst": "Kaiser Permanente" + }, + { + "author_name": "Christopher T Rentsch", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Janet P Tate", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Nitu M Kashyap", + "author_inst": "Yale New Haven Health" + }, + { + "author_name": "Richard C Hintz II", + "author_inst": "Yale Center for Clinical Investigation" + }, + { + "author_name": "Aneesh P Chopra", + "author_inst": "CareJourney" + }, + { + "author_name": "Amy C Justice", + "author_inst": "VA Connecticut Healthcare System & Yale School of Medicine" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.29.20248976", "rel_title": "Laboratory Biomarkers of COVID-19 Disease Severity and Outcome: Findings from a Developing Country", @@ -986963,33 +988385,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.01.02.424974", - "rel_title": "Rapid inactivation of SARS-CoV-2 on copper touch surfaces determined using a cell culture infectivity assay", - "rel_date": "2021-01-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.02.424974", - "rel_abs": "COVID-19, caused by SARS-CoV-2, was first reported in China in 2019 and has transmitted rapidly around the world, currently responsible for 83 million reported cases and over 1.8 million deaths. The mode of transmission is believed principally to be airborne exposure to respiratory droplets from symptomatic and asymptomatic patients but there is also a risk of the droplets contaminating fomites such as touch surfaces including door handles, stair rails etc, leading to hand pick up and transfer to eyes, nose and mouth. We have previously shown that human coronavirus 229E survives for more than 5 days on inanimate surfaces and another laboratory reproduced this for SARS-CoV-2 this year. However, we showed rapid inactivation of Hu-CoV-229E within 10 minutes on different copper surfaces while the other laboratory indicated this took 4 hours for SARS-CoV-2. So why the difference? We have repeated our work with SARS-CoV-2 and can confirm that this coronavirus can be inactivated on copper surfaces in as little as 1 minute. We discuss why the 4 hour result may be technically flawed.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "C William Keevil", - "author_inst": "University of Southampton" - }, - { - "author_name": "Catherine A Bryant", - "author_inst": "University of Southampton" - }, - { - "author_name": "Sandra A Wilks", - "author_inst": "University of Southampton" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.01.02.424917", "rel_title": "Alveolar type II cells harbouring SARS-CoV-2 show senescence with a proinflammatory phenotype", @@ -987633,6 +989028,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2020.12.28.20248926", + "rel_title": "Simulating the impacts of interregional mobility restriction on the spatial spread of COVID-19 in Japan", + "rel_date": "2021-01-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.28.20248926", + "rel_abs": "This study develops a spatial Susceptible-Exposed-Infectious-Recovered (SEIR) model that analyzes the effect of interregional mobility on the spatial spread of the coronavirus disease 2019 (COVID-19) outbreak in Japan. National and local governments have requested that residents refrain from traveling between 47 prefectures during the state of emergency. However, the extent to which restricting the interregional mobility prevents infection expansion has not been elucidated. Our spatial SEIR model describes the spatial spread pattern of COVID-19 when people commute to a prefecture where they work or study during the daytime and return to their residential prefecture at night. We assume that people are exposed to infection risk during their daytime activities. According to our simulation results, interregional mobility restriction can prevent geographical expansion of the infection. However, in prefectures with many infectious individuals, residents are exposed to higher infection risk when their mobility is restricted. Our simulation results also show that interregional mobility restriction plays a limited role in reducing the national total number of infected individuals.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Keisuke Kondo", + "author_inst": "Research Institute of Economy, Trade and Industry" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.12.28.20248922", "rel_title": "The Ugandan Severe Acute Respiratory Syndrome -Coronavirus 2 (SARS-CoV-2) Model: A Data Driven Approach to Estimate Risk", @@ -988365,69 +989779,6 @@ "type": "new results", "category": "systems biology" }, - { - "rel_doi": "10.1101/2020.12.30.424829", - "rel_title": "Process Development and Scale-up Optimization of the SARS-CoV-2 Receptor Binding Domain-Based Vaccine Candidate, RBD219-N1C1", - "rel_date": "2020-12-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.30.424829", - "rel_abs": "A SARS-CoV-2 RBD219-N1C1 (RBD219-N1C1) recombinant protein antigen formulated on Alhydrogel(R) has recently been shown to elicit a robust neutralizing antibody response against SARS-CoV-2 pseudovirus in mice. The antigen has been produced under current good manufacturing practices (cGMP) and is now in clinical testing. Here, we report on process development and scale-up optimization for upstream fermentation and downstream purification of the antigen. This includes production at the 1 and 5 L scale in the yeast, Pichia pastoris, and the comparison of three different chromatographic purification methods. This culminated in the selection of a process to produce RBD219-N1C1 with a yield of >400 mg per liter of fermentation with >92% purity and >39% target product recovery after purification. In addition, we show the results from analytical studies, including SEC-HPLC, DLS, and an ACE2 receptor binding assay that were performed to characterize the purified proteins to select the best purification process. Finally, we propose an optimized upstream fermentation and downstream purification process that generates quality RBD219-N1C1 protein antigen and is fully scalable at a low cost.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Jungsoon Lee", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Zhuyun Liu", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Wen-Hsiang Chen", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Junfei Wei", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Rakhi Kundu", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Rakesh Adhikari", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Joanne Altieri Rivera", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Portia M Gillespie", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Ulrich Strych", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Bin Zhan", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Peter J Hotez", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Maria Elena Bottazzi", - "author_inst": "Baylor College of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.12.23.20248783", "rel_title": "Development of a Multivariable Model for COVID-19 Risk Stratification Based on Gradient Boosting Decision Trees", @@ -989118,6 +990469,157 @@ "type": "new results", "category": "genetics" }, + { + "rel_doi": "10.1101/2020.12.29.424711", + "rel_title": "Deep mining of early antibody response in COVID-19 patients yields potent neutralisers and reveals high level of convergence", + "rel_date": "2020-12-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.29.424711", + "rel_abs": "Passive immunisation using monoclonal antibodies will play a vital role in the fight against COVID-19. Until now, the majority of anti-SARS-CoV-2 antibody discovery efforts have relied on screening B cells of patients in the convalescent phase. Here, we describe deep-mining of the antibody repertoires of hospitalised COVID-19 patients using a combination of phage display technology and B cell receptor (BCR) repertoire sequencing to isolate neutralising antibodies and gain insights into the early antibody response. This comprehensive discovery approach has yielded potent neutralising antibodies with distinct mechanisms of action, including the identification of a novel non-ACE2 receptor blocking antibody that is not expected to be affected by any of the major viral variants reported. The study highlighted the presence of potent neutralising antibodies with near germline sequences within both the IgG and IgM pools at early stages of infection. Furthermore, we highlight a highly convergent antibody response with the same sequences occurring both within this study group and also within the responses described in previously published anti-SARS-CoV-2 studies.", + "rel_num_authors": 34, + "rel_authors": [ + { + "author_name": "Georgia Bullen", + "author_inst": "IONTAS Ltd." + }, + { + "author_name": "Jacob D Galson", + "author_inst": "Alchemab Therapeutics Ltd." + }, + { + "author_name": "Pedro Villar", + "author_inst": "IONTAS Ltd." + }, + { + "author_name": "Lien Moreels", + "author_inst": "IONTAS Ltd." + }, + { + "author_name": "Line Ledsgaard", + "author_inst": "IONTAS Ltd." + }, + { + "author_name": "Giada Mattiuzzo", + "author_inst": "National Institute for Biological Standards and Control" + }, + { + "author_name": "Gareth Hall", + "author_inst": "University of Leicester" + }, + { + "author_name": "Emma M Bentley", + "author_inst": "National Institute for Biological Standards and Control" + }, + { + "author_name": "Edward W Masters", + "author_inst": "IONTAS Ltd." + }, + { + "author_name": "David Tang", + "author_inst": "LifeArc" + }, + { + "author_name": "Sophie Millett", + "author_inst": "LifeArc" + }, + { + "author_name": "Danielle Tongue", + "author_inst": "LifeArc" + }, + { + "author_name": "Richard Brown", + "author_inst": "LifeArc" + }, + { + "author_name": "Ioannis Diamantopoulos", + "author_inst": "IONTAS Ltd." + }, + { + "author_name": "Kothai Parthiban", + "author_inst": "IONTAS Ltd." + }, + { + "author_name": "Claire Tebbutt", + "author_inst": "IONTAS Ltd." + }, + { + "author_name": "Rachael Leah", + "author_inst": "IONTAS Ltd." + }, + { + "author_name": "Krishna Chaitanya", + "author_inst": "IONTAS Ltd." + }, + { + "author_name": "Deividas Pazeraitis", + "author_inst": "IONTAS Ltd." + }, + { + "author_name": "Sachin B Surade", + "author_inst": "IONTAS Ltd." + }, + { + "author_name": "Omodele Ashiru", + "author_inst": "Abcam" + }, + { + "author_name": "Lucia Crippa", + "author_inst": "Abcam" + }, + { + "author_name": "Richard Cowan", + "author_inst": "University of Leicester" + }, + { + "author_name": "Matthew W Bowler", + "author_inst": "European Molecular Biology Laboratory" + }, + { + "author_name": "Jamie I Campbell", + "author_inst": "Abcam" + }, + { + "author_name": "Wing-Yiu Jason Lee", + "author_inst": "Queen Mary University of London" + }, + { + "author_name": "Mark D Carr", + "author_inst": "University of Leicester" + }, + { + "author_name": "David Matthews", + "author_inst": "LifeArc" + }, + { + "author_name": "Paul Pfeffer", + "author_inst": "Queen Mary University of London" + }, + { + "author_name": "Simon E Hufton", + "author_inst": "National Institute for Biological Standards and Control" + }, + { + "author_name": "Kovilen Sawmynaden", + "author_inst": "LifeArc" + }, + { + "author_name": "Jane Osbourn", + "author_inst": "Alchemab Therapeutics Ltd." + }, + { + "author_name": "John McCafferty", + "author_inst": "IONTAS Ltd." + }, + { + "author_name": "Aneesh Karatt-Vellatt", + "author_inst": "IONTAS Ltd." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.12.29.424644", "rel_title": "Defective NETs Clearance contributes to sustained FXII Activation in COVID-19-associated Pulmonary Thrombo-Inflammation", @@ -990046,33 +991548,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.21.20248690", - "rel_title": "Can age-distribution be an indicator of the goodness of COVID-19 testing?", - "rel_date": "2020-12-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.21.20248690", - "rel_abs": "It has been evident that the faster, more accurate, and more comprehensive testing can help policymakers assess the real impact of COVID-19 and help them with when and how strict the mitigation policies should be. Nevertheless, the exact number of infected ones could not be measured due to the lack of comprehensive testing. In this paper, first of all, we will investigate the relation of transmission of COVID-19 with age by observing timed data in multiple countries. Then, we compare the COVID-19 CFR with the age-demography data. and as a result, we have proposed a method for estimating a lower bound for the number of positive cases by using the reported data on the oldest age group and the regions population age-distributions. The proposed estimation method improved the expected similarity between the age-distribution of positive cases and regions populations. Thus, using the publicly accessible data for several developed countries, we show how the improvement of testing over the course of several months has made it clear for the community that different age groups are equally prone to becoming COVID positive. The result shows that the age demography of COVID-19 gets similar to the age-demography of the population, together with the reduction of CFR over time. In addition, countries with less CFR have more similar COVID-19s age-distribution, which is caused by more comprehensive testing, than ones who have higher CFR. This leads us to a better estimation for positive cases in different testing strategies. Having knowledge of this fact helps policymakers enforce more effective policies for controlling the spread of the virus.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Amirhoshang Hoseinpour Dehkordi", - "author_inst": "Institute for Research in Fundamental Sciences" - }, - { - "author_name": "Reza Nemati", - "author_inst": "Biogen, Cambridge, MA, USA" - }, - { - "author_name": "Pouya Tavousi", - "author_inst": "UConn Tech Park, University of Connecticut, Storrs, CT, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.26.424449", "rel_title": "MHC-II constrains the natural neutralizing antibody response to the SARS-CoV-2 spike RBM in humans", @@ -990743,6 +992218,25 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.12.23.424267", + "rel_title": "SARS-CoV-2 mutations among minks show reduced lethality and infectivity to humans", + "rel_date": "2020-12-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.23.424267", + "rel_abs": "SARS-CoV-2 infection in minks has become a serious problem, as the virus may mutate and reinfect humans; some countries have decided to cull minks. Here, the virus sequencing data in minks were analysed and compared to those of human-virus. Although the mink-virus maintained the characteristics of human-virus, some variants rapidly mutated, adapting to minks. Some mink-derived variants infected humans, which accounted for 40% of the total SARS-CoV-2 cases in the Netherlands. These variants appear to be less lethal and infective compared to those in humans. Variants that have mutated further among minks were not found in humans. Such mink-viruses might be suitable for vaccination for humans, such as in the case of the smallpox virus, which is less infective and toxic to humans.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Tomokazu Konishi", + "author_inst": "Akita Prefectural University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.12.26.424450", "rel_title": "The mechanism of SARS-CoV-2 nucleocapsid protein recognition by the human 14-3-3 proteins", @@ -991867,45 +993361,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.12.25.424008", - "rel_title": "Differential Dynamic Behavior of Prefusion Spike Proteins of SARS Coronaviruses 1 and 2", - "rel_date": "2020-12-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.25.424008", - "rel_abs": "The coronavirus spike protein, which binds to the same human receptor in both SARS-CoV-1 and 2, has been implied to be a potential source of their differential transmissibility. However, the mechanistic details of spike protein binding to its human receptor remain elusive at the molecular level. Here, we have used an extensive set of unbiased and biased microsecond-level all-atom molecular dynamics (MD) simulations of SARS-CoV-1 and 2 spike proteins to determine the differential dynamic behavior of prefusion spike protein structure in the two viruses. Our results indicate that the active form of the SARS-CoV-2 spike protein is more stable than that of SARS-CoV-1 and the energy barrier associated with the activation is higher in SARS-CoV-2. Our results also suggest that not only the receptor binding domain (RBD) but also other domains such as the N-terminal domain (NTD) could play a role in the differential binding behavior of SARS-CoV-1 and 2 spike proteins.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Vivek Govind Kumar", - "author_inst": "University of Arkansas" - }, - { - "author_name": "Dylan S Ogden", - "author_inst": "University of Arkansas" - }, - { - "author_name": "Ugochi Isu", - "author_inst": "University of Arkansas" - }, - { - "author_name": "Adithya Polasa", - "author_inst": "University of Arkansas" - }, - { - "author_name": "James Losey", - "author_inst": "University of Arkansas" - }, - { - "author_name": "Mahmoud Moradi", - "author_inst": "University of Arkansas" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2020.12.24.424326", "rel_title": "Influence of HLA class II polymorphism on predicted cellular immunity against SARS-CoV-2 at the population and individual level", @@ -992521,6 +993976,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.12.22.20248259", + "rel_title": "Understanding Covid-19 misinformation and vaccine hesitancy in context: Findings from a qualitative study involving citizens in Bradford, UK", + "rel_date": "2020-12-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.22.20248259", + "rel_abs": "BackgroundCovid-19 vaccines can offer a route out of the pandemic, yet initial research suggests that many are unwilling to be vaccinated. A rise in the spread of misinformation is thought to have played a significant role in this vaccine hesitancy. In order to maximise vaccine uptake it is important to understand why misinformation has been able to take hold at this time and why it may pose a more significant problem within certain populations and places.\n\nObjectiveTo understand peoples Covid-19 beliefs, their interactions with health (mis)information during Covid-19 and attitudes towards a Covid-19 vaccine.\n\nDesign and participantsIn-depth phone interviews were carried out with 20 people from different ethnic groups and areas of Bradford during Autumn 2020. Reflexive thematic analysis was conducted.\n\nResultsParticipants spoke about a wide range of emotive misinformation they had encountered regarding Covid-19, resulting in confusion, distress and mistrust. Vaccine hesitancy could be attributed to three prominent factors: safety concerns, negative stories and personal knowledge. The more confused, distressed and mistrusting participants felt about their social worlds during the pandemic, the less positive they were about a vaccine.\n\nConclusionsCovid-19 vaccine hesitancy needs to be understood in the context of the relationship between the spread of misinformation and associated emotional reactions. Vaccine programmes should provide a focused, localised and empathetic response to counter misinformation.\n\nPatient or public contributionA rapid community and stakeholder engagement process was undertaken to identify Covid-19 related priority topics important to both Bradford citizens and local decision makers.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Bridget Lockyer", + "author_inst": "Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust" + }, + { + "author_name": "Shahid Islam", + "author_inst": "Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust" + }, + { + "author_name": "Aamnah Rahman", + "author_inst": "Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust" + }, + { + "author_name": "Josie Dickerson", + "author_inst": "Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust" + }, + { + "author_name": "Kate Pickett", + "author_inst": "Department of Health Sciences, University of York" + }, + { + "author_name": "Trevor Sheldon", + "author_inst": "Institute of Population Health Sciences, Queen Mary University London" + }, + { + "author_name": "John Wright", + "author_inst": "Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust" + }, + { + "author_name": "Rosemary McEachan", + "author_inst": "Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust" + }, + { + "author_name": "Laura Sheard", + "author_inst": "Department of Health Sciences, University of York" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.12.24.20248519", "rel_title": "Mental health, personality and lifetime psychedelic use during the COVID-19 pandemic", @@ -993649,33 +995155,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2020.12.22.20248614", - "rel_title": "Real-world clinical performance of commercial SARS-CoV-2 rapid antigen tests in suspected COVID-19: A systematic meta-analysis of available data as per November 20, 2020", - "rel_date": "2020-12-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.22.20248614", - "rel_abs": "BackgroundImmunochromatographic rapid antigen tests (RATs) emerged onto the COVID-19 pandemic testing landscape to aid in the rapid diagnosis of people with suspected SARS-CoV-2 infection. RATs are particularly useful where RT-PCR is not immediately available and symptoms suggestive of a high viral load and infectiousness are assumed. Several lateral flow immunoassays have been authorized for use under EUA and/or the CE mark, presenting varying overall clinical performance data generated by the manufacturer or by independent investigators. To compare the real-world clinical performance of commercially available rapid chromatographic immunoassays intended for the qualitative detection of SARS-CoV-2, we performed a systematic meta-analysis of published data.\n\nMethodsWe searched the MEDLINE(R), Embase, BIOSIS and Derwent Drug File (ProQuest)for manufacturer-independent prospective clinical performance studies comparing SARS-CoV-2 RATs and RT-PCR assays. Only studies on lateral flow assays not needing a separate reader for retrieving the result were included, if data were available on viral load, patients symptom status, sample type, and PCR assay used. For better data comparability, recalculation of the studies single performance data confidence intervals using the exact Clopper-Pearson method was applied.\n\nResultsWe could include 19 studies (ten peer-reviewed) presenting detailed clinical performance data on 11,209 samples with 2449 RT-PCR-positives out of study prevalence rates between 1.9-100 % and between 50- 100% symptomatic samples. Four studies directly compared two to three different RATs and 15 studies compared one RAT to RT-PCR. Overall specificity ranged, with one test outlier, between 92.4% (87.4- 95.9) and 100% (99.7-100), and overall clinical sensitivity varied between 28.9% (16.4-44.3) and 98.3% (91.1-99.7), depending on assay, population characteristics, viral load, and symptom status. Sensitivity in high-viral-load samples (cycle threshold [≤]25) showed a considerable heterogeneity among the assays ranging from 66.7% to 100%.\n\nConclusionOnly two RATs offered sufficient manufacturer-independent, real-world performance data supporting use for the detection of current SARS-CoV-2 infection in symptomatic or high-viral-load patient populations. Reliable positive predictive values require testing of symptomatic patients or asymptomatic individuals only in case of a high pre-test probability. If RATs are used for screening of asymptomatic cases in low-prevalence scenarios, a lower positive predictive value of the result has to be considered.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Johannes Hayer", - "author_inst": "Roche Diagnostics GmbH" - }, - { - "author_name": "Dusanka Kasapic", - "author_inst": "Roche Diagnostics International Ltd" - }, - { - "author_name": "Claudia Silke Zemmrich", - "author_inst": "Institure for Pharmacology and Preventive Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.22.20244061", "rel_title": "Predicting the Evolution of COVID-19 Mortality Risk: a Recurrent Neural Network Approach", @@ -994447,6 +995926,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.12.22.20248379", + "rel_title": "Psychiatric morbidities and Coping strategies in patients with different Coronavirus disease-2019 severities and chronic medical diseases: A multicenter cross-sectional study", + "rel_date": "2020-12-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.22.20248379", + "rel_abs": "COVID-19 patients, especially those with chronic medical illnesses (CMI), may use different coping strategies, to reduce their psychological distress while facing the COVID-19 infection. The aim was to compare anxiety, depression and coping styles between patients infected with COVID-19 disease with and without CMI during the peak of COVID-19 disease in Egypt. This is a cross sectional study, that included an online survey consisting of Arabic versions of General Health Questionnaire-12, Taylor Manifest Anxiety Scale (TMAS), Beck Depression Inventory (BDI) and Brief-COPE scale. Questionnaires were distributed to adult patients with a confirmed diagnosis of SARS-CoV-2 virus infection during their quarantine in Egypt. One hundred ninety-nine patients responded to the survey, where 46.73% of them had CMI. Religion, emotional support, use of informational support and acceptance were the most used coping strategies by participants. Avoidant coping strategies were frequently used by divorced patients, home quarantined individuals, patients who developed COVID-19 related anxiety/depression and patients who didnt receive hydroxyl-chloroquine. Approach strategies were frequently used by patients with mild COVID-19. Understanding the used coping strategies has implications for how individuals might be helped to manage their illness during the current presentation and intervene with development of serious long-term mental health conditions.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "hend Ibrahim Shousha", + "author_inst": "Endemic medicine department, Faculty of Medicine, Cairo University, Cairo, Egypt" + }, + { + "author_name": "Nagwan Madbouly", + "author_inst": "Psychiatry Department, Faculty of Medicine, Cairo University, Cairo, Egypt" + }, + { + "author_name": "Shimaa Afify", + "author_inst": "National Hepatology and Tropical Medicine Research Institute, Cairo, Egypt" + }, + { + "author_name": "Noha Asem", + "author_inst": "The Public Health Department, Faculty of Medicine, Cairo University, Cairo, Egypt" + }, + { + "author_name": "Rabab Maher", + "author_inst": "Students Hospital, Cairo University, Cairo, Egypt" + }, + { + "author_name": "suaad Moussa", + "author_inst": "Psychiatry Department, Faculty of Medicine, Cairo University, Cairo, Egypt" + }, + { + "author_name": "Amr Abdalazeem", + "author_inst": "Endemic Medicine Department, Faculty of Medicine, Helwan University, Cairo, Egypt" + }, + { + "author_name": "Eslam Nageb", + "author_inst": "15 Mayo Smart Hospital, Ministry of Health And Population, Cairo, Egypt" + }, + { + "author_name": "Khaled harhira", + "author_inst": "15 Mayo Smart Hospital, Ministry of Health And Population, Cairo, Egypt" + }, + { + "author_name": "Hazem Elmorsy", + "author_inst": "15 Mayo Smart Hospital, Ministry of Health And Population, Cairo, Egypt" + }, + { + "author_name": "Hassan Elgarem", + "author_inst": "Endemic medicine department, Faculty of Medicine, Cairo University, Cairo, Egypt" + }, + { + "author_name": "Dalia Omran", + "author_inst": "Endemic Medicine Department, Faculty of Medicine, Cairo University, Cairo, Egypt" + }, + { + "author_name": "mohamed hassany", + "author_inst": "National Hepatology & Tropical Medicine Research Institute, Cairo, Egypt" + }, + { + "author_name": "Basem elsayed", + "author_inst": "National Hepatology & Tropical Medicine Research Institute, Cairo, Egypt" + }, + { + "author_name": "Mohamed El kassas", + "author_inst": "Endemic medicine department, Faculty of Medicine, Helwan University, Helwan, Egypt" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.12.23.20248794", "rel_title": "How the COVID-19 pandemic affects transgender health care in upper-middle income and high income countries - A worldwide, cross-sectional survey", @@ -995215,29 +996769,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.22.20248752", - "rel_title": "On an optimal testing strategy for workplace settings operating during the COVID-19 pandemic", - "rel_date": "2020-12-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.22.20248752", - "rel_abs": "High quality daily testing for the presence of the SARS-CoV-2 in workplace settings has become part of the standard and mandatory protection measures implemented widely in response to the current pandemic. Such tests are often limited to a small fraction of the attending personnel due to cost considerations, limited availability and processing capabilities and the often cumbersome requirements of the test itself. A maximally efficient use of such an important and frequently scarce resource is clearly required. We here present an optimal testing strategy which minimises the presence of pre-symptomatic and asymptomatic members of the population, derived under a series of simplifying assumptions, which however retain many of the generalities of the problem and yield robust results, as verified through a number of numerical simulations. We show that reduction in overall infected-person-days, IPD, by significant percentages can be achieved, for fixed numbers of tests per day of 5% and 10% of the population, of 30% and 50% in the IPD numbers, respectively.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Xavier Hernandez", - "author_inst": "UNAM" - }, - { - "author_name": "Sergio Valentinotti", - "author_inst": "Laboratorios Liomont S.A. de C.V. Mexico City, Mexico." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.22.20248719", "rel_title": "\"There's No Place Like Home for The Holidays:\" Travel and SARS-CoV-2 Test Positivity Following Thanksgiving Weekend", @@ -996000,6 +997531,85 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.12.22.424069", + "rel_title": "Discovery of Cyclic Peptide Ligands to the SARS-CoV-2 Spike Protein using mRNA Display", + "rel_date": "2020-12-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.22.424069", + "rel_abs": "The COVID-19 pandemic, caused by SARS-CoV-2, has led to substantial morbidity, mortality and disruption globally. Cellular entry of SARS-CoV-2 is mediated by the viral spike protein and affinity ligands to this surface protein have the potential for applications as antivirals and diagnostic reagents. Here, we describe the affinity selection of cyclic peptide ligands to the SARS-CoV-2 spike protein receptor binding domain (RBD) from three distinct libraries (in excess of a trillion molecules each) by mRNA display. We identified six high affinity molecules with dissociation constants (KD) in the nanomolar range (15-550 nM) to the RBD. The highest affinity ligand could be used as an affinity reagent to detect spike protein in solution by ELISA, and the co-crystal structure of this molecule bound to the RBD demonstrated that it binds to a cryptic binding site, displacing a {beta}-strand near the C-terminus. Our findings provide key mechanistic insight into the binding of peptide ligands to the SARS-CoV-2 spike RBD and the ligands discovered in this work may find future use as reagents for diagnostic applications.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Alexander Norman", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Charlotte Franck", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Mary Christie", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Paige Hawkins", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Karishma Patel", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Anneliese Ashhurst", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Anupriya Aggarwal", + "author_inst": "Kirby Institute" + }, + { + "author_name": "Jason KK Low", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Rezwan Siddiquee", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Caroline Ashley", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Megan Steain", + "author_inst": "The University of Sydney" + }, + { + "author_name": "James A Triccas", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Stuart Grant Turville", + "author_inst": "Kirby Institute" + }, + { + "author_name": "Joel Mackay", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Toby Passioura", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Richard J Payne", + "author_inst": "The University of Sydney" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.12.22.423909", "rel_title": "Platycodin D prevents both lysosome- and TMPRSS2-driven SARS-CoV-2 infection in vitro by hindering membrane fusion", @@ -997160,41 +998770,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.22.20248714", - "rel_title": "Is Fear of COVID-19 Higher among Food-Insecure Households? A Model-Based Study, Mediated by Perceived Stress among Iranian Populations", - "rel_date": "2020-12-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.22.20248714", - "rel_abs": "The COVID-19 pandemic is a crisis accompanied with multiple psychological consequences. This cross-sectional study, conducted on 2871 Iranians, examines how food insecurity may be associated with fear of COVID-19. Household Food Insecurity Access Scale, COVID-19 fear scale, Cohens Perceived Stress Scale, and Perceived Social Support Questionnaire were used in gathering data. Data analysis was done using SPSS 22 and Amos 22. The results showed that food insecurity has significantly positive direct and indirect (mediated by perceived stress) correlations with fear of COVID-19 (P<0.05). It was also shown that perceived social support could negatively affect fear of COVID-19, through food insecurity or perceived stress (P<0.05). Among women, the presence of a child under 5 had a significant direct impact on fear of COVID-19 (P<0.05). The crisis caused by COVID-19 highlights the need for increasing social resilience through developing and implementing appropriate food security strategies.\n\nO_TEXTBOXStatement of Relevance\n\nThe COVID-19 pandemic is accompanied with multiple psychological consequences (including the fear of COVID-19), and threatens the food security status of millions of people. In order to assess the food insecurity impact on fear of COVID-19, the present study was conducted on Iranian adults. The proposed model, constructed by structural equation modeling, indicated the direct and indirect effects of food insecurity on fear of COVID-19. It was also shown that perceived social support could affect the fear of COVID-19 through food insecurity or perceived stress. It is concluded that food insecurity imposes further mental burdens during the pandemic, and policymakers should strengthen social resilience against its inter-related health consequences.\n\nC_TEXTBOX", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Neda Ezzeddin", - "author_inst": "Department of Community Nutrition, Faculty of Nutrition Sciences and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran" - }, - { - "author_name": "Hassan Eini-Zinab", - "author_inst": "Department of Community Nutrition, National Nutrition and Food Technology Research Institute; and Faculty of Nutrition Sciences and Food Technology, Shahid Behe" - }, - { - "author_name": "Naser Kalantari", - "author_inst": "Department of Community Nutrition, National Nutrition and Food Technology Research Institute; and Faculty of Nutrition Sciences and Food Technology, Shahid Behe" - }, - { - "author_name": "Mohammad Ahmadi", - "author_inst": "Department of Community Nutrition, Faculty of Nutrition Sciences and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran" - }, - { - "author_name": "Zeinab Beheshti", - "author_inst": "Department of Community Nutrition, Faculty of Nutrition Sciences and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "nutrition" - }, { "rel_doi": "10.1101/2020.12.18.20248255", "rel_title": "Modeling effectiveness of testing strategies to prevent COVID-19 in nursing homes--United States, 2020", @@ -997998,6 +999573,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.20.20240507", + "rel_title": "COVID-19 (Coronavirus Disease) Outbreak Prediction Using a Susceptible-Exposed-Symptomatic Infected-Recovered-Super Spreaders-Asymptomatic Infected-Deceased-Critical (SEIR-PADC) Dynamic Model", + "rel_date": "2020-12-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.20.20240507", + "rel_abs": "Extension of SIR type models has been reported in a number of publications in mathematics community. But little is done on validation of these models to fit adequately with multiple clinical data of an infectious disease. In this paper, we introduce SEIR-PAD model to assess susceptible, exposed, infected, recovered, super-spreader, asymptomatic infected, and deceased populations. SEIR-PAD model consists of 7-set of ordinary differential equations with 8 unknown coefficients which are solved numerically in MATLAB using an optimization algorithm to fit 4-set of COVID-19 clinical data consist of cumulative populations of infected, deceased, recovered, and susceptible. Trends of COVID-19 in Trends in Gulf Cooperation Council (GCC) countries are successfully predicted using available data from outbreak until 23rd June 2020. Promising results of SEIR-PAD model provide insight into better management of COVID-19 pandemic in GCC countries.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Ahmad Sedaghat", + "author_inst": "School of Engineering Australian College of Kuwait Safat 13015, Kuwait" + }, + { + "author_name": "Amir MOSAVI", + "author_inst": "Obuda University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.21.20248610", "rel_title": "Population risk factors for severe disease and mortality in COVID-19: A global systematic review and meta-analysis", @@ -998738,33 +1000336,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.19.20248571", - "rel_title": "COVID-19 PANDEMICS: HOW FAR ARE WE FROM HERD IMMUNITY?", - "rel_date": "2020-12-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.19.20248571", - "rel_abs": "Objectivesto estimate the current number of total infections in a region in order to measure the progress of the epidemic with the purpose of reopening activities and planning the deployment of vaccines.\n\nStudy designWe recovered estimates of the basic reproductive number (R0) and the Infection Fatality Risk (IFR) as well as the number of confirmed cases and deaths in several countries.\n\nMethodsthis works presents an expression to estimate the number of remaining susceptible in a population using the observed number of SARS-CoV-2 related deaths and current estimates of R0 and IFR.\n\nResultsthe epidemic will infect most of the population causing 2.5 deaths per thousand inhabitants on average, and herd immunity will be achieved when the number of deaths per thousand inhabitants is close to two. This work introduces an expression to provide estimates of the number of remaining susceptible in a region using the reported number of deaths.\n\nConclusionsany region with fewer than 2.5 deaths per thousand individuals will continue accumulating deaths until this average is achieved, and the infection rate will exceed the removal rate until the number of deaths is about two deaths per thousand, when herd immunity is reached. Waves may occur in any region where the number of deaths is below the herd immunity level.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "CARLOS M HERNANDEZ-SUAREZ", - "author_inst": "UNIVERSIDAD DE COLIMA" - }, - { - "author_name": "EFREN MURILLO-ZAMORA", - "author_inst": "IMSS" - }, - { - "author_name": "FRANCISCO ESPINOZA-GOMEZ", - "author_inst": "UNIVERSIDAD DE COLIMA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.21.20248586", "rel_title": "Routine SARS-CoV-2 wastewater surveillance results in Turkey to follow Covid-19 outbreak", @@ -999296,6 +1000867,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.12.18.20248511", + "rel_title": "SARS-CoV-2 infections among personnel providing home care services for the elderly in Stockholm, Sweden", + "rel_date": "2020-12-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.18.20248511", + "rel_abs": "BackgroundIn March 2020, Stockholm, Sweden was hit by a severe outbreak of SARS-CoV-2. Four weeks later, a systematic study of testing for past or present infections among healthcare workers in the region was launched. Only a minority of COVID-19 related deaths occurred at hospitals and the study was therefore extended to employees in companies providing home care services for the elderly.\n\nMethodsFive companies offered participation to 438 employees at work and 405 employees (92.5%) were enrolled. Serum samples were analyzed for IgG to SARS-CoV-2 and throat swabs were tested by for the SARS-CoV-2 virus by PCR.\n\nResultsAmong home care employees, 20.1% (81/403) were seropositive, about twice as many as in a simultaneously enrolled reference population (healthcare workers entirely without patient contact, n=3,671; 9.7% seropositivity). Only 13/379 employees (3.4%) had evidence of a current infection (PCR positivity). Among these, 5 were also seropositive (a sign of past infection or lingering infection after symptoms have resolved) and 3 were positive with only low amounts of virus. The combination of high amounts of virus and no antibodies, a characteristic for pre-symptomatic COVID-19, was thus present only in 5 employees (1.3%).\n\nConclusionsPersonnel providing home service for the elderly appear to be a risk group for SARS-CoV-2 infection. Employees likely to be pre-symptomatic for COVID-19 can be readily identified by screening. Increased attention for protection of employees as well as of the elderly they serve is warranted.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Sadaf Sakina Hassan", + "author_inst": "Karolinska Insitutet" + }, + { + "author_name": "Asa Seigerud", + "author_inst": "Roo Hemtjanst" + }, + { + "author_name": "Laila Sara Arroyo Muhr", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Sara Nordqvist-Kleppe", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Elisa Pin", + "author_inst": "Science for Life Laboratory" + }, + { + "author_name": "Anna Manberg", + "author_inst": "Science for Life Laboratory" + }, + { + "author_name": "Sophia Hober", + "author_inst": "KTH Royal Institute of Technology" + }, + { + "author_name": "Peter Nilsson", + "author_inst": "Science for Life Laboratory" + }, + { + "author_name": "Lars Engstrand", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Miriam Elfstrom", + "author_inst": "Karolinska University Hospital" + }, + { + "author_name": "Jonas Blomqvist", + "author_inst": "Karolinska University Hospital" + }, + { + "author_name": "Kalle Conneryd-Lundgren", + "author_inst": "Karolinska University Hospital" + }, + { + "author_name": "Joakim Dillner", + "author_inst": "Karolinska Institutet" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.12.22.423922", "rel_title": "Active learning tools improve the learning outcomes, scientific attitude and critical thinking in higher education: Experiences in an online course during the COVID-19 pandemic", @@ -1000512,113 +1002150,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.21.20248475", - "rel_title": "Clinical outcomes and risk factors for COVID-19 among migrant populations in high-income countries: a systematic review", - "rel_date": "2020-12-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.21.20248475", - "rel_abs": "BackgroundMigrants, including refugees, asylum seekers, labour migrants, and undocumented migrants, now constitute a considerable proportion of most high-income countries populations, including their skilled and unskilled workforces. Migrants may be at increased risk of COVID-19 due to their health and social circumstances, yet the extent to which they are being affected and their predisposing risk factors are not clearly understood. We did a systematic review to assess clinical outcomes of COVID-19 in migrant populations (cases, hospitalisations, deaths), indirect health and social impacts, and to determine key risk factors.\n\nMethodsWe did a systematic review following PRISMA guidelines, registered with PROSPERO (CRD42020222135). We searched databases including PubMed, Global Health, Scopus, CINAHL, and pre-print databases (medRxiv) via the WHO Global Research on COVID-19 database to Nov 18, 2020 for peer-reviewed and grey literature pertaining to migrants (defined as foreign born) and COVID-19 in 82 high-income countries. We used our international networks to source national datasets and grey literature. Data were extracted on our primary outcomes (cases, hospitalisations, deaths) and we evaluated secondary outcomes on indirect health and social impacts, and risk factors, using narrative synthesis.\n\nResults3016 data sources were screened with 158 from 15 countries included in the analysis (35 data sources for primary outcomes: cases [21], hospitalisations [4]; deaths [15]; 123 for secondary outcomes). We found that migrants are at increased risk of infection and are disproportionately represented among COVID-19 cases. Available datasets suggest a similarly disproportionate representation of migrants in reported COVID-19 deaths, as well as increased all-cause mortality in migrants in some countries in 2020. Undocumented migrants, migrant health and care workers, and migrants housed in camps and labour compounds may have been especially affected. In general, migrants have higher levels of many risk factors and vulnerabilities relevant to COVID-19, including increased exposure to SARS-CoV-2 due to high-risk occupations and overcrowded accommodation, and barriers to health care including inadequate information, language barriers, and reduced entitlement to healthcare coverage related to their immigration status.\n\nConclusionsMigrants in high-income countries are at high risk of exposure to, and infection with, COVID-19. These data are of immediate relevance to national public health responses to the pandemic and should inform policymaking on strategies for reducing transmission of COVID-19 in this population. Robust data on testing uptake and clinical outcomes in migrants, and barriers and facilitators to COVID-19 vaccination, are urgently needed, alongside strengthening engagement with diverse migrant groups.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Sally E Hayward", - "author_inst": "Institute for Infection and Immunity, St George's University of London; Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Anna Deal", - "author_inst": "Institute for Infection and Immunity, St George's University of London; Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Cherie Cheng", - "author_inst": "Institute for Infection and Immunity, St George's University of London" - }, - { - "author_name": "Alison F Crawshaw", - "author_inst": "Institute for Infection and Immunity, St George's University of London" - }, - { - "author_name": "Miriam Orcutt", - "author_inst": "Institute for Global Health, University College London" - }, - { - "author_name": "Tushna F Vandrevala", - "author_inst": "Faculty of Business and Social Sciences, Kingston University" - }, - { - "author_name": "Marrie Norredam", - "author_inst": "Danish Research Centre for Migration, Ethnicity and Health, University of Copenhagen" - }, - { - "author_name": "Manuel Carballo", - "author_inst": "International Centre for Migration, Health, and Development" - }, - { - "author_name": "Yusuf Ciftci", - "author_inst": "Doctors of the World UK" - }, - { - "author_name": "Ana Requena-Mendez", - "author_inst": "Department of Medicine-Solna, Karolinska Institutet; and Barcelona Institute for Global Health (ISGlobal-University of Barcelona)" - }, - { - "author_name": "Chris Greenaway", - "author_inst": "Department of Medicine, McGill University" - }, - { - "author_name": "Jessica Carter", - "author_inst": "Institute for Infection and Immunity, St George's University of London" - }, - { - "author_name": "Felicity Knights", - "author_inst": "Institute for Infection and Immunity, St George's University of London" - }, - { - "author_name": "Anushka Mehrotra", - "author_inst": "Institute for Infection and Immunity, St George's University of London" - }, - { - "author_name": "Farah Seedat", - "author_inst": "Public Health England" - }, - { - "author_name": "Kayvan Bozorgmehr", - "author_inst": "Public Health, Bielefeld University; Section for Health Equity Studies & Migration, Heidelberg University Hospital" - }, - { - "author_name": "Apostolos Veizis", - "author_inst": "Medecins Sans Frontieres Greece" - }, - { - "author_name": "Ines Campos-Matos", - "author_inst": "Public Health England; and UCL Collaborative Centre for Inclusion Health" - }, - { - "author_name": "Fatima Wurie", - "author_inst": "Public Health England; and UCL Research Department of Epidemiology and Public Health" - }, - { - "author_name": "Teymur Noori", - "author_inst": "European Centre for Disease Prevention and Control (ECDC)" - }, - { - "author_name": "Martin McKee", - "author_inst": "Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Bernadette Kumar", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Sally Hargreaves", - "author_inst": "Institute for Infection and Immunity, St George's University of London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.21.20248328", "rel_title": "The first wave of the Spanish COVID-19 epidemic was associated with early introductions and fast spread of a dominating genetic variant", @@ -1001522,6 +1003053,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.18.20248512", + "rel_title": "A Working Model to Inform Risk-Based Back to Work Strategies", + "rel_date": "2020-12-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.18.20248512", + "rel_abs": "BackgroundThe coronavirus disease 2019 (COVID-19) pandemic has forced many businesses to close or move to remote work to reduce the potential spread of disease. Employers desiring a return to onsite work want to understand their risk for having an infected employee on site and how best to mitigate this risk. Here, we modelled a range of key metrics to help inform return to work policies and procedures, including evaluating the benefit and optimal design of a SARS-CoV-2 employee screening program.\n\nMethodsWe modeled a range of input variables including prevalence of COVID-19, time infected, number of employees, test sensitivity and specificity, test turnaround time, number of times tested within the infectious period, and sample pooling. We modeled the impact of these input variables on several output variables: number of healthy employees; number of infected employees; number of test positive and test negative employees; number of true positive, false positive, true negative, and false negative employees; positive and negative predictive values; and time an infected, potentially contagious employee is on site.\n\nResultsWe show that an employee screening program can reduce the risk for onsite transmission across different prevalence values and group sizes. For example, at a pre-test asymptomatic community prevalence of 0.5% (5 in 1000) with an employee group size of 500, the risk for at least one infected employee on site is 91.8%, with 3 asymptomatic infected employees predicted within those 500 employees. Implementing a SARS-CoV-2 baseline screen with an 80% sensitivity and 99.5% specificity would reduce the risk of at least one infected employee on site to 39.4% and the predicted number of infected employees onsite (false negatives) to 1. Repetitive testing is required for ongoing vigilance of onsite employees. The expected number of days an infected employee is on site depends on test sensitivity, testing interval, and turnaround time. If the test interval is longer than the infectious period ([~]14 days for COVID-19), testing will not detect the infected employee. Sample pooling reduces the number of tests performed, thereby reducing testing costs. However, the pooling methodology (eg, 1-stage vs 2-stage pooling, pool size) will impact the number of employees that screen positive, thereby affected the number of employees eligible to return to onsite work.\n\nConclusionsThe modeling presented here can be used to help employers understand their risk for having an infected employee on site. Further, it details how an employee screening program can reduce this risk and shows how screening performance and frequency impact the effectiveness of a screening program. The primary factors determining the effectiveness of a screening program are test sensitivity and frequency of testing.\n\nDisclaimerThis publication is offered to businesses/employers as a model of potential risk arising from COVID19 in the workplace. While believed to be based on reliable data, the model described herein has not been prospectively validated and should not be relied upon for any purpose other than as an aid to understand the potential impacts of a number of variables on the risk of having COVID19 positive employees on a worksite. Decisions related to workplace safety; COVID19 related workplace testing; programs and procedures should be based upon your actual data and applicable laws and public health orders.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Kristen Meier", + "author_inst": "Illumina,Inc." + }, + { + "author_name": "Kirsten J. Curnow", + "author_inst": "Illumina, Inc." + }, + { + "author_name": "Darcy Vavrek", + "author_inst": "Illumina, Inc." + }, + { + "author_name": "John Moon", + "author_inst": "Illumina, Inc." + }, + { + "author_name": "Kyle Farh", + "author_inst": "Illumina, Inc." + }, + { + "author_name": "Martin Chian", + "author_inst": "Illumina, Inc." + }, + { + "author_name": "Robert Ragusa", + "author_inst": "Illumina, Inc." + }, + { + "author_name": "Eileen de Feo", + "author_inst": "Illumina, Inc." + }, + { + "author_name": "Phillip G. Febbo", + "author_inst": "Illumina, Inc." + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.20.20248563", "rel_title": "Development and external validation of a logistic regression derived formula based on repeated routine hematological measurements predicting survival of hospitalized Covid-19 patients", @@ -1002554,125 +1004136,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.12.21.20248643", - "rel_title": "Safety and immunogenicity clinical trial of an inactivated SARS-CoV-2 vaccine, BBV152 (a phase 2, double-blind, randomised controlled trial) and the persistence of immune responses from a phase 1 follow-up report", - "rel_date": "2020-12-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.21.20248643", - "rel_abs": "BackgroundBBV152 is a whole-virion inactivated SARS-CoV-2 vaccine (3 {micro}g or 6 {micro}g) formulated with a Toll-like receptor 7/8 agonist molecule adsorbed to alum (Algel-IMDG). Earlier, we reported findings from a phase 1 (vaccination regimen on days 0 and 14) randomised, double-blind trial on the safety and immunogenicity of three different formulations of BBV152 and one control arm containing Algel (without antigen). Two formulations were selected for the phase 2 (days 0 and 28) study. Here, we report interim findings of a controlled, randomised, double-blind trial on the immunogenicity and safety of BBV152: 3 {micro}g and 6 {micro}g with Algel-IMDG.\n\nMethodsWe conducted a double-blind, randomised, multicentre, phase 2 clinical trial to evaluate the immunogenicity and safety of BBV152. A total of 380 healthy children and adults were randomised to receive two vaccine formulations (n=190 each) with 3 {micro}g with Algel-IMDG and 6 {micro}g with Algel-IMDG. Two intramuscular doses of vaccines were administered (four weeks apart). Participants, investigators, and laboratory staff were blinded to the treatment allocation. The primary outcome was seroconversion ([≥]4-fold above baseline) based on wild-type virus neutralisation (PRNT50). Secondary outcomes were reactogenicity and safety. Cell-mediated responses were evaluated. A follow-up blood draw was collected from phase 1 participants at day 104 (three months after the second dose).\n\nFindingsAmong 921 participants screened between Sep 7-13, 2020, 380 participants were randomised to the safety and immunogenicity population. The PRNT50 seroconversion rates of neutralising antibodies on day 56 were 92{middle dot}9% (88{middle dot}2, 96{middle dot}2) and 98{middle dot}3% (95{middle dot}1, 99{middle dot}6) in the 3 {micro}g and 6 {micro}g with Algel-IMDG groups, respectively. Higher neutralising titres (2-fold) were observed in the phase 2 study than in the phase 1 study (p<0.05). Both vaccine groups elicited more Th1 cytokines than Th2 cytokines. After two doses, the proportion (95% CI) of solicited local and systemic adverse reactions were 9.7% (6{middle dot}9, 13{middle dot}2) and 10.3% (7{middle dot}4, 13{middle dot}8) in the 3 {micro}g and 6 {micro}g with Algel-IMDG groups, respectively. No significant difference was observed between the groups. No serious adverse events were reported in this study. Phase 1 follow-up immunological samples at day 104 showed seroconversion in 73{middle dot}5% (63{middle dot}6, 81{middle dot}9), 81{middle dot}1% (71{middle dot}4, 88{middle dot}1), and 73{middle dot}1% (62{middle dot}9, 81{middle dot}8) of individuals in the 3 {micro}g with Algel-IMDG, 6 {micro}g with Algel-IMDG, and 6 {micro}g with Algel groups, respectively.\n\nInterpretationIn the phase 1 trial, BBV152 produced high levels of neutralising antibodies that remained elevated in all participants three months after the second vaccination. In the phase 2 trial, BBV152 led to tolerable safety outcomes and enhanced humoral and cell-mediated immune responses. The safety profile of BBV152 is noticeably lower than the rates for other SARS-CoV-2 vaccine platform candidates. The 6 {micro}g Algel-IMDG formulation was selected for the phase 3 efficacy trial.\n\nFundingThis work was supported and funded by Bharat Biotech International Limited.\n\nClinicaltrials.gov: NCT04471519", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Raches Ella", - "author_inst": "Bharat Biotech International Limited" - }, - { - "author_name": "Siddharth Reddy", - "author_inst": "Bharat Biotech International Ltd" - }, - { - "author_name": "Harsh Jogdand", - "author_inst": "Bharat Biotech International Ltd" - }, - { - "author_name": "Vamshi Sarangi", - "author_inst": "Bharat Biotech International Ltd" - }, - { - "author_name": "Brunda Ganneru", - "author_inst": "Bharat Biotech International Ltd" - }, - { - "author_name": "Sai Prasad", - "author_inst": "Bharat Biotech International Ltd" - }, - { - "author_name": "Dipankar Das", - "author_inst": "Bharat Biotech International Ltd" - }, - { - "author_name": "Dugyala Raju", - "author_inst": "Bharat Biotech International Ltd" - }, - { - "author_name": "Usha Praturi", - "author_inst": "Bharat Biotech International Ltd" - }, - { - "author_name": "Gajanan Sapkal", - "author_inst": "National Institute of Virology" - }, - { - "author_name": "Pragya Yadav", - "author_inst": "National Institute of Virology" - }, - { - "author_name": "Prabhakar Reddy", - "author_inst": "Nizams Institute of Medical Sciences" - }, - { - "author_name": "Savita Verma", - "author_inst": "PGIMS, Rohtak" - }, - { - "author_name": "Chandramani Singh", - "author_inst": "All India Institute of Medical Sciences, Patna" - }, - { - "author_name": "Sagar Vivek Redkar", - "author_inst": "Redkar Hospital" - }, - { - "author_name": "Chandra Sekhar Gillurkar", - "author_inst": "Gillurkar Multi speciality Hospital" - }, - { - "author_name": "Jitendra Singh Kushwaha", - "author_inst": "Prakhar Hospital" - }, - { - "author_name": "Satyajit Mohapatra", - "author_inst": "SRM Medical College Hospital and Research Centre" - }, - { - "author_name": "Sanjay Kumar Rai", - "author_inst": "All India Institute of Medical Sciences, Delhia" - }, - { - "author_name": "Amit Bhate", - "author_inst": "Jeevan Rekha Hospital" - }, - { - "author_name": "Samiran Panda", - "author_inst": "Indian Council of Medical Research" - }, - { - "author_name": "Priya Abraham", - "author_inst": "National Institute of Virology" - }, - { - "author_name": "Nivedita Gupta", - "author_inst": "Indian Council of Medical Research" - }, - { - "author_name": "Krishna Ella", - "author_inst": "Bharat Biotech International Ltd" - }, - { - "author_name": "Balram Bhargava", - "author_inst": "Indian Council of Medical Research" - }, - { - "author_name": "Krishna Mohan Vadrevu", - "author_inst": "Bharat Biotech International Ltd" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.08.20233056", "rel_title": "Minimizing exposure to respiratory droplets, 'jet riders' and aerosols in air-conditioned hospital rooms by a 'Shield-and-Sink' strategy", @@ -1003480,6 +1004943,69 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.12.21.423779", + "rel_title": "Cetylpyridinium chloride-containing mouthwashes reduce in vitro SARS-CoV-2 infectivity", + "rel_date": "2020-12-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.21.423779", + "rel_abs": "Oral mouthwashes decrease the infectivity of several respiratory viruses including SARS-CoV-2. However, the precise agents with antiviral activity present in these oral rinses and their exact mechanism of action remain unknown. Here we show that Cetylpyridinium chloride (CPC), a quaternary ammonium compound present in many oral mouthwashes, reduces SARS-CoV-2 infectivity by inhibiting the viral fusion step with target cells after disrupting the integrity of the viral envelope. We also found that CPC-containing mouth rinses decreased more than a thousand times the infectivity of SARS-CoV-2 in vitro, while the corresponding vehicles had no effect. This activity was effective for different SARS-CoV-2 variants, including the B.1.1.7 variant, predominant in UK, also in the presence of sterilized saliva. CPC-containing mouth rinses could therefore represent a cost-effective measure to reduce SARS-CoV-2 infectivity in saliva, aiding to reduce viral transmission from infected individuals regardless of the variants they are infected with.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Jordana Munoz-Basagoiti", + "author_inst": "AIDS Research Institute IrsiCaixa" + }, + { + "author_name": "Daniel Perez-Zsolt", + "author_inst": "AIDS Research Institute IrsiCaixa" + }, + { + "author_name": "Ruben Leon", + "author_inst": "Dentaid Research Center" + }, + { + "author_name": "Vanessa Blanc", + "author_inst": "Dentaid Research Center" + }, + { + "author_name": "Dalia Raich-Regue", + "author_inst": "AIDS Research Institute IrsiCaixa" + }, + { + "author_name": "Mary Cano-Sarabia", + "author_inst": "Catalan Institute of Nanoscience and Nanotechnology" + }, + { + "author_name": "Benjamin Trinite", + "author_inst": "AIDS Research Institute IrsiCaixa" + }, + { + "author_name": "Edwards Pradenas", + "author_inst": "IrsiCaixa AIDS Research Institute" + }, + { + "author_name": "Julia Blanco", + "author_inst": "AIDS research Institute IrsiCaixa" + }, + { + "author_name": "Joan Gispert", + "author_inst": "Dentaid Research Center" + }, + { + "author_name": "Bonventura Clotet", + "author_inst": "AIDS Research Institute IrsiCaixa" + }, + { + "author_name": "Nuria Izquierdo-Useros", + "author_inst": "AIDS Research Institute IrsiCaixa" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.12.20.423630", "rel_title": "Mutation Landscape of SARS COV2 in Africa", @@ -1004511,41 +1006037,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.18.20248340", - "rel_title": "Forecasting daily confirmed COVID-19 cases in Algeria using ARIMA models", - "rel_date": "2020-12-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.18.20248340", - "rel_abs": "Coronavirus disease has become a worldwide threat affecting almost every country in the world. The aim of this study is to identify the COVID-19 cases (positive, recovery and death) in Algeria using the Double Exponential Smoothing Method and an Autoregressive Integrated Moving Average (ARIMA) model for forecasting the COVID-19 cases.\n\nThe data for this study were obtained from March 21st, 2020 to November 26th, 2020. The daily Algerian COVID-19 confirmed cases were sourced from The Ministry of Health, Population and Hospital Reform of Algeria. Based on the results of PACF, ACF, and estimated parameters of the ARIMA model in the COVID-19 case in Algeria following the ARIMA model (0,1,1). Observed cases during the forecast period were accurately predicted and were placed within the prediction intervals generated by the fitted model. This study shows that ARIMA models with optimally selected covariates are useful tools for monitoring and predicting trends of COVID-19 cases in Algeria.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Abdelaziz MESSIS", - "author_inst": "University of Bordj Bou Arreridj" - }, - { - "author_name": "Ahmed Adjebli", - "author_inst": "University of Bejaia" - }, - { - "author_name": "Riad Ayeche", - "author_inst": "University of Bordj Bou Arreridj" - }, - { - "author_name": "Abderrezak Ghidouche", - "author_inst": "University of Bejaia" - }, - { - "author_name": "Djida Ait ali", - "author_inst": "University of Bejaia" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.18.423104", "rel_title": "Glycyrrhizin effectively neutralizes SARS-CoV-2 in vitro by inhibiting the viral main protease", @@ -1005409,6 +1006900,133 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.17.20248430", + "rel_title": "Risk Factors for SARS-CoV-2 Seropositivity in a Health Care Worker Population", + "rel_date": "2020-12-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.17.20248430", + "rel_abs": "BackgroundProtecting health care workers (HCWs) during the coronavirus disease 2019 (COVID-19) pandemic is essential. Serologic testing can identify HCWs who had minimally symptomatic severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections that were missed by occupational screening based on daily symptom and temperature checks. Recent studies report conflicting results regarding the impact of occupational factors on SARS-CoV-2 seropositivity amongst HCWs.\n\nMethodsThe study population included all hospital workers at an academic medical center in Orange County, California. SARS-CoV-2 seropositivity was assessed from a fingerstick blood specimen using a coronavirus antigen microarray, which compares IgM and IgG antibodies against a panel of SARS-CoV-2 antigens with positive and negative controls to identify prior SARS-CoV-2 infection with 98% specificity and 93% sensitivity. Demographic, occupational, and clinical factors were surveyed and their effect on seropositivity estimated using multivariable logistic regression analysis.\n\nResultsAmongst 1,557 HCWs with complete data, SARS-CoV-2 seropositivity was 10.8%. Risk factors for increased seropositivity included male gender, exposure to COVID-19 outside of work, working in food or environmental services, and working in COVID-19 units. Amongst the 1,103 HCW who were seropositive but missed by occupational screening, additional risk factors included younger age and working in administration.\n\nConclusionsSARS-CoV-2 seropositivity is significantly higher than reported case counts even amongst HCWs who are meticulously screened. Seropositive HCWs missed by occupational screening were more likely to be younger, work roles without direct patient care, or have COVID-19 exposure outside of work.\n\nKey PointsSARS-CoV-2 seropositivity risk factors amongst health care workers included male gender, nonoccupational exposure, food or environmental services role, and COVID-19 unit location. Those missed by occupational screening were younger, in roles without direct patient care, or exposed outside of work.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Sebastian Schubl", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Cesar Figueroa", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Anton Palma", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Rafael de Assis", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Aarti Jain", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Rie Nakajima", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Alguimantas Jasinskas", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Danielle Brabender", + "author_inst": "University of Southern California" + }, + { + "author_name": "Ariana Naaseh", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Oscar Dominguez", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Ava Runge", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Shannon Skochko", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Justine Chinn", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Adam Kelsey", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Kieu Lai", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Weian Zhao", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Peter Horvath", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Delia Tifrea", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Areg Grigorian", + "author_inst": "University of Southern California" + }, + { + "author_name": "Abran Gonzales", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Suzanne Adelsohn", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Frank Zaldivar", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Robert Edwards", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Alpesh Amin", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Michael Stamos", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Philip Barie", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Philip Felgner", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Saahir Khan", + "author_inst": "University of Southern California" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.17.20248401", "rel_title": "Longitudinal analysis of COVID-19 patients shows age-associated T cell changes independent of ongoing ill-health", @@ -1006293,25 +1007911,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.17.20248442", - "rel_title": "Fluoxetine pharmacokinetics and tissue distribution suggest a possible role in reducing SARS-CoV-2 titers", - "rel_date": "2020-12-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.17.20248442", - "rel_abs": "BackgroundRecent in vitro studies have shown fluoxetine inhibits the severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) pathogen and one clinical study reported fluoxetine exposure at a median dose of 20mg in patients with the SARS-Cov-2 coronavirus disease 2019 (COVID-19) had a significantly lower risk of intubation and death. The aim of this study is to conduct in silico population dosing simulations to quantify the percentage of patients achieving a trough level for the effective concentration resulting in 90% inhibition (EC90) of SARS-Cov-2 as reported in Calu-3 human lung cells.\n\nMethodsPopulation pharmacokinetic parameter estimates for a structural one-compartment model with first-order absorption was used to simulate fluoxetine concentration-time data. A population of 1,000 individuals were simulated at standard fluoxetine doses (20mg/day, 40mg/day, and 60mg/day) to estimate the percentage of the patients achieving a trough level for the EC90 SARS-Cov-2 inhibitory concentration at each day throughout a 10-day treatment period. All analyses were conducted via statistical programming in R.\n\nResultsStandard fluoxetine antidepressant doses resulted in a range of 79% to 97% of the patient population achieving a trough target plasma concentration of 25.1 ng/ml which translates to lung-tissue distribution coefficient of 60-times higher (EC90 of 4.02 M). At a dose of 40mg per day, at least 85% of patients will reach the trough target EC90 concentration within 3-days. The findings of this pharmacokinetic dosing study corroborate both in vitro and observational clinical study findings showing fluoxetine inhibits the SARS-Cov-2 pathogen at commonly treated doses in the practice of psychiatry.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Andy R Eugene", - "author_inst": "Medical University of Lublin" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "pharmacology and therapeutics" - }, { "rel_doi": "10.1101/2020.12.17.20248445", "rel_title": "Classification of the infection status of COVID-19 in 186 countries", @@ -1007263,6 +1008862,105 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.12.18.423363", + "rel_title": "Multi-omic profiling reveals widespread dysregulation of innate immunity and hematopoiesis in COVID-19", + "rel_date": "2020-12-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.18.423363", + "rel_abs": "Our understanding of protective vs. pathologic immune responses to SARS-CoV-2, the virus that causes Coronavirus disease 2019 (COVID-19), is limited by inadequate profiling of patients at the extremes of the disease severity spectrum. Here, we performed multi-omic single-cell immune profiling of 64 COVID-19 patients across the full range of disease severity, from outpatients with mild disease to fatal cases. Our transcriptomic, epigenomic, and proteomic analyses reveal widespread dysfunction of peripheral innate immunity in severe and fatal COVID-19, with the most profound disturbances including a prominent neutrophil hyperactivation signature and monocytes with anti-inflammatory features. We further demonstrate that emergency myelopoiesis is a prominent feature of fatal COVID-19. Collectively, our results reveal disease severity-associated immune phenotypes in COVID-19 and identify pathogenesis-associated pathways that are potential targets for therapeutic intervention.\n\nOne Sentence SummarySingle-cell profiling demonstrates multifarious dysregulation of innate immune phenotype associated with COVID-19 severity.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Aaron J. Wilk", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Madeline J. Lee", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Bei Wei", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Benjamin Parks", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Ruoxi Pi", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Giovanny J. Martinez-Colon", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Thanmayi Ranganath", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Nancy Q. Zhao", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Shalina Taylor", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Winston Becker", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "- Stanford COVID-19 Biobank", + "author_inst": "-" + }, + { + "author_name": "David Jimenez-Morales", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Andra L. Blomkalns", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Euan A. Ashley", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Kari C. Nadeau", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Samuel Yang", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Susan Holmes", + "author_inst": "Stanford University" + }, + { + "author_name": "Marlene Rabinovitch", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Angela J. Rogers", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "William J. Greenleaf", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Catherine A. Blish", + "author_inst": "Stanford University School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.12.18.423427", "rel_title": "SARS-CoV-2 spike protein interacts with and activates TLR4", @@ -1008107,33 +1009805,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, - { - "rel_doi": "10.1101/2020.12.16.20248366", - "rel_title": "Effect of COVID-19 on Critical ICU Capacity in US Acute Care Hospitals", - "rel_date": "2020-12-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.16.20248366", - "rel_abs": "ImportanceThe current wave of COVID-19 infections has led to media reports of ICUs across the country reaching critical capacity. But the degree to which this has happened and community and institutional characteristics of hospitals where capacity limits have been reached is largely unknown.\n\nObjectiveTo determine changes in intensive care capacity in US acute care hospitals between September and early December, 2020 and to identify whether hospitals serving more vulnerable populations were more likely to exceed critical-levels of ICU occupancy.\n\nDesign, Setting, and ParticipantsRetrospective observational cohort of US acute care hospitals reporting to the US Department of Health and Human Services (HHS) from September 4, 2020 to December 3, 2020. Hospitals in this cohort were compared to all US acute care hospitals. Multivariate logistic regression was used to assess the relationship between community socioeconomic factors and hospital-structural features with a hospital reaching critical ICU capacity.\n\nExposureCommunity-level socioeconomic status and hospital-structural features\n\nMain Outcomes and MeasuresOur primary outcome was reaching critical ICU capacity (>90%) for at least two weeks since September 4. Secondary outcomes included the weekly capacity and occupancy tabulated by state and by hospital referral region.\n\nResults1,791 hospitals had unsuppressed ICU capacity data in the HHS Protect dataset, with 45% of hospitals reaching critical ICU capacity for at least two weeks during the study period. Hospitals in the South (OR = 2.79, p<0.001), Midwest (OR = 1.76, p=0.01) and West (OR = 1.85, p<0.01) were more likely to reach critical capacity than those in the Northeast. For-profit hospitals (OR = 2.15, p<0.001), rural hospitals (OR = 1.40, p<0.05) and hospitals in areas of high uninsurance (OR = 1.94, p<0.001) were more likely to reach critical ICU capacity, while hospitals with more intensivists (OR = 0.92, p=0.044 and higher nurse-bed ratios (OR = 0.95, p=0.013) were less likely to reach critical capacity.\n\nConclusions and RelevanceNearly half of U.S. hospitals reporting data to HHS Protect have reached critical capacity at some point since September. Those that are better resourced with staff were less likely to do so while for for-profit hospitals and those in poorer communities were more likely to reach capacity. Continued non-pharmacologic interventions are clearly needed to spread of the disease to ensure ICUs remain open for all patients needing critical care.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSWith an increasing number of SARS-CoV2 infections, how has the burden on ICU capacity changed over the past three months and what community and institutional factors are associated with hospitals reaching critical capacity?\n\nFinding45% of US acute care hospitals have reached critical ICU capacity at some point over the past three months. Hospital located in areas with fewer insured people were more likely to reach critical ICU capacity. At an institutional level, for-profit hospitals, rural hospitals, and those that have less baseline staffing of intensivists and nurses were more likely to reach critical ICU capacity.\n\nMeaningThe COVID-19 pandemic appears to be disproportionately straining ICUs with fewer resources and staff, setting up a substantial risk to widen disparities in access to care for already underserved populations.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Thomas C. Tsai", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Benjamin H. Jacobson", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Ashish K. Jha", - "author_inst": "Brown University School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.12.16.20236877", "rel_title": "Renal Involvement in Patients with COVID-19 Pneumonia and Outcomes After Stem Cell Nebulization.", @@ -1008941,6 +1010612,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, + { + "rel_doi": "10.1101/2020.12.15.20248260", + "rel_title": "Accelerated intermittent theta burst as a substitute for patients needing electroconvulsive therapy during the COVID-19 pandemic: study protocol for an open-label clinical trial", + "rel_date": "2020-12-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.15.20248260", + "rel_abs": "BackgroundTreatment resistant depression (TRD) is one of the leading causes of disability in Canada and is associated with significant societal costs. Repetitive transcranial magnetic stimulation (rTMS) is an approved, safe, and well-tolerated intervention for TRD. In the setting of the COVID-19 pandemic, reducing the number of visits to the clinic is a potential approach to significantly minimize exposure and transmission risks to patients. This can be accomplished by administering multiple treatment sessions in a single day, using an rTMS protocol known as accelerated intermittent theta burst stimulation (aiTBS). The objective of this novel study is to assess the feasibility, acceptance and clinical outcomes of a practical high-dose aiTBS protocol, including tapering treatments and symptom-based relapse prevention treatments, in patients with unipolar depression previously responsive to electroconvulsive therapy (ECT) or patients warranting ECT due to symptom severity.\n\nMethodsAll patients with unipolar depression referred to the brain stimulation service at the Centre for Addiction and Mental Health (CAMH) who warrant ECT will be offered screening to assess for eligibility to enroll in this trial. This open label, single group trial consists of 3 phases. In the acute treatment phase, treatment will occur 8 times daily for 5 days a week, until symptom remission is achieved or a maximum of 10 days of treatment. In the tapering phase, treatments will be reduced to 2 treatment days per week for 2 weeks, followed by 1 treatment day per week for 2 weeks. Patients will then enter the symptom-based relapse prevention phase including virtual check-ins and a treatment schedule based on symptom level. Remission, response and change in scores on several clinical measures from baseline to the end of the acute, tapering and relapse prevention phases represent the clinical outcomes of interest.\n\nDiscussionFindings from this novel clinical trial may provide support for the use of aiTBS, including tapering treatments and symptom-based relapse prevention treatments, as a safe and effective alternative intervention for patients needing ECT during the COVID-19 pandemic.\n\nTrial registrationClinicaltrials.gov: NCT04384965", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Daniel M. Blumberger", + "author_inst": "Centre for Addiction and Mental Health" + }, + { + "author_name": "Zafiris J Daskalakis", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Fidel Vila-Rodriguez", + "author_inst": "University of British Columbia" + }, + { + "author_name": "David Boivin-Lafleur", + "author_inst": "Centre for Addiction and Mental Health" + }, + { + "author_name": "Michelle S. Goodman", + "author_inst": "Centre for Addiction and Mental Health" + }, + { + "author_name": "Tyler Kaster", + "author_inst": "Centre for Addiction and Mental Health" + }, + { + "author_name": "Yuliya Knyahnytska", + "author_inst": "Centre for Addiction and Mental Health" + }, + { + "author_name": "Gerasimos Konstantinou", + "author_inst": "Centre for Addiction and Mental Health" + }, + { + "author_name": "Alisson P. Trevizol", + "author_inst": "Centre for Addiction and Mental Health" + }, + { + "author_name": "Daphne Voineskos", + "author_inst": "Centre for Addiction and Mental Health" + }, + { + "author_name": "Cory R. Weissman", + "author_inst": "Centre for Addiction and Mental Health" + }, + { + "author_name": "Jonathan Downar", + "author_inst": "University Health Network" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.12.15.20248235", "rel_title": "Exploring patient experiences of video consultations during Covid-19 in an outpatient care setting using routine feedback data from 955 contacts", @@ -1009601,37 +1011335,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.12.14.20248190", - "rel_title": "Utility of COVID-19 Decision Rules Related to Consecutive Decline in Positivity or Hospitalizations: A Data-driven Simulation Study", - "rel_date": "2020-12-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.14.20248190", - "rel_abs": "The White House issued Guidelines for Opening Up America Again to help state and local officials when reopening their economies. These included a \"downward trajectory of positive tests as a percent of total tests within a 14-day period.\" To examine this rule, we computed the probability of observing continuous decline in positivity when true positivity is in decline using data-driven simulation. Data for COVID-19 positivity reported in New York state from April 14 to May 5, 2020, where a clear reduction was observed, were used. First, a logistic regression model was fitted to the data, considering the fitted values as true positivity. Second, we created observed positivity by randomly selecting 25,000 people per day from a population with those true positivity for 14 days. The simulation was repeated 1,000 times to compute the probability of observing a consecutive decline. As sensitivity analyses, we performed the simulation with different daily numbers of tests (10 to 30,000) and length of observation (7 and 21 days). We further used daily hospitalizations as another metric, using data from the state of Indiana. With 25,000 daily tests, the probability of a consecutive decline in positivity for 14 days was 99.9% (95% CI: 99.7% to 100%). The probability dropped with smaller numbers of tests and longer lengths of consecutive observation, because there is more chance of observing an increase in positivity with smaller numbers of tests and longer observation. The probability of consecutive decline in hospitalizations was [~]0.0% regardless of the length of consecutive observation due to large variance. These results suggest that continuous declines in sample COVID-19 test positivity and hospitalizations may not be observed with sufficient probability, even when population probabilities truly decline. Criteria based on consecutive declines in metrics are unlikely to be useful for making decisions about relaxing COVID-19 mitigation efforts.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Keisuke Ejima", - "author_inst": "Indiana University" - }, - { - "author_name": "Kevin Maki", - "author_inst": "Indiana University" - }, - { - "author_name": "Lilian Golzarri-Arroyo", - "author_inst": "Indiana University" - }, - { - "author_name": "David B. Allison", - "author_inst": "Indiana University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.12.15.20248221", "rel_title": "The association of covid-19 infection with household food insecurity among Iranian population", @@ -1010323,6 +1012026,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.15.20248271", + "rel_title": "Social distancing and preventive practices of government employees in response to COVID-19 in Ethiopia", + "rel_date": "2020-12-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.15.20248271", + "rel_abs": "BackgroundPublic health measures are critical to mitigate the spread of the novel coronavirus disease 2019 (COVID-19) pandemic. Ethiopia has implemented a variety of essential public health measures in response to the spread of the virus. This study aimed to assess social distancing and preventive practices of government employees in response to COVID-19.\n\nMethodsA cross-sectional study was conducted among 1573 government employees selected from 46 public institutions (16 National, 18 from Addis Ababa City Administration, and 12 from Oromia Regional State) located in Addis Ababa. Data were collected from 8th to 19th June 2020 using a paper-based self-administered questionnaire and analyzed using SPSS version 23.0. ANOVA and t-tests were applied to assess the difference between groups. Bivariate and multivariable logistic regression analyses were used to identify factors associated with outcome variables.\n\nResultsThe majority of the participants reported wearing of facemask (96%), avoiding close contact with people including handshaking (94.5%), frequent had washing (94.1%), maintaining physical distancing (89.5%), avoiding mass gatherings (88.1%), and restricting movement and travelling (84.1%). More than 80% of the participants perceived that consistently wearing a facemask is highly effective in preventing the transmission of coronavirus. Participants from Oromia reported statistically significantly lower odds of perceived effectiveness of facemask in preventing coronavirus infection (adjusted OR=0.27, 95% CI:0.17-0.45). About 19% of the respondents reported that they had ever tested for COVID-19. Participants within the age groups of 18-29 were more likely to test for coronavirus than the older age groups. Whilst, respondents from Oromia were less likely to test for coronavirus than those from national level (adjusted OR=0.31, 95% CI:0.16-0.60). About one-third (31.3%) of the respondents strongly agreed that the policy responses that the Government had taken to contain the spread of coronavirus were reasonable, and 38.5% agreed with the policy responses.\n\nConclusionsThe findings showed higher social distancing and preventive practices among the government employees in response to COVID-19. People should properly apply social distancing measures, wearing facemasks, and washing hands frequently with water and soap as a comprehensive package of SARS-CoV-2 prevention and control strategies. Rules and regulations imposed by the Government should be properly enforced in order to control the pandemic.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Wakgari Deressa", + "author_inst": "Department of Preventive Medicine, School of Public Health, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia" + }, + { + "author_name": "Alemayehu Worku", + "author_inst": "Department of Preventive Medicine, School of Public Health, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia" + }, + { + "author_name": "Workeabeba Abebe", + "author_inst": "Department of Pediatrics and Child Health, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia" + }, + { + "author_name": "Sefonias Getachew", + "author_inst": "Department of Preventive Medicine, School of Public Health, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia" + }, + { + "author_name": "Wondwosson Amogne", + "author_inst": "Department of Internal Medicine, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.14.20245266", "rel_title": "Efficacy and Safety of Indomethacin in Covid -19 patients", @@ -1011427,153 +1013165,6 @@ "type": "confirmatory results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.12.16.422677", - "rel_title": "Identification of inhibitors of SARS-CoV-2 3CL-Pro enzymatic activity using a small molecule in-vitro repurposing screen", - "rel_date": "2020-12-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.16.422677", - "rel_abs": "Compound repurposing is an important strategy for the identification of effective treatment options against SARS-CoV-2 infection and COVID-19 disease. In this regard, SARS-CoV-2 main protease (3CL-Pro), also termed M-Pro, is an attractive drug target as it plays a central role in viral replication by processing the viral polyproteins pp1a and pp1ab at multiple distinct cleavage sites. We here report the results of a repurposing program involving 8.7 K compounds containing marketed drugs, clinical and preclinical candidates, and small molecules regarded as safe in humans. We confirmed previously reported inhibitors of 3CL-Pro, and have identified 62 additional compounds with IC50 values below 1 M and profiled their selectivity towards Chymotrypsin and 3CL-Pro from the MERS virus. A subset of 8 inhibitors showed anti-cytopathic effect in a Vero-E6 cell line and the compounds thioguanosine and MG-132 were analysed for their predicted binding characteristics to SARS-CoV-2 3CL-Pro. The X-ray crystal structure of the complex of myricetin and SARS-Cov-2 3CL-Pro was solved at a resolution of 1.77 [A], showing that myricetin is covalently bound to the catalytic Cys145 and therefore inhibiting its enzymatic activity.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=154 SRC=\"FIGDIR/small/422677v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (41K):\norg.highwire.dtl.DTLVardef@17ca2aeorg.highwire.dtl.DTLVardef@19c5159org.highwire.dtl.DTLVardef@1a0adf6org.highwire.dtl.DTLVardef@1fd05cd_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOAbstract Figure.C_FLOATNO Workflow for identification and profiling of inhibitors of SARS-CoV-2 3CL-Pro using a large scale repurposing and bioactive compound collection (rhs). Primary assay principle based on quenched FRET peptide substrate of SARS-CoV-2 3CL-Pro (lhs). Inhibiting compounds reduce fluorescence signal relative to DMSO controls. Hit profiling using X-ray.\n\nC_FIG", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Maria Kuzikov", - "author_inst": "Fraunhofer ITMP" - }, - { - "author_name": "Elisa Costanzi", - "author_inst": "Elettra-Sincrotrone Trieste S.C.p.A." - }, - { - "author_name": "Jeanette Reinshagen", - "author_inst": "Fraunhofer ITMP" - }, - { - "author_name": "Francesca Esposito", - "author_inst": "Dipartimento di Scienze della vita e dell ambiente" - }, - { - "author_name": "Laura Vangeel", - "author_inst": "KU Leuven" - }, - { - "author_name": "Markus Wolf", - "author_inst": "Fraunhofer ITMP" - }, - { - "author_name": "Bernhard Ellinger", - "author_inst": "Fraunhofer ITMP" - }, - { - "author_name": "Carsten Claussen", - "author_inst": "Fraunhofer ITMP" - }, - { - "author_name": "Gerd Geisslinger", - "author_inst": "Institute of Clinical Pharmacology, Goethe-University" - }, - { - "author_name": "Angela Corona", - "author_inst": "University of Cagliari" - }, - { - "author_name": "Daniela Iaconis", - "author_inst": "Dompe Farmaceutici SpA" - }, - { - "author_name": "Carmine Talarico", - "author_inst": "Dompe Farmaceutici SpA" - }, - { - "author_name": "Candida Manelfi", - "author_inst": "Dompe Farmaceutici SpA" - }, - { - "author_name": "Rolando Cannalire", - "author_inst": "University of Naples Federico II" - }, - { - "author_name": "Giulia Rossetti", - "author_inst": "Forschungszentrum Juelich" - }, - { - "author_name": "Jonas Gossen", - "author_inst": "Forschungszentrum Juelich" - }, - { - "author_name": "Simone Albani", - "author_inst": "Forschungszentrum Juelich" - }, - { - "author_name": "Francesco Musiani", - "author_inst": "University of Bologna" - }, - { - "author_name": "Katja Herzog", - "author_inst": "EU-OPENSCREEN ERIC" - }, - { - "author_name": "Yang Ye", - "author_inst": "University of Chinese Academy of Sciences, Beijing" - }, - { - "author_name": "Barbara Giabbai", - "author_inst": "Elettra-Sincrotrone Trieste S.C.p.A." - }, - { - "author_name": "Nicola Demitri", - "author_inst": "Elettra-Sincrotrone Trieste S.C.p.A." - }, - { - "author_name": "Dirk Jochmans", - "author_inst": "REGA Institute - KULeuven" - }, - { - "author_name": "Steven De Jonghe", - "author_inst": "KU Leuven" - }, - { - "author_name": "Jasper Rymenants", - "author_inst": "KU Leuven" - }, - { - "author_name": "Vincenzo Summa", - "author_inst": "University of Naples Federico II" - }, - { - "author_name": "Enzo Tramontano", - "author_inst": "University of Cagliari" - }, - { - "author_name": "Andrea Rosario Beccari", - "author_inst": "Dompe Farmaceutici SpA" - }, - { - "author_name": "Pieter Leyssen", - "author_inst": "KU Leuven" - }, - { - "author_name": "Paola Storici", - "author_inst": "Elettra-Sincrotrone Trieste S.C.p.A." - }, - { - "author_name": "Johan Neyts", - "author_inst": "Rega Institute" - }, - { - "author_name": "Philip Gribbon", - "author_inst": "Fraunhofer ITMP" - }, - { - "author_name": "Andrea Zaliani", - "author_inst": "Fraunhofer ITMP" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2020.12.16.423113", "rel_title": "Detection of long SARS-CoV-2 nucleocapsid sequences in peripheral blood monocytes collected soon after hospital admission", @@ -1012209,6 +1013800,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.08.20244525", + "rel_title": "Amplicon contamination in labs masquerades as COVID19 in surveillance tests", + "rel_date": "2020-12-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.08.20244525", + "rel_abs": "A cohort of laboratorians with positive SARS-CoV2 test results were uncovered during asymptomatic COVID-19 screening programs at six universities. Follow-up PCR and antibody tests showed that most of these cases were not true COVID-19 infection but instead arose from reverse-transcribed and amplified viral sequences (amplicons) that are generated during research. Environmental testing showed widespread contamination of amplicons in lab spaces including notebooks, keyboards, glasses, and doorknobs. Minimizing instances of amplicon contamination and developing protocols for handling suspected cases are critical to propel research efforts and to avoid diverting university and healthcare resources from patients with COVID-19. Removal of these individuals from the standard testing protocol, per CDC guidelines for positive cases, risks the spread of true infection. We discuss potential prevention and mitigation strategies.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Dan Davidi Dr", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Susan Fitzgerald", + "author_inst": "Harvard University" + }, + { + "author_name": "Hannah L Glaspell", + "author_inst": "Cornell University" + }, + { + "author_name": "Samantha Jalbert", + "author_inst": "Harvard University" + }, + { + "author_name": "Stylianos Maheras", + "author_inst": "Harvard University" + }, + { + "author_name": "Stephanie E Mattoon", + "author_inst": "Cornell University" + }, + { + "author_name": "Vanessa M Britto Dr", + "author_inst": "Brown University" + }, + { + "author_name": "Davidson H Hamer Dr", + "author_inst": "Boston University" + }, + { + "author_name": "Giang T Nguyen Dr", + "author_inst": "Harvard University" + }, + { + "author_name": "Judy Platt Dr", + "author_inst": "Boston University" + }, + { + "author_name": "Cecilia W Stuopis Dr", + "author_inst": "MIT" + }, + { + "author_name": "Joshua E Turse Dr", + "author_inst": "Cornell University" + }, + { + "author_name": "Michael Springer Dr", + "author_inst": "Harvard Medical School" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.12.10.20247080", "rel_title": "Does Contact Tracing Work? Quasi-Experimental Evidence from an Excel Error in England", @@ -1013157,57 +1014815,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.12.10.20247155", - "rel_title": "Self-harm presentations to Emergency Departments and Place of Safety during the first wave of the UK COVID-19 pandemic: South London and Maudsley data on service use from February to June 2020.", - "rel_date": "2020-12-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.10.20247155", - "rel_abs": "The lockdown and social distancing policy imposed due to the COVID-19 pandemic has had a substantial impact on both mental health service delivery, and the ways in which people are accessing these services. Previous reports from the South London and Maudsley NHS Trust (SLaM; a large mental health service provider for around 1.2m residents in South London) have highlighted increased use of virtual contacts by mental health teams, with dropping numbers of face-to-face contacts over the first wave of the pandemic. There has been concern that the impact of the COVID-19 pandemic would lead to higher mental health emergencies, particularly instances of self-harm. However, with people advised to stay at home during the first wave lockdown, it is as yet unclear whether this impacted mental health service presentations. Taking advantage of SLaMs Clinical Records Interactive Search (CRIS) data resource with daily updates of information from its electronic mental health records, this paper describes overall presentations to Emergency Department (ED) mental health liaison teams, and those with self-harm. The paper focussed on three periods: i) a pre-lockdown period 1st February to 15th March, ii) a lockdown period 16th March to 10th May and iii) a post-lockdown period 11th May to 28th June. In summary, all attendances to EDs for mental health support decreased during the lockdown period, including those with self-harm. All types of self-harm decreased during lockdown, with self-poisoning remaining the most common. Attendances to EDs for mental health support increased post-lockdown, although were only just approaching pre-lockdown levels by the end of June 2020.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Eleanor Nuzum", - "author_inst": "South London and Maudsley NHS Foundation Trust" - }, - { - "author_name": "Evangelia Martin", - "author_inst": "South London and Maudsley NHS Foundation Trust" - }, - { - "author_name": "Gemma Morgan", - "author_inst": "South London and Maudsley NHS Foundation Trust" - }, - { - "author_name": "Rina Dutta", - "author_inst": "King's College London" - }, - { - "author_name": "Christoph Mueller", - "author_inst": "King's College London" - }, - { - "author_name": "Catherine Polling", - "author_inst": "King's College London" - }, - { - "author_name": "Megan Pritchard", - "author_inst": "King's College London" - }, - { - "author_name": "Sumithra Velupillai", - "author_inst": "King's College London" - }, - { - "author_name": "Robert Stewart", - "author_inst": "King's College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.12.13.20248123", "rel_title": "The seroprevalence and trends of SARS-CoV-2 in Delhi, India: A repeated population-based seroepidemiological study", @@ -1013875,6 +1015482,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.11.20247932", + "rel_title": "COVID-19 TARRACO Cohort Study: Development of a predictive prognostic rule for early assessment of COVID-19 patients in primary care settings.", + "rel_date": "2020-12-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.11.20247932", + "rel_abs": "PURPOSEClinical course in COVID-19 patients is uncertain. This study investigated possible early prognostic factors among middle-aged and older adult and explored prognostic rules stratifying risk of patients.\n\nMETHODSCommunity-based retrospective cohort study that included 282 community-dwelling symptomatic patients [≥]50 years with laboratory-confirmed COVID-19 (hospitalised and/or outpatient) during March-June 2020 in Tarragona (Southern Catalonia, Spain). Relationship between demographics, pre-existing comorbidities and early symptomatology (first 5-days) and risk of suffering critical outcome (ICU-admission/death) across clinical course was evaluated by logistic regression analyses, and simple predictive models were developed.\n\nRESULTSOf the 282 cases (mean age: 65.9 years; 140 men), 154 (54.6%) were hospitalised (30 ICU-admitted) and 45 (16%) deceased. In crude analyses, increasing age, male sex, some comorbidities (renal, respiratory or cardiac disease, diabetes and hypertension) and symptoms (confusion, dyspnea) were associated with an increased risk to suffer critical outcome, whereas other symptoms (rinorrhea, myalgias, headache, anosmia/disgeusia) were related with reduced risk. After multivariable-adjustment only age/years (OR: 1.04; 95% CI: 1.01-1.07; p=0.004), confusion (OR: 5.33; 95% CI: 1.54-18.48; p=0.008), dyspnea (OR: 5.41; 95% CI: 2.74-10.69; p<0.001) and myalgias (OR: 0.30; 95% CI: 0.10-0.93; p=0.038) remained significantly associated with increased or reduced risk. A proposed CD65-M prognostic rule (including the above mentioned 4 variables) showed a good correlation with the risk of suffering critical outcome (area under ROC curve: 0.828; 95% CI: 0.774-0.882).\n\nCONCLUSIONClinical course of COVID-19 is early unpredictable, but simple clinical tools as the proposed CD65-M rule (pending external validation) may be helpful assessing these patients in primary care settings.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Angel Vila-corcoles", + "author_inst": "Primary Care Department Camp de Tarragona. Institut Catala de la Salut, Tarragona, Spain." + }, + { + "author_name": "Eva Satue-Gracia", + "author_inst": "Primary Care Department Camp de Tarragona. Institut Catala de la Salut, Tarragona, Spain." + }, + { + "author_name": "Angel Vila-Rovira", + "author_inst": "Universitary Institute of Primary Care Research IDIAP Jordi Gol. Barcelona, Spain." + }, + { + "author_name": "Cinta de Diego-cabanes", + "author_inst": "Primary Care Department Camp de Tarragona. Institut Catala de la Salut, Tarragona, Spain." + }, + { + "author_name": "Maria Jose Forcadell-Peris", + "author_inst": "Primary Care Department Camp de Tarragona. Institut Catala de la Salut, Tarragona, Spain." + }, + { + "author_name": "Imma Hospital-Guardiola", + "author_inst": "Primary Care Department Camp de Tarragona. Institut Catala de la Salut, Tarragona, Spain." + }, + { + "author_name": "Olga Ochoa-Gondar", + "author_inst": "Primary Care Department Camp de Tarragona. Institut Catala de la Salut, Tarragona, Spain." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.11.20247437", "rel_title": "Clinical and Demographic Characteristics of COVID-19 Patients Admitted in a Tertiary Care Hospital in the Dominican Republic", @@ -1014875,49 +1016525,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.12.11.20235838", - "rel_title": "Unique predictors of intended uptake of a COVID-19 vaccine", - "rel_date": "2020-12-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.11.20235838", - "rel_abs": "IntroductionAn effective vaccine for COVID-19 is only of value if the public has confidence in taking it. There is little data on COVID-19-specific vaccine confidence or its determinants in the United States. The objective of this study was to determine public confidence in a COVID-19 vaccine.\n\nMethodsA cross-sectional survey of Pennsylvanian adults, August-October, 2020, to identify their likelihood of taking an approved, no-cost coronavirus vaccine, general vaccine acceptance, and sociodemographic traits to identify predictors of vaccine acceptance.\n\nResultsOf the 950 respondents, 55% were \"very likely\", 20% \"somewhat likely\", 14% \"unsure\", 4% \"somewhat unlikely\", and 7% \"very unlikely\" to take a coronavirus vaccine, even though 70% had taken the flu vaccine since September 2019. The strongest predictors of vaccine acceptance were trust in the system evaluating vaccines and perceptions of local COVID-19 vaccination norms. The strongest predictors of negative vaccine intentions were worries about unknown side-effects and positive attitudes toward natural infection. Sociodemographic factors, political views, and religiosity did not predict vaccine intentions.\n\nConclusionsFewer adults intend to take a coronavirus vaccine than currently take the flu vaccine. To overcome coronavirus vaccine hesitancy, information campaigns to reinforce positive predictors and overcome negative predictors are indicated.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Robert P. Lennon", - "author_inst": "Pennsylvania State College of Medicine" - }, - { - "author_name": "Meg L. Small", - "author_inst": "The Pennsylvania State University" - }, - { - "author_name": "Rachel A. Smith", - "author_inst": "The Pennsylvania State University" - }, - { - "author_name": "Lauren J. Van Scoy", - "author_inst": "Pennsylvania State College of Medicine" - }, - { - "author_name": "Jessica G. Myrick", - "author_inst": "The Pennsylvania State University" - }, - { - "author_name": "Molly A. Martin", - "author_inst": "The Pennsylvania State University" - }, - { - "author_name": "- Data4Action Research Group", - "author_inst": "-" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.14.20248137", "rel_title": "Assessing Durability of Vaccine Effect Following Blinded Crossover in COVID-19 Vaccine Efficacy Trials", @@ -1015681,6 +1017288,77 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.12.12.422532", + "rel_title": "Generation of a SARS-CoV-2 Replicon as a Model System to Dissect Virus Replication and Antiviral Inhibition", + "rel_date": "2020-12-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.12.422532", + "rel_abs": "SARS-CoV-2 research and antiviral discovery are hampered by the lack of a cell-based virus replication system that can be readily adopted without biosafety level 3 (BSL-3) restrictions. Here, the construction of a non-infectious SARS-CoV-2 reporter replicon and its application in deciphering viral replication mechanisms and evaluating SARS-CoV-2 inhibitors are presented. The replicon genome is replication competent but does not produce progeny virions. Its replication can be inhibited by RdRp mutations or by known SARS-CoV-2 antiviral compounds. Using this system, a high-throughput antiviral assay has also been developed. Significant differences in potencies of several SARS-CoV-2 inhibitors in different cell lines were observed, which highlights the challenges of discovering antivirals capable of inhibiting viral replication in vivo and the importance of testing compounds in multiple cell culture models. The generation of a SARS-CoV-2 replicon provides a powerful platform to expand the global research effort to combat COVID-19.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Xi He", + "author_inst": "Merck & Co., Inc." + }, + { + "author_name": "Shuo Quan", + "author_inst": "Merck & Co., Inc" + }, + { + "author_name": "Min Xu", + "author_inst": "Merck & Co., Inc." + }, + { + "author_name": "Silveria Rodriguez", + "author_inst": "Merck & Co., Inc." + }, + { + "author_name": "Shih Lin Goh", + "author_inst": "Merck& Co., Inc." + }, + { + "author_name": "Jiajie Wei", + "author_inst": "Merck & Co., Inc." + }, + { + "author_name": "Arthur Fridman", + "author_inst": "Merck & Co., Inc." + }, + { + "author_name": "Kenneth A Koeplinger", + "author_inst": "Merck and Co., Inc." + }, + { + "author_name": "Steve S Carroll", + "author_inst": "Merck & Co., Inc." + }, + { + "author_name": "Jay A Grobler", + "author_inst": "Merck & Co., Inc." + }, + { + "author_name": "Amy S Espeseth", + "author_inst": "Merck & Co., Inc." + }, + { + "author_name": "David B Olsen", + "author_inst": "Merck & Co., Inc." + }, + { + "author_name": "Daria J Hazuda", + "author_inst": "Merck & Co., Inc." + }, + { + "author_name": "Dai Wang", + "author_inst": "Merck & Co., Inc." + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.12.13.422548", "rel_title": "Evaluation of in vitro activity of copper gluconate against SARS-CoV-2 using confocal microscopy-based high content screening", @@ -1016528,57 +1018206,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.08.20245977", - "rel_title": "Follow-up study on serum cholesterol profiles in recovered COVID-19 patients", - "rel_date": "2020-12-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.08.20245977", - "rel_abs": "COVID-19 patients develop hypolipidemia. However, it is unknown whether lipid levels have improved in recovered patients. In this study, a 3-6 month follow-up study was performed to examine serum levels of laboratory values in 107 discharged COVID-19 patients (mild = 59; severe/critical = 48; diagnoses on admission). 61 patients had a revisit chest CT scan. A Wilcoxon signed-rank test was used to analyze changes in laboratory values. LDL-c and HDL-c levels were significantly higher at follow-up than at admission in severe/critical cases (p < 0.05). LDL-c levels were significantly higher at follow-up than at admission in mild cases (p < 0.05). With adjustment of the factor of traditional Chinese medicine, LDL-c and HDL-c levels were significantly improved at follow-up than at admission in severe/critical cases (p < 0.05). Increases in HDL-c significantly correlated with increases in numbers of white blood cells (p<0.001) and decreases in levels of C-reactive protein (p < 0.05) during patients recovery. Residue lesions were observed in CT images in 69% (42 of 61) of follow-up patients. We concluded that improvements of LDL-c, HDL-c and incomplete absorption of lung lesions were observed at follow-up for recovered patients, indicating that a long-term recovery process could be required.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Guiling Li", - "author_inst": "Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China" - }, - { - "author_name": "Li Du", - "author_inst": "Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China" - }, - { - "author_name": "Xiaoling Cao", - "author_inst": "Department of Cell Biology and Anatomy, School of Medicine, University of South Carolina, Columbia, South Carolina, USA" - }, - { - "author_name": "Xiuqi Wei", - "author_inst": "Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China" - }, - { - "author_name": "Yao Jiang", - "author_inst": "Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China" - }, - { - "author_name": "Yuqi Lin", - "author_inst": "Department of Laboratory Medicine, Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China" - }, - { - "author_name": "Vi Nguyen", - "author_inst": "Department of Cell Biology and Anatomy, School of Medicine, University of South Carolina, Columbia, South Carolina, USA" - }, - { - "author_name": "Wenbin Tan", - "author_inst": "University of South Carolina, School of Medicine" - }, - { - "author_name": "Hui Wang", - "author_inst": "Department of Laboratory Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.05.20241927", "rel_title": "Neutralising antibodies drive Spike mediated SARS-CoV-2 evasion", @@ -1017570,6 +1019197,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.08.20246090", + "rel_title": "Analysis of the specificity of the SD Biosensor Standard Q Ag-Test based on Slovak mass testing data", + "rel_date": "2020-12-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.08.20246090", + "rel_abs": "From 31.10. - 1.11.2020 Slovakia has used the SD Biosensor Standard Q Ag-Test for nationwide tests for SARS-CoV-2, in which 3,625,332 persons from 79 counties were tested. Based on this data, we calculate that the specificity of the test is at least 99.6% (with a 97.5% one-sided lower confidence bound). Our analysis is based on a worst case approach in which all positives are assumed to be false positives. Therefore, the actual specificity is expected to exceed 99.6%.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Michal Hledik", + "author_inst": "Institute of Science and Technology Austria (IST Austria)" + }, + { + "author_name": "Jitka Polechova", + "author_inst": "Department of Mathematics, University of Vienna, Austria" + }, + { + "author_name": "Mathias Beiglboeck", + "author_inst": "Department of Mathematics, University of Vienna, Austria" + }, + { + "author_name": "Anna Nele Herdina", + "author_inst": "Division of Clinical Virology, Department of Laboratory Medicine, Informatics, and Intelligent Systems, Medical University of Vienna, Austria" + }, + { + "author_name": "Robert Strassl", + "author_inst": "Division of Clinical Virology, Department of Laboratory Medicine, Informatics, and Intelligent Systems, Medical University of Vienna, Austria" + }, + { + "author_name": "Martin Posch", + "author_inst": "Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Austria" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.09.20246421", "rel_title": "Contacts and behaviours of university students during the COVID-19 pandemic at the start of the 2020/21 academic year", @@ -1018486,77 +1020152,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.08.20246124", - "rel_title": "Risk factors for retirement home COVID-19 outbreaks in Ontario, Canada: A population-level cohort study", - "rel_date": "2020-12-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.08.20246124", - "rel_abs": "BackgroundThe epidemiology of COVID-19 in retirement homes (also known as assisted living facilities) is largely unknown. We examined the association between retirement home and community level characteristics and the risk of COVID-19 outbreaks in retirement homes during the first wave of the COVID-19 epidemic.\n\nMethodsWe conducted a population-based retrospective cohort study of licensed retirement homes in Ontario, Canada, from March 1st - September 24th, 2020. Our primary outcome was a COVID-19 outbreak ([≥]1 resident or staff confirmed case by validated nucleic acid amplification assay). We used time-dependent proportional hazards methods to model the associations between retirement home and community level characteristics and COVID-19 outbreaks.\n\nResultsOur cohort included all 770 licensed retirement homes in Ontario, which housed 56,491 residents. There were 172 (22.3%) COVID-19 retirement home outbreaks involving 1,045 (1.9%) residents and 548 staff (1.5%). COVID-19 cases were distributed unevenly across retirement homes, with 1,593 (92.2%) resident and staff cases occurring in 77 (10%) of homes. The adjusted hazard of a COVID-19 outbreak in a retirement home was positively associated with homes that had a large resident capacity, homes that were co-located with a long-term care facility, large corporate owned chains, homes that offered many services onsite, increases in regional COVID-19 incidence, and a higher community-level ethnic concentration.\n\nInterpretationReadily identifiable retirement home-level characteristics are independently associated with COVID-19 outbreaks and may support risk identification. A higher ethnic concentration of the community surrounding a retirement home is associated COVID-19 outbreaks, with an uncertain mechanism.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Andrew P Costa", - "author_inst": "McMaster University" - }, - { - "author_name": "Derek R Manis", - "author_inst": "McMaster University" - }, - { - "author_name": "Aaron Jones", - "author_inst": "McMaster University" - }, - { - "author_name": "Nathan M Stall", - "author_inst": "University of Toronto" - }, - { - "author_name": "Kevin A Brown", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Veronique Boscart", - "author_inst": "Conestoga College Institute of Technology and Advanced Learning" - }, - { - "author_name": "Adriane Castellino", - "author_inst": "Retirement Homes Regulatory Authority" - }, - { - "author_name": "George A. Heckman", - "author_inst": "University of Waterloo" - }, - { - "author_name": "Michael P Hillmer", - "author_inst": "Ontario Ministry of Health" - }, - { - "author_name": "Chloe Ma", - "author_inst": "Retirement Homes Regulatory Authority" - }, - { - "author_name": "Paul Pham", - "author_inst": "Retirement Homes Regulatory Authority" - }, - { - "author_name": "Saad Rais", - "author_inst": "Retirement Homes Regulatory Authority" - }, - { - "author_name": "Samir K Sinha", - "author_inst": "Sinai Health and University Health Network" - }, - { - "author_name": "Jeffrey W Poss", - "author_inst": "University of Waterloo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.09.20246579", "rel_title": "Early initiation of prophylactic anticoagulation for prevention of COVID-19 mortality: a nationwide cohort study of hospitalized patients in the United States", @@ -1019156,6 +1020751,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.10.20238576", + "rel_title": "Intense and Mild Wave of COVID-19 in The Gambia: a Cohort Analysis", + "rel_date": "2020-12-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.10.20238576", + "rel_abs": "BackgroundThe SARS-CoV-2 pandemic is evolving differently in Africa compared to other regions, with lower transmission and milder clinical presentation. Reasons for this are not fully understood. Recent data from Eastern and Southern Africa suggest that transmission may be higher than measured. Detailed epidemiological data in different African settings is urgently needed.\n\nMethodsWe calculated cumulative rates of SAR-CoV-2 infections per 1,000 people at risk in The Gambia (2.42 million individuals) using publicly available data. We evaluated these rates in a cohort of 1,366 employees working at the MRC Unit The Gambia @LSHTM (MRCG) where systematic surveillance of symptomatic cases and contact tracing was implemented. Cumulative rates among the Gambian population were stratified by age groups and, among MRCG staff, by occupational exposure risk. SARS-CoV-2 testing was conducted on oropharyngeal/nasopharyngeal samples with consistent sampling and laboratory procedures across cohorts.\n\nFindingsBy September 2020, 3,579 cases of SARS-CoV-2 and 115 deaths had been identified; with 67% of cases detected in August. Among them, 191 cases were MRCG staff; all of them were asymptomatic/mild, with no deaths. The cumulative incidence rate for SARS-CoV-2 infection among MRCG staff (excluding those with occupational exposure risk) was 129 per 1,000, at least 20-fold higher than the estimations based on diagnosed cases in the adult Gambian population.\n\nInterpretationOur findings are consistent with recent African sero-prevalence studies reporting high community transmission of SAR-CoV-2. Enhanced community surveillance is essential to further understand and predict the future trajectory of the pandemic in Africa.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "- MRCG/GG COVID-19 working group", + "author_inst": "" + }, + { + "author_name": "Anna Roca", + "author_inst": "MRC Unit The Gambia at the LSHTM" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.10.20247346", "rel_title": "What positives can be taken from the COVID-19 pandemic in Australia?", @@ -1020364,61 +1021982,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.12.11.20247650", - "rel_title": "An emergency system for monitoring pulse oximetry, peak expiratory flow and body temperature of patients with COVID-19 at home: Development and preliminary application", - "rel_date": "2020-12-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.11.20247650", - "rel_abs": "BackgroundCOVID-19 is characterized by a rapid change in the patients condition, with major changes occurring over a few days. Our aim was to develop and evaluate an emergency system for monitoring patients with COVID-19, which may be useful in hospitals where more severe patients stay in their homes.\n\nMethodology/Principal findingsThe system consists of the home-based patient unit, which is set up around the patient and the hospital unit, which enables the medical staff to telemonitor the patients condition and help to send medical recommendations. The home unit allows the data transmission from the patient to the hospital, which is performed using a cell phone application. The hospital unit includes a virtual instrument developed in LabVIEW(R) environment that is able to provide a real-time monitoring of the oxygen saturation (SpO2), beats per minute (BPM), body temperature (BT) and peak expiratory flow (PEF). Abnormal events may be fast and automatically identified. After the design details are described, the system is validated by a 30-day home monitoring study in 12 controls and 12 patients with COVID-19 presenting asymptomatic to mild disease. Patients presented reduced SpO2 (p<0.0001) and increased BPM values (p<0.0001). Three patients (25%) presented PEF values between 50 and 80% of the predicted. Three of the 12 monitored patients presented events of desaturation (SpO2<92%). The experimental results were in close agreement with the involved pathophysiology, providing clear evidences that the proposed system can be a useful tool for the remote monitoring of patients with COVID-19.\n\nConclusionsAn emergency system for home monitoring of patients with COVID-19 was developed in the current study. The proposed system allowed us to quickly respond to early abnormalities in these patients. This system may contribute to conserve hospital resources for those most in need, while simultaneously enabling early recognition of patients under acute deterioration, requiring urgent assessment.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Leonardo P Motta", - "author_inst": "State University of Rio de Janeiro" - }, - { - "author_name": "Pedro P F Silva", - "author_inst": "State University of Rio de Janeiro" - }, - { - "author_name": "Bruno M Borguezan", - "author_inst": "State University of Rio de Janeiro" - }, - { - "author_name": "Jorge L M Amaral", - "author_inst": "State University of Rio de Janeiro" - }, - { - "author_name": "Lucimar G Milagres", - "author_inst": "State University of Rio de Janeiro" - }, - { - "author_name": "Marcio N Boia", - "author_inst": "State University of Rio de Janeiro" - }, - { - "author_name": "Marcos R Ferraz", - "author_inst": "State University of Rio de Janeiro" - }, - { - "author_name": "Roberto Mogami", - "author_inst": "State University of Rio de Janeiro" - }, - { - "author_name": "Rodolfo A Nunes", - "author_inst": "State University of Rio de Janeiro" - }, - { - "author_name": "Pedro Lopes de Melo", - "author_inst": "State University of Rio de Janeiro" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2020.12.11.20247668", "rel_title": "Potential role of aberrant mucosal immune response to SARS-CoV-2 in pathogenesis of IgA Nephropathy", @@ -1021454,6 +1023017,117 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2020.12.10.419044", + "rel_title": "A single dose, BCG-adjuvanted SARS-CoV-2 vaccine induces Th1-polarized immunity and high-titre neutralizing antibodies in mice", + "rel_date": "2020-12-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.10.419044", + "rel_abs": "Global control of COVID-19 requires broadly accessible vaccines that are effective against SARS-CoV-2 variants. In this report, we exploit the immunostimulatory properties of bacille Calmette-Guerin (BCG), the existing tuberculosis vaccine, to deliver a vaccination regimen with potent SARS-CoV-2-specific protective immunity. Combination of BCG with a stabilized, trimeric form of SARS-CoV-2 spike antigen promoted rapid development of virus-specific IgG antibodies in the blood of vaccinated mice, that was further augmented by the addition of alum. This vaccine formulation, BCG:CoVac, induced high-titre SARS-CoV-2 neutralizing antibodies (NAbs) and Th1-biased cytokine release by vaccine-specific T cells, which correlated with the early emergence of T follicular helper cells in local lymph nodes and heightened levels of antigen-specific plasma B cells after vaccination. Vaccination of K18-hACE2 mice with a single dose of BCG:CoVac almost completely abrogated disease after SARS-CoV-2 challenge, with minimal inflammation and no detectable virus in the lungs of infected animals. Boosting BCG:CoVac-primed mice with a heterologous vaccine further increased SARS-CoV-2-specific antibody responses, which effectively neutralized B.1.1.7 and B.1.351 SARS-CoV-2 variants of concern. These findings demonstrate the potential for BCG-based vaccination to protect against major SARS-CoV-2 variants circulating globally.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Claudio Counoupas", + "author_inst": "Centenary Institute" + }, + { + "author_name": "Matt D Johnson", + "author_inst": "Centre for Inflammation, Centenary Institute and University of Technology Sydney" + }, + { + "author_name": "Alberto Stella", + "author_inst": "Kirby Institute UNSW" + }, + { + "author_name": "Duc H Nguyen", + "author_inst": "Centre for Inflammation, Centenary Institute and University of Technology Sydney" + }, + { + "author_name": "Angela Ferguson", + "author_inst": "Centenary Institute" + }, + { + "author_name": "Anupriya Aggarwal", + "author_inst": "Kirby Institute UNSW" + }, + { + "author_name": "Nayan Bhattacharyya", + "author_inst": "Centenary Institute" + }, + { + "author_name": "Alice Grey", + "author_inst": "Royal Prince Alfred Hospital" + }, + { + "author_name": "Karishma Patel", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Rezwan Siddiquee", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Erica L Stewart", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Owen Hutchings", + "author_inst": "RPA Virtual Hospital" + }, + { + "author_name": "Carl Feng", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Nicole G. G Hansbro", + "author_inst": "Centre for Inflammation, Centenary Institute and University of Technology Sydney" + }, + { + "author_name": "Umaimainthan Palendira", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Megan Steain", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Bernadette M Saunders", + "author_inst": "Centre for Inflammation, Centenary Institute and University of Technology Sydney" + }, + { + "author_name": "Jason Low", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Joel Mackay", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Anthony Kelleher", + "author_inst": "Kirby Institute UNSW" + }, + { + "author_name": "Warwick Britton", + "author_inst": "Centenary Institute" + }, + { + "author_name": "Stuart Turville", + "author_inst": "Kirby Institute UNSW" + }, + { + "author_name": "Philip M Hansbro", + "author_inst": "Centre for Inflammation, Centenary Institute and University of Technology Sydney" + }, + { + "author_name": "James A Triccas", + "author_inst": "The University of Sydney" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.12.10.419242", "rel_title": "Molnupiravir (EIDD-2801) inhibits SARS-CoV2 replication in Syrian hamsters model", @@ -1022242,101 +1023916,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.12.08.20246025", - "rel_title": "Characterising long-term covid-19: a rapid living systematic review", - "rel_date": "2020-12-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.08.20246025", - "rel_abs": "BackgroundWhile it is now apparent clinical sequelae (often called Long Covid) may persist after acute Covid-19, their nature, frequency, and aetiology are poorly characterised. This study aims to regularly synthesise evidence on Long Covid characteristics, to inform clinical management, rehabilitation, and interventional studies to improve long term outcomes.\n\nMethodsA living systematic review. Medline, CINAHL (EBSCO), Global Health (Ovid), WHO Global Research Database on Covid-19, LitCOVID, and Google Scholar were searched up to 17th March 2021. Published studies including at least 100 people with confirmed or clinically suspected Covid-19 at 12 weeks or more post-onset were included. Results were analysed using descriptive statistics and meta-analyses to estimate prevalence with 95% confidence intervals (CIs).\n\nResultsThirty-nine studies were included: 32 cohort, six cross-sectional, and one case-control. Most showed high or moderate risk of bias. None were set in low-income countries, limited studies included children. Studies reported on 10,951 people (48% female) in 12 countries. Most followed-up post hospital discharge (78%, 8520/10951). The longest mean follow-up was 221.7 (SD: 10.9) days post Covid-19 onset. An extensive range of symptoms with wide prevalence was reported, most commonly weakness (41%; 95% CI 25% to 59%), malaise (33%; 95% CI 15% to 57%), fatigue (31%; 95% CI 24% to 39%), concentration impairment (26%; 95% CI 21% to 32%), and breathlessness (25%; 95% CI 18% to 34%). Other frequent symptoms included musculoskeletal, neurological, and psychological. 37% (95% CI 18% to 60%) of people reported reduced quality of life.\n\nConclusionLong Covid is a complex condition with heterogeneous symptoms. The nature of the studies precludes a precise case definition or evaluation of risk factors. There is an urgent need for prospective, robust, standardised controlled studies into aetiology, risk factors, and biomarkers to characterise Long Covid in different at-risk populations and settings.\n\nSystematic review registrationThe protocol was prospectively registered on the PROSPERO database (CRD42020211131).\n\nSection 1: What is already known?O_LIA significant number of people continue to describe ongoing symptoms long after the acute phase of Covid-19, often referred to as Long Covid.\nC_LIO_LILong Covid is a heterogeneous condition with an uncertain prevalence, for which there is currently no precise case definition.\nC_LI\n\nSection 2: What are the new findings?O_LIThis living systematic review provides a comprehensive summary of peer-reviewed published evidence on persistent symptoms of Covid-19 and will be regularly updated as new evidence emerges.\nC_LIO_LIThe breadth of reported symptoms suggests a complex, heterogeneous condition affecting both those who were hospitalised and those managed in the community.\nC_LIO_LIOur review identifies weakness (41%; 95% CI 25% to 59%), general malaise (33%; 95% confidence interval 15% to 57%), fatigue (31%; 95% CI 24% to 39%), concentration impairment (26%; 95% CI 21% to 32%) and breathlessness (25%; 95% CI 18% to 34%) as the most common symptoms.\nC_LI\n\nSection 3: What do the new findings imply?O_LIThe current evidence base of the clinical spectrum of Long Covid is limited, based on heterogenous data, and vulnerable to biases, hence caution should be used when interpreting or generalising the results.\nC_LIO_LIOur review identifies areas where further Long Covid research is critically needed to help characterise Long Covid in different populations and define its aetiology, risk factors, and biomarkers, as well as the impact on variants of concern and vaccination on long term outcomes.\nC_LI", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Melina Michelen", - "author_inst": "City, University of London" - }, - { - "author_name": "Vincent Cheng", - "author_inst": "University of Bristol" - }, - { - "author_name": "Lakshmi Manoharan", - "author_inst": "University of Oxford" - }, - { - "author_name": "Natalie Elkheir", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Drew Dagens", - "author_inst": "University of Oxford" - }, - { - "author_name": "Claire Hastie", - "author_inst": "Long Covid Support" - }, - { - "author_name": "Margaret O'Hara", - "author_inst": "Long Covid Support" - }, - { - "author_name": "Jake Suett", - "author_inst": "Queen Elizabeth Hospital, Kings Lynn" - }, - { - "author_name": "Dania T Dahmash", - "author_inst": "2.\tISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK" - }, - { - "author_name": "Polina Bugaeva", - "author_inst": "Julius-Maximilians-Universitat Wurzburg, Wurzburg, Germany" - }, - { - "author_name": "Ishmeala Rigby", - "author_inst": "2.\tISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK" - }, - { - "author_name": "Daniel Munblit", - "author_inst": "Imperial College London" - }, - { - "author_name": "Eli Harriss", - "author_inst": "Bodleian Health Care Libraries, University of Oxford, Oxford, UK" - }, - { - "author_name": "Amanda Burls", - "author_inst": "City, University of London" - }, - { - "author_name": "Carol Foote", - "author_inst": "Freelance" - }, - { - "author_name": "Janet T Scott", - "author_inst": "MRC-University of Glasgow Center for Virus research" - }, - { - "author_name": "Gail Carson", - "author_inst": "University of Oxford" - }, - { - "author_name": "Piero L Olliaro", - "author_inst": "University of Oxford" - }, - { - "author_name": "Louise Sigfrid", - "author_inst": "University of Oxford" - }, - { - "author_name": "Charitini Stavropoulou", - "author_inst": "City, University of London" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.12.07.20245001", "rel_title": "Health Signatures During COVID-19: A Precision Fitness Case Study", @@ -1023096,6 +1024675,61 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.12.08.416636", + "rel_title": "Persistent Cellular Immunity to SARS-CoV-2 Infection", + "rel_date": "2020-12-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.08.416636", + "rel_abs": "SARS-CoV-2 is responsible for an ongoing pandemic that affected millions of individuals around the globe. To gain further understanding of the immune response in recovered individuals we measured T cell responses in paired samples obtained an average of 1.3 and 6.1 months after infection from 41 individuals. The data indicate that recovered individuals show persistent polyfunctional SARS-CoV-2 antigen specific memory that could contribute to rapid recall responses. In addition, recovered individuals show enduring immune alterations in relative numbers of CD4+ and CD8+ T cells, expression of activation/exhaustion markers, and cell division.\n\nSummaryWe show that SARS-CoV-2 infection elicits broadly reactive and highly functional memory T cell responses that persist 6 months after infection. In addition, recovered individuals show enduring immune alterations in CD4+ and CD8+ T cells compartments.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Gaelle Breton", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Pilar Mendoza", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Thomas Hagglof", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Thiago Y. Oliveira", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Dennis Schaefer-Babajew", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Christian Gaebler", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Martina Turroja", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Arlene Hurley", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Marina Caskey", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Michel C. Nussenzweig", + "author_inst": "The Rockefeller University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.12.08.416297", "rel_title": "Complete Protection of Nasal and Lung Airways Against SARS-CoV-2 Challenge by Antibody Plus Th1 Dominant N- and S-Specific T-Cell Responses to Subcutaneous Prime and Thermally-Stable Oral Boost Bivalent hAd5 Vaccination in an NHP Study", @@ -1023979,141 +1025613,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.07.20245274", - "rel_title": "Single-cell RNA sequencing reveals in vivo signatures of SARS-CoV-2-reactive T cells through 'reverse phenotyping'", - "rel_date": "2020-12-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.07.20245274", - "rel_abs": "The in vivo phenotypic profile of T cells reactive to severe acute respiratory syndrome (SARS)-CoV-2 antigens remains poorly understood. Conventional methods to detect antigen-reactive T cells require in vitro antigenic re-stimulation or highly individualized peptide-human leukocyte antigen (pHLA) multimers. Here, we used single-cell RNA sequencing to identify and profile SARS-CoV-2-reactive T cells from Coronavirus Disease 2019 (COVID-19) patients. To do so, we induced transcriptional shifts by antigenic stimulation in vitro and took advantage of natural T cell receptor (TCR) sequences of clonally expanded T cells as barcodes for reverse phenotyping. This allowed identification of SARS-CoV-2-reactive TCRs and revealed phenotypic effects introduced by antigen-specific stimulation. We characterized transcriptional signatures of currently and previously activated SARS-CoV-2-reactive T cells, and showed correspondence with phenotypes of T cells from the respiratory tract of patients with severe disease in the presence or absence of virus in independent cohorts. Reverse phenotyping is a powerful tool to provide an integrated insight into cellular states of SARS-CoV-2-reactive T cells across tissues and activation states.", - "rel_num_authors": 30, - "rel_authors": [ - { - "author_name": "David S Fischer", - "author_inst": "Institute of Computational Biology, Helmholtz Zentrum Muenchen, Neuherberg, Germany" - }, - { - "author_name": "Meshal I Ansari", - "author_inst": "Institute of Computational Biology, Helmholtz Zentrum Muenchen, Neuherberg, Germany; Institute of Lung Biology and Disease and Comprehensive Pneumology Center w" - }, - { - "author_name": "Karolin Wagner", - "author_inst": "Institute for Medical Microbiology, Immunology and Hygiene, Technische Universitaet Muenchen (TUM), Munich, Germany" - }, - { - "author_name": "Sebastian Jarosch", - "author_inst": "Institute for Medical Microbiology, Immunology and Hygiene, Technische Universitaet Muenchen (TUM), Munich, Germany" - }, - { - "author_name": "Yiyi Huang", - "author_inst": "Institute of Virology, Technische Universitaet Muenchen (TUM), Munich, Germany" - }, - { - "author_name": "Christoph H Mayr", - "author_inst": "Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Muenchen, Member of the German Center for" - }, - { - "author_name": "Maximilian Strunz", - "author_inst": "Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Muenchen, Member of the German Center for" - }, - { - "author_name": "Niklas J Lang", - "author_inst": "Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Muenchen, Member of the German Center for" - }, - { - "author_name": "Elvira D'Ippolito", - "author_inst": "Institute for Medical Microbiology, Immunology and Hygiene, Technische Universitaet Muenchen (TUM), Munich, Germany" - }, - { - "author_name": "Monika Hammel", - "author_inst": "Institute for Medical Microbiology, Immunology and Hygiene, Technische Universitaet Muenchen (TUM), Munich, Germany" - }, - { - "author_name": "Laura Mateyka", - "author_inst": "Institute for Medical Microbiology, Immunology and Hygiene, Technische Universitaet Muenchen (TUM), Munich, Germany" - }, - { - "author_name": "Simone Weber", - "author_inst": "Institute for Medical Microbiology, Immunology and Hygiene, Technische Universitaet Muenchen (TUM), Munich, Germany" - }, - { - "author_name": "Lisa S Wolff", - "author_inst": "Institute of Virology, Technische Universitaet Muenchen (TUM), Munich, Germany" - }, - { - "author_name": "Klaus Witter", - "author_inst": "Laboratory of Immunogenetics and Molecular Diagnostics, Department of Transfusion Medicine, Cell Therapeutic Agents and Hemostaseology, Hospital of the Ludwig-M" - }, - { - "author_name": "Isis E Fernandez", - "author_inst": "Department of Internal Medicine V, Ludwig-Maximilians University (LMU) Munich, Member of the German Center for Lung Research (DZL), CPC-M bioArchive, Munich, Ge" - }, - { - "author_name": "Gabriela Leuschner", - "author_inst": "Department of Internal Medicine V, Ludwig-Maximilians University (LMU) Munich, Member of the German Center for Lung Research (DZL), CPC-M bioArchive, Munich, Ge" - }, - { - "author_name": "Katrin Milger", - "author_inst": "Department of Internal Medicine V, Ludwig-Maximilians University (LMU) Munich, Member of the German Center for Lung Research (DZL), CPC-M bioArchive, Munich, Ge" - }, - { - "author_name": "Marion Frankenberger", - "author_inst": "Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Muenchen, Member of the German Center for" - }, - { - "author_name": "Lorenz Nowak", - "author_inst": "Department of Internal Medicine V, Hospital of the Ludwig-Maximilians University (LMU) Munich, and Asklepios Lung Clinic Munich-Gauting, Member of the German Ce" - }, - { - "author_name": "Katharina Heinig", - "author_inst": "Department of Internal Medicine V, Hospital of the Ludwig-Maximilians University (LMU) Munich, and Asklepios Lung Clinic Munich-Gauting, Member of the German Ce" - }, - { - "author_name": "Ina Koch", - "author_inst": "Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Muenchen, Member of the German Center for" - }, - { - "author_name": "Mircea G Stoleriu", - "author_inst": "Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Muenchen, Member of the German Center for" - }, - { - "author_name": "Anne Hilgendorff", - "author_inst": "Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Muenchen, Member of the German Center for" - }, - { - "author_name": "Juergen Behr", - "author_inst": "Department of Internal Medicine V, Ludwig-Maximilians University (LMU) Munich, Member of the German Center for Lung Research (DZL), CPC-M bioArchive, Munich, Ge" - }, - { - "author_name": "Andreas Pichlmair", - "author_inst": "Institute of Virology, Technische Universitaet Muenchen (TUM), Munich, Germany; German Center for Infection Research (DZIF), partner site Munich, Munich, German" - }, - { - "author_name": "Benjamin Schubert", - "author_inst": "Institute of Computational Biology, Helmholtz Zentrum Muenchen, Neuherberg, Germany; Department of Mathematics, Technical University of Munich, Garching, German" - }, - { - "author_name": "Fabian J Theis", - "author_inst": "Institute of Computational Biology, Helmholtz Zentrum Muenchen, Neuherberg, Germany; Department of Mathematics, Technical University of Munich, Garching, German" - }, - { - "author_name": "Dirk H Busch", - "author_inst": "Institute for Medical Microbiology, Immunology and Hygiene, Technische Universitaet Muenchen (TUM), Munich, Germany; German Center for Infection Research (DZIF)" - }, - { - "author_name": "Herbert B Schiller", - "author_inst": "Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Muenchen, Member of the German Center for" - }, - { - "author_name": "Kilian Schober", - "author_inst": "Institute for Medical Microbiology, Immunology and Hygiene, Technische Universitaet Muenchen (TUM), Munich, Germany" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.06.20244905", "rel_title": "Optimizing SARS-CoV-2 molecular diagnostic using N gene target: insights about reinfection", @@ -1024784,6 +1026283,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.04.20243410", + "rel_title": "At-home self-testing of teachers with a SARS-CoV-2 rapid antigen test to reduce potential transmissions in schools", + "rel_date": "2020-12-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.04.20243410", + "rel_abs": "BackgroundRapid antigen tests for SARS-CoV-2 became available recently, offering an opportunity to vastly increase testing capacities. Antigen tests offer lower sensitivity than the gold standard, RT-PCR, but rapid sample-to-answer time. High-frequency testing with an antigen test may offset the lower sensitivity, and testing can be done with at-home collection of samples, offering potential benefit in screening efforts. In this study, we set out to evaluate the practical application of self-performed high-frequency antigen test in a school setting.\n\nMethodA total of 711 teachers from 86 schools were enrolled in a seven-week study. After instruction, participants tested themselves every 48 hours at home with a rapid antigen test for SARS-CoV-2 (target: nucleocapsid protein) in a self-collected anterior nasal swab. Positive results in the antigen test were confirmed via RT-PCR from the same sample that had been determined to be positive by the study participant. A questionnaire was given to all participants to evaluate whether the test failed to detect infection.\n\nFindings10 836 tests from 602 teachers were recorded and analyzed. A total of five confirmed cases of viral shedding of SARS-CoV-2 was detected by use of the antigen test. One study participant with a SARS-CoV-2 infection was presymptomatic and four were mildly symptomatic at the time of the antigen test. Sixteen false positive antigen tests (0.15% of all tests) were reported, predominantly when the local incidence in the general population was low. In four cases, the study participant reported that a PCR had detected a SARS-CoV-2 infection, but the antigen test was negative, indicating a false negative result.\n\nInterpretationHigh-frequency, self-performed rapid antigen tests can detect individuals with a SARS-CoV-2 infection, and therefore potentially reduce transmissions. Testing may be most beneficial when applied during high local incidence of SARS-CoV-2 infections and when mild or atypical symptoms are present. To avoid a high rate of false positive results, a test with optimized specificity should be used.\n\nFundingThe study was commissioned and funded by the Hessian Ministry of Education and the Hessian Ministry of Integration and Social Affairs.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Sebastian Hoehl", + "author_inst": "Institute for Medical Virology, Goethe University Frankfurt" + }, + { + "author_name": "Barbara Schenk", + "author_inst": "Institute of Medical Virology, Goethe University Frankfurt" + }, + { + "author_name": "Olga Rudych", + "author_inst": "Institute of Medical Virology, Goethe University Frankfurt" + }, + { + "author_name": "Stephan Goettig", + "author_inst": "Institute of Medical Microbiology, Goethe University Frankfurt" + }, + { + "author_name": "Ivo Foppa", + "author_inst": "Hessisches Landespruefungs- und Untersuchungsamt im Gesundheitswesen (HLPUG), Abteilung I (Gesundheitsschutz)" + }, + { + "author_name": "Niko Kohmer", + "author_inst": "Institute of Medical Virology, Goethe University Frankfurt" + }, + { + "author_name": "Onur Karaca", + "author_inst": "Institute of Medical Virology, Goethe University Frankfurt" + }, + { + "author_name": "Tuna Toptan", + "author_inst": "University Hospital Frankfurt" + }, + { + "author_name": "Sandra Ciesek", + "author_inst": "University Hospital, Goethe University Frankfurt" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.12.04.20243972", "rel_title": "Use of Public Data to Describe COVID-19 Contact Tracing in China during January 20-February 29, 2020", @@ -1025428,37 +1026978,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hiv aids" }, - { - "rel_doi": "10.1101/2020.12.05.20244483", - "rel_title": "Features and outcomes of secondary sepsis and urinary tract infections in COVID-19 patients treated with stem cell nebulization", - "rel_date": "2020-12-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.05.20244483", - "rel_abs": "BackgroundCOVID-19 is the defining global crisis of our time. Secondary complication such as urinary tract infections and sepsis, worsen the already established problem, creating a new challenge.\n\nObjectiveTo characterize the features and outcomes in COVID-19 patients with sepsis and urinary tract infection.\n\nMethodsAn observational and analytical study was conducted within the framework of the SENTAD COVID clinical trial at the Abu Dhabi Stem Cells Center, were the patients received a nebulization therapy with the use of autologous stem cells (group A). Those patients were compared with a not stem cells treated control arm (group B), and both received the UAE COVID 19 standard management. An analysis of the culture samples, antimicrobial agents and the efficacy of the therapy on patients outcomes was done.\n\nResultsA significant difference between the groups was found in the UTI incidence (p=*0.0206). Patients in group A showed a lower tendency to sepsis in comparison with group B (7% vs 21%), HR=0.35, (95% Confidence Interval: 0.13 - 0.91), p=0.0175. It was calculated a NNT=7.3. Candida albicans was the most frequently agent causing sepsis and UTI. The massive use of broad-spectrum antimicrobials was striking.\n\nConclusionsWe found a protective factor of stem cells against secondary infection in COVID 19 cases, in terms of sepsis and UTI. The suggested immunomodulatory effect of stem cells offers a therapeutic strategy to manage the disease and avoid several complications. Antimicrobial agents can lead to increased opportunistic infections, so a rational approach to these treatments must be considered.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Gina Marcela Torres Zambrano", - "author_inst": "ADSCC" - }, - { - "author_name": "Rene Antonio Rivero", - "author_inst": "ADSCC" - }, - { - "author_name": "Carlos Villegas Valverde", - "author_inst": "ADSCC" - }, - { - "author_name": "Yendry Ventura Carmenate", - "author_inst": "ADSCC" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.04.20230755", "rel_title": "Breath biomarkers of pediatric SARS-CoV-2 infection: a pilot study", @@ -1026246,6 +1027765,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.05.20244376", + "rel_title": "Rt2: computing and visualising COVID-19 epidemics temporal reproduction number", + "rel_date": "2020-12-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.05.20244376", + "rel_abs": "Analysing the spread of COVID-19 epidemics in a timely manner is essential for public health authorities. However, raw numbers may be misleading because of spatial and temporal variations. We introduce Rt2, an R-program with a shiny interface, which uses incidence data, i.e. number of new cases per day, to compute variations in the temporal reproduction number ([R]t), which corresponds to the average number of secondary infections caused by an infected person. This number is computed with the R0 package, which better captures past variations, and the EpiEstim package, which provides a more accurate estimate of current values. [R]t can be computed in different countries using either the daily number of new cases or of deaths. For France, these numbers can also be computed at the regional and departmental level using also daily numbers of hospital and ICU admissions. Finally, in addition to [R]t, we represent the incidence using a one-week sliding window to buffer daily variations. Overall, Rt2 provides an accurate and timely overview of the state and speed of spread of COVID-19 epidemics at different scales, using different metrics.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Bastien Reyn\u00e9", + "author_inst": "Universit\u00e9 de Montpellier" + }, + { + "author_name": "Gonch\u00e9 Danesh", + "author_inst": "Universit\u00e9 de Montpellier" + }, + { + "author_name": "Samuel Alizon", + "author_inst": "CNRS" + }, + { + "author_name": "Mircea T. Sofonea", + "author_inst": "Universit\u00e9 de Montpellier" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.06.20244780", "rel_title": "Seasonality and Progression of COVID-19 among Countries With or Without Lock-downs.", @@ -1027070,81 +1028620,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.11.28.20240150", - "rel_title": "Machine learning analysis highlights the down-trending of the proportion of COVID-19 patients with a distinct laboratory result profile", - "rel_date": "2020-12-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.28.20240150", - "rel_abs": "BackgroundNew York City (NYC) experienced an initial surge and gradual decline in the number of SARS-CoV-2 confirmed cases in 2020. A change in the pattern of laboratory test results in COVID-19 patients over this time has not been reported or correlated with patient outcome.\n\nMethodsWe performed a retrospective study of routine laboratory and SARS-CoV-2 RT-PCR test results from 5,785 patients evaluated in a NYC hospital emergency department from March to June employing machine learning analysis.\n\nResultsA COVID-19 high-risk laboratory test result profile (COVID19-HRP), consisting of 21 routine blood tests, was identified to characterize the SARS-CoV-2 patients. Approximately half of the SARS-CoV-2 positive patients had the distinct COVID19-HRP that separated them from SARS-CoV-2 negative patients. SARS-CoV-2 patients with the COVID19-HRP had higher SARS-CoV-2 viral loads, determined by cycle-threshold values from the RT-PCR, and poorer clinical outcome compared to other positive patients without COVID19-HRP. Furthermore, the percentage of SARS-CoV-2 patients with the COVID19-HRP has significantly decreased from March/April to May/June. Notably, viral load in the SARS-CoV-2 patients declined and their laboratory profile became less distinguishable from SARS-CoV-2 negative patients in the later phase.\n\nConclusionsOur study visualized the down-trending of the proportion of SARS-CoV-2 patients with the distinct COVID19-HRP. This analysis could become an important tool in COVID-19 population disease severity tracking and prediction. In addition, this analysis may play an important role in prioritizing high-risk patients, assisting in patient triaging and optimizing the usage of resources.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "He S Yang", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Yu Hou", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Hao Zhang", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Amy Chadburn", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Lars F Westblade", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Richard Fedeli", - "author_inst": "New York-Presbyterian Hospital/Weill Cornell Medical Campus" - }, - { - "author_name": "Peter AD Steel", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Sabrina E Racine-Brzostek", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Priya Velu", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Jorge L Sepulveda", - "author_inst": "George Washington University" - }, - { - "author_name": "Michael J Satlin", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Melissa M Cushing", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Rainu Kaushal", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Zhen Zhao", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Fei Wang", - "author_inst": "Weill Cornell Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.05.413377", "rel_title": "Whole Genome Sequencing for Revealing the Point Mutations of SARS-CoV-2 Genome in Bangladeshi Isolates and their Structural Effects on Viral Proteins", @@ -1027960,6 +1029435,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.02.20242180", + "rel_title": "ABO-RH blood group and risk of covid-19 in a moroccan population", + "rel_date": "2020-12-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.02.20242180", + "rel_abs": "IntroductionGiven the rapid spread, significant morbidity and mortality associated with COVID-19, there has been scientific interest in obtaining data detailing the factors influencing the risk of COVID-19 infection. The aim of this study was to reveal a possible association between the ABO-RH system and the risk of COVID-19 in the Moroccan population.\n\nMaterials and methodsThis is an analytical cross-sectional study. It was carried out on 1094 patients for the diagnosis of Covid-19 by Rt-PCR at the Moulay Ismail military hospital in the province of Meknes. All Rt-PCR negative individuals were used as a comparison group.\n\nResultsAmong the 1094 individuals who were diagnosed, RT-PCR for detection of SARS-CoV-2 was positive for 242 individuals. Comparison of the proportions of blood groups of the two groups showed that the proportion of blood group A in patients with COVID-19 was significantly higher than in people in the comparison group (P = 0.007), while the proportion of blood group O in patients with COVID-19 was significantly lower than in people in the control group (P = 0.017). Comparison of the Rh blood groups of the two groups did not find a significant association (P = 0.608).\n\nConclusionAs demonstrated by several previous studies, we concluded that blood group A was associated with a higher risk of acquiring COVID-19. Equally, the O blood group was associated with a lower risk of infection.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Mourad Belaouni", + "author_inst": "Moulay Ismail military hospital of Meknes" + }, + { + "author_name": "Elhoucine Malki", + "author_inst": "Moulay Ismail Military Hospital of Meknes" + }, + { + "author_name": "Rabii El Bahraouy", + "author_inst": "Moulay Ismail Military Hospital of Meknes" + }, + { + "author_name": "Bouchra El Maliki", + "author_inst": "Hassan II University, Faculty of Medicine and Pharmacy" + }, + { + "author_name": "Mohammed Er-Rami", + "author_inst": "Moulay Ismail Military Hospital of Meknes" + }, + { + "author_name": "Houcine Louzi", + "author_inst": "Moulay Ismail Military Hospital of Meknes" + }, + { + "author_name": "Khaled Lahmadi", + "author_inst": "Moulay Ismail Military Hospital of Meknes" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.02.20242750", "rel_title": "Clinical Evaluation of a COVID-19 Antibody Lateral Flow Assay using Point of Care Samples", @@ -1029144,73 +1030662,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2020.12.04.409144", - "rel_title": "SARS-CoV-2 Spike Protein Impairs Endothelial Function via Downregulation of ACE2", - "rel_date": "2020-12-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.04.409144", - "rel_abs": "Coronavirus disease 2019 (COVID-19) includes the cardiovascular complications in addition to respiratory disease. SARS-CoV-2 infection impairs endothelial function and induces vascular inflammation, leading to endotheliitis. SARS-CoV-2 infection relies on the binding of Spike glycoprotein (S protein) to angiotensin converting enzyme 2 (ACE2) in the host cells. We show here that S protein alone can damage vascular endothelial cells (ECs) in vitro and in vivo, manifested by impaired mitochondrial function, decreased ACE2 expression and eNOS activity, and increased glycolysis. The underlying mechanism involves S protein downregulation of AMPK and upregulation of MDM2, causing ACE2 destabilization. Thus, the S protein-exerted vascular endothelial damage via ACE2 downregulation overrides the decreased virus infectivity.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Cara R. Schiavon", - "author_inst": "Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA" - }, - { - "author_name": "Ming He", - "author_inst": "Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA" - }, - { - "author_name": "Hui Shen", - "author_inst": "Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA" - }, - { - "author_name": "Yichi Zhang", - "author_inst": "Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA" - }, - { - "author_name": "Yoshitake Cho", - "author_inst": "Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA" - }, - { - "author_name": "Leonardo Andrade", - "author_inst": "Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA" - }, - { - "author_name": "Gerry S. Shadel", - "author_inst": "Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA" - }, - { - "author_name": "Mark Hepokoski", - "author_inst": "Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA" - }, - { - "author_name": "Jin Zhang", - "author_inst": "Department of Pharmacology, University of California, San Diego, La Jolla, CA" - }, - { - "author_name": "Jason X.-J. Yuan", - "author_inst": "Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA" - }, - { - "author_name": "Atul Malhotra", - "author_inst": "Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA" - }, - { - "author_name": "Uri Manor", - "author_inst": "Salk Institute for Biological Studies" - }, - { - "author_name": "John Y-J. Shyy", - "author_inst": "Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "pathology" - }, { "rel_doi": "10.1101/2020.12.03.20243311", "rel_title": "Screening for SARS-CoV-2 infection in asymptomatic individuals using the Panbio COVID-19 Antigen Rapid Test (Abbott) compared to RT-qPCR", @@ -1029830,6 +1031281,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.03.20243626", + "rel_title": "A holistic approach for suppression of COVID-19 spread in workplaces and universities", + "rel_date": "2020-12-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.03.20243626", + "rel_abs": "As society has moved past the initial phase of the COVID-19 crisis that relied on broad-spectrum shutdowns as a stopgap method, industries and institutions have faced the daunting question of how to return to a stabilized state of activities and more fully reopen the economy. A core problem is how to return people to their workplaces and educational institutions in a manner that is safe, ethical, grounded in science, and takes into account the unique factors and needs of each organization and community. In this paper, we introduce an epidemiological model (the \"Community-Workplace\" model) that accounts for SARS-CoV-2 transmission within the workplace, within the surrounding community, and between them. We use this multi-group deterministic compartmental model to consider various testing strategies that, together with symptom screening, exposure tracking, and nonpharmaceutical interventions (NPI) such as mask wearing and social distancing, aim to reduce disease spread in the workplace. Our framework is designed to be adaptable to a variety of specific workplace environments to support planning efforts as reopenings continue.\n\nUsing this model, we consider a number of case studies, including an office workplace, a factory floor, and a university campus. Analysis of these cases illustrates that continuous testing can help a workplace avoid an outbreak by reducing undetected infectiousness even in high-contact environments. We find that a university setting, where individuals spend more time on campus and have a higher contact load, requires more testing to remain safe, compared to a factory or office setting. Under the modeling assumptions, we find that maintaining a prevalence below 3% can be achieved in an office setting by testing its workforce every two weeks, whereas achieving this same goal for a university could require as much as fourfold more testing (i.e., testing the entire campus population twice a week). Our model also simulates the dynamics of reduced spread that result from the introduction of mitigation measures when test results reveal the early stages of a workplace outbreak. We use this to show that a vigilant university that has the ability to quickly react to outbreaks can be justified in implementing testing at the same rate as a lower-risk office workplace. Finally, we quantify the devastating impact that an outbreak in a small-town college could have on the surrounding community, which supports the notion that communities can be better protected by supporting their local places of business in preventing onsite spread of disease.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Sarah F Poole", + "author_inst": "Verily Life Sciences" + }, + { + "author_name": "Jessica Gronsbell", + "author_inst": "Verily Life Sciences" + }, + { + "author_name": "Dale Winter", + "author_inst": "Verily Life Sciences" + }, + { + "author_name": "Stefanie Nickels", + "author_inst": "Verily Life Sciences" + }, + { + "author_name": "Roie Levy", + "author_inst": "Verily Life Sciences" + }, + { + "author_name": "Bin Fu", + "author_inst": "Verily Life Sciences" + }, + { + "author_name": "Maximilien Burq", + "author_inst": "Verily Life Sciences" + }, + { + "author_name": "Sohrab Saeb", + "author_inst": "Verily Life Sciences" + }, + { + "author_name": "Matthew D Edwards", + "author_inst": "Verily Life Sciences" + }, + { + "author_name": "Michael K Behr", + "author_inst": "Verily Life Sciences" + }, + { + "author_name": "Vignesh Kumaresan", + "author_inst": "Verily Life Sciences" + }, + { + "author_name": "Alexander R Macalalad", + "author_inst": "Verily Life Sciences" + }, + { + "author_name": "Sneh Shah", + "author_inst": "Verily Life Sciences" + }, + { + "author_name": "Michelle Prevost", + "author_inst": "Verily Life Sciences" + }, + { + "author_name": "Nigel Snoad", + "author_inst": "Verily Life Sciences" + }, + { + "author_name": "Michael P Brenner", + "author_inst": "Google Research" + }, + { + "author_name": "Lance J Myers", + "author_inst": "Verily Life Sciences" + }, + { + "author_name": "Paul Varghese", + "author_inst": "Verily Life Sciences" + }, + { + "author_name": "Robert M Califf", + "author_inst": "Verily Life Sciences" + }, + { + "author_name": "Vindell Washington", + "author_inst": "Verily Life Sciences" + }, + { + "author_name": "Vivian S Lee", + "author_inst": "Verily Life Sciences" + }, + { + "author_name": "Menachem Fromer", + "author_inst": "Verily Life Sciences" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.03.20243584", "rel_title": "A Stochastic Compartmental Model for COVID-19", @@ -1030562,81 +1032116,6 @@ "type": "new results", "category": "physiology" }, - { - "rel_doi": "10.1101/2020.11.30.20240010", - "rel_title": "Is Point-of-Care testing feasible and safe in care homes in England? An exploratory usability and accuracy evaluation of Point-of-Care Polymerase Chain Reaction test for SARS-COV-2", - "rel_date": "2020-12-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.30.20240010", - "rel_abs": "IntroductionReliable rapid testing on COVID-19 is needed in care homes to reduce the risk of outbreaks and enable timely care. Point-of-care testing (POCT) in care homes could provide rapid actionable results. This study aimed to examine the usability and test performance of point of care polymerase chain reaction (PCR) for COVID-19 in care homes.\n\nMethodsPoint-of-care PCR for detection of SARS-COV2 was evaluated in a purposeful sample of four UK care homes. Test agreement with laboratory real-time PCR and usability and use errors were assessed.\n\nResultsPoint of care and laboratory polymerase chain reaction (PCR) tests were performed on 278 participants. The point of care and laboratory tests returned uncertain results or errors for 17 and 5 specimens respectively. Agreement analysis was conducted on 256 specimens. 175 were from staff: 162 asymptomatic; 13 symptomatic. 69 were from residents: 59 asymptomatic; 10 symptomatic. Asymptomatic specimens showed 83.3% (95% CI: 35.9%-99.6%) positive agreement and 98.7% negative agreement (95% CI: 96.2%-99.7%), with overall prevalence and bias-adjusted kappa (PABAK) of 0.965 (95% CI: 0.932 - 0.999). Symptomatic specimens showed 100% (95% CI: 2.5%-100%) positive agreement and 100% negative agreement (95% CI: 85.8%-100%), with overall PABAK of 1. No usability-related hazards emerged from this exploratory study.\n\nConclusionApplications of point-of-care PCR testing in care homes can be considered with appropriate preparatory steps and safeguards. Agreement between POCT and laboratory PCR was good. Further diagnostic accuracy evaluations and in-service evaluation studies should be conducted, if the test is to be implemented more widely, to build greater certainty on this initial exploratory analysis.\n\nKey pointsO_LIPoint of care tests (POCT) in care homes are feasible and could increase testing capacity for the control of COVID-19 infection.\nC_LIO_LIThe test of agreement between POCT and laboratory PCR for care home residents and the staff was good.\nC_LIO_LIAdoption of POCT in care homes can be considered with appropriate preparatory steps and safeguards in place.\nC_LIO_LIRepetitive errors and test malfunctioning can be mitigated with bespoke training for care home staff.\nC_LIO_LIIntegrated care pathways should be investigated to test the high variability of the context of use.\nC_LI", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Massimo Micocci", - "author_inst": "NIHR London In Vitro Diagnostics Co-operative, Dept of Surgery and Cancer, Faculty of Medicine, Imperial College London St. Mary's Hospital London" - }, - { - "author_name": "Adam Gordon", - "author_inst": "Division of Medical Sciences and Graduate Entry Medicine, University of Nottingham, Nottingham, UK;NIHR Applied Research Collaboration-East Midlands (ARC-EM), N" - }, - { - "author_name": "Mikyung Kelly Seo", - "author_inst": "NIHR London In Vitro Diagnostics Co-operative, Dept of Surgery and Cancer, Faculty of Medicine, Imperial College London St. Mary's Hospital London" - }, - { - "author_name": "Joy A Allen", - "author_inst": "NIHR Newcastle In Vitro Diagnostics Co-operative, Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK" - }, - { - "author_name": "Kerrie Davies", - "author_inst": "Healthcare Associated Infections Research Group, University of Leeds and Leeds Teaching Hospitals NHS Trust, Leeds, UK" - }, - { - "author_name": "Dan Lasserson", - "author_inst": "Warwick Medical School, University of Warwick, UK" - }, - { - "author_name": "Carl Thompson", - "author_inst": "School of Healthcare, University of Leeds, Leeds, UK" - }, - { - "author_name": "Karen Spilsbury", - "author_inst": "School of Healthcare, University of Leeds, Leeds, UK; NIHR Applied Research Collaboration Yorkshire and Humber, UK" - }, - { - "author_name": "Cyd Akrill", - "author_inst": "Springfield Healthcare, Leeds, UK" - }, - { - "author_name": "Ros Heath", - "author_inst": "Landermeads Nursing Home, Nottingham, UK" - }, - { - "author_name": "Anita Astle", - "author_inst": "Wren Hall Nursing Home, Selston, UK" - }, - { - "author_name": "Claire Sharpe", - "author_inst": "Ashmere Nottinghamshire Ltd, Notts, UK" - }, - { - "author_name": "Rafael Perera", - "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, UK" - }, - { - "author_name": "Gail Hayward", - "author_inst": "NIHR Community Healthcare MedTech and IVD Co-operative,Oxford,UK" - }, - { - "author_name": "Peter Buckle", - "author_inst": "NIHR London In Vitro Diagnostics Co-operative, Dept of Surgery and Cancer, Faculty of Medicine, Imperial College London St. Mary's Hospital London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2020.11.26.20229989", "rel_title": "Application of respiratory metagenomics for COVID-19 patients on the intensive care unit to inform appropriate initial antimicrobial treatment and rapid detection of nosocomial transmission", @@ -1031292,6 +1032771,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.12.01.20242313", + "rel_title": "Effect of Vitamin D deficiency on COVID-19 status: A systematic review", + "rel_date": "2020-12-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.01.20242313", + "rel_abs": "BackgroundOne major micronutrient known to have a possible protective effect against COVID-19 disease is vitamin D. This systematic review sought to identify and synthesise available evidence to aid the understanding of the possible effect of vitamin D deficiency on COVID-19 status and health outcomes in COVID-19 patients.\n\nMethodsThree databases PubMed, ScienceDirect, and Google Scholar were searched systematically to obtain English language journal article published within 1/12/2019 and 3/11/2020. The search consisted of the terms (\"Vitamin D,\" OR \"25{square}Hydroxyvitamin D,\" OR \"Low Vitamin D.\") AND (\"COVID-19\" OR \"2019-nCoV\" OR \"Coronavirus\" OR \"SARS-CoV-2\") AND (\"disease severity\" OR \"IMV\" OR \"ICU admission\" OR \"mortality\" OR \"hospitalization\" OR \"infection\"). We followed the recommended PRISMA guidelines in executing this study. After going through the screening of the articles, eleven articles were included in the review.\n\nFindingsAlmost all the included studies reported a positive association between Vitamin D sufficiency and COVID-19 status and health outcomes. Vitamin D deficient patients (< 25 ng/mL) are 5.84 times [aOR=6.84, p=0.01] more likely to die from COVID-19 compared to the vitamin D sufficient people. Another study also found that Vitamin D deficiency is associated with higher risk of death with Hazard ratio (HR) 14.73, p<0.001. Vitamin D deficient (<12 ng/mL) people were 2.2 times [aOR=3.2, p=0.07] more likely to develop severe COVID-19 after adjusting for age, gender, obesity, cardiac disease, and kidney disease compared to the vitamin D sufficient people. One study found that after controlling for confounders, patients with low 25(OH)D (<30 ng/mL) level are more likely [aOR=1.45, p=<0.001] to be COVID-19 infected compared to the patients with 25(OH)D level >=30 ng/mL.\n\nConclusionFindings from the study included suggest Vitamin D may serve as a mitigating effect for covid-19 infection, severity and mortality. We recommend the need to encourage people to eat foods rich in vitamin D such as fish, red meat, liver and egg yolks whiles at the same time providing vitamin D supplements for individuals with COVID-19 in order to boost their immune systems.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Pranta Das", + "author_inst": "University of Dhaka" + }, + { + "author_name": "Nandeeta Samad", + "author_inst": "North South University" + }, + { + "author_name": "Bright Opoku Ahinkorah", + "author_inst": "University of Technology Sydney" + }, + { + "author_name": "Prince Peprah", + "author_inst": "University of New South Wales" + }, + { + "author_name": "Aliu Mohammed", + "author_inst": "University of Cape Coast" + }, + { + "author_name": "Abdul-Aziz Seidu", + "author_inst": "University of Cape Coast" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.12.01.20241729", "rel_title": "International estimates of intended uptake and refusal of COVID-19 vaccines: A rapid systematic review and meta-analysis of large nationally representative samples", @@ -1032004,25 +1033522,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.12.01.20242263", - "rel_title": "A Novel Model for Simulating COVID-19 Dynamics Through Layered Infection States that Integrate Concepts from Epidemiology, Biophysics and Medicine: SEI3R2S-Nrec", - "rel_date": "2020-12-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.01.20242263", - "rel_abs": "IntroductionEffectively modeling SARS-CoV-2/COVID-19 dynamics requires careful integration of population health (public health motivation) and recovery dynamics (medical interventions motivation). This manuscript proposes a minimal pandemic model, which conceptually separates \"complex adaptive systems\" (CAS) associated with social behavior and infrastructure (e.g., tractable input events modulating exposure) from idealized bio-CAS (e.g., the immune system). The proposed model structure extends the classic simple SEIR (susceptible, exposed, infected, resistant/recovered) uni-causal compartmental model, widely used in epidemiology, into an 8th-order functional network SEI3R2S-Nrec model structure, with infection partitioned into three severity states (e.g., starts in I1 [mostly asymptomatic], then I2 if notable symptoms, then I3 if ideally hospitalized) that connect via a lattice of fluxes to two \"resistant\" (R) states. Here Nrec (\"not recovered\") represents a placeholder for better tying emerging COVID-19 medical research findings with those from epidemiology.\n\nMethodsBorrowing from fuzzy logic, a given model represents a \"Universe of Discourse\" (UoD) that is based on assumptions. Nonlinear flux rates are implemented using the classic Hill function, widely used in the biochemical and pharmaceutical fields and intuitive for inclusion within differential equations. There is support for \"encounter\" input events that modulate ongoing E (exposures) fluxes via S{leftrightarrow}I1 and other I1/2/3 encounters, partitioned into a \"social/group\" (uSG(t)) behavioral subgroup (e.g., ideally informed by evolving science best-practices), and a smaller uTB(t) subgroup with added \"spreader\" lifestyle and event support. In addition to signal and flux trajectories (e.g., plotted over 300 days), key cumulative output metrics include fluxes such as I3[->]D deaths, I2[->]I3 hospital admittances, I1[->]I2 related to \"cases\" and R1+R2 resistant. The code, currently available as a well-commented Matlab Live Script file, uses a common modeling framework developed for a portfolio of other physiological models that tie to a planned textbook; an interactive web-based version will follow.\n\nResultsDefault population results are provided for the USA as a whole, three states in which this author has lived (Arizona, Wisconsin, Oregon), and several special hypothetical cases of idealized UoDs (e.g., nursing home; healthy lower-risk mostly on I1[->]R1 path to evaluate reinfection possibilities). Often known events were included (e.g., pulses for holiday weekends; Trump/governor-inspired summer outbreak in Arizona). Runs were mildly tuned by the author, in two stages: i) mild model-tuning (e.g., for risk demographics such as obesity), then ii) iterative input tuning to obtain similar overall March-thru-November curve shapes and appropriate cumulative numbers (recognizing limitations of data like \"cases\"). Predictions are consistent deaths, and CDC estimates of actual cases and immunity (e.g., antibodies). Results could be further refined by groups with more resources (human, data access, computational). It is hoped that its structure and causal predictions might prove helpful to policymakers, medical professionals, and \"on the ground\" managers of science-based interventions.\n\nDiscussion and Future DirectionsThese include: i) sensitivity of the model to parameters; ii) possible next steps for this SEI3R2S-Nrec framework such as dynamic sub-models to better address compartment-specific forms of population diversity (e.g., for E [host-parasite biophysics], Is [infection diversity], and/or Rs [immune diversity]); iii) models potential utility as a framework for applying optimal/feedback control engineering to help manage the ongoing pandemic response in the context of competing subcriteria and emerging new tools (e.g., more timely testing, vaccines); and iv) ways in which the Nrec medical submodel could be expanded to provide refined estimates of the types of tissue damage, impairments and dysfunction that are known byproducts of the COVID-19 disease process, including as a function of existing comorbidities.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Jack M Winters", - "author_inst": "Marquette University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.01.20241778", "rel_title": "Large parallel screen of saliva and nasopharyngeal swabs in a test center setting proofs utility of saliva as alternate specimen for SARS-CoV-2 detection by RT-PCR", @@ -1032778,6 +1034277,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "surgery" }, + { + "rel_doi": "10.1101/2020.11.27.20239913", + "rel_title": "Wearing masks and establishing COVID-19 areas reduces secondary attack risk in nursing homes", + "rel_date": "2020-12-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.27.20239913", + "rel_abs": "BackgroundCOVID-19 is spreading rapidly in nursing homes (NHs). It is urgent to evaluate the effect of infection prevention and control (IPC) measures to reduce COVID spreading.\n\nMethodsWe analysed COVID-19 outbreaks in 12 NH using rRT-PCR for SARS-CoV-2. We estimated secondary attack risks (SARs) and identified cofactors associated with the proportion of infected residents.\n\nResultsThe SAR was below 5%, suggesting a high efficiency of IPC measures. Mask-wearing or establishment of COVID-19 zones for infected residents were associated with lower SAR.\n\nConclusionsWearing masks and isolating potentially infected residents appear to limit SARS-CoV-2 spread in nursing homes.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Bastien Reyn\u00e9", + "author_inst": "Montpellier University" + }, + { + "author_name": "Christian Selinger", + "author_inst": "IRD" + }, + { + "author_name": "Mircea T. Sofonea", + "author_inst": "Univ. Montpellier" + }, + { + "author_name": "St\u00e9phanie Miot", + "author_inst": "CHU de Montpellier" + }, + { + "author_name": "Amandine Pisoni", + "author_inst": "CHU de Montpellier" + }, + { + "author_name": "Edouard TUAILLON", + "author_inst": "Montpellier University" + }, + { + "author_name": "Jean J Bousquet", + "author_inst": "CHU" + }, + { + "author_name": "Hubert Blain", + "author_inst": "CHU de Montpellier" + }, + { + "author_name": "Samuel Alizon", + "author_inst": "CNRS" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "geriatric medicine" + }, { "rel_doi": "10.1101/2020.11.23.20237404", "rel_title": "A COVID-19 transmission model informing medication development and supply chain needs", @@ -1033454,81 +1035004,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.30.20241265", - "rel_title": "Detection of the Novel SARS-CoV-2 European Lineage B.1.177 in Ontario, Canada", - "rel_date": "2020-12-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.30.20241265", - "rel_abs": "BackgroundTravel-related dissemination of SARS-CoV-2 continues to contribute to the global pandemic. A novel SARS-CoV-2 lineage (B.1.177) reportedly arose in Spain in the summer of 2020, with subsequent spread across Europe linked to travel by infected individuals. Surveillance and monitoring through the use of whole genome sequencing (WGS) offers insights into the global and local movement of pathogens such as SARS-CoV-2 and can detect introductions of novel variants.\n\nMethodsWe analyzed the genomes of SARS-CoV-2 sequenced for surveillance purposes from specimens received by Public Health Ontario (Sept 6 - Oct 10, 2020), collected from individuals in eastern Ontario. Taxonomic lineages were identified using pangolin (v2.08) and phylogenetic analysis incorporated publicly available genomes covering the same time period as the study sample. Epidemiological data collected from laboratory requisitions and standard reportable disease case investigation was integrated into the analysis.\n\nResultsGenomic surveillance identified a COVID-19 case with SARS-CoV-2 lineage B.1.177 from an individual in eastern Ontario in late September, 2020. The individual had recently returned from Europe. Genomic analysis with publicly available data indicate the most closely related genomes to this specimen were from Southern Europe. Genomic surveillance did not identify further cases with this lineage.\n\nConclusionsGenomic surveillance allowed for early detection of a novel SARS-CoV-2 lineage in Ontario which was deemed to be travel related. This type of genomic-based surveillance is a key tool to measure the effectiveness of public health measures such as mandatory self-isolation for returned travellers, aimed at preventing onward transmission of newly introduced lineages of SARS-CoV-2.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Jennifer L. Guthrie", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Sarah Teatero", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Sandra Zittermann", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Yao Chen", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Ashleigh Sullivan", - "author_inst": "Public Health Agency of Canada" - }, - { - "author_name": "Heather Rilkoff", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Esha Joshi", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Karthikeyan Sivaraman", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Richard de Borja", - "author_inst": "Ontario Institute for Cancer Research" - }, - { - "author_name": "Yogi Sundaravadanam", - "author_inst": "Ontario Institute for Cancer Research" - }, - { - "author_name": "Michael Laszloffy", - "author_inst": "Ontario Institute for Cancer Research" - }, - { - "author_name": "Lawrence Heisler", - "author_inst": "Ontario Institute for Cancer Research" - }, - { - "author_name": "Vanessa G. Allen", - "author_inst": "Ontario Institute for Cancer Research" - }, - { - "author_name": "Jared T. Simpson", - "author_inst": "Ontario Institute for Cancer Research" - }, - { - "author_name": "Nahuel Fittipaldi", - "author_inst": "Public Health Ontario" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.30.20241257", "rel_title": "Predictive accuracy of computer-aided versions of the on-admission National Early Warning Score in estimating the risk of COVID-19 for unplanned admission to hospital: a retrospective development and validation study", @@ -1034192,6 +1035667,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, + { + "rel_doi": "10.1101/2020.11.30.20241406", + "rel_title": "A Healthy Buildings Guideline for the COVID-19 Pandemic and Beyond", + "rel_date": "2020-12-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.30.20241406", + "rel_abs": "Public health experts have confirmed that airborne transmission of SARS-CoV-2 (COVID-19) is one of the primary mechanisms of infection (CDC, 2020). In addition to social distancing, mask wearing and hand washing, experts now recommend increasing the ventilation and filtration of indoor air. While there is widespread consensus on this general approach, to date there are no published guidelines for the levels of ventilation, filtration, etc. that are required to control the pandemic. This is an urgent concern because colder weather in the Northern Hemisphere has moved social activity indoors where the risk of infection is higher.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Clifford Federspiel", + "author_inst": "Vigilent" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.12.02.408229", "rel_title": "Novel Mutations in NSP1 and PLPro of SARS-CoV-2 NIB-1 Genome Mount for Effective Therapeutics", @@ -1035224,209 +1036718,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.12.01.404483", - "rel_title": "Topoisomerase 1 inhibition therapy protects against SARS-CoV-2-induced inflammation and death in animal models.", - "rel_date": "2020-12-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.01.404483", - "rel_abs": "The ongoing pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is currently affecting millions of lives worldwide. Large retrospective studies indicate that an elevated level of inflammatory cytokines and pro-inflammatory factors are associated with both increased disease severity and mortality. Here, using multidimensional epigenetic, transcriptional, in vitro and in vivo analyses, we report that Topoisomerase 1 (Top1) inhibition suppresses lethal inflammation induced by SARS-CoV-2. Therapeutic treatment with two doses of Topotecan (TPT), a FDA-approved Top1 inhibitor, suppresses infection-induced inflammation in hamsters. TPT treatment as late as four days post-infection reduces morbidity and rescues mortality in a transgenic mouse model. These results support the potential of Top1 inhibition as an effective host-directed therapy against severe SARS-CoV-2 infection. TPT and its derivatives are inexpensive clinical-grade inhibitors available in most countries. Clinical trials are needed to evaluate the efficacy of repurposing Top1 inhibitors for COVID-19 in humans.", - "rel_num_authors": 47, - "rel_authors": [ - { - "author_name": "Jessica Sook Yuin Ho", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA." - }, - { - "author_name": "Bobo Wing-Yee Mok", - "author_inst": "Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, L-501, Li Ka Shing" - }, - { - "author_name": "Laura Campisi", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA." - }, - { - "author_name": "Tristan Jordan", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA." - }, - { - "author_name": "Soner Yildiz", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA." - }, - { - "author_name": "Natasha N Gaudreault", - "author_inst": "Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS, 66506, USA" - }, - { - "author_name": "David A Meekins", - "author_inst": "Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS, 66506, USA" - }, - { - "author_name": "Sabarish V Indran", - "author_inst": "Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS, 66506, USA" - }, - { - "author_name": "Igor Morozov", - "author_inst": "Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS, 66506, USA" - }, - { - "author_name": "Jessie D Trujillo", - "author_inst": "Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS, 66506, USA" - }, - { - "author_name": "Yesai S Fstkchyan", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA." - }, - { - "author_name": "Raveen Rathnasinghe", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA." - }, - { - "author_name": "Zeyu Zhu", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA." - }, - { - "author_name": "Simin Zheng", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA." - }, - { - "author_name": "Nan Zhao", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA." - }, - { - "author_name": "Kris White", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA." - }, - { - "author_name": "Helen Ray-Jones", - "author_inst": "MRC London Institute of Medical Sciences, London W12 0NN, UK" - }, - { - "author_name": "Valeriya Malysheva", - "author_inst": "MRC London Institute of Medical Sciences, London W12 0NN, UK" - }, - { - "author_name": "Michiel J Thiecke", - "author_inst": "Enhanc3D Genomics Ltd, Cambridge CB22 0AT" - }, - { - "author_name": "Siu-Ying Lau", - "author_inst": "Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, L-501, Li Ka Shing" - }, - { - "author_name": "Honglian Liu", - "author_inst": "Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, L-501, Li Ka Shing" - }, - { - "author_name": "Anna Junxia Zhang", - "author_inst": "Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, L-501, Li Ka Shing" - }, - { - "author_name": "Andrew Chak-Yiu Lee", - "author_inst": "Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, L-501, Li Ka Shing" - }, - { - "author_name": "Wen-Chun Liu", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA." - }, - { - "author_name": "Teresa Aydillo", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA." - }, - { - "author_name": "Betsaida S Melo", - "author_inst": "Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.; Icahn Institute of Genomics and Multiscale Biology, Icahn Scho" - }, - { - "author_name": "Ernesto Guccione", - "author_inst": "Tisch Cancer Institute, Department of Oncological Sciences and Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York City, N" - }, - { - "author_name": "Robert Sebra", - "author_inst": "Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.; Icahn Institute of Genomics and Multiscale Biology, Icahn Scho" - }, - { - "author_name": "Elaine Shum", - "author_inst": "Division of Medical Oncology and Hematology, NYU Langone Perlmutter Cancer Center, New York, NY 10016, USA." - }, - { - "author_name": "Jan Bakker", - "author_inst": "Pontificia Universidad Catolica de Chile, Santiago, Chile; Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands; Editor in Chief, Journal " - }, - { - "author_name": "David A Kaufman", - "author_inst": "Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, NYU School of Medicine" - }, - { - "author_name": "Andre Moreira", - "author_inst": "Department of Pathology, New York University School of Medicine" - }, - { - "author_name": "Mariano Carossino", - "author_inst": "Louisiana Animal Disease Diagnostic Laboratory and Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Roug" - }, - { - "author_name": "Udeni B R Balasuriya", - "author_inst": "Louisiana Animal Disease Diagnostic Laboratory and Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Roug" - }, - { - "author_name": "Minji Byun", - "author_inst": "Department of Medicine, Clinical Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA." - }, - { - "author_name": "Randy A Albrecht", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Me" - }, - { - "author_name": "Michael Schotsaert", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Me" - }, - { - "author_name": "Adolfo Garcia-Sastre", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Me" - }, - { - "author_name": "Sumit K Chanda", - "author_inst": "Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037." - }, - { - "author_name": "Anand D Jeyasekharan", - "author_inst": "Department of Haematology-Oncology, National University Hospital and Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore." - }, - { - "author_name": "Benjamin R TenOever", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Me" - }, - { - "author_name": "Mikhail Spivakov", - "author_inst": "MRC London Institute of Medical Sciences, London W12 0NN, UK" - }, - { - "author_name": "Sven Heinz", - "author_inst": "Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92092, USA" - }, - { - "author_name": "Honglin Chen", - "author_inst": "Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, L-501, Li Ka Shing" - }, - { - "author_name": "Christopher Benner", - "author_inst": "Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92092, USA" - }, - { - "author_name": "Juergen A Richt", - "author_inst": "Center of Excellence for Emerging and Zoonotic Animal Diseases (CEEZAD), Kansas State University, Manhattan, KS; Diagnostic Medicine and Pathobiology, College o" - }, - { - "author_name": "Ivan Marazzi", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA." - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.12.01.406611", "rel_title": "Designed proteins assemble antibodies into modular nanocages", @@ -1036522,6 +1037813,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.29.20240374", + "rel_title": "Impact of the COVID-19 pandemic on infant and pediatric asthma: a multi-center survey using an administrative database in Japan", + "rel_date": "2020-11-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.29.20240374", + "rel_abs": "BackgroundLimited data are available on the relationship between infant and pediatric asthma and severe acute respiratory syndrome coronavirus 2 (COVID-19).\n\nPolitical limitations such as school closure may affect the treatment behavior of pediatric asthma. To investigate the trends of treatment behavior in the field of pediatrics during the COVID-19 pandemic.\n\nMethodsThis is a retrospective observational study using Diagnosis Procedure Combination (DPC) data from the Quality Indicator/Improvement Project (QIP) database. We identified children with asthma aged 15 years or younger who were patients from July 1, 2018, to June 30, 2020. The main outcome was a comparison between asthma patients treatment behavior before the COVID-19 pandemic and during the COVID-19 pandemic.\n\nWe statistically tested the admission volume changes based on the discharge date after adjusting for seasonality through a Fourier term using an interrupted time-series analysis (ITS).\n\nResultsWe identified 10,481 inpatients cases in 67 hospitals and 258,911 out-patients cases in 180 hospitals who were diagnosed with asthma. We performed ITS analysis for inpatients. The reduction in the number of patients during this period was estimated to be 232 (P=0.001). In addition, ITS analysis was performed for patients aged <3 years. The reduced number of patients during this period was estimated to be 155 (P<0.001).\n\nConclusionsWe found that the number of pediatric asthma patients dramatically decreased during the COVID-19 pandemic. We need to continue research into the trends of pediatric asthma patients after the COVID-19 pandemic in Japan.\n\nKey MessagesThere are increasingly available data on the relationship between adults asthma and COVID-19. However, in the fields of pediatrics, limited data are available. Patients with moderate to severe asthma who needed hospitalization dramatically decreased during the COVID-19 pandemic. Besides, doctors prescribed nebulizers more than metered-dose inhalers by the clinical guideline recommendation. Our findings reinforce the value of political inventions, such as school closure reduced the number of asthma attacks in infants and school-age children.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Seiko Bun", + "author_inst": "Kyoto University" + }, + { + "author_name": "Kenji Kishimoto", + "author_inst": "Kyoto university" + }, + { + "author_name": "Jung-ho Shin", + "author_inst": "Kyoto university" + }, + { + "author_name": "Daisuke Takada", + "author_inst": "Kyoto university" + }, + { + "author_name": "Tetsuji Morishita", + "author_inst": "Kyoto university" + }, + { + "author_name": "Susumu Kunisawa", + "author_inst": "Kyoto university" + }, + { + "author_name": "Yuichi Imanaka", + "author_inst": "Kyoto University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2020.11.25.20239038", "rel_title": "COVID-19 Workplace Outbreaks by Industry Sector and their Associated Household Transmission, Ontario, Canada, January to June, 2020", @@ -1037294,49 +1038628,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.26.20239186", - "rel_title": "Characteristics of COVID-19 patients admitted to a tertiary care hospital in Pune, India, and cost-effective predictors of intensive care treatment requirement", - "rel_date": "2020-11-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.26.20239186", - "rel_abs": "BackgroundMaharashtra is one of the worst affected states in this pandemic.2 As of 30th September, Maharashtra has in total 1.4 million cases with 38,000 deaths. Objective was to study associations of severity of disease and need for ICU treatment in COVID-19 patients.\n\nMethodsA retrospective study of clinical course in 800 hospitalized COVID-19 patients, and a predictive model of need for ICU treatment. Eight hundred consecutive patients admitted with confirmed COVID-19 disease.\n\nResultsAverage age was 41 years, 16% were <20 years of age, 55% were male, 50% were asymptomatic and 16% had at least one comorbidity. Using MoHFW India severity guidelines, 73% patients had mild, 6% moderate and 20% severe disease. Severity was associated with higher age, symptomatic presentation, elevated neutrophil and reduced lymphocyte counts and elevated inflammatory markers. Seventy-seven patients needed ICU treatment: they were older (56 years), more symptomatic and had lower SpO2 and abnormal chest X-ray and deranged hematology and biochemistry at admission. A model trained on the first 500 patients, using above variables predicted need for ICU treatment with sensitivity 80%, specificity 88% in subsequent 300 patients; exclusion of expensive laboratory tests did not affect accuracy.\n\nConclusionIn the early phase of COVID- 19 epidemic, a significant proportion of hospitalized patients were young and asymptomatic. Need for ICU treatment was predicted by simple measures including higher age, symptomatic onset, low SpO2 and abnormal chest X-ray. We propose a cost-effective model for referring patients for treatment at specialized COVID-19 hospitals.\n\nKey MessagesO_LIOf 800 patients, 73% had mild, 6% moderate and 20% had severe disease.\nC_LIO_LISeventy-seven patients (9.6%) required ICU treatment, 25 (3%) died.\nC_LIO_LIICU treatment was predicted by higher age, more symptomatic presentation, lower SpO2 and pneumonia on chest X-ray at admission.\nC_LIO_LIA machine learning model features in first 500 patients accurately predicted ICU treatment in subsequent 300 patients.\nC_LIO_LIA good clinical protocol, SpO2 and chest X-ray are adequate to predict and triage COVID-19 patients for hospital admissions in resource poor environments.\nC_LI", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Urvi B Shukla", - "author_inst": "Symbiosis University Hospital and Research Centre (SUHRC), Symbiosis International (Deemed University), Lavale, Mulshi, Pune, Maharashtra 412115" - }, - { - "author_name": "Sharvari Rahul Shukla", - "author_inst": "Symbiosis Statistical Institute, Symbiosis International (Deemed University), A 106, ICC Trade Tower 403A, International Convention Centre, Senapati Bapat Road," - }, - { - "author_name": "Sachin B Palve", - "author_inst": "Department of Community Medicine, Symbiosis Medical College for Women, Symbiosis International (Deemed University), Lavale, Mulshi, Pune, Maharashtra 412115" - }, - { - "author_name": "Rajiv Yeravdekar", - "author_inst": "Symbiosis Institute of Health Sciences, Symbiosis International (Deemed University), Senapati Bapat Road, Pune 411016" - }, - { - "author_name": "Vijay Natarajan", - "author_inst": "Symbiosis University Hospital and Research Centre (SUHRC), Symbiosis International (Deemed University), Lavale, Mulshi, Pune, Maharashtra 412115" - }, - { - "author_name": "Pradeep Tiwari", - "author_inst": "Diabetes Unit, KEM Hospital Research Center, Rasta Peth, Pune-411011" - }, - { - "author_name": "Chittaranjan S Yajnik", - "author_inst": "Diabetes Unit, KEM Hospital Research Center, Rasta Peth, Pune-411011" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.26.20239202", "rel_title": "The impact of the COVID-19 pandemic and related control measures on cancer diagnosis in Catalonia:A time-series analysis of primary care electronic health records covering about 5 million people.", @@ -1037964,6 +1039255,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.11.27.20240002", + "rel_title": "Comparative Genomic Study for Revealing the Complete Scenario of COVID-19 Pandemic in Bangladesh", + "rel_date": "2020-11-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.27.20240002", + "rel_abs": "As the COVID-19 pandemic continues to ravage across the globe and take millions of lives and like many parts of the world, the second wave of the pandemic hit Bangladesh, this study aimed at understanding its causative agent, SARS-CoV-2 at the genomic and proteomic level and provide precious insights about the pathogenesis, evolution, strengths and weaknesses of the virus. As of Mid-June 2021, over 1500 SARS-CoV-2 genomes have been sequenced across the country. From our analyses, it was discovered that the wave-2 samples had a significantly greater average rate of mutation/sample (30.79%) than the wave-1 samples (12.32%). Wave-2 samples also had a higher frequency of deletion, and transversion events. During the first wave, the GR clade was the most predominant but it was replaced by the GH clade in the latter wave. The B.1.1.25 variant showed the highest frequency in wave-1 while in case of wave-2, the B.1.351.3 variant, was the most common one. A notable presence of the delta variant, which is currently at the center of concern, was also observed. Comparison of the Spike protein found in the reference and the 3 most common lineages found in Bangladesh namely, B.1.1.7, B.1.351, B.1.617 in terms of their ability to form stable complexes with ACE2 receptor revealed that B.1.617 had the potential to be more transmissible than others. Importantly, no indigenous variants have been detected so far which implies that the successful prevention of import of foreign variants can diminish the outbreak in the country.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Ishtiaque Ahammad", + "author_inst": "Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka-1349, Bangladesh" + }, + { + "author_name": "Mohammad Uzzal Hossain", + "author_inst": "Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka-1349, Bangladesh" + }, + { + "author_name": "Anisur Rahman", + "author_inst": "Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Sonapur, Noakhali-3814, Bangladesh" + }, + { + "author_name": "Zeshan Mahmud Chowdhury", + "author_inst": "Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka-1229, Bangladesh" + }, + { + "author_name": "Arittra Bhattacharjee", + "author_inst": "Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka-1349, Bangladesh; Department of Biochemistry and Microbiology, No" + }, + { + "author_name": "Md. Tabassum Hossain Emon", + "author_inst": "Department of Biotechnology and Genetic Engineering, Life Science Faculty, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902, Bangladesh" + }, + { + "author_name": "Keshob Chandra Das", + "author_inst": "Molecular Biotechnology, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka-1349, Bangladesh" + }, + { + "author_name": "Chaman Ara Keya", + "author_inst": "Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka-1229, Bangladesh" + }, + { + "author_name": "Md. Salimullah", + "author_inst": "Molecular Biotechnology, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka-1349, Bangladesh" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.28.20239848", "rel_title": "Prevalence of IgG antibodies against SARS-CoV-2 among healthcare workers in a tertiary pediatric hospital in Poland", @@ -1038864,29 +1040206,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.11.28.20240127", - "rel_title": "Contribution of age-related effects to COVID-19 differences of crude fatality ratios in two Argentine provinces between March and August 2020", - "rel_date": "2020-11-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.28.20240127", - "rel_abs": "The following paper presents temporary estimations of CFR (the ratio between deaths and infected positive cases) attributed to COVID-19 for two provinces in Argentina (Jujuy and Buenos Aires Province), using public data provided by the Argentine Ministry of Health. In order to make comparisons between jurisdictions, we applied a series of exploratory measures (which resulted in excluding many other jurisdictions from the comparison), and later on the Kitagawa decomposition procedure, trying to separate rate (\"net\" fatality) and structure components (age-attributable effects) from CFR estimations in those provinces. After the decomposition we can observe that between almost non existant differences on average, the magnitude of structure and net rate effects tend to go into different directions across age groups, indicating some premature mortality in Buenos Aires and an excess net CFR in Jujuy for older age-groups", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Octavio Nicolas Bramajo", - "author_inst": "Center for Demographic Studies, Barcelona" - }, - { - "author_name": "Maria Florencia Bathory", - "author_inst": "Universidad Nacional de Lujan, Argentina" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.11.28.20240333", "rel_title": "COVID-19 Outbreak and Voluntary Demand for Non-COVID-19 Healthcare: Evidence from Taiwan", @@ -1039454,6 +1040773,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.29.20238402", + "rel_title": "Change of dominant strain during dual SARS-CoV-2 infection", + "rel_date": "2020-11-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.29.20238402", + "rel_abs": "BackgroundThe effect of SARS-CoV-2 mutations and viral load on the severity of COVID-19 is not well understood. The possibility of reinfection with SARS-CoV-2 has already been reported, but dual infection with SARS-CoV-2 is poorly described and is currently under discussion. We describe a study of two strains of SARS-CoV-2 detected in the same patient during the same disease presentation.\n\nMethodsTwo nasopharyngeal swabs were obtained eight days apart from the patient in their 90s, diagnosed with lobar pneumonia (J18.1). Both tests were positive for SARS-CoV-2 with high viral load (Ct = 13). We have performed high-throughput sequencing of SARS-CoV-2 genomes from both swabs.\n\nFindingsGenomic analysis of SARS-CoV-2 revealed the presence of two genetically distant strains in both swabs. Detected strains belong to different phylogenetic clades (GH and GR) and differ in the seven nucleotide positions. The relative abundance of strains was 70% (GH) and 30% (GR) in the first swab, and 3% (GH) and 97% (GR).\n\nInterpretationOur findings suggest that the patient was infected by two genetically distinct SARS-CoV-2 strains at the same time. One of the possible explanations is that the second infection occurred in the hospital. Change of the dominant strain ratio during disease manifestation could be explained by the advantage or higher virulence of the strain belonging to the clade GR.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "A E Samoilov", + "author_inst": "Central Research Institute of Epidemiology of The Federal Service on Customers' Rights Protection and Human Well-being Surveillance" + }, + { + "author_name": "V V Kaptelova", + "author_inst": "Central Research Institute of Epidemiology of The Federal Service on Customers' Rights Protection and Human Well-being Surveillance" + }, + { + "author_name": "A Y Bukharina", + "author_inst": "Central Research Institute of Epidemiology of The Federal Service on Customers' Rights Protection and Human Well-being Surveillance" + }, + { + "author_name": "O Y Shipulina", + "author_inst": "Central Research Institute of Epidemiology of The Federal Service on Customers' Rights Protection and Human Well-being Surveillance" + }, + { + "author_name": "E V Korneenko", + "author_inst": "Central Research Institute of Epidemiology of The Federal Service on Customers' Rights Protection and Human Well-being Surveillance" + }, + { + "author_name": "A V Lukyanov", + "author_inst": "Central Research Institute of Epidemiology of The Federal Service on Customers' Rights Protection and Human Well-being Surveillance" + }, + { + "author_name": "A A Grishaeva", + "author_inst": "Central Research Institute of Epidemiology of The Federal Service on Customers' Rights Protection and Human Well-being Surveillance" + }, + { + "author_name": "A A Ploskireva", + "author_inst": "Central Research Institute of Epidemiology of The Federal Service on Customers' Rights Protection and Human Well-being Surveillance" + }, + { + "author_name": "Anna S Speranskaya", + "author_inst": "Central Research Institute of Epidemiology of The Federal Service on Customers' Rights Protection and Human Well-being Surveillance" + }, + { + "author_name": "V G Akimkin", + "author_inst": "Central Research Institute of Epidemiology of The Federal Service on Customers' Rights Protection and Human Well-being Surveillance" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.29.20240408", "rel_title": "A psychrometric model to predict the biological decay of the SARS-CoV-2 virus in aerosols", @@ -1040454,29 +1041828,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.24.20238303", - "rel_title": "Dental practice in Pre- COVID19 and Future Perspectives", - "rel_date": "2020-11-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.24.20238303", - "rel_abs": "ObjectivesTo assess the trends in dental practice in pre-COVID19 times and future perspectives.\n\nMethodsThe cross-sectional study was conducted among the dental professionals across India. The snowball and convenience sampling methods were used to ensure maximum participation of the subjects. An online structured questionnaire was created using free-access Google Forms application and was sent to the dental professionals via E-mail, WhatsApp mobile application and through other social media platforms. Initially, a pilot study was conducted among 30 dentists to check for the validity. The questionnaire was administered between the months of May 2020 - July 2020 and was sent to 650 dentists from various parts of the country. Data were compiled and subjected to statistical analysis.\n\nResultsThe questionnaire was sent to 650 dental professionals. Out of 650, 120 (18.4%) participants took part in the survey. Majority of the respondents had 1 to 3 years of experience in dental practice (n=51, 42.5%). It was noted that majority of the participants were into consultation practice (n=69, 57.5%). 65.8% participants reported that they can withstand upto 6 months from economic view point. Difficulty in paying salaries, reduced incomes is some of the main problems encountered by dental professionals. Increasing the price of treatment, reducing co-workers are a few strategies planned by dental professionals to mitigate the economic burden caused by COVID19 pandemic.\n\nConclusionMajority of dental professionals in India are dependent on private practice and consultation practice. Due to COVID19, source of income has disrupted for majority of the younger dental professionals.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Ashwin Parakkaje Subramanya", - "author_inst": "Krishnadevaraya College of Dental Sciences and Hospital" - }, - { - "author_name": "Prabhuji MLV", - "author_inst": "Krishnadevaraya College of Dental Sciences and Hospital" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "dentistry and oral medicine" - }, { "rel_doi": "10.1101/2020.11.25.20238527", "rel_title": "Performance of prediction models for short term outcome in COVID-19 patients in the emergency department: a retrospective study", @@ -1041068,6 +1042419,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.27.401893", + "rel_title": "Effect of RBD mutation (Y453F) in spike glycoprotein of SARS-CoV-2 on neutralizing antibody affinity", + "rel_date": "2020-11-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.27.401893", + "rel_abs": "Natural selection \"adaptation\" in the coronavirus can occur during coronavirus amplification in vivo in farmed minks. Natural selection in such viruses is observed by introduction of mutations in SARS- CoV-2 that are not observed during the growth process in humans. Infection with a mutant (Y453F) of SARS-CoV-2 from farmed minks is known to widely spread among humans. We investigated the virological characteristics of this SARS-CoV-2 mutant (Y453F) using three-dimensional protein structural analysis. Our experimental study suggests that virus variants with the Y453F mutation partially escaped detection by four neutralizing monoclonal antibodies. The spread of SARS-CoV-2 variants mediated by millions of infected farmed minks is uncontrolled; consequently, raising a concern that infection of SARS-CoV-2 mutants that cause serious symptoms in humans may spread globally.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Takma Hayashi", + "author_inst": "National Hospital Organization Kyoto Medical Center" + }, + { + "author_name": "Nobuo Yaegashi", + "author_inst": "Tohoku University School of Medicine" + }, + { + "author_name": "Ikuo Konishi", + "author_inst": "Kyoto University School of Medicine / National Hospital Organization Kyoto Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.11.24.20237842", "rel_title": "Positive rates predict death rates of Covid-19 locally and worldwide 13 days ahead", @@ -1041628,45 +1043006,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.25.20237115", - "rel_title": "Impact of non-pharmaceutical interventions for SARS-CoV-2 on norovirus outbreaks: an analysis of outbreaks reported by 9 US States", - "rel_date": "2020-11-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.25.20237115", - "rel_abs": "ImportanceThe impact of non-pharmaceutical interventions (NPIs) in response to the SARS-CoV-2 pandemic on incidence of other infectious diseases is still being assessed.\n\nObjectiveTo determine if the observed change in reported norovirus outbreaks in the United States was best explained by underreporting, seasonal trends, or reduced exposure due to NPIs. We also aimed to assess if the change in reported norovirus outbreaks varied by setting.\n\nDesignAn ecologic, interrupted time series analysis of norovirus outbreaks from nine states reported to the National Outbreak Reporting System (NORS) from July 2012-July 2020.\n\nSettingSurveillance data from Massachusetts, Michigan, Minnesota, Ohio, Oregon, South Carolina, Tennessee, Virginia, and Wisconsin were included in the analysis.\n\nParticipants9,226 reports of acute gastroenteritis outbreaks with norovirus as an epidemiologically suspected or laboratory-confirmed etiology were included in the analysis, resulting in more than 8 years of follow up. Outbreak reports from states that participated in NoroSTAT for at least 4 years were included in the analysis (range: 4-8 years).\n\nExposureThe main exposure of interest was time period: before (July 2012-February 2020) or after (April 2020-July 2020) the start of NPIs in the United States\n\nMain outcomeThe main outcome of interest was monthly rate of reported norovirus outbreaks. As a secondary outcome, we also examined the average outbreak size.\n\nResultsWe found that the decline in norovirus outbreak reports was significant for all 9 states considered (pooled incidence rate ratio (IRR) comparing April 2020-July 2020 vs. all pre-COVID months for each state= 0.14, 95% CI: 0.098, 0.21; P=<0.0001), even after accounting for typical seasonal decline in incidence during the summer months. These patterns were similar across a variety of settings, including nursing homes, child daycares, healthcare settings, and schools. The average outbreak size was also reduced by 61% (95% CI: 56%, 42.7%; P=<0.0001), suggesting that the decline does not reflect a tendency to report only more severe outbreaks due to strained surveillance systems, but instead reflects a decline in incidence.\n\nConclusions and relevanceWhile NPIs implemented during the spring and summer of 2020 were intended to reduce transmission of SARS-CoV-2, these changes also appear to have impacted the incidence of norovirus, a non-respiratory pathogen. These results suggest that NPIs may provide benefit for preventing transmission of other human pathogens, reducing strain to health systems during the continued SARS-CoV-2 pandemic.\n\nDisclaimerThe findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the US Centers for Disease Control and Prevention (CDC).", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Alicia Nicole Mullis Kraay", - "author_inst": "Emory University" - }, - { - "author_name": "Peichun Han", - "author_inst": "Emory University" - }, - { - "author_name": "Anita K Kambhampati", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Mary E Wikswo", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Sara A Mirza", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Benjamin A Lopman", - "author_inst": "Emory University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.24.20235887", "rel_title": "Toward Understanding COVID-19 Pneumonia: A Deep-learning-based Approach for Severity Analysis and Monitoring the Disease", @@ -1042634,6 +1043973,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.24.20237263", + "rel_title": "The Unyvero Hospital-Acquired pneumonia panel for diagnosis of secondary bacterial pneumonia in COVID-19 patients", + "rel_date": "2020-11-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.24.20237263", + "rel_abs": "The study was undertaken to evaluate the performance of Unyvero Hospitalized Pneumonia Panel (HPN) Application, a multiplex PCR based method for the detection of bacterial pathogens from lower respiratory tract (LRT) samples, obtained from COVID-19 patients with suspected secondary hospital-acquired pneumonia. Residual LRT samples obtained from critically ill COVID-19 patients with predetermined microbiological culture results were tested using the Unyvero HPN Application. Performance evaluation of the HPN Application was carried out using the standard-of-care (SoC) microbiological culture findings as the reference method. Eighty-three LRT samples were used in the evaluation. The HPN Application had a full concordance with SoC findings in 59/83 (71%) samples. The new method detected additional bacterial species in 21 (25%) and failed at detecting a bacterial species present in lower respiratory culture in 3 (3.6%) samples. Overall the sensitivity, specificity, positive and negative predictive values of the HPN Application were 95.1% (95%CI: 96.5-98.3%); 98.3% (95% CI: 97.5-98.9%); 71.6% (95% CI: 61.0-80.3%) and 99.8% (95% CI: 99.3-99.9%) respectively. In conclusion, the HPN Application demonstrated higher diagnostic yield in comparison with the culture and generated results within 5 hours.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Chaitanya Tellapragada", + "author_inst": "Karolinska Institute" + }, + { + "author_name": "Christian Giske", + "author_inst": "Karolinska Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.24.20236802", "rel_title": "Characteristics, outcomes, and mortality amongst 133,589 patients with prevalent autoimmune diseases diagnosed with, and 48,418 hospitalised for COVID-19: a multinational distributed network cohort analysis", @@ -1043746,45 +1045108,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2020.11.24.396671", - "rel_title": "Evolutionary analysis of SARS-CoV-2 spike protein for its different clades", - "rel_date": "2020-11-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.24.396671", - "rel_abs": "ObjectiveThe spike protein of SARS-CoV-2 has become the main target for antiviral and vaccine development. Despite its relevance, there is scarce information about its evolutionary traces. The aim of this study was to investigate the diversification patterns of the spike for each clade of SARS-CoV-2 through different approaches.\n\nMethodsTwo thousand and one hundred sequences representing the seven clades of the SARS-CoV-2 were included. Patterns of genetic diversifications and nucleotide evolutionary rate were estimated for the spike genomic region.\n\nResultsThe haplotype networks showed a star shape, where multiple haplotypes with few nucleotide differences diverge from a common ancestor. Four hundred seventy nine different haplotypes were defined in the seven analyzed clades. The main haplotype, named Hap-1, was the most frequent for clades G (54%), GH (54%), and GR (56%) and a different haplotype (named Hap-252) was the most important for clades L (63.3%), O (39.7%), S (51.7%), and V (70%). The evolutionary rate for the spike protein was estimated as 1.08 x 10-3 nucleotide substitutions/site/year. Moreover, the nucleotide evolutionary rate after nine months of pandemic was similar for each clade.\n\nConclusionsIn conclusion, the present evolutionary analysis is relevant since the spike protein of SARS-CoV-2 is the target for most therapeutic candidates; besides, changes in this protein could have consequences on viral transmission, response to antivirals and efficacy of vaccines. Moreover, the evolutionary characterization of clades improves knowledge of SARS-CoV-2 and deserves to be assessed in more detail since re-infection by different phylogenetic clades has been reported.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Matias Javier Pereson Sr.", - "author_inst": "Universidad de Buenos Aires. Facultad de Farmacia y Bioquimica. Instituto de Investigaciones en Bacteriologia y Virologia Molecular (IBaViM). Buenos Aires, Arge" - }, - { - "author_name": "Diego Flichman Sr.", - "author_inst": "Instituto de Investigaciones Biomedicas en Retrovirus y Sindrome de Inmunodeficiencia Adquirida INBIRS. Consejo Nacional de Investigaciones Cientificas y Tecnic" - }, - { - "author_name": "Alfredo Martinez Sr.", - "author_inst": "Virology Section, Centro de Educacion Medica e Investigaciones Clinicas Norberto Quirno CEMIC. Buenos Aires, Argentina" - }, - { - "author_name": "Patricia Bare Sr.", - "author_inst": "Instituto de Medicina Experimental IMEX. Academia Nacional de Medicina. Buenos Aires, Argentina." - }, - { - "author_name": "Gabriel Garcia Sr.", - "author_inst": "Universidad de Buenos Aires. Facultad de Farmacia y Bioquimica. Instituto de Investigaciones en Bacteriologia y Virologia Molecular (IBaViM). Buenos Aires, Arge" - }, - { - "author_name": "Federico Di Lello Sr.", - "author_inst": "Universidad de Buenos Aires. Facultad de Farmacia y Bioquimica. Instituto de Investigaciones en Bacteriologia y Virologia Molecular (IBaViM). Buenos Aires, Arge" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2020.11.25.398578", "rel_title": "SARS-CoV-2 utilizes a multipronged strategy to suppress host protein synthesis", @@ -1044524,6 +1045847,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.22.20236448", + "rel_title": "Interventions for treatment of COVID-19: second edition of a living systematic review with meta-analyses and trial sequential analyses (The LIVING Project)", + "rel_date": "2020-11-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.22.20236448", + "rel_abs": "BackgroundCOVID-19 is a rapidly spreading disease that has caused extensive burden to individuals, families, countries, and the world. Effective treatments of COVID-19 are urgently needed. This is the second edition of a living systematic review of randomized clinical trials assessing the effects of all treatment interventions for participants in all age groups with COVID-19.\n\nMethods and findingsWe planned to conduct aggregate data meta-analyses, trial sequential analyses, network meta-analysis, and individual patient data meta-analyses. Our systematic review was based on PRISMA and Cochrane guidelines, and our eight-step procedure for better validation of clinical significance of meta-analysis results. We performed both fixed-effect and random-effects meta-analyses. Primary outcomes were all-cause mortality and serious adverse events. Secondary outcomes were admission to intensive care, mechanical ventilation, renal replacement therapy, quality of life, and non-serious adverse events. According to the number of outcome comparisons, we adjusted our threshold for significance to p = 0.033. We used GRADE to assess the certainty of evidence. We searched relevant databases and websites for published and unpublished trials until November 2, 2020. Two reviewers independently extracted data and assessed trial methodology.\n\nWe included 82 randomized clinical trials enrolling a total of 40,249 participants. 81 out of 82 trials were at overall high risk of bias.\n\nMeta-analyses showed no evidence of a difference between corticosteroids versus control on all-cause mortality (risk ratio [RR] 0.89; 95% confidence interval [CI] 0.79 to 1.00; p = 0.05; I2 = 23.1%; eight trials; very low certainty), on serious adverse events (RR 0.89; 95% CI 0.80 to 0.99; p = 0.04; I2 = 39.1%; eight trials; very low certainty), and on mechanical ventilation (RR 0.86; 95% CI 0.55 to 1.33; p = 0.49; I2 = 55.3%; two trials; very low certainty). The fixed-effect meta-analyses showed indications of beneficial effects. Trial sequential analyses showed that the required information size for all three analyses was not reached.\n\nMeta-analysis (RR 0.93; 95% CI 0.82 to 1.07; p = 0.31; I2 = 0%; four trials; moderate certainty) and trial sequential analysis (boundary for futility crossed) showed that we could reject that remdesivir versus control reduced the risk of death by 20%. Meta-analysis (RR 0.82; 95% CI 0.68 to 1.00; p = 0.05; I2 = 38.9%; four trials; very low certainty) and trial sequential analysis (required information size not reached) showed no evidence of difference between remdesivir versus control on serious adverse events. Fixed-effect meta-analysis showed indications of a beneficial effect of remdesivir on serious adverse events.\n\nMeta-analysis (RR 0.40; 95% CI 0.19 to 0.87; p = 0.02; I2 = 0%; two trials; very low certainty) showed evidence of a beneficial effect of intravenous immunoglobulin versus control on all-cause mortality, but trial sequential analysis (required information size not reached) showed that the result was severely underpowered to confirm or reject realistic intervention effects.\n\nMeta-analysis (RR 0.63; 95% CI 0.35 to 1.14; p = 0.12; I2 = 77.4%; five trials; very low certainty) and trial sequential analysis (required information size not reached) showed no evidence of a difference between tocilizumab versus control on serious adverse events. Fixed-effect meta-analysis showed indications of a beneficial effect of tocilizumab on serious adverse events. Meta-analysis (RR 0.70; 95% CI 0.51 to 0.96; p = 0.02; I2 = 0%; three trials; very low certainty) showed evidence of a beneficial effect of tocilizumab versus control on mechanical ventilation, but trial sequential analysis (required information size not reached) showed that the result was severely underpowered to confirm of reject realistic intervention effects.\n\nMeta-analysis (RR 0.32; 95% CI 0.15 to 0.69; p < 0.00; I2 = 0%; two trials; very low certainty) showed evidence of a beneficial effect of bromhexidine versus standard care on non-serious adverse events, but trial sequential analysis (required information size not reached) showed that the result was severely underpowered to confirm or reject realistic intervention effects.\n\nMeta-analyses and trial sequential analyses (boundary for futility crossed) showed that we could reject that hydroxychloroquine versus control reduced the risk of death and serious adverse events by 20%.\n\nMeta-analyses and trial sequential analyses (boundary for futility crossed) showed that we could reject that lopinavir-ritonavir versus control reduced the risk of death, serious adverse events, and mechanical ventilation by 20%.\n\nAll remaining outcome comparisons showed that we did not have enough information to confirm or reject realistic intervention effects. Nine single trials showed statistically significant results on our outcomes, but were underpowered to confirm or reject realistic intervention effects. Due to lack of data, it was not relevant to perform network meta-analysis or possible to perform individual patient data meta-analyses.\n\nConclusionsNo evidence-based treatment for COVID-19 currently exists. Very low certainty evidence indicates that corticosteroids might reduce the risk of death, serious adverse events, and mechanical ventilation; that remdesivir might reduce the risk of serious adverse events; that intraveneous immunoglobin might reduce the risk of death and serious adverse events; that tocilizumab might reduce the risk of serious adverse events and mechanical ventilation; and that bromhexidine might reduce the risk of non-serious adverse events. More trials with low risks of bias and random errors are urgently needed. This review will continuously inform best practice in treatment and clinical research of COVID-19.\n\nSystematic review registration PROSPERO CRD42020178787\n\nAuthor summaryWhy was this study done?\n\nO_LISevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has spread rapidly worldwide, causing an international outbreak of the corona virus disease 2019 (COVID-19).\nC_LIO_LIThere is a need for a living systematic review evaluating the beneficial and harmful effects of all possible interventions for treatment of COVID-19.\nC_LI\n\nWhat did the researchers do and find?\n\nO_LIWe conducted the second edition of our living systematic review with meta-analyses and Trial sequential analyses to compare the effects of all treatment interventions for COVID-19.\nC_LIO_LIVery low certainty evidence indicated that corticosteroids might reduce the risk of death, serious adverse events, and mechanical ventilation; that remdesivir might reduce the risk of serious adverse events; that intraveneous immunoglobin might reduce the risk of death and serious adverse events; that tocilizumab might reduce the risk of serious adverse events and mechanical ventilation; and that bromhexidine might reduce the risk of non-serious adverse events.\nC_LIO_LINine single trials showed statistically significant results on our predefined outcomes but were underpowered to confirm or reject realistic intervention effects.\nC_LIO_LINone of the remaining trials showed evidence of a difference of the experimental interventions on our predefined outcomes.\nC_LI\n\nWhat do these findings mean?\n\nO_LINo evidence-based treatment for COVID-19 currently exists\nC_LIO_LIMore high quality, low risk of bias randomized clinical trials are urgently needed.\nC_LI", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Sophie Juul", + "author_inst": "Copenhagen Trial Unit, Centre for Clinical Intervention Research, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark" + }, + { + "author_name": "Emil Eik Nielsen", + "author_inst": "Copenhagen Trial Unit, Centre for Clinical Intervention Research, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark and Department of Interna" + }, + { + "author_name": "Joshua Feinberg", + "author_inst": "Copenhagen Trial Unit, Centre for Clinical Intervention Research, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark" + }, + { + "author_name": "Faiza Siddiqui", + "author_inst": "Copenhagen Trial Unit, Centre for Clinical Intervention Research, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark" + }, + { + "author_name": "Caroline Kamp Joergensen", + "author_inst": "Copenhagen Trial Unit, Centre for Clinical Intervention Research, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark" + }, + { + "author_name": "Emily Barot", + "author_inst": "Copenhagen Trial Unit, Centre for Clinical Intervention Research, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark" + }, + { + "author_name": "Johan Holgersson", + "author_inst": "Lund University, Helsingborg Hospital, Department of Clinical Sciences Lund, Anesthesia & Intensive Care, Lund, Sweden" + }, + { + "author_name": "Niklas Nielsen", + "author_inst": "Lund University, Helsingborg Hospital, Department of Clinical Sciences Lund, Anesthesia & Intensive Care, Lund, Sweden" + }, + { + "author_name": "Peter Bentzer", + "author_inst": "Lund University, Helsingborg Hospital, Department of Clinical Sciences Lund, Anesthesia & Intensive Care, Lund, Sweden" + }, + { + "author_name": "Areti Angeliki Veroniki", + "author_inst": "Department of Primary Education, School of Education, University of Ioannina, Ioannina, Greece and Knowledge Translation Program, Li Ka Shing Knowledge Institut" + }, + { + "author_name": "Lehana Thabane", + "author_inst": "Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada" + }, + { + "author_name": "Fanlong Bu", + "author_inst": "Centre for Evidence-based Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China" + }, + { + "author_name": "Sarah Klingenberg", + "author_inst": "Copenhagen Trial Unit, Centre for Clinical Intervention Research, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark" + }, + { + "author_name": "Christian Gluud", + "author_inst": "Copenhagen Trial Unit, Centre for Clinical Intervention Research, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark" + }, + { + "author_name": "Janus Christian Jakobsen", + "author_inst": "Copenhagen Trial Unit, Centre for Clinical Intervention Research, Copnehagen University Hospital, Rigshospitalet, Copenhagen, Denmark and Faculty of Health Scie" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.22.20236091", "rel_title": "Comparing COVID-19 vaccine allocation strategies in India: a mathematical modelling study", @@ -1045420,49 +1046818,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.23.20237255", - "rel_title": "A simple, effective enclosure with disposable coverings for inexpensive containment of aerosolized COVID viruses during tracheal intubation and extubation", - "rel_date": "2020-11-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.23.20237255", - "rel_abs": "Structured AbstractO_ST_ABSBackgroundC_ST_ABSSARS-CoV-2 (COVID-19) is a severe respiratory virus that can be transmitted through aerosol particles produced by coughing, talking, and breathing. Medical procedures used to treat severe cases such as tracheal intubation, extubation, and tracheal suctioning produce infectious aerosol particles. This presents significant risk for viral exposure of nearby healthcare workers during and following tracheal operations. This study looks at an enclosure to limit medical personnels exposure to these particles.\n\nMethodsA low-cost plastic enclosure was designed to reduce aerosol spread and viral transmission during intubation and extubation procedures. The enclosure consists of clear polycarbonate for maximum visibility. Large side cutouts provide health care providers with ease of access to the patient. Aerosol particle instruments measured the aerosol containment efficacy after applying various types of plastic coverings to seal the side openings. The use of negative pressure was also tested.\n\nResultsThe enclosure with 2 layers of plastic coverings sealing the side openings reduced total escaped particle number concentrations (diameter > 0.01 m) by over 93% at 3 inches away from all openings. Concentration decay experiments indicated that the enclosure without active suction should be left on the patient for 15-20 minutes following a tracheal manipulation to allow sufficient time for >90% of aerosol particles to settle upon interior surfaces. This decreases to 5 minutes when 30 LPM suction is applied.\n\nConclusionsThis enclosure is an inexpensive, easily implemented additional layer of protection that can be used to reduce the risk of SARS-CoV-2 aerosol transmission between patients and healthcare workers.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Luke W Monroe", - "author_inst": "Carnegie Mellon University" - }, - { - "author_name": "Jack S Johnson", - "author_inst": "Carnegie Mellon University" - }, - { - "author_name": "Howard B Gutstein", - "author_inst": "Allegeny Health Network" - }, - { - "author_name": "John P Lawrence", - "author_inst": "Allegheny Health Network" - }, - { - "author_name": "Keith Lejeune", - "author_inst": "Allegheny Health Network" - }, - { - "author_name": "Ryan C Sullivan", - "author_inst": "Carnegie Mellon Unversity" - }, - { - "author_name": "Coty N Jen", - "author_inst": "Carnegie Mellon University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.11.23.20237503", "rel_title": "Evolution of Human Respiratory Virus Epidemics", @@ -1046102,6 +1047457,49 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.11.24.396028", + "rel_title": "Protective face mask filter capable of inactivating SARS-CoV-2, and methicillin-resistant Staphylococcus aureus and Staphylococcus epidermidis", + "rel_date": "2020-11-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.24.396028", + "rel_abs": "Face masks have globally been accepted to be an effective protective tool to prevent bacterial and viral transmission, especially against indoor aerosol transmission. However, commercial face masks contain filters that are made of materials that are not capable of inactivating neither SARS-CoV-2 nor multidrug-resistant bacteria. Therefore, symptomatic and asymptomatic individuals can infect other people even if they wear them because some viable viral or bacterial loads can escape from the masks. Furthermore, viral or bacterial contact transmission can occur after touching the mask, which constitutes an increasing source of contaminated biological waste. Additionally, bacterial pathogens contribute to the SARS-CoV-2 mediated pneumonia disease complex and their resistance to antibiotics in pneumonia treatment is increasing at an alarming rate. In this regard, herein, we report the development of a novel protective non-woven face mask filter fabricated with a biofunctional coating of benzalkonium chloride that is capable of inactivating SARS-CoV-2 in one minute of contact, and the life-threatening methicillin-resistant Staphylococcus aureus and Staphylococcus epidermidis. Nonetheless, despite the results obtained, further studies are needed to ensure the safety and correct use of this technology for the mass production and commercialization of this broad-spectrum antimicrobial face mask filter. Our novel protective non-woven face mask filter would be useful for many health care workers and researchers working in this urgent and challenging field.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Miguel Mart\u00ed", + "author_inst": "Universidad Cat\u00f3lica de Valencia San Vicente M\u00e1rtir" + }, + { + "author_name": "Alberto Tu\u00f1\u00f3n-Molina", + "author_inst": "Universidad Cat\u00f3lica de Valencia San Vicente M\u00e1rtir" + }, + { + "author_name": "Finn Lillelund Aachmann", + "author_inst": "Norwegian University of Science and Technology" + }, + { + "author_name": "Yukiko Muramoto", + "author_inst": "Kyoto University" + }, + { + "author_name": "Takeshi Noda", + "author_inst": "Kyoto University" + }, + { + "author_name": "Kazuo Takayama", + "author_inst": "Kyoto University" + }, + { + "author_name": "\u00c1ngel Serrano-Aroca", + "author_inst": "Universidad Cat\u00f3lica de Valencia San Vicente M\u00e1rtir" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2020.11.23.393488", "rel_title": "LinearTurboFold: Linear-Time RNA Structural Alignment and Conserved Structure Prediction with Applications to Coronaviruses", @@ -1047082,65 +1048480,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.22.20236240", - "rel_title": "Dynamics of ORF1ab and N Gene among hospitalized COVID-19 positive cohorts: A hospital based retrospective study", - "rel_date": "2020-11-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.22.20236240", - "rel_abs": "1.ObjectiveThe present study hospital based retrospective study aimed at investigating the dynamics of ORF1ab and N gene from hospitalized COVID-19 positive cohorts considering the Ct values of both genes.\n\nStudy design and MethodologyRetrospective analyses of Ct values were done from 115 hospitalized COVID-19 positive patients in different time interval. Patients were admitted to the hospital either by RAT or/and RT-PCR and first RT-PCR testing were made after 9 days of incubation followed by testing in every 3 days of interval till negative, subsequently release of the patients.\n\nResultsWe have looked into the dynamics of ORF1ab and N gene and found that N gene require longer duration of days with 12.68 (S.D.{+/-}3.24) to become negative than ORF1ab with 12.09 (S.D.{+/-}2.88) days and it differs significantly (p=0.012; p<0.05). The persistent of N gene found in 46 patients out of 115 (39.65%) to the succeeding reading after 3 days. We have also looked into the mean differences in the between N and ORF1ab genes every readings separately and found that there were no significant differences between the mean Ct value of ORF1ab and N gene except in the day 3 (p=0.015; p<0.05). Further, we have looked into the relationship of age and gender of patients with the duration of positivity; however we did not find any significant role.\n\nConclusionIn COVID-19 hospital positive cohorts, the persistent of positivity of N gene is significantly for more duration than ORF1ab. As the SARS-CoV-2 is a new virus and study on it is evolving, so, exhaustive study is required on the dynamic of N gene positivity persistent in relation to the other pathophysiological parameters for the management and control of COVID-19.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Pojul Loying", - "author_inst": "Department of Microbiology, Gauhati Medical College and Hospital, Guwahati-781032, Assam, India" - }, - { - "author_name": "Vaishali Sarma", - "author_inst": "Department of Microbiology, Gauhati Medical College and Hospital, Guwahati-781032, Assam, India" - }, - { - "author_name": "Suranjana C. Hazarika", - "author_inst": "Department of Microbiology, Gauhati Medical College and Hospital, Guwahati-781032, Assam, India" - }, - { - "author_name": "Monjuri Kataki", - "author_inst": "Department of Microbiology, Gauhati Medical College and Hospital, Guwahati-781032, Assam, India" - }, - { - "author_name": "Dina Raja", - "author_inst": "Department of Microbiology, Gauhati Medical College and Hospital, Guwahati-781032, Assam, India" - }, - { - "author_name": "Divyashree Medhi", - "author_inst": ". Department of Microbiology, Gauhati Medical College and Hospital, Guwahati-781032, Assam, India" - }, - { - "author_name": "Ridip Dutta", - "author_inst": ". Department of Microbiology, Gauhati Medical College and Hospital, Guwahati-781032, Assam, India" - }, - { - "author_name": "Achu Chena", - "author_inst": "Department of Microbiology, Gauhati Medical College and Hospital, Guwahati-781032, Assam, India" - }, - { - "author_name": "Divya Daimary", - "author_inst": "Department of Microbiology, Gauhati Medical College and Hospital, Guwahati-781032, Assam, India" - }, - { - "author_name": "Aakangkhita Choudhurydo", - "author_inst": "Department of Microbiology, Gauhati Medical College and Hospital, Guwahati-781032, Assam, India" - }, - { - "author_name": "Lahari Saikia", - "author_inst": "Department of Microbiology, Gauhati Medical College and Hospital, Guwahati-781032, Assam, India" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.20.20234500", "rel_title": "ANTIBODY RESPONSE TO COVID-19 INFECTION- CLINICAL VARIABLES AT PLAY", @@ -1047800,6 +1049139,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "endocrinology" }, + { + "rel_doi": "10.1101/2020.11.21.20236042", + "rel_title": "High resolution proximity statistics as early warning for US universities reopening during COVID-19", + "rel_date": "2020-11-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.21.20236042", + "rel_abs": "Reopening of colleges and universities for the Fall semester of 2020 across the United States has caused significant COVID-19 case spikes, requiring reactive responses such as temporary closures and switching to online learning. Until sufficient levels of immunity are reached through vaccination, Institutions of Higher Education will need to balance academic operations with COVID-19 spread risk within and outside the student community. In this work, we study the impact of proximity statistics obtained from high resolution mobility traces in predicting case rate surges in university counties. We focus on 50 land-grant university counties (LGUCs) across the country and show high correlation (PCC > 0.6) between proximity statistics and COVID-19 case rates for several LGUCs during the period around Fall 2020 reopenings. These observations provide a lead time of up to [~]3 weeks in preparing resources and planning containment efforts. We also show how features such as total population, population affiliated with university, median income and case rate intensity could explain some of the observed high correlation. We believe these easily explainable mobility metrics along with other disease surveillance indicators can help universities be better prepared for the Spring 2021 semester.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Zakaria Mehrab", + "author_inst": "University of Virginia" + }, + { + "author_name": "Akhilandeshwari goud Ranga", + "author_inst": "University of Virginia" + }, + { + "author_name": "Debarati Sarkar", + "author_inst": "University of Virginia" + }, + { + "author_name": "Srinivasan Venkatramanan", + "author_inst": "University of Virginia" + }, + { + "author_name": "Youngyun Chung Baek", + "author_inst": "University of Virginia" + }, + { + "author_name": "Samarth Swarup", + "author_inst": "University of Virginia" + }, + { + "author_name": "Madhav Marathe", + "author_inst": "University of Virginia" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.20.20235648", "rel_title": "Distribution of Incubation Period of COVID-19 in the Canadian Context: Modeling and Computational Study", @@ -1048536,81 +1049918,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.11.21.392753", - "rel_title": "Challenges for targeting SARS-CoV-2 proteases as a therapeutic strategy for COVID-19", - "rel_date": "2020-11-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.21.392753", - "rel_abs": "Two proteases produced by the SARS-CoV-2 virus, Mpro and PLpro, are essential for viral replication and have become the focus of drug development programs for treatment of COVID-19. We screened a highly focused library of compounds containing covalent warheads designed to target cysteine proteases to identify new lead scaffolds for both Mpro and PLpro proteases. These efforts identified a small number of hits for the Mpro protease and no viable hits for the PLpro protease. Of the Mpro hits identified as inhibitors of the purified recombinant protease, only two compounds inhibited viral infectivity in cellular infection assays. However, we observed a substantial drop in antiviral potency upon expression of TMPRSS2, a transmembrane serine protease that acts in an alternative viral entry pathway to the lysosomal cathepsins. This loss of potency is explained by the fact that our lead Mpro inhibitors are also potent inhibitors of host cell cysteine cathepsins. To determine if this is a general property of Mpro inhibitors, we evaluated several recently reported compounds and found that they are also effective inhibitors of purified human cathepsin L and B and showed similar loss in activity in cells expressing TMPRSS2. Our results highlight the challenges of targeting Mpro and PLpro proteases and demonstrate the need to carefully assess selectivity of SARS-CoV-2 protease inhibitors to prevent clinical advancement of compounds that function through inhibition of a redundant viral entry pathway.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Kas Steuten", - "author_inst": "Stanford University" - }, - { - "author_name": "Heeyoung Kim", - "author_inst": "Heidelberg University" - }, - { - "author_name": "John C. Widen", - "author_inst": "Stanford University" - }, - { - "author_name": "Brett M. Babin", - "author_inst": "Stanford University" - }, - { - "author_name": "Ouma Onguka", - "author_inst": "Stanford University" - }, - { - "author_name": "Scott Lovell", - "author_inst": "Stanford University" - }, - { - "author_name": "Oguz Bolgi", - "author_inst": "University of Freiburg" - }, - { - "author_name": "Berati Cerikan", - "author_inst": "Heidelberg University" - }, - { - "author_name": "Mirko Cortese", - "author_inst": "Heidelberg University" - }, - { - "author_name": "Ryan K. Muir", - "author_inst": "Stanford University" - }, - { - "author_name": "John M. Bennett", - "author_inst": "Stanford University" - }, - { - "author_name": "Ruth Geiss-Friedlander", - "author_inst": "University of Freiburg" - }, - { - "author_name": "Christoph Peters", - "author_inst": "University of Freiburg" - }, - { - "author_name": "Ralf Bartenschlager", - "author_inst": "Heidelberg University" - }, - { - "author_name": "Matthew Bogyo", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.11.22.393009", "rel_title": "In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1", @@ -1049402,6 +1050709,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.11.19.20231670", + "rel_title": "Are pregnant women satisfied with perinatal standards of care during COVID-19 pandemic?", + "rel_date": "2020-11-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.19.20231670", + "rel_abs": "COVID-19 restrictive measures severely impacted maternity services worldwide, but little is known about the differences in womens concerns, perception of the modifications of maternity services and childbirth programs at different times during the pandemic. Here we report data from the first COVID-19 wave in Italy, during the 2020 national lockdown (March-April) and soon after lockdown release (May).\n\n1307 pregnant women answered the survey during national lockdown (phase 1) or after restrictive measures were released (phase 2). Women reported a significantly higher COVID-19 concern during phase 1 than during phase 2 (2.34 SD 0.5 vs 2.12 SD 0.5 on a Likert scale 0-3; p<0.001). Several domains of perinatal care were affected during COVID-19 lockdown: while antenatal visits, the use of technology to keep in touch with healthcare professionals, and closeness of caregivers were generally more appreciated (especially during phase 2), women reported the greatest difficulties in receiving clear information on hospitalization, birth plan and partners presence at birth.\n\nItalian pregnant womens worries about the effects of the pandemic on health and their perception of quality in the organization of maternity services improved during lockdown, but they continued to represent a challenge in May, especially regarding organizational aspects of hospitalization and childbirth.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Claudia Ravaldi", + "author_inst": "PeaRL Perinatal Research Laboratory, University of Florence; CiaoLapo Foundation for Perinatal Health, Prato, Italy" + }, + { + "author_name": "Laura Mosconi", + "author_inst": "CiaoLapo Foundation for Perinatal Health, Prato, Italy" + }, + { + "author_name": "Giada Crescioli", + "author_inst": "PeaRL Perinatal Research Laboratory, University of Florence; CiaoLapo Foundation for Perinatal Health, Prato, Italy" + }, + { + "author_name": "Valdo Ricca", + "author_inst": "Department of Health Sciences, University of Florence, Florence, Italy" + }, + { + "author_name": "Alfredo Vannacci", + "author_inst": "PeaRL Perinatal Research Laboratory, University of Florence; CiaoLapo Foundation for Perinatal Health, Prato, Italy" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.11.20.20235291", "rel_title": "Isolation thresholds for curbing SARS-CoV-2 resurgence", @@ -1050718,49 +1052060,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.11.18.20234146", - "rel_title": "Quantifying Covid19-Vaccine Location Strategies For Germany", - "rel_date": "2020-11-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.18.20234146", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSBackgroundC_ST_ABSVaccines are an important tool to limit the health and economic damage of the Covid-19 pandemic. Several vaccine candidate already provided promising effectiveness data, but it is crucial for an effective vaccination campaign that people are willing and able to get vaccinated as soon as possible. Taking Germany as an example, we provide insights of using a mathematical approach for the planning and location of vaccination sites to optimally administer vaccines against Covid-19.\n\nMethodsWe used mathematical programming for computing an optimal selection of vaccination sites out of a given set (i.e., university hospitals, health department related locations and general practices). Different patient-to-facility assignments and doctor-to-facility assignments and different constraints on the number of vaccinees per site or maximum travel time are used.\n\nResultsIn order to minimize the barriers for people to get vaccinated, i.e., limit the one-way travel journey (airline distance) by around 35 km for 75 % of the population (with a maximum of 70 km), around 80 well-positioned facilities can be enough. If only the 38 university hospitals are being used, the 75 % distance increases to around 50 km (with a maximum of 145 km). Using all 400 health departments or all 56 000 general practices can decrease the journey length significantly, but comes at the price of more required staff and possibly wastage of only partially used vaccine containers.\n\nConclusionsIn the case of free assignments, the number of required physicians can in most scenarios be limited to 2 000, which is also the minimum with our assumptions. However, when travel distances for the patients are to be minimized, capacities of the facilities must be respected, or administrative assignments are prespecified, an increased number of physicians is unavoidable.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Neele Leithaeuser", - "author_inst": "Fraunhofer ITWM" - }, - { - "author_name": "Johanna Schneider", - "author_inst": "Fraunhofer ITWM" - }, - { - "author_name": "Sebastian Johann", - "author_inst": "TU Kaiserslautern" - }, - { - "author_name": "Sven Krumke", - "author_inst": "TU Kaiserslautern" - }, - { - "author_name": "Manuel Streicher", - "author_inst": "TU Kaiserslautern" - }, - { - "author_name": "Eva Schmidt", - "author_inst": "TU Kaiserslautern" - }, - { - "author_name": "Stefan Scholz", - "author_inst": "RKI" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2020.11.17.20233569", "rel_title": "Biofunctionalized Two-dimensional MoS2 Receptors for Rapid Response Modular Electronic SARS-CoV-2 and Influenza A Antigen Sensors", @@ -1051660,6 +1052959,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.18.20232546", + "rel_title": "Prolonged presence of replication-competent SARS-CoV-2 in mildly symptomatic individuals: A Report of 2 Cases", + "rel_date": "2020-11-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.18.20232546", + "rel_abs": "It has been estimated that individuals with COVID-19 can shed replication-competent virus up to a maximum of twenty days after initiation of symptoms. This report describes two patients with mild forms of the disease who shed replication-competent virus for 24 and 37 days, respectively, after symptom onset.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Maria Cassia Mendes-Correa", + "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo-Laboratorio de Investigacao Medica em Virologia (LIM52)-Instituto de Medicina Tropical de Sao Paulo" + }, + { + "author_name": "Fabio Eudes Leal", + "author_inst": "Universidade Municipal de Sao Caetano do Sul (USCS)" + }, + { + "author_name": "Lucy S Villas-Boas", + "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo-Laboratorio de Investigacao Medica em Virologia (LIM52)-Instituto de Medicina Tropical de Sao Paulo" + }, + { + "author_name": "Steven Sol Witkin", + "author_inst": "Weill Cornell Medicine, USA" + }, + { + "author_name": "Anderson de Paula", + "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo-Laboratorio de Investigacao Medica em Virologia (LIM52)-Instituto de Medicina Tropical de Sao Paulo" + }, + { + "author_name": "Tania Regina Tozetto-Mendoza", + "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo-Laboratorio de Investigacao Medica em Virologia (LIM52)-Instituto de Medicina Tropical de Sao Paulo" + }, + { + "author_name": "Noely Evangelista Ferreira", + "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo-Laboratorio de Investigacao Medica em Virologia (LIM52)-Instituto de Medicina Tropical de Sao Paulo" + }, + { + "author_name": "Gislaine Curty", + "author_inst": "Instituto Nacional do Cancer" + }, + { + "author_name": "Pedro Santos de Carvalho", + "author_inst": "Instituto Nacional do Cancer" + }, + { + "author_name": "Lewis F Buss", + "author_inst": "Departamento de Molestias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de Sao Paulo" + }, + { + "author_name": "Silvia F Costa", + "author_inst": "Departamento de Molestias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de Sao Paulo" + }, + { + "author_name": "Flavia Mendes da Cunha Carvalho", + "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo" + }, + { + "author_name": "Joyce Kawakami", + "author_inst": "Instituto do Coracao do Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo" + }, + { + "author_name": "Noemi Nosomi Taniwaki", + "author_inst": "Instituto Adolf Lutz de Sao Paulo" + }, + { + "author_name": "Heuder Paiao", + "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo" + }, + { + "author_name": "Joao Carlos da Silva Bizario", + "author_inst": "Universidade Municipal de Sao Caetano do Sul" + }, + { + "author_name": "Jaqueline Goes de Jesus", + "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo-Instituto de Medicina Tropical de Sao Paulo" + }, + { + "author_name": "Ester Cerdeira Sabino", + "author_inst": "Departamento de Molestias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de Sao Paulo" + }, + { + "author_name": "Camila Malta Romano", + "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo-Laboratorio de Investigacao Medica em Virologia (LIM52)-Instituto de Medicina Tropical de Sao Paulo" + }, + { + "author_name": "Regina Maura Zetone Grepan", + "author_inst": "Universidade Municipal de Sao Caetano do Sul" + }, + { + "author_name": "Antonio Sesso", + "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo-Instituto de Medicina Tropical de Sao Paulo" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.18.20234351", "rel_title": "The potential impact of School Closure Relative to Community-based Non-pharmaceutical Interventions on COVID-19 Cases in Ontario, Canada", @@ -1052836,53 +1054234,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.11.18.20234468", - "rel_title": "Assessment of COVID-19 vaccine acceptance among healthcare workers in Los Angeles", - "rel_date": "2020-11-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.18.20234468", - "rel_abs": "ImportanceHealthcare workers (HCW) are slated to be early recipients of SARS-CoV-2 vaccines due to increased risk of exposure to patients with COVID-19, and will be tasked with administering approved vaccines to the general population. As lynchpins of the vaccination effort, HCWs opinions of a vaccines safety and efficacy may affect both public perception and uptake of the vaccine. Therefore, it is crucial to understand and address potential hesitancy prior to vaccine administration.\n\nObjectiveTo understand healthcare workers attitudes about vaccine safety, efficacy, and acceptability in the context of the COVID-19 pandemic, including acceptance of a novel coronavirus vaccine.\n\nDesign, Setting, ParticipantsA cross-sectional survey was distributed to participants enrolled in a longitudinal cohort study surveilling SARS-CoV-2 infection among 1,093 volunteer sampled University of California, Los Angeles (UCLA) Health System employees. Surveys were completed online between September 24 and October 16, 2020. In total, 609 participants completed this supplemental survey.\n\nResultsWe averaged a 9-statement Likert scale matrix scored from 1 (\"strongly disagree\") to 5 (\"strongly agree\") and found respondents overwhelmingly confident about vaccine safety (4.47); effectiveness (4.44); importance, self-protection, and community health (4.67). Notably, 47.3% of respondents reported unwillingness to participate in a coronavirus vaccine trial, and most (66.5%) intend to delay vaccination. The odds of reporting intent to delay coronavirus vaccine uptake were 4.15 times higher among nurses, 2.45 times higher among other personnel with patient contact roles, and 2.15 times higher among those without patient contact compared to doctors. Evolving SARS-CoV-2 science (76.0%), current political climate (57.6%), and fast-tracked vaccine development timeline (83.4%) were cited as primary variables impacting HCW decisions to undergo vaccination. Of note, these results were obtained prior to release of Phase III data from companies manufacturing vaccines in the U.S.\n\nConclusions and RelevanceDespite overall confidence in vaccines, a majority of HCW expressed concerns over a novel coronavirus vaccine. A large proportion plan to delay vaccine uptake due to concerns about expedited development, emerging scientific discoveries, and the political climate. Forthcoming vaccination campaigns must address these unique points of coronavirus vaccine hesitancy in order to achieve adequate vaccine coverage.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Adva Gadoth", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Megan Halbrook", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Rachel Martin-Blais", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Ashley N. Gray", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Nicole H. Tobin", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Kathie G. Ferbas", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Grace M. Aldrovandi", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Anne W Rimoin", - "author_inst": "University of California, Los Angeles" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.11.19.20234815", "rel_title": "Forecasting the spread of COVID19 in Hungary", @@ -1053578,6 +1054929,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2020.11.15.20231845", + "rel_title": "A Predictive Internet-Based Model for COVID-19 Hospitalization Census", + "rel_date": "2020-11-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.15.20231845", + "rel_abs": "The COVID-19 pandemic has strained hospital resources and necessitated the need for predictive models to forecast patient care demands in order to allow for adequate staffing and resource allocation. Recently, other studies have looked at associations between Google Trends data and the number of COVID-19 cases. Expanding on this approach, we propose a vector error correction model (VECM) for the number of COVID-19 patients in a healthcare system (Census) that incorporates Google search term activity and healthcare chatbot scores. The VECM provided a good fit to Census and very good forecasting performance as assessed by hypothesis tests and mean absolute percentage prediction error. Although our study and model have limitations, we have conducted a broad and insightful search for candidate Internet variables and employed rigorous statistical methods. We have demonstrated the VECM can potentially be a valuable component to a COVID-19 surveillance program in a healthcare system.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Philip J Turk", + "author_inst": "Atrium Health" + }, + { + "author_name": "Thao P Tran", + "author_inst": "Atrium Health" + }, + { + "author_name": "Geoff A Rose", + "author_inst": "Atrium Health" + }, + { + "author_name": "Andrew D McWilliams", + "author_inst": "Atrium Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.16.20232223", "rel_title": "Clinical Profile of First 1000 COVID-19 Cases Admitted at Tertiary Care Hospitals and the Correlates of their Mortality: An Indian Experience", @@ -1054406,45 +1055788,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.16.20232843", - "rel_title": "Effectiveness of Second Wave COVID-19 Response Strategies in Australia", - "rel_date": "2020-11-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.16.20232843", - "rel_abs": "BackgroundThere is a significant challenge in responding to second waves of COVID-19 cases, with governments being hesitant in introducing hard lockdown measures given the resulting economic impact. In addition, rising case numbers reflect an increase in coronavirus transmission some time previously, so timing of response measures is highly important. Australia experienced a second wave from June 2020 onwards, confined to greater Melbourne, with initial social distancing measures failing to reduce rapidly increasing case numbers. We conducted a detailed analysis of this outbreak, together with an evaluation of the effectiveness of alternative response strategies, to provide guidance to countries experiencing second waves of SARS-Cov-2 transmission.\n\nMethodAn individual-based transmission model was used to 1) describe a second-wave COVID-19 epidemic in Australia; 2) evaluate the impact of lockdown strategies used; and 3) evaluate effectiveness of alternative mitigation strategies. The model was calibrated using daily diagnosed case data prior to lockdown. Specific social distancing interventions were modelled by adjusting person-to-person contacts in mixing locations.\n\nResultsModelling earlier activation of lockdown measures are predicted to reduce total case numbers by more than 50%. Epidemic peaks and duration of the second wave were also shown to reduce. Our results suggest that activating lockdown measures when second-wave case numbers first indicated exponential growth, would have been highly effective in reducing COVID-19 cases. The model was shown to realistically predict the epidemic growth rate under the social distancing measures applied, validating the methods applied.\n\nConclusionsThe timing of social distancing activation is shown to be critical to their effectiveness. Data showing exponential rise in cases, doubling every 7-10 days, can be used to trigger early lockdown measures. Such measures are shown to be necessary to reduce daily and total case numbers, and the consequential health burden, so preventing health care facilities being overwhelmed. Early control of second wave resurgence potentially permits strict lockdown measures to be eased earlier.\n\nAll authors have seen and approved the manuscript. Research funding from Department of Health, Western Australia and Department of Health, Queensland is acknowledged. The authors confirm that these organisations had no influence on the submitted work, nor are there any competing interests.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "George J Milne", - "author_inst": "University of Western Australia" - }, - { - "author_name": "Simon Xie", - "author_inst": "the University of Western Australia" - }, - { - "author_name": "Dana Poklepovich", - "author_inst": "University of Western Australia" - }, - { - "author_name": "Dan O'Halloran", - "author_inst": "Department of Health, Queensland" - }, - { - "author_name": "Matthew Yap", - "author_inst": "University of Western Australia" - }, - { - "author_name": "David Whyatt", - "author_inst": "University of Western Australia" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.16.20232876", "rel_title": "Adverse effects of remdesivir, hydroxychloroquine, and lopinavir/ritonavir when used for COVID-19: systematic review and meta-analysis of randomized trials", @@ -1055088,6 +1056431,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.11.17.20233197", + "rel_title": "Age Specific Months of Mortality (MOMa) from Endemic and Pandemic (Covid 19) diseases", + "rel_date": "2020-11-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.17.20233197", + "rel_abs": "People do not naturally understand risk. We fear things that happen rarely like kidnapping while ignoring common risks like motor vehicle crashes. We also do not fully comprehend the large effect that age has on risk. In this paper, I introduce a concept that I call age specific months of mortality, abbreviated MOMa, a statistic that will allow people to understand their risk of death within their age group. In a year without excess mortality, i.e. no pandemic, individual causes of death will add up to a total of 12 MOMa. Excess mortality, e.g. a pandemic, adds MOMa beyond 12. For people in their 20s, the MOMa is 5 for accidents, 1.9 for suicide, 1.6 for homicide, and 1.2 for Covid-19. For people in their 60s, the MOMa is 12 for Covid-19, 4 for cancer, 2.6 for coronary heart, and treatment of Covid-19 with dexamethasone reduces MOMa from 12 to 7 months.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Christopher Rembold", + "author_inst": "university of virginia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.11.17.20228122", "rel_title": "Delayed Stroke Treatment during COVID-19 Pandemic in China", @@ -1055804,41 +1057166,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.17.20233718", - "rel_title": "On short-term trends and predictions for COVID-19 in France and the USA: comparison with Australia", - "rel_date": "2020-11-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.17.20233718", - "rel_abs": "In Europe and the USA daily new COVID-19 cases have recently been occurring in record numbers, which has created an alarming situation. The CDC in conjunction with several University groups gives forecasts for each county in the USA for several weeks at a time, but they have very large confidence intervals typified by the most recent national prediction of between 310,000 and 710,000 new cases for the week ending November 21, 2020. We have examined recent data for France and the USA over 10, 15 and 20 days. Using such data with simple fitting techniques, which do not require knowledge of any parameters, it has been possible to predict new case numbers fairly accurately for a week or more. A best-fitting polynomial of high order was only useful for a few days, after which it severely overestimated case numbers. A more detailed analysis with confidence intervals was performed for polynomials of orders one to six, which showed that lower order polynomials were more useful for prediction. Using the packages PCHIP and a POLYFIT (with degree one) in MATLAB gave smooth curves from which future case numbers could be reasonably well estimated. With PCHIP the average errors over 7 days were remarkably small, being -0.16% for France and +0.19% for the USA. A comparison is made between the temporal patterns of new cases for France, the USA and Australia. For Australia the second wave has dwindled to close to zero due to hard lock down conditions, which are discussed.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Henry C Tuckwell", - "author_inst": "UNIVERSITY OF ADELAIDE" - }, - { - "author_name": "Mohsen Dorraki", - "author_inst": "University of Adelaide" - }, - { - "author_name": "Stephen J Salamon", - "author_inst": "University of Adelaide" - }, - { - "author_name": "Andrew Allison", - "author_inst": "University of Adelaide" - }, - { - "author_name": "Derek Abbott", - "author_inst": "University of Adelaide" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.16.20231746", "rel_title": "Assessing the impact of non-pharmaceutical interventions on the dynamics of COVID-19: A mathematical modelling study in the case of Ethiopia", @@ -1056530,6 +1057857,45 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.11.17.387555", + "rel_title": "Replicating bacterium-vectored vaccine expressing SARS-CoV-2 Membrane and Nucleocapsid proteins protects against severe COVID-19 disease in hamsters", + "rel_date": "2020-11-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.17.387555", + "rel_abs": "An inexpensive readily manufactured COVID-19 vaccine that protects against severe disease is needed to combat the pandemic. We have employed the LVS {Delta}capB vector platform, previously used successfully to generate potent vaccines against the Select Agents of tularemia, anthrax, plague, and melioidosis, to generate a COVID-19 vaccine. The LVS {Delta}capB vector, a replicating intracellular bacterium, is a highly attenuated derivative of a tularemia vaccine (LVS) previously administered to millions of people. We generated vaccines expressing SARS-CoV-2 structural proteins and evaluated them for efficacy in the golden Syrian hamster, which develops severe COVID-19 disease. Hamsters immunized intradermally or intranasally with a vaccine co-expressing the Membrane (M) and Nucleocapsid (N) proteins, then challenged 5-weeks later with a high dose of SARS-CoV-2, were protected against severe weight loss and lung pathology and had reduced viral loads in the oropharynx and lungs. Protection by the vaccine, which induces murine N-specific interferon-gamma secreting T cells, was highly correlated with pre-challenge serum anti-N TH1-biased IgG. This potent vaccine against severe COVID-19 should be safe and easily manufactured, stored, and distributed, and given the high homology between MN proteins of SARS-CoV and SARS-CoV-2, has potential as a universal vaccine against the SARS subset of pandemic causing {beta}-coronaviruses.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Marcus A Horwitz", + "author_inst": "UCLA" + }, + { + "author_name": "Qingmei A Jia", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Helle Bielefeldt-Ohmann", + "author_inst": "University of Queensland" + }, + { + "author_name": "Rachel Maison", + "author_inst": "Colorado State University" + }, + { + "author_name": "Sasa Maslesa-Galic", + "author_inst": "UCLA" + }, + { + "author_name": "Richard A Bowen", + "author_inst": "Colorado State University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.11.17.387902", "rel_title": "Sequential ER stress and inflammatory responses are induced by SARS-CoV-2 ORF3 through ERphagy", @@ -1057486,29 +1058852,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2020.11.16.20231399", - "rel_title": "Simple Accurate Regression-Based Forecasting of Intensive Care Unit Admissions due to COVID-19 in Ontario, Canada", - "rel_date": "2020-11-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.16.20231399", - "rel_abs": "The pandemic caused by SARS-CoV-2 has proven challenging clinically, and at the population level, due to heterogeneity in both transmissibility and severity. Recent case incidence in Ontario, Canada (autumn 2020) has outstripped incidence in seen during the first (spring) pandemic wave; but has been associated with a lower incidence of intensive care unit (ICU) admissions and deaths. We hypothesized that differential ICU burden might be explained by increased testing volumes, as well as the shift in mean case age from older to younger. We constructed a negative binomial regression model using only three covariates, at a 2-week lag: log10(weekly cases); log10(weekly deaths); and mean weekly case age. This model reproduced observed ICU admission volumes, and demonstrated good preliminary predictive validity. Furthermore, when admissions were used in combination with ICU length of stay, our modeled estimates demonstrated excellent convergent validity with ICU occupancy data reported by the Canadian Institute for Health Information. Our approach needs external validation in other settings and at larger and smaller geographic scales, but appears to be a useful short-term forecasting tool for ICU resource demand; we also demonstrate that the virulence of SARS-CoV-2 infection has not meaningfully changed in Ontario between the first and second waves, but the demographics of those infected, and the fraction of cases identified, have.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "David Fisman", - "author_inst": "University of Toronto" - }, - { - "author_name": "Ashleigh Tuite", - "author_inst": "University of Toronto" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.17.387092", "rel_title": "Mosaic RBD nanoparticles elicit neutralizing antibodies against SARS-CoV-2 and zoonotic coronaviruses", @@ -1058532,6 +1059875,33 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.11.12.20229468", + "rel_title": "Continued Age Shift of Confirmed Positive COVID-19 Incidence Over Time to Children and Young Adults: Washington State March - August 2020", + "rel_date": "2020-11-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.12.20229468", + "rel_abs": "BackgroundAs the coronavirus (COVID-19) epidemic passed the initial infection peak in Washington State, phased re-opening lifted stay-at-home orders and restrictions leading to increased non-essential work, social activities and gathering, especially among younger persons.\n\nMethodsA longitudinal cohort analysis of Washington State Department of Health COVID-19 confirmed case age distribution 1) March-April 2020 (N=13,934) and 2) March-August 2020 (N=76,032) for proportional change over time using chi square tests for significance.\n\nResultsFrom March 1st to April 19, 2020 COVID-19 case positive age distribution shifted with a 10% decline in cases age 60 years and older and a 20% increase in age 0-19/20-39 years (chi-square = 223.10, p <.001). Number of cases over the eight-week analysis period were 0-19 years n = 515, 20-39 years n = 4078, 40-59 years n =4788, 60-79 years n = 3221, 80+ years n = 1332. After the peak (March 22, 2020), as incidence declined in older age groups, the combined percentage of cases age 0-19 and 20-39 increased from 20% to 40% of total cases. During this time testing expanded with more testing among older age groups while case positivity shifted young. Percent positive cases by age through August 2020 increased to a consistent average of 60% less than age 40 [age 0-19 increased to 19% (N = 10257), age 20-39 increased to 42% (N = 30215)].\n\nConclusionsAn increased share of COVID-19 incidence among children (age 0-19) and young adults (age 20-39) indicates their elevated role in propagating the epidemic by creating a reservoir of disease with risk of spillovers to more vulnerable older persons and those with comorbid conditions. Media savvy and age appropriate COVID-19 messaging may increase mitigation compliance among these less vulnerable, more mobile and lower priority vaccination age groups. As vaccines become available, mitigation will continue to be a priority to reduce overall population incidence.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Judith Malmgren", + "author_inst": "University of Washington" + }, + { + "author_name": "Boya Guo", + "author_inst": "University of Washington" + }, + { + "author_name": "Henry Kaplan", + "author_inst": "Swedish Cancer Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.12.20229658", "rel_title": "Clinico-pathological features in fatal Covid-19 Infection: A Preliminary Experience of a Tertiary Care Centre in North India using Post-Mortem Minimally Invasive Tissue Biopsies", @@ -1059648,45 +1061018,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.12.20230870", - "rel_title": "Optimizing COVID-19 control with asymptomatic surveillance testing in a university environment", - "rel_date": "2020-11-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.12.20230870", - "rel_abs": "The high proportion of transmission events derived from asymptomatic or presymptomatic infections make SARS-CoV-2, the causative agent in COVID-19, difficult to control through the traditional non-pharmaceutical interventions (NPIs) of symptom-based isolation and contact tracing. As a consequence, many US universities developed asymptomatic surveillance testing labs, to augment NPIs and control outbreaks on campus throughout the 2020-2021 academic year (AY); several of those labs continue to support asymptomatic surveillance efforts on campus in AY2021-2022. At the height of the pandemic, we built a stochastic branching process model of COVID-19 dynamics at UC Berkeley to advise optimal control strategies in a university environment. Our model combines behavioral interventions in the form of group size limits to deter superspreading, symptom-based isolation, and contact tracing, with asymptomatic surveillance testing. We found that behavioral interventions offer a cost-effective means of epidemic control: group size limits of six or fewer greatly reduce superspreading, and rapid isolation of symptomatic infections can halt rising epidemics, depending on the frequency of asymptomatic transmission in the population. Surveillance testing can overcome uncertainty surrounding asymptomatic infections, with the most effective approaches prioritizing frequent testing with rapid turnaround time to isolation over test sensitivity. Importantly, contact tracing amplifies population-level impacts of all infection isolations, making even delayed interventions effective. Combination of behavior-based NPIs and asymptomatic surveillance also reduces variation in daily case counts to produce more predictable epidemics. Furthermore, targeted, intensive testing of a minority of high transmission risk individuals can effectively control the COVID-19 epidemic for the surrounding population. Even in some highly vaccinated university settings in AY2021-2022, asymptomatic surveillance testing offers an effective means of identifying breakthrough infections, halting onward transmission, and reducing total caseload. We offer this blueprint and easy-to-implement modeling tool to other academic or professional communities navigating optimal return-to-work strategies.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Cara E. Brook", - "author_inst": "UC Berkeley" - }, - { - "author_name": "Graham R Northrup", - "author_inst": "UC Berkeley" - }, - { - "author_name": "Alexander J. Ehrenberg", - "author_inst": "UC Berkeley" - }, - { - "author_name": "- The IGI Testing Consortium", - "author_inst": "" - }, - { - "author_name": "Jennifer A. Doudna", - "author_inst": "University of California Berkeley" - }, - { - "author_name": "Mike Boots", - "author_inst": "UC Berkeley" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.13.20231316", "rel_title": "Evaluation of the Panbio rapid antigen test for SARS-CoV-2 in primary health care centers and test sites.", @@ -1060282,6 +1061613,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.13.20230060", + "rel_title": "ELIPSE-COL: A novel ELISA test based on rational envisioned synthetic peptides for detection of SARS-CoV-2 infection in Colombia.", + "rel_date": "2020-11-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.13.20230060", + "rel_abs": "BackgroundCOVID-19 pandemic caused by infection with the betacoronavirus SARS-CoV-2 is the greatest public health defiant on a global scale in the last 100 years. Governments and health Institutes face challenges during the pandemic, related to the diagnosis, mitigation, treatment, and timely detection after the epidemic peak for the prevention of new infections and the evaluation of the real impact of the COVID-19 disease in different geographic areas. To develop a valuable tool to study the seroprevalence of SARS-CoV-2 infection in Colombia, an \"in-house\" ELISA was achieved for the detection of IgG anti-SARS-CoV-2 antibodies in serum.\n\nMethodsThe test was standardized using an antigenic epitope \"Pool\" of the synthetic peptide as antigen derived from antigenic regions of the spike, nucleocapsid, envelope, and membrane structural proteins, which were designed, based on the genomic information of SARS-CoV-2 circulating in Colombia. In the ELISA standardization process, 94 positive sera were used, including sera from asymptomatic and symptomatic patients (mild and severe) and 123 negative sera, including pre-pandemic historical negatives originating from patients living in arbovirus endemic areas or patients with a history of respiratory diseases and sera from patients with a negative rRT-PCR test for SARS-CoV-2.\n\nResultsThe in-house peptide ELIPSE-COL test showed promising performance, being able to detect reactivity in sera from asymptomatic and symptomatic patients. The sensitivity and specificity of the assay were 91.4% and 83.7% respectively.\n\nConclusionELIPSE-COL assay was developed as an ELISA test using synthetic peptides for the study of the seroprevalence of SARS-CoV-2 infection in Colombia.\n\nSUMMARY BOXO_LIDetection of IgG anti-SARS-CoV-2 antibodies is required for the evaluation of the pandemic impact and vaccination strategies.\nC_LIO_LIELIPSE-COL is an in-house test based on synthetic peptides as antigen derived from antigenic regions of the spike, nucleocapsid, envelope, and membrane structural proteins.\nC_LIO_LIThe sensitivity and specificity of the assay were 91.4% and 83.7% respectively suggesting a promising performance.\nC_LIO_LIELIPSE-COL test is a valuable tool for the study of seroprevalence in Colombia.\nC_LI", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Adriana Arevalo", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Carlos Franco-Munoz", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Sofia Duque-Beltran", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Lyda Munoz-Galindo", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Maria Teresa Herrera-Sepulveda", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Jose Manuel Lozano", + "author_inst": "Universidad Nacional de Colombia" + }, + { + "author_name": "Luz Mary Salazar", + "author_inst": "Universidad Nacional de Colombia" + }, + { + "author_name": "Martha Lucia Ospina-Martinez", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Marcela Mercado-Reyes", + "author_inst": "Instituto Nacional de Salud" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.13.20231209", "rel_title": "Severe COVID-19 Is Fueled by Disrupted Gut Barrier Integrity", @@ -1061194,105 +1062576,6 @@ "type": "new results", "category": "systems biology" }, - { - "rel_doi": "10.1101/2020.11.15.383323", - "rel_title": "Immunological memory to SARS-CoV-2 assessed for greater than six months after infection", - "rel_date": "2020-11-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.15.383323", - "rel_abs": "Understanding immune memory to SARS-CoV-2 is critical for improving diagnostics and vaccines, and for assessing the likely future course of the COVID-19 pandemic. We analyzed multiple compartments of circulating immune memory to SARS-CoV-2 in 254 samples from 188 COVID-19 cases, including 43 samples at [≥] 6 months post-infection. IgG to the Spike protein was relatively stable over 6+ months. Spike-specific memory B cells were more abundant at 6 months than at 1 month post symptom onset. SARS-CoV-2-specific CD4+ T cells and CD8+ T cells declined with a half-life of 3-5 months. By studying antibody, memory B cell, CD4+ T cell, and CD8+ T cell memory to SARS-CoV-2 in an integrated manner, we observed that each component of SARS-CoV-2 immune memory exhibited distinct kinetics.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Jennifer M Dan", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Jose Mateus", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Yu Kato", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Kathryn M Hastie", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Esther D Yu", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Caterina Faliti", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Alba Grifoni", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Sydney I Ramirez", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Sonya Haupt", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "April Frazier", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Catherine Nakao", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Vamseedhar Rayaprolu", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Stephen A Rawlings", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Bjoern Peters", - "author_inst": "La Jolla Institute Immunology" - }, - { - "author_name": "Florian Krammer", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Viviana Simon", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Erica O Saphire", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Davey Smith", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Daniela Weiskopf", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Alessandro Sette", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Shane Crotty", - "author_inst": "La Jolla Institute for Immunology" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.11.16.385278", "rel_title": "High resolution profiling of pathways of escape for SARS-CoV-2 spike-binding antibodies", @@ -1061948,6 +1063231,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.11.20230250", + "rel_title": "Modelling the positive testing rate of COVID-19 in South Africa Using A Semi-Parametric Smoother for Binomial Data", + "rel_date": "2020-11-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.11.20230250", + "rel_abs": "The current outbreak of COVID-19 is a major pandemic that has shaken up the entire world in a short time. South Africa has the highest number of COVID-19 cases in Africa and understanding the countrys disease trajectory is important for government policy makers to plan the optimal COVID-19 intervention strategy. The number of cases is highly correlated with the number of COVID-19 tests undertaking. Thus, current methods of understanding the COVID-19 transmission process in the country based only on the number of cases can be misleading. In light of this, we propose to estimate both the probability of positive cases per tests conducted (the positive testing rate) and the rate in which the positive testing rate changes over time (its derivative) using a flexible semi-parametric model.\n\nWe applied the method to the observed positive testing rate in South Africa with data obtained from March 5th to September 2nd 2020. We found that the positive testing rate was declining from early March when the disease was first observed until early May where it kept on increasing. In the month of July 2020, the infection reached its peak then its started to decrease again indicating that the intervention strategy is effective. From mid August, 2020, the rate of change of the positive testing rate indicates that decline in the positive testing rate is slowing down, suggesting that a less effective intervention is currently implemented.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Olajumoke Evangelina Owokotomo", + "author_inst": "Data Science Institute, Center for Statistics, I-BioStat, Hasselt University" + }, + { + "author_name": "Samue Manda", + "author_inst": "Biostatistics Research Unit at South African Medical Research Council South Africa" + }, + { + "author_name": "Adetayo Kasim", + "author_inst": "Department of Anthropology Durham Research Methods Centre, Durham University, UK" + }, + { + "author_name": "Jurgen Claesen", + "author_inst": "Data Science Institute, Center for Statistics, I-BioStat, Hasselt University" + }, + { + "author_name": "Ziv Shkedy", + "author_inst": "Data Science Institute, Center for Statistics, I-BioStat, Hasselt University" + }, + { + "author_name": "Tarylee Reddy", + "author_inst": "Biostatistics Research Unit at South African Medical Research Council South Africa" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.12.20230508", "rel_title": "Asymptomatic and symptomatic SARS-CoV-2 infections elicit polyfunctional antibodies.", @@ -1063220,53 +1064542,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.09.20228189", - "rel_title": "Predictors of adverse outcome in patients with suspected COVID-19 managed in a virtual hospital setting: a cohort study", - "rel_date": "2020-11-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.09.20228189", - "rel_abs": "ObjectiveIdentify predictors of adverse outcome in a Virtual Hospital (VH) setting for COVID 19.\n\nDesignReal-world prospective observational study.\n\nSettingVirtual hospital remote assessment service in West Hertfordshire NHS Trust, UK.\n\nParticipantsPatients with suspected COVID-19 illness enrolled directly from the community (post-accident and emergency (A&E) or medical intake assessment) or post-inpatient admission.\n\nMain outcome measureDeath or (re-)admission to inpatient hospital care over 28 days.\n\nResults900 patients with a clinical diagnosis of COVID-19 (455 referred from A&E or medical intake and 445 post-inpatient) were included in the analysis. 76 (8.4%) of these experienced an adverse outcome (15 deaths in admitted patients, 3 deaths in patients not admitted, and 58 additional inpatient admissions). Predictors of adverse outcome were increase in age (OR 1.04 [95%CI: 1.02, 1.06] per year of age), history of cancer (OR 2.87 [95%CI: 1.41, 5.82]), history of mental health problems (OR 1.76 [95%CI: 1.02, 3.04]), severely impaired renal function (OR for eGFR <30 = 9.09 [95%CI: 2.01, 41.09]) and having a positive SARS-CoV-2 PCR result (OR 2.0 [95% CI: 1.11, 3.60]).\n\nConclusionsThese predictors may help direct intensity of monitoring for patients with suspected or confirmed COVID-19 who are being remotely monitored by primary or secondary care services. Further research is needed to identify the reasons for increased risk of adverse outcome associated with cancer and mental health problems.\n\nARTICLE SUMMARYO_ST_ABSStrengths and limitations of this studyC_ST_ABSO_LIThe study uses anonymised data from all patients registered for the virtual hospital between 17/03/20 and 17/05/20, and therefore selection bias is not an issue.\nC_LIO_LIAt the time of this study, this was the only service providing remote follow-up for patients with suspected COVID-19 in the area, and therefore our findings are likely to be relevant to primary care patients receiving remote follow-up.\nC_LIO_LIWe were able to collect reliable data on a wide range of clinical and demographic features, and reliably follow all patients for the primary outcome for at least two weeks following their discharge from the VH.\nC_LIO_LIWe were not able to extract detailed symptom or clinical examination data, and there were significant amounts of missing data for some variables.\nC_LIO_LIOur study is likely underpowered to detect all predictors, especially in the analysis of our two sub-groups\nC_LI", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Nick A Francis", - "author_inst": "University of Southampton" - }, - { - "author_name": "Beth Stuart", - "author_inst": "University of Southampton" - }, - { - "author_name": "Matthew Knight", - "author_inst": "2.\tWest Hertfordshire Hospitals NHS Trust" - }, - { - "author_name": "Rama Vancheeswaran", - "author_inst": "West Hertfordshire Hospitals NHS Trust" - }, - { - "author_name": "Charles Oliver", - "author_inst": "West Hertfordshire Hospitals NHS Trust" - }, - { - "author_name": "Merlin Willcox", - "author_inst": "University of Southampton" - }, - { - "author_name": "Andrrew Barlow", - "author_inst": "West Hertfordshire Hospitals NHS Trust" - }, - { - "author_name": "Michael Moore", - "author_inst": "University of Southampton" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.10.20227397", "rel_title": "For a structured response to the psychosocial consequences of the restrictive measures imposed by the global COVID-19 health pandemic: The MAVIPAN longitudinal prospective cohort study protocol.", @@ -1063970,6 +1065245,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.11.20230177", + "rel_title": "Age differential analysis of COVID-19 second wave in Europe reveals highest incidence among young adults", + "rel_date": "2020-11-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.11.20230177", + "rel_abs": "Most of the western nations have been unable to suppress the COVID-19 and are currently experiencing second or third surges of the pandemic. Here, we analyze data of incidence by age groups in 25 European countries, revealing that the highest incidence of the current second wave is observed for the group comprising young adults (aged 18-29 years old) in all but 3 of the countries analyzed. We discuss the public health implications of our findings.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Alberto Aleta", + "author_inst": "ISI Foundation" + }, + { + "author_name": "Yamir Moreno", + "author_inst": "University of Zaragoza" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.12.20230292", "rel_title": "Comparison of seven commercial SARS-CoV-2 rapid Point-of-Care Antigen tests", @@ -1064886,37 +1066184,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.10.20229278", - "rel_title": "Changing probability of experiencing food insecurity by socioeconomic and demographic groups during the COVID-19 pandemic in the UK", - "rel_date": "2020-11-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.10.20229278", - "rel_abs": "BackgroundFood supply concerns have featured prominently in the UK response to the COVID-19 pandemic. We assess changes in food insecurity in the UK population from April to July 2020.\n\nMethodWe analyze 11,095 respondents from the April through July waves of the Understanding Society COVID-19 longitudinal study survey linked with Wave 9 of the UK Understanding Society study. Food insecurity was defined as having used a food bank in the last 4 weeks; being hungry but not eating in the last week; or not able to eat healthy and nutritious food in the last week. Unadjusted estimates to examine changes in population prevalence and logistic regression were used to assess the association between employment transitions and food insecurity.\n\nFindingsThe prevalence of reporting at least one form of food insecurity rose from 7{middle dot}1% in April to 20{middle dot}2% by July 2020. Some of the largest increases were among Asian respondents (22{middle dot}91 percentage points), the self-employed (15{middle dot}90 percentage points), and 35-44-year-olds (17{middle dot}08 percentage points). In logistic regression models, those moving from employment to unemployment had higher odds of reporting food insecurity relative to furloughed individuals (OR = 2{middle dot}23; 95% CI: 1{middle dot}20-4{middle dot}131) and to the persistently employed (OR=2{middle dot}38; 95% CI: 1{middle dot}33-4{middle dot}27), adjusting for sociodemographic characteristics. Furloughed individuals did not differ significantly in their probability of experiencing food insecurity compared to the persistently employed (OR=1{middle dot}07; 95% CI: 0{middle dot}83 to 1{middle dot}37).\n\nInterpretationFood insecurity has increased substantially in the UK. Steps are needed to provide subsidies or food support to vulnerable groups.\n\nO_TEXTBOXEvidence before this studyWe searched Google Scholar with the terms \"COVID-19\" and \"food insecurity\" and \"UK\"; and \"food insecurity\" and \"UK\" and \"coronavirus\", published between January 1st and October 31st, 2020. One cross-sectional report was identified, which found higher levels of food insecurity in early April 2020 relative to 2018. Importantly, the report relied on items used to measure food insecurity that referred to a 12-month time span in 2018 and then a 30-day time span in April 2020, a potential source of bias for examining changes in population prevalence over time.\n\nAdded value of this studyHere we provide the first longitudinal national probability study that tracks temporal changes in population prevalence of food insecurity several months following the initial COVID-19-related lockdown measures in the UK. The prevalence of food insecurity rose for all socioeconomic and demographic and groups from April to July 2020, but did so for some more than others. Some of the largest increases in food insecurity were among Asian respondents, the self-employed, respondents aged 35-44, and those living in Scotland, London, and the North West of England. At the individual level, losing employment was associated with a higher odds of food insecurity compared to those furloughed under the Coronavirus Job Retention Scheme and the persistently employed. Importantly, furloughed individuals did not differ in their probability of food insecurity relative to the persistently employed.\n\nImplications of all the available evidenceThis study documents an alarming increase in food insecurity in the United Kingdom during the pandemic, with important implications for policy. While Coronavirus the Job Retention Scheme appeared to have conferred some protection, it is clear that not enough has been done to mitigate overall increases food insecurity in the UK. Steps are needed to provide subsidies or food support, especially since during the pandemic emergency food assistance may not be readily accessible. Taken together our results show that, while COVID is first of all a health crisis, it also has potential to become an escalating social and economic crisis if steps are not taken to protect the weak.\n\nC_TEXTBOX", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Jonathan Koltai", - "author_inst": "Bocconi University" - }, - { - "author_name": "Veronica Toffolutti", - "author_inst": "Bocconi University" - }, - { - "author_name": "Martin McKee", - "author_inst": "The London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "David Stuckler", - "author_inst": "Bocconi University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.11.10.20223495", "rel_title": "Addressing a complicated problem: can COVID-19 asymptomatic cases be detected and epidemics stopped, when testing is limited and the location of such cases unknown?", @@ -1065768,6 +1067035,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.10.20226688", + "rel_title": "Natural history, trajectory, and management of mechanically ventilated COVID-19 patients in the United Kingdom.", + "rel_date": "2020-11-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.10.20226688", + "rel_abs": "BackgroundTo date the description of mechanically ventilated patients with Coronavirus Disease 2019 (COVID-19) has focussed on admission characteristics with no consideration of the dynamic course of the disease. Here, we present a data-driven analysis of granular, daily data from a representative proportion of patients undergoing invasive mechanical ventilation (IMV) within the United Kingdom (UK) to evaluate the complete natural history of COVID-19.\n\nMethodsWe included adult patients undergoing IMV within 48 hours of ICU admission with complete clinical data until intensive care unit (ICU) death or discharge. We examined factors and trajectories that determined disease progression and responsiveness to interventions used in acute respiratory distress syndrome (ARDS). Our data visualisation tool is available as a web-based widget (https://www.CovidUK.ICU).\n\nFindingsData for 633 adults with COVID-19 who were mechanically ventilated between 01 March 2020 and 31 August 2020 were analysed. Mortality, intensity of mechanical ventilation and severity of organ injury increased with severity of hypoxaemia. Median PaO2/FiO2 in non-survivors on the day of death was 12.3(8.9-18.4) kPa suggesting severe refractory hypoxaemia as a major contributor to mortality. Non-resolution of hypoxaemia over the first week of IMV was associated with higher ICU mortality (60.4% versus 17.6%; P<0.001). The reported ideal body weight overestimated our calculated ideal body weight derived from reported height, with three-quarters of all reported tidal volume values were above 6mL/kg of ideal body weight. Overall, 76% of patients with moderate hypoxaemia and 46% with severe did not undergo prone position at any stage of admission. Furthermore, only 45% showed a persistent oxygenation response on prone position. Non-responders to prone position show higher lactate, D-Dimers, troponin, cardiovascular component of the sequential organ failure assessment (SOFA) score, and higher ICU mortality (69.5% versus 31.1%; P<0.001). There was no difference in number of prone sessions between survivors and non-survivors, however, patients who died without receiving prone position had a greater number of missed opportunities for prone intervention (7(3-15.5) versus 2(0-6); P<0.001).\n\nInterpretationA sizeable proportion of patients with progressive worsening of hypoxaemia had no application of and were refractory to evidence based ARDS strategies and showed a higher mortality. Strategies for early recognition and management of COVID-19 patients refractory to conventional management strategies will be critical to improving future outcomes.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSBeyond the regular literature expertise of our consortium, we enhanced our literature review - due to the fast-evolving Covid-19 publication situation-by searching PubMed for articles published in English or with English language abstracts on October 26, 2020 (and before), with the terms \"mechanical ventilation\", \"prone position\", \"AND (\"coronavirus\" OR \"COVID-19\"). Studies including patients not receiving ventilation were excluded, as were those reporting on paediatric and single-centre populations. Note, that neither of those studies analysed the data with respect to the temporal evolution of patients and at our level of granularity. Only four multicentre studies reported detailed ventilator settings and outcomes in ventilated patients with COVID-19. All studies showed only ventilator settings with restricted time points either on admission or the first 4 days of admission. None enabled granular visualisation and analysis of longitudinal ICU trajectory and management.\n\nAdded value of this studyThis study provides a comprehensive analysis and visualisation of routine clinical measurements tracking the whole ICU time course of patients undergoing invasive mechanical ventilation for COVID-19. Mechanically ventilated patients with COVID-19 have a different natural history and trajectory from descriptions of non-COVID ARDS patients, not predictable from admission physiology. Refractory hypoxaemia is an attributable factor associated with poor outcomes in Covid-19 and hence, understanding of use and utility of evidence-based ARDS interventions is clinically crucial. Opportunities to apply prone positioning appropriately are frequently missed, application of high levels of PEEP, and higher tidal volume delivery than planned is common. Lack of responsiveness to advanced ARDS management is associated with hypercoagulation and cardiovascular instability. These data may help homogenise future clinical management protocols and suggest change-of-practice trials.\n\nImplications of all the available evidenceThis study shows that disease progression in Covid-19 during the first surge occurred more frequently and for longer than other forms of respiratory failure from pre-Covid19 studies. Furthermore, variations in clinical practise occur across sites which may benefit from standardisation of evidence-based practise. Patients that do not resolve hypoxaemia over the first week have a significantly higher mortality, and, crucially, that a significant proportion are refractory to prone interventions and show variability in responses to PEEP changes. Opportunities to implement prone position were missed in many patients and this was compounded with its reduced effect on oxygenation with delayed application. This lack of responsiveness is related to indices of inflammation, thrombosis, and cardiac dysfunction suggesting that pulmonary thrombosis could influence prone responsiveness and should be pro-actively investigated in the setting of refractory Covid-19 ARDS. Prediction of failure to resolve or respond to ARDS interventions could further focus research on this group with worse outcome.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Brijesh V Patel", + "author_inst": "Division of Anaesthetics, Pain Medicine & Intensive Care, Department of Surgery & Cancer, Faculty of Medicine, Imperial College London; Department of Adult Inte" + }, + { + "author_name": "Shlomi Haar", + "author_inst": "Imperial College London" + }, + { + "author_name": "Rhodri Handslip", + "author_inst": "Division of Anaesthetics, Pain Medicine & Intensive Care, Department of Surgery & Cancer, Faculty of Medicine, Imperial College London; Department of Adult Inte" + }, + { + "author_name": "Teresa Mei-Ling Lee", + "author_inst": "Division of Anaesthetics, Pain Medicine & Intensive Care, Department of Surgery & Cancer, Faculty of Medicine, Imperial College London; Department of Adult Inte" + }, + { + "author_name": "Sunil Patel", + "author_inst": "Division of Anaesthetics, Pain Medicine & Intensive Care, Department of Surgery & Cancer, Faculty of Medicine, Imperial College London; Department of Adult Inte" + }, + { + "author_name": "Feargus Hosking-Jervis", + "author_inst": "Department of Surgery & Cancer, Imperial College London" + }, + { + "author_name": "Donna Kelly", + "author_inst": "Department of Critical Care, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom" + }, + { + "author_name": "Alex Harston", + "author_inst": "Brain and Behaviour Lab, Dept. of Bioengineering and Behaviour Analytics Lab, Data Science Institute, Imperial College London, London, United Kingdom" + }, + { + "author_name": "Barnaby Sanderson", + "author_inst": "Department of Critical Care, Guy's and St Thomas' NHS Foundation Trust, St Thomas' Hospital, London, United Kingdom" + }, + { + "author_name": "Barbara Borgatta", + "author_inst": "Aintree University Hospital Foundation Trust, Liverpool, United Kingdom" + }, + { + "author_name": "Kate Colette Tatham", + "author_inst": "Dept of Anaesthetics & Critical Care, The Royal Marsden NHS Foundation Trust, London, UK" + }, + { + "author_name": "Ingeborg Welters", + "author_inst": "Department of Critical Care, Liverpool University Hospitals NHS Foundation Trust and University of Liverpool, United Kingdom" + }, + { + "author_name": "Luigi Camporota", + "author_inst": "Department of Critical Care, Guy's and St Thomas' NHS Foundation Trust, St Thomas' Hospital, London, United Kingdom" + }, + { + "author_name": "Anthony C Gordon", + "author_inst": "Division of Anaesthetics, Pain Medicine & Intensive Care, Department of Surgery & Cancer, Faculty of Medicine, Imperial College London; Department of Anaesthesi" + }, + { + "author_name": "Matthieu Komorowski", + "author_inst": "Division of Anaesthetics, Pain Medicine & Intensive Care, Department of Surgery & Cancer, Faculty of Medicine, Imperial College London; Department of Anaesthesi" + }, + { + "author_name": "David antcliffe", + "author_inst": "Division of Anaesthetics, Pain Medicine & Intensive Care, Department of Surgery & Cancer, Faculty of Medicine, Imperial College London; Department of Anaesthesi" + }, + { + "author_name": "John R Prowle", + "author_inst": "Critical Care and Peri-operative Medicine Research Group, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary U" + }, + { + "author_name": "Zudin Puthucheary", + "author_inst": "Critical Care and Peri-operative Medicine Research Group, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary U" + }, + { + "author_name": "Aldo A Faisal", + "author_inst": "Dept. Of Computing & Dept. Of Bioengineering and Behaviour Analytics Lab, Data Science Institute and UKRI Centre for Doctoral Training in AI for Healthcare, Imp" + }, + { + "author_name": "- United Kingdom COVID-ICU National Service Evaluation", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.11.10.20229237", "rel_title": "Non-COVID-19 patients in times of pandemic: decreased emergency department visits and increased out-of-hospital mortality in Northern Italy", @@ -1066616,85 +1067978,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.09.20228106", - "rel_title": "EPIDEMIOLOGICAL AND CLINICAL CHARACTERISTICS OF COVID-19 PATIENTS IN KENYA", - "rel_date": "2020-11-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.09.20228106", - "rel_abs": "BackgroundMore than 49,000 cases of infection and 900 deaths from COVID-19 have been recorded in the Kenya. However, the characteristics and risk factors for severe outcomes among hospitalized COVID-19 patients in this setting have not been described.\n\nMethodsWe extracted demographic, laboratory, clinical and outcome data from medical records of RT-PCR confirmed SARS-CoV2 patients admitted in six hospitals in Kenya between March and September, 2020. We used Cox proportional hazards regressions to determine factors related to in-hospital mortality.\n\nResultsData from 787 COVID-19 patients was available. The median age was 43 years (IQR 30-53), with 505 (64%) males. At admission, 455 (58%) were symptomatic. The commonest symptoms were cough (337, 43%), loss of taste or smell (279, 35%), and fever (126, 16%). Co-morbidities were reported in 340 (43%), with cardiovascular disease, diabetes and HIV documented in 130 (17%), 116 (15%), 53 (7%) respectively. 90 (11%) were admitted to ICU for a mean of 11 days, 52 (7%) were ventilated with a mean of 10 days, 107 (14%) died. The risk of death increased with age [hazard ratio (HR) 1.57 (95% CI 1.13 - 2.19)] for persons >60 years compared to those <60 years old; having co-morbidities [HR 2.34 (1.68 - 3.25)]; and among males [HR 1.76 (1.27, 2.44)] compared to females. Elevated white blood cell count and aspartate aminotransferase were associated with higher risk of death.\n\nConclusionsWe identify the risk factors for mortality that may guide stratification of high risk patients.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Loice Achieng Ombajo", - "author_inst": "University of Nairobi" - }, - { - "author_name": "Nyamai Mutono", - "author_inst": "Washington State University" - }, - { - "author_name": "Paul Sudi", - "author_inst": "Kenyatta National Hospital" - }, - { - "author_name": "Mbuvi Mutua", - "author_inst": "Kenyatta National Hospital" - }, - { - "author_name": "Mohammed Sood", - "author_inst": "Coast General Teaching and Referral Hospital" - }, - { - "author_name": "Alliyy Muhammad Loo", - "author_inst": "Coast General Teaching and Referral Hospital" - }, - { - "author_name": "Phoebe Juma", - "author_inst": "University of Nairobi" - }, - { - "author_name": "Jackline Odhiambo", - "author_inst": "The Nairobi Hospital" - }, - { - "author_name": "Reena Shah", - "author_inst": "AgaKhan University Hospital" - }, - { - "author_name": "Frederick Wangai", - "author_inst": "University of Nairobi" - }, - { - "author_name": "Marybeth Maritim", - "author_inst": "University of Nairobi" - }, - { - "author_name": "Omu Anzala", - "author_inst": "Kenya-AIDS Vaccine Initiative/Institute of Clinical Research" - }, - { - "author_name": "Patrick Amoth", - "author_inst": "Ministry of Health, Kenya" - }, - { - "author_name": "Evans Kamuri", - "author_inst": "Kenyatta National Hospital" - }, - { - "author_name": "Waweru Munyu", - "author_inst": "Avenue Healthcare" - }, - { - "author_name": "Sam Mwangi Thumbi", - "author_inst": "Washington State University, Paul G Allen School for Global Animal Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.08.20227702", "rel_title": "Development of a highly sensitive point-of-care test to detect SARS-CoV-2 from saliva combining a simple RNA extraction method with colorimetric reverse transcription loop-mediated isothermal amplification detection", @@ -1067510,6 +1068793,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.09.20223396", + "rel_title": "Age-Specific SARS-CoV-2 Infection Fatality and Case Identification Fraction in Ontario, Canada", + "rel_date": "2020-11-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.09.20223396", + "rel_abs": "BackgroundSARS-CoV-2 is a novel pandemic pathogen that displays great variability in virulence across cases. Due to limitations in diagnostic testing only a subset of infections are identified. Underestimation of true infections makes calculation of infection fatality ratios (IFR) challenging.\n\nSeroepidemiology allows estimation of true cumulative incidence of infection in populations, for estimation of IFR.\n\nMethodsSeroprevalence estimates were derived using retention samples stored by Canadian Blood Services in May 2020. These were compared to non-long-term care-linked case and fatality data from the same period. Estimates were combined to generate IFR and case identification fraction estimates.\n\nResultsOverall IFR was estimated to be 0.80% (0.75 to 0.85%), consistent with estimates from other jurisdictions. IFR increased exponentially with age from 0.01% (0.002 to 0.04%) in those aged 20-29 years, to 12.71% (4.43 to 36.50%) in those aged 70 and over. We estimated that 5.88 infections (3.70 to 9.21) occurred for every case identified, with a higher fraction of cases identified in those aged 70 and older (42.0%) than those aged 20-29 (9.4%). IFR estimates in those aged 60 and older were identical to pooled estimates from other countries.\n\nConclusionsTo our knowledge these are the first Canadian estimates SARS-CoV-2 IFR and case identification fraction. Notwithstanding biases associated with donor sera they are similar to estimates from other countries, and approximately 80-fold higher than estimates for influenza A (H1N1) during the 2009 epidemic. Ontarios first COVID-19 pandemic wave is likely to have been accurately characterized due to a high case identification fraction.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "David Fisman", + "author_inst": "University of Toronto" + }, + { + "author_name": "Steven J. Drews", + "author_inst": "Canadian Blood Services" + }, + { + "author_name": "Ashleigh Tuite", + "author_inst": "University of Toronto" + }, + { + "author_name": "Sheila O'Brien", + "author_inst": "Canadian Blood Services" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.11.20229914", "rel_title": "Comparative analysis of point-of-care lateral flow immunoassays for the detection of IgM and IgG anti-SARS-CoV-2 antibodies in healthcare workers", @@ -1068794,65 +1070108,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hiv aids" }, - { - "rel_doi": "10.1101/2020.11.09.20228858", - "rel_title": "Can we predict the severe course of COVID-19? A systematic review and meta-analysis of indicators of clinical outcome.", - "rel_date": "2020-11-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.09.20228858", - "rel_abs": "BackgroundCOVID-19 has been reported in over 40million people globally with variable clinical outcomes. In this systematic review and meta-analysis, we assessed demographic, laboratory and clinical indicators as predictors for severe courses of COVID-19.\n\nMethodsWe systematically searched multiple databases (PubMed, Web of Science Core Collection, MedRvix and bioRvix) for publications from December 2019 to May 31st 2020. Random-effects meta-analyses were used to calculate pooled odds ratios and differences of medians between (1) patients admitted to ICU versus non-ICU patients and (2) patients who died versus those who survived. We adapted an existing Cochrane risk-of-bias assessment tool for outcome studies.\n\nResultsOf 6,702 unique citations, we included 88 articles with 69,762 patients. There was concern for bias across all articles included. Age was strongly associated with mortality with a difference of medians (DoM) of 13.15 years (95% confidence interval (CI) 11.37 to 14.94) between those who died and those who survived. We found a clinically relevant difference between non-survivors and survivors for C-reactive protein (CRP; DoM 69.10, CI 50.43 to 87.77), lactate dehydrogenase (LDH; DoM 189.49, CI 155.00 to 223.98), cardiac troponin I (cTnI; DoM 21.88, CI 9.78 to 33.99) and D-Dimer (DoM 1.29mg/L, CI 0.9 - 1.69). Furthermore, cerebrovascular disease was the co-morbidity most strongly associated with mortality (Odds Ratio 3.45, CI 2.42 to 4.91) and ICU admission (Odds Ratio 5.88, CI 2.35 to 14.73).\n\nDiscussionThis comprehensive meta-analysis found age, cerebrovascular disease, CRP, LDH and cTnI to be the most important risk-factors in predicting severe COVID-19 outcomes and will inform decision analytical tools to support clinical decision-making.\n\nSummaryIn this systematic review we meta-analyzed 88 articles for risk factors of ICU admission and mortality in COVID-19. We found age, cerebrovascular disease, CRP, LDH and cTnI are the most important risk-factors for ICU admission or mortality.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Stephan Katzenschlager", - "author_inst": "Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany" - }, - { - "author_name": "Alexandra J Zimmer", - "author_inst": "Departments of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Canada" - }, - { - "author_name": "Claudius Gottschalk", - "author_inst": "Heidelberg University Hospital" - }, - { - "author_name": "Juergen Grafeneder", - "author_inst": "Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria" - }, - { - "author_name": "Alexander Seitel", - "author_inst": "Division of Computer Assisted Medical Interventions, German Cancer Research Center (DKFZ), Heidelberg, Germany" - }, - { - "author_name": "Lena Maier-Hein", - "author_inst": "Division of Computer Assisted Medical Interventions, German Cancer Research Center (DKFZ), Heidelberg, Germany" - }, - { - "author_name": "Andrea Benedetti", - "author_inst": "Departments of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Canada" - }, - { - "author_name": "Jan Larmann", - "author_inst": "Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany" - }, - { - "author_name": "Markus A Weigand", - "author_inst": "Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany" - }, - { - "author_name": "Sean McGrath", - "author_inst": "Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, USA" - }, - { - "author_name": "Claudia Denkinger", - "author_inst": "University of Heidelberg" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.11.378018", "rel_title": "The repurposed drugs suramin and quinacrine inhibit cooperatively in vitro SARS-CoV-2 3CLpro", @@ -1069972,6 +1071227,89 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.11.11.378778", + "rel_title": "Rapid generation of potent antibodies by autonomous hypermutation in yeast", + "rel_date": "2020-11-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.11.378778", + "rel_abs": "The predominant approach for antibody generation remains animal immunization, which can yield exceptionally selective and potent antibody clones owing to the powerful evolutionary process of somatic hypermutation. However, animal immunization is inherently slow, has poor compatibility with certain antigens (e.g., integral membrane proteins), and suffers from self-tolerance and immunodominance, which limit the functional spectrum of antibodies that can be obtained. Here, we describe Autonomous Hypermutation yEast surfAce Display (AHEAD), a synthetic recombinant antibody generation technology that imitates somatic hypermutation inside engineered yeast. In AHEAD, antibody fragments are encoded on an error-prone orthogonal DNA replication system, resulting in Saccharomyces cerevisiae populations that continuously mutate surface-displayed antibody repertoires. Simple cycles of yeast culturing and enrichment for antigen binding drive the evolution of high-affinity antibody clones in a readily parallelizable process that takes as little as 2 weeks. We applied AHEAD to generate nanobodies against the SARS-CoV-2 S glycoprotein, a GPCR, and other targets. The SARS-CoV-2 nanobodies, concurrently evolved from an open-source naive nanobody library in 8 independent experiments, reached subnanomolar affinities through the sequential fixation of multiple mutations over 3-8 AHEAD cycles that saw [~]580-fold and [~]925-fold improvements in binding affinities and pseudovirus neutralization potencies, respectively. These experiments highlight the defining speed, parallelizability, and effectiveness of AHEAD and provide a template for streamlined antibody generation at large with salient utility in rapid response to current and future viral outbreaks.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Alon Wellner", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Conor McMahon", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Morgan S.A. Gilman", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Jonathan R. Clements", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Sarah Clark", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Kianna M. Nguyen", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Ming H. Ho", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Jung-Eun Shin", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Jared Feldman", + "author_inst": "Ragon Institute of MGH, MIT and Harvard" + }, + { + "author_name": "Blake M. Hauser", + "author_inst": "Ragon Institute of MGH, MIT and Harvard" + }, + { + "author_name": "Timothy M. Caradonna", + "author_inst": "Ragon Institute of MGH, MIT and Harvard" + }, + { + "author_name": "Laura M. Wingler", + "author_inst": "Duke University Medical Center" + }, + { + "author_name": "Aaron G. Schmidt", + "author_inst": "Ragon Institute of MGH, MIT and Harvard" + }, + { + "author_name": "Debora S. Marks", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Jonathan Abraham", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Andrew C. Kruse", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Chang C. Liu", + "author_inst": "University of California, Irvine" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2020.11.11.377713", "rel_title": "In silico analyses on the comparative sensing of SARS-CoV-2 mRNA by intracellular TLRs of human", @@ -1070860,29 +1072198,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.11.07.20227306", - "rel_title": "COVID-19 detection on IBM quantum computer with classical-quantum transfer learning", - "rel_date": "2020-11-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.07.20227306", - "rel_abs": "Diagnose the infected patient as soon as possible in the coronavirus 2019 (COVID-19) outbreak which is declared as a pandemic by the world health organization (WHO) is extremely important. Experts recommend CT imaging as a diagnostic tool because of the weak points of the nucleic acid amplification test (NAAT). In this study, the detection of COVID-19 from CT images, which give the most accurate response in a short time, was investigated in the classical computer and firstly in quantum computers. Using the quantum transfer learning method, we experimentally perform COVID-19 detection in different quantum real processors (IBMQx2, IBMQ-London and IBMQ-Rome) of IBM, as well as in different simulators (Pennylane, Qiskit-Aer and Cirq). By using a small number of data sets such as 126 COVID-19 and 100 Normal CT images, we obtained a positive or negative classification of COVID-19 with 90% success in classical computers, while we achieved a high success rate of 94-100% in quantum computers. Also, according to the results obtained, machine learning process in classical computers requiring more processors and time than quantum computers can be realized in a very short time with a very small quantum processor such as 4 qubits in quantum computers. If the size of the data set is small; Due to the superior properties of quantum, it is seen that according to the classification of COVID-19 and Normal, in terms of machine learning, quantum computers seem to outperform traditional computers.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Erdi Acar", - "author_inst": "Department of Computer Engineering, Institute of Science, Canakkale Onsekiz Mart University" - }, - { - "author_name": "Ihsan Yilmaz", - "author_inst": "Department of Computer Engineering, Faculty of Engineering, Canakkale Onsekiz Mart University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.11.08.20227934", "rel_title": "Spatial dynamics of SARS-Cov-2 and reduced risk of contagion: evidence from the second Italian epidemic wave", @@ -1071570,6 +1072885,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.08.20184663", + "rel_title": "Mathematical modeling of the SARS-CoV-2 epidemic in Qatar and its impact on the national response to COVID-19", + "rel_date": "2020-11-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.08.20184663", + "rel_abs": "BackgroundMathematical modeling constitutes an important tool for planning robust responses to epidemics. This study was conducted to guide the Qatari national response to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic. The study investigated the time course of the epidemic, forecasted healthcare needs, predicted the impact of social and physical distancing restrictions, and rationalized and justified easing of restrictions.\n\nMethodsAn age-structured deterministic model was constructed to describe SARS-CoV-2 transmission dynamics and disease progression throughout the population.\n\nResultsThe enforced social and physical distancing interventions flattened the epidemic curve, reducing the peaks for incidence, prevalence, acute-care hospitalization, and intensive care unit (ICU) hospitalizations by 87%, 86%, 76%, and 78%, respectively. The daily number of new infections was predicted to peak at 12,750 on May 23, and active-infection prevalence was predicted to peak at 3.2% on May 25. Daily acute-care and ICU-care hospital admissions and occupancy were forecast accurately and precisely. By October 15, 2020, the basic reproduction number R0 had varied between 1.07-2.78, and 50.8% of the population were estimated to have been infected (1.43 million infections). The proportion of actual infections diagnosed was estimated at 11.6%. Applying the concept of Rt tuning, gradual easing of restrictions was rationalized and justified to start on June 15, 2020, when Rt declined to 0.7, to buffer the increased interpersonal contact with easing of restrictions and to minimize the risk of a second wave. No second wave has materialized as of October 15, 2020, five months after the epidemic peak.\n\nConclusionsUse of modeling and forecasting to guide the national response proved to be a successful strategy, reducing the toll of the epidemic to a manageable level for the healthcare system.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Houssein H. Ayoub", + "author_inst": "Qatar University" + }, + { + "author_name": "Hiam Chemaitelly", + "author_inst": "Weill Cornell Medicine-Qatar" + }, + { + "author_name": "Shaheen Seedat", + "author_inst": "Weill Cornell Medicine-Qatar" + }, + { + "author_name": "Monia Makhoul", + "author_inst": "Weill Cornell Medicine-Qatar" + }, + { + "author_name": "Zaina Al Kanaani", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Abdullatif Al Khal", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Einas Al Kuwari", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Adeel A Butt", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Peter Coyle", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Andrew Jeremijenko", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Anvar Hassan Kaleeckal", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Ali Nizar Latif", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Riyazuddin Mohammad Shaik", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Hadi M. Yassine", + "author_inst": "Qatar University" + }, + { + "author_name": "Mohamed G. Al Kuwari", + "author_inst": "Primary Health Care Corporation, Doha, Qatar" + }, + { + "author_name": "Hamad Eid Al Romaihi", + "author_inst": "Ministry of Public Health" + }, + { + "author_name": "Mohamed H. Al-Thani", + "author_inst": "Ministry of Public Health" + }, + { + "author_name": "Roberto Bertollini", + "author_inst": "Ministry of Public Health" + }, + { + "author_name": "Laith J Abu-Raddad", + "author_inst": "Weill Cornell Medicine-Qatar" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.07.20227447", "rel_title": "A fair efficacy formula for assessing the effectiveness of contact tracing applications", @@ -1072422,65 +1073828,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.11.06.20227264", - "rel_title": "The role of children in the transmission chain of SARS-CoV-2: a systematic review and update of current evidence", - "rel_date": "2020-11-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.06.20227264", - "rel_abs": "Decisions on school closures and on safe schooling during the COVID-19 pandemic should be evidence-based. We conducted a systematic literature review to assess child-to-child and child-to-adult SARS-CoV-2 transmission and to characterise the potential role of school closures on community transmission. 1337 peer-reviewed articles published through August 31, 2020 were screened; 22 were included in this review. The literature appraised provides sufficient evidence that children can both be infected by and transmit SARS-CoV-2 in community, household and school settings. Transmission by children was most frequently documented in household settings, while examples of children as index cases in school settings were rare. Included studies suggested that school closures may help to reduce SARS- CoV-2 transmission, but the societal, economic, and educational impacts of prolonged school closures must be considered. In-school mitigation measures, alongside continuous surveillance and assessment of emerging evidence, will promote the protection and educational attainment of students and support the educational workforce.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Jonathan E. Suk", - "author_inst": "European Centre for Disease Prevention and Control" - }, - { - "author_name": "Constantine Vardavas", - "author_inst": "School of Medicine, University of Crete, Greece" - }, - { - "author_name": "Katerina Nikitara", - "author_inst": "School of Medicine, University of Crete, Greece" - }, - { - "author_name": "Revati Phalkey", - "author_inst": "Division of Epidemiology and Public Health, School of Medicine, University of Nottingham, UK" - }, - { - "author_name": "Jo Leonardi-Bee", - "author_inst": "Division of Epidemiology and Public Health, School of Medicine, University of Nottingham, UK" - }, - { - "author_name": "Anastasia Pharris", - "author_inst": "European Centre for Disease Prevention and Control" - }, - { - "author_name": "Emma Wiltshire", - "author_inst": "European Centre for Disease Prevention and Control, Stockholm, Sweden" - }, - { - "author_name": "Tjede Funk", - "author_inst": "European Centre for Disease Prevention and Control, Stockholm, Sweden" - }, - { - "author_name": "Lisa Ferland", - "author_inst": "European Centre for Disease Prevention and Control, Stockholm, Sweden" - }, - { - "author_name": "Nick Bundle", - "author_inst": "European Centre for Disease Prevention and Control, Stockholm, Sweden" - }, - { - "author_name": "Jan C. Semenza", - "author_inst": "European Centre for Disease Prevention and Control, Stockholm, Sweden" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.11.05.20226761", "rel_title": "Genetic variants are identified to increase risk of COVID-19 related mortality from UK Biobank data", @@ -1073016,6 +1074363,81 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.11.09.372169", + "rel_title": "Identification of a unique TCR repertoire, consistent with a superantigen selection process in Children with Multi-system Inflammatory Syndrome", + "rel_date": "2020-11-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.09.372169", + "rel_abs": "Multisystem Inflammatory Syndrome in Children (MIS-C), a hyperinflammatory syndrome associated with SARS-CoV-2 infection, shares many clinical features with toxic shock syndrome, which is triggered by bacterial superantigens. The superantigen specificity for binding different V{beta}-chains results in V{beta}-skewing, whereby T cells with specific V{beta}-chains and diverse antigen specificity are overrepresented in the TCR repertoire. Here, we characterized the TCR repertoire of MIS-C patients and found a profound expansion of TCR Beta Variable gene (TRBV)11-2. Furthermore, TRBV11-2 skewing was remarkably correlated with MIS-C severity and serum cytokine levels. Further analysis of TRBJ gene usage and CDR3 length distribution of MIS-C expanding TRBV11-2 clones revealed extensive junctional diversity, indicating a superantigen-mediated selection process for TRBV expansion. In silico modelling indicates that polyacidic residues in TCR V{beta}11-2 engage in strong interactions with the superantigen-like motif of SARS-CoV-2 spike glycoprotein. Overall, our data indicate that the immune response in MIS-C is consistent with superantigenic activation.\n\nHighlightsO_LIMultisystem Inflammatory Disease in Children (MIS-C) patients exhibit T cell receptor (TCR) repertoire skewing, with expansion of T cell Receptor Beta Variable gene (TRBV)11-2\nC_LIO_LITRBV11-2 skewing correlates with MIS-C severity and cytokine storm\nC_LIO_LIJ gene/CDR3 diversity in MIS-C patients is compatible with a superantigen selection process\nC_LIO_LIIn silico modelling indicates TCR V{beta}11-2 engages in CDR3-independent interactions with the polybasic insert P681RRAR in the SAg-like motif of SARS-CoV-2 spike\nC_LI", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Rebecca A Porritt", + "author_inst": "Cedars Sinai Medical Center" + }, + { + "author_name": "Lisa Paschold", + "author_inst": "Martin-Luther-University Halle-Wittenberg" + }, + { + "author_name": "Magali Noval Rivas", + "author_inst": "Cedars Sinai Medical Center" + }, + { + "author_name": "Mary Hongying Cheng", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Lael M Yonker", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Harsha Chandnani", + "author_inst": "Loma Linda University Hospital" + }, + { + "author_name": "Merrick Lopez", + "author_inst": "Loma Linda University Hospital" + }, + { + "author_name": "Donjete Simnica", + "author_inst": "Martin-Luther-University Halle-Wittenberg" + }, + { + "author_name": "Christoph Schultheiss", + "author_inst": "Martin-Luther-University Halle-Wittenberg" + }, + { + "author_name": "Chintda Santiskulvong", + "author_inst": "Cedars Sinai Medical Center" + }, + { + "author_name": "Jennifer Van Eyk", + "author_inst": "Cedars Sinai Medical Center" + }, + { + "author_name": "Alessio Fasano", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Ivet Bahar", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Mascha Binder", + "author_inst": "Martin-Luther-University Halle-Wittenberg" + }, + { + "author_name": "Moshe Arditi", + "author_inst": "Cedars Sinai Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.11.09.375139", "rel_title": "Gain-of-function assay for SARS-CoV-2 Mpro inhibition in living cells", @@ -1074415,45 +1075837,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.05.20226712", - "rel_title": "COVID-19 isolation and containment strategies for ships: Lessons from the USS Theodore Roosevelt outbreak", - "rel_date": "2020-11-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.05.20226712", - "rel_abs": "The control of shipborne disease outbreaks represents a vexing but entirely predictable challenge at the start of any pandemic. Passenger ships, with large numbers of people confined in close quarters, can serve as incubators of disease, seeding the pandemic across the globe as infected passengers return home. Short-term steps taken by local authorities can exacerbate this problem, creating humanitarian crises and worsening the scale of the outbreak. In this work, we have undertaken a model-based examination of the USS Theodore Roosevelt outbreak to understand the dynamics of COVID-19 spread aboard the aircraft carrier. We have used a series of counterfactual \"what-if\" analyses to better understand the options available to public health authorities in such situations. The models suggest that rapid mass evacuation and widespread surveillance testing can be effective in these settings. Our results lead to a set of generalizable recommendations for disease control that are broadly applicable to the current COVID-19 crisis as well as to future pandemics.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Madison Stoddard", - "author_inst": "Fractal Therapeutics, Cambridge, MA" - }, - { - "author_name": "Kaitlyn Johnson", - "author_inst": "Department of Integrative Biology, The University of Texas at Austin" - }, - { - "author_name": "Douglas White", - "author_inst": "Independent Researcher" - }, - { - "author_name": "Ryan Nolan", - "author_inst": "Halozyme Therapeutics, San Diego, CA" - }, - { - "author_name": "Natasha Hochberg", - "author_inst": "Department of Epidemiology, Boston University School of Public Health" - }, - { - "author_name": "Arijit Chakravarty", - "author_inst": "Fractal Therapeutics, Cambridge, MA" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.06.20226894", "rel_title": "Synchronization in Epidemic Growth and the Impossibility of Selective Containment", @@ -1075141,6 +1076524,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.11.06.20227108", + "rel_title": "Primary school staff reflections on school closures due to COVID-19 and recommendations for the future: a national qualitative survey", + "rel_date": "2020-11-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.06.20227108", + "rel_abs": "School closures due to the COVID-19 global pandemic are likely to have a range of negative consequences spanning the domains of child development, education and health, in addition to the widening of inequalities and inequities. Research is required to improve understanding of the impact of school closures on the education, health and wellbeing of pupils and school staff, the challenges posed during reopening and importantly to identify how countries can return to in-school education and to inform policy. This qualitative study aimed to reflect on the perspectives and experiences of primary school staff (pupils aged 3-11) in Wales regarding school closures and the initial reopening of schools and to identify recommendations for the future. A total of 208 school staff completed a national online survey through the HAPPEN primary school network, consisting of questions about school closures (March to June 2020), the phased reopening of schools (June to July 2020) and a return to full-time education. Thematic analysis of survey responses highlighted that primary school staff perceive that gaps in learning, health and wellbeing have increased and inequalities have widened during school closures. Findings from this study identified five recommendations; (i) prioritise the health and wellbeing of pupils and staff; (ii) focus on enabling parental engagement and support; (iii) improve digital competence amongst pupils, teachers and parents; (iv) consider opportunities for smaller class sizes and additional staffing; and (v) improve the mechanism of communication between schools and families, and between government and schools.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Emily Marchant", + "author_inst": "Swansea University" + }, + { + "author_name": "Charlotte Todd", + "author_inst": "Swansea University" + }, + { + "author_name": "Michaela James", + "author_inst": "Swansea University" + }, + { + "author_name": "Tom Crick", + "author_inst": "Swansea University" + }, + { + "author_name": "Russell Dwyer", + "author_inst": "St Thomas Community Primary School" + }, + { + "author_name": "Sinead Brophy", + "author_inst": "Swansea University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.11.04.20225920", "rel_title": "Characterising heterogeneity and sero-reversion in antibody responses to mild SARS-CoV-2 infection: a cohort study using time series analysis and mechanistic modelling", @@ -1076165,57 +1077587,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.04.20225888", - "rel_title": "Point-of-care detection of SARS-CoV-2 in nasopharyngeal swab samples using an integrated smartphone-based centrifugal microfluidic platform", - "rel_date": "2020-11-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.04.20225888", - "rel_abs": "With its origin estimated around December 2019 in Wuhan, China, the ongoing 2020 SARS-CoV-2 pandemic is a major global health challenge, resulting in more than 45 million infections and 1.2 million deaths. The demand for scalable, rapid and sensitive viral diagnostics is thus particularly pressing at present to help contain the rapid spread of infection and prevent overwhelming the capacity of health systems. While high-income countries have managed to rapidly expand diagnostic capacities, such is not the case in resource-limited settings of low- to medium-income countries.\n\nAiming at developing cost-effective viral load detection systems for point-of-care COVID-19 diagnostics in resource-limited and resource-rich settings alike, we report the development of an integrated modular centrifugal microfluidic platform to perform loop-mediated isothermal amplification (LAMP) of viral RNA directly from heat-inactivated nasopharyngeal swab samples. The discs were pre-packed with dried n-benzyl-n-methylethanolamine modified agarose beads used as a versatile post-nucleic acid amplification signal enhancement strategy, allowing fluorescence detection via a smartphone camera and simple optics. The platform provided sample-to-answer analysis within 1 hour from sample collection and a detection limit between 100 and 1000 RNA copies in 10 L reaction volume. Furthermore, direct detection of non-extracted SARS-CoV-2 RNA in nasopharyngeal swab samples from patients with Ct values below 26 (n=25 plus 6 PCR negative samples) was achieved with [~]94% sensitivity and 100% specificity, thus being fit-for-purpose to diagnose patients with a high risk of viral transmission. These results show significant promise towards bringing routine point-of-care COVID-19 diagnostics closer to resource-limited settings.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Ruben R. G. Soares", - "author_inst": "KTH Royal Institute of Technology, Division of Nanobiotechnology, Department of Protein Science, Science for Life Laboratory, Solna, Sweden" - }, - { - "author_name": "Ahmad S. Akhtar", - "author_inst": "KTH Royal Institute of Technology, Division of Nanobiotechnology, Department of Protein Science, Science for Life Laboratory, Solna, Sweden" - }, - { - "author_name": "Ines F. Pinto", - "author_inst": "KTH Royal Institute of Technology, Division of Nanobiotechnology, Department of Protein Science, Science for Life Laboratory, Solna, Sweden" - }, - { - "author_name": "Noa Lapins", - "author_inst": "KTH Royal Institute of Technology, Division of Nanobiotechnology, Department of Protein Science, Science for Life Laboratory, Solna, Sweden" - }, - { - "author_name": "Donal Barrett", - "author_inst": "Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden" - }, - { - "author_name": "Gustaf Sandh", - "author_inst": "Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden." - }, - { - "author_name": "Xiushan Yin", - "author_inst": "Applied Biology Laboratory, Shenyang University of Chemical Technology, Shenyang, China; Biotech and Biomedicine Science Co. Ltd, Shenyang, China" - }, - { - "author_name": "Vicent Pelechano", - "author_inst": "Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden" - }, - { - "author_name": "Aman Russom", - "author_inst": "KTH Royal Institute of Technology, Division of Nanobiotechnology, Department of Protein Science, Science for Life Laboratory, Solna, Sweden; AIMES - Center for " - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.04.20225805", "rel_title": "Development of an automated chemiluminescence assay system for quantitative measurement of multiple anti-SARS-CoV-2 antibodies", @@ -1076951,6 +1078322,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.05.20224618", + "rel_title": "Evaluation of a home-based 7-day infection control strategy for healthcare workers following high-risk exposure to SARS-CoV-2: a cohort study", + "rel_date": "2020-11-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.05.20224618", + "rel_abs": "BackgroundEvidence-based infection control strategies are needed for healthcare workers (HCWs) following high-risk exposure to SARS-CoV-2. This study evaluated the negative predictive value (NPV) of a home-based 7-day infection control strategy.\n\nMethodsHCWs advised by their Infection Control or Occupational Health officer to self-isolate due to a high-risk SARS-CoV-2 exposure were enrolled between May-September 2020. The strategy consisted of symptom-triggered nasopharyngeal SARS-CoV-2 RNA testing from day 0-6 post exposure, followed by standardized home-based nasopharyngeal swab and saliva testing on day 7. The NPV of this strategy was calculated for i) clinical COVID-19 diagnosis from day 8-14 post exposure, and for ii) asymptomatic SARS-CoV-2 detected by standardized nasopharyngeal swab and saliva specimens collected at days 9-10 and 14 post exposure. Interim results are reported in the context of a second wave threatening this essential workforce.\n\nResultsAmong 30 HCWs enrolled to date (age 31{+/-}9 years, 24 [80.0%] female), 3 were diagnosed with COVID-19 by day 14 post exposure (secondary attack rate 10.0%), with all cases detected by the 7-day infection control strategy: NPV for subsequent clinical COVID-19 or asymptomatic SARS-CoV-2 detection by day 14 was 100.0% (95%CI: 93.1-100.0%).\n\nInterpretationAmong HCWs with high-risk exposure to SARS-CoV-2, a home-based 7-day infection control strategy may have a high NPV for subsequent COVID-19 and asymptomatic SARS-CoV-2 detection. While ongoing data collection and data sharing are needed to improve the precision of the estimated NPV, we report interim results to inform infection control strategies in light of a second wave threatening this essential workforce.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Carla Benea", + "author_inst": "Research Institute McGill University Health Center" + }, + { + "author_name": "Laura Rendon", + "author_inst": "Research Institute McGill University Health Center" + }, + { + "author_name": "Jesse Papenburg", + "author_inst": "Department of Medicine, McGill University; Research Institute of the McGill University Health Centre" + }, + { + "author_name": "Charles Frenette", + "author_inst": "Department of Medicine, McGill University" + }, + { + "author_name": "Ahmed Imcaoudene", + "author_inst": "Department of Medicine, McGill University" + }, + { + "author_name": "Emily McDonald", + "author_inst": "Department of Medicine, McGill University; Research Institute of the McGill University Health Centre" + }, + { + "author_name": "Quoc Dinh Nguyen", + "author_inst": "Centre hospitalier de l'Universite de Montreal; Centre de recherche du centre hospitalier de l'Universite de Montreal" + }, + { + "author_name": "Ewa Rajda", + "author_inst": "Department of Medicine, McGill University" + }, + { + "author_name": "Estelle Tran", + "author_inst": "Department of Medicine, McGill University" + }, + { + "author_name": "Andrea Benedetti", + "author_inst": "Department of Medicine, McGill University; Research Institute of the McGill University Health Centre; Department of Epidemiology, Biostatistical and Occupationa" + }, + { + "author_name": "Marcel A Behr", + "author_inst": "Department of Medicine, McGill University; Research Institute of the McGill University Health Centre; Department of Epidemiology, Biostatistical and Occupationa" + }, + { + "author_name": "Benjamin M Smith", + "author_inst": "Department of Medicine, McGill University; Research Institute of the McGill University Health Centre; Department of Epidemiology, Biostatistical and Occupationa" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.05.20226522", "rel_title": "What support do frontline workers want? A qualitative study of health and social care workers experiences and views of psychosocial support during the COVID-19 pandemic.", @@ -1078199,41 +1079633,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.11.04.368431", - "rel_title": "Identification, Isolation, Propagation And Inactivation Of SARS-CoV2 Isolated From Egypt", - "rel_date": "2020-11-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.04.368431", - "rel_abs": "Severe Acute Respiratory Syndrome Coronavirus 2 causes the novel pandemic Pneumonia disease. It is a positive single strand ssRNA virus that infect human. COVID-19 appeared in Egypt in Feb 2020. The samples were taken from patients with COVID-19 symptoms at military hospital in Egypt and transported to the main chemical laboratories under all the biosafety measures according to WHO guidelines. All samples were tested with RT-PCR. Positive samples were cultured using VeroE6 cell lines. The propagated virus was isolated and inactivated. The isolated virus was sequenced using next generation sequencing and submitted into gene bank. This study provides an isolation, propagation and inactivation methodology which is valuable for production of inactivated vaccines against SARS-CoV2 in Egypt.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Mohamed Gomaa Seadawy", - "author_inst": "Main chemical laboratories, Egypt Army" - }, - { - "author_name": "Ahmed Fawzy Gad", - "author_inst": "main chemical laboratories, Egypt Army" - }, - { - "author_name": "Bassem Elasyed Harty", - "author_inst": "main chemical laboratories, Egypt Army" - }, - { - "author_name": "Mohamed Shamel Eldesoky", - "author_inst": "main chemical laboratories, Egypt Army" - }, - { - "author_name": "Mostafa Fetooh Mohamed", - "author_inst": "main chemical laboratories, Egypt Army" - } - ], - "version": "1", - "license": "cc_no", - "type": "confirmatory results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.11.04.361154", "rel_title": "Intranasal fusion inhibitory lipopeptide prevents direct contact SARS-CoV-2 transmission in ferrets", @@ -1079032,6 +1080431,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.04.20151290", + "rel_title": "ZINC SUFFICIENCY STATUS AND COVID-19 MORTALITY IN SOCIALLY SIMILAR EUROPEAN POPULATIONS - AN EPIDEMIOLOGICAL TIME-SERIES ANALYSIS", + "rel_date": "2020-11-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.04.20151290", + "rel_abs": "The impact of Zinc (Zn) sufficiency/supplementation on COVID-19 associated mortality and incidence (SARS-CoV-2 infections) remains unknown. During an infection, the levels of free Zn are reduced as part of nutritional immunity to limit the growth and replication of pathogen and the ensuing inflammatory damage. Considering its key role in immune competency and frequently recorded deficiency in large sections of different populations, Zn has been prescribed for both prophylactic and therapeutic purposes in COVID-19 without any corroborating evidence for its protective role. Multiple trials are underway evaluating the effect of Zn supplementation on COVID-19 outcome in patients getting standard of care treatment. However, the trial designs presumably lack the power to identify negative effects of Zn supplementation, especially in the vulnerable groups of elderly and patients with comorbidities (contributing 9 out of 10 deaths; up to >8000-fold higher mortality). In this study, we have analyzed COVID-19 mortality and incidence (case) data from 23 socially similar European populations with comparable confounders (population: 522.47 million; experiencing up to >150 fold difference in death rates) and at the matching stage of the pandemic (12 March - 26 June 2020; 1st wave of COVID-19 incidence and mortality). Our results suggest a positive correlation between populations Zn-sufficiency status and COVID-19 mortality (r(23): 0.7893-0.6849, p-value<0.0003) as well as incidence [r(23):0.8084 to 0.5658; p-value<0.005]. The observed association is contrary to what would be expected if Zn sufficiency was protective in COVID-19. Thus, controlled trials or retrospective analyses of the adverse event patients data should be undertaken to correctly guide the practice of Zn supplementation in COVID-19.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Samer Singh", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Amita Diwaker", + "author_inst": "Institute of Medical Sciences, Banaras Hindu University" + }, + { + "author_name": "Brijesh P Singh", + "author_inst": "Banaras Hindu University, Varanasi INDIA" + }, + { + "author_name": "Rakesh K Singh", + "author_inst": "Institute of Science, Banaras Hindu University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.04.20225706", "rel_title": "Higher risk of mental health deterioration during the Covid-19 lockdown among students rather than non-students. The French Confins study", @@ -1080500,29 +1081930,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.31.20223727", - "rel_title": "A Two-Region SEIR COVID-19 Epidemic Model for the Island of Ireland", - "rel_date": "2020-11-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.31.20223727", - "rel_abs": "The island of Ireland consists of two countries, Ireland and Northern Ireland, which are separated by a land border. We develop a model for the COVID-19 epidemic which consists of two SEIR models, one for each country, coupled through border interaction terms. The model incorporates symptomatic and presymptomatic infectives, but not asymptomatic infectives, together with a simple isolation/quarantine model. The objective of the work is to explore how the two-region epidemic could evolve by examining selected regions of parameter space. In this context we examine the effect of the border status on evolution of the epidemic. We found that, even though the border interaction parameters are relatively small, the open border could significantly affect the course of the epidemic in some of the scenarios studied. We also looked for and found examples of sensitive dependence on several parameters.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "James J Grannell", - "author_inst": "University College Cork" - }, - { - "author_name": "James R Grannell", - "author_inst": "Dublin Institute for Advanced Studies" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.30.20223412", "rel_title": "Modelling and Forecasting The Number of Confirmed Cases and Deaths from COVID-19 Pandemic in USA from April 12th to May 21st, 2020", @@ -1081186,6 +1082593,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.30.20223594", + "rel_title": "Personalized Prescription of ACEI/ARBs for Hypertensive COVID-19 Patients", + "rel_date": "2020-11-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.30.20223594", + "rel_abs": "The COVID-19 pandemic has prompted an international effort to develop and repurpose medications and procedures to effectively combat the disease. Several groups have focused on the potential treatment utility of angiotensin-converting-enzyme inhibitors (ACEIs) and angiotensin-receptor blockers (ARBs) for hypertensive COVID-19 patients, with inconclusive evidence thus far. We couple electronic medical record (EMR) and registry data of 3,643 patients from Spain, Italy, Germany, Ecuador, and the US with a machine learning framework to personalize the prescription of ACEIs and ARBs to hypertensive COVID-19 patients. Our approach leverages clinical and demographic information to identify hospitalized individuals whose probability of mortality or morbidity can decrease by prescribing this class of drugs. In particular, the algorithm proposes increasing ACEI/ARBs prescriptions for patients with cardiovascular disease and decreasing prescriptions for those with low oxygen saturation at admission. We show that personalized recommendations can improve patient outcomes by 1.0% compared to the standard of care when applied to external populations. We develop an interactive interface for our algorithm, providing physicians with an actionable tool to easily assess treatment alternatives and inform clinical decisions. This work offers the first personalized recommendation system to accurately evaluate the efficacy and risks of prescribing ACEIs and ARBs to hypertensive COVID-19 patients.\n\nHighlights- This paper introduces a data-driven approach for personalizing the prescription of ACE inhibitors (ACEIs) and angiotensin-receptor blockers (ARBs) for hypertensive COVID-19 patients.\n- Leveraging an international cohort of more than 3,500 patients, we identify clinical and demographic characteristics that may affect the effectiveness of ACEIs/ARBs for COVID-19 patients, such as low oxygen saturation at admission.\n- We developed a user-friendly online application that is available to physicians to facilitate interpretation and communication of the results of the algorithm.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Dimitris Bertsimas", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Alison Borenstein", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Luca Mingardi", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Omid Nohadani", + "author_inst": "Benefits Science Technologies" + }, + { + "author_name": "Agni Orfanoudaki", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Bartolomeo Stellato", + "author_inst": "Princeton University" + }, + { + "author_name": "Holly Wiberg", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Pankaj Sarin", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Dirk Varelmann", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Vicente Estrada", + "author_inst": "Hospital Clinico San Carlos" + }, + { + "author_name": "Carlos Macaya", + "author_inst": "Hospital Clinico San Carlos" + }, + { + "author_name": "Ivan Nunez Gil", + "author_inst": "Hospital Clinico San Carlos" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.31.20220608", "rel_title": "A household case evidences shorter shedding of SARS-CoV-2 in naturally infected cats compared to their human owners.", @@ -1081958,29 +1083428,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.02.20224352", - "rel_title": "Emergence of Novel SARS-CoV-2 Variants in the Netherlands", - "rel_date": "2020-11-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.02.20224352", - "rel_abs": "In this study, we analyzed SARS-CoV-2 genomes in the Netherlands, in the context of global viral population since the beginning of the pandemic. We have identified the most variant sites on the whole genome as well as the stable, conserved ones on the S and N proteins. We found four mutations, S:D614G, NSP12b:P314L, NSP3:F106F, to be the most frequent ones that dominate the SARS-CoV-2 population outside of China. We detected novel variants of SARS-CoV-2 almost unique to the Netherlands that form localized clusters, indicating community spread. We emphasize that while SARS-CoV-2 is evolving, and the number of mutations from the reference sequence is increasing, we observe only little diversity in the new variants as we enter the later stages of the pandemic. Our analyses suggest we have diverged away from the current SARS-CoV-2 reference enough that the reference should be re-evaluated to represent the current viral population more accurately. We assert our work provides valuable information on the genetic diversity of SARS-CoV-2 and its local dynamics in the Netherlands, especially for DNA-based diagnostic, therapeutic or vaccine development against COVID-19. We suggest sequence-based analyses should opt for a consensus representation to adequately cover the genomic variation observed.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Aysun Urhan", - "author_inst": "Delft University of Technology" - }, - { - "author_name": "Thomas Abeel", - "author_inst": "Delft University of Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.02.20224253", "rel_title": "Risk factors for outcomes of COVID-19 patients: an observational study of 795 572 patients in Russia", @@ -1082728,6 +1084175,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.11.02.20215657", + "rel_title": "COVID-19 Medical Vulnerability Indicators: A Local Data Model for Equity in Public Health Decision-Making", + "rel_date": "2020-11-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.02.20215657", + "rel_abs": "ObjectiveTo develop indicators of vulnerability for coronavirus disease 2019 (covid-19) infection in Los Angeles County (LAC) by race and neighborhood characteristics.\n\nDesignDevelopment of indicators that combines pre-existing medical vulnerabilities with social and built-environment data by zip code tabulation areas (ZCTAs).\n\nSettingNeighborhoods in LAC categorized by race/ethnicity ranked into quintiles by relative vulnerability: Non-Hispanic white; Black; Latinx; Cambodians, Hmong and Laotians combined (CHL); and Other Asians.\n\nData SourcesAskCHIS Neighborhood Edition, American Community Survey 2014-2018, and California Department of Parks and Recreation.\n\nMain Outcome Measures1) Pre-Existing Health Condition, 2) Barriers to Accessing Healthcare, 3) Built Environment Risk, and 4) CDCs Social Vulnerability.\n\nResultsNeighborhoods most vulnerable to COVID-19 are characterized by significant clustering of racial minorities, low income households and unmet medical needs. An overwhelming 73% of Blacks reside in the neighborhoods with the two highest quintiles of pre-existing health conditions, followed by Latinx (70%) and CHL (60%), while 60% of whites reside in low or the lowest vulnerable neighborhoods. For the Barriers to Accessing Healthcare indicator, 40% of Latinx reside in the highest vulnerability places followed by Blacks, CHL and other Asians (29%, 22%, and 16% respectively), compared with only 7% of Whites reside in such neighborhoods. The Built Environment Indicator finds CHL (63%) followed by Latinx (55%) and Blacks (53%) reside in the neighborhoods designated as high or the highest vulnerability compared to 32% of Whites residing in these neighborhoods. The Social Vulnerability Indicator finds 42% of Blacks and Latinx and 38% of CHL residing in neighborhoods of high vulnerability compared with only 8% of Whites residing these neighborhoods.\n\nConclusionsVulnerability to covid-19 infections differs by neighborhood and racial/ethnic groups. Our vulnerability indicators when utilized in decision-making of re-openings or resource distribution such as testing, vaccine distribution, hotel rooms for quarantine and other covid-19-related resources can provide an equity driven data approach for the most vulnerable.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Paul M Ong", + "author_inst": "University of California, Los Angeles (UCLA) Center for Neighborhood Knowledge" + }, + { + "author_name": "Chhandara Pech", + "author_inst": "University of California, Los Angeles (UCLA) Center for Neighborhood Knowledge" + }, + { + "author_name": "Nataly Rios Gutierrez", + "author_inst": "University of California, Los Angeles (UCLA) Center for Neighborhood Knowledge" + }, + { + "author_name": "Vickie M Mays", + "author_inst": "University of California, Los Angeles" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.11.03.20219121", "rel_title": "SARS-CoV-2 antibody prevalence and symptoms in a local Austrian population", @@ -1083624,53 +1085102,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.11.03.20224998", - "rel_title": "Safety, Tolerability, and Immunogenicity of COVID-19 Vaccines: A Systematic Review and Meta-Analysis", - "rel_date": "2020-11-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.03.20224998", - "rel_abs": "We aimed to summarize reliable medical evidence by the meta-analysis of all published clinical trials that investigated the safety, tolerability, and immunogenicity of vaccine candidates against coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The PubMed, Cochrane Library, EMBASE, and medRxiv databases were used to select the studies. 7094 articles were identified initially and 43 were retrieved for more detailed evaluation. 5 randomized, double-blind, placebo-controlled trials were selected. A total of 1604 subjects with either vaccines or placebo infections were included in the meta-analysis within the scope of these articles. According to the results, there is an increase in total adverse events for subjects with either low (95% CI: 1.90-4.29) or high (CI: 2.65-5.63) dose vaccination. The adverse effects of COVID-19 vaccine are mainly local ones including pain, itching, and redness, and no significant difference was identified in the systemic reactions. All adverse effects were transient and resolved within a few days. Moreover, the neutralizing and IgG antibody levels post different dose vaccinations were all significantly increased at day 14/21 (P = 0.0004 and P = 0.0003, respectively) and day 28/35 (P < 0.00001) in vaccine groups compared to placebo controls. Besides, the levels of neutralizing and IgG antibodies were also elevated significantly at from day 14 to 35, versus day 0 (All P < 0.001). In conclusion, our analysis suggests that the current COVID-19 vaccine candidates are safe, tolerated, and immunogenic, which provides important information for further development, evaluation, and clinical application of COVID-19 vaccine.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Ping Yuan", - "author_inst": "Tongji University School of Medicine" - }, - { - "author_name": "Pu Ai", - "author_inst": "Tongji University School of Medicine" - }, - { - "author_name": "Yihan Liu", - "author_inst": "Tongji University School of Medicine" - }, - { - "author_name": "Zisheng Ai", - "author_inst": "Tongji University School of Medicine" - }, - { - "author_name": "Yi Wang", - "author_inst": "Tongji University School of Medicine" - }, - { - "author_name": "Weijun Cao", - "author_inst": "Tongji University School of Medicine" - }, - { - "author_name": "Xiaohuan Xia", - "author_inst": "Tongji University School of Medicine" - }, - { - "author_name": "Jialin Zheng", - "author_inst": "Tongji University School of Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.02.20224311", "rel_title": "Covid-19 fatality prediction in people with diabetes and prediabetes using a simple score at hospital admission", @@ -1084406,6 +1085837,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.28.20221887", + "rel_title": "Frequency and profile of objective cognitive deficits in hospitalized patients recovering from COVID-19", + "rel_date": "2020-11-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.28.20221887", + "rel_abs": "BackgroundCognitive impairment is common following critical illness. A number of case reports and case series have suggested that cognitive deficits occur in patients with COVID-19. This study evaluated the frequency, severity, and profile of cognitive dysfunction in hospitalized patients recovering from COVID-19.\n\nMethodsWe obtained and analyzed cross-sectional neuropsychological data from a cohort of N=57 patients participating in inpatient rehabilitation. Our primary outcome measure was the Brief Memory and Executive Test (BMET). We calculated the frequency of impairment based on clinician diagnosis and by the BMET subtests using age-normed classification of impairment. We explored associations with intubation and extubation as markers of illness severity and complications, as well as psychiatric diagnosis.\n\nOutcomesOur sample was 75% male, 61% non-white, with a mean age of 64.5 (SD = 13.9) years. Patients were evaluated at a mean of 43.2 days post-admission. 88% had documented hypoxemic respiratory failure and 77% required intubation. 81% of patients had cognitive impairment, ranging from mild to severe. Deficits were most common in working memory (55% of patients impaired), set-shifting (47%), divided attention (46%), and processing speed (40%). Executive dysfunction was not significantly associated with intubation length or the time from extubation to assessment, nor was it associated with the presence of a psychiatric diagnosis.\n\nInterpretationMedically stable inpatients recovering from COVID-19 commonly have deficits in attention and executive functions. These deficits were not significantly correlated with length of intubation or time since extubation. Findings provide an early benchmark for studying the evolution of cognitive difficulties after COVID-19 and suggest that easy to disseminate interventions that remediate attention and executive dysfunctions may be important in this population.\n\nFundingThe authors have no funding for this study to report.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Abhishek Jaywant", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "W Michael Vanderlind", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "George S Alexopoulos", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Chaya B Fridman", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Roy H Perlis", + "author_inst": "Massachusetts General Hospital/Harvard Medical School" + }, + { + "author_name": "Faith M Gunning", + "author_inst": "Weill Cornell Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.10.28.20219816", "rel_title": "A Multi-Factor Risk Model for Severe Covid-19 for Vaccine Prioritization and Monitoring Based on a 15 Million Medicare Cohort", @@ -1085226,33 +1086696,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.28.20221770", - "rel_title": "The association between socioeconomic status and mobility reductions in the early stage of England's COVID-19 pandemic", - "rel_date": "2020-11-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.28.20221770", - "rel_abs": "This study uses mobile phone data to examine how socioeconomic status was associated with the extent of mobility reduction during the spring 2020 lockdown in England in a manner that considers both potentially confounding effects and spatial dependency and heterogeneity. It shows that socioeconomic status as approximated through income and occupation was strongly correlated with the extent of mobility reduction. It also demonstrates that the specific nature of the association of socioeconomic status with mobility reduction varied markedly across England. Finally, the analysis suggests that the ability to restrict everyday mobility in response to a national lockdown is distributed in a spatially uneven manner, and may need to be considered a luxury or, failing that, a tactic of survival for specific social groups.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Won Do Lee", - "author_inst": "Transport Studies Unit, School of Geography and the Environment, University of Oxford" - }, - { - "author_name": "Matthias Qian", - "author_inst": "Sa\u00efd Business School, University of Oxford" - }, - { - "author_name": "Tim Schwanen", - "author_inst": "Transport Studies Unit, School of Geography and the Environment, University of Oxford" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.28.20221820", "rel_title": "Simulating Pandemic Disease Spread and the Impact of Interventions in Complex Societal Networks", @@ -1085848,6 +1087291,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.30.20222935", + "rel_title": "Association of COVID-19 RT-qPCR test false-negative rate with patient age, sex and time since diagnosis", + "rel_date": "2020-11-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.30.20222935", + "rel_abs": "BackgroundRoutine testing for SARS-CoV-2 in the community is essential for guiding key epidemiological decisions from the quarantine of individual patients to enrolling regional and national preventive measures. Yet, the primary testing tool, the RT-qPCR based testing, is notoriously known for its low sensitivity, i.e. high risk of missed detection of carriers. Quantifying the false-negative rate (FNR) of the RT-qPCR test at the community settings and its dependence on patient demographic and disease progression is therefore key in designing and refining strategies for disease spread prevention.\n\nMethodsAnalyzing 843,917 test results of 521,696 patients, we identified false-negative (FN) and true-positive (TP) results as negative and positive results preceded by a COVID-19 diagnosis and followed by a later positive test. Regression analyses were used to determine associations of false-negative results with time of sampling after diagnosis, patient demographics and viral loads based on RT-qPCR Ct values of the next positive tests.\n\nFindingsThe overall FNR was 22.8%, which is consistent with previous studies. Yet, this rate was much lower at the first 5 days following diagnosis (10.7%) and only increased in later dates. Furthermore, the FNR was strongly associated with demographics, with odds ratio of 1.74 (95% CI: 1.58-1.90) for women over men and 1.36 (95% CI: 1.34-1.39) for 10 years younger patients. Finally, FNR was associated with viral loads (p-value 0.0005), with a difference of 1.50 (95% CI: 0.70-2.30) between the average Ct of the N gene in a positive test following a false-negative compared to a positive test following a true-positive.\n\nInterpretationOur results show that in the first few days following diagnosis, when results are critical for quarantine decisions, RT-qPCR testing is more reliable than previously reported. Yet the reliability of the test result is reduced in later days as well as for women and younger patients, where the viral loads are typically lower.\n\nFundingThis research was supported by the ISRAEL SCIENCE FOUNDATION (grant No. 3633/19) within the KillCorona - Curbing Coronavirus Research Program.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Matan Levine-Tiefenbrun", + "author_inst": "Technion-Israel Institute of Technology" + }, + { + "author_name": "Idan Yelin", + "author_inst": "Technion-Israel Institute of Technology" + }, + { + "author_name": "Hedva Uriel", + "author_inst": "Technion - Israel Institute of Technology" + }, + { + "author_name": "Jacob Kuint", + "author_inst": "Maccabi Healthcare Services, Israel" + }, + { + "author_name": "Licita Schreiber", + "author_inst": "Maccabi Healthcare Services, Israel" + }, + { + "author_name": "Esma Herzel", + "author_inst": "Maccabi Healthcare Services, Israel" + }, + { + "author_name": "Rachel Katz", + "author_inst": "Maccabi Healthcare Services, Israel" + }, + { + "author_name": "Amir Ben-Tov", + "author_inst": "Maccabi Healthcare Services, Israel" + }, + { + "author_name": "Tal Patalon", + "author_inst": "Maccabi Healthcare Services, Israel" + }, + { + "author_name": "Gabriel Chodick", + "author_inst": "Maccabi Healthcare Services, Israel" + }, + { + "author_name": "Roy Kishony", + "author_inst": "Technion - Israel Institute of Technology" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.30.20223198", "rel_title": "Analytical and Clinical Performance of the Panbio COVID-19 Antigen-Detecting Rapid Diagnostic Test", @@ -1087139,29 +1088641,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.10.30.20222786", - "rel_title": "Deep Learning Model for Improving the Characterization of Coronavirus on Chest X-ray Images Using CNN", - "rel_date": "2020-11-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.30.20222786", - "rel_abs": "The novel Coronavirus, also known as Covid19, is a pandemic that has weighed heavily on the socio-economic affairs of the world. Although researches into the production of relevant vaccine are being advanced, there is, however, a need for a computational solution to mediate the process of aiding quick detection of the disease. Different computational solutions comprised of natural language processing, knowledge engineering and deep learning have been adopted for this task. However, deep learning solutions have shown interesting performance compared to other methods. This paper therefore aims to advance the application deep learning technique to the problem of characterization and detection of novel coronavirus. The approach adopted in this study proposes a convolutional neural network (CNN) model which is further enhanced using the technique of data augmentation. The motive for the enhancement of the CNN model through the latter technique is to investigate the possibility of further improving the performances of deep learning models in detection of coronavirus. The proposed model is then applied to the COVID-19 X-ray dataset in this study which is the National Institutes of Health (NIH) Chest X-Ray dataset obtained from Kaggle for the purpose of promoting early detection and screening of coronavirus disease. Results obtained showed that our approach achieved a performance of 100% accuracy, recall/precision of 0.85, F-measure of 0.9, and specificity of 1.0. The proposed CNN model and data augmentation solution may be adopted in pre-screening suspected cases of Covid19 to provide support to the use of the well-known RT-PCR testing.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Olaide Nathaniel Oyelade", - "author_inst": "Ahmadu Bello University, Zaria-Nigeria" - }, - { - "author_name": "Absalom E Ezugwu", - "author_inst": "University of KwaZulu-Natal" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.10.29.20222414", "rel_title": "How well does societal mobility restriction help control the COVID-19 pandemic? Evidence from real-time evaluation", @@ -1088049,6 +1089528,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.30.20215335", + "rel_title": "Innate immunity plays a key role in controlling viral load in COVID-19: mechanistic insights from a whole-body infection dynamics model", + "rel_date": "2020-11-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.30.20215335", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a pathogen of immense public health concern. Efforts to control the disease have only proven mildly successful, and the disease will likely continue to cause excessive fatalities until effective preventative measures (such as a vaccine) are developed. To develop disease management strategies, a better understanding of SARS-CoV-2 pathogenesis and population susceptibility to infection are needed. To this end, physiologically-relevant mathematical modeling can provide a robust in silico tool to understand COVID-19 pathophysiology and the in vivo dynamics of SARS-CoV-2. Guided by ACE2-tropism (ACE2 receptor dependency for infection) of the virus, and by incorporating cellular-scale viral dynamics and innate and adaptive immune responses, we have developed a multiscale mechanistic model for simulating the time-dependent evolution of viral load distribution in susceptible organs of the body (respiratory tract, gut, liver, spleen, heart, kidneys, and brain). Following calibration with in vivo and clinical data, we used the model to simulate viral load progression in a virtual patient with varying degrees of compromised immune status. Further, we conducted global sensitivity analysis of model parameters and ranked them for their significance in governing clearance of viral load to understand the effects of physiological factors and underlying conditions on viral load dynamics. Antiviral drug therapy, interferon therapy, and their combination was simulated to study the effects on viral load kinetics of SARS-CoV-2. The model revealed the dominant role of innate immunity (specifically interferons and resident macrophages) in controlling viral load, and the impotance of timing when initiating therapy following infection.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=118 SRC=\"FIGDIR/small/20215335v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (43K):\norg.highwire.dtl.DTLVardef@54d70eorg.highwire.dtl.DTLVardef@1f2f0ecorg.highwire.dtl.DTLVardef@a71f28org.highwire.dtl.DTLVardef@1eeaeb8_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Prashant Dogra", + "author_inst": "Houston Methodist Research Institute" + }, + { + "author_name": "Javier Ruiz-Ramirez", + "author_inst": "Houston Methodist Research Institute" + }, + { + "author_name": "Kavya Sinha", + "author_inst": "Houston Methodist Hospital" + }, + { + "author_name": "Joseph D. Butner", + "author_inst": "Houston Methodist Research Institute" + }, + { + "author_name": "Maria J. Pelaez", + "author_inst": "Houston Methodist Research Institute" + }, + { + "author_name": "Manmeet Rawat", + "author_inst": "University of New Mexico School of Medicine" + }, + { + "author_name": "Venkata K. Yellepeddi", + "author_inst": "University of Utah" + }, + { + "author_name": "Renata Pasqualini", + "author_inst": "Rutgers New Jersey Medical School" + }, + { + "author_name": "Wadih Arap", + "author_inst": "Rutgers New Jersey Medical School" + }, + { + "author_name": "H. Dirk Sostman", + "author_inst": "Houston Methodist Academic Institute" + }, + { + "author_name": "Vittorio Cristini", + "author_inst": "Houston Methodist Research Institute" + }, + { + "author_name": "Zhihui Wang", + "author_inst": "Houston Methodist Research Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.30.20223123", "rel_title": "High prevalence of SARS-CoV-2 swab positivity and increasing R number in England during October 2020: REACT-1 round 6 interim report", @@ -1088945,53 +1090487,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.11.03.365270", - "rel_title": "The ACE2-binding interface of SARS-CoV-2 Spike inherently deflects immune recognition", - "rel_date": "2020-11-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.03.365270", - "rel_abs": "The COVID-19 pandemic remains a global threat, and host immunity remains the main mechanism of protection against the disease. The spike protein on the surface of SARS-CoV-2 is a major antigen and its engagement with human ACE2 receptor plays an essential role in viral entry into host cells. Consequently, antibodies targeting the ACE2-interacting surface (ACE2IS) located in the receptor-binding domain (RBD) of the spike protein can neutralize the virus. However, the understanding of immune responses to SARS-CoV-2 is still limited, and it is unclear how the virus protects this surface from recognition by antibodies. Here, we designed an RBD mutant that disrupts the ACE2IS and used it to characterize the prevalence of antibodies directed to the ACE2IS from convalescent sera of 94 COVID19-positive patients. We found that only a small fraction of RBD-binding antibodies targeted the ACE2IS. To assess the immunogenicity of different parts of the spike protein, we performed in vitro antibody selection for the spike and the RBD proteins using both unbiased and biased selection strategies. Intriguingly, unbiased selection yielded antibodies that predominantly targeted regions outside the ACE2IS, whereas ACE2IS-binding antibodies were readily identified from biased selection designed to enrich such antibodies. Furthermore, antibodies from an unbiased selection using the RBD preferentially bound to the surfaces that are inaccessible in the context of whole spike protein. These results suggest that the ACE2IS has evolved less immunogenic than the other regions of the spike protein, which has important implications in the development of vaccines against SARS-CoV-2.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Takamitsu Hattori", - "author_inst": "New York University Grossman School of Medicine" - }, - { - "author_name": "Akiko Koide", - "author_inst": "New York University Grossman School of Medicine" - }, - { - "author_name": "Tatyana Panchenko", - "author_inst": "New York University Grossman School of Medicine" - }, - { - "author_name": "Larizbeth A Romero", - "author_inst": "New York University Grossman School of Medicine" - }, - { - "author_name": "Kai Wen Teng", - "author_inst": "New York University Grossman School of Medicine" - }, - { - "author_name": "Takuya Tada", - "author_inst": "New York University Grossman School of Medicine" - }, - { - "author_name": "Nathaniel R Landau", - "author_inst": "New York University Grossman School of Medicine" - }, - { - "author_name": "Shohei Koide", - "author_inst": "New York University Grossman School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.11.03.366641", "rel_title": "Early immune response in mice immunized with a semi-split inactivated vaccine against SARS-CoV-2 containing S protein-free particles and subunit S protein", @@ -1089779,6 +1091274,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.01.362319", + "rel_title": "Robust SARS-CoV-2-specific T-cell immunity is maintained at 6 months following primary infection", + "rel_date": "2020-11-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.01.362319", + "rel_abs": "The immune response to SARS-CoV-2 is critical in both controlling primary infection and preventing re-infection. However, there is concern that immune responses following natural infection may not be sustained and that this may predispose to recurrent infection. We analysed the magnitude and phenotype of the SARS-CoV-2 cellular immune response in 100 donors at six months following primary infection and related this to the profile of antibody level against spike, nucleoprotein and RBD over the previous six months. T-cell immune responses to SARS-CoV-2 were present by ELISPOT and/or ICS analysis in all donors and are characterised by predominant CD4+ T cell responses with strong IL-2 cytokine expression. Median T-cell responses were 50% higher in donors who had experienced an initial symptomatic infection indicating that the severity of primary infection establishes a setpoint for cellular immunity that lasts for at least 6 months. The T-cell responses to both spike and nucleoprotein/membrane proteins were strongly correlated with the peak antibody level against each protein. The rate of decline in antibody level varied between individuals and higher levels of nucleoprotein-specific T cells were associated with preservation of NP-specific antibody level although no such correlation was observed in relation to spike-specific responses. In conclusion, our data are reassuring that functional SARS-CoV-2-specific T-cell responses are retained at six months following infection although the magnitude of this response is related to the clinical features of primary infection.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Jianmin Zuo", + "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham" + }, + { + "author_name": "Alex Dowell", + "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham" + }, + { + "author_name": "Hayden Pearce", + "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham" + }, + { + "author_name": "Kriti Verma", + "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham" + }, + { + "author_name": "Heather Long", + "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham" + }, + { + "author_name": "Jusnara Begum", + "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham" + }, + { + "author_name": "Felicity Aiano", + "author_inst": "Immunisation and Countermeasures Division, National Infection Service, PHE Colindale. 61 Colindale Avenue, London NW9 5EQ." + }, + { + "author_name": "Zahin Amin-Chowdhury", + "author_inst": "Immunisation and Countermeasures Division, National Infection Service, PHE Colindale. 61 Colindale Avenue, London NW9 5EQ." + }, + { + "author_name": "Bassam Hallis", + "author_inst": "Immunoassay Lab, National Infection Service, Porton Down SP4 0JG" + }, + { + "author_name": "Lorrain Stapley", + "author_inst": "Immunoassay Lab, National Infection Service, Porton Down SP4 0JG" + }, + { + "author_name": "Ray Borrow", + "author_inst": "Sero-epidemiology Unit, PHE, Manchester Royal Infirmary, Manchester, M13 9WL" + }, + { + "author_name": "Ezra Linley", + "author_inst": "Sero-epidemiology Unit, PHE, Manchester Royal Infirmary, Manchester, M13 9WL" + }, + { + "author_name": "Shazaad Ahmad", + "author_inst": "Manchester University NHS Foundation Trust" + }, + { + "author_name": "Ben Parker", + "author_inst": "NIHR Manchester Clinical Research Facility, Manchester Royal Infirmary, Oxford Rd, Manchester, M13 9WL" + }, + { + "author_name": "Alex Horsley", + "author_inst": "University of Manchester and NIHR Manchester Clinical Research Facility, Manchester University NHS Foundation Trust, Manchester M23 9LT" + }, + { + "author_name": "Gayatri Amirthalingam", + "author_inst": "Immunisation and Countermeasures Division, National Infection Service, PHE Colindale. 61 Colindale Avenue, London NW9 5EQ." + }, + { + "author_name": "Kevin Brown", + "author_inst": "Immunisation and Countermeasures Division, National Infection Service, PHE Colindale. 61 Colindale Avenue, London NW9 5EQ." + }, + { + "author_name": "Mary E Ramsay", + "author_inst": "Immunisation and Countermeasures Division, National Infection Service, PHE Colindale. 61 Colindale Avenue, London NW9 5EQ." + }, + { + "author_name": "Shamez Ladhani", + "author_inst": "Immunisation and Countermeasures Division, National Infection Service, PHE Colindale. 61 Colindale Avenue, London NW9 5EQ." + }, + { + "author_name": "Paul Moss", + "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.11.02.363242", "rel_title": "Ivermectin reduces coronavirus infection in vivo: a mouse experimental model", @@ -1090523,45 +1092113,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2020.10.30.362335", - "rel_title": "Boceprevir, calpain inhibitors II and XII, and GC-376 have broad-spectrum antiviral activity against coronaviruses in cell culture", - "rel_date": "2020-11-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.30.362335", - "rel_abs": "As the COVID-19 pandemic continues to fold out, the morbidity and mortality are increasing daily. Effective treatment for SARS-CoV-2 is urgently needed. We recently discovered four SARS-CoV-2 main protease (Mpro) inhibitors including boceprevir, calpain inhibitors II and XII and GC-376 with potent antiviral activity against infectious SARS-CoV-2 in cell culture. Despite the weaker enzymatic inhibition of calpain inhibitors II and XII against Mpro compared to GC-376, calpain inhibitors II and XII had more potent cellular antiviral activity. This observation promoted us to hypothesize that the cellular antiviral activity of calpain inhibitors II and XII might also involve the inhibition of cathepsin L in addition to Mpro. To test this hypothesis, we tested calpain inhibitors II and XII in the SARS-CoV-2 pseudovirus neutralization assay in Vero E6 cells and found that both compounds significantly decreased pseudoviral particle entry into cells, indicating their role in inhibiting cathepsin L. The involvement of cathepsin L was further confirmed in the drug time-of-addition experiment. In addition, we found that these four compounds not only inhibit SARS-CoV-2, but also SARS-CoV, MERS-CoV, as well as human coronaviruses (CoVs) 229E, OC43, and NL63. The mechanism of action is through targeting the viral Mpro, which was supported by the thermal shift binding assay and enzymatic FRET assay. We further showed that these four compounds have additive antiviral effect when combined with remdesivir. Altogether, these results suggest that boceprevir, calpain inhibitors II and XII, and GC-376 are not only promising antiviral drug candidates against existing human coronaviruses, but also might work against future emerging CoVs.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Yanmei Hu", - "author_inst": "University of Arizona" - }, - { - "author_name": "Chunlong Ma", - "author_inst": "University of Arizona" - }, - { - "author_name": "Tommy Szeto", - "author_inst": "University of Arizona" - }, - { - "author_name": "Brett Hurst", - "author_inst": "Utah State University" - }, - { - "author_name": "Bart Tarbet", - "author_inst": "Utah State University" - }, - { - "author_name": "Jun Wang", - "author_inst": "University of Arizona" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2020.10.31.362848", "rel_title": "Tetravalent SARS-CoV-2 Neutralizing Antibodies Show Enhanced Potency and Resistance to Escape Mutations", @@ -1091265,6 +1092816,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.29.20222224", + "rel_title": "Projecting the impact of behaviour and isolation interventions and super spreader events from mass gatherings and international travel on Malaysia's COVID-19 epidemic trajectories using an augmented SEIR model", + "rel_date": "2020-10-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.29.20222224", + "rel_abs": "BackgroundVarious levels of lockdown implemented to contain the rapid spread of COVID-19 are not long-term solutions due to socioeconomic implications.\n\nMethodsTo inform safe reopening, we used an augmented SEIR model to project the impact of 1) interventions and potential new epidemic trajectories arising from super spreader (SS) events and/or international travel and 2) re-introducing strong behavioural interventions on resurgence trajectories.\n\nResultsOur model suggests that 50% behaviour intervention effectiveness (BIE) (from enforced social distancing during lockdown, early in the epidemic), along with 50% isolation intervention effectiveness (IIE) (from increased testing and isolating infected individuals) was achieved during lockdown, which curbed COVID-19 transmission in Malaysia. Post-lockdown, BIE plays a minimal role if IIE reaches or exceeds 46.9% when other variables are held constant. At IIE of 30% and BIE of 21.3%, SS events of 5,000 active cases risks COVID-19 resurgence, with 4-year projected 12.9mn cumulative cases and 1.1mn deaths. Earlier action to increase BIE to 50% on day 98 compared to day 111, prevented an additional 21,401 recovered cases and 257 deaths.\n\nConclusionUntil a safe and effective vaccine is widely available, the risk of COVID-19 resurgence from large SS events warrants caution in decisions to allow for mass gatherings and regular international travel.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Aidonna Jan Ayub", + "author_inst": "Khazanah Research Institute" + }, + { + "author_name": "Gregory Wai Son Ho", + "author_inst": "Khazanah Research Institute" + }, + { + "author_name": "Khayriyyah Mohd Hanafiah", + "author_inst": "Universiti Sains Malaysia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.28.20221655", "rel_title": "Pre-existing conditions are associated with long-COVID patients hospitalization, despite confirmed clearance of SARS-CoV-2 virus", @@ -1092301,33 +1093879,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.10.30.361873", - "rel_title": "Amino acid transporter B0AT1 influence on ADAM17 interactions with SARS-CoV-2 receptor ACE2 putatively expressed in intestine, kidney, and cardiomyocytes", - "rel_date": "2020-10-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.30.361873", - "rel_abs": "SARS-CoV-2 exhibits significant experimental and clinical gastrointestinal, renal, and cardiac muscle tropisms responsible for local tissue-specific and systemic pathophysiology capriciously occurring in about half of COVID-19 patients. The underlying COVID-19 mechanisms engaged by these extra-pulmonary organ systems are largely unknown. We approached this knowledge gap by recognizing that neutral amino acid transporter B0AT1 (alternately called NBB, B, B0 in the literature) is a common denominator expressed nearly exclusively by three particular cell types: intestinal epithelia, renal proximal tubule epithelium, and cardiomyocytes. B0AT1 provides uptake of glutamine and tryptophan. The gut is the main depot expressing over 90% of the bodys entire pool of SARS-CoV-2 receptor angiotensin converting enzyme-2 (ACE2) and B0AT1. Recent cryo-EM studies established that ACE2 forms a thermodynamically favored dimer-of-heterodimers complex with B0AT1 assembled in the form of a dimer of two ACE2:B0AT1 heterodimers anchored in plasma membranes. Prior epithelial cell studies demonstrated ACE2 chaperone trafficking of B0AT1. This contrasts with monomeric expression of ACE2 in lung pneumocytes, in which B0AT1 is undetectable. The cell types in question also express a disintegrin and metalloproteinase-17 (ADAM17) known to cleave and shed the ectodomain of monomeric ACE2 from the cell surface, thereby relinquishing protection against unchecked renin-angiotensin-system (RAS) events of COVID-19. The present study employed molecular docking modeling to examine the interplaying assemblage of ACE2, ADAM17 and B0AT1. We report that in the monomer form of ACE2, neck region residues R652-N718 provide unimpeded access to ADAM17 active site pocket, but notably R708 and S709 remained >10-15 [A] distant. In contrast, interference of ADAM17 docking to ACE2 in a dimer-of-heterodimers arrangement was directly correlated with the presence of a neighboring B0AT1 subunit complexed to the partnering ACE2 subunit of the 2ACE2:2B0AT1] dimer of heterodimers, representing the expression pattern putatively exclusive to intestinal, renal and cardiomyocyte cell types. The monomer and dimer-of-heterodimers docking models were not influenced by the presence of SARS-CoV-2 receptor binding domain (RBD) complexed to ACE2. The results collectively provide the underpinnings for understanding the role of B0AT1 involvement in COVID-19 and the role of ADAM17 steering ACE2 events in intestinal and renal epithelial cells and cardiomyocytes, with implications useful for consideration in pandemic public hygiene policy and drug development.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Jacob T. Andring", - "author_inst": "University of Florida College of Medicine" - }, - { - "author_name": "Robert McKenna", - "author_inst": "University of Florida College of Medicine" - }, - { - "author_name": "Bruce R. Stevens", - "author_inst": "University of Florida College of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.10.29.339317", "rel_title": "COVID Moonshot: Open Science Discovery of SARS-CoV-2 Main Protease Inhibitors by Combining Crowdsourcing, High-Throughput Experiments, Computational Simulations, and Machine Learning", @@ -1093583,6 +1095134,77 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.10.29.360586", + "rel_title": "Distinct cellular immune profiles in the airways and blood of critically ill patients with COVID 19", + "rel_date": "2020-10-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.29.360586", + "rel_abs": "Our understanding of the coronavirus disease-19 (COVID-19) immune response is almost exclusively derived from studies that examined blood. To gain insight in the pulmonary immune response we analysed BALF samples and paired blood samples from 17 severe COVID-19 patients. Macrophages and T cells were the most abundant cells in BALF. In the lungs, both CD4 and CD8 T cells were predominantly effector memory cells and expressed higher levels of the exhaustion marker PD-1 than in peripheral blood. Prolonged ICU stay associated with a reduced proportion of activated T cells in peripheral blood and even more so in BALF. T cell activation in blood, but not in BALF, was higher in fatal COVID-19 cases. Increased levels of inflammatory mediators were more pronounced in BALF than in plasma. In conclusion, the bronchoalveolar immune response in COVID-19 has a unique local profile that strongly differs from the immune profile in peripheral blood.\n\nSummaryThe bronchoalveolar immune response in severe COVID-19 strongly differs from the peripheral blood immune profile. Fatal COVID-19 associated with T cell activation blood, but not in BALF.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Anno Saris", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Tom DY Reijnders", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Esther J Nossent", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Alex R Schuurman", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Jan Verhoeff", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Saskia D van Asten", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Hetty J Bontkes", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Siebe G Blok", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Janwillem Duitman", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Harm Jan Bogaard", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Leo Heunks", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Rene Lutter", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Tom van der Poll", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Juan J Garcia Vallejo", + "author_inst": "Amsterdam UMC" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.10.29.361048", "rel_title": "COVID-19 cytokines and the hyperactive immune response: Synergism of TNF-\u03b1 and IFN-\u03b3 in triggering inflammation, tissue damage, and death", @@ -1095099,45 +1096721,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.27.357418", - "rel_title": "High-throughput fluorescent assay for inhibitor screening of proteases from RNA viruses", - "rel_date": "2020-10-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.27.357418", - "rel_abs": "Spanish flu and other influenza outbreaks, the recent Zika epidemics, and the ongoing COVID-19 pandemic are the most profound examples of severe widespread diseases that are caused by RNA viruses. Perhaps less well known yet dangerous RNA viruses cause deadly diseases such as polio, Ebola, measles, rubella, yellow fever, dengue fever and many others. To combat a particular viral disease by diminishing its spread and number of fatal cases, effective vaccines and antivirals are indispensable. Therefore, quick access to the means of discovery of new treatments for any epidemic outbreak is of great interest and in vitro biochemical assays are the basis of drug discovery. The recent outbreak of the coronavirus pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) demands an affordable and reliable assay for testing antivirals. Here, we developed a quick and inexpensive high-throughput fluorescent assay to test inhibitors of viral proteases. Accordingly, we employed this assay to sample inhibitors for papain-like protease from SARS-CoV-2. In addition, we validated this assay for screening inhibitors of flaviviral protease from the tick-borne encephalitis virus to emphasize a broad range of applications of our approach. This fluorescent high-throughput assay is based on fluorescent energy transfer (FRET) between two distinct fluorescent proteins (eGFP and mCherry) connected via a substrate polypeptide. When the substrate is cleaved, FRET is abolished and the change in fluorescence corresponds to reaction progress. Our data show that this assay can be used for testing the inhibitors in the 96 or 384 well plates format with robust and reproducible outcomes.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Bara Cihlova", - "author_inst": "Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic" - }, - { - "author_name": "Andrea Huskova", - "author_inst": "Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic" - }, - { - "author_name": "Jiri B\u00f6serle", - "author_inst": "Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic" - }, - { - "author_name": "Radim Nencka", - "author_inst": "Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic" - }, - { - "author_name": "Evzen Boura", - "author_inst": "Institute of Organic Chemistry and Biochemistry" - }, - { - "author_name": "Jan Silhan", - "author_inst": "Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.10.27.20211631", "rel_title": "Optimal COVID-19 quarantine and testing strategies", @@ -1095997,6 +1097580,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.22.20217885", + "rel_title": "Pre-endoscopy SARS-CoV-2 testing strategy during COVID-19 pandemic: The care must go on", + "rel_date": "2020-10-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.22.20217885", + "rel_abs": "BackgroundIn response to the COVID-19 pandemic, endoscopic societies have recommended reduction of endoscopic procedures. In particular non-urgent endoscopies should be postponed. However, this might lead to unnecessary delay in diagnosing gastrointestinal conditions.\n\nMethodsRetrospectively we analysed the gastrointestinal endoscopies performed at the Central Endoscopy Unit of Saarland University Medical Center during seven weeks from 23 March to 10 May 2020 and present our real-world single-center experience with an individualized rtPCR-based pre-endoscopy SARS-CoV-2 testing (\"PECo\") strategy.\n\nResultsAltogether 359 gastrointestinal endoscopies were performed. The PECo strategy enabled us to conservatively handle endoscopy program reduction (44% reduction as compared 2019). The results of COVID-19 rtPCR from nasopharyngeal swabs were available in 89% of patients prior to endoscopies. Apart from six patients with known COVID-19, all other tested patients were negative. The frequencies of endoscopic therapies and clinically significant findings did not differ between patients with or without SARS-CoV-2 tests.\n\nConclusionA reasonable reduction of the endoscopy program in the setting of structured SARS-CoV-2 testing is feasible and safe. The PECo strategy allows continuation of endoscopic procedures in a region with intermediate frequency of COVID-19 when hospital capacities are not overwhelmed by the pandemic. Thus, the study might help to develop new strategies during future waves of COVID-19 or local outbreaks.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Markus Casper", + "author_inst": "Saarland University Medical Center" + }, + { + "author_name": "Matthias C Reichert", + "author_inst": "Saarland University Medical Center" + }, + { + "author_name": "Juergen Rissland", + "author_inst": "Saarland University Medical Center" + }, + { + "author_name": "Markus Casper", + "author_inst": "Saarland University Medical Center" + }, + { + "author_name": "Frank Lammert", + "author_inst": "Saarland University Medical Center" + }, + { + "author_name": "Marcin Krawczyk", + "author_inst": "Saarland University Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "gastroenterology" + }, { "rel_doi": "10.1101/2020.10.22.20215277", "rel_title": "The importance of the human factor during the evolution of SARS-CoV-2 pandemic: the successful case of the Italian strategy", @@ -1096681,41 +1098303,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.10.23.20218271", - "rel_title": "Online information on face masks in Italian and English websites: issues and responsibilities of search engines", - "rel_date": "2020-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.23.20218271", - "rel_abs": "Countries have major differences in the acceptance of face mask use for the prevention of COVID-19. We analyzed 450 webpages returned by searching the string \"are face masks dangerous\" in Italy, the UK and the USA using three search engines (Bing, Duckduckgo and Google). The majority (64-79%) were pages from news outlets, with few (2-6%) pages from government and public health agencies. Webpages with a positive stance on masks were more frequent in English (50%) than in Italian (36%), and those with a negative stance were more frequent in Italian (28% vs. 19% in English). Google returned the highest number of mask-positive pages and Duckduckgo the lowest. Google also returned the lowest number of pages mentioning conspiracy theories and Duckduckgo the highest. Webpages in Italian scored lower than those in English in transparency (reporting authors, their credentials and backing the information with references). When issues about the use of face masks were analyzed, mask effectiveness was the most discussed followed by hypercapnia (accumulation of carbon dioxide), contraindication in respiratory disease, and hypoxia, with issues related to their contraindications in mental health conditions and disability mentioned by very few pages. This study suggests that: 1) public health agencies should increase their web presence in providing correct information on face masks; 2) search engines should improve the information quality criteria in their ranking; 3) the public should be more informed on issues related to the use of masks and disabilities, mental health and stigma arising for those people who cannot wear masks.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Shaily Meta", - "author_inst": "Brighton and Sussex Medical School" - }, - { - "author_name": "Daria Ghezzi", - "author_inst": "Homerton College, Cambridge University" - }, - { - "author_name": "Alessia Catalani", - "author_inst": "Universita di Urbino, Italy" - }, - { - "author_name": "Tania Vanzolini", - "author_inst": "Universita di Urbino, Italy" - }, - { - "author_name": "Pietro Ghezzi", - "author_inst": "Brighon & Sussex Medical School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.10.23.20218412", "rel_title": "The COVID-19 Suffolk Events Toolkit (C-SET): A structured approach to conducting COVID-secure events", @@ -1097375,6 +1098962,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.23.20218479", + "rel_title": "COVID -19: could green tea catechins reduce the risks?", + "rel_date": "2020-10-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.23.20218479", + "rel_abs": "PurposeSeveral lines of emerging pharmacological and epidemiological evidence imply that overall risks related to COVID-19 may be reduced by green tea catechins. Therefore, it may be expected that countries with higher per/capita green tea consumption would be less affected by COVID-19. The aim of this study was to assess this possibility.\n\nMethodsAmong countries with at least 3 million population (n=134), countries with relatively high (above 150 g) per/capita green tea consumption have been identified (n=21); (ii) normalized to population values of COVID-19 cases (morbidity) and deaths (mortality) for groups of countries with high and low per/capita green tea consumption were compared.\n\nResultsStriking differences in COVID-19 morbidity and mortality between groups of countries with high and low green tea consumption were found. The differences were still observed after the adjustment for the onset of the disease. An analysis using multiple linear regression approach suggests that the associations are present at the level of individual countries.\n\nConclusionEvidence supporting the idea that green tea constituents could reduce overall risks related to COVID-19 has been obtained. The results are promising and are in line with emerging evidence from other studies including pharmacological ones. Nevertheless, because of limitations of this study the idea still should be considered as a hypothesis requiring further assessment. Several vaccines are currently validated for COVID-19 prevention and mass vaccination has already been started in many countries. Still, it is likely that the development of an efficient drug therapy that reduces COVID-19 severity/mortality would be important for rather prolonged time. In this context, the results obtained in this study may have significant implications.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Maksim Storozhuk", + "author_inst": "Bogomoletz Institute of Physiology, National Academy of Sciences of Ukraine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.25.20216937", "rel_title": "Reducing Covid-19 risk in schools: a qualitative examination of staff and family views and concerns", @@ -1098231,33 +1099837,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.10.25.20219105", - "rel_title": "PUBLIC TRANSIT RIDERSHIP ANALYSIS DURING THE COVID-19 PANDEMIC", - "rel_date": "2020-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.25.20219105", - "rel_abs": "This study investigates the effect of the coronavirus (COVID-19) pandemic on public transport ridership in Baltimore and nine other U.S. cities similar to Baltimore, in terms of population and service area, during the first five months of 2020. The analysis is based on ridership numbers, vehicle revenue hours, and vehicles operated in maximum service. A compliance analysis was done between 2020 and 2019, as well as a monthly analysis of 2020 by mode and type of services. In comparison to 2019, the ridership decreases from March, the start of the pandemic, while all ten cities experienced the most decrease in ridership in April.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Samira Ahangari", - "author_inst": "Morgan State University" - }, - { - "author_name": "Celeste Chavis", - "author_inst": "Morgan State University" - }, - { - "author_name": "Mansoureh Jeihani", - "author_inst": "Morgan State University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.10.25.20219006", "rel_title": "Determinants of psychological distress during the COVID-19 pandemic and the lockdown measures: a nationwide on-line survey in Greece and Cyprus", @@ -1099001,6 +1100580,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.26.20219576", + "rel_title": "Impact of the COVID-19 pandemic on remote mental healthcare and prescribing in psychiatry", + "rel_date": "2020-10-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.26.20219576", + "rel_abs": "ObjectivesThe recent COVID-19 pandemic has disrupted mental healthcare delivery, with many services shifting from in- person to remote patient contact. We investigated the impact of the pandemic on the use of remote consultation and on the prescribing of psychiatric medications.\n\nDesign and settingThe Clinical Record Interactive Search tool (CRIS) was used to examine de-identified electronic health records (EHRs) of people receiving mental healthcare from the South London and Maudsley (SLaM) NHS Foundation Trust. Data from the period before and after the onset of the pandemic were analysed using linear regression, and visualised using locally estimated scatterplot smoothing (LOESS).\n\nParticipantsAll patients receiving care from SLaM between 7th January 2019 and 20th September 2020 (around 37,500 patients per week).\n\nOutcome measuresO_LIThe number of clinical contacts (in-person, remote or non-attended) with mental healthcare professionals per week\nC_LIO_LIPrescribing of antipsychotic and mood stabiliser medications per week\nC_LI\n\nResultsFollowing the onset of the pandemic, the frequency of in-person contacts was significantly reduced compared to that in the previous year ({beta} coefficient: -5829.6 contacts, 95% CI -6919.5 to -4739.6, p<0.001), while the frequency of remote contacts significantly increased ({beta} coefficient: 3338.5 contacts, 95% CI 3074.4 to 3602.7, p<0.001). Rates of remote consultation were lower in older adults than in working age adults, children and adolescents. Despite this change in the type of patient contact, antipsychotic and mood stabiliser prescribing remained at similar levels.\n\nConclusionsThe COVID-19 pandemic has been associated with a marked increase in remote consultation, particularly among younger patients. However, there was no evidence that this has led to changes in psychiatric prescribing. Nevertheless, further work is needed to ensure that older patients are able to access mental healthcare remotely.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Rashmi Patel", + "author_inst": "King's College London (Institute of Psychiatry, Psychology and Neuroscience), London, UK" + }, + { + "author_name": "Jessica Irving", + "author_inst": "King's College London (Institute of Psychiatry, Psychology and Neuroscience), London, UK" + }, + { + "author_name": "Aimee Brinn", + "author_inst": "King's College London (Institute of Psychiatry, Psychology and Neuroscience), London, UK" + }, + { + "author_name": "Matthew Broadbent", + "author_inst": "South London and Maudsley NHS Foundation Trust, London, UK" + }, + { + "author_name": "Hitesh Shetty", + "author_inst": "South London and Maudsley NHS Foundation Trust, London, UK" + }, + { + "author_name": "Megan Pritchard", + "author_inst": "South London and Maudsley NHS Foundation Trust, London, UK" + }, + { + "author_name": "Johnny Downs", + "author_inst": "King's College London (Institute of Psychiatry, Psychology and Neuroscience), London, UK" + }, + { + "author_name": "Robert Stewart", + "author_inst": "King's College London (Institute of Psychiatry, Psychology and Neuroscience), London, UK" + }, + { + "author_name": "Robert Harland", + "author_inst": "South London and Maudsley NHS Foundation Trust, London, UK" + }, + { + "author_name": "Philip McGuire", + "author_inst": "King's College London (Institute of Psychiatry, Psychology and Neuroscience), London, UK" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.10.26.20219634", "rel_title": "Who is (Not) Complying with the Social Distancing Directive and Why? Testing a General Framework of Compliance with Multiple Measures of Social Distancing", @@ -1099813,29 +1101447,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.10.26.20219519", - "rel_title": "Symptoms at presentation for patients admitted to hospital with Covid-19: results from the ISARIC prospective multinational observational study", - "rel_date": "2020-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.26.20219519", - "rel_abs": "BackgroundThe ISARIC prospective multinational observational study is the largest cohort of hospitalized patients with COVID-19. We present relationships of age, sex, and nationality to presenting symptoms.\n\nMethodsInternational, prospective observational study of 60109 hospitalized symptomatic patients with laboratory-confirmed COVID-19 recruited from 43 countries between 30 January and 3 August 2020. Logistic regression was performed to evaluate relationships of age and sex to published COVID-19 case definitions and the most commonly reported symptoms.\n\nResults Typical symptoms of fever (69%), cough (68%) and shortness of breath (66%) were the most commonly reported. 92% of patients experienced at least one of these. Prevalence of typical symptoms was greatest in 30-to 60-year-olds (respectively 80%, 79%, 69%; at least one 95%). They were reported less frequently in children ([≤]18 years: 69%, 48%, 23%; 85%), older adults ([≥]70 years: 61%, 62%, 65%; 90%), and women (66%, 66%, 64%; 90%; vs men 71%, 70%, 67%; 93%). The most common atypical presentation under 60 years of age was nausea and vomiting, and over 60 years was confusion. Regression models showed significant differences in symptoms with sex, age and country.\n\nInterpretationAdults over 60 and children admitted to hospital with COVID-19 are less likely to present with typical symptoms. Nausea and vomiting are common atypical presentations under 30 years. Confusion is a frequent atypical presentation of COVID-19 in adults over 60 years. Women are less likely to experience typical symptoms than men.\n\nSummaryAdults over 60 and children admitted to hospital with COVID-19 are less likely to have typical symptoms. Nausea and vomiting are common atypical presentations under 30 and confusion over 60. Women are less likely to experience typical symptoms than men.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "- ISARIC Clinical Characterisation Group", - "author_inst": "" - }, - { - "author_name": "Mark G Pritchard", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.10.26.20219592", "rel_title": "Intention to have the seasonal influenza vaccination during the COVID-19 pandemic among eligible adults in the UK", @@ -1100847,6 +1102458,145 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.10.27.20219097", + "rel_title": "Co-infection in critically ill patients with COVID-19: An observational cohort study from England", + "rel_date": "2020-10-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.27.20219097", + "rel_abs": "ObjectiveTo describe the incidence and nature of co-infection in critically ill adults with COVID-19 infection in England.\n\nMethodsA retrospective cohort study of adults with COVID-19 admitted to seven intensive care units (ICUs) in England up to 18 May 2020, was performed. Patients with completed ICU stays were included. The proportion and type of organisms were determined at <48 and >48 hours following hospital admission, corresponding to community and hospital-acquired co-infections.\n\nResultsOf 254 patients studied (median age 59 years (IQR 49-69); 64.6% male), 139 clinically significant organisms were identified from 83(32.7%) patients. Bacterial co-infections were identified within 48 hours of admission in 14(5.5%) patients; the commonest pathogens were Staphylococcus aureus (four patients) and Streptococcus pneumoniae (two patients). The proportion of pathogens detected increased with duration of ICU stay, consisting largely of Gram-negative bacteria, particularly Klebsiella pneumoniae and Escherichia coli. The co-infection rate >48 hours after admission was 27/1000 person-days (95% CI 21.3-34.1). Patients with co-infections were more likely to die in ICU (crude OR 1.78,95% CI 1.03-3.08, p=0.04) compared to those without co-infections.\n\nConclusionWe found limited evidence for community-acquired bacterial co-infection in hospitalised adults with COVID-19, but a high rate of Gram-negative infection acquired during ICU stay.", + "rel_num_authors": 31, + "rel_authors": [ + { + "author_name": "Vadsala Baskaran", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Hannah Lawrence", + "author_inst": "Department of Respiratory Medicine, Nottingham University Hospital NHS Trust, Nottingham NG5 1PB, UK" + }, + { + "author_name": "Louise Lansbury", + "author_inst": "Division of Epidemiology and Public Health, School of Medicine, University of Nottingham, Clinical Sciences Building, Nottingham City Hospital Campus, Hucknall " + }, + { + "author_name": "Karmel Webb", + "author_inst": "Division of Epidemiology and Public Health, School of Medicine, University of Nottingham, Clinical Sciences Building, Nottingham City Hospital Campus, Hucknall " + }, + { + "author_name": "Shahideh Safavi", + "author_inst": "NIHR Nottingham Biomedical Research Centre, Queen's Medical Centre, Nottingham NG7 2UH, UK" + }, + { + "author_name": "Izzah Zainuddin", + "author_inst": "Department of Respiratory Medicine, Nottingham University Hospital NHS Trust, Nottingham NG5 1PB, UK" + }, + { + "author_name": "Tausif Huq", + "author_inst": "Department of Respiratory Medicine, Nottingham University Hospital NHS Trust, Nottingham NG5 1PB, UK" + }, + { + "author_name": "Charlotte Eggleston", + "author_inst": "Department of Respiratory Medicine, Nottingham University Hospital NHS Trust, Nottingham NG5 1PB, UK" + }, + { + "author_name": "Jayne Ellis", + "author_inst": "University College London Hospitals NHS Foundation Trust, 250 Euston Rd, London NW1 2PG, UK" + }, + { + "author_name": "Clare Thakker", + "author_inst": "University College London Hospitals NHS Foundation Trust, 250 Euston Rd, London NW1 2PG, UK" + }, + { + "author_name": "Bethan Charles", + "author_inst": "Salford Royal NHS Foundation Trust, Stott Ln, Salford M6 8HD, UK" + }, + { + "author_name": "Sara Boyd", + "author_inst": "Guy's and St Tomas' NHS Foundation Trust, Great Maze Pond, London SE1 9RT, UK" + }, + { + "author_name": "Tom Williams", + "author_inst": "Guy's and St Tomas' NHS Foundation Trust, Great Maze Pond, London SE1 9RT, UK" + }, + { + "author_name": "Claire Phillips", + "author_inst": "Brighton and Sussex University Hospitals NHS trust, Eastern Road, Brighton BN2 1ES, UK" + }, + { + "author_name": "Ethan Redmore", + "author_inst": "Brighton and Sussex University Hospitals NHS trust, Eastern Road, Brighton BN2 1ES, UK" + }, + { + "author_name": "Sarah Platt", + "author_inst": "Newcastle Upon Tyne Hospitals NHS Foundation Trust, Freeman Rd, High Heaton, Newcastle upon Tyne NE7 7DN, UK" + }, + { + "author_name": "Eve Hamilton", + "author_inst": "Newcastle Upon Tyne Hospitals NHS Foundation Trust, Freeman Rd, High Heaton, Newcastle upon Tyne NE7 7DN, UK" + }, + { + "author_name": "Andrew Barr", + "author_inst": "Newcastle Upon Tyne Hospitals NHS Foundation Trust, Freeman Rd, High Heaton, Newcastle upon Tyne NE7 7DN, UK" + }, + { + "author_name": "Lucy Venyo", + "author_inst": "Newcastle Upon Tyne Hospitals NHS Foundation Trust, Freeman Rd, High Heaton, Newcastle upon Tyne NE7 7DN, UK" + }, + { + "author_name": "Peter Wilson", + "author_inst": "University College London Hospitals NHS Foundation Trust, 250 Euston Rd, London NW1 2PG, UK" + }, + { + "author_name": "Tom Bewick", + "author_inst": "University Hospitals of Derby and Burton NHS Foundation Trust, Uttoxeter Road, Derby DE22 3NE, UK" + }, + { + "author_name": "Priya Daniel", + "author_inst": "University Hospitals of Derby and Burton NHS Foundation Trust, Uttoxeter Road, Derby DE22 3NE, UK" + }, + { + "author_name": "Paul Dark", + "author_inst": "Division of Infection, Immunity and Respiratory Medicine, NIHR Manchester Biomedical Research Centre, University of Manchester, Manchester, M23 9PT" + }, + { + "author_name": "Adam R Jeans", + "author_inst": "Salford Royal NHS Foundation Trust, Stott Ln, Salford M6 8HD, UK" + }, + { + "author_name": "Jamie McCanny", + "author_inst": "Guy's and St Thomas' NHS Foundation Trust, Great Maze Pond, London SE1 9RT, UK" + }, + { + "author_name": "Jonathan D Edgeworth", + "author_inst": "Guy's and St Thomas' NHS Foundation Trust, Great Maze Pond, London SE1 9RT, UK" + }, + { + "author_name": "Martin J Llewelyn", + "author_inst": "Brighton and Sussex University Hospitals NHS trust, Eastern Road, Brighton BN2 1ES, UK" + }, + { + "author_name": "Matthias L Schmid", + "author_inst": "Newcastle Upon Tyne Hospitals NHS Foundation Trust, Freeman Rd, High Heaton, Newcastle upon Tyne NE7 7DN, UK" + }, + { + "author_name": "Tricia M McKeever", + "author_inst": "Division of Epidemiology and Public Health, School of Medicine, University of Nottingham, Clinical Sciences Building, Nottingham City Hospital Campus, Hucknall " + }, + { + "author_name": "Martin Beed", + "author_inst": "Department of Critical Care, Nottingham University Hospital NHS Trust, Nottingham NG5 1PB, UK" + }, + { + "author_name": "Wei Shen Lim", + "author_inst": "Department of Respiratory Medicine, Nottingham University Hospital NHS Trust, Nottingham NG5 1PB, UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2020.10.27.20220400", "rel_title": "The Incidence and Severity of COVID-19 in Adult Professional Soccer Players", @@ -1101971,93 +1103721,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.10.26.354969", - "rel_title": "Origin of imported SARS-CoV-2 strains in The Gambia identified from whole genome sequences", - "rel_date": "2020-10-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.26.354969", - "rel_abs": "Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a positive-sense single stranded RNA virus with high human transmissibility. This study generated Whole Genome data to determine the origin and pattern of transmission of SARS-CoV-2 from the first six cases tested in The Gambia. Total RNA from SARS-CoV-2 was extracted from inactivated nasopharyngeal-oropharyngeal swabs of six cases and converted to cDNA following the ARTIC COVID-19 sequencing protocol. Libraries were constructed with the NEBNext ultra II DNA library prep kit for Illumina and Oxford Nanopore Ligation sequencing kit and sequenced on Illumina MiSeq and Nanopore GridION, respectively. Sequencing reads were mapped to the Wuhan reference genome and compared to eleven other SARS-CoV-2 strains of Asian, European and American origins. A phylogenetic tree was constructed with the consensus genomes for local and non-African strains. Three of the Gambian strains had a European origin (UK and Spain), two strains were of Asian origin (Japan). In The Gambia, Nanopore and Illumina sequencers were successfully used to identify the sources of SARS-CoV-2 infection in COVID-19 cases.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Abdoulie Kanteh", - "author_inst": "Medical Research Council" - }, - { - "author_name": "Jarra Manneh", - "author_inst": "MRCG at LSHTM" - }, - { - "author_name": "Sona Jabang", - "author_inst": "MRCG at LSHTM" - }, - { - "author_name": "Kujabi Mariama A.", - "author_inst": "MRCG at LSHTM" - }, - { - "author_name": "Sanyang Bakary", - "author_inst": "MRCG at LSHTM" - }, - { - "author_name": "Oboh Mary A.", - "author_inst": "MRCG at LSHTM" - }, - { - "author_name": "Abdoulie Bojang", - "author_inst": "MRCG at LSHTM" - }, - { - "author_name": "Haruna Jallow", - "author_inst": "Ministry of Health" - }, - { - "author_name": "Davis Nwakanma", - "author_inst": "MRCG at LSHTM" - }, - { - "author_name": "Ousman Secka", - "author_inst": "MRCG at LSHTM" - }, - { - "author_name": "Anna Rocca", - "author_inst": "MRCG at LSHTM" - }, - { - "author_name": "Alfred Amambua-Ngwa", - "author_inst": "MRCG at LSHTM" - }, - { - "author_name": "Martin Antonio", - "author_inst": "MRCG at LSHTM" - }, - { - "author_name": "Ignatius Baldeh", - "author_inst": "Ministry of Health" - }, - { - "author_name": "Karen Forrest", - "author_inst": "MRCG at LSHTM" - }, - { - "author_name": "Ahmadou Lamin Samateh", - "author_inst": "Ministry of Health: Gambia" - }, - { - "author_name": "Umberto D\u2019Alessandro", - "author_inst": "MRCG at LSHTM" - }, - { - "author_name": "Abdul Karim Sesay", - "author_inst": "MRCG at LSHTM" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.10.26.355206", "rel_title": "Positive outcomes of COVID-19 research-related gender policy changes", @@ -1102537,6 +1104200,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.22.20216481", + "rel_title": "Hardness of Herd Immunity and Success Probability of Quarantine Measures: A Branching Process Approach", + "rel_date": "2020-10-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.22.20216481", + "rel_abs": "Herd immunity refers to the collective resistance of a population against the spreading of an infection as an epidemic. Understanding the dependencies of herd immunity on various epidemiological parameters is of immense importance for strategizing control measures against an infection in a population. Using an age-dependent branching process model of infection propagation, we obtain interesting functional dependencies of herd immunity on the incubation period of the contagion, contact rate, and the probability of disease transmission from an infected to a susceptible individual. We show that herd immunity is difficult to achieve in case of a high incubation period of the contagion. We derive a method to quantify the success probabilities of quarantine measures to mitigate infection from a population, before achieving herd immunity. We provide a mechanistic derivation of the distribution of generation time from basic principles, which is of central importance to estimate the reproduction number R0, but has been assumed in an ad hoc manner in epidemiological studies, by far. This derivation of the generation time distribution has the generality to be applied in the study of many other age-dependent branching processes, such as the growth of bacterial colonies, various problems in evolutionary and population biology etc.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Sujit Kumar Nath", + "author_inst": "University of Leeds" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.22.20217752", "rel_title": "Lockdown related travel behavior undermines thecontainment of SARS-CoV-2", @@ -1103421,45 +1105103,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.21.20217174", - "rel_title": "Mortality among Adults Ages 25-44 in the United States During the COVID-19 Pandemic.", - "rel_date": "2020-10-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.21.20217174", - "rel_abs": "IntroductionCoronavirus disease-19 (COVID-19) has caused a marked increase in all-cause deaths in the United States, mostly among adults aged 65 and older. Because younger adults have far lower infection fatality rates, less attention has been focused on the mortality burden of COVID-19 in this demographic.\n\nMethodsWe performed an observational cohort study using public data from the National Center for Health Statistics at the United States Centers for Disease Control and Prevention, and CDC Wonder. We analyzed all-cause mortality among adults ages 25-44 during the COVID-19 pandemic in the United States. Further, we compared COVID-19-related deaths in this age group during the pandemic period to all drug overdose deaths and opioid-specific overdose deaths in each of the ten Health and Human Services (HHS) regions during the corresponding period of 2018, the most recent year for which data are available.\n\nResultsAs of September 6, 2020, 74,027 all-cause deaths occurred among persons ages 25-44 years during the period from March 1st to July 31st, 2020, 14,155 more than during the same period of 2019, a 23% relative increase (incident rate ratio 1.23; 95% CI 1.21-1.24), with a peak of 30% occurring in May (IRR 1.30; 95% CI 1.27-1.33). In HHS Region 2 (New York, New Jersey), HHS Region 6 (Arkansas, Louisiana, New Mexico, Oklahoma, Texas), and HHS Region 9 (Arizona, California, Hawaii, Nevada), COVID-19 deaths exceeded 2018 unintentional opioid overdose deaths during at least one month. Combined, 2,450 COVID-19 deaths were recorded in these three regions during the pandemic period, compared to 2,445 opioid deaths during the same period of 2018.\n\nMeaningWe find that COVID-19 has likely become the leading cause of death--surpassing unintentional overdoses--among young adults aged 25-44 in some areas of the United States during substantial COVID-19 outbreaks.\n\nNoteThe data presented here have since been updated. As a result, an additional 1,902 all-cause deaths occurring among US adults ages 25-44 during the period of interest are not accounted for in this manuscript.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Jeremy S Faust", - "author_inst": "Brigham and Women's Hospital, Department of Emergency Medicine, Harvard Medical School" - }, - { - "author_name": "Harlan Krumholz", - "author_inst": "Yale University" - }, - { - "author_name": "Katherine L Dickerson", - "author_inst": "Harvard Affiliated Emergency Medicine Residency" - }, - { - "author_name": "Zhenqiu Lin", - "author_inst": "Yale New Haven Hospital Center for Outcomes Research and Evaluation" - }, - { - "author_name": "Cleavon Gilman", - "author_inst": "Emergency Medicine Department Yuma Regional Medical Center" - }, - { - "author_name": "Rochelle P. Walensky", - "author_inst": "Massachusetts General Hospital Division of Infectious Diseases Harvard Medical School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.21.20217158", "rel_title": "Cost and social distancing dynamics in a mathematical model of COVID-19 with application to Ontario, Canada", @@ -1104099,6 +1105742,41 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2020.10.23.351353", + "rel_title": "Evidence for ZAP-independent CpG reduction in SARS-CoV-2 genome, and pangolin coronavirus origin of 5'UTR", + "rel_date": "2020-10-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.23.351353", + "rel_abs": "SARS-CoV-2, the causative agent of COVID-19, has an RNA genome, which is, overall, closely related to the bat coronavirus sequence RaTG13. However, the ACE2-binding domain of this virus is more similar to a coronavirus isolated from a Guangdong pangolin. In addition to this unique feature, the genome of SARS-CoV-2 (and its closely related coronaviruses) has a low CpG content. This has been postulated to be the signature of an evolutionary pressure exerted by the host antiviral protein ZAP. Here, we analyzed the sequences of a wide range of viruses using both alignment-based and alignment free approaches to investigate the origin of SARS-CoV-2 genome. Our analyses revealed a high level of similarity between the 5UTR of SARS-CoV-2 and that of the Guangdong pangolin coronavirus. This suggests bat and pangolin coronaviruses might have recombined at least twice (in the 5UTR and ACE2 binding regions) to seed the formation of SARS-CoV-2. An alternative hypothesis is that the lineage preceding SARS-CoV-2 is a yet to be sampled bat coronavirus whose ACE2 binding domain and 5UTR are distinct from other known bat coronaviruses. Additionally, we performed a detailed analysis of viral genome compositions as well as expression and RNA binding data of ZAP to show that the low CpG abundance in SARS-CoV-2 is not related to an evolutionary pressure from ZAP.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Ali Afrasiabi", + "author_inst": "Systems Biology and Health Data Analytics Lab, The Graduate School of Biomedical Engineering, UNSW Sydney" + }, + { + "author_name": "Hamid Alinejad-Rokny", + "author_inst": "Systems Biology and Health Data Analytics Lab, The Graduate School of Biomedical Engineering, UNSW Sydney" + }, + { + "author_name": "Nigel Lovell", + "author_inst": "The Graduate School of Biomedical Engineering, UNSW Sydney" + }, + { + "author_name": "Zhenming Xu", + "author_inst": "UNIVERSITY OF TEXAS HLTH SCI CTR SAN ANTONIO" + }, + { + "author_name": "Diako Ebrahimi", + "author_inst": "Texas Biomedical Research Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.10.20.20216440", "rel_title": "Covid-19 in children: is there any correlation with renal function and severity of the disease?", @@ -1104931,97 +1106609,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.21.20216689", - "rel_title": "Serological surveillance of SARS-CoV-2: trends and humoral response in a cohort of public health workers", - "rel_date": "2020-10-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.21.20216689", - "rel_abs": "BackgroundAntibody waning after SARS-CoV-2 infection may result in reduction in long-term immunity following natural infection and vaccination, and is therefore a major public health issue. We undertook prospective serosurveillance in a large cohort of healthy adults from the start of the epidemic in England.\n\nMethodsClinical and non-clinical healthcare workers were recruited across three English regions and tested monthly from March to November 2020 for SARS-CoV-2 spike (S) protein and nucleoprotein (N) antibodies using five different immunoassays. In positive individuals, antibody responses and long-term trends were modelled using mixed effects regression.\n\nFindingsIn total, 2246 individuals attended 12,247 visits and 264 were seropositive in [≥]2 assays. Most seroconversions occurred between March and April 2020. The assays showed >85% agreement for ever-positivity, although this changed markedly over time. Antibodies were detected earlier with Abbott (N) but declined rapidly thereafter. With the EuroImmun (S) and receptor-binding domain (RBD) assays, responses increased for 4 weeks then fell until week 12-16 before stabilising. For Roche (N), responses increased until 8 weeks, stabilised, then declined, but most remained above the positive threshold. For Roche (S), responses continued to climb over the full 24 weeks, with no sero-reversions. Predicted proportions sero-reverting after 52 weeks were 100% for Abbott, 59% (95% credible interval 50-68%) Euroimmun, 41% (30-52%) RBD, 10% (8-14%) Roche (N) <2% Roche (S).\n\nInterpretationTrends in SARS-CoV-2 antibodies following infection are highly dependent on the assay used. Ongoing serosurveillance using multiple assays is critical for monitoring the course and long-term progression of SARS-CoV-2 antibodies.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Ross J Harris", - "author_inst": "Public Health England" - }, - { - "author_name": "Heather J Whitaker", - "author_inst": "Public Health England" - }, - { - "author_name": "Nick J Andrews", - "author_inst": "Public Health England" - }, - { - "author_name": "Felicity Aiano", - "author_inst": "Public Health England" - }, - { - "author_name": "Zahin Amin-Chowdhury", - "author_inst": "Public Health England" - }, - { - "author_name": "Jessica Flood", - "author_inst": "Public Health England" - }, - { - "author_name": "Ray Borrow", - "author_inst": "Public Health England" - }, - { - "author_name": "Ezra Linley", - "author_inst": "Public Health England" - }, - { - "author_name": "Shazaad Ahmad", - "author_inst": "Manchester University NHS Foundation Trust" - }, - { - "author_name": "Lorraine Stapley", - "author_inst": "Public Health England" - }, - { - "author_name": "Bassam Hallis", - "author_inst": "Public Health England" - }, - { - "author_name": "Gayatri Amirthalingam", - "author_inst": "Public Health England" - }, - { - "author_name": "Katja Hoschler", - "author_inst": "Public Health England" - }, - { - "author_name": "Ben Parker", - "author_inst": "Public Health England" - }, - { - "author_name": "Alex Horsley", - "author_inst": "Manchester University NHS Foundation Trust" - }, - { - "author_name": "Timothy J G Brooks", - "author_inst": "Public Health England" - }, - { - "author_name": "Kevin Brown", - "author_inst": "Public Health England" - }, - { - "author_name": "Mary Ramsay", - "author_inst": "Public Health England" - }, - { - "author_name": "Shamez Ladhani", - "author_inst": "Public Health England, St. Georges University of London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.21.20206078", "rel_title": "Comparison of three nasopharyngeal swab types and the impact of physiochemical properties for optimal SARS-CoV-2 detection", @@ -1105617,6 +1107204,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.21.20216077", + "rel_title": "Nasopharyngeal aspirates vs. nasal swabs for the detection of respiratory pathogens: results of a rapid review protocol", + "rel_date": "2020-10-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.21.20216077", + "rel_abs": "BackgroundNasal pathogen detection sensitivities are often as low as 70% despite advances in molecular diagnostics. It has been suggested that this is linked, in part, to the choice of sampling method.\n\nMethodsA diagnostic test accuracy review for sensitivity, using recently developed Cochrane methods for conducting rapid reviews, and the PRISMA protocol was undertaken, with QUADAS-2 risk of bias assessments and meta-analysis of included studies. Sensitivities were calculated by a consensus standard of positivity by either method as the gold standard. Insufficient and/or inaccurate, cross sectional or anatomical site pooling methodologies were excluded.\n\nResultsOf 13 included studies, 8 had high risk of bias, and 5 had high applicability concerns. There were no statistical differences in pooled sensitivities between collection methods for 8 different viruses, and neither with use of PCR, Immunofluorescence nor culture. In a single study, Influenza H1N1 favoured nasopharyngeal swabs, with aspirates having 93.3% of the sensitivity of swabs (p>0.001). Similar equivocal sensitivities were noticed in detecting bacteria.\n\nConclusionsThe chain of sampling, from anatomical site to laboratory results, features different potential foci along which sensitivity may be lost. A sufficient body of evidence exists that use of a different sampling method will not yield more respiratory pathogens. The new Cochrane Rapid Reviews guidance helped rapidly answer this relevant and timely clinical question.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Matthew Francis Flynn", + "author_inst": "Ulster University" + }, + { + "author_name": "Martin Kelly", + "author_inst": "Western Health and Social Care Trust" + }, + { + "author_name": "James S Dooley", + "author_inst": "Ulster University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.21.20216747", "rel_title": "The wide spectrum of neuropsychiatric complications in Covid-19 patients within a multidisciplinary hospital context", @@ -1106569,73 +1108183,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.20.20216259", - "rel_title": "Population-based prevalence surveys during the COVID-19 pandemic: a systematic review", - "rel_date": "2020-10-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.20.20216259", - "rel_abs": "Population-based prevalence surveys of COVID-19 contribute to establish the burden and epidemiology of infection, the role of asymptomatic and mild infections in transmission, and allow more precise decisions about reopen policies. We performed a systematic review to evaluate qualitative aspects of these studies, their reliability, and biases. The available data described 37 surveys from 19 countries, mostly from Europe and America and using antibody testing. They reached highly heterogeneous sample sizes and prevalence estimates. Disproportional prevalence was observed in minority communities. Important risk of bias was detected in four domains: sample size, data analysis with sufficient coverage, measurements in standard way, and response rate. The correspondence analysis showed few consistent patterns for high risk of bias. Intermediate risk of bias was related to American and European studies, blood samples and prevalence >1%. Low risk of bias was related to Asian studies, RT-PCR tests and prevalence <1%.\n\nOne sentence summaryPopulation-based prevalence surveys of COVID-19 until September 2020 were mostly conducted in Europe and Americas, used antibody testing, and had important risks of bias.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Vinicius Bonetti Franceschi Jr.", - "author_inst": "UFRGS" - }, - { - "author_name": "Andressa Schneiders Santos Jr.", - "author_inst": "UFCSPA" - }, - { - "author_name": "Andressa Barreto Glaeser Jr.", - "author_inst": "UFCSPA" - }, - { - "author_name": "Janini Cristina Paiz Jr.", - "author_inst": "UFRGS" - }, - { - "author_name": "Gabriel Dickin Caldana Jr.", - "author_inst": "UFCSPA" - }, - { - "author_name": "Carem Luana Machado Lessa Jr.", - "author_inst": "UFCSPA" - }, - { - "author_name": "Amanda de Menezes Mayer Jr.", - "author_inst": "UFRGS" - }, - { - "author_name": "Julia Goncalves Kuchle Jr.", - "author_inst": "UFCSPA" - }, - { - "author_name": "Paulo Ricardo Gazzola Zen Sr.", - "author_inst": "UFCSPA" - }, - { - "author_name": "Alvaro Vigo Sr.", - "author_inst": "UFRGS" - }, - { - "author_name": "Ana Trindade Winck Sr.", - "author_inst": "UFCSPA" - }, - { - "author_name": "Liane Nanci Rotta Sr.", - "author_inst": "UFCSPA" - }, - { - "author_name": "Claudia Elizabeth Thompson Sr.", - "author_inst": "UFCSPA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.20.20216267", "rel_title": "COVID-19's unfortunate events in schools: mitigating classroom clusters in the context of variable transmission", @@ -1107307,6 +1108854,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.20.20215715", + "rel_title": "Challenges Faced by Dialysis Unit Staff during COVID -19 times-A Qualitative Study", + "rel_date": "2020-10-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.20.20215715", + "rel_abs": "IntroductionThe novel SARS COV2-Covid -19 has become a global pandemic since January 2020 and has been spreading exponentially. Dialysis patients with lowered immunity are at high risk. The dialysis patients come for repeated treatment. Hence the dialysis staffs are also at great risk of contracting COVID-19.\n\nObjectiveTo study the challenges faced by the dialysis staff during the COVID-19 pandemic in a rural hemodialysis unit.\n\nMaterial and MethodsThe study was conducted in the hemodialysis unit of Sri ManakulaVinayagar Medical College Hospital, Puducherry, India. We did free list and pile sorting to understand the salient problems and its structure as perceived by the team members. We found Smiths S value for free list. Multidimensional scaling and Hierarchical cluster analysis were done to pile sort data. Data was analyzed using Anthropac 4.983/X. In addition, group interview was done to get in-depth information and validate the findings obtained from the free list and pile sort exercise.\n\nResultsTwelve salient items were generated from the free list. In pile sort, we got three broad domains-the shortage of personal safety equipment, the lack of personal safety and presence of logistical and operational problems. Relative to other items, testing by RT-PCR was surprisingly not perceived to be important for them.\n\nConclusionAddressing the shortage of personal safety equipment, impediments to personal safety and giving credence to the feelings, fears and needs of the dialysis staff in a dialysis unit during COVID -19 pandemic are paramount in ensuring their safety and improving working dynamics.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "P RAVI KUMAR", + "author_inst": "Sri Manakula Vinayagar Medical college & Hospital,Madagadipet,Puducherry 605107,India" + }, + { + "author_name": "Amol R Dongre", + "author_inst": "Sri Manakula Vinayagar Medical College and Hospital, Madagadipet,Puducherry 605107" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "nephrology" + }, { "rel_doi": "10.1101/2020.10.19.20215228", "rel_title": "Use of dried blood spot samples for SARS-CoV-2 antibody detection using the Roche Elecsys high throughput immunoassay", @@ -1108170,73 +1109740,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.20.20204651", - "rel_title": "Characteristics and outcomes of clinically diagnosed RT-PCR swab negative COVID-19: a retrospective cohort study", - "rel_date": "2020-10-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.20.20204651", - "rel_abs": "Patients with strong clinical features of COVID-19 with negative real time polymerase chain reaction (RT-PCR) SARS-CoV-2 testing are not currently included in official statistics. The scale, characteristics and clinical relevance of this group are thus unknown. We performed a retrospective cohort study in two large London hospitals to characterize the demographic, clinical, and hospitalization outcome characteristics of swab-negative clinical COVID-19 patients. We found 1 in 5 patients with a negative swab and clinical suspicion of COVID-19 received a clinical diagnosis of COVID-19 within clinical documentation, discharge summary or death certificate. We compared this group to a similar swab positive cohort and found similar demographic composition, symptomology and laboratory findings. Swab-negative clinical COVID-19 patients had better outcomes, with shorter length of hospital stay, reduced need for >60% supplementary oxygen and reduced mortality. Patients with strong clinical features of COVID-19 that are swab-negative are a common clinical challenge. Health systems must recognize and plan for the management of swab-negative patients in their COVID-19 clinical management, infection control policies and epidemiological assessments.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Paul Middleton", - "author_inst": "Imperial College London" - }, - { - "author_name": "Pablo N Perez-Guzman", - "author_inst": "Imperial College London" - }, - { - "author_name": "Alexandra Cheng", - "author_inst": "Imperial College Healthcare Trust" - }, - { - "author_name": "Naveenta Kumar", - "author_inst": "Imperial College London" - }, - { - "author_name": "Mara Kont", - "author_inst": "Imperial College London" - }, - { - "author_name": "Anna Daunt", - "author_inst": "Imperial College London" - }, - { - "author_name": "Sujit Mukherjee", - "author_inst": "Imperial College London" - }, - { - "author_name": "Graham Cooke", - "author_inst": "Imperial College" - }, - { - "author_name": "Timothy B Hallett", - "author_inst": "Imperial College London" - }, - { - "author_name": "Katharina D Hauck", - "author_inst": "Imperial College London" - }, - { - "author_name": "Peter J White", - "author_inst": "Imperial College London" - }, - { - "author_name": "Mark R Thursz", - "author_inst": "Imperial College London" - }, - { - "author_name": "Shevanthi Nayagam", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.20.20210195", "rel_title": "Tocilizumab is associated with reduction in inflammation and improvement in P/F ratio in critically sick COVID19 patients", @@ -1109100,6 +1110603,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.19.20214015", + "rel_title": "Percentage HScore confirms low incidence of secondary haemophagocytic lymphohistiocytosis in hospitalised COVID-19 patients", + "rel_date": "2020-10-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.19.20214015", + "rel_abs": "ObjectiveIt has been assumed that a significant proportion of COVID-19 patients show evidence of hyperinflammation of which secondary haemophagocytic lymphohistiocytosis (sHLH) is the most severe manifestation. To facilitate diagnosis of sHLH the HScore has been developed and validated. We set out to examine the prevalence of sHLH-like hyperinflammation in COVID-19.\n\nMethodsWe retrospectively examined HScore parameters in 626 COVID-19 cases admitted to our institute of which 567 were suitable for analysis and compared these to a cohort of confirmed infection associated sHLH cases. To account for missing data, we calculated the maximum possible HScore of the recorded parameters (%HScore).\n\nResultsEarly measurement of HScore parameters (day -1 to 4 from diagnosis) strongly predicted the %HScore over the course of the admission (p <0.0001). The retrospective cohort of sHLH showed significantly higher %HScores as compared to COVID-19 (median 73.47 vs 18.13 respectively, p <0.0001). The overall prevalence of individuals with an 80% probability of sHLH in our COVID-19 cohort was 1.59% on admission and only rose to 4.05% during the whole disease course. In the small cohort with scores suggestive of sHLH, there was no excess mortality compared with the whole cohort. %HScores were higher in younger patients (p<0.0001) and did not reliably predict outcome at any cut-off value (AUROC 0.533, p=0.211; OR 0.99).\n\nConclusionSurprisingly, these findings show that sHLH-type hyperinflammation is not prevalent in COVID-19, and %HScores do not predict outcome. Therefore, new algorithms are required to optimise case selection for clinical trials of targeted anti-inflammatory interventions.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Michael R Ardern-Jones", + "author_inst": "University of Southampton" + }, + { + "author_name": "Matthew Stammers", + "author_inst": "University Hospitals Southampton NHS Foundation Trust" + }, + { + "author_name": "Hang T.T. Phan", + "author_inst": "NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK" + }, + { + "author_name": "Florina Borca", + "author_inst": "NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK" + }, + { + "author_name": "Anastasia Koutalopoulou", + "author_inst": "Division of Medicine, University Hospitals Southampton NHS Foundation Trust, Southampton General Hospital, Southampton, SO16 6YD, United Kingdom" + }, + { + "author_name": "Ying Teo", + "author_inst": "Division of Medicine, University Hospitals Southampton NHS Foundation Trust, Southampton General Hospital, Southampton, SO16 6YD, United Kingdom" + }, + { + "author_name": "James Batchelor", + "author_inst": "Clinical Informatics Research Unit Faculty of Medicine, University of Southampton, Southampton, UK" + }, + { + "author_name": "Trevor Smith", + "author_inst": "Division of Medicine, University Hospitals Southampton NHS Foundation Trust, Southampton General Hospital, Southampton, SO16 6YD, United Kingdom" + }, + { + "author_name": "Andrew Duncombe", + "author_inst": "Department of Haematology, University Hospitals Southampton NHS Foundation Trust, Southampton, SO16 6YD, UK" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2020.10.19.20214528", "rel_title": "SI epidemic model applied to COVID-19 data in mainland China", @@ -1109784,69 +1111338,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.10.14.20212670", - "rel_title": "Intrinsic Signal Amplification by Type-III CRISPR-Cas Systems Provides a Sequence-Specific Viral Diagnostic", - "rel_date": "2020-10-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.14.20212670", - "rel_abs": "To combat viral pandemics, there is an urgent need for inexpensive new technologies that enable fast, reliable, and scalable detection of viruses. Here we repurposed the type III CRISPR-Cas system for sensitive and sequence specific detection of SARS-CoV-2 in an assay that can be performed in one hour or less. RNA recognition by type III systems triggers Cas10-mediated polymerase activity, which simultaneously generates pyrophosphates, protons and cyclic oligonucleotides. We show that amplified products of the Cas10-polymerase are detectable using colorimetric or fluorometric readouts.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Andrew Santiago-Frangos", - "author_inst": "Montana State University" - }, - { - "author_name": "Artem A. Nemudryi", - "author_inst": "Montana State University" - }, - { - "author_name": "Anna Nemudraia", - "author_inst": "Montana State University" - }, - { - "author_name": "Laina N. Hall", - "author_inst": "Montana State University" - }, - { - "author_name": "Pushya Krishna", - "author_inst": "Montana State University" - }, - { - "author_name": "Tanner Wiegand", - "author_inst": "Montana State University" - }, - { - "author_name": "Royce A. Wilkinson", - "author_inst": "Montana State University" - }, - { - "author_name": "Deann T. Snyder", - "author_inst": "Montana State University" - }, - { - "author_name": "Jodi F. Hedges", - "author_inst": "Montana State University" - }, - { - "author_name": "Mark A. Jutila", - "author_inst": "Montana State University" - }, - { - "author_name": "Matthew P. Taylor", - "author_inst": "Montana State University" - }, - { - "author_name": "Blake Wiedenheft", - "author_inst": "Montana State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.10.15.20213504", "rel_title": "Experiences of Women Who Gave Birth in US Hospitals During the COVID-19 Pandemic", @@ -1110786,6 +1112277,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2020.10.15.20213058", + "rel_title": "Correlation between Chest CT Severity Scores and the Clinical Parameters of Adult Patients with COVID-19 pneumonia", + "rel_date": "2020-10-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.15.20213058", + "rel_abs": "PurposeOur aim is to correlate the clinical condition of patients with COVID-19 infection with the 25 Point CT severity score by Chang et al (devised for assessment of ARDS in patients with SARS in 2005).\n\nMaterial and MethodsData of consecutive symptomatic patients who were suspected to have COVID-19 infection and presented to our hospital, was collected from March to April 2020. All patients underwent two consecutive RT-PCR tests and had a non-contrast HRCT scan done at presentation. From the original cohort of 1062 patients, 160 patients were excluded leaving a total number of 902 patients.\n\nResultsThe mean age was 44.2 {+/-}11.9 years [85.3%males, 14.7%females]. CT severity score found to be positively correlated with lymphopenia, increased serum CRP, d-dimer and ferritin levels (p < 0.0001). The oxygen requirements as well as length of hospital stay were increasing with the increase of scan severity.\n\nConclusionThe 25-point CT severity score correlates well with the COVID-19 clinical severity. Our data suggest that chest CT scoring system can aid in predicting COVID-19 disease outcome and significantly correlates with lab tests and oxygen requirements.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Ghufran Saeed", + "author_inst": "Sheikh Khalifa Medical City" + }, + { + "author_name": "Waqar Gaba", + "author_inst": "SKMC" + }, + { + "author_name": "Asad Shah", + "author_inst": "SKMC" + }, + { + "author_name": "Abeer Al Helali", + "author_inst": "SKMC" + }, + { + "author_name": "Emadullah Raidullah", + "author_inst": "SKMC" + }, + { + "author_name": "Ameirah Al Ali", + "author_inst": "SKMC" + }, + { + "author_name": "Mohammed Elghazali", + "author_inst": "SKMC" + }, + { + "author_name": "Deena Ahmed", + "author_inst": "SKMC" + }, + { + "author_name": "Shaikha Al Kaabi", + "author_inst": "SKMC" + }, + { + "author_name": "Safaa Almazrouei", + "author_inst": "SKMC" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2020.10.15.20213629", "rel_title": "Correlation of COVID-19 Mortality with Clinical Parameters in an Urban and Suburban Nursing Home Population", @@ -1111494,45 +1113040,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.18.20214643", - "rel_title": "Impact of COVID-19 pandemic and lockdown measures on mental health of children and adolescents in Greece", - "rel_date": "2020-10-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.18.20214643", - "rel_abs": "BackgroundMental health effects of the COVID-19 pandemic and the subsequent lockdown measures are expected to be profound.\n\nAimThe aim of the present study was to investigate the impact of the pandemic and the lockdown on childrens and adolescents mental health in Greece.\n\nMethodsA cross-sectional survey of 1,232 Greek parents of children and adolescents aged < 18 years was conducted in March and May 2020. Parents provided information about sociodemographic characteristics, family everyday life during the lockdown and the pandemic psychological impact on their children.\n\nResultsApproximately one-third (35.1%) of parents reported that the psychological health of their children was considerably affected. The most significant concern was social isolation. Unemployment, increased family conflicts, no opportunity for tele-work and a deteriorating psychological health of the parent, as well as childrens previous history of physical health conditions were all significantly associated with adverse mental health impact.\n\nConclusionA considerable proportion of children and adolescents may experience adverse mental health effects due to the COVID-19 pandemic and the lockdown measures, and socioeconomic inequalities may be associated with these effects.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Konstantina Magklara", - "author_inst": "First Department of Psychiatry, Medical School, University of Athens, Athens, Greece" - }, - { - "author_name": "Helen Lazaratou", - "author_inst": "First Department of Psychiatry, Medical School, University of Athens, Athens, Greece." - }, - { - "author_name": "Anastasia Barbouni", - "author_inst": "School of Public Health, Department of Public and Community Health, University of West Attica, Athens, Greece." - }, - { - "author_name": "Konstantinos Poulas", - "author_inst": "Department of Pharmacy, University of Patras, Rio, Greece." - }, - { - "author_name": "Konstantinos Farsalinos", - "author_inst": "School of Public Health, Department of Public and Community Health, University of West Attica, Athens, Greece; Department of Pharmacy, University of Patras, Rio" - }, - { - "author_name": "- Coronavirus Greece Research Group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.10.17.20214056", "rel_title": "The implications of religious event and holidays on the transmission of SARS-CoV2 : the impact of behavioral changes on transmission", @@ -1112104,6 +1113611,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.18.20214585", + "rel_title": "Evaluating the use of the reproduction number as an epidemiological tool, using spatio-temporal trends of the Covid-19 outbreak in England", + "rel_date": "2020-10-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.18.20214585", + "rel_abs": "The time-varying reproduction number (Rt: the average number secondary infections caused by each infected person) may be used to assess changes in transmission potential during an epidemic. While new infections are not usually observed directly, they can be estimated from data. However, data may be delayed and potentially biased. We investigated the sensitivity of Rt estimates to different data sources representing Covid-19 in England, and we explored how this sensitivity could track epidemic dynamics in population sub-groups.\n\nWe sourced public data on test-positive cases, hospital admissions, and deaths with confirmed Covid-19 in seven regions of England over March through August 2020. We estimated Rt using a model that mapped unobserved infections to each data source. We then compared differences in Rt with the demographic and social context of surveillance data over time.\n\nOur estimates of transmission potential varied for each data source, with the relative inconsistency of estimates varying across regions and over time. Rt estimates based on hospital admissions and deaths were more spatio-temporally synchronous than when compared to estimates from all test-positives. We found these differences may be linked to biased representations of subpopulations in each data source. These included spatially clustered testing, and where outbreaks in hospitals, care homes, and young age groups reflected the link between age and severity of disease.\n\nWe highlight that policy makers could better target interventions by considering the source populations of Rt estimates. Further work should clarify the best way to combine and interpret Rt estimates from different data sources based on the desired use.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Katharine Sherratt", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Sam Abbott", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Sophie Meakin", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Joel Hellewell", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "James D Munday", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Nikos Bosse", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "- CMMID Covid-19 working group", + "author_inst": "" + }, + { + "author_name": "Mark Jit", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Sebastian Funk", + "author_inst": "London School of Hygiene & Tropical Medicine" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.18.20209189", "rel_title": "Evaluation of Nowcasting for Real-Time COVID-19 Tracking - New York City, March-May 2020", @@ -1113224,29 +1114782,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2020.10.19.345066", - "rel_title": "Mutational analysis and assessment of its impact on proteins of SARS-CoV-2 genomes from India", - "rel_date": "2020-10-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.19.345066", - "rel_abs": "The ongoing global pandemic of SARS-CoV-2 implies a corresponding accumulation of mutations. Herein the mutational status of 611 genomes from India along with their impact on proteins was ascertained. After excluding gaps and ambiguous sequences, a total of 493 variable sites (152 parsimony informative and 341 singleton) were observed. The most prevalent reference nucleotide was C (209) and substituted one was T (293). NSP3 had the highest incidence of 101 sites followed by S protein (74 sites), NSP12b (43 sites) and ORF3a (31 sites). The average number of mutations per sample for males and females was 2.56 and 2.88 respectively suggesting a higher contribution of mutations from females. Non-uniform geographical distribution of mutations implied by Odisha (30 samples, 109 mutations) and Tamil Nadu (31 samples, 40 mutations) suggests that sequences in some regions are mutating faster than others. There were 281 mutations (198 Neutral and 83 Disease) affecting amino acid sequence. NSP13 has a maximum of 14 Disease variants followed by S protein and ORF3a with 13 each. Further, constitution of Disease mutations in genomes from asymptomatic people was mere 11% but those from deceased patients was over three folds higher at 38% indicating contribution of these mutations to the pathophysiology of the SARS-CoV-2.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Rezwanuzzaman Laskar", - "author_inst": "Aliah University" - }, - { - "author_name": "Safdar Ali", - "author_inst": "Aliah University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.10.19.345140", "rel_title": "COVID-19: Variant screening, an important step towards precision epidemiology", @@ -1113974,6 +1115509,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.10.15.20208454", + "rel_title": "Modelling SARS-CoV-2 transmission in a UK university setting", + "rel_date": "2020-10-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.15.20208454", + "rel_abs": "Around 40% of school leavers in the UK attend university and individual universities generally host thousands of students each academic year. Bringing together these student communities during the COVID-19 pandemic may require strong interventions to control transmission. Prior modelling analyses of SARS-CoV-2 transmission within universities using compartmental modelling approaches suggest that outbreaks are almost inevitable.\n\nWe constructed a network-based model to capture the interactions of a student population in different settings (housing, social and study). For a single academic term of a representative campus-based university, we ran a susceptible-latent-infectious-recovered type epidemic process, parameterised according to available estimates for SARS-CoV-2. We investigated the impact of: adherence to (or effectiveness of) isolation and test and trace measures; room isolation of symptomatic students; and supplementary mass testing.\n\nWith all adhering to test, trace and isolation measures, we found that 22% (7% - 41%) of the student population could be infected during the autumn term, compared to 69% (56% - 76%) when assuming zero adherence to such measures. Irrespective of the adherence to isolation measures, on average a higher proportion of students resident on-campus became infected compared to students resident off-campus. Room isolation generated minimal benefits. Regular mass testing, together with high adherence to isolation and test and trace measures, could substantially reduce the proportion infected during the term compared to having no testing.\n\nOur findings suggest SARS-CoV-2 may readily transmit in a university setting if there is limited adherence to nonpharmaceutical interventions and/or there are delays in receiving test results. Following isolation guidance and effective contact tracing curbed transmission and reduced the expected time an adhering student would spend in isolation.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Edward M Hill", + "author_inst": "University of Warwick" + }, + { + "author_name": "Benjamin D Atkins", + "author_inst": "University of Warwick" + }, + { + "author_name": "Matt J Keeling", + "author_inst": "University of Warwick" + }, + { + "author_name": "Michael Tildesley", + "author_inst": "University of Warwick" + }, + { + "author_name": "Louise Dyson", + "author_inst": "University of Warwick" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.14.20212720", "rel_title": "Predictors of severe symptomatic laboratory-confirmed SARS-COV-2 reinfection", @@ -1114817,49 +1116387,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.07.20207019", - "rel_title": "Understanding the value of clinical symptoms of COVID-19. A logistic regression model", - "rel_date": "2020-10-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.07.20207019", - "rel_abs": "BackgroundThe new coronavirus SARS-CoV-2, the causative agent of COVID-19, is responsible for the current pandemic outbreak worldwide. However, there is limited information regarding the set of specific symptoms of COVID-19. Therefore, the objective of this study was to describe the main symptoms associated with COVID-19 to aid in the clinical diagnosis for the rapid identification of cases.\n\nMethods and findingsA cross sectional study of all those diagnosed by RT-PCR for SARS-CoV-2 between April 1 and May 24 in Argentina was conducted. The data includes clinical and demographic information from all subjects at the time of presentation, which were uploaded to the centralized national reporting system at health centers. A total of 67318 individuals were included in this study, where 12% tested positive for SARS-CoV-2. The study population was divided in two age groups, a group aged 0 to 55 years-old (<56 group), (median = 32, n=48748) and another group aged 56 to 103 years-old ([≥]56 group) (median =72, n=18570). Multivariate logistic regression analyses showed that out of a total of 23 symptoms, only five were found to have a positive association with COVID-19: anosmia (odds ratio [OR] 10.40, 95% confidence interval [CI] 8.20-13.10, <56 group; OR 6.09 CI 3.05-12.20, [≥]56 group) dysgeusia (OR 3.67, CI 2.7-4.9, <56 group; OR 3.53 CI 1.52-8.18, [≥]56 group), low grade fever (37.5-37.9{degrees} C) (OR 1.61, CI 1.20-2.05, <56 group; OR 1.80 CI 1.07-3.06, [≥]56 group), cough (OR 1.20, CI 1.05-1.38, <56 group; OR 1.37 CI 1.04-1.80, [≥]56 group) and headache only in <56 group (OR 1.71, CI 1.48-1.99). In turn, at the time of presentation, the symptoms associated with respiratory problems: chest pain, tachypnea, dyspnea, respiratory failure and use of accessory muscles for breathing, had a negative association with COVID-19 (OR <1) or did not present statistical relevance (OR = 1).\n\nWith the intention of helping the clinical diagnosis, we designed a model to be able to identify possible cases of COVID-19. This model included 16 symptoms, the age and sex of the individuals, and was able to detect 80% of those infected with SARS-CoV-2 with a specificity of 46%.\n\nConclusionsThe analysis of symptoms opens the opportunity for a guidance and improved symptoms based definition of suspected cases of COVID-19, where multiple factors (age, sex, symptoms and interaction between symptoms) are considered. We present a tool to help identify COVID-19 cases to provide quick information to aid decision-making by health personnel and program managers.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Pedro Emanuel Fleitas", - "author_inst": "Instituto de Investigaciones de Enfermedades Tropicales (IIET-CONICET), Universidad Nacional de Salta" - }, - { - "author_name": "Jorge A Paz", - "author_inst": "Instituto de Estudios Laborales y del Desarrollo Economico (IELDE), Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Universidad Nacional d" - }, - { - "author_name": "Mario I Simoy", - "author_inst": "Instituto de Investigaciones en Energia no Convencional (INENCO), Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET) Universidad Nacional de S" - }, - { - "author_name": "Carlos Vargas", - "author_inst": "Instituto de Investigaciones de Enfermedades Tropicales (IIET-CONICET), Universidad Nacional de Salta" - }, - { - "author_name": "Ruben O Cimino", - "author_inst": "Instituto de Investigaciones de Enfermedades Tropicales (IIET-CONICET), Universidad Nacional de Salta" - }, - { - "author_name": "Alejandro J Krolewiecki", - "author_inst": "Instituto de Investigaciones de Enfermedades Tropicales (IIET-CONICET), Universidad Nacional de Salta" - }, - { - "author_name": "Juan P Aparicio", - "author_inst": "Instituto de Investigaciones en Energia no Convencional (INENCO), Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Universidad Nacional de " - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pathology" - }, { "rel_doi": "10.1101/2020.10.15.20213249", "rel_title": "Title: COVID-19 and frontline health workers in West Africa: a scoping review", @@ -1115623,6 +1117150,45 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.10.15.339473", + "rel_title": "Additional analyses exploring the hypothesized transdifferentiation of plasmablasts to developing neutrophils in severe COVID-19", + "rel_date": "2020-10-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.15.339473", + "rel_abs": "We thank Alquicira-Hernandez et al. for their reanalysis of our single-cell transcriptomic dataset profiling peripheral immune responses to severe COVID-19. We agree that careful analysis of single-cell sequencing data is important for generating cogent hypotheses but find several aspects of their criticism of our analysis to be problematic. Here we respond briefly to misunderstandings and inaccuracies in their commentary that may have led to misinformed interpretation of our results.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Aaron J Wilk", + "author_inst": "Stanford University" + }, + { + "author_name": "Arjun Rustagi", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Nancy Q Zhao", + "author_inst": "Stanford University" + }, + { + "author_name": "Beth A Martin", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Angela J Rogers", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Catherine A Blish", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_no", + "type": "contradictory results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.10.16.342097", "rel_title": "Duple extinguishment of COVID-19: single compound synergized inhibition of SARS-CoV-2 replication and direct suppression of inflammatory cytokines in vitro/vivo", @@ -1116503,45 +1118069,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "sports medicine" }, - { - "rel_doi": "10.1101/2020.10.13.20212233", - "rel_title": "Heterogeneity in transmissibility and shedding SARS-CoV-2 via droplets and aerosols", - "rel_date": "2020-10-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.13.20212233", - "rel_abs": "Which virological factors mediate overdispersion in the transmissibility of emerging viruses remains a longstanding question in infectious disease epidemiology. Here, we use systematic review to develop a comprehensive dataset of respiratory viral loads (rVLs) of SARS-CoV-2, SARS-CoV-1 and influenza A(H1N1)pdm09. We then comparatively meta-analyze the data and model individual infectiousness by shedding viable virus via respiratory droplets and aerosols. Our analyses indicate heterogeneity in rVL as an intrinsic virological factor facilitating greater overdispersion for SARS-CoV-2 in the COVID-19 pandemic than A(H1N1)pdm09 in the 2009 influenza pandemic. For COVID-19, case heterogeneity remains broad throughout the infectious period, including for pediatric and asymptomatic infections. Hence, many COVID-19 cases inherently present minimal transmission risk, whereas highly infectious individuals shed tens to thousands of SARS-CoV-2 virions/min via droplets and aerosols while breathing, talking and singing. Coughing increases the contagiousness, especially in close contact, of symptomatic cases relative to asymptomatic ones. Infectiousness tends to be elevated between 1-5 days post-symptom onset. Our findings show how individual case variations influence virus transmissibility and present considerations for disease control in the COVID-19 pandemic.\n\nSignificance StatementFor some emerging infectious diseases, including COVID-19, few cases cause most secondary infections. Others, like influenza A(H1N1)pdm09, spread more homogenously. The virological factors that mediate such distinctions in transmissibility remain unelucidated, prohibiting the development of specific disease control measures. We find that intrinsic case variation in respiratory viral load (rVL) facilitates overdispersion, and superspreading, for COVID-19 but more homogeneous transmission for A(H1N1)pdm09. We interpret the influence of heterogeneity in rVL on individual infectiousness by modelling likelihoods of shedding viable virus via respiratory droplets and aerosols. We analyze the distribution and kinetics of SARS-CoV-2 rVL, including across age and symptomatology subgroups. Our findings compare individual infectiousness across COVID-19 and A(H1N1)pdm09 cases and present quantitative guidance on triaging COVID-19 contact tracing.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Paul Z Chen", - "author_inst": "University of Toronto" - }, - { - "author_name": "Niklas Bobrovitz", - "author_inst": "University of Toronto" - }, - { - "author_name": "Zahra Premji", - "author_inst": "University of Calgary" - }, - { - "author_name": "Marion Koopmans", - "author_inst": "Erasmus University Medical Center" - }, - { - "author_name": "David N Fisman", - "author_inst": "University of Toronto" - }, - { - "author_name": "Frank X Gu", - "author_inst": "University of Toronto" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.15.20209817", "rel_title": "Repurposed antiviral drugs for COVID-19; interim WHO SOLIDARITY trial results", @@ -1117269,6 +1118796,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.11.20210864", + "rel_title": "Awareness, Perception and Practice Of COVID 19 Prevention among Residents of a State in the South-South Region Of Nigeria: Implications for Public Health Control Efforts", + "rel_date": "2020-10-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.11.20210864", + "rel_abs": "BackgroundThis research explored awareness, perception, and practice of COVID 19 prevention among residents of communities in all the local government areas (districts) in Rivers State during the early stages of the pandemic response.\n\nDesignThis was a descriptive cross-sectional survey which employed an interviewer-administered four-page questionnaire built into the Open Data Kit application for android phones. Knowledge and practice scores were computed by scoring every correct response/action as 1 and wrong responses as 0. Knowledge was graded as excellent for scores of [≥]80%, good for scores of 50-79% and poor for scores of <50%. Respondents who washed all critical parts of the hand were categorized as having correct handwashing practice.\n\nSettingRivers State in the South-South region of Nigeria had recorded over 2000 cases of COVID 19 as of 18th August 2020, ranking 5th among the high burden states in Nigeria. As with any epidemic of an infectious nature, panic, fear, and misconceptions are rife. Risk communication utilizes multi-faceted activities geared towards facilitating correct and consistent knowledge and prevention practice.\n\nParticipantsStudy involved 1,294 adult community residents in the 23 districts of the state.\n\nResultsThe respondents were aged between 18 and 80 years with average age of 39.6 years (SD = 11.9 years). A total of 710 (54.9%) were male, 476 (36.8%) were unemployed with 685 (52.9%) having secondary education. Almost all respondents 1,271 (98.2%) had heard about COVID 19. The three most common sources of information about COVID 19 were radio jingles 1102 (86.7%), television adverts 940 (74.0%) and announcements in Church 612 (48.2%). Overall, 608 (47.0%) of the respondents had poor knowledge of COVID 19. About 1167 (90.2%) of the respondents who were aware of COVID 19 acknowledged that COVID 19 is a problem in the state while 443 (34.9%) respondents believed they were unlikely contract the virus. Only 505 (39.0%) of the respondents washed all critical parts of the hand correctly.\n\nConclusionsRisk communication interventions during pandemics need to be based on an understanding of the gaps in knowledge, attitude, perceptions, and practice. Broadcast media has a pivotal role to play in risk communication for behaviour change for the control of current and future epidemics in this population.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Golden Owhonda", + "author_inst": "Rivers State Ministry of Health" + }, + { + "author_name": "Omosivie Maduka", + "author_inst": "University of Port Harcourt" + }, + { + "author_name": "Ifeoma Nwadiuto", + "author_inst": "Rivers State Ministry of Health" + }, + { + "author_name": "Charles Tobin-West", + "author_inst": "University of Port Harcourt" + }, + { + "author_name": "Esther Azi", + "author_inst": "University of Port Harcourt" + }, + { + "author_name": "Chibianotu Ojimah", + "author_inst": "World Health Organization, Rivers State Field Office" + }, + { + "author_name": "Datonye Alasia", + "author_inst": "University of Port Harcourt" + }, + { + "author_name": "Ayo-Maria Olofinuka", + "author_inst": "World Health Organization" + }, + { + "author_name": "Vetty Agala", + "author_inst": "Rivers State Ministry of Health, Hospital Management Board" + }, + { + "author_name": "John Nwolim Paul", + "author_inst": "Rivers State Ministry of Health" + }, + { + "author_name": "Doris Nria", + "author_inst": "Rivers State Ministry of Health" + }, + { + "author_name": "Chinenye Okafor", + "author_inst": "World Health Organization Rivers State Field Office" + }, + { + "author_name": "Ifeoma Ndekwu", + "author_inst": "Stakeholder Democratic Network" + }, + { + "author_name": "Chikezie Opara", + "author_inst": "Stakeholder Democracy Network" + }, + { + "author_name": "Chris Newsom", + "author_inst": "Stakeholder Democratic Network" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.10.11.20210922", "rel_title": "Symptoms associated with SARS-CoV-2 infection in a community-based population: Results from an epidemiological study", @@ -1117925,57 +1119527,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.10.12.20211086", - "rel_title": "Using Automated-Machine Learning to Predict COVID-19 Patient Survival: Identify Influential Biomarkers", - "rel_date": "2020-10-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.12.20211086", - "rel_abs": "BackgroundIn a pandemic, it is important for clinicians to stratify patients and decide who receives limited medical resources. In this study, we used automated machine learning (autoML) to develop and compare between multiple machine learning (ML) models that predict the chance of patient survival from COVID-19 infection and identified the best-performing model. In addition, we investigated which biomarkers are the most influential in generating an accurate model. We believe an ML model such as this could be a useful tool for clinicians stratifying hospitalized SARS-CoV-2 patients.\n\nMethodsThe data was retrospectively collected from Clinical Looking Glass (CLG) on all patients testing positive for COVID-19 through a nasopharyngeal specimen by real-time RT-PCR and admitted between 3/1/2020-7/3/2020 (4376 patients) at our institution. We collected 47 biomarkers from each patient within 36 hours before or after the index time: RT-PCR positivity, and tracked whether a patient survived or not for one month following this time. We utilized the autoML from H2O.ai, an open source package for R language. The autoML generated 20 ML models and ranked them by area under the precision-recall curve (AUCPR) on the test set. We selected the best model (model_var_47) and chose a threshold probability that maximized F2 score to make a binary classifier: dead or alive. Subsequently, we ranked the relative importance of variables that generated model_var_47 and chose the 10 most influential variables. Next, we reran the autoML with these 10 variables and likewise selected the model with the best AUCPR on the test set (model_var_10). Again, threshold probability that maximized F2 score for model_var_10 was chosen to make a binary classifier. We calculated and compared the sensitivity, specificity, and positive predicate value (PPV) for model_var_10 and model_var_47.\n\nResultsThe best model that autoML generated using all 47 variables was the stacked ensemble model of all models (AUCPR = 0.836). The most influential variables were: systolic and diastolic blood pressure, age, respiratory rate, pulse oximetry, blood urea nitrogen, lactate dehydrogenase, d-dimer, troponin, and glucose. When the autoML was retrained with these 10 most important variables, it did not significantly affect the performance (AUCPR= 0.828). For the binary classifiers, sensitivity, specificity, and PPV of model_var_47 was 83.6%, 87.7%, and 69.8% respectively, while for model_var_10 they were 90.9%, 71.1%, and 51.8% respectively.\n\nConclusionsBy using autoML, we developed high-performing models that predict patient mortality from COVID-19 infection. In addition, we identified the most important biomarkers correlated with mortality. This ML model can be used as a decision supporting tool for medical practitioners to efficiently triage COVID-19 infected patients. From our literature review, this will be the largest COVID-19 patient cohort to train ML models and the first to utilize autoML. The COVID-19 survival calculator based on this study can be found at https://www.tsubomitech.com/.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Kenji Ikemura", - "author_inst": "Tsubomi Technology, Montefiore Medical Center" - }, - { - "author_name": "Doctor Y Goldstein", - "author_inst": "Montefiore Medical Center" - }, - { - "author_name": "James Szymanski", - "author_inst": "Montefiore Medical Center, Albert Einstein College of Medicine" - }, - { - "author_name": "Eran Bellin", - "author_inst": "Montefiore Medical Center" - }, - { - "author_name": "Lindsay Stahl", - "author_inst": "Montefiore Medical Center" - }, - { - "author_name": "Yukako Yagi", - "author_inst": "Memorial Sloan Kettering Cancer Center" - }, - { - "author_name": "Mahmoud Saada", - "author_inst": "Tsubomi Technology" - }, - { - "author_name": "Katelyn Simone", - "author_inst": "Tsubomi Technology" - }, - { - "author_name": "Morayma Reyes Gil", - "author_inst": "Montefiore Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.10.12.20210609", "rel_title": "Rapid detection of SARS-CoV-2 antibodies in oral fluids", @@ -1118811,6 +1120362,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.12.20211599", + "rel_title": "Less severe course of COVID-19 is associated with elevated levels of antibodies against seasonal human coronaviruses OC43 and HKU1 (HCoV OC43, HCoV HKU1)", + "rel_date": "2020-10-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.12.20211599", + "rel_abs": "The clinical course of COVID-19 is very heterogeneous: Most infected individuals can be managed in an outpatient setting, but a substantial proportion of patients requires intensive care, resulting in a high rate of fatalities. Recently, an association between contact to small children and mild course of COVID-19 was reported. We performed an observational study to assess the impact of previous infections with seasonal coronaviruses on COVID-19 severity. 60 patients with confirmed COVID-19 infections were included (age 30 - 82 years; 52 males, 8 females): 19 inpatients with critical disease, 16 inpatients with severe or moderate disease and 25 outpatients (age and gender matched to inpatients). Patients with critical disease had significantly lower levels of HCoV OC43- (p=0.016) and HCoV HKU1-specific (p=0.023) antibodies at the first encounter compared to other COVID-19 patients. Our results indicate that previous infections with seasonal coronaviruses might protect against a severe course of disease. This finding should be validated in other settings and could contribute to identify persons at risk before an infection.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Martin Dugas", + "author_inst": "University of Muenster" + }, + { + "author_name": "Tanja Grote-Westrick", + "author_inst": "University Hospital Muenster" + }, + { + "author_name": "Richard Vollenberg", + "author_inst": "University Hospital Muenster" + }, + { + "author_name": "Eva Lorentzen", + "author_inst": "University Hospital Muenster" + }, + { + "author_name": "Tobias Brix", + "author_inst": "University of Muenster" + }, + { + "author_name": "Hartmut Schmidt", + "author_inst": "University Hospital Muenster" + }, + { + "author_name": "Phil-Robin Tepasse", + "author_inst": "University Hospital Muenster" + }, + { + "author_name": "Joachim Kuehn", + "author_inst": "University Hospital Muenster" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.12.20211748", "rel_title": "Prone positioning of non-intubated patients with COVID-19 - A Systematic Review and Meta-analysis", @@ -1119719,105 +1121317,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.13.20211367", - "rel_title": "Innate lymphoid cell composition associates with COVID-19 disease severity", - "rel_date": "2020-10-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.13.20211367", - "rel_abs": "ObjectivesThe role of innate lymphoid cells (ILCs) in coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is unknown. Understanding the immune response in COVID-19 could contribute to unravel the pathogenesis and identification of treatment targets. To describe the phenotypic landscape of circulating ILCs in COVID-19 patients and to identify ILC phenotypes correlated to serum biomarkers, clinical markers, and laboratory parameters relevant in COVID-19.\n\nMethodsBlood samples collected from moderately (n=11) and severely ill (n=12) COVID-19 patients as well as healthy control donors (n=16), were analyzed with 18-parameter flow cytometry. Using supervised and unsupervised approaches, we examined the ILC activation status and homing profile. Clinical and laboratory parameters were obtained from all COVID-19 patients and serum biomarkers were analyzed with multiplex immunoassays.\n\nResultsILCs were largely depleted from the circulation of COVID-19 patients compared with healthy controls. Remaining circulating ILCs from patients revealed increased frequencies of ILC2 in moderate COVID-19, with a concomitant decrease of ILC precursors (ILCp), as compared with controls. ILC2 and ILCp showed an activated phenotype with increased CD69 expression, whereas expression levels of the chemokine receptors CXCR3 and CCR4 were significantly altered in ILC2 and ILCp, and ILC1, respectively. The activated ILC profile of COVID-19 patients was associated with soluble inflammatory markers, while frequencies of ILC subsets were correlated with laboratory parameters that reflect the disease severity.\n\nConclusionThis study provides insights into the potential role of ILCs in immune responses against SARS-CoV-2, particularly linked to the severity of COVID-19.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Marina Garcia", - "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden" - }, - { - "author_name": "Efthymia Kokkinou", - "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden" - }, - { - "author_name": "Anna Carrasco Garcia", - "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden" - }, - { - "author_name": "Tiphaine Parrot", - "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden" - }, - { - "author_name": "Laura M. Palma Medina", - "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden" - }, - { - "author_name": "Kimia T. Maleki", - "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden" - }, - { - "author_name": "Wanda Christ", - "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden" - }, - { - "author_name": "Renata Varnaite", - "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden" - }, - { - "author_name": "Iva Filipovic", - "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden" - }, - { - "author_name": "Hans-Gustaf Ljunggren", - "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden" - }, - { - "author_name": "Niklas K. Bjorkstrom", - "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden" - }, - { - "author_name": "Elin Folkesson", - "author_inst": "Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden.Division of Infectious Diseases, Department of Medicine Solna, Karolinska I" - }, - { - "author_name": "Olav Rooyackers", - "author_inst": "Division of Anesthesiology and Intensive Care; Department of Clinical Science, Technology and Intervention; Karolinska Institutet, Huddinge, Sweden" - }, - { - "author_name": "Lars I. Eriksson", - "author_inst": "Department of Physiology and Pharmacology, Section for Anesthesiology and Intensive Care, Karolinska Institutet, Stockholm, Sweden. Function Perioperative Medic" - }, - { - "author_name": "Anders Sonnerborg", - "author_inst": "Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden. Division of Infectious Diseases and Dermatology, Department of Medicine Hu" - }, - { - "author_name": "Soo Aleman", - "author_inst": "Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden. Division of Infectious Diseases and Dermatology, Department of Medicine Hu" - }, - { - "author_name": "Kristoffer Stralin", - "author_inst": "Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden. Division of Infectious Diseases and Dermatology, Department of Medicine Hu" - }, - { - "author_name": "Sara Gredmark-Russ", - "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden. Department of Infecti" - }, - { - "author_name": "Jonas Klingstrom", - "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden" - }, - { - "author_name": "Jenny Mjosberg", - "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden" - }, - { - "author_name": "- the Karolinska KI/K COVID-19 Study Group", - "author_inst": "-" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.12.20211722", "rel_title": "Impact of COVID-19 Restrictions on People with Hypertension", @@ -1120529,6 +1122028,65 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.10.14.339689", + "rel_title": "COVID19: Exploring uncommon epitopes for a stable immune response through MHC1 binding", + "rel_date": "2020-10-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.14.339689", + "rel_abs": "The COVID19 pandemic has resulted in 1,092,342 deaths as of 14th October 2020, indicating the urgent need for a vaccine. This study highlights novel protein sequences generated by shot gun sequencing protocols that could serve as potential antigens in the development of novel subunit vaccines and through a stringent inclusion criterion, we characterized these protein sequences and predicted their 3D structures. We found distinctly antigenic sequences from the SARS-CoV-2 that have led to identification of 4 proteins that demonstrate an advantageous binding with Human leukocyte antigen-1 molecules. Results show how previously unexplored proteins may serve as better candidates for subunit vaccine development due to their high stability and immunogenicity, reinforce by their HLA-1 binding propensities and low global binding energies. This study thus takes a unique approach towards furthering the development of vaccines by employing multiple consensus strategies involved in immuno-informatics technique.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Folagbade Muyiwa Abitogun", + "author_inst": "University College Hospital, Ibadan, Nigeria" + }, + { + "author_name": "Rajvee Srivastava", + "author_inst": "Biological Life Science Division, Ahmedabad University, Gujarat, India" + }, + { + "author_name": "Siddhant Sharma", + "author_inst": "Department of Biochemistry, Deshbandhu College, University of Delhi, New Delhi, India" + }, + { + "author_name": "Viktoria Komarysta", + "author_inst": "Department of Botany and Plant Ecology, V.N Karazin Kharkiv National University, Kharkiv, Ukraine" + }, + { + "author_name": "Eva Akurut", + "author_inst": "Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Uganda" + }, + { + "author_name": "Nirvana Munir", + "author_inst": "Faculty of Pharmacy and Biotechnology, German University in Cairo (GUC), Cairo, Egypt." + }, + { + "author_name": "Lawrence Macalalad", + "author_inst": "Department of Biology, College of Science, Pamantasan ng Lungsod ng Maynila (PLM), Manila, Philippines" + }, + { + "author_name": "Olawale Ojo-Rowland", + "author_inst": "Department of Medical Microbiology, State Specialist Hosipital, Akure, Ondo State, Nigeria" + }, + { + "author_name": "Opelopejesu Owolabi", + "author_inst": "Future Health Systems, Faculty of Public Health, University of Ibadan, Oyo State, Nigeria" + }, + { + "author_name": "Abayomi Giwa", + "author_inst": "Department of Physiology, Babcock University, Ogun State, Nigeria" + }, + { + "author_name": "Surajit Debnath", + "author_inst": "Department of Medical Laboratory Technology, Women Polytechnic, Tripura, India" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.10.12.336818", "rel_title": "Structural stability of SARS-CoV-2 degrades with temperature", @@ -1121341,20 +1122899,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.08.20209122", - "rel_title": "Duration of Oxygen Requirement and Predictors in Severe COVID-19 Patients in Ethiopia: A Survival Analysis", - "rel_date": "2020-10-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.08.20209122", - "rel_abs": "BackgroundWith the rising number of new cases of COVID-19, understanding the oxygen requirement of severe patients assists in identifying at risk groups and in making an informed decision on building hospitals capacity in terms of oxygen facility arrangement. Therefore, the study aimed to estimate time to getting off supplemental oxygen therapy and identify predictors among COVID-19 patients admitted to Millennium COVID-19 Care Center in Ethiopia.\n\nMethodsA prospective observational study was conducted among 244 consecutively admitted COVID-19 patients from July to September, 2020. Kaplan Meier plots, median survival times and Log-rank test were used to describe the data and compare survival distribution between groups. Cox proportional hazard survival model was used to identify determinants of time to getting off supplemental oxygen therapy, where hazard ratio (HR), P-value and 95%CI for HR were used for testing significance and interpretation of results.\n\nResultsMedian time to getting off supplemental oxygen therapy among the studied population was 6 days (IQR, 4.3-20.0). Factors that affect time to getting off supplemental oxygen therapy were age group (AHR=0.52,95%CI=0.32,0.84, p-value=0.008 for [≥]70 years) and shortness of breath (AHR=0.71,95%CI=0.52,0.96, p-value=0.026).\n\nConclusionsAverage duration of supplemental oxygen therapy requirement among COVID-19 patients was 6 days and being 70 years and older and having shortness of breath were found to be associated with prolonged duration of supplemental oxygen therapy requirement. This result can be used as a guide in planning institutional resource allocation and patient management to provide a well-equipped care to prevent complications and death from the disease.", - "rel_num_authors": 0, - "rel_authors": null, - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.09.20209379", "rel_title": "Cardiac Arrhythmias in Patients with COVID-19: A Systematic review and Meta-analysis", @@ -1122570,6 +1124114,121 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.10.13.334532", + "rel_title": "Sequential infection with influenza A virus followed by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) leads to more severe disease and encephalitis in a mouse model of COVID-19.", + "rel_date": "2020-10-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.13.334532", + "rel_abs": "COVID-19 is a spectrum of clinical symptoms in humans caused by infection with SARS-CoV-2, a recently emerged coronavirus that rapidly caused a pandemic. Coalescence of this virus with seasonal respiratory viruses, particularly influenza virus is a global health concern. To investigate this, transgenic mice expressing the human ACE2 receptor driven by the epithelial cell cytokeratin-18 gene promoter (K18-hACE2) were first infected with IAV followed by SARS-CoV-2. The host response and effect on virus biology was compared to K18-hACE2 mice infected with IAV or SARS-CoV-2 only. Infection of mice with each individual virus resulted in a disease phenotype compared to control mice. Although SARS-CoV-2 RNA synthesis appeared significantly reduced in the sequentially infected mice, they exhibited more rapid weight loss, more severe lung damage and a prolongation of the innate response compared to singly infected or control mice. The sequential infection also exacerbated the extrapulmonary encephalitic manifestations associated with SARS-CoV-2 infection. Conversely, prior infection with a commercially available, multivalent live-attenuated influenza vaccine (Fluenz tetra) elicited the same reduction in SARS-CoV-2 RNA synthesis albeit without the associated increase in disease severity. This suggests that the innate immune response stimulated by infection with IAV is responsible for the observed inhibition of SARS-CoV-2, however, infection with attenuated, apathogenic influenza vaccine does not result in an aberrant immune response and enhanced disease severity. Taken together, the data suggest that the concept of twinfection is deleterious and mitigation steps should be instituted as part of a comprehensive public health response to the COVID-19 pandemic.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Jordan J. Clark", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Rebekah Penrice-Randal", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Parul Sharma", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Anja Kipar", + "author_inst": "University of Zurich" + }, + { + "author_name": "Xiaofeng Dong", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Shaun Pennington", + "author_inst": "Liverpool School of Tropical Medicine" + }, + { + "author_name": "Amy E Marriott", + "author_inst": "Liverpool School of Tropical Medicine" + }, + { + "author_name": "Stefano Colombo", + "author_inst": "Liverpool School of Tropical Medicine" + }, + { + "author_name": "Andrew D. Davidson", + "author_inst": "University of Bristol" + }, + { + "author_name": "Maia Kavanagh Williamson", + "author_inst": "University of Bristol" + }, + { + "author_name": "David A Matthews", + "author_inst": "University of Bristol" + }, + { + "author_name": "Lance Turtle", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Tessa Prince", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Grant Hughes", + "author_inst": "Liverpool School of Tropical Medicine" + }, + { + "author_name": "Edward I Patterson", + "author_inst": "Liverpool School of Tropical Medicine" + }, + { + "author_name": "Ghada Shawli", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Krishanthi Subramaniam", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Jo Sharp", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Lynn McLaughlin", + "author_inst": "University of Liverpool" + }, + { + "author_name": "En-Min Zhou", + "author_inst": "North West A and F University" + }, + { + "author_name": "Joseph D Turner", + "author_inst": "Liverpool School of Tropical Medicine" + }, + { + "author_name": "Giancarlo Biagini", + "author_inst": "Liverpool School of Tropical Medicine" + }, + { + "author_name": "Andrew Owen", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Julian Alexander Hiscox", + "author_inst": "University of Liverpool" + }, + { + "author_name": "James P Stewart", + "author_inst": "University of Liverpool" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.10.13.337774", "rel_title": "Degradation of SARS-CoV-2 receptor ACE2 by tobacco carcinogen-induced Skp2 in lung epithelial cells", @@ -1123398,89 +1125057,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.10.06.20207902", - "rel_title": "Evaluation of saliva sampling procedures for SARS-CoV-2 diagnostics reveals differential sensitivity and association with viral load", - "rel_date": "2020-10-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.06.20207902", - "rel_abs": "Nasopharyngeal sampling has been the preferential collection method for SARS-CoV-2 diagnostics. Alternative sampling procedures that are less invasive and do not require a healthcare professional would be more preferable for patients and health professionals. Saliva collection has been proposed as such a possible alternative sampling procedure. We evaluated the sensitivity of SARS-CoV-2 testing on two different saliva collection devices (spitting versus swabbing) compared to nasopharyngeal swabs in over 2500 individuals that were either symptomatic or had high-risk contacts with infected individuals. We observed an overall poor sensitivity in saliva for SARS-CoV-2 detection (30.8% and 22.4% for spitting and swabbing, respectively). However, when focusing on individuals with medium to high viral load, sensitivity increased substantially (97.0% and 76.7% for spitting and swabbing, respectively), irrespective of symptomatic status. Our results suggest that saliva cannot readily replace nasopharyngeal sampling for SARS-CoV-2 diagnostics but may enable identification of cases with medium to high viral loads.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Pieter Mestdagh", - "author_inst": "Ghent University" - }, - { - "author_name": "Michel Gillard", - "author_inst": "UCB" - }, - { - "author_name": "Marc Arbyn", - "author_inst": "Sciensano" - }, - { - "author_name": "Jean-Paul Pirnay", - "author_inst": "Queen Astrid Military Hospital" - }, - { - "author_name": "Jeroen Poels", - "author_inst": "Federal Agency for Medicines and Health Products" - }, - { - "author_name": "Jan Hellemans", - "author_inst": "Biogazelle" - }, - { - "author_name": "Eliana Peeters", - "author_inst": "Sciensano" - }, - { - "author_name": "Veronik Hutse", - "author_inst": "Sciensano" - }, - { - "author_name": "Celine Vermeiren", - "author_inst": "UCB" - }, - { - "author_name": "Maxime Boutier", - "author_inst": "UCB" - }, - { - "author_name": "Veerle De Wever", - "author_inst": "UCB" - }, - { - "author_name": "Patrick Soentjens", - "author_inst": "Queen Astrid Military Hospital" - }, - { - "author_name": "Sarah Djebara", - "author_inst": "Queen Astrid Military Hospital" - }, - { - "author_name": "Hugues Malonne", - "author_inst": "Federal Agency for Medicines and Health Products" - }, - { - "author_name": "Emmanuel Andre", - "author_inst": "KU Leuven" - }, - { - "author_name": "John Smeraglia", - "author_inst": "UCB" - }, - { - "author_name": "Jo Vandesompele", - "author_inst": "Biogazelle" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.11.20210740", "rel_title": "Outcomes of COVID-19: disparities by ethnicity", @@ -1124227,6 +1125803,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.07.20208520", + "rel_title": "Variability of Salivary and Nasal Specimens for SARS-CoV-2 Detection", + "rel_date": "2020-10-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.07.20208520", + "rel_abs": "In a large cohort of ambulatory confirmed COVID-19 patients with multiple self-collected sample time points, we compared 202 matched nasal-oropharyngeal swabs and oral salivary fluid sample pairs by RT-PCR. Nasal-oropharyngeal swabs were more sensitive than this salivary sample type (oral crevicular fluid) suggesting that not all saliva sample types have equivalent sensitivity. However, all samples that were Vero E6-TMPRSS2 cell culture positive (e.g., infectious virus) were also oral fluid RT-PCR positive suggesting that oral fluid may find the patients most likely to transmit disease to others.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Yukari C Manabe", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Carolyn Reuland", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Tong Yu", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Razvan Azamfirei", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Taylor Church", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Diane M Brown", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Thelio T Sewell", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Justin P Hardick", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Paul W Blair", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Christopher D Heaney", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Andrew Pekosz", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "David L Thomas", + "author_inst": "Johns Hopkins University School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.07.20207647", "rel_title": "Rapid detection of SARS-CoV2 by Ambient Mass Spectrometry Techniques", @@ -1125015,77 +1126654,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2020.10.10.20210070", - "rel_title": "Severe COVID-19 patients display a back boost of seasonal coronavirus-specific antibodies", - "rel_date": "2020-10-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.10.20210070", - "rel_abs": "Severe acquired respiratory syndrome coronavirus-2 (SARS-CoV-2) is the cause of coronavirus disease (COVID-19). In severe COVID-19 cases, higher antibody titers against seasonal coronaviruses have been observed than in mild cases. To investigate antibody cross-reactivity as potential explanation for severe disease, we determined the kinetics, breadth, magnitude and level of cross-reactivity of IgG against SARS-CoV-2 and seasonal CoV nucleocapsid and spike from 17 severe COVID-19 cases at the clonal level. Although patients mounted a mostly type-specific SARS-CoV-2 response, B-cell clones directed against seasonal CoV dominated and strongly increased over time. Seasonal CoV IgG responses that did not neutralize SARS-CoV-2 were boosted well beyond detectable cross-reactivity, particularly for HCoV-OC43 spike. These findings support a back-boost of poorly protective coronavirus-specific antibodies in severe COVID-19 patients that may negatively impact de novo SARS-CoV-2 immunity, reminiscent of original antigenic sin.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Brenda M. Westerhuis", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Muriel Aguilar-Bretones", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Matthijs P. Raadsen", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Erwin de Bruin", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Nisreen M.A. Okba", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Bart L. Haagmans", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Thomas Langerak", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Henrik Endeman", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Johannes P.C. van den Akker", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Diederik A.M.P.J. Gommers", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Eric C.M. van Gorp", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Barry H.G. Rockx", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Marion P.G. Koopmans", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Gijsbert P. van Nierop", - "author_inst": "Erasmus MC" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.09.20165431", "rel_title": "Machine learning based prognostic model and mobile application software platform for predicting infection susceptibility of COVID-19 using health care data", @@ -1125765,6 +1127333,49 @@ "type": "confirmatory results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2020.10.12.335562", + "rel_title": "Sequences in the cytoplasmic tail of SARS-CoV-2 spike facilitate syncytia formation", + "rel_date": "2020-10-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.12.335562", + "rel_abs": "The Spike (S) protein of SARS-CoV-2 binds ACE2 to direct fusion with host cells. S comprises a large external domain, a transmembrane domain (TMD) and a short cytoplasmic tail. Understanding the intracellular trafficking of S is relevant to SARS-CoV-2 infection, and to vaccines expressing full-length S from mRNA or adenovirus vectors. We have applied proteomics to identify cellular factors that interact with the cytoplasmic tail of S. We confirmed interactions with the COPI and COPII vesicle coats, ERM family actin regulators, and the WIPI3 autophagy component. The COPII binding-site promotes exit from the endoplasmic reticulum (ER), and although COPI-binding should retain S in the early Golgi where viral budding occurs, there is a suboptimal histidine residue in the recognition motif. As a result, S leaks to the surface where it accumulates and can direct the formation of multinucleate syncytia. Thus, the trafficking signals in the tail of S indicate that syncytia play a role in the SARS-CoV-2 lifecycle.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Jerome Cattin-Ortola", + "author_inst": "MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK" + }, + { + "author_name": "Lawrence Welch", + "author_inst": "MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK" + }, + { + "author_name": "Sarah L Maslen", + "author_inst": "MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK" + }, + { + "author_name": "J Mark Skehel", + "author_inst": "MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK" + }, + { + "author_name": "Guido Papa", + "author_inst": "MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK" + }, + { + "author_name": "Leo C James", + "author_inst": "MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK" + }, + { + "author_name": "Sean Munro", + "author_inst": "MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2020.10.12.335331", "rel_title": "Integrated analysis of multimodal single-cell data", @@ -1126741,65 +1128352,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.09.20199778", - "rel_title": "Exclusion of bacterial co-infection in COVID-19 using baseline inflammatory markers and their response to antibiotics", - "rel_date": "2020-10-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.09.20199778", - "rel_abs": "BackgroundCOVID-19 is infrequently complicated by secondary bacterial infection, but nevertheless antibiotic prescriptions are common. We used community-acquired pneumonia (CAP) as a benchmark to define the processes that occur in a bacterial pulmonary infection, and tested the hypothesis that baseline inflammatory markers and their response to antibiotic therapy could distinguish CAP from COVID-19.\n\nMethodsIn patients admitted to Royal Free Hospital (RFH) and Barnet Hospital (BH) we defined CAP by lobar consolidation on chest radiograph, and COVID-19 by SARS-CoV-2 detection by PCR. Data were derived from routine laboratory investigations.\n\nResultsOn admission all CAP and >90% COVID-19 patients received antibiotics. We identified 106 CAP and 619 COVID-19 patients at RFH. CAP was characterised by elevated white cell count (WCC) and C-reactive protein (CRP) compared to COVID-19 (median WCC 12.48 (IQR 8.2-15.3) vs 6.78 (IQR 5.2-9.5) x106 cells/ml and median CRP CRP 133.5 (IQR 65-221) vs 86 (IQR 42-160) mg/L). Blood samples collected 48-72 hours into admission revealed decreasing CRP in CAP but not COVID-19 (CRP difference -33 (IQR -112 to +3.5) vs +15 (IQR -15 to +70) mg/L respectively). In the independent validation cohort (BH) consisting of 169 CAP and 181 COVID-19 patients, admission WCC >8.2x106 cells/ml or falling CRP during admission identified 95% of CAP cases, and predicted the absence of bacterial co-infection in 45% of COVID-19 patients.\n\nConclusionsWe propose that in COVID-19 the absence of both elevated baseline WCC and antibiotic-related decrease in CRP can exclude bacterial co-infection and facilitate antibiotic stewardship efforts.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Claire Y Mason", - "author_inst": "Royal Free London NHS Trust" - }, - { - "author_name": "Tanmay Kanitkar", - "author_inst": "Royal Free London NHS Trust" - }, - { - "author_name": "Charlotte J Richardson", - "author_inst": "Royal Free London NHS Trust" - }, - { - "author_name": "Marisa Lanzman", - "author_inst": "Royal Free London NHS Trust" - }, - { - "author_name": "Zak Stone", - "author_inst": "Royal Free London NHS Trust" - }, - { - "author_name": "Tabitha Mahungu", - "author_inst": "Royal Free London NHS Trust" - }, - { - "author_name": "Damien Mack", - "author_inst": "Royal Free London NHS Trust" - }, - { - "author_name": "Emmanuel Q Wey", - "author_inst": "Royal Free London NHS Trust" - }, - { - "author_name": "Lucy Lamb", - "author_inst": "Royal Free London NHS Trust" - }, - { - "author_name": "Indran Balakrishnan", - "author_inst": "Royal Free London NHS Trust" - }, - { - "author_name": "Gabriele Pollara", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.08.20208546", "rel_title": "SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay", @@ -1127635,6 +1129187,61 @@ "type": "new results", "category": "neuroscience" }, + { + "rel_doi": "10.1101/2020.10.09.334052", + "rel_title": "Kidney injury molecule-1 is a potential receptor for SARS-CoV-2", + "rel_date": "2020-10-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.09.334052", + "rel_abs": "COVID-19 patients present high incidence of kidney abnormalities, which are associated with poor prognosis and high mortality. Identification of SARS-CoV-2 in kidney of COVID-19 patients suggests renal tropism and direct infection. Presently, it is generally recognized that SARS-CoV-2 initiates invasion through binding of receptor-binding domain (RBD) of spike protein to host cell-membrane receptor ACE2, however, whether there is additional target of SARS-CoV-2 in kidney remains unclear. Kidney injury molecule-1 (KIM1) is a transmembrane protein that drastically up-regulated after renal injury. Here, binding between SARS-CoV2-RBD and the extracellular Ig V domain of KIM1 was identified by molecular simulations and co-immunoprecipitation, which was comparable in affinity to that of ACE2 to SARS-CoV-2. Moreover, KIM1 facilitated cell entry of SARS-CoV2-RBD, which was potently blockaded by a rationally designed KIM1-derived polypeptide. Together, the findings suggest KIM1 may mediate and exacerbate SARS-CoV-2 infection in a vicious cycle, and KIM1 could be further explored as a therapeutic target.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Chen Yang", + "author_inst": "Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Yu Zhang", + "author_inst": "Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Hong Chen", + "author_inst": "Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Yuchen Chen", + "author_inst": "Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Dong Yang", + "author_inst": "Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "ZiWei Shen", + "author_inst": "Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Xiaomu Wang", + "author_inst": "Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Xinran Liu", + "author_inst": "Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Mingrui Xiong", + "author_inst": "Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Kun Huang", + "author_inst": "Tongji Medical College, Huazhong University of Science and Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2020.10.09.334136", "rel_title": "Soluble Spike DNA vaccine provides long-term protective immunity against SAR-CoV-2 in mice and nonhuman primates", @@ -1128575,45 +1130182,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.07.20208918", - "rel_title": "Cardiovascular drugs and COVID-19 clinical outcomes: a living systematic review and meta-analysis", - "rel_date": "2020-10-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.07.20208918", - "rel_abs": "OBJECTIVETo continually evaluate the rapidly evolving evidence base on the role of cardiovascular drugs in COVID-19 clinical outcomes (susceptibility to infection, hospitalization, hospitalization length, disease severity, and all-cause mortality).\n\nDESIGNLiving systematic review and meta-analysis.\n\nDATA SOURCESEligible publications identified from >500 databases indexed through 31st July 2020 and additional studies from reference lists, with planned continual surveillance for at least two years.\n\nSTUDY SELECTIONObservational and interventional studies that report on the association between cardiovascular drugs and COVID-19 clinical outcomes.\n\nDATA EXTRACTIONSingle-reviewer extraction and quality evaluation (using ROBINS-I), with half the records independently extracted and evaluated by a second reviewer.\n\nRESULTSOf 23,427 titles screened, 175 studies were included in the quantitative synthesis. The most reported drug classes were angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin receptor blockers (ARBs) with ACEI/ARB exposure being associated with higher odds of testing positive for COVID-19 (pooled unadjusted OR 1.15, 95% CI 1.02 to 1.30). Among patients with COVID-19, unadjusted estimates showed that ACEI/ARB exposure was associated with being hospitalized (OR 2.25, 1.70 to 2.98) and having severe disease (OR 1.50, 1.27 to 1.77) but not with the length of hospitalization (mean difference -0.45, -1.33 to 0.43 days) or all-cause mortality (OR 1.25, CI 0.98 to 1.58). However, after adjustment, ACEI/ARB exposure was not associated with testing positive for COVID-19 (pooled adjusted OR 1.01, 0.93 to 1.10), being hospitalized (OR 1.16, 0.80 to 1.68), having severe disease (1.04, 0.76 to 1.42), or all-cause mortality (0.86, 0.64 to 1.15). Similarly, subgroup analyses involving only hypertensive patients revealed that ACEI/ARB exposure was not associated with being hospitalized (OR 0.84, 0.58 to 1.22), disease severity (OR 0.88, 0.68 to 1.14) or all-cause mortality (OR 0.77, 0.54 to 1.12) while it decreased the length of hospitalization (mean difference -0.71, -1.11 to -0.30 days). After adjusting for relevant covariates, other cardiovascular drug classes were mostly not found to be associated with poor COVID-19 clinical outcomes. However, the validity of these findings is limited by a high level of heterogeneity in terms of effect sizes and a serious risk of bias, mainly due to confounding in the included studies.\n\nCONCLUSIONOur comprehensive review shows that ACEI/ARB exposure is associated with COVID-19 outcomes such as susceptibility to infection, severity, and hospitalization in unadjusted analyses. However, after adjusting for potential confounding factors, this association is not evident. Patients on cardiovascular drugs should continue taking their medications as currently recommended. Higher quality evidence in the form of randomized controlled trials will be needed to determine any adverse or beneficial effects of cardiovascular drugs.\n\nPRIMARY FUNDING SOURCENone\n\nSYSTEMATIC REVIEW REGISTRATIONPROSPERO (CRD42020191283)", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Innocent Gerald Asiimwe", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Sudeep Pushpakom", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Richard Turner", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Ruwanthi Kolamunnage-Dona", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Andrea Jorgensen", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Munir Pirmohamed", - "author_inst": "University of Liverpool" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.07.20208231", "rel_title": "Role of high-dose exposure in transmission hot zones as a driver of SARS-CoV2 dynamics", @@ -1129332,6 +1130900,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.26.20201954", + "rel_title": "Personal protective equipment for reducing the risk of COVID-19 infection among healthcare workers involved in emergency trauma surgery during the pandemic: a systematic review protocol", + "rel_date": "2020-10-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.26.20201954", + "rel_abs": "ObjectiveThe objective of this broad evidence synthesis is to identify and summarize the available literature regarding the efficacy of different personal protective equipment (PPE) for reducing the risk of COVID-19 infection in health personnel caring for patients undergoing trauma surgery in low-resource environments (LREs).\n\nIntroductionMany healthcare facilities in low-and middle-income countries are inadequately resourced and may lack optimal organization and governance, especially concerning surgical health systems. COVID-19 has the potential to decimate these already strained surgical healthcare services unless health systems take stringent measures to protect healthcare workers from viral exposure and ensure the continuity of specialized care for the patients.\n\nInclusion criteriaThis review will preferentially consider systematic reviews of experimental and quasi-experimental studies, as well as individual studies of such designs, evaluating the effect of different PPE on the risk of COVID-19 infection in healthcare workers (HCWs) involved in emergency trauma surgery.\n\nMethodsWe will conduct several searches in the L{middle dot}OVE (Living OVerview of Evidence) platform for COVID-19, a system that performs automated regular searches in PubMed, Embase, Cochrane Central Register of Controlled Trials (CENTRAL), and over thirty other sources. The search results will be presented according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) flow diagram. Critical appraisal of the eligible studies for methodological quality will be conducted. Data will be extracted using the standardized data extraction tool in Covidence. Studies will, when possible, be pooled in a statistical meta-analysis using JBI SUMARI. The Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) approach for grading the certainty of evidence will be followed, and a Summary of Findings (SoF) will be created.\n\nSystematic review registration numberCRD42020198267", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Dylan Griswold", + "author_inst": "Division of Neurosurgery, Department of Clinical Neurosciences, Addenbrookes Hospital & University of Cambridge, Cambridge, UK" + }, + { + "author_name": "Andres Gempeler", + "author_inst": "Clinical Research Center, Fundacion Valle del Lili, Cali, Colombia" + }, + { + "author_name": "Angelos Kolias", + "author_inst": "Division of Neurosurgery, Department of Clinical Neurosciences, Addenbrookes Hospital & University of Cambridge, Cambridge, UK" + }, + { + "author_name": "Peter J Hutchinson", + "author_inst": "Division of Neurosurgery, Department of Clinical Neurosciences, Addenbrookes Hospital & University of Cambridge, Cambridge, UK" + }, + { + "author_name": "Andres M Rubiano", + "author_inst": "Neuroscience Institute, INUB-MEDITECH Research Group, El Bosque University, Bogota, Colombia" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.10.06.20204487", "rel_title": "System Dynamics Model of Possible Covid-19 Trajectories Under Various Non-Pharmaceutical Intervention Options in Low Resource Setting.", @@ -1130140,65 +1131743,6 @@ "type": "new results", "category": "scientific communication and education" }, - { - "rel_doi": "10.1101/2020.10.05.20207506", - "rel_title": "Developing multiplex ddPCR assays for SARS-CoV-2 detection based on probe mix and amplitude based multiplexing", - "rel_date": "2020-10-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.05.20207506", - "rel_abs": "Multiplexing has been highlighted to save on costs, increase sample throughput, and maximize on the number of targets that can be sensitively detected within a small sample. With the ongoing SARS-CoV-2 pandemic, different articles have been published highlighting the superiority of droplet digital PCR (ddPCR) over the gold reverse transcription PCR (RT-PCR) in SARS-CoV-2 detection. However, few studies have been reported on developing multiplex ddPCR assays for SARS-CoV-2 detection and their performance. In this study, we developed simplex (1 target), duplex (2 targets), triplex probe mix (3 targets), and fourplex (4 targets) assays based on a two color ddPCR system for SARS-CoV-2 detection. Results showed that the fourplex assay had the similar limits of detection and accuracy to the lower multiplex assays. Analyzing 94 clinical isolates demonstrated that the ddPCR triplex probe mix assay had better sensitivity than the RT-qPCR assay. Additionally, the ddPCR multiplex assay showed that remdesivir could inhibit the growth of SARS-CoV-2 in vitro while another testing drug couldnt. Conclusively, our research shows that developing multiplex ddPCR assays is possible by combing probe mix and amplitude based multiplexing, which will help in developing multiplexed ddPCR assays for different SARS-CoV-2 applications.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Raphael Nyaruaba", - "author_inst": "Wuhan Institute of Virology" - }, - { - "author_name": "Changchang Li", - "author_inst": "Wuhan Institute of Virology" - }, - { - "author_name": "Caroline Mwaliko", - "author_inst": "Wuhan Institute of Virology" - }, - { - "author_name": "Matilu Mwau", - "author_inst": "Kenya Medical Research Institute" - }, - { - "author_name": "Nelson Odiwuor", - "author_inst": "Wuhan Institute of Virology" - }, - { - "author_name": "Elishiba Muturi", - "author_inst": "Wuhan Institute of Virology" - }, - { - "author_name": "Caroline Muema", - "author_inst": "Wuhan Institute of Virology" - }, - { - "author_name": "Jin Xiong", - "author_inst": "Wuhan Institute of Virology" - }, - { - "author_name": "Junhua Li", - "author_inst": "Wuhan Institute of Virology" - }, - { - "author_name": "Junping Yu", - "author_inst": "Wuhan Institute of Virology" - }, - { - "author_name": "Hongping Wei", - "author_inst": "Wuhan Institute of Virology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.05.20207241", "rel_title": "Efficacy of face masks, neck gaiters and face shields for reducing the expulsion of simulated cough-generated aerosols", @@ -1130918,6 +1132462,41 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.10.07.325910", + "rel_title": "Production of ORF8 protein from SARS-CoV-2 using an inducible virus-mediated expression-system in suspension-cultured tobacco BY-2 cells", + "rel_date": "2020-10-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.07.325910", + "rel_abs": "COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which spread worldwide in 2020, is an urgent problem to be overcome. The ORF8 of SARS-CoV-2 has been suggested to be associated with the symptoms of COVID-19, according to reports of clinical studies. However, little is known about the function of ORF8. As one of the ways to advance the functional analysis of ORF8, mass production of ORF8 with the correct three-dimensional structure is necessary. In this study, we attempted to produce ORF8 protein by chemically inducible protein production system using tobacco BY-2 cells. An ORF8-producing line was generated by the Agrobacterium method. As a result, the production of ORF8 of 8.8 {+/-} 1.4 mg/L of culture medium was confirmed. SDS-PAGE and nuclear magnetic resonance (NMR) analysis confirmed that the ORF8 produced by this system is a dimeric form with a single structure, unlike that produced in Escherichia coli. Furthermore, it was suggested that the ORF8 produced by this system was glycosylated. Through this study, we succeeded in producing ORF8 folded into a single structure in a chemically inducible protein production system using tobacco BY-2 cells. It is expected that the functional analysis of ORF8 will be advanced using the ORF8 produced by this system and that it will greatly contribute to the development of antibodies and therapeutic agents targeting ORF8.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Tomohiro Imamura", + "author_inst": "Ishikawa Prefectural University" + }, + { + "author_name": "Noriyoshi Isozumi", + "author_inst": "Japan Advanced Institute of Science and Technology (JAIST)" + }, + { + "author_name": "Yasuki Higashimura", + "author_inst": "Ishikawa Prefectural University" + }, + { + "author_name": "Shinya Ohki", + "author_inst": "Japan Advanced Institute of Science and Technology (JAIST)" + }, + { + "author_name": "Masashi Mori", + "author_inst": "Ishikawa Prefectural University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "plant biology" + }, { "rel_doi": "10.1101/2020.10.07.328302", "rel_title": "Extremely potent human monoclonal antibodies from convalescent Covid-19 patients", @@ -1131910,49 +1133489,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.10.04.20206011", - "rel_title": "Temporal Analysis of COVID-19 Convalescent Plasma Donations Reveals Significant Decrease in Neutralizing Capacity Over Time", - "rel_date": "2020-10-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.04.20206011", - "rel_abs": "COVID-19 convalescent plasma (CCP) received approval for use under an Emergency Use Authorization by the FDA for treatment of seriously ill patients. Use of CCP units with a signal-to-cutoff ratio of [≥]12 using the Ortho VITROS SARS-CoV-2 IgG test (OVSARS2IgG) is authorized. Little is known about the relationship between this ratio and the neutralizing capacity of plasma/sera against genuine SARS-CoV-2 virus. We measured the neutralizing capacity of 981 samples from 196 CCP donors 7-119 days post initial donation (DPID). Neutralizing capacity was assessed for 50% (PRNT50) and 90% (PRNT90) reduction of infectious virus using the gold standard plaque reduction neutralization test (PRNT). Importantly, while 32.7%/79.5% (PRNT90/PRNT50) of donations met the FDA minimum titer of 1:80 initially, only 14.0%/48.8% (PRNT90/PRNT50) met this cut-off [≥]85 DPID. A subset of 91 donations were evaluated using the OVSARS2IgG and compared to PRNT titers for diagnostic accuracy. The correlation of OVSARS2IgG results to neutralizing capacity allowed extrapolation to CCP therapy efficacy results. CCP with OVSARS2IgG ratios in the therapeutically beneficial group had neutralizing titers of [≥]1:640 (PRNT50) and/or [≥]1:80 (PRNT90). This information provides a new basis for refining the recommended properties of CCP that is used to treat severe COVID-19.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Roxie Girardin", - "author_inst": "NYSDOH" - }, - { - "author_name": "Alan lI Dupuis", - "author_inst": "NYSDOH" - }, - { - "author_name": "Anne F. Payne", - "author_inst": "NYSDOH" - }, - { - "author_name": "Timothy J Sullivan", - "author_inst": "NYSDOH" - }, - { - "author_name": "Donna Strauss", - "author_inst": "NYBC" - }, - { - "author_name": "Monica M. Parker", - "author_inst": "NYSDOH" - }, - { - "author_name": "Kathleen McDonough", - "author_inst": "NYSDOH" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.10.05.20207118", "rel_title": "Multi-omics highlights ABO plasma protein as a causal risk factor for COVID-19", @@ -1132468,6 +1134004,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.03.20206151", + "rel_title": "Impact of pre-existing SARS-CoV-2 reactive T cells in uninfected individuals on COVID-19 mortality in different countries", + "rel_date": "2020-10-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.03.20206151", + "rel_abs": "Several recent studies identified SARS-CoV-2 reactive T cells in people without exposure to the virus. However, pathophysiological implications of these findings remain unknown. Here, the potential impact of pre-existing T cell reactivity against SARS-CoV-2 in uninfected individuals on markedly different COVID-19 mortality levels in different countries has been investigated. The inverse correlation is documented between the prevalence of pre-existing SARS-CoV-2 reactive T cells in people without exposure to the virus and COVID-19 mortality rates in different countries. In countries with similar levels of pre-existing SARS-CoV-2 cross-reactive T cells in uninfected individuals, differences in COVID-19 mortality appear linked with the extend and consistency of implementations of social measures designed to limit the transmission of SARS-CoV-2 (lockdown; physical distancing; mask wearing). Collectively, these observations support the model that the level of pre-existing SARS-CoV-2 reactive T cells is one of the important determinants of the innate herd immunity against COVID-19. Together with the consistent social measures directed to limit the virus spread, high levels of pre-existing SARS-CoV-2 reactive T cells appear significant determinants diminishing the COVID-19 mortality. Observations reported in this contribution should have significant impact on definitions of the herd immunity threshold required to effectively stop the pandemic in different countries across the globe.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Gennadi Glinsky", + "author_inst": "University of California San Diego" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.03.20206243", "rel_title": "Diagnostic performance of the combined nasal and throat swab in patients admitted to hospital with suspected COVID-19", @@ -1133232,77 +1134787,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.10.05.20206953", - "rel_title": "Scalable, effective, and rapid decontamination of SARS-CoV-2 contaminated N95 respirators using germicidal ultra-violet C (UVC) irradiation device", - "rel_date": "2020-10-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.05.20206953", - "rel_abs": "ImportanceParticulate respirators such as N95 masks are an essential component of personal protective equipment (PPE) for front-line workers. This study describes a rapid and effective UVC irradiation system that would facilitate the safe re-use of N95 respirators and provides supporting information for deploying UVC for decontamination of SARS-CoV-2 during the COVID19 pandemic.\n\nObjectiveTo assess the inactivation potential of the proposed UVC germicidal device as a function of time by using 3M(R) 8211 - N95 particulate respirators inoculated with SARS-CoV-2.\n\nDesignA germicidal UVC device to deliver tailored UVC dose was developed and snippets (2.5cm2) of the 3M-N95 respirator were inoculated with 106 plaque-forming units (PFU) of SARS-CoV-2 and were UV irradiated. Different exposure times were tested (0-164 seconds) by fixing the distance between the lamp (10 cm) and the mask while providing an exposure of at least 5.43 mWcm-2.\n\nSettingThe current work is broadly applicable for healthcare-settings, particularly during a pandemic such as COVID-19.\n\nParticipantsNot applicable.\n\nMain Outcome(s) and Measure(s)Primary measure of outcome was titration of infectious virus recovered from virus-inoculated respirator pieces after UVC exposure. Other measures included the method validation of the irradiation protocol, using lentiviruses (biosafety level-2 agent) and establishment of the germicidal UVC exposure protocol.\n\nResultsAn average of 4.38x103 PFUml-1(SD 772.68) was recovered from untreated masks while 4.44x102 PFUml-1(SD 203.67), 4.00x102 PFUml-1(SD 115.47), 1.56x102 PFUml-1(SD 76.98) and 4.44x101 PFUml-1(SD 76.98) was recovered in exposures 2s,6s,18s and 54 seconds per side respectively. The germicidal device output and positioning was monitored and a minimum output of 5.43 mWcm-2 was maintained. Infectious SARS-CoV-2 was not detected by plaque assays (minimal level of detection is 67 PFUml-1) on N95 respirator snippets when irradiated for 120s per side or longer suggesting 3.5 log reduction in 240 seconds of irradiation.\n\nConclusions and RelevanceA scalable germicidal UVC device to deliver tailored UVC dose for rapid decontamination of SARS-CoV-2 was developed. UVC germicidal irradiation of N95 snippets inoculated with SARS-CoV-2 for 120s per side resulted in 100% (3.5 log in total) reduction of virus. These data support the reuse of N95 particle-filtrate apparatus upon irradiation with UVC and supports use of UVC-based decontamination of SARS-CoV-2 virus during the COVID19 pandemic.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Raveen Rathnasinghe", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Robert F Karlicek", - "author_inst": "Rensselaer Polytechnic Institute" - }, - { - "author_name": "Michael Schotsaert", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Mattheos A Koffas", - "author_inst": "Rensselaer Polytechnic Institute" - }, - { - "author_name": "Brigitte Arduini", - "author_inst": "Rensselaer Polytechnic Institute" - }, - { - "author_name": "Sonia Jangra", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Bowen Wang", - "author_inst": "Rensselaer Polytechnic Institute" - }, - { - "author_name": "Jason L. Davis", - "author_inst": "Rensselaer Polytechnic Institute" - }, - { - "author_name": "Mohammed Alnaggar", - "author_inst": "Rensselaer Polytechnic Institute" - }, - { - "author_name": "Anthony Costa", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Richard Vincent", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Adolfo Garcia-Sastre", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Deepak Vashishth", - "author_inst": "Rensselaer Polytechnic Institute" - }, - { - "author_name": "Priti Balchandani", - "author_inst": "Icahn School of Medicine at Mount Sinai" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.10.05.20201574", "rel_title": "Prevalence of SARS-CoV-2 in human post-mortem ocular tissues", @@ -1134066,6 +1135550,129 @@ "type": "new results", "category": "pathology" }, + { + "rel_doi": "10.1101/2020.10.06.323634", + "rel_title": "Multi-Clonal Live SARS-CoV-2 In Vitro Neutralization by Antibodies Isolated from Severe COVID-19 Convalescent Donors", + "rel_date": "2020-10-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.06.323634", + "rel_abs": "The interactions between antibodies, SARS-CoV-2 and immune cells contribute to the pathogenesis of COVID-19 and protective immunity. To understand the differences between antibody responses in mild versus severe cases of COVID-19, we analyzed the B cell responses in patients 1.5 months post SARS-CoV-2 infection. Severe and not mild infection correlated with high titers of IgG against Spike receptor binding domain (RBD) that were capable of viral inhibition. B cell receptor (BCR) sequencing revealed two VH genes, VH3-38 and VH3-53, that were enriched during severe infection. Of the 22 antibodies cloned from two severe donors, six exhibited potent neutralization against live SARS-CoV-2, and inhibited syncytia formation. Using peptide libraries, competition ELISA and RBD mutagenesis, we mapped the epitopes of the neutralizing antibodies (nAbs) to three different sites on the Spike. Finally, we used combinations of nAbs targeting different immune-sites to efficiently block SARS-CoV-2 infection. Analysis of 49 healthy BCR repertoires revealed that the nAbs germline VHJH precursors comprise up to 2.7% of all VHJHs. We demonstrate that severe COVID-19 is associated with unique BCR signatures and multi-clonal neutralizing responses that are relatively frequent in the population. Moreover, our data support the use of combination antibody therapy to prevent and treat COVID-19.", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Michael Mor", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Michal Werbner", + "author_inst": "Bar-Ilan University" + }, + { + "author_name": "Joel Alter", + "author_inst": "Bar-Ilan University" + }, + { + "author_name": "Modi Safra", + "author_inst": "Bar-Ilan University" + }, + { + "author_name": "Elad Chomsky", + "author_inst": "ImmunAi" + }, + { + "author_name": "Smadar Hada-Neeman", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Ksenia Polonsky", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Cameron Nowell", + "author_inst": "Monash Institute of Pharmaceutical Sciences" + }, + { + "author_name": "Alex Clark", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Anna Roitburd-Berman", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Noam Ben-Shalom", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Michal Navon", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Dor Rafael", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Hila Sharim", + "author_inst": "ImmunAi" + }, + { + "author_name": "Evgeny Kiner", + "author_inst": "ImmunAi" + }, + { + "author_name": "Eric Griffis", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Jonathan M. Gershoni", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Oren Kobiler", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Sandra Lawrynowicz Leibel", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Oren Zimhony", + "author_inst": "Hebrew University" + }, + { + "author_name": "Aaron F. Carlin", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Gur Yaari", + "author_inst": "Bar-Ilan University" + }, + { + "author_name": "Moshe Dassau", + "author_inst": "Bar-Ilan University" + }, + { + "author_name": "Meital Gal-Tanamy", + "author_inst": "Bar-Ilan University" + }, + { + "author_name": "David Hagin", + "author_inst": "Ichilov Hospital" + }, + { + "author_name": "Ben A. Croker", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Natalia Freund", + "author_inst": "Tel Aviv University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.10.06.328138", "rel_title": "The strength of a NES motif in the nucleocapsid protein of human coronaviruses is related to genus, but not to pathogenic capacity", @@ -1134710,29 +1136317,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.02.20205716", - "rel_title": "Metabolic syndrome increases COVID-19-related mortality in the UK Biobank sample", - "rel_date": "2020-10-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.02.20205716", - "rel_abs": "Previous studies link obesity, components of metabolic health, such as hypertension or inflammation, to increased hospitalisations and death rates of patients with COVID-19. Here, in two overlapping samples of over 1,000 individuals from the UK Biobank we investigate whether metabolic health as measured by waist circumference, dyslipidaemia, hypertension, diabetes, and systemic inflammation is related to increased COVID-19 infection and mortality rates. Using logistic regression and controlling for confounding variables such as socioeconomic status, age, sex or ethnicity, we find that individuals with worse metabolic health (measured on average eleven years prior to 2020) have an increased risk for COVID-19-related death (adjusted odds ratio: 1.67). We also find that specific factors contributing to increased mortality are increased serum glucose levels, systolic blood pressure and waist circumference.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Filip Morys", - "author_inst": "Montreal Neurological Institute, McGill University" - }, - { - "author_name": "Alain Dagher", - "author_inst": "Montreal Neurological Institute, McGill University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.05.326637", "rel_title": "In vitro efficacy of Artemisinin-based treatments against SARS-CoV-2", @@ -1135464,6 +1137048,217 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.02.20204578", + "rel_title": "Extremely preterm infant admissions within the SafeBoosC-III consortium during the COVID-19 lockdown", + "rel_date": "2020-10-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.02.20204578", + "rel_abs": "ObjectiveTo evaluate if the number of admitted extremely preterm (EP) infants (born before 28 weeks of gestational age) has changed in the neonatal intensive care units (NICUs) of the SafeBoosC-III consortium during the global lockdown when compared to the corresponding time period in 2019.\n\nDesignThis is a retrospective, observational study. Forty-six out of 79 NICUs (58%) from 17 countries participated. Principal investigators were asked to report the following information: 1) Total number of EP infant admissions to their NICU in the three months where the lockdown restrictions were most rigorous during the first phase of the COVID-19 pandemic, 2) Similar EP infant admissions in the corresponding three months of 2019, 3) the level of local restrictions during the lockdown period and 4) the local impact of the COVID-19 lockdown on the everyday life of a pregnant woman.\n\nResultsThere was no significant difference between the number of EP infant admissions during the three most rigorous lockdown months of the COVID-19 pandemic compared to the corresponding three months in 2019 (n=428 versus n=457 respectively, p=0.33). There were no significant changes within individual geographic regions and no significant association between the level of lockdown restrictions and change in the number of EP infant admissions (p=0.334).\n\nConclusionThis larger ad hoc study did not confirm previous studies report of a major reduction in the number of extremely preterm births during the first phase of the COVID-19 pandemic.", + "rel_num_authors": 49, + "rel_authors": [ + { + "author_name": "Marie Isabel Rasmussen", + "author_inst": "Department of Neonatology, Rigshospitalet, Copenhagen" + }, + { + "author_name": "Mathias Luehr Hansen", + "author_inst": "Department of Neonatology, Rigshospitalet, Copenhagen" + }, + { + "author_name": "Gerhard Pichler", + "author_inst": "Department of Pediatrics, Medical University of Graz, Graz, Austria" + }, + { + "author_name": "Eugene Dempsey", + "author_inst": "Infant Centre and Department of Paediatrics and Child Health, University College Cork, College Road, Cork, Ireland" + }, + { + "author_name": "Adelina Pellicer", + "author_inst": "Department of Neonatology, La Paz University Hospital, Madrid, Spain" + }, + { + "author_name": "Afif EL-Khuffash", + "author_inst": "Department of Pediatrics, The Royal College of Surgeons in Ireland, Dublin, Ireland" + }, + { + "author_name": "Shashidhar A", + "author_inst": "St. Johns Medical College Hospital, Bengaluru, India" + }, + { + "author_name": "Salvador Piris-Borregas", + "author_inst": "Department of Neonatology, 12 Octubre University Hospital. Madrid" + }, + { + "author_name": "Miguel Alsina", + "author_inst": "Neonatology Department, Hospital Clinic-Maternintat, Barcelona, Spain" + }, + { + "author_name": "Merih Cetinkaya", + "author_inst": "Department of Neonatology, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul, Turkey" + }, + { + "author_name": "Lina Chalak", + "author_inst": "Division of Pediatrics - Neonatal-Perinatal, UT Southwestern, United States" + }, + { + "author_name": "Hilal Ozkan", + "author_inst": "Division of Neonatology, Department of Pediatrics, Uludag University Medical Faculty, Turkey" + }, + { + "author_name": "Mariana Baserga", + "author_inst": "Division of Neonatology, Department of Pediatrics, University of Utah, United States" + }, + { + "author_name": "Jan Sirc", + "author_inst": "Institute for the Care of Mother and Child, Prague, Czech Republic" + }, + { + "author_name": "Hans Fuchs", + "author_inst": "Center for Pediatrics, Department of Neonatology, Medical Center, University of Freiburg, Germany" + }, + { + "author_name": "Ebru Ergenekon", + "author_inst": "Department of Neonatology, Gazi University Hospital, Yenimahalle/Ankara, Turkey" + }, + { + "author_name": "Luis Arruza", + "author_inst": "Division of Neonatology. Instituto del Nino y del Adolescente. Hospital Clinico San Carlos-IdISSC, Madrid, Spain" + }, + { + "author_name": "Amit Mathur", + "author_inst": "Department of Neonatal-Perinatal Medicine, Saint Louis University School of Medicine, Missouri, United States" + }, + { + "author_name": "Martin Stocker", + "author_inst": "Neonatal and Pediatric Intensive Care Unit, Children's Hospital Lucerne, Switzerland" + }, + { + "author_name": "Olalla Otero-Vaccarello", + "author_inst": "Department of Neonatology, Hospital Universitario de Tarragona Juan XXIII, Tarragona, Spain" + }, + { + "author_name": "Tomasz Szczapa", + "author_inst": "Department of Neonatology, Neonatal Biophysical Monitoring and Cardiopulmonary Therapies Research Unit, Poznan University of Medical Sciences, Poznan, Poland." + }, + { + "author_name": "Kosmas Sarafidis", + "author_inst": "First Department of Neonatology, Aristotle University, Hippokrateion General Hospital, Thessaloniki, Greece" + }, + { + "author_name": "Barbara Krolak-Olejnik", + "author_inst": "Department of Neonatology, Wroclaw Medical University, Poland" + }, + { + "author_name": "Asli Memisoglu", + "author_inst": "Department of Neonatology, Marmara University Pendik Training and Research Hospital, Pendik/Istanbul, Turkey" + }, + { + "author_name": "Hallvard Reigstad", + "author_inst": "Department of Neonatology, Haukeland University Hospital, Bergen, Norway" + }, + { + "author_name": "Elzbieta Rafinska-Wazny", + "author_inst": "Department of Neonatology, Centrum Medyczne 'Ujastek', Krakow, Poland" + }, + { + "author_name": "Eleftheria Hatzidaki", + "author_inst": "Department of Neonatology & NICU, University Hospital of Heraklion, Crete, Greece" + }, + { + "author_name": "Zhang Peng", + "author_inst": "Department of Neonatology, Childrens Hospital of Fudan University, Shanghai, China" + }, + { + "author_name": "Despoina Gkentzi", + "author_inst": "NICU, Department of Pediatrics, University General Hospital of Patras, Patras, Greece" + }, + { + "author_name": "Renaud Viellevoye", + "author_inst": "Department of Pediatrics, Neonatal Intensive Care Unit, CHR Liege, Belgium" + }, + { + "author_name": "Julie De Buyst", + "author_inst": "NICU, Tivoli Hospital, La Louviere, Belgium" + }, + { + "author_name": "Emmanuele Mastretta", + "author_inst": "S.C. Neonatologia - Pres Osp S.Anna - Citta della Salute e della Scienza di Torino, Italy" + }, + { + "author_name": "Ping Wang", + "author_inst": "Department of Neonatology, Guangzhou Women and Childrens Medical Center, Guangzhou, China" + }, + { + "author_name": "Gitte Hahn", + "author_inst": "Department of Neonatology, Rigshospitalet, Copenhagen, Denmark" + }, + { + "author_name": "Lars Bender", + "author_inst": "Department of Neonatology, Aalborg Universitets Hospital, Aalborg, Denmark" + }, + { + "author_name": "Luc Cornette", + "author_inst": "Department of Neonatology, AZ St-Jan Bruges, Belgium" + }, + { + "author_name": "Jakub Tkaczyk", + "author_inst": "Department of Neonatology, University Hospital Motol, Prague, Czech Republic" + }, + { + "author_name": "Ruth del Rio", + "author_inst": "Department of Neonatology, Hospital Sant Joan de Deu, Barcelona, Spain" + }, + { + "author_name": "Monica Fumagalli", + "author_inst": "Department of Neonatology, Fondazione IRCCS Ca Granda Ospedale Maggiore Policlinico Milan, Milan, Italy, Department of Clinical Sciences and Community Health, U" + }, + { + "author_name": "Evangelina Papathoma", + "author_inst": "Neonatal Intensive Care Unit, 'Alexandra' University and State Maternity Hospital, Athens, Greece" + }, + { + "author_name": "Maria Wilinska", + "author_inst": "Neonatology Department, Centre of Postgraduate Medical Education, Warsaw, Poland" + }, + { + "author_name": "Gunnar Naulers", + "author_inst": "Department of Neonatology, University Hospital Leuven, Leuven, Belgium" + }, + { + "author_name": "Iwona Sadowska-Kakrawczenko", + "author_inst": "Department of Neonatology, Collegium Medicum in Bydgoszcz Nicolaus Copernicus University in Torun, Poland" + }, + { + "author_name": "Chantal Lecart", + "author_inst": "Department of Neonatology, GHdC Charleroi, Belgium" + }, + { + "author_name": "Maria Luz Couce", + "author_inst": "Neonatology Department, University Clinical Hospital of Santiago de Compostela, Health Research Institute of Santiago de Compostela, Spain" + }, + { + "author_name": "Siv Fredly", + "author_inst": "Department of Neonatology, Oslo University Hospital, Norway" + }, + { + "author_name": "Anne Marie Heuchan", + "author_inst": "Department of Neonatology, Royal Hospital for Children, United Kingdom" + }, + { + "author_name": "Tanja Karen", + "author_inst": "Department of Neonatology, University Hospital Zurich, Switzerland" + }, + { + "author_name": "Gorm Greisen", + "author_inst": "Department of Neonatology, Rigshospitalet, Copenhagen, Denmark" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2020.10.02.20205914", "rel_title": "Willingness of Nigerian residents to disclose COVID-19 symptoms and take COVID-19 test", @@ -1136220,65 +1138015,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "geriatric medicine" }, - { - "rel_doi": "10.1101/2020.10.01.20205393", - "rel_title": "A Mechanism for Severity of Disease in Older Patients with COVID-19: The Nexus between Telomere Length and Lymphopenia", - "rel_date": "2020-10-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.01.20205393", - "rel_abs": "BackgroundLymphopenia due to a plummeting T-cell count is a major feature of severe COVID-19. T-cell proliferation is telomere length (TL)-dependent and TL shortens with age. Older persons are disproportionally affected by severe COVID-19, and we hypothesized that those with short TL have less capacity to mount an adequate T-cell proliferative response to SARS-CoV-2. This hypothesis predicts that among older patients with COVID-19, shorter telomeres of peripheral blood mononuclear cells (PBMCs) will be associated with a lower lymphocyte count.\n\nMethodsOur sample comprised 17 COVID-19 and 21 non-COVID-19 patients, aged 87 {+/-} 8 (mean {+/-} SD) and 87 {+/-} 9 years, respectively. We measured TL by the Telomere Shortest Length Assay, a novel method that measures and tallies the short telomeres directly relevant to telomere-mediated biological processes. The primary analysis quantified TL as the proportion of telomeres shorter than 2 kilobases. For comparison, we also quantified TL by Southern blotting, which measures the mean length of telomeres.\n\nResultsLymphocyte count (109/L) was 0.91 {+/-} 0.42 in COVID-19 patients and 1.50 {+/-} 0.50 in non-COVID-19 patients (P < 0.001). In COVID-19 patients, but not in non-COVID-19 patients, lymphocyte count was inversely correlated with the proportion of telomeres shorter than 2 kilobases (P = 0.005) and positively correlated with the mean of telomeres measured by TeSLA (P = 0.03). Lymphocyte counts showed no statistically significant correlations with Southern blotting results in COVID-19 or non-COVID-19 patients.\n\nConclusionsThese results support the hypothesis that a compromised TL-dependent T-cell proliferative response contributes to lymphopenia and the resulting disproportionate severity of COVID-19 among old adults. We infer that infection with SARS-CoV-2 uncovers the limits of the TL reserves of older persons.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Athanase Benetos", - "author_inst": "Universite de Lorraine" - }, - { - "author_name": "Tsung-Po Lai", - "author_inst": "Rutgers University" - }, - { - "author_name": "Simon Toupance", - "author_inst": "Universite de Lorraine" - }, - { - "author_name": "Carlos Labat", - "author_inst": "Universite de Lorraine" - }, - { - "author_name": "Simon Verhulst", - "author_inst": "Groningen Institute for Evolutionary Life Sciences, University of Groningen," - }, - { - "author_name": "Christine Perret-Guillaume", - "author_inst": "Universite de Lorraine" - }, - { - "author_name": "Sylvie Gautier", - "author_inst": "Universite de Lorraine" - }, - { - "author_name": "Marie-Noelle Ungeheuer", - "author_inst": "Institut Pasteur, Clinical Investigation and Access to Bioresources Department, Paris," - }, - { - "author_name": "Daniel Levy", - "author_inst": "National Heart, Lung, and Blood Institute's Framingham Heart Study" - }, - { - "author_name": "Ezra Susser", - "author_inst": "Mailman School of Public Health, Columbia University" - }, - { - "author_name": "Abraham Aviv", - "author_inst": "Center of Human Development and Aging, Rutgers New Jersey Medical School," - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.01.20203836", "rel_title": "Evaluation of the accuracy, ease of use and limit of detection of novel, rapid, antigen-detecting point-of-care diagnostics for SARS-CoV-2", @@ -1137166,6 +1138902,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.01.20205096", + "rel_title": "Interactions between seasonal human coronaviruses and implications for the SARS-CoV-2 pandemic: A retrospective study in Stockholm, Sweden, 2009-2020", + "rel_date": "2020-10-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.01.20205096", + "rel_abs": "ObjectivesThe four seasonal coronaviruses 229E, NL63, OC43, and HKU1 are frequent causes of respiratory infections and show annual and seasonal variation. Increased understanding about these patterns could be informative about the epidemiology of SARS-CoV-2.\n\nMethodsResults from PCR diagnostics for the seasonal coronaviruses, and other respiratory viruses, were obtained for 55,190 clinical samples analysed at the Karolinska University Hospital, Stockholm, Sweden, between 14 September 2009 and 2 April 2020.\n\nResultsSeasonal coronaviruses were detected in 2,130 samples (3.9%) and constituted 8.1% of all virus detections. OC43 was most commonly detected (28.4% of detections), followed by NL63 (24.0%), HKU1 (17.6%), and 229E (15.3%). The overall fraction of positive samples was similar between seasons, but at species level there were distinct biennial alternating peak seasons for the Alphacoronaviruses, 229E and NL63, and the Betacoronaviruses, OC43 and HKU1, respectively. The Betacoronaviruses peaked earlier in the winter season (Dec-Jan) than the Alphacoronaviruses (Feb-Mar). Coronaviruses were detected across all ages, but diagnostics were more frequently requested for paediatric patients than adults and the elderly. OC43 and 229E incidence was relatively constant across age strata, while that of NL63 and HKU1 decreased with age.\n\nConclusionsBoth the Alphacoronaviruses and Betacoronaviruses showed alternating biennial winter incidence peaks, which suggests some type of immune mediated interaction. Symptomatic reinfections in adults and the elderly appear relatively common. Both findings may be of relevance for the epidemiology of SARS-CoV-2.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Robert Dyrdak", + "author_inst": "Karolinska Institutet; Karolinska University Hospital" + }, + { + "author_name": "Emma B Hodcroft", + "author_inst": "University of Basel" + }, + { + "author_name": "Martina Wahlund", + "author_inst": "Karolinska University Hospital; Karolinska Institutet" + }, + { + "author_name": "Richard A Neher", + "author_inst": "University of Basel" + }, + { + "author_name": "Jan Albert", + "author_inst": "Karolinska Institutet; Karolinska University Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.30.20204727", "rel_title": "High prevalence of SARS-CoV-2 swab positivity in England during September 2020: interim report of round 5 of REACT-1 study", @@ -1137962,61 +1139733,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.09.29.20202846", - "rel_title": "SARS-CoV-2 antibody responses in patients with aggressive haematological malignancies", - "rel_date": "2020-10-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.29.20202846", - "rel_abs": "The development of antibody responses to SARS-CoV-2 is an indicator of seroprevalence and may afford protection from infection. It has been presumed that antibody responses to SARS-CoV-2 will be impaired in patients with aggressive haematological malignancy (PHM) due to underlying immunological dysfunction caused by malignancy or systemic anti-cancer treatment (SACT), placing them at increased risk. Here we analysed longitudinal serum samples from ten hospitalised PHM with aggressive disease and on SACT, collected up to 103 days post-onset of COVID-19 symptoms. We found that the majority (8/9) of PHM with confirmed SARS-CoV-2 infection seroconverted and developed antibodies to the major SARS-CoV-2 antigens (S1 and N) with most (6/8) produced neutralising antibody responses. Furthermore, the dynamics of antibody responses were broadly similar to that reported for the general population, except for a possible delay to seroconversion. Our finding that PHM on SACT can make functional antibody responses to SARS-CoV-2 has important implications for patient management and serological monitoring of SARS-CoV-2 in high-risk groups.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Luke Muir", - "author_inst": "University College London" - }, - { - "author_name": "Jiexin Zheng", - "author_inst": "University College London NHS Foundation Trust" - }, - { - "author_name": "Chloe Rees-Spear", - "author_inst": "University College London" - }, - { - "author_name": "Annachiara Rosa", - "author_inst": "The Francis Crick Institute, London" - }, - { - "author_name": "Christopher Earl", - "author_inst": "The Francis Crick Institute, London" - }, - { - "author_name": "Peter Cherepanov", - "author_inst": "The Francis Crick Institute, London" - }, - { - "author_name": "Rajeev Gupta", - "author_inst": "University College London NHS Foundation Trust" - }, - { - "author_name": "Asim Khwaja", - "author_inst": "University College London NHS Foundation Trust" - }, - { - "author_name": "Clare Jolly", - "author_inst": "University College London" - }, - { - "author_name": "Laura E McCoy", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "hematology" - }, { "rel_doi": "10.1101/2020.09.29.20201509", "rel_title": "SARS-CoV-2 antibody testing in a UK population: detectable IgG for up to 20 weeks post infection.", @@ -1138888,6 +1140604,189 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.28.20201475", + "rel_title": "Large scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management", + "rel_date": "2020-09-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.28.20201475", + "rel_abs": "The COVID-19 pandemic has spread rapidly throughout the world. In the UK, the initial peak was in April 2020; in the county of Norfolk (UK) and surrounding areas, which has a stable, low-density population, over 3,200 cases were reported between March and August 2020. As part of the activities of the national COVID-19 Genomics Consortium (COG-UK) we undertook whole genome sequencing of the SARS-CoV-2 genomes present in positive clinical samples from the Norfolk region. These samples were collected by four major hospitals, multiple minor hospitals, care facilities and community organisations within Norfolk and surrounding areas. We combined clinical metadata with the sequencing data from regional SARS-CoV-2 genomes to understand the origins, genetic variation, transmission and expansion (spread) of the virus within the region and provide context nationally. Data were fed back into the national effort for pandemic management, whilst simultaneously being used to assist local outbreak analyses. Overall, 1,565 positive samples (172 per 100,000 population) from 1,376 cases were evaluated; for 140 cases between two and six samples were available providing longitudinal data. This represented 42.6% of all positive samples identified by hospital testing in the region and encompassed those with clinical need, and health and care workers and their families. 1,035 cases had genome sequences of sufficient quality to provide phylogenetic lineages. These genomes belonged to 26 distinct global lineages, indicating that there were multiple separate introductions into the region.\n\nFurthermore, 100 genetically-distinct UK lineages were detected demonstrating local evolution, at a rate of [~]2 SNPs per month, and multiple co-occurring lineages as the pandemic progressed. Our analysis: identified a sublineage associated with 6 care facilities; found no evidence of reinfection in longitudinal samples; ruled out a nosocomial outbreak; identified 16 lineages in key workers which were not in patients indicating infection control measures were effective; found the D614G spike protein mutation which is linked to increased transmissibility dominates the samples and rapidly confirmed relatedness of cases in an outbreak at a food processing facility. The large-scale genome sequencing of SARS-CoV-2-positive samples has provided valuable additional data for public health epidemiology in the Norfolk region, and will continue to help identify and untangle hidden transmission chains as the pandemic evolves.\n\nMajor pointsIn Norfolk and surrounding regions\n\nO_LI100 distinct UK lineages were identified.\nC_LIO_LI16 UK lineages found in key workers were not observed in patients or in community care.\nC_LIO_LI172 genomes from SARS-CoV-2 positive samples sequenced per 100,000 population representing 42.6% of all positive cases.\nC_LIO_LISARS-CoV-2 genomes from 1035 cases sequenced to a high quality.\nC_LIO_LIOnly 5 countries, out of 103, have sequenced more SARS-CoV-2 genomes than have been sequenced in Norfolk for this paper.\nC_LIO_LISamples covered the entire first wave, March to August 2020.\nC_LIO_LIStable evolutionary rate of 2 SNPs per month.\nC_LIO_LID614G mutation is the dominant genotype and associated with increased transmission.\nC_LIO_LINo evidence of reinfection in 42 cases with longitudinal samples.\nC_LIO_LIWGS identified a sublineage associated with care facilities.\nC_LIO_LIWGS ruled out nosocomial outbreaks.\nC_LIO_LIRapid WGS confirmed the relatedness of cases from an outbreak at a food processing facility.\nC_LI", + "rel_num_authors": 42, + "rel_authors": [ + { + "author_name": "Andrew J Page", + "author_inst": "Quadram Institute Bioscience" + }, + { + "author_name": "Alison E Mather", + "author_inst": "Quadram Institute Bioscience" + }, + { + "author_name": "Thanh Le Viet", + "author_inst": "Quadram Institute Bioscience" + }, + { + "author_name": "Emma J Meader", + "author_inst": "Norfolk and Norwich University Hospital" + }, + { + "author_name": "Nabil-Fareed J Alikhan", + "author_inst": "Quadram Institute Bioscience" + }, + { + "author_name": "Gemma L Kay", + "author_inst": "Quadram Institute Bioscience" + }, + { + "author_name": "Leonardo de Oliveira Martins", + "author_inst": "Quadram Institute Bioscience" + }, + { + "author_name": "Alp Aydin", + "author_inst": "Quadram Institute Bioscience" + }, + { + "author_name": "David J Baker", + "author_inst": "Quadram Institute Bioscience" + }, + { + "author_name": "Alexander J. Trotter", + "author_inst": "Quadram Institute Bioscience" + }, + { + "author_name": "Steven Rudder", + "author_inst": "Quadram Institute Bioscience" + }, + { + "author_name": "Ana P Tedim", + "author_inst": "Quadram Institute Bioscience" + }, + { + "author_name": "Anastasia Kolyva", + "author_inst": "Norfolk and Norwich University Hospital" + }, + { + "author_name": "Rachael Stanley", + "author_inst": "Norfolk and Norwich University Hospital" + }, + { + "author_name": "Maria Diaz", + "author_inst": "Quadram Institute Bioscience" + }, + { + "author_name": "Will Potter", + "author_inst": "Norfolk and Norwich University Hospital" + }, + { + "author_name": "Claire Stuart", + "author_inst": "Norfolk and Norwich University Hospital" + }, + { + "author_name": "Lizzie Meadows", + "author_inst": "Quadram Institute Bioscience" + }, + { + "author_name": "Andrew Bell", + "author_inst": "Quadram Institute Bioscience" + }, + { + "author_name": "Ana Victoria Gutierrez", + "author_inst": "Quadram Institute Bioscience" + }, + { + "author_name": "Nicholas M Thomson", + "author_inst": "Quadram Institute Bioscience" + }, + { + "author_name": "Evelien M Adriaenssens", + "author_inst": "Quadram Institute Bioscience" + }, + { + "author_name": "Tracey Swingler", + "author_inst": "Quadram Institute Bioscience" + }, + { + "author_name": "Rachel AJ Gilroy", + "author_inst": "Quadram Institute Bioscience" + }, + { + "author_name": "Luke Griffith", + "author_inst": "University of East Anglia" + }, + { + "author_name": "Dheeraj K Sethi", + "author_inst": "Norfolk and Norwich University Hospital" + }, + { + "author_name": "Dinesh Aggarwal", + "author_inst": "Public Health England" + }, + { + "author_name": "Colin S Brown", + "author_inst": "Public Health England" + }, + { + "author_name": "Rose K Davidson", + "author_inst": "University of East Anglia" + }, + { + "author_name": "Robert A Kingsley", + "author_inst": "Quadram Institute Bioscience" + }, + { + "author_name": "Luke Bedford", + "author_inst": "Ipswich Hospital" + }, + { + "author_name": "Lindsay J Coupland", + "author_inst": "Norfolk and Norwich University Hospital" + }, + { + "author_name": "Ian G Charles", + "author_inst": "Quadrum Institute Bioscience" + }, + { + "author_name": "Ngozi Elumogo", + "author_inst": "Norfolk and Norwich University Hospital" + }, + { + "author_name": "John Wain", + "author_inst": "Quadram Institute Bioscience" + }, + { + "author_name": "Reenesh Prakash", + "author_inst": "Norfolk and Norwich University Hospital" + }, + { + "author_name": "Mark A Webber", + "author_inst": "Quadram Institute Bioscience" + }, + { + "author_name": "SJ Louise Smith", + "author_inst": "Norfolk County Council" + }, + { + "author_name": "Meera Chand", + "author_inst": "Public Health England" + }, + { + "author_name": "Samir Dervisevic", + "author_inst": "Norfolk and Norwich University Hospital" + }, + { + "author_name": "Justin O'Grady", + "author_inst": "Quadram Institute Bioscience" + }, + { + "author_name": "- The COVID-19 Genomics UK (COG-UK) consortium", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.30.20203315", "rel_title": "Widening the gap: greater racial and ethnic disparities in COVID-19 burden after accounting for missing race/ethnicity data", @@ -1139700,49 +1141599,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2020.09.30.20204529", - "rel_title": "Projected HIV and Bacterial STI Incidence Following COVID-Related Sexual Distancing and Clinical Service Interruption", - "rel_date": "2020-09-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.30.20204529", - "rel_abs": "BackgroundThe global COVID-19 pandemic has the potential to indirectly impact the transmission dynamics and prevention of HIV and other sexually transmitted infections (STI). Studies have already documented reductions in sexual activity (\"sexual distancing\") and interruptions in HIV/STI services, but it is unknown what combined impact these two forces will have on longer-term HIV/STI epidemic trajectories.\n\nMethodsWe adapted a network-based model of co-circulating HIV, gonorrhea, and chlamydia for a population of men who have sex with men (MSM) in the Atlanta area. Model scenarios varied the timing, overlap, and relative extent of COVID-related sexual distancing in casual and one-time partnership networks and service interruption within four service categories (HIV screening, HIV PrEP, HIV ART, and STI treatment).\n\nResultsA 50% relative decrease in sexual partnerships and interruption of all clinical services, both lasting 18 months, would generally offset each other for HIV (total 5-year population impact for Atlanta MSM: -227 cases), but have net protective effect for STIs (-23,800 cases). Greater relative reductions and longer durations of service interruption would increase HIV and STI incidence, while greater relative reductions and longer durations of sexual distancing would decrease incidence of both. If distancing lasted only 3 months but service interruption lasted 18 months, the total 5-year population impact would be an additional 890 HIV cases and 57,500 STI cases.\n\nConclusionsThe counterbalancing impact of sexual distancing and clinical service interruption depends on the infection and the extent and durability of these COVID-related changes. If sexual behavior rebounds while service interruption persists, we project an excess of hundreds of HIV cases and thousands of STI cases just among Atlanta MSM over the next 5 years. Immediate action to limit the impact of service interruptions is needed to address the indirect effects of the global COVID pandemic on the HIV/STI epidemic.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Samuel M Jenness", - "author_inst": "Emory University" - }, - { - "author_name": "Adrien Le Guillou", - "author_inst": "Emory University" - }, - { - "author_name": "Christina Chandra", - "author_inst": "Emory University" - }, - { - "author_name": "Laura M Mann", - "author_inst": "Emory University" - }, - { - "author_name": "Travis Sanchez", - "author_inst": "Emory University" - }, - { - "author_name": "Daniel Westreich", - "author_inst": "University of North Carolina" - }, - { - "author_name": "Julia L Marcus", - "author_inst": "Harvard Medical School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "hiv aids" - }, { "rel_doi": "10.1101/2020.09.28.20202804", "rel_title": "Mitigating the transmission of infection and death due to SARS-CoV-2 through non-pharmaceutical interventions and repurposing drugs", @@ -1140410,6 +1142266,73 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.09.30.320762", + "rel_title": "Hallmarks of Alpha- and Betacoronavirus non-structural protein 7+8 complexes", + "rel_date": "2020-09-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.30.320762", + "rel_abs": "Coronaviruses infect many different species including humans. The last two decades have seen three zoonotic coronaviruses with SARS-CoV-2 causing a pandemic in 2020. Coronaviral non-structural proteins (nsp) built up the replication-transcription complex (RTC). Nsp7 and nsp8 interact with and regulate the RNA-dependent RNA-polymerase and other enzymes in the RTC. However, the structural plasticity of nsp7+8 complex has been under debate. Here, we present the framework of nsp7+8 complex stoichiometry and topology based on a native mass spectrometry and complementary biophysical techniques of nsp7+8 complexes from seven coronaviruses in the genera Alpha- and Betacoronavirus including SARS-CoV-2. Their complexes cluster into three groups, which systematically form either heterotrimers or heterotetramers or both, exhibiting distinct topologies. Moreover, even at high protein concentrations mainly heterotetramers are observed for SARS-CoV-2 nsp7+8. From these results, the different assembly paths can be pinpointed to specific residues and an assembly model is proposed.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Boris Krichel", + "author_inst": "Heinrich Pette Institute, Leibniz Institute for Experimental Virology" + }, + { + "author_name": "Ganesh Bylapudi", + "author_inst": "Justus Liebig University Giessen" + }, + { + "author_name": "Christina Schmidt", + "author_inst": "European XFEL GmbH" + }, + { + "author_name": "Clement Blanchet", + "author_inst": "EMBL Hamburg" + }, + { + "author_name": "Robin Schubert", + "author_inst": "European XFEL GmbH" + }, + { + "author_name": "Lea Brings", + "author_inst": "European XFEL GmbH" + }, + { + "author_name": "Martin Koehler", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Renato Zenobi", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Dmitri Svergun", + "author_inst": "EMBL Hamburg" + }, + { + "author_name": "Kristina Lorenzen", + "author_inst": "European XFEL GmbH" + }, + { + "author_name": "Ramakanth Madhugiri", + "author_inst": "Justus Liebig University Giessen" + }, + { + "author_name": "John Ziebuhr", + "author_inst": "Justus Liebig University Giessen" + }, + { + "author_name": "Charlotte Uetrecht", + "author_inst": "Heinrich Pette Institute, Leibniz Institute for Experimental Virology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2020.09.29.319061", "rel_title": "BANCOVID, the first D614G variant mRNA-based vaccine candidate against SARS-CoV-2 elicits neutralizing antibody and balanced cellular immune response", @@ -1141758,73 +1143681,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.27.20202655", - "rel_title": "Assessment of Commercial SARS-CoV-2 Antibody Assays, Jamaica", - "rel_date": "2020-09-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.27.20202655", - "rel_abs": "The performance of the Roche Elecsys(R) Anti-SARS-CoV-2, Abbott Architect SARS-CoV-2 IgG, Euroimmun SARS-CoV-2 IgA, Euroimmun SARS-CoV-2 IgG ELISA, and Trillium IgG/IgM rapid assays was evaluated in Jamaica, the largest country of the English-speaking Caribbean. Diagnostic sensitivities of the assays were assessed by testing serum samples from SARS-CoV-2 PCR-confirmed persons. Serum samples collected [≥]14 days after onset of symptoms, or [≥]14 days after an initial SARS-CoV-2 RT-PCR positive test for asymptomatics, showed diagnostic sensitivities ranging from 67.9-75.0% when including all possible disease severities and increased to 90.0-95.0% when examining those with moderate to critical disease. Grouping moderate to critical disease showed a significant association with a SARS-CoV-2 antibody positive result for all assays. Diagnostic specificity, assessed by testing serum samples collected during 2018-2019 from healthy persons and from persons with antibodies to a wide range of viral infections, ranged from 96.7-100.0%. For all assays examined, SARS-CoV-2 real-time PCR cycle threshold (Ct) values of the initial nasopharyngeal swab sample testing positive were significantly different for samples testing antibody positive versus negative. These data from a predominantly African descent Caribbean population shows comparable diagnostic sensitivities and specificities for all testing platforms assessed and limited utility of these tests for persons with asymptomatic and mild infections.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Tiffany R Butterfield", - "author_inst": "The University of the West Indies" - }, - { - "author_name": "Alrica Bruce-Mowatt", - "author_inst": "The University of the West Indies" - }, - { - "author_name": "Yakima Z R Phillips", - "author_inst": "The University of the West Indies" - }, - { - "author_name": "Nicole Brown", - "author_inst": "The University of the West Indies" - }, - { - "author_name": "Keisha Francis", - "author_inst": "The University of the West Indies" - }, - { - "author_name": "Jabari Brown", - "author_inst": "The University of the West Indies" - }, - { - "author_name": "Devon Taylor", - "author_inst": "AstraZeneca" - }, - { - "author_name": "Carl A Bruce", - "author_inst": "The University of the West Indies" - }, - { - "author_name": "Donovan McGrowder", - "author_inst": "The University of the West Indies" - }, - { - "author_name": "Gilian Wharfe", - "author_inst": "The University of the West Indies" - }, - { - "author_name": "Simone L Sandiford", - "author_inst": "The University of the West Indies" - }, - { - "author_name": "Tamara K Thompson", - "author_inst": "The University of the West Indies" - }, - { - "author_name": "Joshua J Anzinger", - "author_inst": "The University of the West Indies" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.27.20202747", "rel_title": "Cardiovascular disease and severe hypoxemia associated with higher rates of non-invasive respiratory support failure in COVID-19", @@ -1142344,6 +1144200,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.09.28.20203083", + "rel_title": "Impact of stopping therapy during the SARS-CoV-2 pandemic in persons with lymphoma", + "rel_date": "2020-09-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.28.20203083", + "rel_abs": "IntroductionThe severe acute respiratory syndrome-2 (SARS-CoV-2) pandemic disrupted medical care for persons with cancer including those with lymphoma. Many professional societies recommend postponing, decreasing or stopping anti-cancer therapy in selected persons during the pandemic. However, although seemingly sensible these recommendations are not evidence-based and their impact on anxiety and health-related quality-of-life (HRQoL) is unknown.\n\nMethodsSurveyed 2532 subjects including 1060 persons with lymphoma, 948 caregivers and 524 normal, uninvolved persons using a purposed-designed questionnaire on a patient organization website. Respondents also completed the Zung Self-Rating Anxiety and patient respondents, the EORTC QLQ-C30 instruments to quantify anxiety and HRQoL. We also evaluated caregiver support and an online education programme of the Chinese Society of Clinical Oncology (CSCO). Data of HRQoL from a 2019 pre-pandemic online survey of 1106 persons with lymphoma was a control.\n\nResults33% (95% Confidence Interval [CI] 30, 36%) of lymphoma patients and 31% (28, 34%) of caregivers but only 21% (17, 24%) of normal individuals had any level of anxiety (both pair-wise P < 0.001). Amongst lymphoma respondents physical exercise and better caregiver support were associated with less anxiety whereas female sex, receiving therapy and reduced therapy intensity were associated with more anxiety. Paradoxically, lymphoma respondents during the pandemic had better HRQoL than pre-pandemic controls. Reduced therapy intensity was associated with worse HRQoL whereas respondents who scored caregiver support and the online patient education programme high had better HRQoL.\n\nConclusionsDuring the SARS-CoV-2 pandemic lymphoma patients and their caregivers had significantly higher incidence of anxiety compared with normals. Lymphoma respondents reported better HRQoL compared with pre-pandemic controls. Reduced therapy-intensity in patients with cancer may have unanticipated adverse effects on anxiety and HRQoL. Regular and intense support by caregivers and online education programmes alleviate anxiety and improve HRQoL.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Shenmiao Yang", + "author_inst": "Peking Univeristy Institute of Hematology" + }, + { + "author_name": "Dong Dong", + "author_inst": "JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, SAR China" + }, + { + "author_name": "Hongfei Gu", + "author_inst": "Chinese lymphoma patients organization, House086, Beijing, China" + }, + { + "author_name": "Robert Peter Gale", + "author_inst": "Haematology Research Centre, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom" + }, + { + "author_name": "Jun Ma", + "author_inst": "Harbin Institute of Hematology & Oncology, Harbin, China." + }, + { + "author_name": "Xiaojun Huang", + "author_inst": "Peking University Peoples Hospital, Peking University Institute of Hematology. National Clinical Research Center for Hematologic Disease, Beijing, China" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "hematology" + }, { "rel_doi": "10.1101/2020.09.29.20203737", "rel_title": "Seroprevalence of SARS CoV-2 antibodies in healthcare workers and administration employees: a prospective surveillance study at a 1,400-bed university hospital in Germany", @@ -1143224,57 +1145119,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.09.29.20203802", - "rel_title": "Temporal Changes in Clinical Practice with COVID-19 Hospitalized Patients: Potential Explanations for Better In-Hospital Outcomes", - "rel_date": "2020-09-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.29.20203802", - "rel_abs": "Background/Aims: We reviewed demographic and clinical profiles, along with measures of hospital-based clinical practice to identify temporal changes in clinical practice that may have affected in-hospital outcomes of patients with COVID-19. Methods: Data consisted of sociodemographic and clinical data captured in University of Pittsburgh Medical Center (UPMC) electronic medical record (EMR) systems, linked by common variables (deidentified). The analysis population included hospitalized patients (across 21 hospitals) with a primary diagnosis of COVID-19 infection during the period March 14-August 31, 2020. The primary outcome was a composite of in-hospital mechanical ventilation/mortality. We compared temporal trends in patient characteristics, clinical practice, and hospital outcomes using 4 time-defined epochs for calendar year 2020: March 14-March 31 (epoch 1); April 1-May 15, (epoch 2), May 16-June 28 (epoch 3); and June 29-August 31 (epoch 4). We report unadjusted survival estimates, followed by propensity score analyses to adjust for differences in patient characteristics, to compare in-hospital outcomes of epoch 4 patients (recently treated) to epoch 1-3 patients (earlier treated). Results: Mean number of hospital admissions was 9.9 per day during epoch 4, which was ~2- to 3-fold higher than the earlier epochs. Presenting characteristics of the 1,076 COVID-19 hospitalized patients were similar across the 4 epochs, including mean age. The crude rate of mechanical ventilation/mortality was lower in epoch 4 patients (17%) than in epoch 1-3 patients (23% to 35%). When censoring for incomplete patient follow-up, the rate of mechanical ventilation/mortality was lower in epoch 4 patients (p<0.0001), as was the individual component of mechanical ventilation (p=0.0002) and mortality (p=0.02). In propensity score adjusted analyses, the in-hospital relative risk (RR) of mechanical ventilation/mortality was lower in epoch 4 patients (RR=0.67, 95% CI: 0.48, 0.93). For the outcome being discharged alive within 3, 5, or 7 days of admission, adjusted odds ranged from 1.6- to 1.7-fold higher among epoch 4 patients compared to earlier treated patients. The better outcomes in epoch 4 patients were principally observed in patients under the age of 75 years. Patient level dexamethasone use was 55.6% in epoch 4 compared to 15% or less of patients in the earlier epochs. Most patients across epochs received anticoagulation drugs (principally heparin). Overall steroid (81.7% vs. 54.3%, p<0.0001) and anticoagulation use (90.4% vs. 80.7%, p=0.0001) was more frequent on the day or day after hospitalization in epoch 4 patients compared to earlier treated patients. Conclusions: In our large system, recently treated hospitalized COVID-19 patients had lower rates of in-hospital mechanical ventilation/mortality and shorter length of hospital stay. Alongside of this was a change to early initiation of glucocorticoid therapy and anticoagulation. The extent to which the improvement in patient outcomes was related to changes in clinical practice remains to be established.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Kevin E Kip", - "author_inst": "University of Pittsburgh Medical Center" - }, - { - "author_name": "Graham Snyder", - "author_inst": "University of Pittsburgh School of Medicine" - }, - { - "author_name": "Donald M Yealy", - "author_inst": "University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center" - }, - { - "author_name": "John W Mellors", - "author_inst": "University of Pittsburgh School of Medicine" - }, - { - "author_name": "Tami Minnier", - "author_inst": "Wolff Center, University of Pittsburgh Medical Center" - }, - { - "author_name": "Michael P Donahoe", - "author_inst": "University of Pittsburgh School of Medicine" - }, - { - "author_name": "Jeffrey McKibben", - "author_inst": "University of Pittsburgh Medical Center" - }, - { - "author_name": "Kevin Collins", - "author_inst": "University of Pittsburgh Medical Center" - }, - { - "author_name": "Oscar C Marroquin", - "author_inst": "University of Pittsburgh Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.26.20202234", "rel_title": "A Multi-center Study of COVID-19 with Multivariate Prognostic Analysis", @@ -1144074,6 +1145918,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.27.20202465", + "rel_title": "Seroprevalence of anti-SARS-CoV-2 IgG at the epidemic peak in French Guiana", + "rel_date": "2020-09-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.27.20202465", + "rel_abs": "Background SARS-CoV-2 seroprevalence studies are crucial for clarifying dynamics in affected countries and determining the route that has already been achieved towards herd immunity. While Latin America has been heavily affected by the pandemic, only a few seroprevalence studies have been conducted there. Methods A cross-sectional survey was performed between 15 July 2020 and 23 July 2020 in 4 medical biology laboratories and 5 health centers of French Guiana, representing a period shortly after the epidemic peak. Samples were screened for the presence of anti-SARS-CoV-2 IgG directed against domain S1 of the SARS-CoV-2 spike protein using the anti-SARS-CoV-2 enzyme-linked immunosorbent assay (ELISA) from Euroimmun. Results The overall seroprevalence was 15.4% [9.3%-24.4%] among 480 participants, ranging from 4.0% to 25.5% across the different municipalities. The seroprevalence did not differ according to gender (p=0.19) or age (p=0.51). Among SARS-CoV-2 positive individuals, we found that 24.6% [11.5%-45.2%] reported symptoms consistent with COVID-19. Conclusions Our findings revealed high levels of infection across the territory but a low number of resulting deaths, which can be explained by the young population structure.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Claude Flamand", + "author_inst": "Epidemiology unit, Institut Pasteur in French Guiana" + }, + { + "author_name": "Antoine Enfissi", + "author_inst": "Laboratory of virology, Institut Pasteur in French Guiana" + }, + { + "author_name": "Sarah Bailly", + "author_inst": "Epidemiology unit, Institut Pasteur in French Guiana" + }, + { + "author_name": "Christelle ALVES SARMENTO", + "author_inst": "Epidemiology unit, Institut Pasteur in French Guiana" + }, + { + "author_name": "Emmanuel Beillard", + "author_inst": "Medical Biology Laboratory, Institut Pasteur in French Guiana" + }, + { + "author_name": "Melanie Gaillet", + "author_inst": "Health Centers Department, Cayenne Hospital Center" + }, + { + "author_name": "Celine Michaud", + "author_inst": "Health Centers Department, Cayenne Hospital Center" + }, + { + "author_name": "Veronique Servas", + "author_inst": "Health Centers Department, Cayenne Hospital Center" + }, + { + "author_name": "Nathalie Clement", + "author_inst": "Clinical Core of the Center for Translational Sciences, Institut Pasteur" + }, + { + "author_name": "Anais Perilhou", + "author_inst": "Clinical Core of the Center for Translational Sciences, Institut Pasteur" + }, + { + "author_name": "Thierry Carage", + "author_inst": "Carage Medical Biology Laboratory" + }, + { + "author_name": "Didier Musso", + "author_inst": "Laboratoires Eurofins Labazur Guyane" + }, + { + "author_name": "Jean-Francois Carod", + "author_inst": "Medical Biology laboratory, Centre Hospitalier Ouest Guyanais" + }, + { + "author_name": "Stephanie Eustache", + "author_inst": "Epidemiology unit, Institut Pasteur in French Guiana" + }, + { + "author_name": "Celine Tourbillon", + "author_inst": "Epidemiology unit, Institut Pasteur in French Guiana" + }, + { + "author_name": "Elodie Boizon", + "author_inst": "Epidemiology unit, Institut Pasteur in French Guiana" + }, + { + "author_name": "Samantha James", + "author_inst": "Epidemiolody unit, Institut Pasteur in French Guiana" + }, + { + "author_name": "Felix Djossou", + "author_inst": "Infectious and Tropical Diseases Unit, Cayenne Hospital Center" + }, + { + "author_name": "Henrik Salje", + "author_inst": "Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS" + }, + { + "author_name": "Simon Cauchemez", + "author_inst": "Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS" + }, + { + "author_name": "Dominique Rousset", + "author_inst": "Laboratory of Virology, Institut Pasteur in French Guiana" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.26.20189522", "rel_title": "Clinical Course And Risk Factors For In-hospital Death In Critical COVID-19 In Wuhan, China", @@ -1144862,57 +1146805,6 @@ "type": "new results", "category": "animal behavior and cognition" }, - { - "rel_doi": "10.1101/2020.09.28.316448", - "rel_title": "Impact of COVID-19 on Hospital Admission of Acute Stroke patients in Bangladesh", - "rel_date": "2020-09-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.28.316448", - "rel_abs": "BackgroundWith the proposed pathophysiologic mechanism of neurologic injury by SARS COV-2 the frequency of stroke and henceforth the related hospital admissions were expected to rise. In this paper we investigate this presumption by comparing the frequency of admissions of stroke cases in Bangladesh before and during the pandemic.\n\nMethodsWe conducted a retrospective analysis of stroke admissions in a 100-bed stroke unit at the National Institute of Neurosciences and Hospital (NINS&H) which is considerably a large stroke unit. We considered all the admitted cases from the 1st January to the 30th June, 2020. We used Poisson regressions to determine whether statistically significant changes in admission counts can be found before and after 25 March since when there is a surge in COVID-19 infections.\n\nResultsA total of 1394 stroke patients got admitted during the study period. Half of the patients were older than 60 years, whereas only 2.6% were 30 years old or younger with a male-female ratio of 1.06:1. From January to March, 2020 the mean rate of admission was 302.3 cases per month which dropped to 162.3 cases per month from April to June with an overall reduction of 46.3% in acute stroke admission per month. In those two periods, reductions in average admission per month for ischemic stroke (IST), intracerebral hemorrhage (ICH), subarachnoid hemorrhage (SAH) and venous stroke (VS) were 45.5%, 37.2%, 71.4% and 39.0%, respectively. Based on weekly data, results of Poisson regressions confirm that the average number of admissions per week dropped significantly during the last three months of the sample period. Further, in the first three months, a total of 22 cases of hyperacute stroke management were done whereas in the last three months there was an 86.4% reduction in the number of hyperacute stroke patients getting reperfusion treatment. Only 38 patients (2.7%) were later found to be RT- PCR for SARS Cov-2 positive based on nasal swab testing.\n\nConclusionOur study revealed more than fifty percent reduction in acute stroke admission during the COVID-19 pandemic. It is still elusive whether the reduction is related to the fear of getting infected by COVID-19 from hospitalization or the overall restriction on public movement and stay-home measures.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "A T M Hasibul Hasan", - "author_inst": "National Institute of Neurosciences & Hospital" - }, - { - "author_name": "Subir Chandra Das", - "author_inst": "National Institute of Neurosciences & Hospital" - }, - { - "author_name": "Muhammad Sougatul Islam", - "author_inst": "BioTED" - }, - { - "author_name": "Mohaimen Mansur", - "author_inst": "Institute of Statistical Research and Training" - }, - { - "author_name": "Md Shajedur Rahman Shawon", - "author_inst": "Center for Big Data Research in Health" - }, - { - "author_name": "Rashedul Hassan", - "author_inst": "Green Life Medical College and Hospital" - }, - { - "author_name": "Mohammad Shah Jahirul Hoque Chowdhury", - "author_inst": "National Institute of Neurosciences & Hospital" - }, - { - "author_name": "Md Badrul Alam Mondal", - "author_inst": "National Institute of Neurosciences & Hospital" - }, - { - "author_name": "Quazi Deen Mohammad", - "author_inst": "National Institute of Neurosciences & Hospital" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "neuroscience" - }, { "rel_doi": "10.1101/2020.09.25.20198986", "rel_title": "Influence of COVID-19 confinement measures on appendectomies in Germany - administrative claims data analysis of 9,797 patients", @@ -1145532,6 +1147424,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "endocrinology" }, + { + "rel_doi": "10.1101/2020.09.25.20201939", + "rel_title": "INFERRED RESOLUTION THROUGH HERD IMMMUNITY OF FIRST COVID-19 WAVE IN MANAUS, BRAZILIAN AMAZON", + "rel_date": "2020-09-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.25.20201939", + "rel_abs": "INTRODUCTORY PARAGRAPHAs in many other settings, peak excess mortality preceded the officially reported first wave peak of the COVID-19 epidemic in Manaus, Brazil, reflecting delayed case recognition and limited initial access to diagnostic testing. To avoid early information bias, we used detailed age and gender stratified death certificate and hospitalisation data to evaluate the epidemics trajectory and infer the cause of its decline using a stochastic model. Our results are consistent with heterogenous transmission reducing over time due to the development of herd immunity. Relative to a baseline model that assumed homogenous mixing across Manaus, a model that permitted a small, self-isolated population fraction raised the estimated herd-immunity threshold from 28% to 30% and reduced the final attack rate from 86% to 65%. In the latter scenario, a substantial proportion of vulnerable, older individuals remained susceptible to infection. Given uncertainties regarding the distancing behaviours of population subgroups with different social and economic characteristics, and the duration of sterilising or transmission-modifying immunity in exposed individuals, we conclude that the potential for epidemic outbreaks remains, but that future waves of infection are likely to be much less pronounced than that already experienced.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Thomas Prowse", + "author_inst": "University of Adelaide" + }, + { + "author_name": "Tara Purcell", + "author_inst": "The University of Melbourne and Royal Melbourne Hospital" + }, + { + "author_name": "Djane Clarys Baia-da-Silva", + "author_inst": "Fundacao de Medicina Tropical Dr Heitor Vieira Dourado" + }, + { + "author_name": "Vanderson Sampaio", + "author_inst": "Fundacao de Vigilancia em Saude; Fundacao de Medicina Tropical Dr Heitor Vieira Dourado" + }, + { + "author_name": "Wuelton Marcelo Monteiro", + "author_inst": "Universidade do Estado do Amazonas; Fundacao de Medicina Tropical Dr Heitor Vieira Dourado" + }, + { + "author_name": "James Wood", + "author_inst": "UNSW" + }, + { + "author_name": "Ivo Mueller", + "author_inst": "Walter + Eliza Hall Institute, Univ. of Melbourne, and Institut Pasteur" + }, + { + "author_name": "Jodie McVernon", + "author_inst": "The University of Melbourne, Murdoch Childrens Research Institute" + }, + { + "author_name": "Marcus Lacerda", + "author_inst": "Fundacao de Medicina Tropical Dr. Heitor Vieira Dourado" + }, + { + "author_name": "Joshua Ross", + "author_inst": "University of Adelaide" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.25.20201582", "rel_title": "Airway emergency management in a pediatric hospital before and during the COVID-19 pandemic", @@ -1146336,49 +1148283,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.23.20200030", - "rel_title": "Epidemiological characterization of symptomatic and asymptomatic COVID-19 cases and positivity in subsequent RT-PCR tests in the United Arab Emirates", - "rel_date": "2020-09-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.23.20200030", - "rel_abs": "BackgroundThe COVID-19 RT-PCR confirmed cases could be symptomatic or asymptomatic. In the United Arab Emirates (UAE), the identified COVID-19 RT-PCR confirmed cases are yet to be characterized. In this study, we characterized the first cohort of COVID-19 RT-PCR confirmed cases reported in the Abu Dhabi Emirate, UAE, according to symptomatic state, and identified factors associated with the symptomatic state. Also, the strength of association between the symptomatic state and testing positive in three subsequent RT-PCR testing rounds was examined and quantified.\n\nMethodWe analyzed data collected from the first cohort of the RT-PCR confirmed COVID-19 cases reported to the health authorities in the Abu Dhabi Emirate - UAE between February 28 and April 08, 2020. Self-reported sociodemographic, working status, travel history, and chronic comorbidities of 1,249 COVID-19 cases were analyzed according to symptomatic state (symptomatic and asymptomatic). After the first RT-PCR confirmatory test, the results of three subsequent testing rounds were also analyzed.\n\nResultsA total of 791 confirmed cases with a mean age of 35.6 years{+/-}12.7 (range: 1-81 years) and information on symptomatic state were analyzed. Nearly, 56.0% were asymptomatic cases. The most frequent two symptoms were fever (58.0%) and cough (41.0%). The mean age of symptomatic (36.3 year {+/-}12.6SD) was significantly higher than that of asymptomatic cases (34.5 year {+/-}12.7SD). Compared to non-working populations, working in public places (aOR, 1.76, 95% CI: 1.11-2.80), healthcare settings (aOR, 2.09, 95% CI: 1.01-4.31), or in aviation and tourism sector (aOR, 2.24, 95% CI: 1.14-4.40), were independently associated with symptomatic state. Reporting at least one chronic comorbidity was also associated with symptomatic cases (aOR, 1.76, 5% CI: 1.03-3.01). Compared to asymptomatic, symptomatic COVID-19 cases had consistent odds of two or more of testing positive to COVID-19 in three subsequent testing rounds.\n\nConclusionsA substantial proportion of the diagnosed COVID-19 cases in the Abu Dhabi Emirate was asymptomatic. Quarantine of asymptomatic cases along with prevention measures and raising awareness of populations working in high-risk settings is warranted. Further follow up research is needed to understand viral clearance and clinical outcomes according to the symptomatic state of the COVID-19 cases.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Rami H. Al-Rifai", - "author_inst": "United Arab Emirates University" - }, - { - "author_name": "Juan Acuna", - "author_inst": "Khalifa University" - }, - { - "author_name": "Farida Ismail Al Hossany", - "author_inst": "Abu Dhabi Public Health Center" - }, - { - "author_name": "Bashir Aden", - "author_inst": "Abu Dhabi Public Health Center" - }, - { - "author_name": "Shamma Abdullah Al Memari", - "author_inst": "Abu Dhabi Public Health Center" - }, - { - "author_name": "Shereena Khamis Al Mazrouei", - "author_inst": "Abu Dhabi Public Health Center" - }, - { - "author_name": "Luai A. Ahmed", - "author_inst": "United Arab Emirates University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.24.20200337", "rel_title": "Title: Risk factors for severe disease in patients admitted with COVID-19 to a hospital in London, England: a retrospective cohort study", @@ -1147330,6 +1149234,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.09.23.20200006", + "rel_title": "FeverIQ - A Privacy-Preserving COVID-19 SymptomTracker with 3.6 Million Reports", + "rel_date": "2020-09-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.23.20200006", + "rel_abs": "Population-scale COVID-19 management benefits from timely and honest information from billions of people. Here, we provide a first report on the FeverIQ symptom tracker, a global effort to collect symptom and test data which has received more than 3.6 million submissions. Unlike other trackers, FeverIQ uses secure multiparty computation (SMC) to cryptographically guarantee user privacy while providing insights to scientists and public health efforts. We performed basic integrity checks of the FeverIQ dataset, such as by comparing it to other publicly released data. We then trained a linear classifier on diagnosis scores which were computed securely, without unprotected symptom data ever leaving a users phone or computer. FeverIQ is currently the worlds largest application of SMC in a health context, demonstrating the practicality of privacy-preserving analytics for population-scale digital health interventions.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Ankit Ranjan", + "author_inst": "Nuffield Department of Surgical Sciences, University of Oxford" + }, + { + "author_name": "Serena Li", + "author_inst": "Henry M. Gunn High School" + }, + { + "author_name": "Boyuan Chen", + "author_inst": "Enya Inc." + }, + { + "author_name": "Alan Chiu", + "author_inst": "Enya Inc." + }, + { + "author_name": "Karthik Jagadeesh", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Jan Liphardt", + "author_inst": "Department of Bioengineering, Stanford University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.09.24.20200782", "rel_title": "Risk assessment of COVID-19 airborne infection during hybrid learning", @@ -1148106,45 +1150049,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2020.09.24.20200238", - "rel_title": "EXTENDING THE SUSCEPTIBLE-EXPOSED-INFECTED-REMOVED(SEIR) MODEL TO HANDLE THE HIGH FALSE NEGATIVE RATE AND SYMPTOM-BASED ADMINISTRATION OF COVID-19 DIAGNOSTIC TESTS: SEIR-fansy", - "rel_date": "2020-09-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.24.20200238", - "rel_abs": "The false negative rate of the diagnostic RT-PCR test for SARS-CoV-2 has been reported to be substantially high. Due to limited availability of testing, only a non-random subset of the population can get tested. Hence, the reported test counts are subject to a large degree of selection bias. We consider an extension of the Susceptible-Exposed-Infected-Removed (SEIR) model under both selection bias and misclassification. We derive closed form expression for the basic reproduction number under such data anomalies using the next generation matrix method. We conduct extensive simulation studies to quantify the effect of misclassification and selection on the resultant estimation and prediction of future case counts. Finally we apply the methods to reported case-death-recovery count data from India, a nation with more than 5 million cases reported over the last seven months. We show that correcting for misclassification and selection can lead to more accurate prediction of case-counts (and death counts) using the observed data as a beta tester. The model also provides an estimate of undetected infections and thus an under-reporting factor. For India, the estimated under-reporting factor for cases is around 21 and for deaths is around 6. We develop an R-package (SEIRfansy) for broader dissemination of the methods.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Ritwik Bhaduri", - "author_inst": "Indian Statistical Institute" - }, - { - "author_name": "Ritoban Kundu", - "author_inst": "Indian Statistical Institute" - }, - { - "author_name": "Soumik Purkayastha", - "author_inst": "University of Michigan" - }, - { - "author_name": "Mike Kleinsasser", - "author_inst": "University of Michigan" - }, - { - "author_name": "Lauren J Beesley", - "author_inst": "University of Michigan" - }, - { - "author_name": "Bhramar Mukherjee", - "author_inst": "University of Michigan" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.24.20200386", "rel_title": "Accessioning and automation compatible anterior nares swab design", @@ -1149060,6 +1150964,65 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.09.25.313270", + "rel_title": "SARS-CoV-2 and Malayan pangolin coronavirus infect human endoderm, ectoderm and induced lung progenitor cells", + "rel_date": "2020-09-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.25.313270", + "rel_abs": "Since the infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in several somatic cells, little is known about the infection of SASRS-CoV-2 and its related pangolin coronavirus (GX_P2V). Here we present for the first time that SARS-CoV-2 pseudovirus and GX_P2V could infect lung progenitor and even anterior foregut endoderm cells causing these cells death, which differentiated from human embryonic stem cells (hESCs). The infection and replication of SARS-CoV-2 and GX_P2V were inhibited when treated with whey protein of breastmilk and Remdesivir, confirming that these two viruses could infect lung progenitor and even anterior foregut endoderm. Moreover, we found that SARS-CoV-2 pseudovirus could infect endoderm and ectoderm. We found that whey protein blocked SARS-CoV-2 infecting these cells. In line with the SARS-CoV-2 results, GX_P2V could also infected endoderm and ectoderm, and also was inhibited by Remdesivir treatment. Although expressing coronavirus related receptor such as ACE2 and TMPRSS2, mesoderm cells are not permissive for SARS-CoV-2 and GX_P2V infection, which needed further to study the mechanisms. Interestingly, we also found that hESCs, which also express ACE2 and TMPRSS2 markers, are permissive for GX_P2V but not SARS-CoV-2 pseudovirus infection and replication, indicating the widespread cell types for GX_P2V infection. Heparin treatment blocked efficiently viral infection. These results provided insight that these stem cells maybe provided a stable repository of coronavirus function or genome. The potential consequence of SARS-CoV-2 and animal coronavirus such as GX_P2V infection in hESCs, germ layer and induced progenitors should be closely monitored.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Kuanhui Xiang", + "author_inst": "Peking University Health Science Center" + }, + { + "author_name": "Bixia Hong", + "author_inst": "Beijing University of Chemical Technology" + }, + { + "author_name": "Xinyuan Lai", + "author_inst": "Peking University Health Science Center" + }, + { + "author_name": "Yangzhen Chen", + "author_inst": "Beijing University of Chemical Technology" + }, + { + "author_name": "Tianming Luo", + "author_inst": "Peking University Health Science Center" + }, + { + "author_name": "Xiaoping An", + "author_inst": "Beijing University of Chemical Technology" + }, + { + "author_name": "Lihua Song", + "author_inst": "Beijing University of Chemical Technology" + }, + { + "author_name": "Hui Zhuang", + "author_inst": "Peking University Health Science Center" + }, + { + "author_name": "Huahao Fan", + "author_inst": "Beijing University of Chemical Technology" + }, + { + "author_name": "Tong Li", + "author_inst": "Peking University Health Science Center" + }, + { + "author_name": "Yi-Gang Tong", + "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P. R. China" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.09.25.313148", "rel_title": "Rapid behavioral response of urban birds to covid-19 lockdown", @@ -1149900,69 +1151863,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2020.09.24.312298", - "rel_title": "Functional genomic screens identify human host factors for SARS-CoV-2 and common cold coronaviruses", - "rel_date": "2020-09-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.24.312298", - "rel_abs": "The Coronaviridae are a family of viruses that causes disease in humans ranging from mild respiratory infection to potentially lethal acute respiratory distress syndrome. Finding host factors that are common to multiple coronaviruses could facilitate the development of therapies to combat current and future coronavirus pandemics. Here, we conducted parallel genome-wide CRISPR screens in cells infected by SARS-CoV-2 as well as two seasonally circulating common cold coronaviruses, OC43 and 229E. This approach correctly identified the distinct viral entry factors ACE2 (for SARS-CoV-2), aminopeptidase N (for 229E) and glycosaminoglycans (for OC43). Additionally, we discovered phosphatidylinositol phosphate biosynthesis and cholesterol homeostasis as critical host pathways supporting infection by all three coronaviruses. By contrast, the lysosomal protein TMEM106B appeared unique to SARS-CoV-2 infection. Pharmacological inhibition of phosphatidylinositol phosphate biosynthesis and cholesterol homeostasis reduced replication of all three coronaviruses. These findings offer important insights for the understanding of the coronavirus life cycle as well as the potential development of host-directed therapies.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Ruofan Wang", - "author_inst": "Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA" - }, - { - "author_name": "Camille R. Simoneau", - "author_inst": "Gladstone Institutes, San Francisco, CA 94158, USA" - }, - { - "author_name": "Jessie Kulsuptrakul", - "author_inst": "Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA" - }, - { - "author_name": "Mehdi Bouhaddou", - "author_inst": "Gladstone Institutes, San Francisco, CA 94158, USA" - }, - { - "author_name": "Katherine Travisano", - "author_inst": "Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA" - }, - { - "author_name": "Jennifer M. Hayashi", - "author_inst": "Gladstone Institutes, San Francisco, CA 94158, USA" - }, - { - "author_name": "Jared Carlson-Stevermer", - "author_inst": "Synthego Corporation, Menlo Park, CA 94025" - }, - { - "author_name": "Jennifer Oki", - "author_inst": "Synthego Corporation, Menlo Park, CA 94025" - }, - { - "author_name": "Kevin Holden", - "author_inst": "Synthego Corporation, Menlo Park, CA 94025" - }, - { - "author_name": "Nevan J. Krogan", - "author_inst": "Gladstone Institutes, San Francisco, CA 94158, USA" - }, - { - "author_name": "Melanie Ott", - "author_inst": "Gladstone Institutes, San Francisco, CA 94158, USA" - }, - { - "author_name": "Andreas S Puschnik", - "author_inst": "Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.09.24.312355", "rel_title": "A vaccine built from potential immunogenic pieces derived from the SARS-CoV-2 spike glycoprotein", @@ -1150850,6 +1152750,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.21.20198796", + "rel_title": "Dynamic Change of COVID-19 Seroprevalence among Asymptomatic Population in Tokyo during the Second Wave", + "rel_date": "2020-09-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.21.20198796", + "rel_abs": "ImportanceFatality rates related to COVID-19 in Japan have been low compared to Western Countries and have decreased despite the absence of lockdown. Serological tests monitored across the course of the second wave can provide insights into the population-level prevalence and dynamic patterns of COVID-19 infection.\n\nObjectiveTo assess changes in COVID-19 seroprevalence among asymptomatic employees working in Tokyo during the second wave.\n\nDesignWe conducted an observational cohort study. Healthy volunteers working for a Japanese company in Tokyo were enrolled from disparate locations to determine seropositivity against COVID19 from May 26 to August 25, 2020. COVID-19 IgM and IgG antibodies were determined by a rapid COVID19 IgM/IgG test kit using fingertip blood. Across the company, tests were performed and acquired weekly. For each participant, serology tests were offered twice, separated by approximately a month, to provide self-reference of test results and to assess for seroconversion and seroreversion.\n\nSettingWorkplace setting within a large company.\n\nParticipantsHealthy volunteers from 1877 employees of a large Japanese company were recruited to the study from 11 disparate locations across Tokyo. Participants having fever, cough, or shortness of breath at the time of testing were excluded.\n\nMain Outcome(s) and Measure(s)Seropositivity rate (SPR) was calculated by pooled data from each two-weeks window across the cohort. Either IgM or IgG positivity was defined as seropositive. Changes in immunological status against SARS-CoV-2 were determined by comparing results between two tests obtained from the same individual.\n\nResultsSix hundred fifteen healthy volunteers (mean + SD 40.8 + 10.0; range 19 - 69; 45.7 % female) received at least one test. Seroprevalence increased from 5.8 % to 46.8 % over the course of the summer. The most dramatic increase in SPR occurred in late June and early July, paralleling the rise in daily confirmed cases within Tokyo, which peaked on August 4. Out of the 350 individuals (mean + SD 42.5 + 10.0; range 19 - 69; 46.0 % female) who completed both offered tests, 21.4 % of those individuals who tested seronegative became seropositive and seroreversion was found in 12.2 % of initially seropositive participants. 81.1% of IgM positive cases at first testing became IgM negative in approximately one month.\n\nConclusions and RelevanceCOVID-19 infection may have spread widely across the general population of Tokyo despite the very low fatality rate. Given the temporal correlation between the rise in seropositivity and the decrease in reported COVID-19 cases that occurred without a shut-down, herd immunity may be implicated. Sequential testing for serological response against COVID-19 is useful for understanding the dynamics of COVID-19 infection at the population-level.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Sawako Hibino", + "author_inst": "Y's Science Clinic Hiroo, Medical Corporation Koshikai" + }, + { + "author_name": "Kazutaka Hayashida", + "author_inst": "Boston children's hospital" + }, + { + "author_name": "Andrew C Ahn", + "author_inst": "Beth Israel Deaconess Medical School" + }, + { + "author_name": "Yasutaka Hayashida", + "author_inst": "Y's Science Clinic Hiroo, Medical Corporation Koshikai" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.22.20199497", "rel_title": "An analysis of clinical and geographical metadata of over 75,000 records in the GISAID COVID-19 database", @@ -1151654,121 +1153585,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.21.20199109", - "rel_title": "Nature and dimensions of the cytokine storm and its attenuation by convalescent plasma in severe COVID-19", - "rel_date": "2020-09-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.21.20199109", - "rel_abs": "In a randomized control trial on convalescent plasma therapy (CPT) in severe COVID-19, we characterized the nature, in terms of abundance of forty eight cytokines, and dimensions, in terms of their interrelationships, of the hyper-immune activation-associated cytokine storm in patients suffering from acute respiratory distress syndrome. We found reduced plasma level of the chemokine MCP3 to be a key correlate for clinical improvement, irrespective of therapeutic regimen. We also identified an anti-inflammatory role of CPT independent of its neutralizing antibody content, and a linear regression analysis revealed that neutralizing antibodies as well as the anti-inflammatory effect of CPT both contribute to marked immediate reductions in hypoxia, as compared to patients on standard therapy.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Purbita Bandopadhyay", - "author_inst": "CSIR-Indian Institute of Chemical Biology" - }, - { - "author_name": "Ranit D'Rozario", - "author_inst": "CSIR-Indian Institute of Chemical Biology" - }, - { - "author_name": "Abhishake Lahiri", - "author_inst": "CSIR-Indian Institute of Chemical Biology" - }, - { - "author_name": "Jafar Sarif", - "author_inst": "CSIR-Indian Institute of Chemical Biology" - }, - { - "author_name": "Yogiraj Ray", - "author_inst": "ID & BG Hospital" - }, - { - "author_name": "Shekhar Ranjan Paul", - "author_inst": "ID & BG Hospital" - }, - { - "author_name": "Rammohan Roy", - "author_inst": "ID & BG Hospital" - }, - { - "author_name": "Rajsekhar Maiti", - "author_inst": "ID & BG Hospital" - }, - { - "author_name": "Kausik Chaudhuri", - "author_inst": "ID & BG Hospital" - }, - { - "author_name": "Sougata Bagchi", - "author_inst": "ID & BG Hospital" - }, - { - "author_name": "Ayan Maiti", - "author_inst": "ID & BG Hospital" - }, - { - "author_name": "Md. Masoom Parwez", - "author_inst": "ID & BG Hospital" - }, - { - "author_name": "Biswanath Sharma Sarkar", - "author_inst": "ID & BG Hospital" - }, - { - "author_name": "Devlina Roy", - "author_inst": "ID & BG Hospital" - }, - { - "author_name": "Rahul Chakraborty", - "author_inst": "ID & BG Hospital" - }, - { - "author_name": "Janani Srinivasa Vasudevan", - "author_inst": "CSIR-Institute of Genomics & Integrative Biology" - }, - { - "author_name": "Sachin Sharma", - "author_inst": "CSIR-Institute of Genomics & Integrative Biology" - }, - { - "author_name": "Durba Biswas", - "author_inst": "Medical College Hospital" - }, - { - "author_name": "Chikam Maiti", - "author_inst": "Medical College Hospital" - }, - { - "author_name": "Bibhuti Saha", - "author_inst": "School of Tropical Medicine" - }, - { - "author_name": "Prasun Bhattacharya", - "author_inst": "Medical College Hospital" - }, - { - "author_name": "Rajesh Pandey", - "author_inst": "CSIR-Institute of Genomics & Integrative Biology" - }, - { - "author_name": "Shilpak Chatterjee", - "author_inst": "CSIR-Indian Institute of Chemical Biology" - }, - { - "author_name": "Sandip Paul", - "author_inst": "CSIR-Indian Institute of Chemical Biology" - }, - { - "author_name": "Dipyaman Ganguly", - "author_inst": "CSIR-Indian Institute of Chemical Biology" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.20.20198192", "rel_title": "Panbio antigen rapid test is reliable to diagnose SARS-CoV-2 infection in the first 7 days after the onset of symptoms", @@ -1152632,6 +1154448,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.20.20197368", + "rel_title": "Modelling the risk of SARS-CoV-2 infection through PPE doffing in a hospital environment", + "rel_date": "2020-09-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.20.20197368", + "rel_abs": "Self-contamination during doffing of personal protective equipment (PPE) is a concern for healthcare workers (HCW) following SARS-CoV-2 positive patient care. Staff may subconsciously become contaminated through improper glove removal, so quantifying this risk is critical for safe working procedures. HCW surface contact sequences on a respiratory ward were modelled using a discrete-time Markov chin for: IV-drip care, blood pressure monitoring and doctors' rounds. Accretion of viral RNA on gloves during care was modelled using a stochastic recurrence relation. The HCW then doffed PPE and contaminated themselves in a fraction of cases based on increasing case load. The risk of infection from this exposure was quantified using a dose-response methodology. A parametric study was conducted to analyse the effect of: 1a) increasing patient numbers on the ward, 1b) the proportion of COVID-19 cases, 2) the length of a shift and 3) the probability of touching contaminated PPE. The driving factors for infection risk were surface contamination and number of surface contacts. HCWs on a 100% COVID-19 ward were less than 2-fold more at risk than on a 50% COVID ward (1.6% vs 1%), whilst on a 5% COVID-19 ward, the risk dropped to 0.1% per shift (sd=0.6%). IV-drip care resulted in higher risk than blood pressure monitoring (1.1% vs 1% p<0.0001), whilst doctors' rounds produced a 0.6% risk (sd=0.8%). Recommendations include supervised PPE doffing procedures such as the \"doffing buddy\" scheme, maximising hand hygiene compliance post-doffing and targeted surface cleaning for surfaces away from the patient vicinity.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Marco-Felipe King", + "author_inst": "University of Leeds" + }, + { + "author_name": "Amanda Marie Wilson", + "author_inst": "University of Arizona" + }, + { + "author_name": "Mark H Weir", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Martin Lopez-Garcia", + "author_inst": "University of Leeds" + }, + { + "author_name": "Jessica Proctor", + "author_inst": "University of Leeds" + }, + { + "author_name": "Waseem Hiwar", + "author_inst": "University of Leeds" + }, + { + "author_name": "Amirul Khan", + "author_inst": "University of Leeds" + }, + { + "author_name": "Louise A Fletcher", + "author_inst": "University of Leeds" + }, + { + "author_name": "P Andrew Sleigh", + "author_inst": "University of Leeds" + }, + { + "author_name": "Ian Clifton", + "author_inst": "Leeds Cystic Fibrosis Trust Strategic Research Centre" + }, + { + "author_name": "Stephanie Jane Dancer", + "author_inst": "Hairmyres Hospital" + }, + { + "author_name": "Mark H. Wilcox", + "author_inst": "eLeeds Teaching Hospital & University of Leeds" + }, + { + "author_name": "Kelly A. Reynolds", + "author_inst": "University of Arizona" + }, + { + "author_name": "Catherine J Noakes", + "author_inst": "University of Leeds" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.09.11.20193029", "rel_title": "Covid-19 Cases in India: A Visual Exploratory Data Analysis Model", @@ -1153600,41 +1155487,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.22.20196048", - "rel_title": "College Openings, Mobility, and the Incidence of COVID-19 Cases", - "rel_date": "2020-09-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.22.20196048", - "rel_abs": "School and college reopening-closure policies are considered one of the most promising non-pharmaceutical interventions for mitigating infectious diseases. Nonetheless, the effectiveness of these policies is still debated, largely due to the lack of empirical evidence on behavior during implementation. We examined U.S. college reopenings association with changes in human mobility within campuses and in COVID-19 incidence in the counties of the campuses over a twenty-week period around college reopenings in the Fall of 2020. We used an integrative framework, with a difference-in-differences design comparing areas with a college campus, before and after reopening, to areas without a campus and a Bayesian approach to estimate the daily reproductive number (Rt). We found that college reopenings were associated with increased campus mobility, and increased COVID-19 incidence by 3.4 cases per 100,000 (95% confidence interval [CI]: 1.5 - 5.4), or a 25% increase relative to the pre-period mean. This reflected our estimate of increased transmission locally after reopening. A greater increase in county COVID-19 incidence resulted from campuses that drew students from counties with high COVID-19 incidence in the weeks before reopening ({chi}2(2) = 10.19, p = 0.006). Even by Fall of 2021, large shares of populations remained unvaccinated, increasing the relevance of understanding non-pharmaceutical decisions over an extended period of a pandemic. Our study sheds light on movement and social mixing patterns during the closure-reopening of colleges during a public health threat, and offers strategic instruments for benefit-cost analyses of school reopening/closure policies.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Martin S Andersen", - "author_inst": "University of North Carolina at Greensboro" - }, - { - "author_name": "Ana I Bento", - "author_inst": "Indiana University" - }, - { - "author_name": "Anirban Basu", - "author_inst": "University of Washington" - }, - { - "author_name": "Chris Marsicano", - "author_inst": "Davidson College" - }, - { - "author_name": "Kosali Simon", - "author_inst": "Indiana University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.09.23.20190090", "rel_title": "Short-term Neuropsychiatric Outcomes and Quality of Life in COVID-19 Survivors", @@ -1154326,6 +1156178,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.21.20199018", + "rel_title": "Epidemiology of COVID-19 vs. Influenza: Differential Failure of COVID-19 Mitigation among Hispanics", + "rel_date": "2020-09-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.21.20199018", + "rel_abs": "BACKGROUNDDuring the early phases of the COVID-19 pandemic, predominantly African-American or Hispanic communities were disproportionately impacted. We sought to better understand the epidemiology of COVID-19 among hospitalized Hispanic patients by comparing individual and census-tract level characteristics of patients diagnosed with COVID-19 to those diagnosed with influenza, another viral infection with respiratory transmission. We evaluated the temporal changes in epidemiology across race-ethnicity related to a shelter-in-place mandate.\n\nMETHODSWe evaluated patients hospitalized at Cook County Health, the safety-net health system for the Chicago metropolitan area. Among self-identified hospitalized Hispanic patients, we compared those with influenza (2019-2020 influenza season) to COVID-19 infection during March 16, 2020 through May 11, 2020. We used multivariable analysis to identify differences in individual and census-tract level characteristics between the two groups.\n\nRESULTSRelative to non-Hispanic blacks and whites, COVID-19 rapidly increased among Hispanics during promotion of social-distancing policies. Whereas non-Hispanic blacks were more likely to be hospitalized for influenza, Hispanic patients predominated among COVID-19 infections (40% relative increase compared to influenza). In the comparative analysis of influenza and COVID-19, Hispanic patients with COVID-19 were more likely to reside in census tracts with higher proportions of residents with the following characteristics: Hispanic; no high school diploma; non-US citizen; limited English speaking ability; employed in manufacturing or construction; and, overcrowding. By multivariable analysis, Hispanic patients hospitalized with COVID-19 compared to those with influenza were more likely to be male (adjusted OR=1.8; 95% CI 1.1 to 2.9) or obese (aOR=2.5; 95% CI 1.5 to 4.2), and to reside in a census tract with [≥]40% of residents without a high-school diploma (aOR=2.5; 95% CI 1.3 to 4.8).\n\nCONCLUSIONSThe rapid and disproportionate increase in COVID-19 hospitalizations among Hispanics after the shelter-in-place mandate indicates that public health strategies were inadequate in protecting this population. In particular, those residing in neighborhoods with lower levels of educational attainment.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "William E Trick", + "author_inst": "Cook County Health" + }, + { + "author_name": "Sheila Badri", + "author_inst": "Cook County Health" + }, + { + "author_name": "Kruti Doshi", + "author_inst": "Cook County Health" + }, + { + "author_name": "Huiyuan Zhang", + "author_inst": "Cook County Health" + }, + { + "author_name": "Katayoun Rezai", + "author_inst": "Cook County Health" + }, + { + "author_name": "Michael J Hoffman", + "author_inst": "Cook County Health" + }, + { + "author_name": "Robert A Weinstein", + "author_inst": "Cook County Health and Rush University Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.09.19.20198051", "rel_title": "COVID-19: Risks of Re-emergence, Re-infection, and Control Measures -- A Long Term Modelling Study", @@ -1155226,61 +1157121,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.22.20199489", - "rel_title": "Aerosol transmission of COVID-19 and infection risk in indoor environments", - "rel_date": "2020-09-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.22.20199489", - "rel_abs": "The role of aerosolized SARS-CoV-2 viruses in airborne transmission of COVID-19 is debated. The transmitting aerosol particles are generated through the breathing and vocalization by infectious subjects. Some authors state that this represents the dominant route of spreading, while others dismiss the option. Public health organizations generally categorize it as a secondary transmission pathway. Here we present a simple, easy-to-use spreadsheet algorithm to estimate the infection risk for different indoor environments, constrained by published data on human aerosol emissions, SARS-CoV-2 viral loads, infective dose and other parameters. We evaluate typical indoor settings such as an office, a classroom, a choir practice room and reception/party environments. These are examples, and the reader is invited to use the algorithm for alternative situations and assumptions. Our results suggest that aerosols from highly infective subjects can effectively transmit COVID-19 in indoor environments. This \"highly infective\" category represents about one fifth of the patients tested positive for SARS-CoV-2. We find that \"super infective\" subjects, representing the top few percent of positive-tested ones, plus an unknown fraction of less, but still highly infective, high aerosol-emitting subjects, may cause COVID-19 clusters (>10 infections), e.g. in classrooms, during choir singing and at receptions. The highly infective ones also risk causing such events at parties, for example. In general, active room ventilation and the ubiquitous wearing of face masks (i.e. by all subjects) may reduce the individual infection risk by a factor of five to ten, similar to high-volume HEPA air filtering. The most effective mitigation measure studied is the use of high-quality masks, which can drastically reduce the indoor infection risk through aerosols.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Jos Lelieveld", - "author_inst": "Max Planck Institute for Chemistry" - }, - { - "author_name": "Frank Helleis", - "author_inst": "Max Planck Institute for Chemistry" - }, - { - "author_name": "Stephan Borrmann", - "author_inst": "Max Planck Institute for Chemistry" - }, - { - "author_name": "Yafang Cheng", - "author_inst": "Max Planck Institute for Chemistry" - }, - { - "author_name": "Frank Drewnick", - "author_inst": "Max Planck Institute for Chemistry" - }, - { - "author_name": "Gerald Haug", - "author_inst": "Max Planck Institute for Chemistry" - }, - { - "author_name": "Thomas Klimach", - "author_inst": "Max Planck Institute for Chemistry" - }, - { - "author_name": "J. Sciare", - "author_inst": "The Cyprus Institute, Climate and Atmosphere Research Center" - }, - { - "author_name": "Hang Su", - "author_inst": "Max Planck Institute for Chemistry" - }, - { - "author_name": "Ulrich Poeschl", - "author_inst": "Max Planck Institute for Chemistry" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.21.20196428", "rel_title": "Sharing a household with children and risk of COVID-19: a study of over 300,000 adults living in healthcare worker households in Scotland", @@ -1155995,6 +1157835,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.16.20196063", + "rel_title": "Initial Model for USA CoVID-19 Resurgence", + "rel_date": "2020-09-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.16.20196063", + "rel_abs": "Early CoVID-19 growth obeys: N{t*}=NI exp[+Ko t* ], with Ko=[(ln2)/(tdbl)], where tdbl is the pandemic growth doubling time. Given N{t*}, the daily number of new CoVID-19 cases is {rho}{t*} = dN{t*}/d{t*}. Implementing society-wide Social Distancing increases the tdbl doubling time, and a linear function of time for tdbl was used in our Initial Model: No[t] = 1 exp[+KA t / (1 + {gamma}o t) ] = eGo exp(-Zo[t] ) , to describe these changes, where the [t]-axis is time-shifted from the t*-axis, back to the pandemic start, and Go = [ KA / {gamma}o ]. While this No[t] successfully modeled the USA CoVID-19 progress from 3/2020 to 6/2020, this equation could not easily model some quickly decreasing {rho}[t] cases (\"fast pandemic shutoff\"), indicating that a second process was involved. This situation was most evident in the initial CoVID-19 data from China, South Korea, and Italy. Modifying Zo[t] to allow exponential cutoffs: Zo[t] {equiv} +[Go / (1+{gamma}o t)] [exp(-{delta}ot)] = Zo[t] exp(-{delta}ot) , NA[t] = eGo exp(-ZA[t]) , resulted in an Enhanced Initial Model (EIM) that significantly improved data fits for these cases. After 6/2020, many regions of the USA \"opened up\", loosening their Social Distancing requirements, which led to a sudden USA CoVID-19 Resurgence. Extrapolating the USA No[t] 3/2020-6/2020 results to 9/2020 as an Initial Model Baseline (IMB), and subtracting this IMB from the newer USA data gives a Resurgence Only function, which is analyzed here. This USA CoVID-19 Resurgence function differs significantly from the No[t] IMB functional form, but it was well-modeled by the NA[t] fast pandemic shutoff function. These results indicate that: (a) the gradual increase in tdbl doubling time from society-wide shut-downs is likely due to eliminating of a large number of population gathering points that could have enabled CoVID-19 spread; and (b) having a non-zero {delta}o fast pandemic shutoff is likely due to more people wearing masks more often [with 12 Figures].", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Genghmun Eng", + "author_inst": "Retired Scientist" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.19.20197749", "rel_title": "How super-spreader cities, highways, hospital bed availability, and dengue fever influenced the COVID-19 epidemic in Brazil", @@ -1156947,57 +1158806,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.16.20195941", - "rel_title": "SARS-CoV-2 PCR cycle threshold at hospital admission associated with Patient Mortality", - "rel_date": "2020-09-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.16.20195941", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cycle threshold (Ct) has been suggested as an approximate measure of initial viral burden. The relationship of initial Ct at hospitalization and patient mortality has not been thoroughly investigated. Methods and findings We conducted a retrospective study of all SARS-CoV-2 positive, hospitalized patients from 3/26/2020 to 8/5/2020 who had SARS CoV-2 Ct data within 48 hours of admission (n=1044). Only patients with complete survival data discharged (n=774) or died in hospital (n=270), were included in our analysis. Laboratory, demographic, and clinical data were extracted from electronic medical records. Multivariable logistic regression was applied to examine the relationship of patient mortality with Ct values while adjusting for established risk factors. Ct values were analyzed both as continuous variables and subdivided into quartiles to better illustrate their relationship with outcomes, and other covariates. Cumulative incidence curves were created to assess whether there was a survival difference in the setting of the competing risks of death versus patient discharge. In this cohort the mean Ct at admission was higher for survivors (28.6, SD=5.8) compared to non-survivors (24.8, SD=6.0, P<0.001). Patients with a lower Ct value on admission were found to have a higher odds ratio (0.91, CI 0.89-0.94, p<0.001) of in hospital mortality after adjusting for age, gender, body mass index (BMI) and history of hypertension and diabetes. Patients with Ct values in 3rd Quartile (Ct 27.4-32.8) and 4th Quartile (Ct >32.9) have a lower odds of in-hospital death (P<0.001) in comparison to the 1st Quartile. On comparing between Ct quartiles, the mortality, BMI and glomerular filtration rate (GFR) were significantly different (p<0.05) between the groups. The cumulative incidence of all-cause mortality and discharge was found to differ between Ct quartiles (Grays Test P<0.001 for both.) Conclusion: SARS-CoV-2 Ct at admission was found to be an independent predictor of in patient mortality. However, further study is needed on how to best clinically utilize such information given the result variation due to specimen quality, phase of disease, and the limited discriminative ability of the test.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Jui Choudhuri", - "author_inst": "Montefiore Medical Center" - }, - { - "author_name": "James Carter", - "author_inst": "Montefiore Medical Center" - }, - { - "author_name": "Randin Nelson", - "author_inst": "Montefiore Medical Center" - }, - { - "author_name": "Karin Skalina", - "author_inst": "Montefiore Medical Center" - }, - { - "author_name": "Marika Osterbur-Badhey", - "author_inst": "Montefiore Medical Center" - }, - { - "author_name": "Andrew Johnson", - "author_inst": "Montefiore Medical Center" - }, - { - "author_name": "Doctor Y Goldstein", - "author_inst": "Montefiore Medical Center" - }, - { - "author_name": "Monika Paroder", - "author_inst": "Montefiore Medical Center" - }, - { - "author_name": "James Szymanski", - "author_inst": "Montefiore Medical Center, Albert Einstein College of Medicine" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.19.20196915", "rel_title": "The Effects of Indias COVID-19 Lockdown on Critical Non-COVID Health Care and Outcomes", @@ -1157513,6 +1159321,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2020.09.15.20195099", + "rel_title": "Early Release Estimates for SARS-CoV-2 Prevalence and Antibody Response Interim Weighting for Probability-Based Sample Surveys", + "rel_date": "2020-09-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.15.20195099", + "rel_abs": "Many months into the SARS-CoV-2 pandemic, basic epidemiologic parameters describing burden of disease are lacking. To reduce selection bias in current burden of disease estimates derived from diagnostic testing data or serologic testing in convenience samples, we are conducting a national probability-based sample SARS-CoV-2 serosurvey. Sampling from a national address-based frame and using mailed recruitment materials and test kits will allow us to estimate national prevalence of SARS-CoV-2 infection and antibodies, overall and by demographic, behavioral, and clinical characteristics. Data will be weighted for unequal selection probabilities and non-response and will be adjusted to population benchmarks. Due to the urgent need for these estimates, expedited interim weighting of serosurvey responses will be undertaken to produce early release estimates, which will be published on the study website, COVIDVu.org. Here, we describe a process for computing interim survey weights and guidelines for release of interim estimates.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Heather Bradley", + "author_inst": "Georgia State University School of Public Health" + }, + { + "author_name": "Mansour Fahimi", + "author_inst": "Marketing Systems Group" + }, + { + "author_name": "Travis Sanchez", + "author_inst": "Emory University Rollins School of Public Health" + }, + { + "author_name": "Ben Lopman", + "author_inst": "Emory University Rollins School of Public Health" + }, + { + "author_name": "Martin Frankel", + "author_inst": "Baruch College, City University of New York" + }, + { + "author_name": "Colleen Kelley", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Richard Rothenberg", + "author_inst": "Georgia State University School of Public Health" + }, + { + "author_name": "Aaron J Siegler", + "author_inst": "Emory University Rollins School of Public Health" + }, + { + "author_name": "Patrick S Sullivan", + "author_inst": "Emory University Rollins School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.15.20159749", "rel_title": "Limited specificity of commercially available SARS-CoV-2 IgG ELISAs in serum samples of African origin", @@ -1158385,37 +1160244,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.09.15.20194951", - "rel_title": "COVID-19 incidence and mortality in the Metropolitan Region, Chile: time, space, and structural factors", - "rel_date": "2020-09-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.15.20194951", - "rel_abs": "Chile has been heavily affected by the COVID-19 pandemic. This article analyzes the association of different groups of factors-demographic, health-related, and socioeconomic-on COVID-19-related outcomes. Using the municipalities of the Metropolitan Region the study looks at the role of time dynamics, space and place in cases and deaths during a 100-days period. Results show that common and idiosyncratic elements that explain the prevalence and dynamics of infections and mortality, with an important role of social determinants of health, particularly multidimensional poverty index and use of public transportation, in explaining differences in outcomes. The article contributes to the understanding of the determinants of COVID-19 outcomes in a specific region, but also highligths the need to consider time-space dynamics and social determinants as key in the analysis. The results are specially relevant for similar research in unequal settings.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Pablo Villalobos Dintrans", - "author_inst": "Universidad de Santiago" - }, - { - "author_name": "Claudio Castillo", - "author_inst": "Universidad de Santiago" - }, - { - "author_name": "Felipe de la Fuente", - "author_inst": "Universidad de Chile" - }, - { - "author_name": "Matilde Maddaleno", - "author_inst": "Universidad de Santiago" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.09.15.20195255", "rel_title": "Knowledge, attitudes and practices associated with the COVID-19 among slum dwellers resided in Dhaka City: A Bangladeshi interview-based survey", @@ -1159275,6 +1161103,157 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, + { + "rel_doi": "10.1101/2020.09.15.20195305", + "rel_title": "Proteomics identifies a type I IFN, prothrombotic hyperinflammatory circulating COVID-19 neutrophil signature distinct from non-COVID-19 ARDS", + "rel_date": "2020-09-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.15.20195305", + "rel_abs": "Understanding the mechanisms by which infection with SARS-CoV-2 leads to acute respiratory distress syndrome (ARDS) is of significant clinical interest given the mortality associated with severe and critical coronavirus induced disease 2019 (COVID-19). Neutrophils play a key role in the lung injury characteristic of non-COVID-19 ARDS, but a relative paucity of these cells is observed at post-mortem in lung tissue of patients who succumb to infection with SARS-CoV-2. With emerging evidence of a dysregulated innate immune response in COVID-19, we undertook a functional proteomic survey of circulating neutrophil populations, comparing patients with COVID-19 ARDS, non-COVID-19 ARDS, moderate COVID-19, and healthy controls. We observe that expansion of the circulating neutrophil compartment and the presence of activated low and normal density mature and immature neutrophil populations occurs in both COVID-19 and non-COVID-19 ARDS. In contrast, release of neutrophil granule proteins, neutrophil activation of the clotting cascade and formation of neutrophil platelet aggregates is significantly increased in COVID-19 ARDS. Importantly, activation of components of the neutrophil type I IFN responses is specific to infection with SARS-CoV-2 and linked to metabolic rewiring. Together this work highlights how differential activation of circulating neutrophil populations may contribute to the pathogenesis of ARDS, identifying processes that are specific to COVID-19 ARDS.", + "rel_num_authors": 34, + "rel_authors": [ + { + "author_name": "Leila Reyes", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Manuel Alejandro Sanchez-Garcia", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Tyler Morrison", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Andrew JM Howden", + "author_inst": "University of Dundee" + }, + { + "author_name": "Emily R Watts", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Simone Arienti", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Pranvera Sadiku", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Patricia Coelho", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Ananda S Mirchandani", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Ailiang Zhang", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "David Hope", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Sarah K Clark", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Jo Singleton", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Shonna Johnston", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Robert Grecian", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Azin Poon", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Sarah McNamara", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Isla Harper", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Max Head Fourman", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Alejandro J Brenes", + "author_inst": "University of Dundee" + }, + { + "author_name": "Shalini Pathak", + "author_inst": "University of Dundee" + }, + { + "author_name": "Amy Lloyd", + "author_inst": "University of Dundee" + }, + { + "author_name": "Gio Rodriguez Blanco", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Alex Von Kriegsheim", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Bart Ghesquiere", + "author_inst": "Vesalius Research Centre" + }, + { + "author_name": "Wesley Vermaelen", + "author_inst": "Vesalius Research Centre" + }, + { + "author_name": "Camila T Cologna", + "author_inst": "Vesalius Research Centre" + }, + { + "author_name": "Kevin Dhaliwal", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Nik Hirani", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "David Dockrell", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Moira KB Whyte", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "David M Griffith", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Doreen A Cantrell", + "author_inst": "University of Dundee" + }, + { + "author_name": "Sarah R Walmsley", + "author_inst": "University of Edinburgh" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.09.16.20182915", "rel_title": "COVID-19 epidemic modelling and the effect of publichealth interventions in India- SEIQHRF model", @@ -1160171,89 +1162150,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.16.20190694", - "rel_title": "KIM-1/TIM-1 is a Receptor for SARS-CoV-2 in Lung and Kidney", - "rel_date": "2020-09-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.16.20190694", - "rel_abs": "SARS-CoV-2 precipitates respiratory distress by infection of airway epithelial cells and is often accompanied by acute kidney injury. We report that Kidney Injury Molecule-1/T cell immunoglobulin mucin domain 1 (KIM-1/TIM-1) is expressed in lung and kidney epithelial cells in COVID-19 patients and is a receptor for SARS-CoV-2. Human and mouse lung and kidney epithelial cells express KIM-1 and endocytose nanoparticles displaying the SARS-CoV-2 spike protein (virosomes). Uptake was inhibited by anti-KIM-1 antibodies and TW-37, a newly discovered inhibitor of KIM-1-mediated endocytosis. Enhanced KIM-1 expression by human kidney tubuloids increased uptake of virosomes. KIM-1 binds to the SARS-CoV-2 Spike protein in vitro. KIM-1 expressing cells, not expressing angiotensin-converting enzyme 2 (ACE2), are permissive to SARS-CoV-2 infection. Thus, KIM-1 is an alternative receptor to ACE2 for SARS-CoV-2. KIM-1 targeted therapeutics may prevent and/or treat COVID-19.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Yutaro Mori", - "author_inst": "Brigham and Women's Hospital, Harvard Medical School" - }, - { - "author_name": "Corby Fink", - "author_inst": "Western University" - }, - { - "author_name": "Takaharu Ichimura", - "author_inst": "Brigham and Women's Hospital, Harvard Medical School" - }, - { - "author_name": "Keisuke Sako", - "author_inst": "Brigham and Women's Hospital, Harvard Medical School" - }, - { - "author_name": "Makiko Mori", - "author_inst": "Brigham and Women's Hospital, Harvard Medical School" - }, - { - "author_name": "Nathan N Lee", - "author_inst": "Brigham and Women's Hospital, Harvard Medical School" - }, - { - "author_name": "Philipp Aschauer", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Krishna M Padmanabha Das", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "SoonGweon Hong", - "author_inst": "Brigham and Women's Hospital, Harvard Medical School" - }, - { - "author_name": "Minsun Song", - "author_inst": "Brigham and Women's Hospital, Harvard Medical School" - }, - { - "author_name": "Robert F Padera Jr.", - "author_inst": "Brigham and Women's Hospital, Harvard Medical School" - }, - { - "author_name": "Astrid Weins", - "author_inst": "Brigham and Women's Hospital, Harvard Medical School" - }, - { - "author_name": "Luke P Lee", - "author_inst": "Brigham and Women's Hospital, Harvard Medical School" - }, - { - "author_name": "Mahmoud L Nasr", - "author_inst": "Brigham and Women's Hospital, Harvard Medical School" - }, - { - "author_name": "Gregory A Dekaban", - "author_inst": "Western University" - }, - { - "author_name": "Jimmy D Dikeakos", - "author_inst": "Western University" - }, - { - "author_name": "Joseph V Bonventre", - "author_inst": "Brigham and Women's Hospital, Harvard Medical School" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.15.20195396", "rel_title": "A COVID-19 Nursing Home Transmission Study: sequence and metadata from weekly testing in an extensive nursing home outbreak", @@ -1161009,6 +1162905,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.16.20196188", + "rel_title": "Multifractal behavior of SARS-CoV-2 COVID-19 pandemic spread, case of: Algeria, Russia, USA and Italy.", + "rel_date": "2020-09-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.16.20196188", + "rel_abs": "Here, the multifractal behavior of the SARS-CoV-2 COVID-19 pandemic daily and death cases is investigated through the so-called Wavelet Transform Modulus Maxima lines (WTMM) method, data available via the World Health Organization (WHO) dashboard of Algeria, Russia, USA and Italy are analyzed. The obtained results show the multifractal behavior of the COVID-19 pandemic data with different spectra of singularities. Keywords: Multifractal behavior, daily and death cases, WTMM, COVID-19 pandemic data", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Sid-Ali Ouadfeul", + "author_inst": "Algerian Petroleum Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.17.20196501", "rel_title": "Epidemiology of SARS-CoV-2 infection in Karnataka State, South India: Transmission dynamics of symptomatic vs. asymptomatic infections", @@ -1161977,49 +1163892,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2020.09.16.20195289", - "rel_title": "THE REMOTE ANALYSIS OF BREATH SOUND IN COVID-19 PATIENTS: A SERIES OF CLINICAL CASES", - "rel_date": "2020-09-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.16.20195289", - "rel_abs": "BackgroundRespiratory sounds have been recognized as a possible indicator of behavior and health. Computer analysis of these sounds can indicate of characteristic sound changes caused by COVID-19 and can be used for diagnosis of this illness.\n\nPurposeThe communication aim is development of fast remote computer-assistance diagnosis of COVID-19, based on analysis of respiratory sounds.\n\nMaterials and MethodsFast Fourier transform (FFT) was applied for analyses of respiratory sounds recorded near the mouth of 9 COVID-19 patients and 4 healthy volunteers. Sampling rate was 48 kHz.\n\nResultsComparing of FFT spectrums of the respiratory sounds of the patients and volunteers we proposed numerical healthy-ill criterions.\n\nConclusionsThe proposed computer method, based on analysis of the FFT spectrums of respiratory sounds of the patients and volunteers, allows one to automatically diagnose COVID-19 with sufficiently high diagnostic values. This method can be applied at development of noninvasive self-testing kits for COVID-19.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Evgeny G. Furman", - "author_inst": "E.A.Vagner Perm State Medical University" - }, - { - "author_name": "Artem Charushin", - "author_inst": "E.A.Vagner Perm State Medical University" - }, - { - "author_name": "Ekaterina Eirikh", - "author_inst": "Perm Regional Clinical Infectious Diseases Hospital" - }, - { - "author_name": "Sergey Malinin", - "author_inst": "E.A.Vagner Perm State Medical University" - }, - { - "author_name": "Valerii Sheludko", - "author_inst": "E.A.Vagner Perm State Medical University" - }, - { - "author_name": "Vladimir Sokolovsky", - "author_inst": "Ben-Gurion University of the Negev" - }, - { - "author_name": "Gregory Furman", - "author_inst": "Ben-Gurion University of the Negev" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2020.09.16.20195982", "rel_title": "Variation of SARS-CoV-2 viral loads by sample type, disease severity and time: a systematic review", @@ -1162939,6 +1164811,69 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.09.15.20195511", + "rel_title": "Inflammatory leptomeningeal cytokines mediate delayed COVID-19 encephalopathy", + "rel_date": "2020-09-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.15.20195511", + "rel_abs": "SARS-CoV-2 infection induces a wide spectrum of neurologic dysfunction. Here we show that a particularly vulnerable population with neurologic manifestations of COVID-19 harbor an influx of inflammatory cytokines within the cerebrospinal fluid in the absence of viral neuro-invasion. The majority of these inflammatory mediators are driven by type 2 interferon and are known to induce neuronal injury in other disease models. Levels of matrix metalloproteinase-10 within the spinal fluid correlate with the degree of neurologic dysfunction. Furthermore, this neuroinflammatory process persists weeks following convalescence from the acute respiratory infection. These prolonged neurologic sequelae following a systemic cytokine release syndrome lead to long-term neurocognitive dysfunction with a wide range of phenotypes.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Jan Remsik", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "Jessica A Wilcox", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "N. Esther Babady", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "Tracy McMillen", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "Behroze A Vachha", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "Neil A Halpern", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "Vikram Dhawan", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "Marc Rosenblum", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "Christine A. Iacobuzio-Donahue", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "Edward K Avila", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "Bianca Santomasso", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "Adrienne Boire", + "author_inst": "Memorial Sloan Kettering Cancer Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2020.09.16.20195552", "rel_title": "How the clinical research community responded to the COVID-19 pandemic: An analysis of the COVID-19 clinical studies in ClinicalTrials.gov", @@ -1164047,141 +1165982,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2020.09.17.300335", - "rel_title": "Structural and Functional Comparison of SARS-CoV-2-Spike Receptor Binding Domain Produced in Pichia pastoris and Mammalian Cells", - "rel_date": "2020-09-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.17.300335", - "rel_abs": "The yeast Pichia pastoris is a cost-effective and easily scalable system for recombinant protein production. In this work we compared the conformation of the receptor binding domain (RBD) from SARS-CoV-2 Spike protein expressed in P. pastoris and in the well established HEK-293T mammalian cell system. RBD obtained from both yeast and mammalian cells was properly folded, as indicated by UV-absorption, circular dichroism and tryptophan fluorescence. They also had similar stability, as indicated by temperature-induced unfolding (observed Tm were 50 {degrees}C and 52 {degrees}C for RBD produced in P. pastoris and HEK-293T cells, respectively). Moreover, the stability of both variants was similarly reduced when the ionic strength was increased, in agreement with a computational analysis predicting that a set of ionic interactions may stabilize RBD structure. Further characterization by HPLC, size-exclusion chromatography and mass spectrometry revealed a higher heterogeneity of RBD expressed in P. pastoris relative to that produced in HEK-293T cells, which disappeared after enzymatic removal of glycans. The production of RBD in P. pastoris was scaled-up in a bioreactor, with yields above 45 mg/L of 90% pure protein, thus potentially allowing large scale immunizations to produce neutralizing antibodies, as well as the large scale production of serological tests for SARS-CoV-2.", - "rel_num_authors": 30, - "rel_authors": [ - { - "author_name": "- Argentinian AntiCovid Consortium", - "author_inst": "-" - }, - { - "author_name": "Claudia R. Arbeitman", - "author_inst": "Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET). Godoy Cruz 2290 C1425FQB, Buenos Aires, Argentina." - }, - { - "author_name": "Gabriela Auge", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiologia y Biologia Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Matias Blaustein", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiologia y Biologia Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Luis Bredeston", - "author_inst": "Universidad de Buenos Aires. Facultad de Farmacia y Bioquimica. Departamento de Quimica Biologica. Junin 965 C1113AAD. Buenos Aires, Argentina." - }, - { - "author_name": "Enrique S. Corapi", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiologia y Biologia Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Patricio O. Craig", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Quimica Biologica. Buenos Aires, Argentina." - }, - { - "author_name": "Leandro A. Cossio", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiologia y Biologia Molecular y Celular. Laboratorio de Agrobiotecnolog" - }, - { - "author_name": "Liliana Dain", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiologia y Biologia Molecular y Celular. Buenos Aires, Argentina. Centr" - }, - { - "author_name": "Fernanda Elias", - "author_inst": "Instituto de Ciencia y Tecnologia Dr. Cesar Milstein (Consejo Nacional de Investigaciones Cientificas y Tecnicas-Fundacion Pablo Cassara). Saladillo 2468 (C1440" - }, - { - "author_name": "Natalia B. Fernandez", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiologia y Biologia Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Javier Gasulla", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiologia y Biologia Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Natalia Gorojovsky", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Quimica Biologica. Buenos Aires, Argentina." - }, - { - "author_name": "Gustavo E. Gudesblat", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiologia y Biologia Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Maria G. Herrera", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiologia y Biologia Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Lorena I. Iba\u00f1ez", - "author_inst": "Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET). Instituto de Ciencia y Tecnologia Dr. Cesar Milstein, Saladillo 2468, C1440FFX Buenos Aire" - }, - { - "author_name": "Tommy Idrovo", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiologia y Biologia Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Matias Iglesias Rando", - "author_inst": "Universidad de Buenos Aires. Facultad de Farmacia y Bioquimica. Departamento de Quimica Biologica. Junin 965 C1113AAD, Buenos Aires, Argentina." - }, - { - "author_name": "Laura Kamenetzky", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiologia y Biologia Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Alejandro D Nadra", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiologia y Biologia Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Diego G. Noseda", - "author_inst": "Universidad Nacional de San Martin - CONICET. Instituto de Investigaciones Biotecnologicas (IIBio). San Martin, Buenos Aires, Argentina." - }, - { - "author_name": "Carlos H. Pavan", - "author_inst": "Universidad de Buenos Aires, Facultad de Farmacia y Bioquimica. Buenos Aires, Argentina." - }, - { - "author_name": "Maria F. Pavan", - "author_inst": "Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET). Instituto de Ciencia y Tecnologia Dr. Cesar Milstein, Saladillo 2468, C1440FFX Buenos Aire" - }, - { - "author_name": "Maria F. Pignataro", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiologia y Biologia Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Ernesto Roman", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Quimica Biologica. Buenos Aires, Argentina." - }, - { - "author_name": "Lucas A.M Ruberto", - "author_inst": "Universidad de Buenos Aires. Facultad de Farmacia y Bioquimica. Departamento de Microbiologia, Inmunologia, Biotecnologia y Genetica. Buenos Aires, Argentina." - }, - { - "author_name": "Natalia Rubinstein", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiologia y Biologia Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Javier Santos", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiologia y Biologia Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Francisco Velazquez", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiologia y Biologia Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Alicia M. Zelada", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiologia y Biologia Molecular y Celular. Laboratorio de Agrobiotecnolog" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.09.17.302232", "rel_title": "Fixed single-cell RNA sequencing for understanding virus infection and host response", @@ -1164897,6 +1166697,77 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2020.09.14.296178", + "rel_title": "SARS-CoV-2 protein Nsp1 alters actomyosin cytoskeleton and phenocopies arrhythmogenic cardiomyopathy-related PKP2 mutant", + "rel_date": "2020-09-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.14.296178", + "rel_abs": "Mutations in desmosomal Plakophilin-2 (PKP2) are the most prevalent drivers of arrhythmogenic cardiomyopathy (ACM) and a common cause of sudden cardiac death in young athletes. However, partner proteins that elucidate PKP2 cellular mechanism to understand cardiac dysfunction in ACM are mostly unknown. Here we identify the actin-based motor proteins Myh9 and Myh10 as key PKP2 interactors, and demonstrate that the expression of the ACM-related PKP2 mutant R735X alters actin fiber organization and cell mechanical stiffness. We also show that SARS-CoV-2 Nsp1 protein acts similarly to this known pathogenic R735X mutant, altering the actomyosin component distribution on cardiac cells. Our data reveal that the viral Nsp1 hijacks PKP2 into the cytoplasm and mimics the effect of delocalized R735X mutant. These results demonstrate that cytoplasmic PKP2, wildtype or mutant, induces the collapse of the actomyosin network, since shRNA-PKP2 knockdown maintains the cell structure, validating a critical role of PKP2 localization in the regulation of actomyosin architecture. The fact that Nsp1 and PKP2 mutant R735X share similar phenotypes also suggests that direct SARS-CoV-2 heart infection could induce a transient ACM-like disease in COVID-19 patients, which may contribute to right ventricle dysfunction, observed in patients with poor survival prognosis.\n\nHighlightsThe specific cardiac isoform Plakophilin-2a (PKP2) interacts with Myh9 and Myh10.\n\nPKP2 delocalization alters actomyosin cytoskeleton component organization. SARS-CoV-2 Nsp1 protein hijacks PKP2 from the desmosome into the soluble fraction where it is downregulated.\n\nViral Nsp1 collapses the actomyosin cytoskeleton and phenocopies the arrhythmogenic cardiomyopathy-related mutant R735X.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Cristina Marquez-Lopez", + "author_inst": "Centro Nacional de Investigaciones Cardiovasculares (CNIC)" + }, + { + "author_name": "Marta Roche-Molina", + "author_inst": "Centro Nacional de Investigaciones Cardiovasculares (CNIC)" + }, + { + "author_name": "Nieves Garc\u00eda-Quint\u00e1ns", + "author_inst": "Centro Nacional de Investigaciones Cardiovasculares (CNIC)" + }, + { + "author_name": "Silvia Sacristan", + "author_inst": "Centro Nacional de Investigaciones Cardiovasculares (CNIC)" + }, + { + "author_name": "David Siniscalco", + "author_inst": "Materials Science Factory, Instituto de Ciencia de Materiales de Madrid (ICMM), CSIC" + }, + { + "author_name": "Andr\u00e9s Gonzalez-Guerra", + "author_inst": "Centro Nacional de Investigaciones Cardiovasculares (CNIC)" + }, + { + "author_name": "Emilio Camafeita", + "author_inst": "Centro Nacional de Investigaciones Cardiovasculares" + }, + { + "author_name": "Mariya Lytvyn", + "author_inst": "Centro Nacional de Investigaciones Cardiovasculares (CNIC)" + }, + { + "author_name": "Mar\u00eda Isabel Guill\u00e9n", + "author_inst": "Centro Nacional de Investigaciones Cardiovasculares (CNIC)" + }, + { + "author_name": "David Sanz-Rosa", + "author_inst": "Centro Nacional de Investigaciones Cardiovasculares (CNIC)" + }, + { + "author_name": "Daniel Mart\u00edn-P\u00e9rez", + "author_inst": "Centro Nacional de Investigaciones Cardiovasculares (CNIC)" + }, + { + "author_name": "Cristina Sanchez-Ramos", + "author_inst": "Centro Nacional de Investigaciones Cardiovasculares (CNIC)" + }, + { + "author_name": "Ricardo Garcia", + "author_inst": "Materials Science Factory, Instituto de Ciencia de Materiales de Madrid (ICMM), CSIC" + }, + { + "author_name": "Juan Antonio Bernal", + "author_inst": "Centro Nacional de Investigaciones Cardiovasculares (CNIC)" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.09.12.20193235", "rel_title": "The impact of COVID-19 in diabetic kidney disease and chronic kidney disease: A population-based study", @@ -1165709,37 +1167580,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, - { - "rel_doi": "10.1101/2020.09.14.20194068", - "rel_title": "Mathematical Modelling of the Spread of the Coronavirus under Social Restrictions", - "rel_date": "2020-09-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.14.20194068", - "rel_abs": "BackgroundCOVID-19 has affected most countries and declared as pandemic. Most countries have implemented some social restrictions to control it. In this work we will use mathematical modelling to assess the current social restrictions in controlling the spread of the disease.\n\nMethodsWe formulate a simple susceptible-infectious-recovery (SIR) model to describe the spread of the coronavirus under social restrictions. The transmission rate in this model is considered variable to catch social restrictions impact. We analyze this model, then fit the model to 160 days induced death data in Italy, Iran, USA, Germany, France, India, Spain and China. we estimate some factors that help in understanding not only the spread of the disease but also assess the current social restriction in controlling this disease.\n\nResultsWe find a formula for the basic reproduction function (R(t)) and the maximum number of daily infected people. Then estimate the models parameters with 95% confidence intervals in these countries. We notice that the model has excellent fit to the disease death data in all considered countries except Iran. The percentage of disease death estimated by the model in Germany and France are 3.8% and 1.2% respectively, which are close to reported percentages values. Finally, we estimate the time, after first reported death, spent under social restrictions to reduce the basic reproduction function (R(t)) to one unit. The times to do that in Italy, USA, Germany, France, Spain and China are 40, 50, 34,58, 31, and 15 days respectively. However, the Indian social restrictions in the 160 days were not enough to reach R(t) = 1.\n\nConclusionThe transmission rate is between 0.1035-1.6076 and recovery rate is between 0-0.2456. The disease death rates calculated for Germany and France are more realistic than others with average value 0.0023. Extending the same social restrictions for enough time could control the disease in Italy, USA, Germany, France, India, Spain and China. While, more social restrictions are needed to control the disease in India.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Mo'tassem Al-arydah", - "author_inst": "Department of mathematics, Khalifa University" - }, - { - "author_name": "Khalid Dib", - "author_inst": "Department of Mathematics, Khalifa University" - }, - { - "author_name": "Hailay Weldegiorgis Berhe", - "author_inst": "Department of mathematics, Mekelle University" - }, - { - "author_name": "Kalyanasundaram Madhu", - "author_inst": "Department of Mathematics, Khalifa University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.10.20191486", "rel_title": "Characterization and Phase 1 Trial of a B Cell Activating Anti-CD73 Antibody for the Immunotherapy of COVID-19", @@ -1166747,6 +1168587,49 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.09.15.275891", + "rel_title": "Rational design of a new class of protease inhibitors for the potential treatment of coronavirus diseases", + "rel_date": "2020-09-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.15.275891", + "rel_abs": "The coronavirus main protease, Mpro, is a key protein in the virus life cycle and a major drug target. Based on crystal structures of SARSCoV2 Mpro complexed with peptidomimetic inhibitors, we recognized a binding characteristic shared with proline-containing inhibitors of hepatitis C virus protease. Initial tests showed that this subclass of HCV protease inhibitors indeed exhibited activity against Mpro. Postulating a benefit for a preorganized backbone conformation, we designed new ketoamide-based Mpro inhibitors based on central proline rings. One of the designed compounds, ML1000, inhibits Mpro with low-nanomolar affinity and suppresses SARSCoV2 viral replication in human cells at sub-micromolar concentrations. Our findings identify ML1000 as a promising new pre-organized scaffold for the development of anti-coronavirus drugs.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Michael Westberg", + "author_inst": "Stanford University" + }, + { + "author_name": "Yichi Su", + "author_inst": "Stanford University" + }, + { + "author_name": "Xinzhi Zou", + "author_inst": "Stanford University" + }, + { + "author_name": "Lin Ning", + "author_inst": "Stanford University" + }, + { + "author_name": "Brett Hurst", + "author_inst": "Utah State University" + }, + { + "author_name": "Bart Tarbet", + "author_inst": "Utah State University" + }, + { + "author_name": "Michael Lin", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.09.14.296889", "rel_title": "CROssBAR: Comprehensive Resource of Biomedical Relations with Deep Learning Applications and Knowledge Graph Representations", @@ -1167391,81 +1169274,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.09.13.20192682", - "rel_title": "The impact of digital contact tracing on the SARS-CoV-2 pandemic - a comprehensive modelling study", - "rel_date": "2020-09-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.13.20192682", - "rel_abs": "Contact tracing is one of several strategies employed in many countries to curb the spread of SARS-CoV-2. Digital contact tracing (DCT) uses tools such as cell-phone applications to improve tracing speed and reach. We model the impact of DCT on the spread of the virus for a large epidemiological parameter space consistent with current literature on SARS-CoV-2. We also model DCT in combination with random testing (RT) and social distancing (SD).\n\nModelling is done with two independently developed individual-based (stochastic) models that use the Monte Carlo technique, benchmarked against each other and against two types of deterministic models.\n\nFor current best estimates of the number of asymptomatic SARS-CoV-2 carriers (approximately 40%), their contagiousness (similar to that of symptomatic carriers), the reproductive number before interventions (R0 at least 3) we find that DCT must be combined with other interventions such as SD and/or RT to push the reproductive number below one. At least 60% of the population would have to use the DCT system for its effect to become significant. On its own, DCT cannot bring the reproductive number below 1 unless nearly the entire population uses the DCT system and follows quarantining and testing protocols strictly. For lower uptake of the DCT system, DCT still reduces the number of people that become infected.\n\nWhen DCT is deployed in a population with an ongoing outbreak where [Formula] of the population have already been infected, the gains of the DCT intervention come at the cost of requiring up to 15% of the population to be quarantined (in response to being traced) on average each day for the duration of the epidemic, even when there is sufficient testing capability to test every traced person.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Tina R Pollmann", - "author_inst": "Technical University of Munich" - }, - { - "author_name": "Julia Pollmann", - "author_inst": "University clinic Heidelberg" - }, - { - "author_name": "Christoph Wiesinger", - "author_inst": "Technical University of Munich" - }, - { - "author_name": "Christian Haack", - "author_inst": "Technical University of Munich" - }, - { - "author_name": "Lolian Shtembari", - "author_inst": "Max Planck Institute for Physics" - }, - { - "author_name": "Andrea Turcati", - "author_inst": "Technical University of Munich" - }, - { - "author_name": "Birgit Neumair", - "author_inst": "Technical University of Munich" - }, - { - "author_name": "Stephan Meighen-Berger", - "author_inst": "Technical University of Munich" - }, - { - "author_name": "Giovanni Zattera", - "author_inst": "Technical University of Munich" - }, - { - "author_name": "Matthias Neumair", - "author_inst": "Technical University of Munich" - }, - { - "author_name": "Uljana Apel", - "author_inst": "Technical University of Munich" - }, - { - "author_name": "Augustine Okolie", - "author_inst": "Technical University of Munich" - }, - { - "author_name": "Johannes Mueller", - "author_inst": "Technical University of Munich, Helmholtz Center Munich" - }, - { - "author_name": "Stefan Schoenert", - "author_inst": "Technical University of Munich" - }, - { - "author_name": "Elisa Resconi", - "author_inst": "Technical University of Munich" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.09.13.20186692", "rel_title": "Secondary traumatic stress and burnout in healthcare workers during COVID-19 outbreak", @@ -1168249,6 +1170057,41 @@ "type": "new results", "category": "systems biology" }, + { + "rel_doi": "10.1101/2020.09.14.296806", + "rel_title": "Single-cell RNA Expression of SARS-CoV-2 Cell Entry Factors in Human Endometrium during Preconception", + "rel_date": "2020-09-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.14.296806", + "rel_abs": "We investigated potential SARS-CoV-2 tropism in human endometrium by single-cell RNA-sequencing of viral entry-associated genes in healthy women. Percentages of endometrial cells expressing ACE2, TMPRSS2, CTSB, or CTSL were <2%, 12%, 80%, and 80%, respectively, with 0.7% of cells expressing all four genes. Our findings imply low efficiency of SARS-CoV-2 infection in the endometrium before embryo implantation, providing information to assess preconception risk in asymptomatic carriers.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Felipe Vilella Mitjana", + "author_inst": "Incliva" + }, + { + "author_name": "Wanxin Wang", + "author_inst": "Stanford University" + }, + { + "author_name": "Inmaculada Moreno Gimeno", + "author_inst": "Igenomix Foundation, INCLIVA" + }, + { + "author_name": "Stephen Quake", + "author_inst": "Department of Bioengineering, Stanford University" + }, + { + "author_name": "Carlos Simon", + "author_inst": "Department of Obstetrics & Gynecology, University of Valencia" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2020.09.13.295691", "rel_title": "Ambroxol Hydrochloride Inhibits the Interaction between Severe Acute Respiratory Syndrome Coronavirus 2 Spike Protein's Receptor Binding Domain and Recombinant Human ACE2.", @@ -1169049,25 +1170892,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2020.09.11.20192997", - "rel_title": "Ventilation and the SARS-CoV-2 CoronavirusAnalysis of outbreaks in a restaurant and on a bus in China,and at a Call Center in South Korea", - "rel_date": "2020-09-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.11.20192997", - "rel_abs": "In a previous paper [10] a model of the distribution of respiratory droplets and aerosols by Lagrangian turbulent air-flow was developed. It is used to show how the SARS-CoV-2 Coronavirus can be spread by the breathing of single infected person. The model shows that the concentration of viruses in the cloud, exhaled by one person, can increase to infectious levels within a certain amount of time, in a confined space where the air re-circulates. In [10] the model was used to analyze the air-flow and SARS-CoV-2 Coronavirus build-up in a restaurant in Guangzhou, China [23, 22]. In this paper, we add the analysis of two more cases, an outbreak among lay-Buddhists, on a bus [30], traveling to a ceremony in Zhejiang province, China, and an outbreak in a Call Center in Seoul, Korea [24]. The analysis and comparison of these three cases, leads to the conclusion that the SARS-CoV-2 Coronavirus attacks in two steps: The first step is a linear spread between individuals with a couple of days delay. The second step is an polynomial spread effected by the air-conditioning system affecting a much larger number of people. Thus in the second step, the ventilation can become the super-spreader.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Bjorn Birnir", - "author_inst": "University of California Santa Barbara" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.11.20192849", "rel_title": "Ignoring the elephant in the room: factors contributing to inadequate access to contraception and sources of contraception during novel coronavirus diseases 2019 in South Africa.", @@ -1169839,6 +1171663,45 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.09.09.290718", + "rel_title": "Daytime variation in SARS-CoV-2 infection and cytokine production", + "rel_date": "2020-09-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.09.290718", + "rel_abs": "S. Ray and A. Reddy recently anticipated the implication of circadian rhythm in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of the coronavirus disease (Covid-19). In addition to its key role in the regulation of biological functions, the circadian rhythm has been suggested as a regulator of viral infections. Specifically, the time of day of infection was found critical for illness progression, as has been reported for influenza, respiratory syncytial and parainfluenza type 3 viruses. We analyzed circadian rhythm implication in SARS-CoV-2 virus infection of isolated human monocytes, key actor cells in Covid-19 disease, from healthy subjects. The circadian gene expression of Bmal1 and Clock genes was investigated with q-RTPCR. Monocytes were infected with SARS-CoV-2 virus strain and viral infection was investigated by One-Step qRT-PCR and immunofluorescence. Interleukin (IL)-6, IL-1{beta} and IL-10 levels were also measured in supernatants of infected monocytes. Using Cosinor analysis, we showed that Bmal1 and Clock transcripts exhibited circadian rhythm in monocytes with an acrophase and a bathyphase at Zeitgeber Time (ZT)6 and ZT17. After forty-eight hours, the amount of SARS-CoV-2 virus increased in the monocyte infected at ZT6 compared to ZT17. The high virus amount at ZT6 was associated with significant increased release in IL-6, IL-1{beta} and IL-10 compared to ZT17. Our results suggest that time day of SARS-CoV-2 infection affects viral infection and host immune response. They support consideration of circadian rhythm in SARS-CoV-2 disease progression and we propose circadian rhythm as a novel target for managing viral progression.\n\nImportanceThe implication of circadian rhythm (CR) in pathogenesis of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has been recently anticipated. The time of day of infection is critical for illness progression as reported for influenza, respiratory syncytial and parainfluenza type 3 viruses. In this study, we wondered if SARS-CoV-2 infection and cytokine production by human monocytes, innate immune cells affected by Covid-19, were regulated by CR. Our results suggest that time day of SARS-CoV-2 infection affects viral infection and host immune response. They support consideration of circadian rhythm in SARS-CoV-2 disease progression and we propose circadian rhythm as a novel target for managing viral progression.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Aissatou Bailo Diallo", + "author_inst": "Aix-Marseille Univ, IRD, APHM, MEPHI, IHU-M\u00e9diterran\u00e9e Infection" + }, + { + "author_name": "Laetitia Gay", + "author_inst": "Aix-Marseille Univ, IRD, APHM, MEPHI, IHU-M\u00e9diterran\u00e9e Infection" + }, + { + "author_name": "Benjamin Coiffard", + "author_inst": "Aix-Marseille Univ, MEPHI, IRD, APHM, Marseille, France" + }, + { + "author_name": "Marc Leone", + "author_inst": "Aix-Marseille Univ, MEPHI, IRD, APHM, Marseille, France" + }, + { + "author_name": "Soraya Mezouar", + "author_inst": "Aix-Marseille Univ, IRD, APHM, MEPHI, IHU-M\u00e9diterran\u00e9e Infection" + }, + { + "author_name": "Jean-Louis M\u00e8ge", + "author_inst": "IHU M\u00e9diterran\u00e9e infection" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.09.09.20191353", "rel_title": "Covid-19 epidemic curve in Brazil: A sum of multiple epidemics, whose income inequality and population density in the states are correlated with growth rate and daily acceleration", @@ -1170731,49 +1172594,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.10.20192070", - "rel_title": "Modelling the first wave of the COVID-19 epidemic in the Czech Republic and the role of government interventions", - "rel_date": "2020-09-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.10.20192070", - "rel_abs": "In the Czech Republic, the first COVID-19 cases were confirmed on 1 March 2020; early population interventions were adopted in the following weeks. A simple epidemiological model was developed to help decision-makers understand the course of the epidemic and perform short-term predictions. In this paper, we present the use of the model and estimated changes in the reproduction number (decrease from > 2.00 to < 1.00 over March and April) following adopted interventions.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Ondrej Majek", - "author_inst": "Institute of Health Information and Statistics of the Czech Republic" - }, - { - "author_name": "Ondrej Ngo", - "author_inst": "Institute of Health Information and Statistics of the Czech Republic" - }, - { - "author_name": "Jiri Jarkovsky", - "author_inst": "Institute of Health Information and Statistics of the Czech Republic" - }, - { - "author_name": "Martin Komenda", - "author_inst": "Institute of Health Information and Statistics of the Czech Republic" - }, - { - "author_name": "Jarmila Razova", - "author_inst": "Ministry of Health of the Czech Republic" - }, - { - "author_name": "Ladislav Dusek", - "author_inst": "Institute of Health Information and Statistics of the Czech Republic" - }, - { - "author_name": "Tomas Pavlik", - "author_inst": "Institute of Health Information and Statistics of the Czech Republic" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.10.20192153", "rel_title": "Modeling the dynamics of SARS-CoV-2 immunity waning, antigenic drifting, and population serology patterns", @@ -1171349,6 +1173169,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.09.11.20191692", + "rel_title": "Hyaluronan is abundant in COVID-19 respiratory secretions", + "rel_date": "2020-09-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.11.20191692", + "rel_abs": "Thick, viscous respiratory secretions are a major pathogenic feature of COVID-19 disease, but the composition and physical properties of these secretions are poorly understood. We characterized the composition and rheological properties (i.e. resistance to flow) of respiratory secretions collected from intubated COVID-19 patients. We found the percent solids and protein content are all greatly elevated in COVID-19 compared to heathy control samples and closely resemble levels seen in cystic fibrosis (CF), a genetic disease known for thick, tenacious respiratory secretions. DNA and hyaluronan are major components of respiratory secretions in COVID-19 and are likewise abundant in cadaveric lung tissues from these patients. COVID-19 secretions exhibited heterogeneous rheological behaviors with thicker samples showing increased sensitivity to DNase and hyaluronidase treatment. These results highlight the dramatic biophysical properties of COVID-19 respiratory secretions and suggest that DNA and hyaluronan may be viable therapeutic targets in COVID-19 infection.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Michael J. Kratochvil", + "author_inst": "Stanford University" + }, + { + "author_name": "Gernot Kaber", + "author_inst": "Stanford University" + }, + { + "author_name": "Pamela C. Cai", + "author_inst": "Stanford University" + }, + { + "author_name": "Elizabeth B Burgener", + "author_inst": "Stanford University" + }, + { + "author_name": "Graham Barlow", + "author_inst": "Stanford University" + }, + { + "author_name": "Samuel Yang", + "author_inst": "Stanford University" + }, + { + "author_name": "Mark R Nicolls", + "author_inst": "Stanford University" + }, + { + "author_name": "Michael G. Ozawa", + "author_inst": "Stanford University" + }, + { + "author_name": "Donald P. Regula", + "author_inst": "Stanford University" + }, + { + "author_name": "Nadine Nagy", + "author_inst": "Stanford University" + }, + { + "author_name": "Carlos E. Milla", + "author_inst": "Stanford University" + }, + { + "author_name": "Angela J. Rogers", + "author_inst": "Stanford University" + }, + { + "author_name": "Andrew J Spakowitz", + "author_inst": "Stanford University" + }, + { + "author_name": "Sarah C. Heilshorn", + "author_inst": "Stanford University" + }, + { + "author_name": "Paul L. Bollyky", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.11.20192492", "rel_title": "Resurgence of SARS-CoV-2 in England: detection by community antigen surveillance", @@ -1172353,73 +1174248,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.09.10.20192336", - "rel_title": "Lessons from the COVID-19 pandemic: People's experiences and satisfaction with telehealth during the COVID-19 pandemic in Australia", - "rel_date": "2020-09-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.10.20192336", - "rel_abs": "Objectives: To determine how participants perceived telehealth consults in comparison to traditional in-person visits, and to investigate whether people believe that telehealth services would be useful beyond the pandemic. Design: A national cross-sectional community survey. Participants: Australian adults aged 18 years and over (n=1369). Main outcome measures: Telehealth experiences. Results: Of the 596 telehealth users, the majority of respondents (62%) rated their telehealth experience as \"just as good\" or \"better\" than a traditional in-person medical appointment. On average, respondents perceived that telehealth would be moderately to very useful for medical appointments after the COVID-19 pandemic is over (M=3.67 out of 5, SD=1.1). Being male (p=0.007), having a history of both depression and anxiety (p=0.037), or lower patient activation (individuals' willingness to take on the role of managing their health/healthcare) (p=0.037) were associated with a poorer telehealth experience. Six overarching themes were identified from free-text responses of why telehealth experience was poorer than a traditional in-person medical appointment: communication is not as effective; limitations with technology; issues with obtaining prescriptions and pathology; reduced confidence in doctor; additional burden for complex care; and inability to be physically examined. Conclusions: Telehealth appointments were reported to be comparable to traditional in-person medical appointments by most of our sample. Telehealth should continue to be offered as a mode of healthcare delivery while the pandemic continues and may be worthwhile beyond the pandemic.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Jennifer MJ Isautier", - "author_inst": "University of Sydney" - }, - { - "author_name": "Tessa Copp", - "author_inst": "University of Sydney" - }, - { - "author_name": "Julie Ayre", - "author_inst": "University of Sydney" - }, - { - "author_name": "Erin Cvejic", - "author_inst": "University of Sydney" - }, - { - "author_name": "Gideon Meyerowitz-Katz", - "author_inst": "University of Wollongong" - }, - { - "author_name": "Carys Batcup", - "author_inst": "University of Sydney" - }, - { - "author_name": "Carissa Bonner", - "author_inst": "University of Sydney" - }, - { - "author_name": "Rachael Dodd", - "author_inst": "University of Sydney" - }, - { - "author_name": "Brooke Nickel", - "author_inst": "University of Sydney" - }, - { - "author_name": "Kristen Pickles", - "author_inst": "The University of Sydney" - }, - { - "author_name": "Samuel Cornell", - "author_inst": "University of Sydney" - }, - { - "author_name": "Thomas Dakin", - "author_inst": "University of Sydney" - }, - { - "author_name": "Kirsten J McCaffery", - "author_inst": "University of Sydney" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.09.11.20192518", "rel_title": "Retrospective study of COVID-19 seroprevalence among tissue donors at the onset of the outbreak before implementation of strict lockdown measures in France", @@ -1173219,6 +1175047,41 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2020.09.10.290932", + "rel_title": "SARS-CoV-2 NSP1 C-terminal region (residues 130-180) is an intrinsically disordered region", + "rel_date": "2020-09-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.10.290932", + "rel_abs": "Nonstructural protein 1 (NSP1) of SARS-CoV-2 plays a key role in downregulation of RIG-I pathways and interacts with 40 S ribosome. Recently, the cryo-EM structure in complex with 40S ribosome is deciphered. However, the structure of full length NSP1 without any partner has not been studies. Also, the conformation of NSP1-C terminal region in isolation is not been studied. In this study, we have investigated the conformational dynamics of NSP1C-terminal region (NSP1-CTR; amino acids 130-180) in isolation and under different solvent environments. The NSP1-CTR is found to be intrinsically disordered in aqueous solution. Further, we used alpha helix inducer, trifluoroethanol, and found induction of alpha helical conformation using CD spectroscopy. Additionally, in the presence of SDS, NSP1-CTR is showing a conformational change from disordered to ordered, possibly gaining alpha helix in part. But in presence of neutral lipid DOPC, a slight change in conformation is observed. This implies the possible role of hydrophobic interaction and electrostatic interaction on the conformational changes of NSP1. The changes in structural conformation were further studied by fluorescence-based studies, which showed significant blue shift and fluorescence quenching in the presence of SDS and TFE. Lipid vesicles also showed fluorescence-based quenching. In agreement to these result, fluorescence lifetime and fluorescence anisotropy decay suggests a change in conformational dynamics. The zeta potential studies further validated that the conformational dynamics is mostly because of hydrophobic interaction. In last, these experimental studies were complemented through Molecular Dynamics (MD) simulation which have also shown a good correlation and testify our experiments. We believe that the intrinsically disordered nature of the NSP1-CTR will have implications in disorder based binding promiscuity with its interacting proteins.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Amit Kumar", + "author_inst": "Indian Institute of Technology Mandi" + }, + { + "author_name": "Ankur Kumar", + "author_inst": "Indian Institute of Technology Mandi" + }, + { + "author_name": "Prateek Kumar", + "author_inst": "Indian Institute of Technology Mandi" + }, + { + "author_name": "Neha Garg", + "author_inst": "Banaras Hindu University Varanasi" + }, + { + "author_name": "Rajanish Giri", + "author_inst": "Indian Institute of Technology Mandi" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2020.09.09.20191684", "rel_title": "Malaria Endemicity Influence on COVID -19 Mortality: New Evidence Added to BCG and TB Prevalence", @@ -1173863,109 +1175726,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.09.20191205", - "rel_title": "Evolution of immunity to SARS-CoV-2", - "rel_date": "2020-09-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.09.20191205", - "rel_abs": "The durability of infection-induced SARS-CoV-2 immunity has major implications for public health mitigation and vaccine development. Animal studies1,2 and the scarcity of confirmed re-infection3 suggests immune protection is likely, although the durability of this protection is debated. Lasting immunity following acute viral infection requires maintenance of both serum antibody and antigen-specific memory B and T lymphocytes and is notoriously pathogen specific, ranging from life-long for smallpox or measles4, to highly transient for common cold coronaviruses (CCC)5. Neutralising antibody responses are a likely correlate of protective immunity and exclusively recognise the viral spike (S) protein, predominantly targeting the receptor binding domain (RBD) within the S1 sub-domain6. Multiple reports describe waning of S-specific antibodies in the first 2-3 months following infection7-12. However, extrapolation of early linear trends in decay might be overly pessimistic, with several groups reporting that serum neutralisation is stable over time in a proportion of convalescent subjects8,12-17. While SARS-CoV-2 specific B and T cell responses are readily induced by infection6,13,18-24, the longitudinal dynamics of these key memory populations remains poorly resolved. Here we comprehensively profiled antibody, B and T cell dynamics over time in a cohort recovered from mild-moderate COVID-19. We find that binding and neutralising antibody responses, together with individual serum clonotypes, decay over the first 4 months post-infection, as expected, with a similar decline in S-specific CD4+ and circulating T follicular helper (cTFH) frequencies. In contrast, S-specific IgG+ memory B cells (MBC) consistently accumulate over time, eventually comprising a significant fraction of circulating MBC. Modelling of the concomitant immune kinetics predicts maintenance of serological neutralising activity above a titre of 1:40 in 50% of convalescent subjects to 74 days, with probable additive protection from B and T cells. Overall, our study suggests SARS-CoV-2 immunity after infection is likely to be transiently protective at a population level. SARS-CoV-2 vaccines may require greater immunogenicity and durability than natural infection to drive long-term protection.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Adam K Wheatley", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Jennifer A Juno", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Jing J Wang", - "author_inst": "Flinders University" - }, - { - "author_name": "Kevin J Selva", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Arnold Reynaldi", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Hyon-Xhi Tan", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Wen Shi Lee", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Kathleen M Wragg", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Hannah G Kelly", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Robyn Esterbauer", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Samantha K Davis", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Helen E Kent", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Francesca L Mordant", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Timothy E Schlub", - "author_inst": "University of New South Wales" - }, - { - "author_name": "David L Gordon", - "author_inst": "Flinders Medical Centre" - }, - { - "author_name": "David S Khoury", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Kanta Subbarao", - "author_inst": "WHO Collaborating Centre for Reference and Research on Influenza" - }, - { - "author_name": "Deborah Cromer", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Tom P Gordon", - "author_inst": "Flinders University" - }, - { - "author_name": "Amy W Chung", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Miles P Davenport", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Stephen J Kent", - "author_inst": "University of Melbourne" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.09.20187625", "rel_title": "Quantifying proximity, confinement, and interventions in disease outbreaks: a decision support framework for air-transported pathogens", @@ -1174597,6 +1176357,41 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2020.09.09.273268", + "rel_title": "Epigenetic Evolution of ACE2 and IL-6 Genes as Non-Canonical Interferon-Stimulated Genes Correlate to COVID-19 Susceptibility in Vertebrates", + "rel_date": "2020-09-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.09.273268", + "rel_abs": "Current novel coronavirus disease (COVID-19) has spread globally within a matter of months. The virus establishes a success in balancing its deadliness and contagiousness, and causes substantial differences in susceptibility and disease progression in people of different ages, genders and pre-existing comorbidities. Since these host factors are subjected to epigenetic regulation, relevant analyses on some key genes underlying COVID-19 pathogenesis were performed to longitudinally decipher their epigenetic correlation to COVID-19 susceptibility. The genes of host angiotensin-converting enzyme 2 (ACE2, as the major virus receptor) and interleukin (IL)-6 (a key immune-pathological factor triggering cytokine storm) were shown to evince active epigenetic evolution via histone modification and cis/trans-factors interaction across different vertebrate species. Extensive analyses revealed that ACE2 ad IL-6 genes are among a subset of non-canonical interferon-stimulated genes (non-ISGs), which have been designated recently for their unconventional responses to interferons (IFNs) and inflammatory stimuli through an epigenetic cascade. Furthermore, significantly higher positive histone modification markers and position weight matrix (PWM) scores of key cis-elements corresponding to inflammatory and IFN signaling, were discovered in both ACE2 and IL6 gene promoters across representative COVID-19-susceptible species compared to unsusceptible ones. Findings characterize ACE2 and IL-6 genes as non-ISGs that respond differently to inflammatory and IFN signaling from the canonical ISGs and their epigenetic properties may serve as biomarkers to longitudinally predict COVID-19 susceptibility in vertebrates and partially explain COVID-19 inequality in people of different subgroups.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Eric R. Sang", + "author_inst": "Tennessee State University" + }, + { + "author_name": "Yun Tian", + "author_inst": "Tennessee State University" + }, + { + "author_name": "Yuanying Gong", + "author_inst": "Tennessee State University" + }, + { + "author_name": "Laura C Miller", + "author_inst": "USDA-ARS" + }, + { + "author_name": "Yongming Sang", + "author_inst": "Tennessee State University" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2020.09.10.286948", "rel_title": "Real-time conformational dynamics of SARS-CoV-2 spikes on virus particles", @@ -1175565,117 +1177360,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.07.20189357", - "rel_title": "COMBINATION OF TOCILIZUMAB AND STEROIDS TO IMPROVE MORTALITY IN PATIENTS WITH SEVERE COVID-19 INFECTION: A SPANISH, MULTICENTER, COHORT STUDY", - "rel_date": "2020-09-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.07.20189357", - "rel_abs": "BackgroundWe aimed to determine the impact of tocilizumab use in severe COVID-19 pneumonia mortality.\n\nMethodsWe performed a multicentre retrospective cohort study in 18 tertiary hospitals in Spain, from March to April 2020. Consecutive patients admitted with severe COVID-19 treated with tocilizumab were compared to patients not treated with tocilizumab, adjusting by Inverse Probability of the Treatment Weights (IPTW). Tocilizumab effect in patients receiving steroids during the 48h following inclusion was analyzed.\n\nResultsDuring the study period, 506 patients with severe COVID-19 fulfilled inclusion criteria. Among them, 268 were treated with tocilizumab and 238 patients were not. Median time to tocilizumab treatment from onset of symptoms was 11 days (IQR 8-14). Global mortality was 23.7%. Mortality was lower in patients treated with tocilizumab than in controls (16.8% versus 31.5%, HR 0.514 [95CI 0.355-0.744], p< 0.001; weighted HR 0.741 [95CI 0.619-0.887], p = 0.001). Tocilizumab treatment reduced mortality by 14.7% relative to no tocilizumab treatment (RRR 46.7%). We calculated a number necessary to treat of 7. Among patients treated with steroids, mortality was lower in patients treated with tocilizumab than in those treated with steroids alone (10.9% versus 40.2%, HR 0.511 [95CI 0.352-0.741], p = 0.036; weighted HR 0.6 [95CI 0.449-0.804], p< 0.001) (Interaction p = 0.094).\n\nConclusionsThese results show that survival of patients with severe COVID-19 is higher in patients treated with tocilizumab than in those not treated, and that tocilizumab effect adds to that of steroids administered to non-intubated cases with COVID-19 during the first 48 hours of presenting with respiratory failure despite of oxygen therapy. Randomised controlled studies are needed to confirm these results.\n\nSummaryWe investigated in-hospital mortality of patients with severe SARS-CoV-2 pneumonia in a multicenter series of patients treated with tocilizumab compared to controls, and adjusted using IPTW. Our results show a beneficial impact of tocilizumab treatment in SARS-CoV-2 pneumonia, that adds to that of steroids.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Belen Ruiz-Antoran", - "author_inst": "Hospital Universitario Puerta de Hierro Majadahonda" - }, - { - "author_name": "Aranzazu Sancho-Lopez", - "author_inst": "Hospital Universitario Puerta de Hierro Majadahonda" - }, - { - "author_name": "Ferran Torres", - "author_inst": "Hospital Clinic, Barcelona" - }, - { - "author_name": "Victor Moreno-Torres", - "author_inst": "Hospital Universitario Puerta de Hierro-Majadahonda" - }, - { - "author_name": "Itziar de Pablo Lopez de Abechuco", - "author_inst": "Hospital Universitario Ramon y Cajal" - }, - { - "author_name": "Paulina Garcia Lopez", - "author_inst": "Hospital Universitario Torrecardenas" - }, - { - "author_name": "Francisco Abad-Santos", - "author_inst": "Hospital Universitario La Princesa" - }, - { - "author_name": "Clara Maria Rosso Fernandez", - "author_inst": "Hospital Universitario Virgen del Rocio" - }, - { - "author_name": "Ana Aldea-Perona", - "author_inst": "Consorcio Parc Salut Mar" - }, - { - "author_name": "Eva Montane", - "author_inst": "Hospital Universitario Germans Trias i Pujol" - }, - { - "author_name": "Ruth M Aparicio-Hernandez", - "author_inst": "Hospital Universitario Central de la Defensa Gomez Ulla" - }, - { - "author_name": "Roser LLop Rius", - "author_inst": "Hospital Universitari de Bellvitge" - }, - { - "author_name": "Consuelo Pedros", - "author_inst": "Hospital General Universitari de Valencia" - }, - { - "author_name": "Paloma Gijon", - "author_inst": "Hospital General Universitario Gregorio Maranon" - }, - { - "author_name": "Carolina Hernandez Carballo", - "author_inst": "Hospital Universitario Nuestra Senora Candelaria" - }, - { - "author_name": "Maria Jose Pedrosa Martinez", - "author_inst": "Hospital Universitario Puerto Real" - }, - { - "author_name": "Guillermo Prada-Ramallal", - "author_inst": "Fundacion Instituto de Investigacion Sanitaria de Santiago de Compostela (FIDIS)" - }, - { - "author_name": "Lourdes Cabrera Garcia", - "author_inst": "Hospital Universitario Clinico San Carlos" - }, - { - "author_name": "Josefa Andrea Aguilar Garcia", - "author_inst": "Hospital Costa del Sol Marbella" - }, - { - "author_name": "Rocio Sanjuan-Jimenez", - "author_inst": "Hospital Universitario Virgen de la Victoria" - }, - { - "author_name": "Evelyn Iveth Ortiz Barraza", - "author_inst": "Hospital Universitario Ramon y Cajal" - }, - { - "author_name": "Enrique Sanchez Chica", - "author_inst": "Hospital Universitario Puerta de Hierro Majadahonda" - }, - { - "author_name": "Ana Fernandez-Cruz", - "author_inst": "Hospital Universitario Puerta de Hierro Majadahonda" - }, - { - "author_name": "- TOCICOV-study group.", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.07.20189852", "rel_title": "Network for subclinical prognostication of COVID 19 Patients from data of thoracic roentgenogram: A feasible alternative screening technology", @@ -1176335,6 +1178019,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.07.20188813", + "rel_title": "Tracking Smell Loss to Identify Healthcare Workers with SARS-CoV-2 Infection", + "rel_date": "2020-09-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.07.20188813", + "rel_abs": "BackgroundHealthcare workers (HCW) treating COVID-19 patients are at high risk for infection and may also spread infection through their contact with vulnerable patients. Smell loss has been associated with SARS-CoV-2 infection, but it is unknown whether monitoring for smell loss can be used to identify asymptomatic infection among high risk individuals, like HCW.\n\nMethodsWe performed a prospective cohort study, tracking 473 HCW across three months to determine if smell loss could predict SARS-CoV-2 infection in this high-risk group. HCW subjects completed a longitudinal, novel behavioral at-home assessment of smell function with household items, as well as detailed symptom surveys that included a parosmia screening questionnaire, and RT-qPCR testing to identify SARSCoV-2 infection.\n\nResultsSARS-CoV-2 was identified in 17 (3.6%) of 473 HCW. Among the 17 infected HCW, 53% reported smell loss, and were more likely to report smell loss than COVID-negative HCW on both the at-home assessment and the screening questionnaire (P < .01). 67% reported smell loss prior to having a positive SARS-CoV-2 test, and smell loss was reported a median of two days before testing positive. Neurological symptoms were reported more frequently among COVID-positive HCW who reported smell loss (P < .01).\n\nConclusionsIn this prospective study of HCW, self-reported changes in smell using two different measures were predictive of COVID-19 infection. Smell loss frequently preceded a positive test and was associated with neurological symptoms.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Julian J Weiss", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Tuki N Attuquayefio", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Elizabeth B White", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Fangyong Li", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Rachel S Herz", + "author_inst": "Alpert Medical School of Brown University" + }, + { + "author_name": "Theresa L White", + "author_inst": "Le Moyne College, SUNY Upstate Medical University" + }, + { + "author_name": "Melissa Campbell", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Bertie Geng", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Rupak Datta", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Anne L Wyllie", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Nathan D Grubaugh", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Arnau Casanovas-Massana", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "M Catherine Muenker", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Ryan Handoko", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Akiko Iwasaki", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "- The Yale IMPACT Research Team", + "author_inst": "" + }, + { + "author_name": "Richard A Martinello", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Albert I Ko", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Dana M Small", + "author_inst": "Yale University" + }, + { + "author_name": "Shelli F Farhadian", + "author_inst": "Yale School of Medicine" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.09.20190389", "rel_title": "Passive, open access data measures movement and predicts COVID-19 cases", @@ -1177035,65 +1178814,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.07.20190074", - "rel_title": "Clinical Outcomes of Critically Ill Patients with COVID-19 by Race", - "rel_date": "2020-09-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.07.20190074", - "rel_abs": "BackgroundStudies of COVID-19 have shown that African Americans have been affected by the virus at a higher rate compared to other races. This cohort study investigated comorbidities and clinical outcomes by race among COVID-19 patients admitted to the intensive care unit.\n\nMethodsThis is a case series of critically ill patients admitted with COVID-19 to a tertiary referral teaching hospital in Atlanta, Georgia. The study included all critically ill hospitalized patients between March 6, 2020 and May 5, 2020. Clinical outcomes during hospitalization included mechanical ventilation, renal replacement therapy and mortality stratified by race.\n\nResultsOf 288 patients included (mean age, 63 {+/-} 16 years; 45% female), 210 (73%) were African American. African Americans had significantly higher rates of comorbidities compared to other races, including hypertension (80% vs 59%, p=0.001), diabetes (49% vs 34%, p=0.026) and mean BMI (33 kg/m2 vs 28 kg/m2, p<0.001). Despite African Americans requiring continuous renal replacement therapy during hospitalization at higher rates than other races (27% vs 13%, p=0.011), rates of intubation, intensive care unit length of stay, and overall mortality (30% vs 24%, p=0.307) were similar.\n\nConclusionThis racially diverse series of critically ill COVID-19 patients shows that despite higher rates of comorbidities at hospital admission in African Americans compared with other races, there was no significant difference in mortality.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Fahad Marmarchi", - "author_inst": "Emory University" - }, - { - "author_name": "Michael Liu", - "author_inst": "Emory University" - }, - { - "author_name": "Srikant Rangaraju", - "author_inst": "Emory University" - }, - { - "author_name": "Sara C Auld", - "author_inst": "Emory University" - }, - { - "author_name": "Maria Christina Creel-Bulos", - "author_inst": "Emory University" - }, - { - "author_name": "Christine L Kempton", - "author_inst": "Emory University" - }, - { - "author_name": "Milad Sharifpour", - "author_inst": "Emory University" - }, - { - "author_name": "Manila Gaddh", - "author_inst": "Emory University" - }, - { - "author_name": "Roman Sniecinski", - "author_inst": "Emory University" - }, - { - "author_name": "Cheryl L Maier", - "author_inst": "Emory University" - }, - { - "author_name": "Fadi Nahab", - "author_inst": "Emory University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.07.20190173", "rel_title": "Functionalized TiO2 nanotube-based Electrochemical Biosensor for Rapid Detection of SARS-CoV-2", @@ -1178153,6 +1179873,101 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.09.09.287508", + "rel_title": "Interaction network of SARS-CoV-2 with host receptome through spike protein", + "rel_date": "2020-09-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.09.287508", + "rel_abs": "Host cellular receptors are key determinants of virus tropism and pathogenesis. Virus utilizes multiple receptors for attachment, entry, or specific host responses. However, other than ACE2, little is known about SARS-CoV-2 receptors. Furthermore, ACE2 cannot easily interpret the multi-organ tropisms of SARS-CoV-2 nor the clinical differences between SARS-CoV-2 and SARS-CoV. To identify host cell receptors involved in SARS-CoV-2 interactions, we performed genomic receptor profiling to screen almost all human membrane proteins, with SARS-CoV-2 capsid spike (S) protein as the target. Twelve receptors were identified, including ACE2. Most receptors bind at least two domains on S protein, the receptor-binding-domain (RBD) and the N-terminal-domain (NTD), suggesting both are critical for virus-host interaction. Ectopic expression of ASGR1 or KREMEN1 is sufficient to enable entry of SARS-CoV-2, but not SARS-CoV and MERS-CoV. Analyzing single-cell transcriptome profiles from COVID-19 patients revealed that virus susceptibility in airway epithelial ciliated and secretory cells and immune macrophages highly correlates with expression of ACE2, KREMEN1 and ASGR1 respectively, and ACE2/ASGR1/KREMEN1 (ASK) together displayed a much better correlation than any individual receptor. Based on modeling of systemic SARS-CoV-2 host interactions through S receptors, we revealed ASK correlation with SARS-CoV-2 multi-organ tropism and provided potential explanations for various COVID-19 symptoms. Our study identified a panel of SARS-CoV-2 receptors with diverse binding properties, biological functions, and clinical correlations or implications, including ASGR1 and KREMEN1 as the alternative entry receptors, providing insights into critical interactions of SARS-CoV-2 with host, as well as a useful resource and potential drug targets for COVID-19 investigation.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Yunqing Gu", + "author_inst": "Fudan University" + }, + { + "author_name": "Jun Cao", + "author_inst": "Fudan University" + }, + { + "author_name": "Xinyu Zhang", + "author_inst": "Fudan University" + }, + { + "author_name": "Hai Gao", + "author_inst": "Fudan University" + }, + { + "author_name": "Yuyan Wang", + "author_inst": "Fudan University" + }, + { + "author_name": "Jia Wang", + "author_inst": "Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences" + }, + { + "author_name": "Jinlan Zhang", + "author_inst": "Fudan University" + }, + { + "author_name": "Guanghui Shen", + "author_inst": "Fudan University" + }, + { + "author_name": "Xiaoyi Jiang", + "author_inst": "Fudan University" + }, + { + "author_name": "Jie Yang", + "author_inst": "Fudan University" + }, + { + "author_name": "Xichen Zheng", + "author_inst": "Fudan University" + }, + { + "author_name": "Jianqing Xu", + "author_inst": "Fudan University" + }, + { + "author_name": "Cheng Cheng Zhang", + "author_inst": "University of Texas Southwestern Medical Center" + }, + { + "author_name": "Fei Lan", + "author_inst": "Fudan University" + }, + { + "author_name": "Di Qu", + "author_inst": "Fudan University" + }, + { + "author_name": "Yun Zhao", + "author_inst": "Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences" + }, + { + "author_name": "Guoliang Xu", + "author_inst": "Fudan University" + }, + { + "author_name": "Youhua Xie", + "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Fudan University" + }, + { + "author_name": "Min Luo", + "author_inst": "Fudan University" + }, + { + "author_name": "Zhigang Lu", + "author_inst": "Fudan University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.09.08.286732", "rel_title": "Rapid, high-yield production of full-length SARS-CoV-2 spike ectodomain by transient gene expression in CHO cells", @@ -1178993,25 +1180808,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.06.20189423", - "rel_title": "Covid-19 vs BCG Universal Immunization: Statistical Significance at Six Months of Exposure", - "rel_date": "2020-09-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.06.20189423", - "rel_abs": "With a time-adjusted dataset of Covid-19 statistical data by reporting jurisdiction at the time point of six months after the local epidemics landfall we perform a statistical analysis of the significance of the correlation hypothesis between universal BCG immunization and milder Covid-19 scenarios proposed in the earlier studies. With the data accumulated to date the statistical significance of the BCG immunization correlation hypothesis is evaluated both qualitatively and quantitatively with the conclusion that it has achieved a significant level of confidence. The conclusions of this research can be used in public policy as well as the rationale to investigate the nature and working of a potential broad immunity mechanism associated with an early-age BCG exposure.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Serge Dolgikh", - "author_inst": "National Aviation University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.06.20189506", "rel_title": "Unequal Lives: A Sociodemographic Analysis of Covid19 Transmission and Mortality in India", @@ -1180943,6 +1182739,57 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.09.07.286906", + "rel_title": "In vitro study of BromAc on SARS-CoV-2 spike and envelope proteins shows synergy and disintegration at modest concentrations", + "rel_date": "2020-09-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.07.286906", + "rel_abs": "Background and objectivesSARS-CoV-2 infection is the cause of a worldwide pandemic, currently with limited therapeutic options. Whilst vaccines are at the forefront of the therapeutic initiative, drug repurposing remains a promising approach for SARS-CoV-2 treatment. BromAc (Bromelain & Acetylcysteine) has synergistic action against glycoproteins by the synchronous breakage of glycosidic linkages and disulfide bonds. The spike protein of SARS-CoV-2, formed of glycoprotein and disulfide bridges for stabilization, represents an attractive target as it is essential for binding to the ACE2 receptor in host cells present in nasal mucosa. We sought to determine the effect of BromAc on the Spike and Envelope proteins and its potential to reduce infectivity in host cells.\n\nDesignRecombinant Spike and Envelope proteins were treated by single agent and combination BromAc at 50 and 100 {micro}g/20mg/mL and analyzed by electrophoresis. Ultraviolet analysis of disulfide bond reduction was performed for both Spike and Envelope proteins after treatment with Acetylcysteine. In vitro whole virus culture inactivation of pre-treated wild type and an S1/S2 Spike mutant SARS-CoV-2 with BromAc from 25 to 250 {micro}g/20mg/mL was measured by cytopathic effect, cell lysis assay, and replication capacity by RT-PCR.\n\nResultsRecombinant Spike and Envelope SARS-CoV-2 proteins were fragmented by BromAc at both 50 and 100 {micro}g/20mg/mL whilst single agents had minimal effect. Spike and Envelope protein disulfide bonds were reduced by Acetylcysteine. In vitro whole virus culture of both wild type and Spike mutant SARS-CoV-2 demonstrated a concentration-dependent inactivation from BromAc treatment but not from single agents.\n\nConclusionBromAc disintegrates SARS-CoV-2 Spike and Envelope proteins. In vitro tests on whole virus support this finding with inactivation of its replication capacity most strongly at 100 and 250 {micro}g/20mg/mL BromAc, even in Spike mutant virus. Clinical testing through nasal administration in patients with early SARS-CoV-2 infection is imminent.\n\nAuthor SummaryThere is currently no suitable therapeutic treatment for early SARS-CoV-2 aimed to prevent disease progression. BromAc is under clinical development by the authors for mucinous cancers due to its ability to alter complex glycoproteins structure. The potential of BromAc on SARS-CoV-2 Spike and Envelope glycoproteins stabilized by disulfide bonds was examined and found to disintegrate recombinant Spike and Envelope proteins whilst reducing disulfide stabilizer bridges. BromAc also showed an inhibitory effect on wild-type and Spike mutant SARS-CoV-2 by inactivation of its replication capacity in vitro. Hence, BromAc may be an effective therapeutic agent for early SARS-CoV-2 infection, despite mutations, and even have potential as a prophylactic in people at high risk of infection.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Javed Akhter", + "author_inst": "St George Hospital" + }, + { + "author_name": "Gregory Queromes", + "author_inst": "CIRI (Centre International de Recherche en Infectiologie)" + }, + { + "author_name": "Krishna Pillai", + "author_inst": "St George Hospital" + }, + { + "author_name": "Vahan Kepenekian", + "author_inst": "Hospices Civils de Lyon, Lyon, France; EMR 3738 (CICLY), Lyon 1 Universite, Lyon, France" + }, + { + "author_name": "Samina Badar", + "author_inst": "UNSW" + }, + { + "author_name": "Ahmed Mekkawy", + "author_inst": "UNSW" + }, + { + "author_name": "Emilie Frobert", + "author_inst": "CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Universite Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, " + }, + { + "author_name": "Sarah Valle", + "author_inst": "UNSW" + }, + { + "author_name": "David L Morris", + "author_inst": "University of New South Wales, St George Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.09.07.286567", "rel_title": "Interaction of human ACE2 to membrane-bound SARS-CoV-1 and SARS-CoV-2 S glycoproteins", @@ -1181915,53 +1183762,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.05.20188805", - "rel_title": "Health professionals practice and associated factors towards precautionary measures for COVID-19 pandemic in public health facilities of Gamo zone, southern Ethiopia: a cross-sectional study", - "rel_date": "2020-09-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.05.20188805", - "rel_abs": "IntroductionCoronavirus disease-2019 (COVID-19) is a highly contagious acute respiratory disease, which caused by a novel coronavirus. The disease disrupts health systems and resulting in social, political, and economic crises. Health professionals are in front of this pandemic and always work in a high-risk environment. Currently, there is no vaccine or drug for the disease. Therefore, strictly practicing precautionary measures are the only option to save the life. Some studies reported health professionals practice of precautionary measures for COVID-19. Nevertheless, a few have identified factors affecting. As such, this study aimed to fill those research gaps in the study setting.\n\nMethodsIn this cross-sectional study, 428 health professionals were involved from the public health facilities of the Gamo zone, southern Ethiopia. A simple random sampling method was employed, and the data collected by the interviewer-administered Open Data Kit survey tool and observational checklist. The data analyzed in Stata version 15 and a binary logistic regression model used to identify factors. In this study, a statistically significant association was declared at P < 0.05.\n\nResultsIn this study, 35.3% (95%CI: 30.7%, 39.8%) of health professionals had a good practice on precautionary measures for the COVID-19 pandemic. Use hand sanitizer or wash hands continuously with soap and water (68.9%), cover nose and mouth with a tissue during sneezing or coughing (67.3%), and use facemask in crowds (56.8%) were the most common practice reported by study participants. Marital status, being married (AOR = 1.84, 95%CI: 1.06, 3.18), good knowledge on the COVID-19 pandemic (AOR = 2.02, 95%CI: 1.02, 3.18), and positive attitude towards precautionary measures for COVID-19 were factors showed signification association with the practice.\n\nConclusionsThe magnitude of good practice of precautionary measures for the COVID-19 pandemic among health professionals was low. As such, different interventions to improve the knowledge and attitude of health professionals in the health care system are highly needed to boost the practice and to advance service delivery.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Abera Mersha", - "author_inst": "Arba Minch University" - }, - { - "author_name": "Shitaye Shibiru", - "author_inst": "Arba Minch University" - }, - { - "author_name": "Meseret Girma", - "author_inst": "Arba Minch University" - }, - { - "author_name": "Gistane Ayele", - "author_inst": "Arba Minch University" - }, - { - "author_name": "Agegnehu Bante", - "author_inst": "Arba Minch University" - }, - { - "author_name": "Mekidim Kassa", - "author_inst": "Arba Minch University" - }, - { - "author_name": "Sintayehu Abebe", - "author_inst": "Arba Minch University" - }, - { - "author_name": "Misgun Shewangizaw", - "author_inst": "Arba Minch University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.04.20187088", "rel_title": "Serological Responses to Human Virome Define Clinical Outcomes of Italian Patients Infected with SARS-CoV-2", @@ -1182673,6 +1184473,61 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.09.05.284604", + "rel_title": "Genomic analysis reveals local transmission of SARS-CoV-2 in early pandemic phase in Peru", + "rel_date": "2020-09-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.05.284604", + "rel_abs": "The dissemination of cases of the new SAR-COV-2 coronavirus represents a serious public health problem for Latin America and Peru. For this reason, it is important to characterize the genome of the isolates that circulate in Latin America. To characterize the complete genome of first samples of the virus circulating in Peru, we amplified seven overlapping segments of the viral genome by RT-PCR and sequenced using Miseq platform. The results indicate that the genomes of the Peruvian SARS-COV-2 samples belong to the genetic groups G and S. Likewise, a phylogenetic and MST analysis of the isolates confirm the introduction of multiple isolates from Europe and Asia that, after border closing, were transmitted locally in the capital and same regions of the country. These Peruvian samples (56%) grouped into two clusters inside G clade and share B.1.1.1 lineage. The characterization of these isolates must be considered for the use and design of diagnostic tools, and effective treatment and vaccine formulations.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Carlos Padilla Rojas Sr.", + "author_inst": "Instituto Nacional de Salud, Peru" + }, + { + "author_name": "Karolyn Vega Chozo", + "author_inst": "Instituto Nacional de Salud, Peru" + }, + { + "author_name": "Marco Galarza Perez", + "author_inst": "Instituto Nacional de Salud, Peru" + }, + { + "author_name": "Henri Bailon Calderon", + "author_inst": "Instituto Nacional de Salud, Peru" + }, + { + "author_name": "Priscila Lope Pari", + "author_inst": "Instituto Nacional de Salud, Peru" + }, + { + "author_name": "Johana Balbuena Torres", + "author_inst": "Instituto Nacional de Salud, Peru" + }, + { + "author_name": "David Garcia Neyra", + "author_inst": "Instituto Nacional de Salud, Peru" + }, + { + "author_name": "Maribel Huaringa Nunez", + "author_inst": "Instituto Nacional de Salud, Peru" + }, + { + "author_name": "Nancy Rojas Serrano", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Omar Caceres Rey", + "author_inst": "Instituto Nacional de Salud" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.09.04.283853", "rel_title": "Pre-clinical studies of a recombinant adenoviral mucosal vaccine to prevent SARS-CoV-2 infection", @@ -1183517,29 +1185372,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.03.20187880", - "rel_title": "Forecasting the outbreak of COVID-19 in Lebanon", - "rel_date": "2020-09-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.03.20187880", - "rel_abs": "This note explores the spread of the Coronavirus disease 2019 (COVID-19) in Lebanon using available data until August 25th, 2020 and forecasts the number of infections until the end of September using four diffierent scenarios for mitigation measures reflected in the reproductive number Rt. Mitigation measures in Lebanon date back to early March soon after the first confirmed cases, and have been gradually lifted as of May. Thereafter, the country has witnessed a slow yet steady increase in the number of cases that has been significantly exacerbated after the explosion at Beirut harbor on August 4. Furthermore, we estimate the daily active cases in need of intensive care compared to the available number of beds and we assess accordingly that this capacity will be exhausted within a short span of time, unless severe measures are imposed.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Omar El Deeb", - "author_inst": "Lebanese International University and Lebanese University" - }, - { - "author_name": "Maya Jalloul", - "author_inst": "Lebanese American University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.04.20187963", "rel_title": "Estimating COVID-19 hospital demand using a non-parametric model: a case study in Galicia (Spain)", @@ -1184127,6 +1185959,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.03.20179598", + "rel_title": "Multiplexed, Microscale, Microarray-based Serological Assay for Antibodies Against All Human-Relevant Coronaviruses", + "rel_date": "2020-09-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.03.20179598", + "rel_abs": "Rapid, sensitive, and precise multiplexed assays for serological analysis during candidate COVID-19 vaccine development would streamline clinical trials. The VaxArray Coronavirus (CoV) SeroAssay quantifies IgG antibody binding to 9 pandemic, potentially pandemic, and endemic human CoV spike antigens in 2 hours with automated results analysis. IgG antibodies in serum bind to the CoV spike protein capture antigens printed in a microarray format and are labeled with a fluorescent anti-species IgG secondary label. The assay demonstrated excellent lower limits of quantification ranging from 0.3 - 2.0 ng/mL and linear dynamic ranges of 76 to 911-fold. Average precision of 11% CV and accuracy (% recovery) of 92.5% over all capture antigens were achieved over 216 replicates representing 3 days and 3 microarray lots. Clinical performance on 263 human serum samples (132 SARS-CoV-2 negatives and 131 positives based on donor-matched RT-PCR and/or date of collection) produced 98.5% PPA (sensitivity) and 100% NPA (specificity).", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Erica D Dawson", + "author_inst": "InDevR, Inc." + }, + { + "author_name": "Laura R Kuck", + "author_inst": "InDevR, Inc." + }, + { + "author_name": "Rebecca H Blair", + "author_inst": "InDevR, Inc." + }, + { + "author_name": "Amber W Taylor", + "author_inst": "InDevR, Inc." + }, + { + "author_name": "Evan Toth", + "author_inst": "InDevR, Inc." + }, + { + "author_name": "Vijaya Knight", + "author_inst": "Children's Hospital of Colorado" + }, + { + "author_name": "Kathy L Rowlen", + "author_inst": "InDevR, Inc." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.03.20187393", "rel_title": "Effect of Renin-Angiotensin-Aldosterone System inhibitors on outcomes of COVID-19 patients with hypertension: Systematic review and Meta-analysis", @@ -1185051,49 +1186926,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2020.09.01.20186445", - "rel_title": "Healthcare Worker Attendance During the Early Stages of the COVID-19 Pandemic: A Longitudinal Analysis of Daily Fingerprint-Verified Data from All Public-Sector Secondary and Tertiary Care Facilities in Bangladesh", - "rel_date": "2020-09-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.01.20186445", - "rel_abs": "BackgroundThe COVID-19 pandemic has overwhelmed hospitals in several areas in high-income countries. An effective response to this pandemic requires healthcare workers (HCWs) to be present at work, particularly in low- and middle-income countries (LMICs) where they are already in critically low supply. To inform whether and to what degree policymakers in Bangladesh, and LMICs more broadly, should expect a drop in HCW attendance as COVID-19 continues to spread, this study aims to determine how HCW attendance has changed during the early stages of the COVID-19 pandemic in Bangladesh.\n\nMethodsThis study analyzed daily fingerprint-verified attendance data from all 527 public-sector secondary and tertiary care facilities in Bangladesh to describe HCW attendance from January 26, 2019 to March 22, 2020, by cadre, hospital type, and geographic division. We then regressed HCW attendance onto fixed effects for day-of-week, month, and hospital, as well as indicators for each of three pandemic periods: a China-focused period (January 11, 2020 [first confirmed COVID-19 death in China] until January 29, 2020), international-spread period (January 30, 2020 [World Health Organizations declaration of a global emergency] until March 6, 2020), and local-spread period (March 7, 2020 [first confirmed COVID-19 case in Bangladesh] until the end of the study period).\n\nFindingsOn average between January 26, 2019 and March 22, 2020, 34{middle dot}1% of doctors, 64{middle dot}6% of nurses, and 70{middle dot}6% of other healthcare staff were present for their scheduled shift. HCWs attendance rate increased with time in 2019 among all cadres. Nurses attendance level dropped by 2{middle dot}5% points (95% CI; -3{middle dot}2% to -1{middle dot}8%) and 3{middle dot}5% points (95% CI; -4{middle dot}5% to -2{middle dot}5%) during the international-spread and the local-spread periods of the COVID-19 pandemic, relative to the China-focused period. Similarly, the attendance level of other healthcare staff declined by 0{middle dot}3% points (95% CI; -0{middle dot}8% to 0{middle dot}2%) and 2{middle dot}3% points (95% CI; -3{middle dot}0% to -1{middle dot}6%) during the international-spread and local-spread periods, respectively. Among doctors, however, the international-spread and local-spread periods were associated with a statistically significant increase in attendance by 3{middle dot}7% points (95% CI; 2{middle dot}5% to 4{middle dot}8%) and 4{middle dot}9% points (95% CI; 3{middle dot}5% to 6{middle dot}4%), respectively. The reduction in attendance levels across all HCWs during the local-spread period was much greater at large hospitals, where the majority of COVID-19 testing and treatment took place, than that at small hospitals.\n\nConclusionsAfter a year of significant improvements, HCWs attendance levels among nurses and other healthcare staff (who form the majority of Bangladeshs healthcare workforce) have declined during the early stages of the COVID-19 pandemic. This finding may portend an even greater decrease in attendance if COVID-19 continues to spread in Bangladesh. Policymakers in Bangladesh and similar LMICs should undertake major efforts to achieve high attendance levels among HCWs, particularly nurses, such as by providing sufficient personal protective equipment as well as monetary and non-monetary incentives.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Duy Do", - "author_inst": "Heidelberg Institute of Global Health, University of Heidelberg; Stanford University" - }, - { - "author_name": "Malabika Sarker", - "author_inst": "James P. Grant School of Public Health, BRAC University; Heidelberg Institute of Global Health, University of Heidelberg" - }, - { - "author_name": "Simiao Chen", - "author_inst": "Heidelberg Institute of Global Health" - }, - { - "author_name": "Ali Lenjani", - "author_inst": "Heidelberg Institute of Global Health, University of Heidelberg" - }, - { - "author_name": "Pauli Tikka", - "author_inst": "Heidelberg Institute of Global Health, University of Heidelberg" - }, - { - "author_name": "Till Barnighausen", - "author_inst": "Heidelberg Institute of Global Health, University of Heidelberg; Peking Union Medical College, Beijing, China; Harvard T.H. Chan School of Public Health, Harvar" - }, - { - "author_name": "Pascal Geldsetzer", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.09.01.20186411", "rel_title": "The Impact of Psychology Interventions on Changing Mental Health Status and Sleep Quality in University Students during the COVID-19 Pandemic", @@ -1185749,6 +1187581,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.02.20186783", + "rel_title": "PI3K/mTOR and topoisomerase inhibitors with potential activity against SARS-CoV-2 infection", + "rel_date": "2020-09-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.02.20186783", + "rel_abs": "There is an urgent need to identify therapies to prevent and treat SARS-CoV-2 infection. We performed a statistical evaluation of in vitro gene expression profiles reflecting exposure to 1,835 drugs, and found topoisomerase inhibitors and PI3K/mTOR pathway inhibitors among the strongest candidates for reduced expression of ACE2, a host gene associated with SARS-CoV-2 infection. Retrospective clinical data suggest that patients on these agents may be less likely to test positive for SARS-CoV-2.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "James Robert White", + "author_inst": "Resphera Biosciences" + }, + { + "author_name": "Michael Bonner Foote", + "author_inst": "Memorial Sloan Kettering Cancer Center, New York, NY, USA" + }, + { + "author_name": "Justin Jee", + "author_inst": "Memorial Sloan Kettering Cancer Center, New York, NY, USA" + }, + { + "author_name": "Guillem Argil\u00e9s", + "author_inst": "Memorial Sloan Kettering Cancer Center, New York, NY, USA" + }, + { + "author_name": "Jonathan C.M. Wan", + "author_inst": "Memorial Sloan Kettering Cancer Center, New York, NY, USA" + }, + { + "author_name": "Luis Alberto Diaz Jr.", + "author_inst": "Memorial Sloan Kettering Cancer Center, New York, NY, USA" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.02.20183830", "rel_title": "Pooling saliva to increase SARS-CoV-2 testing capacity", @@ -1186665,37 +1188536,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2020.09.02.20185660", - "rel_title": "Onset of effects of non-pharmaceutical interventions on COVID-19 worldwide", - "rel_date": "2020-09-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.02.20185660", - "rel_abs": "During the initial phase of the global COVID-19 outbreak, most countries responded with non-pharmaceutical interventions (NPIs). The effectiveness of these NPIs has been investigated with simulation studies, that rely on assumptions and by empirical studies with few countries and controversial results. However, it has not been investigated in detail how long different NPIs need to be in place to take effect, or how long they should be in place for their maximum effect to unfold. We used global data and a non-parametric machine learning model to estimate the effects of NPIs in relation to how long they have been in place. Here we show that closure and regulation of schools was the most important NPI, associated with a pronounced effect about 10 days after implementation. Restrictions of mass gatherings and restrictions and regulations of businesses were found to have a more gradual effect, and social distancing was associated with a delayed effect starting about 18 days after implementation. Generally, effects increased until about 40 to 50 days after implementation. Our results can inform political decisions regarding the choice of NPIs and how long they need to be in place to take effect.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Elisabeth Lucia Zeilinger", - "author_inst": "Faculty of Psychology, University of Vienna" - }, - { - "author_name": "Ingo W. Nader", - "author_inst": "IT Power Services GmbH, Vienna, Austria" - }, - { - "author_name": "Dana Jomar", - "author_inst": "IT Power Services GmbH, Vienna, Austria" - }, - { - "author_name": "Clemens Zauchner", - "author_inst": "IT Power Services GmbH, Vienna, Austria" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.09.01.20179879", "rel_title": "Exploring options for reprocessing of N95 Filtering Facepiece Respirators (N95-FFRs) amidst COVID-19 pandemic: a systematic review", @@ -1187327,6 +1189167,33 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.09.03.281600", + "rel_title": "Boosting the analysis of protein interfaces with Multiple Interface String Alignment: illustration on the spikes of coronaviruses", + "rel_date": "2020-09-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.03.281600", + "rel_abs": "We introduce Multiple Interface String Alignment (MISA), a visualization tool to display coherently various sequence and structure based statistics at protein-protein interfaces (SSE elements, buried surface area, {Delta}ASA, B factor values, etc). The amino-acids supporting these annotations are obtained from Voronoi interface models. The benefit of MISA is to collate annotated sequences of (homologous) chains found in different biological contexts i.e. bound with different partners or unbound. The aggregated views MISA/SSE, MISA/BSA, MISA/{Delta} ASAetc make it trivial to identify commonalities and differences between chains, to infer key interface residues, and to understand where conformational changes occur upon binding. As such, they should prove of key relevance for knowledge based annotations of protein databases such as the Protein Data Bank.\n\nIllustrations are provided on the receptor binding domain (RBD) of coronaviruses, in complex with their cognate partner or (neutralizing) antibodies. MISA computed with a minimal number of structures complement and enrich findings previously reported.\n\nThe corresponding package is available from the Structural Bioinformatics Library (http://sbl.inria.fr)", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Stephane Bereux", + "author_inst": "Inria and Ecole Polytechnique" + }, + { + "author_name": "Bernard Delmas", + "author_inst": "INRAe" + }, + { + "author_name": "Frederic Cazals", + "author_inst": "Inria" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.09.03.280446", "rel_title": "A Single Dose of Self-Transcribing and Replicating RNA Based SARS-CoV-2 Vaccine Produces Protective Adaptive Immunity In Mice", @@ -1188159,49 +1190026,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.08.28.20184234", - "rel_title": "Comparative analysis of immune-associated genes in COVID-19, cardiomyopathy and venous thromboembolism", - "rel_date": "2020-09-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.28.20184234", - "rel_abs": "As of 28 August 2020, there have been 5.88 million Coronavirus Disease 2019 (COVID19) cases and 181,000 COVID-19 related deaths in the United States alone. Given the lack of an effective pharmaceutical treatment for COVID-19, the high contagiousness of the disease and its varied clinical outcomes, identifying patients at risk of progressing to severe disease is crucial for the allocation of valuable healthcare resources during this pandemic. Current research has shown that there is a higher prevalence of cardiovascular comorbidities amongst patients with severe COVID-19 or COVID-19-related deaths, but the link between cardiovascular disease and poorer prognosis is poorly understood. We believe that pre-existing immune dysregulation that accompanies cardiovascular disease predisposes patients to a harmful inflammatory immune response, leading to their higher risk of severe disease. Thus, in this project, we aim to characterize immune dysregulation in patients with cardiomyopathy, venous thromboembolism and COVID-19 patients by looking at immune-associated gene dysregulation, immune infiltration and dysregulated immunological pathways and gene signatures.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Grant E Castaneda", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Abby C Lee", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Wei Tse Li", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Chengyu Chen", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Jaideep Chakladar", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Eric Chang", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Weg Ongkeko", - "author_inst": "University of California, San Diego" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.29.20184127", "rel_title": "The evolution of Covid-19 in Italy during the Summer 2020: analysis and interpretation of an unpredicted rest period", @@ -1188853,6 +1190677,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.08.29.20184366", + "rel_title": "Potential Community and Campus Covid-19 Outcomes Under University and College Reopening Scenarios", + "rel_date": "2020-09-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.29.20184366", + "rel_abs": "BackgroundSignificant uncertainty exists about the safety of, and best strategies for, reopening colleges and universities while the Covid-19 pandemic is not well-controlled. Little also is known about the effects that on-campus outbreaks may have on local non-student and/or higher-risk communities. Model-based analysis can help inform decision and policy making across a wide range of assumptions and uncertainties.\n\nObjectiveTo evaluate the potential range of campus and community Covid-19 exposures, infections, and mortality due to various university and college reopening plans and precautions.\n\nMethodsWe developed and calibrated campus-only, community-only, and campus-x-community epidemic models using standard susceptible-exposed-infected-recovered differential equation and agent-based modeling methods. Input parameters for campus and surrounding communities were estimated via published and grey literature, scenario development, expert opinion, Monte Carlo simulation, and accuracy optimization algorithms; models were cross-validated against each other using February-June 2020 county, state, and country data. Campus opening plans (spanning various fully open, hybrid, and fully virtual approaches) were identified from websites, publications, communications, and surveys. All scenarios were simulated assuming 16-week semesters and best/worst case ranges for disease prevalence among community residents and arriving students, precaution compliance, contact frequency, virus attack rates, and tracing and isolation effectiveness. Day-to-day student and community differences in exposures, infections, and mortality were estimated under each scenario as compared to regular and no re-opening; 10% trimmed medians, standard deviations, and probability intervals were computed to omit extreme outlier scenarios. Factorial analyses were conducted to identify inputs with largest and smallest impacts on outcomes.\n\nResultsAs a base case, predicted 16-week student infections and mortality under normal operaions with no precautions (or no compliance) ranged from 472 to 9,484 (4.7% to 94.8%) and 2 to 61 (0.02% to 0.61%) per 10,000 student population, respectively. In terms of contact tracing and isolation resources, as many as 17 to 1,488 total exposures per 10,000 students could occur on a given day throughout the semester needing to be located, tested, and if warranted quarantined. Attributable total additional predicted community exposures, infections, and mortality ranged from 1 to 187, 13 to 820, and 1 to 21, respectively, assuming the university takes no additional precautions to limit exposure risk. The mean (SD) number of days until 1% and 5% of on-campus students are infected was 11 (3) and 76 (17) days, respectively; 34.8% of replications resulted in more than 10% students infected by semester end. The diffusion first inflection \"point of no return\" occurred on average on day 84 (+/-20 days, 95% interval). Common re-opening precaution strategies reduced the above consequences by 24% to 26% fewer infections (now 360 to 6,976 per 10,000 students) and 36% to 50% fewer mortalities (now 1 to 39 per 10,000 students). Perfect testing and immediate quarantining of all students on arrival to campus at semester start further reduced infections by 58% to 95% (now 200 to 468 per 10,000 students) and mortalities by 95% to 100% (now 0 to 3 per 10,000 students). Uncertainties in many factors, however, produced tremendous variability in all median estimates, ranging by -67% to +370%.\n\nConclusionsConsequences of re-opening college and university physical campuses on student and community Covid-19 exposures, infections, and mortality are very highly unpredictable, de-pending on a combination of random chance, controllable (e.g. physical layouts), and uncontrollable (e.g. human behavior) factors. Important implications at government and academic institution levels include clear needs for specific criteria to adapt campus operations mid-semester, methods to detect when this is necessary, and well-executed contingency plans for doing so.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "James C Benneyan", + "author_inst": "Northeastern University" + }, + { + "author_name": "Christopher Gehrke", + "author_inst": "Northeastern University" + }, + { + "author_name": "Iulian Ilies", + "author_inst": "Northeastern University" + }, + { + "author_name": "Nicole Nehls", + "author_inst": "Northeastern University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.08.29.20184093", "rel_title": "Quantifying the Risk of Indoor Drainage System in Multi-unit Apartment Building as a Transmission Route of SARS-CoV-2", @@ -1189957,41 +1191812,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "otolaryngology" }, - { - "rel_doi": "10.1101/2020.08.31.20175828", - "rel_title": "COVID-19 Detection From Chest Radiographs Using Machine Learning and Convolutional Neural Networks", - "rel_date": "2020-09-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.31.20175828", - "rel_abs": "Accurate and efficient diagnosis of potential COVID-19 patients is vital in the fight against the current pandemic. However, even the gold-standard COVID-19 test--reverse transcription polymerase chain reaction--suffers from a high false negative rate and a turnaround time of up to one week, preventing the infected from accessing the timely care they require, and impeding efforts to isolate positive cases. To address these shortcomings, this study develops a machine learning model based on the DenseNet-201 deep convolutional neural network, that can classify COVID-19 from chest radiographs in less than one minute and far more accurately than conventional tests (F1-score: 0.96; precision: 0.95; recall: 0.98). It uses a significantly larger dataset and more control classes than previously published models, demonstrating the promise of a machine learning approach for accurate and efficient COVID-19 screening. A live web application of the trained model can be accessed at https://cov2d19-classifier.herokuapp.com/.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Andrew C. Li", - "author_inst": "Newton South High School" - }, - { - "author_name": "David T. Lee", - "author_inst": "Shrewsbury High School" - }, - { - "author_name": "Kristoff K. Misquitta", - "author_inst": "Stuyvesant High School" - }, - { - "author_name": "Kaiji Uno", - "author_inst": "Brookline High School" - }, - { - "author_name": "Sasha Wald", - "author_inst": "Stuyvesant High School" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.08.31.20184838", "rel_title": "A comprehensive analysis of recovered COVID-19 patients and dynamic trend in antibodies over 3 months using ELISA and CLIA methods.", @@ -1190879,6 +1192699,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2020.08.31.20185157", + "rel_title": "ASSOCIATION OF HYPERGLYCEMIA WITH HOSPITAL MORTALITY IN COVID-19 PATIENTS WITHOUT DIABETES: A COHORT STUDY", + "rel_date": "2020-09-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.31.20185157", + "rel_abs": "ObjectiveDiabetes is a known risk factor for mortality in Coronavirus disease 2019 (COVID-19) patients. Our objective was to identify prevalence of hyperglycemia in COVID-19 patients with and without diabetes and quantify its association with COVID-19 disease course.\n\nResearch Design and MethodsIn this observational cohort study, all consecutive COVID-19 patients admitted to John H Stroger Jr. Hospital, Chicago, IL from March 15, 2020 to May 15, 2020 were included. The primary outcome was hospital mortality and the main predictor was hyperglycemia (any blood glucose [≥]7.78 mmol/L during hospitalization).\n\nResultsOf 403 COVID-19 patients studied, 228 (57%) developed hyperglycemia. Of these, 83 (21%) had hyperglycemia without diabetes. A total of 51 (12.7%) patients died. Compared to the reference group no-diabetes/no-hyperglycemia patients the no-diabetes/hyperglycemia patients showed higher mortality (1.8% versus 20.5%, adjusted odds ratio 21.94 (95% confidence interval 4.04-119.0), p < 0.001); improved prediction of death (p=0.0162) and faster progression to death (p=0.0051). Hyperglycemia within the first 24 and 48 hours was also significantly associated with mortality (odds ratio 2.15 and 3.31, respectively). Further, compared to the same reference group, no-diabetes/hyperglycemia patients had higher risk of ICU admission (p<0.001), mechanical ventilation (p<0.001) and acute respiratory distress syndrome (p<0.001) and a longer hospital stay in survivors (p<0.001).\n\nConclusionsHyperglycemia in the absence of diabetes was common (21% of hospitalized COVID-19 patients) and was associated with an increased risk of and faster progression to death. Development of hyperglycemia in COVID-19 patients who do not have diabetes is an early indicator of poor prognosis.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Manju Mamtani", + "author_inst": "M&H Research, LLC" + }, + { + "author_name": "Ambarish M Athavale", + "author_inst": "Division of Nephrology, Department of Medicine, Cook County Health, Chicago, Illinois" + }, + { + "author_name": "Mohan Abraham", + "author_inst": "Division of Nephrology, Department of Medicine, Cook County Health, Chicago, Illinois" + }, + { + "author_name": "Jane Vernik", + "author_inst": "Division of Nephrology, Department of Medicine, Cook County Health, Chicago, Illinois" + }, + { + "author_name": "Amatur Amarah", + "author_inst": "Division of Nephrology, Department of Medicine, Cook County Health, Chicago, Illinois" + }, + { + "author_name": "Juan Ruiz", + "author_inst": "Division of Nephrology, Department of Medicine, Cook County Health, Chicago, Illinois" + }, + { + "author_name": "Amit Joshi", + "author_inst": "Division of Nephrology, Department of Medicine, Cook County Health, Chicago, Illinois" + }, + { + "author_name": "Matthew Itteera", + "author_inst": "Division of Nephrology, Department of Medicine, Cook County Health, Chicago, Illinois" + }, + { + "author_name": "Sara Zhukovsky", + "author_inst": "Rush Medical College, Chicago, Illinois" + }, + { + "author_name": "Ravi Prakash Madaiah", + "author_inst": "Cerner Corporation, Kansas City, Missouri" + }, + { + "author_name": "Blaine C White", + "author_inst": "Department of Emergency Medicine, Wayne State University School of Medicine, Detroit, Michigan, USA" + }, + { + "author_name": "Peter Hart", + "author_inst": "Division of Nephrology, Department of Medicine, Cook County Health, Chicago, Illinois" + }, + { + "author_name": "Hemant Kulkarni", + "author_inst": "M&H Research, LLC" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "endocrinology" + }, { "rel_doi": "10.1101/2020.09.01.20182642", "rel_title": "Covid-19 SEIDRD Modelling for Pakistan with implementation of seasonality, healthcare capacity and behavioral risk reduction", @@ -1191759,61 +1193646,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.31.20185488", - "rel_title": "SARS-CoV-2 Viral RNA Load Dynamics in the Nasopharynx of Infected Children", - "rel_date": "2020-09-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.31.20185488", - "rel_abs": "It is important to understand the temporal trend of pediatric severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral load to estimate the transmission potential of children in schools and communities. We determined differences in SARS-CoV-2 viral load dynamics between nasopharyngeal samples of infected asymptomatic and symptomatic children. The daily cycle threshold values of SARS-CoV-2 in the nasopharynx of a cohort of infected children were collected for analysis. Among 17 infected children, 10 (58.8%) were symptomatic. Symptomatic children, when compared to asymptomatic children, had higher viral load (mean cycle threshold on day 7 of illness 28.6 versus 36.7, p = 0.02). Peak SARS-CoV-2 viral loads occured around days 2-3 of illness/days of diagnosis in infected children. After adjusting for the estimated date of infection, the higher SARS-CoV-2 viral loads in symptomatic children remained. We postulate that symptomatic SARS-CoV-2-infected children may have higher transmissibility than asymptomatic children. As peak viral load in infected children occurred in the early stage of illness, viral shedding and transmission in the pre-symptomatic phase probable. Our study highlights the importance of screening for SARS-CoV-2 in children with epidemiological risk factors, even when they are asymptomatic in order to improve containment of the virus in the community, including educational settings.\n\nKey pointsO_LISymptomatic children had higher SARS-CoV-2 viral loads in the nasopharynx than asymptomatic children, which may indicate that symptomatic children have higher transmissibility.\nC_LIO_LIPeak SARS-CoV-2 viral loads occurred early around 2-3 days post symptom onset iin children and therefore, pre-symptomatic transmission of the virus is probable.\nC_LIO_LISymptom based screening for SARS-CoV-2 may not be effective in diagnosing coronavirus disease 2019 (COVID-19) in children as a proportion of children may be asymptomatic or pauci-symptomatic.\nC_LIO_LIChildren with high epidemiological risk factors should be screened or isolated as they may be carriers of the virus and contribute to transmission.\nC_LI", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Kai-qian Kam", - "author_inst": "KK Women's and Children's Hospital" - }, - { - "author_name": "Koh Cheng Thoon", - "author_inst": "KK Women's and Children's Hospital" - }, - { - "author_name": "Matthias Maiwald", - "author_inst": "KK Women's and Children's Hospital" - }, - { - "author_name": "Chia Yin Chong", - "author_inst": "KK Women's and Children's Hospital" - }, - { - "author_name": "Han Yang Soong", - "author_inst": "KK Women's and Children's Hospital" - }, - { - "author_name": "Liat Hui Loo", - "author_inst": "KK Women's and Children's Hospital" - }, - { - "author_name": "Woon Hui Natalie Tan", - "author_inst": "KK Women's and Children's Hospital" - }, - { - "author_name": "Jiahui Li", - "author_inst": "KK Women's and Children's Hospital" - }, - { - "author_name": "Karen Donceras Nadua", - "author_inst": "KK Women's and Children's Hospital" - }, - { - "author_name": "Chee Fu Yung", - "author_inst": "KK Women's and Children's Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.31.20185223", "rel_title": "Adjusting COVID-19 Reports for Countries Age Disparities: A Comparative Framework for Reporting Performances", @@ -1192545,6 +1194377,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.27.20183442", + "rel_title": "Tocilizumab in Hospitalized Patients With COVID-19 Pneumonia", + "rel_date": "2020-09-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.27.20183442", + "rel_abs": "BACKGROUNDCOVID-19 is associated with immune dysregulation and hyperinflammation. Tocilizumab is an anti-interleukin-6 receptor antibody.\n\nMETHODSPatients hospitalized with severe COVID-19 pneumonia receiving standard care were randomized (2:1) to double-blinded intravenous tocilizumab 8 mg/kg or placebo. The primary outcome measure was clinical status on a 7-category ordinal scale at day 28 (1, discharged/ready for discharge; 7, death).\n\nRESULTSOverall, 452 patients were randomized; the modified-intention-to-treat population included 294 tocilizumab-treated and 144 placebo-treated patients. Clinical status at day 28 was not statistically significantly improved for tocilizumab versus placebo (P=0.36). Median (95% CI) ordinal scale values at day 28: 1.0 (1.0 to 1.0) for tocilizumab and 2.0 (1.0 to 4.0) for placebo (odds ratio, 1.19 [0.81 to 1.76]). There was no difference in mortality at day 28 between tocilizumab (19.7%) and placebo (19.4%) (difference, 0.3% [95% CI, -7.6 to 8.2]; nominal P=0.94). Median time to hospital discharge was 8 days shorter with tocilizumab than placebo (20.0 and 28.0, respectively; nominal P=0.037; hazard ratio 1.35 [95% CI 1.02 to 1.79]). Median duration of ICU stay was 5.8 days shorter with tocilizumab than placebo (9.8 and 15.5, respectively; nominal P=0.045). In the safety population, serious adverse events occurred in 34.9% of 295 patients in the tocilizumab arm and 38.5% of 143 in the placebo arm.\n\nCONCLUSIONSIn this randomized placebo-controlled trial in hospitalized COVID-19 pneumonia patients, tocilizumab did not improve clinical status or mortality. Potential benefits in time to hospital discharge and duration of ICU stay are being investigated in ongoing clinical trials.\n\nTrial registrationClinicalTrials.gov NCT04320615", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Ivan Rosas", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Norbert Br\u00e4u", + "author_inst": "James J. Peters Veterans Affairs Medical Center, Bronx and Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Michael Waters", + "author_inst": "eStudy Site" + }, + { + "author_name": "Ronaldo C. Go", + "author_inst": "Hacksensack University Medical Center" + }, + { + "author_name": "Bradley D. Hunter", + "author_inst": "Intermountain Healthcare" + }, + { + "author_name": "Sanjay Bhagani", + "author_inst": "Royal Free Hospital" + }, + { + "author_name": "Daniel Skiest", + "author_inst": "University of Massachusetts Medical School-Baystate" + }, + { + "author_name": "Mariam S. Aziz", + "author_inst": "Rush University Medical Center" + }, + { + "author_name": "Nichola Cooper", + "author_inst": "Imperial College London" + }, + { + "author_name": "Ivor S. Douglas", + "author_inst": "Denver Health Medical Center and University of Colorado, Anschutz School of Medicine" + }, + { + "author_name": "Sinisa Savic", + "author_inst": "Leeds Teaching Hospitals NHS Trust and National Institute for Health Research, Leeds Biomedical Research Centre" + }, + { + "author_name": "Taryn Youngstein", + "author_inst": "Imperial College London" + }, + { + "author_name": "Lorenzo Del Sorbo", + "author_inst": "University Health Network" + }, + { + "author_name": "Antonio Cubillo Gracian", + "author_inst": "Hospital Universitario HM Sanchinarro, Centro Integral, Oncologico Clara Campal and Departamento de Ciencias Medicas Clinicas, Facultad de Medicina, Universidad" + }, + { + "author_name": "David J. De La Zerda", + "author_inst": "University of Miami Miller School of Medicine" + }, + { + "author_name": "Andrew Ustianowski", + "author_inst": "North Manchester General Hospital" + }, + { + "author_name": "Min Bao", + "author_inst": "Genentech" + }, + { + "author_name": "Sophie Dimonaco", + "author_inst": "Roche Products Ltd" + }, + { + "author_name": "Emily Graham", + "author_inst": "Roche Products Ltd" + }, + { + "author_name": "Balpreet Matharu", + "author_inst": "Roche Products Ltd" + }, + { + "author_name": "Helen Spotswood", + "author_inst": "Roche Products Ltd" + }, + { + "author_name": "Larry Tsai", + "author_inst": "Genentech" + }, + { + "author_name": "Atul Malhotra", + "author_inst": "University of California San Diego" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.26.20180968", "rel_title": "Racial and workplace disparities in seroprevalence of SARS-CoV-2 in Baton Rouge, Louisiana, July 15-31, 2020", @@ -1193713,45 +1195652,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.08.27.20178160", - "rel_title": "Joint Investigation of Two-Month Post-Diagnosis IgG Antibody Levels and Psychological Measures for Assessing Longer Term Multi-Faceted Recovery among COVID-19 Cases in Northern Cyprus", - "rel_date": "2020-09-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.27.20178160", - "rel_abs": "Following the outbreak of COVID-19, multidisciplinary research focusing on the long-term effects of the COVID-19 infection and the complete longer term recovery is still scarce. With regards to long-term consequences, biomarkers of physiological effects as well as the psychological experiences are of significant importance for comprehensively understanding the whole COVID-19 recovery period. The present research surveys the IgG antibody titers and the impact of COVID-19 as a traumatic experience in the aftermath of the active infection period, around two months after diagnosis, in a subset of COVID-19 patients from the first wave of the outbreak in Northern Cyprus. Associations of antibody titers and psychological survey measures with baseline characteristics and disease severity were explored, and correlations among various measures were evaluated. Of the 47 serology tests conducted for presence of IgG antibodies, 39 (83%) were positive. We identified trends demonstrating individuals experiencing severe or critical COVID-19 disease and/or those with comorbidities are more heavily impacted both physiologically and mentally, with higher IgG titers and negative psychological experience compared to those with milder disease and without comorbidities. We also observed that more than half of the COVID-19 cases had negative psychological experiences, being subjected to discrimination and verbal harassment/insult, by family/friends. In summary, as the first study co-evaluating immune response together with mental status, our findings suggest that further multidisciplinary research in larger sample populations as well as community intervention plans are needed to holistically address the physiological and psychological effects of COVID-19 among the cases in the long-term.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Burc Barin", - "author_inst": "The Emmes Company, Rockville, Maryland, USA." - }, - { - "author_name": "Banu Elcin Yoldascan", - "author_inst": "Department of Public Health, Faculty of Medicine, Cyprus International University, Nicosia, North Cyprus" - }, - { - "author_name": "Fatma Savaskan", - "author_inst": "Headnursing Department, Burhan Nalbantoglu State Hospital, Nicosia, North Cyprus" - }, - { - "author_name": "Goncagul Ozbalikci", - "author_inst": "Microbiology Laboratory, Burhan Nalbantoglu State Hospital, Nicosia, North Cyprus" - }, - { - "author_name": "Tugce Karaderi", - "author_inst": "Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Medical and Health Sciences, University of Copenhagen, Copenhag" - }, - { - "author_name": "Huseyin Cakal", - "author_inst": "School of Psychology, Keele University, Keele, ST5 5BG, Staffordshire, UK." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.08.26.20182824", "rel_title": "Beyond Six Feet: A Guideline to Limit Indoor Airborne Transmission of COVID-19", @@ -1194319,6 +1196219,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.27.20182550", + "rel_title": "MAIT cell activation and dynamics associated with COVID-19 disease severity and outcome", + "rel_date": "2020-09-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.27.20182550", + "rel_abs": "Severe COVID-19 is characterized by excessive inflammation of the lower airways. The balance of protective versus pathological immune responses in COVID-19 is incompletely understood. Mucosa-associated invariant T (MAIT) cells are antimicrobial T cells that recognize bacterial metabolites, and can also function as innate-like sensors and mediators of antiviral responses. Here, we investigated the MAIT cell compartment in COVID-19 patients with moderate and severe disease, as well as in convalescence. We show profound and preferential decline in MAIT cells in circulation of patients with active disease paired with strong activation, as well as significant MAIT cell enrichment and pro-inflammatory IL-17A bias in the airways. Unsupervised analysis identified MAIT cell CD69high and CXCR3low immunotypes associated with poor clinical outcome. MAIT cell levels normalized in the convalescent phase, consistent with dynamic recruitment to the tissues and subsequent release with disease resolution. These findings indicate that MAIT cells are engaged in the immune response against SARS-CoV-2 and suggest their involvement in COVID-19 immunopathogenesis.\n\nOne sentence summaryMAIT cells are strongly activated by SARS-CoV-2 infection in a manner associated with disease severity and outcome, they decline in blood, are enriched in the airways as a prominent IL-17A expressing subset, and dynamically recover in circulation during convalescence.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Tiphaine Parrot", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Jean-Baptiste Gorin", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Andrea Ponzetta", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Kimia T Maleki", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Tobias Kammann", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Johanna Emgard", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Andre Perez Potti", + "author_inst": "Karrolinska Institutet" + }, + { + "author_name": "Takuya Sekine", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Olga Rivera-Ballesteros", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "- Karolinska COVID-19 Study Group", + "author_inst": "" + }, + { + "author_name": "Elin Folkesson", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Olav Rooyackers", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Lars I Eriksson", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Anna Norrby-Teglund", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Hans-Gustaf Ljunggren", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Niklas K Bjorkstrom", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Soo Aleman", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Marcus Buggert", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Jonas Klingstrom", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Kristoffer Stralin", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Johan K. Sandberg", + "author_inst": "Karolinska Institutet" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.27.20182832", "rel_title": "Analysis and validation of a highly sensitive one-step nested quantitative real-time polymerase chain reaction assay for specific detection of severe acute respiratory syndrome coronavirus 2", @@ -1194987,45 +1196986,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.08.28.20183681", - "rel_title": "Systematic review and meta-analysis of the prevalence of common respiratory viruses in children < 2 years with bronchiolitis reveal a weak role played by the SARS-CoV-2", - "rel_date": "2020-09-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.28.20183681", - "rel_abs": "Introduction The advent of genome amplification assays has allowed description of new respiratory viruses and to reconsider the role played by certain respiratory viruses in bronchiolitis. This systematic review and meta-analysis was initiated to clarify the prevalence of respiratory viruses in children with bronchiolitis in the coronavirus disease 2019 pandemic context.\n\nMethodsWe performed an electronic search through Pubmed and Global Index Medicus databases. We included observational studies reporting the detection rate of common respiratory viruses in children with bronchiolitis using molecular assays. Data was extracted and the quality of the included articles was assessed. We conducted sensitivity, subgroups, publication bias, and heterogeneity analyses using a random effect model.\n\nResultsThe final meta-analysis included 51 studies. Human respiratory syncytial virus (HRSV) was largely the most commonly detected virus 59.2%; 95% CI [54.7; 63.6]). The second predominant virus was Rhinovirus (RV) 19.3%; 95% CI [16.7; 22.0]) followed by Human bocavirus (HBoV) 8.2%; 95% CI [5.7; 11.2]). Other reported viruses included Human Adenovirus (HAdV) 6.1%; 95% CI [4.4; 8.0]), Human Metapneumovirus (HMPV) 5.4%; 95% CI [4.4; 6.4]), Human Parainfluenzavirus (HPIV) 5.4%; 95% CI [3.8; 7.3]), Influenza 3.2%; 95% CI [2.2; 4.3], mild Human Coronavirus (HCoV) 2.9%; 95% CI [2.0; 4.0]), and Enterovirus (EV) 2.9%; 95% CI [1.6; 4.5]). HRSV was the predominant virus involved in multiple detection and most codetections were HRSV + RV 7.1%, 95% CI [4.6; 9.9]) and HRSV + HBoV 4.5%, 95% CI [2.4; 7.3]).\n\nConclusionsThe present study has shown that HRSV is the main cause of bronchiolitis in children, we also have Rhinovirus, and Bocavirus which also play a significant role. No study has reported the presence of Severe Acute Respiratory Syndrome Coronavirus-2 in children with bronchiolitis to date.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Sebastien Kenmoe", - "author_inst": "Centre Pasteur of Cameroon" - }, - { - "author_name": "Cyprien Kengne-Nde", - "author_inst": "National AIDS Control Committee, Epidemiological Surveillance, Evaluation and Research Unit, P.O. Box 1459 Yaounde, Cameroon" - }, - { - "author_name": "Jean Thierry Ebogo-Belobo", - "author_inst": "Medical Research Centre, Institut of Medical Research and Medicinal Plants Studies, Yaounde, Cameroon" - }, - { - "author_name": "Donatien Serge Mbaga", - "author_inst": "Department of Microbiology, Faculty of Science, The University of Yaounde I, Yaounde, Cameroon" - }, - { - "author_name": "Abdou Fatawou Modiyinji", - "author_inst": "Department of Virology, Centre Pasteur of Cameroon, 451 Rue 2005, P.O. Box 1274 Yaounde, Cameroon" - }, - { - "author_name": "Richard Njouom", - "author_inst": "Department of Virology, Centre Pasteur of Cameroon, 451 Rue 2005, P.O. Box 1274 Yaounde, Cameroon" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2020.08.26.20180992", "rel_title": "Survival and 30-days hospital outcome in hospitalized COVID-19 patients in Upper Egypt: Multi-center study", @@ -1195905,6 +1197865,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.27.20183293", + "rel_title": "Factors Associated with Good Patient Outcomes Following Convalescent Plasma in COVID-19: A Prospective Phase II Clinical Trial", + "rel_date": "2020-09-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.27.20183293", + "rel_abs": "We conducted a prospective single-arm open-label phase II clinical trial assessing the safety and efficacy of convalescent plasma in hospitalized COVID-19 patients. Convalescent plasma with sufficient IgG titer (1:320) obtained from recovered donors was administered to adult patients with either severe or critical COVID-19 illness. Primary outcomes were adverse events in association with plasma administration, and hospital mortality. Secondary outcomes included disease progression, recovery, length of stay, and hospital discharge. Of the 38 patients included in the analysis, 24 (63%) recovered and were discharged, and 14 (37%) died. Patients who received convalescent plasma early in the disease course (severe illness group) as compared to the patients that received convalescent plasma later in disease progression (critical illness group) had significantly lower hospital mortality 13% vs 55% (p<0.02) and shorter mean hospital length of stay 15.4 vs 33 days (p<0.01). One patient experienced a transient transfusion reaction. No other adverse effects of convalescent plasma infusion were observed. Our results suggest that convalescent plasma is safe and has the potential for positive impact on clinical outcomes including recovery and survival if given to patients early in the course of COVID-19 disease.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Danyal Ibrahim", + "author_inst": "Trinity Health Of New England" + }, + { + "author_name": "Latha Dulipsingh", + "author_inst": "Saint Francis Hospital" + }, + { + "author_name": "Lisa Zapatka", + "author_inst": "Trinity Health Of New England" + }, + { + "author_name": "Reginald Eadie", + "author_inst": "Trinity Health Of New England" + }, + { + "author_name": "Rebecca Crowell", + "author_inst": "Saint Francis Hospital" + }, + { + "author_name": "Kendra Williams", + "author_inst": "Saint Francis Hospital" + }, + { + "author_name": "Dorothy Wakefield", + "author_inst": "Saint Francis Hospital" + }, + { + "author_name": "Lisa Cook", + "author_inst": "Saint Francis Hospital" + }, + { + "author_name": "Jennifer Puff", + "author_inst": "Saint Francis Hospital" + }, + { + "author_name": "Syed A Hussain", + "author_inst": "Trinity Health Of New England" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.30.20177543", "rel_title": "Bronchoscopy on Intubated COVID-19 Patients is Associated with Low Infectious Risk to Operators at a High-Volume Center Using an Aerosol-minimizing Protocol", @@ -1196849,93 +1198864,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.31.274704", - "rel_title": "Engineered Trimeric ACE2 Binds and Locks \"Three-up\" Spike Protein to Potently Inhibit SARS-CoVs and Mutants", - "rel_date": "2020-09-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.31.274704", - "rel_abs": "SARS-CoV-2 enters cells via ACE-2, which binds the spike protein with moderate affinity. Despite a constant background mutational rate, the virus must retain binding with ACE2 for infectivity, providing a conserved constraint for SARS-CoV-2 inhibitors. To prevent mutational escape of SARS-CoV-2 and to prepare for future related coronavirus outbreaks, we engineered a de novo trimeric ACE2 (T-ACE2) protein scaffold that binds the trimeric spike protein with extremely high affinity (KD < 1 pM), while retaining ACE2 native sequence. T-ACE2 potently inhibits all tested pseudotyped viruses including SARS-CoV-2, SARS-CoV, eight naturally occurring SARS-CoV-2 mutants, two SARSr-CoVs as well as authentic SARS-CoV-2. The cryo-EM structure reveals that T-ACE2 can induce the transit of spike protein to \"three-up\" RBD conformation upon binding. T-ACE2 thus represents a promising class of broadly neutralizing proteins against SARS-CoVs and mutants.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Liang Guo", - "author_inst": "Westlake University" - }, - { - "author_name": "Wenwen Bi", - "author_inst": "Westlake University" - }, - { - "author_name": "Xinling Wang", - "author_inst": "Fudan University" - }, - { - "author_name": "Wei Xu", - "author_inst": "Fudan University" - }, - { - "author_name": "Renhong Yan", - "author_inst": "Westlake University" - }, - { - "author_name": "Yuanyuan Zhang", - "author_inst": "Westlake University" - }, - { - "author_name": "Kai Zhao", - "author_inst": "Westlake University" - }, - { - "author_name": "Yaning Li", - "author_inst": "Westlake University" - }, - { - "author_name": "Mingfeng Zhang", - "author_inst": "Westlake University" - }, - { - "author_name": "Xingyue Bao", - "author_inst": "Westlake University" - }, - { - "author_name": "Xia Cai", - "author_inst": "Fudan University" - }, - { - "author_name": "Yutang Li", - "author_inst": "Fudan University" - }, - { - "author_name": "Di Qu", - "author_inst": "Fudan University" - }, - { - "author_name": "Shibo Jiang", - "author_inst": "Fudan University" - }, - { - "author_name": "Youhua Xie", - "author_inst": "Fudan University" - }, - { - "author_name": "Qiang Zhou", - "author_inst": "Westlake University" - }, - { - "author_name": "Lu Lu", - "author_inst": "Fudan University" - }, - { - "author_name": "Bobo Dang", - "author_inst": "Westlake University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2020.08.31.276675", "rel_title": "Characterization of neutralizing versus binding antibodies and memory B cells in COVID-19 recovered individuals from India", @@ -1197587,6 +1199515,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.25.20182170", + "rel_title": "Transfer learning to detect COVID-19 automatically from X-ray images, using convolutional neural networks", + "rel_date": "2020-08-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.25.20182170", + "rel_abs": "Novel coronavirus pneumonia (COVID-19) is a contagious disease that has already caused thousands of deaths and infected millions of people worldwide. Thus, all technological gadgets that allow the fast detection of COVID-19 infection with high accuracy can offer help to healthcare professionals. This study is purposed to explore the effectiveness of artificial intelligence (AI) in the rapid and reliable detection of COVID-19 based on chest X-ray imaging. In this study, reliable pre-trained deep learning algorithms were applied to achieve the automatic detection of COVID-19-induced pneumonia from digital chest X-ray images.\n\nMoreover, the study aims to evaluate the performance of advanced neural architectures proposed for the classification of medical images over recent years. The data set used in the experiments involves 274 COVID-19 cases, 380 viral pneumonia, and 380 healthy cases, which was derived from several open sources of X-Rays, and the data available online. The confusion matrix provided a basis for testing the post-classification model. Furthermore, an open-source library PYCM was used to support the statistical parameters. The study revealed the superiority of Model vgg16 over other models applied to conduct this research where the model performed best in terms of overall scores and based-class scores. According to the research results, deep Learning with X-ray imaging is useful in the collection of critical biological markers associated with COVID-19 infection. The technique is conducive for the physicians to make a diagnosis of COVID-19 infection. Meanwhile, the high accuracy of this computer-aided diagnostic tool can significantly improve the speed and accuracy of COVID-19 diagnosis.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Mundher Taresh Sr.", + "author_inst": "Hunan University" + }, + { + "author_name": "Ningbo Zhu Sr.", + "author_inst": "Hunan University" + }, + { + "author_name": "Talal Ahmed Ali Ali Sr.", + "author_inst": "Hunan University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2020.08.24.20180877", "rel_title": "Interplay of antibody and cytokine production reveals CXCL-13 as a potential novel biomarker of lethal SARS-CoV-2 infection", @@ -1198935,33 +1200890,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "anesthesia" }, - { - "rel_doi": "10.1101/2020.08.25.20182071", - "rel_title": "Efficacy of Localized Lockdowns in the SARS-CoV-2 Pandemic", - "rel_date": "2020-08-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.25.20182071", - "rel_abs": "Non-pharmaceutical interventions, such as social distancing and lockdowns, have been essential to control the COVID-19 pandemic. In particular, localized lockdowns in small geographic areas have become an important policy intervention to prevent viral spread in cases of resurgence. These localized lockdowns can result in lower social and economic costs compared to larger-scale suppression strategies. Using an integrated dataset from Chile (March 3 through June 15, 2020) and a novel synthetic control approach, in this paper we estimate the effect of localized lockdowns, disentangling its direct and indirect causal effects on SARS-CoV-2 transmission. Our results show that the effects of localized lockdowns are strongly modulated by their duration and are influenced by indirect effects from neighboring geographic areas. Our estimates suggest that extending localized lockdowns can slow down the pandemic; however, localized lockdowns on their own are insufficient to control pandemic growth in the presence of indirect effects from contiguous neighboring areas that do not have lockdowns. These results provide critical empirical evidence about the effectiveness of localized lockdowns in interconnected geographic areas.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Yige Li", - "author_inst": "Department of Health Care Policy, Harvard Medical School; Department of Biostatistics, Harvard School of Public Health" - }, - { - "author_name": "Eduardo A Undurraga", - "author_inst": "Pontificia Universidad Catolica de Chile; Millennium Initiative for Collaborative Research in Bacterial Resistance MICROB-R; Research Center for Integrated Disa" - }, - { - "author_name": "Jose Ramon Zubizarreta", - "author_inst": "Department of Health Care Policy, Harvard Medical School; Department of Biostatistics, Harvard School of Public Health; Department of Statistics, Harvard Facult" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.25.20182105", "rel_title": "DNA Methylation Architecture of the ACE2 gene in Nasal Cells", @@ -1199909,6 +1201837,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.28.271965", + "rel_title": "Structure-Altering Mutations of the SARS-CoV-2 Frame Shifting RNA Element", + "rel_date": "2020-08-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.28.271965", + "rel_abs": "With the rapid rate of Covid-19 infections and deaths, treatments and cures besides hand washing, social distancing, masks, isolation, and quarantines are urgently needed. The treatments and vaccines rely on the basic biophysics of the complex viral apparatus. While proteins are serving as main drug and vaccine targets, therapeutic approaches targeting the 30,000 nucleotide RNA viral genome form important complementary approaches. Indeed, the high conservation of the viral genome, its close evolutionary relationship to other viruses, and the rise of gene editing and RNA-based vaccines all argue for a focus on the RNA agent itself. One of the key steps in the viral replication cycle inside host cells is the ribosomal frameshifting required for translation of overlapping open reading frames. The frameshifting element (FSE), one of three highly conserved regions of coronaviruses, includes an RNA pseudoknot considered essential for this ribosomal switching. In this work, we apply our graph-theory-based framework for representing RNA secondary structures, \"RAG\" (RNA-As Graphs), to alter key structural features of the FSE of the SARS-CoV-2 virus. Specifically, using RAG machinery of genetic algorithms for inverse folding adapted for RNA structures with pseudoknots, we computationally predict minimal mutations that destroy a structurally-important stem and/or the pseudoknot of the FSE, potentially dismantling the virus against translation of the polyproteins. Additionally, our microsecond molecular dynamics simulations of mutant structures indicate relatively stable secondary structures. These findings not only advance our computational design of RNAs containing pseudoknots; they pinpoint to key residues of the SARS-CoV-2 virus as targets for anti-viral drugs and gene editing approaches.\n\nSIGNIFICANCESince the outbreak of Covid-19, numerous projects were launched to discover drugs and vaccines. Compared to protein-focused approaches, targeting the RNA genome, especially highly conserved crucial regions, can destruct the virus life cycle more fundamentally and avoid problems of viral mutations. We choose to target the small frame-shifting element (FSE) embedded in the Open Reading Frame 1a,b of SARS-CoV-2. This FSE is essential for translating overlapping reading frames and thus controlling the viral protein synthesis pathway. By applying graph-theory-based computational algorithms, we identify structurally crucial residues in the FSE as potential targets for anti-viral drugs and gene editing.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Tamar Schlick", + "author_inst": "New York University" + }, + { + "author_name": "Qiyao Zhu", + "author_inst": "New York University" + }, + { + "author_name": "Swati Jain", + "author_inst": "New York University" + }, + { + "author_name": "Shuting Yan", + "author_inst": "New York University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.08.30.273235", "rel_title": "The global landscape of SARS-CoV-2 genomes, variants, and haplotypes in 2019nCoVR", @@ -1200929,113 +1202888,6 @@ "type": "confirmatory results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.08.28.244269", - "rel_title": "Immune response to vaccine candidates based on different types of nanoscaffolded RBD domain of the SARS-CoV-2 spike protein", - "rel_date": "2020-08-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.28.244269", - "rel_abs": "Effective and safe vaccines against SARS-CoV-2 are highly desirable to prevent casualties and societal cost caused by Covid-19 pandemic. The receptor binding domain (RBD) of the surface-exposed spike protein of SARS-CoV-2 represents a suitable target for the induction of neutralizing antibodies upon vaccination. Small protein antigens typically induce weak immune response while particles measuring tens of nanometers are efficiently presented to B cell follicles and subsequently to follicular germinal center B cells in draining lymph nodes, where B cell proliferation and affinity maturation occurs. Here we prepared and analyzed the response to several DNA vaccines based on genetic fusions of RBD to four different scaffolding domains, namely to the foldon peptide, ferritin, lumazine synthase and {beta}-annulus peptide, presenting from 6 to 60 copies of the RBD on each particle. Scaffolding strongly augmented the immune response with production of neutralizing antibodies and T cell response including cytotoxic lymphocytes in mice upon immunization with DNA plasmids. The most potent response was observed for the 24-residue {beta}-annulus peptide scaffold that forms large soluble assemblies, that has the advantage of low immunogenicity in comparison to larger scaffolds. Our results support the advancement of this vaccine platform towards clinical trials.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Dusko Lainscek", - "author_inst": "National institute of chemistry" - }, - { - "author_name": "Tina Fink", - "author_inst": "National institute of chemistry" - }, - { - "author_name": "Vida Forstneric", - "author_inst": "National institute of chemistry" - }, - { - "author_name": "Iva Hafner-Bratkovic", - "author_inst": "National institute of chemistry" - }, - { - "author_name": "Sara Orehek", - "author_inst": "National institute of chemistry" - }, - { - "author_name": "Ziga Strmsek", - "author_inst": "National institute of chemistry" - }, - { - "author_name": "Mateja Mancek Keber", - "author_inst": "National institute of chemistry" - }, - { - "author_name": "Peter Pecan", - "author_inst": "National institute of chemistry" - }, - { - "author_name": "Hana Esih", - "author_inst": "National institute of chemistry" - }, - { - "author_name": "Spela Malensek", - "author_inst": "National institute of chemistry" - }, - { - "author_name": "Jana Aupic", - "author_inst": "National institute of chemistry" - }, - { - "author_name": "Petra Dekleva", - "author_inst": "National institute of chemistry" - }, - { - "author_name": "Tjasa Plaper", - "author_inst": "National institute of chemistry" - }, - { - "author_name": "Sara Vidmar", - "author_inst": "National institute of chemistry" - }, - { - "author_name": "Lucija Kadunc", - "author_inst": "National institute of chemistry" - }, - { - "author_name": "Mojca Bencina", - "author_inst": "National institute of chemistry" - }, - { - "author_name": "Florence Pojer", - "author_inst": "EPFL" - }, - { - "author_name": "Kelvin Lau", - "author_inst": "EPFL" - }, - { - "author_name": "David Hacker", - "author_inst": "EPFL" - }, - { - "author_name": "Bruno Correia", - "author_inst": "Ecole Polytechnique Federale de Lausanne" - }, - { - "author_name": "David Peterhoff", - "author_inst": "University Regensburg" - }, - { - "author_name": "Ralf Wagner", - "author_inst": "University Regensburg" - }, - { - "author_name": "Roman Jerala", - "author_inst": "National institute of chemistry" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.08.28.271635", "rel_title": "SARS-CoV-2 spike D614G variant exhibits highly efficient replication and transmission in hamsters", @@ -1201731,6 +1203583,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.08.28.270306", + "rel_title": "Prunella vulgaris extract and suramin block SARS-coronavirus 2 virus Spike protein D614 and G614 variants mediated receptor association and virus entry in cell culture system", + "rel_date": "2020-08-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.28.270306", + "rel_abs": "Until now, no approved effective vaccine and antiviral therapeutic are available for treatment or prevention of SARS-coronavirus 2 (SCoV-2) virus infection. In this study, we established a SCoV-2 Spike glycoprotein (SP), including a SP mutant D614G, pseudotyped HIV-1-based vector system and tested their ability to infect ACE2-expressing cells. This study revealed that a C-terminal 17 amino acid deletion in SCoV-2 SP significantly increases the incorporation of SP into the pseudotyped viruses and enhanced its infectivity, which may be helpful in the design of SCoV2-SP-based vaccine strategies. Moreover, based on this system, we have demonstrated that an aqueous extract from the Chinese herb Prunella vulgaris (CHPV) and a compound, suramin, displayed potent inhibitory effects on both wild type and mutant (G614) SCoV-2 SP pseudotyped virus (SCoV-2-SP-PVs)-mediated infection. The 50% inhibitory concentration (IC50) for CHPV and suramin on SCoV-2-SP-PVs are 30, and 40 g/ml, respectively. To define the mechanisms of their actions, we demonstrated that both CHPV and suramin are able to directly interrupt SCoV-2-SP binding to its receptor ACE2 and block the viral entry step. Importantly, our results also showed that CHPV or suramin can efficiently reduce levels of cytopathic effect caused by SARS-CoV-2 virus (hCoV-19/Canada/ON-VIDO-01/2020) infection in Vero cells. Furthermore, our results demonstrated that the combination of CHPV/suramin with an anti-SARS-CoV-2 neutralizing antibody mediated more potent blocking effect against SCoV2-SP-PVs. Overall, this study provides evidence that CHPV and suramin has anti-SARS-CoV-2 activity and may be developed as a novel antiviral approach against SARS-CoV-2 infection.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Zhujun Ao", + "author_inst": "University of Manitoba" + }, + { + "author_name": "Mable Chan", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Maggie Jing Ouyang", + "author_inst": "University of Manitoba" + }, + { + "author_name": "Titus Abiola Olukitibi", + "author_inst": "University of Manitoba" + }, + { + "author_name": "Mona Mahmoudi", + "author_inst": "University of Manitoba" + }, + { + "author_name": "Darwyn Kobasa", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Xiaojian Yao", + "author_inst": "University of Manitoba" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.08.28.271957", "rel_title": "Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2", @@ -1202558,25 +1204453,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2020.08.20.20178913", - "rel_title": "Chest X-ray image analysis and classification for COVID-19 pneumonia detection using Deep CNN", - "rel_date": "2020-08-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.20.20178913", - "rel_abs": "In order to speed up the discovery of COVID-19 disease mechanisms, this research developed a new diagnosis platform using deep convolutional neural network (CNN) which is able to assist radiologists with diagnosis by distinguishing COVID-19 pneumonia from non-COVID-19 pneumonia in patients at Middlemore Hospital based on chest X-rays classification and analysis. Such a tool can save time in interpreting chest X-rays and increase the accuracy and thereby enhance our medical capacity for detection and diagnosis COVID-19. The research idea is that a set of X-ray medical lung images (which include normal, infected by bacteria, infected by virus including COVID-19) were used to train a deep CNN which can be able to distinguish between the noise and the useful information and then uses this training to interpret new images by recognizing patterns that indicate certain diseases such as coronavirus infection in the individual images. The supervised learning method is used as the process of learning from the training dataset can be thought of as a doctor supervising the learning process. It becomes more accurate as the number of analyzed images growing. In this way, it imitates the training for a doctor, but the theory is that since it is capable of learning from a far larger set of images than any human, can have the potential of being more accurate.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Terry Gao Sr.", - "author_inst": "CMDHB" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.08.24.20180836", "rel_title": "Perceptions of Risk of Attending Hospital during the COVID-19 Pandemic: a UK public opinion survey", @@ -1203240,6 +1205116,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.08.24.20180943", + "rel_title": "Monitoring COVID-19 related public Interest and population Health Literacy in South Asia: An Internet Search-Interest Based Model", + "rel_date": "2020-08-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.24.20180943", + "rel_abs": "BackgroundInformation epidemiology based on internet search data can be used to model COVID-19 pandemic progressions and monitor population health literacy. However, the applicability of internet searches to monitor COVID-19 infections and public health awareness in South Asian countries are unclear.\n\nObjectivesTo assess the association of public interest and health literacy in COVID-19 with the actual number of infected cases for countries in South Asia.\n\nMethodsGoogle Trends data from January to March 2020 were used to correlate public interest and health literacy with official data on COVID-19 cases using the relative search volume (RSV) index. Public interest in COVID-19 was retrieved in RSV indices with the search term \"Coronavirus (Virus)\". Similarly, an OR combination of search terms \"hand wash\", \"face mask\", \"hand sanitizer\", \"face shield\" and \"gloves\" were used to retrieve RSV indices as a surrogate of population health literacy in COVID-19. Daily confirmed COVID-19 cases were obtained from the COVID-19 data repository managed by the Johns Hopkins University. Country-level time-lag correlation analyses were performed for a time lag between 30 and +30 days.\n\nResultsCOVID-19-related worldwide public interest reached a peak on March 16, 2020, right after the WHO announcement of coronavirus outbreak as a pandemic. COVID-19 related public interest reached the highest peak in South Asian countries a few days after each county reported 100th confirmed cases. There were significant positive correlations between COVID-19 related public interest and daily laboratory confirmed cases in countries expect Nepal, Bhutan, and Sri Lanka. The highest public interest in South Asian Countries was on average 12 days before the local maximum of new confirmed cases. Similarly, web searches related to personal hygiene and COVID-19 preventive measures in south Asia correlated to the number of confirmed cases as well as national restriction measures.\n\nConclusionPublic interest indicated by RSV indices can help to monitor the progression of an outbreak such as the current COVID-19 pandemic particularly in countries with a lack of diagnostic and surveillance capacity, and thereby distribute appropriate health information to the general public.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Hasan Symum", + "author_inst": "University of South Florida" + }, + { + "author_name": "Kh Mohammed Ali", + "author_inst": "Dhaka Medical College Hospital, Dhaka, Bangladesh" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.08.24.20155713", "rel_title": "In-house assembled protective devices in laboratory safety against SARS-nCoV-2 in clinical biochemistry laboratory of a COVID dedicated hospital", @@ -1204336,125 +1206235,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.08.26.268854", - "rel_title": "Furin Cleavage Site Is Key to SARS-CoV-2 Pathogenesis", - "rel_date": "2020-08-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.26.268854", - "rel_abs": "SARS-CoV-2 has resulted in a global pandemic and shutdown economies around the world. Sequence analysis indicates that the novel coronavirus (CoV) has an insertion of a furin cleavage site (PRRAR) in its spike protein. Absent in other group 2B CoVs, the insertion may be a key factor in the replication and virulence of SARS-CoV-2. To explore this question, we generated a SARS-CoV-2 mutant lacking the furin cleavage site ({Delta}PRRA) in the spike protein. This mutant virus replicated with faster kinetics and improved fitness in Vero E6 cells. The mutant virus also had reduced spike protein processing as compared to wild-type SARS-CoV-2. In contrast, the {Delta}PRRA had reduced replication in Calu3 cells, a human respiratory cell line, and had attenuated disease in a hamster pathogenesis model. Despite the reduced disease, the {Delta}PRRA mutant offered robust protection from SARS-CoV-2 rechallenge. Importantly, plaque reduction neutralization tests (PRNT50) with COVID-19 patient sera and monoclonal antibodies against the receptor-binding domain found a shift, with the mutant virus resulting in consistently reduced PRNT50 titers. Together, these results demonstrate a critical role for the furin cleavage site insertion in SARS-CoV-2 replication and pathogenesis. In addition, these findings illustrate the importance of this insertion in evaluating neutralization and other downstream SARS-CoV-2 assays.\n\nImportanceAs COVID-19 has impacted the world, understanding how SARS-CoV-2 replicates and causes virulence offers potential pathways to disrupt its disease. By removing the furin cleavage site, we demonstrate the importance of this insertion to SARS-CoV-2 replication and pathogenesis. In addition, the findings with Vero cells indicate the likelihood of cell culture adaptations in virus stocks that can influence reagent generation and interpretation of a wide range of data including neutralization and drug efficacy. Overall, our work highlights the importance of this key motif in SARS-CoV-2 infection and pathogenesis.\n\nArticle SummaryA deletion of the furin cleavage site in SARS-CoV-2 amplifies replication in Vero cells, but attenuates replication in respiratory cells and pathogenesis in vivo. Loss of the furin site also reduces susceptibility to neutralization in vitro.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Bryan A Johnson", - "author_inst": "UTMB" - }, - { - "author_name": "Xuping Xie", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Birte Kalveram", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Kumari G Lokugamage", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Antonio Muruato", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Jing Zou", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Xianwen Zhang", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Terry Juelich", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Jennifer K Smith", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Lihong Zhang", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Craig Schindewolf", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Michelle N Vu", - "author_inst": "University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Abigail Vanderheiden", - "author_inst": "Emory University" - }, - { - "author_name": "Jessica A Plante", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Kenneth S Plante", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Benhur Lee", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Scott Weaver", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Mehul Suthar", - "author_inst": "Emory University" - }, - { - "author_name": "Andrew Laurence Routh", - "author_inst": "University of Texas Medical Branch, Galveston" - }, - { - "author_name": "Ping Laurence Ren", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Zhiqiang Ku", - "author_inst": "University of Texas Health Science Center at Houston" - }, - { - "author_name": "Zhiqiang An", - "author_inst": "University of Texas Health Science Center at Houston" - }, - { - "author_name": "Kari Debbink", - "author_inst": "Bowie State University" - }, - { - "author_name": "Pei Yong Shi", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Alexander N. Freiberg", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Vineet D Menachery", - "author_inst": "University of Texas Medical Branch" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.08.25.267351", "rel_title": "Molecular dynamics reveals complex compensatory effects of ionic strength on the SARS-CoV-2 Spike/hACE-2 interaction", @@ -1205350,6 +1207130,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.22.20179937", + "rel_title": "Seroprevalence of anti-SARS-CoV-2 IgG antibody in hospitalized patients in a tertiary referral center in North India", + "rel_date": "2020-08-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.22.20179937", + "rel_abs": "BackgroundSeroprevalence of IgG antibodies against SARS-CoV-2 is an important tool to estimate the true extent of infection in a population. However, seroprevalence studies have been scarce in South East Asia including India, which, as of now, carries the third largest burden of confirmed cases in the world. The present study aimed to estimate the seroprevalence of anti-SARS-CoV-2 IgG antibody among hospitalized patients at one of the largest government hospital in India.\n\nMethodThis cross-sectional study, conducted at a tertiary care hospital in North India, recruited consecutive patients who were negative for SARS-CoV-2 by RT-PCR or CB-NAAT. Anti-SARS-CoV-2 IgG antibody levels targeting recombinant spike receptor-binding domain (RBD) protein of SARS CoV-2 were estimated in serum sample by the ELISA method.\n\nResultsA total of 212 hospitalized patients were recruited in the study with mean age ({+/-}SD) of 41.2 ({+/-}15.4) years and 55% male population. Positive serology against SARS CoV-2 was detected in 19.8% patients(95% CI 14.7-25.8). Residency in Delhi conferred a higher frequency of seropositivity 26.5% (95% CI 19.3-34.7) as compared to that of other states 8% (95% CI 3.0-16.4) with p value 0.001. No particular age groups or socio-economic strata showed a higher proportion of seropositivity.\n\nConclusionAround, one-fifth of hospitalized patients, who were not diagnosed with COVID-19 before, demonstrated seropositivity against SARS-CoV-2. While there was no significant difference in the different age groups and socio-economic classes; residence in Delhi was associated with increased risk (relative risk of 3.62, 95% CI 1.59-8.21)", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Animesh Ray", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Komal Singh", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Souvick Chattopadhyay", + "author_inst": "Translational Health Science and Technology Institute, Faridabad, Haryana" + }, + { + "author_name": "Farha Mehdi", + "author_inst": "Translational Health Science and Technology Institute, Faridabad, Haryana" + }, + { + "author_name": "Gaurav Batra", + "author_inst": "Translational Health Science and Technology Institute, Faridabad, Haryana" + }, + { + "author_name": "Aakansha Gupta", + "author_inst": "All India Institute Of Medical Sciences, New Delhi" + }, + { + "author_name": "Ayush Agarwal", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Bhavesh M", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Shubham Sahni", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Chaithra R", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Shubham Agarwal", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Chitrakshi Nagpal", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Gagantej B H", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Umang Arora", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Kartikeya Kumar Sharma", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Ranveer Singh Jadon", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Ashish Datt Upadhyay", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Neeraj Nischal", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Naval K Vikram", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Manish Soneja", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "R M Pandey", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Naveet Wig", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.22.20179929", "rel_title": "SARS-CoV-2 transmission and control in a hospital setting: an individual-based modelling study", @@ -1206022,37 +1207905,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.08.23.20180349", - "rel_title": "A deterministic linear infection model to inform Risk-Cost-Benefit Analysis of activities during the SARS-CoV-2 pandemic", - "rel_date": "2020-08-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.23.20180349", - "rel_abs": "August 16, 2020\n\nRisk-cost-benefit analysis requires the enumeration of decision alternatives, their associated outcomes, and the quantification of uncertainty. Public and private decision-making surrounding the COVID-19 pandemic must contend with uncertainty about the probability of infection during activities involving groups of people, in order to decide whether that activity is worth undertaking. We propose a deterministic linear model of SARS-CoV-2 infection probability that can produce estimates of relative risk for diverse activities, so long as those activities meet a list of assumptions, including that they do not last longer than one day. We show how the model can be used to inform decisions facing governments and industry, such as opening stadiums or flying on airplanes. We prove that the model is a good approximation of a more refined model in which we assume infections come from a series of independent risks. The linearity assumption makes interpreting and using the model straightforward, and we argue that it does so without significantly diminishing the reliability of the model.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "John E. McCarthy", - "author_inst": "Washington University" - }, - { - "author_name": "Bob A. Dumas", - "author_inst": "Omnium LLC" - }, - { - "author_name": "Myles Terence McCarthy", - "author_inst": "University of Illinois" - }, - { - "author_name": "Barry D Dewitt", - "author_inst": "Carnegie Mellon University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.08.24.20180661", "rel_title": "FLOW CYTOMETRY MULTIPLEXED METHOD FOR THE DETECTION OF NEUTRALIZING HUMAN ANTIBODIES TO THE NATIVE SARS-CoV-2 SPIKE PROTEIN", @@ -1206999,6 +1208851,41 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2020.08.25.254474", + "rel_title": "Experimental infection of cattle with SARS-CoV-2", + "rel_date": "2020-08-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.25.254474", + "rel_abs": "Six cattle (Bos taurus) were intranasally inoculated with SARS-CoV-2 and kept together with three naive in-contact animals. Low-level virus replication and a specific sero-reactivity were observed in two inoculated animals, despite the presence of high antibody titers against a bovine betacoronavirus. The in-contact animals did not become infected.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Lorenz Ulrich", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Kerstin Wernike", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Donata Hoffmann", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Thomas C. Mettenleiter", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Martin Beer", + "author_inst": "Friedrich-Loeffler-Institut" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.08.24.265645", "rel_title": "SARS-CoV-2 3CLpro Whole Human Proteome Cleavage Prediction and Enrichment/Depletion Analysis", @@ -1207931,37 +1209818,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.08.21.20179317", - "rel_title": "Health Disparities and COVID-19: A Retrospective Study Examining Individual and Community Factors Causing Disproportionate COVID-19 Outcomes in Cook County, Illinois, March 16-May 31, 2020", - "rel_date": "2020-08-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.21.20179317", - "rel_abs": "BackgroundEarly data from the COVID-19 pandemic suggests that the disease has had a disproportionate impact on communities of color causing higher infection and mortality rates within those communities.\n\nMethodsThis study used demographic data from the 2018 US census estimates, mortality data from the Cook County Medical Examiners office, and testing results from the Illinois Department of Public Health to perform both bivariate and multivariate regression analyses to explore the role race plays in COVID-19 outcomes at the individual and community levels.\n\nResultsPrincipal findings show that: 1) while Black Americans make up 22% of Cook Countys population, they account for 36% of the countys COVID-19 related deaths; 2) the average age of death from COVID-19 is seven years younger for minorities compared to Non-Hispanic White (White) decedents; 3) minorities were more likely than Whites to have seven of the top 10 co-morbidities at death; 4) residents of predominantly minority areas were twice as likely to test positive for COVID-19 (p = 0.0001, IRR 1.94, 95% CI 1.50, 2.50) than residents of predominantly White areas; and 5) residents of predominantly minority areas were 1.43 times more likely to die of COVID-19 than those in predominantly White areas (p = 0.03).\n\nConclusionsThere are notable differences in COVID-19 related outcomes between racial and ethnic groups at individual and community levels. We hope that this study will scientifically illustrate the health disparities experienced by communities of color and help to address the underlying systemic inequalities still prevalent within our country.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Larissa Unruh", - "author_inst": "Cook County Health" - }, - { - "author_name": "Sadhana Dharmapuri", - "author_inst": "Cook County Health" - }, - { - "author_name": "Xia Yinglin", - "author_inst": "University of Illinois" - }, - { - "author_name": "Kenneth Soyemi", - "author_inst": "Cook County Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.08.21.20178574", "rel_title": "SARS-CoV-2 infection and transmission in educational settings: cross-sectional analysis of clusters and outbreaks in England", @@ -1208777,6 +1210633,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.21.20179663", + "rel_title": "How do socio-demographic status and personal attributes influence adherence to COVID-19 preventive behaviours?", + "rel_date": "2020-08-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.21.20179663", + "rel_abs": "This study assesses how socio-demographic status and personal attributes influence protection behaviours during a pandemic, with protection behaviours being assessed through three perspectives - social distancing, personal protection behaviour and social responsibility awareness. The COVID-19 preventive behaviours were explored and compared based on the social-demographic and personal attributes of individuals. Using a publicly available and recently collected dataset on Japanese citizens during the COVID-19 early outbreak and exploiting both Classification and Regression Tree (CART) and regression analysis, the study notes that socio-demographic and personal attributes of individuals indeed shape the subjective prevention actions and thereby the control of the spread of a pandemic. Three socio-demographic attributes - sex, marital family status and having children - appear to have played an influential role in Japanese citizens abiding by the COVID-19 protection behaviours, especially with women having children being noted more conscious than the male counterparts. Work status also appears to have some impact especially concerning social distancing and personal protection behaviour. Among the personality attributes, smoking behaviour appeared as a contributing factor with non-smokers or less-frequent smokers more compliant to the protection behaviours. Overall, the findings imply the need of public policy campaigning to account for variations in protection behaviour due to socio-demographic and personal attributes during a pandemic.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Shahadat Uddin", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Tasadduq Imam", + "author_inst": "CQUniversity (Melbourne)" + }, + { + "author_name": "Matloob Khushi", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Arif Khan", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Mohammad Ali Moni", + "author_inst": "University of New south Wales" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.08.21.20179499", "rel_title": "The effect of BMI and physical activity levels on the duration of symptomatic days with Covid-19 infection", @@ -1209501,33 +1211392,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.20.20178962", - "rel_title": "Estimation of case-fatality rate in COVID-19 patients with hypertension and diabetes mellitus in the New York State", - "rel_date": "2020-08-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.20.20178962", - "rel_abs": "We estimated the case-fatality rate (CFR) and ratios (RR) in adult COVID-19 cases with hypertension and diabetes mellitus in the New York State. We found that the elderly population had a higher CFR, but the elevated CFR ratios associated with comorbidities are more pronounced for the younger population.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Yang Ge", - "author_inst": "The University of Georgia" - }, - { - "author_name": "Shengzhi Sun", - "author_inst": "Boston University" - }, - { - "author_name": "Ye Shen", - "author_inst": "The University of Georgia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.20.20178657", "rel_title": "COVID-19 in a cohort of pregnant women and their descendants. Cohort profile in the MOACC-19 study", @@ -1210231,6 +1212095,181 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2020.08.19.20177493", + "rel_title": "Ensemble Forecasts of Coronavirus Disease 2019 (COVID-19) in the U.S.", + "rel_date": "2020-08-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.19.20177493", + "rel_abs": "BackgroundThe COVID-19 pandemic has driven demand for forecasts to guide policy and planning. Previous research has suggested that combining forecasts from multiple models into a single \"ensemble\" forecast can increase the robustness of forecasts. Here we evaluate the real-time application of an open, collaborative ensemble to forecast deaths attributable to COVID-19 in the U.S.\n\nMethodsBeginning on April 13, 2020, we collected and combined one- to four-week ahead forecasts of cumulative deaths for U.S. jurisdictions in standardized, probabilistic formats to generate real-time, publicly available ensemble forecasts. We evaluated the point prediction accuracy and calibration of these forecasts compared to reported deaths.\n\nResultsAnalysis of 2,512 ensemble forecasts made April 27 to July 20 with outcomes observed in the weeks ending May 23 through July 25, 2020 revealed precise short-term forecasts, with accuracy deteriorating at longer prediction horizons of up to four weeks. At all prediction horizons, the prediction intervals were well calibrated with 92-96% of observations falling within the rounded 95% prediction intervals.\n\nConclusionsThis analysis demonstrates that real-time, publicly available ensemble forecasts issued in April-July 2020 provided robust short-term predictions of reported COVID-19 deaths in the United States. With the ongoing need for forecasts of impacts and resource needs for the COVID-19 response, the results underscore the importance of combining multiple probabilistic models and assessing forecast skill at different prediction horizons. Careful development, assessment, and communication of ensemble forecasts can provide reliable insight to public health decision makers.", + "rel_num_authors": 40, + "rel_authors": [ + { + "author_name": "Evan L Ray", + "author_inst": "University of Massachusetts Amherst" + }, + { + "author_name": "Nutcha Wattanachit", + "author_inst": "University of Massachusetts Amherst" + }, + { + "author_name": "Jarad Niemi", + "author_inst": "Iowa State University" + }, + { + "author_name": "Abdul Hannan Kanji", + "author_inst": "University of Massachusetts Amherst" + }, + { + "author_name": "Katie House", + "author_inst": "University of Massachusetts Amherst" + }, + { + "author_name": "Estee Y Cramer", + "author_inst": "University of Massachusetts Amherst" + }, + { + "author_name": "Johannes Bracher", + "author_inst": "Heidelberg Institute for Theoretical Studies and Karlsruhe Institute of Technology" + }, + { + "author_name": "Andrew Zheng", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Teresa K Yamana", + "author_inst": "Columbia University, Mailman School of Public Health" + }, + { + "author_name": "Xinyue Xiong", + "author_inst": "Northeastern University" + }, + { + "author_name": "Spencer Woody", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Yuanjia Wang", + "author_inst": "Columbia University" + }, + { + "author_name": "Lily Wang", + "author_inst": "Iowa State University" + }, + { + "author_name": "Robert L Walraven", + "author_inst": "unaffiliated" + }, + { + "author_name": "Vishal Tomar", + "author_inst": "Auquan Ltd" + }, + { + "author_name": "Katherine Sherratt", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Daniel Sheldon", + "author_inst": "University of Massachusetts Amherst" + }, + { + "author_name": "Robert C Reiner", + "author_inst": "University of Washington" + }, + { + "author_name": "B. Aditya Prakash", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Dave Osthus", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Michael Lingzhi Li", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Elizabeth C Lee", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Ugur Koyluoglu", + "author_inst": "Oliver Wyman" + }, + { + "author_name": "Pinar Keskinocak", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Youyang Gu", + "author_inst": "unaffiliated" + }, + { + "author_name": "Quanquan Gu", + "author_inst": "University of California Los Angeles" + }, + { + "author_name": "Glover E George", + "author_inst": "US Army Engineer Research and Development Center" + }, + { + "author_name": "Guido Espa\u00f1a", + "author_inst": "University of Notre Dame" + }, + { + "author_name": "Sabrina Corsetti", + "author_inst": "University of Michigan" + }, + { + "author_name": "Jagpreet Chhatwal", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Sean Cavany", + "author_inst": "University of Notre Dame" + }, + { + "author_name": "Hannah Biegel", + "author_inst": "University of Arizona" + }, + { + "author_name": "Michal Ben-Nun", + "author_inst": "Predictive Science Inc" + }, + { + "author_name": "Jo Walker", + "author_inst": "U.S. Centers for Disease Control and Prevention" + }, + { + "author_name": "Rachel Slayton", + "author_inst": "U.S. Centers for Disease Control and Prevention" + }, + { + "author_name": "Velma Lopez", + "author_inst": "U.S. Centers for Disease Control and Prevention" + }, + { + "author_name": "Matthew Biggerstaff", + "author_inst": "U.S. Centers for Disease Control and Prevention" + }, + { + "author_name": "Michael A Johansson", + "author_inst": "U.S. Centers for Disease Control and Prevention" + }, + { + "author_name": "Nicholas G Reich", + "author_inst": "University of Massachusetts - Amherst" + }, + { + "author_name": "- COVID-19 Forecast Hub Consortium", + "author_inst": "" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.18.20177691", "rel_title": "Genetically-predicted vitamin D status, ambient UVB during the pandemic and COVID-19 risk in UK Biobank: Mendelian Randomisation study", @@ -1210979,33 +1213018,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.19.20177840", - "rel_title": "Effects of (Un)lockdown on COVID-19 transmission: A mathematical study of different phases in India", - "rel_date": "2020-08-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.19.20177840", - "rel_abs": "The novel coronavirus (SARS-CoV-2), identified in China at the end of the December 2019 is causing a potentially fatal respiratory syndrome (COVID-19), has meanwhile led to outbreak all over the globe. India has now become the third worst hit country globally with 16,38,870 confirmed cases and 35,747 confirmed deaths due to COVID-19 as of 31 July 2020. In this paper we have used mathematical modelling approach to study the effects of lockdowns and un-lockdowns on the pandemic evolution in India. This, study is based on SIDHARTHE model, which is an extension of classical SIR (Susceptible-Infected-Recovered) model. The SIDHARTHE model distinguish between the diagnosed and undiagnosed cases, which is very important because undiagnosed individuals are more likely to spread the virus than diagnosed individuals. We have stratified the lockdowns and un-lockdowns into seven phases and have computed the basic reproduction number R0 for each phase. We have calibrated our model results with real data from 20 March 2020 to 31 July 2020. Our results demonstrate that different strategies implemented by GoI, have delayed the peak of pandemic by approximately 100 days. But due to underdiagnosis of the infected asymptomatic subpopulation, a sudden outbreak of cases can be observed in India.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Rohit Kumar", - "author_inst": "JNU" - }, - { - "author_name": "Md. Zubbair Malik", - "author_inst": "JNU" - }, - { - "author_name": "Sapna Ratan Shah", - "author_inst": "JNU" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.19.20178137", "rel_title": "Testing for coronavirus (SARS-CoV-2) infection in populations with low infection prevalence: the largely ignored problem of false positives and the value of repeat testing", @@ -1211673,6 +1213685,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2020.08.20.20178301", + "rel_title": "SARS-Cov-2 proliferation: an analytical aggregate-level model", + "rel_date": "2020-08-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.20.20178301", + "rel_abs": "An intuitive mathematical model describing the virus proliferation is presented and its parameters estimated from time series of observed reported CoViD-19 cases in Germany. The model replicates the main essential characteristics of the proliferation in a stylized form, and thus can support the systematic reasoning about interventional measures (or their lifting) that were discussed during summer and which currently become relevant again in some countries. The model differs in form from elementary SIR models, but is contained in the general Kermack-McKendrick (1927) model. It is maintained that (compared to elementary SIR models) the model is more faithfully representing real proliferation at the instantaneous level, leading to overall more plausible association of model parameters to physical transmission and recovery parameters. The main policy-oriented results are that (1) mitigation measures imposed in March 2020 in Germany were absolutely necessary to avoid health care resource exhaustion, (2) fast response is key to containment in case of renewed outbreaks. Two model generalizations aiming to better represent the true infectiousness profile and aiming to incorporate recurring susceptibility are stated and numerical results for the latter are presented.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Thomas Pitschel", + "author_inst": "Goethe University Frankfurt" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.19.20178368", "rel_title": "Inhaled corticosteroids downregulate SARS-CoV-2-related gene expression in COPD: results from a RCT", @@ -1212621,61 +1214652,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.17.20175950", - "rel_title": "Decline of SARS-CoV-2 specific IgG, IgM and IgA in convalescent COVID-19 patients within 100 days after hospital discharge", - "rel_date": "2020-08-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.17.20175950", - "rel_abs": "Monitoring the levels of SARS-CoV-2 specific antibodies such as IgG, M and A in COVID-19 patient is an alternative method for diagnosing SARS-CoV-2 infection and an simple way to monitor immune responses in convalescent patients and after vaccination. Here, we assessed the levels of SARS-CoV-2 RBD specific antibodies in twenty-seven COVID-19 convalescent patients over 28-99 days after hospital discharge. Almost all patient who had severe or moderate COVID-19 symptoms and a high-level of IgG during the hospitalization showed a significant reduction at revisit. The remaining patients who had a low-level IgG during hospitalization stayed low at revisit. As expected, IgM levels in almost all convalescent patients reduced significantly or stayed low at revisit. The RBD-specific IgA levels were also reduced significantly at revisit. We also attempted to estimate decline rates of virus-specific antibodies using a previously established exponential decay model of antibody kinetics after infection. The predicted days when convalescent patients RBD-specific IgG reaches to an undetectable level are approximately 273 days after hospital discharge, while the predicted decay times are 150 days and 108 days for IgM and IgA, respectively. This investigation and report will aid current and future studies to develope SARS-CoV-2 vaccines that are potent and long-lasting.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Huan Ma", - "author_inst": "Division of Life Sciences and Medicine, University of Science and Technology of China" - }, - { - "author_name": "Dan Zhao", - "author_inst": "Division of Life Sciences and Medicine, University of Science and Technology of China" - }, - { - "author_name": "Weihong Zeng", - "author_inst": "Division of Life Sciences and Medicine, University of Science and Technology of China" - }, - { - "author_name": "Yunru Yang", - "author_inst": "Division of Life Sciences and Medicine, University of Science and Technology of China" - }, - { - "author_name": "Xiaowen Hu", - "author_inst": "Division of Life Sciences and Medicine, University of Science and Technology of China" - }, - { - "author_name": "Peigen Zhou", - "author_inst": "Department of Statistics, University of Wisconsin-Madison, Madison, WI 53706, USA" - }, - { - "author_name": "Jianping Weng", - "author_inst": "Division of Life Sciences and Medicine, University of Science and Technology of China" - }, - { - "author_name": "Linzhao Cheng", - "author_inst": "Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei Anhui 230026, China, and Johns Hopkins University School of Medicin" - }, - { - "author_name": "Xueying Zheng", - "author_inst": "Division of Life Sciences and Medicine, University of Science and Technology of China" - }, - { - "author_name": "Tengchuan Jin", - "author_inst": "Division of Life Sciences and Medicine, University of Science and Technology of China" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.18.20177204", "rel_title": "Clinical Characterisation of Lateral Flow Assays for Detection of COVID-19 Antibodies in a population", @@ -1213515,6 +1215491,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2020.08.19.20172924", + "rel_title": "First study on surveillance of SARS-CoV-2 RNA in wastewater systems and related environments in Wuhan: Post-lockdown", + "rel_date": "2020-08-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.19.20172924", + "rel_abs": "Wastewater-based epidemiology (WBE) has emerged as an effective environmental surveillance tool in monitoring fecal-oral pathogen infections within a community. Congruently, SARS-CoV-2 virus, the etiologic agent of COVID-19, has been demonstrated to infect the gastrointestinal tissues, and be shed in feces. In the present study, SARS-CoV-2 RNA was concentrated from wastewater, sludge, surface water, ground water, and soil samples of municipal and hospital wastewater systems and related environment in Wuhan during the COVID-19 middle and low risk periods, and the viral RNA copies quantified using RT-qPCR. From the findings of this study, during the middle risk period, one influent sample and three secondary treatment effluents collected from Waste Water Treatment Plant 2 (WWTP2), as well as two influent samples from wastewater system of Hospital 2 were SARS-CoV-2 RNA positive. One sludge sample collected from Hospital 4; which was obtained during low risk period, was positive for SARS-CoV-2 RNA. These study findings demonstrate the significance of WBE in continuous surveilling and monitoring of SARS-CoV-2 at the community level, even when the COVID19 prevalence is low. Therefore, the application of WBE is principally useful in tracking the level of infections in communities and the risk assessment of the secondary environment.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Lu Zhao", + "author_inst": "Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, Ch" + }, + { + "author_name": "Evans Atoni", + "author_inst": "Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, Ch" + }, + { + "author_name": "Yao Du", + "author_inst": "School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China" + }, + { + "author_name": "Huaiyu Zhang", + "author_inst": "Central and Southern China Municipal Design & Research Institute Co., Ltd., Wuhan China" + }, + { + "author_name": "Oscar Donde", + "author_inst": "Department of Environmental Science, Egerton University, P. O. Box 536-20115, Egerton, Kenya" + }, + { + "author_name": "Doudou Huang", + "author_inst": "Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, Ch" + }, + { + "author_name": "Shuqi Xiao", + "author_inst": "Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, Ch" + }, + { + "author_name": "Teng Ma", + "author_inst": "School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China" + }, + { + "author_name": "Zhu Shu", + "author_inst": "School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China" + }, + { + "author_name": "Zhiming Yuan", + "author_inst": "Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, Ch" + }, + { + "author_name": "Lei Tong", + "author_inst": "School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China" + }, + { + "author_name": "Han Xia", + "author_inst": "Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, Ch" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.20.259242", "rel_title": "In Silico Modeling of Virus Particle Propagation and Infectivity along the Respiratory Tract: A Case Study for SARS-COV-2", @@ -1214255,57 +1216294,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.17.20177006", - "rel_title": "Single-strand RPA for rapid and sensitive detection of SARS-CoV-2 RNA", - "rel_date": "2020-08-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.17.20177006", - "rel_abs": "We report the single-strand Recombinase Polymerase Amplification (ssRPA) method, which merges the fast, isothermal amplification of RPA with subsequent rapid conversion of the double-strand DNA amplicon to single strands, and hence enables facile hybridization-based, high-specificity readout. We demonstrate the utility of ssRPA for sensitive and rapid (4 copies per 50 {micro}L reaction within 10 min, or 8 copies within 8 min) visual detection of SARS-CoV-2 RNA spiked samples, as well as clinical saliva and nasopharyngeal swabs in VTM or water, on lateral flow devices. The ssRPA method promises rapid, sensitive, and accessible RNA detection to facilitate mass testing in the COVID-19 pandemic.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Youngeun Kim", - "author_inst": "Harvard University, Wyss Institute" - }, - { - "author_name": "Adam B Yaseen", - "author_inst": "Harvard University, Wyss Institute" - }, - { - "author_name": "Jocelyn Y Kishi", - "author_inst": "Harvard University, Wyss Institute" - }, - { - "author_name": "Fan Hong", - "author_inst": "Harvard University, Wyss Institute" - }, - { - "author_name": "Sinem K Saka", - "author_inst": "Harvard University, Wyss Institute" - }, - { - "author_name": "Kuanwei Sheng", - "author_inst": "Harvard University, Wyss Institute" - }, - { - "author_name": "Nikhil Gopalkrishnan", - "author_inst": "Harvard University, Wyss Institute" - }, - { - "author_name": "Thomas E Schaus", - "author_inst": "Harvard University, Wyss Institute" - }, - { - "author_name": "Peng Yin", - "author_inst": "Harvard University, Wyss Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.18.20177295", "rel_title": "A Syndromic Surveillance Tool to Detect Anomalous Clusters of COVID-19 Symptoms in the United States", @@ -1215141,6 +1217129,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.18.20177451", + "rel_title": "Investigating dynamics of COVID-19 spread and containment with agent-based modeling", + "rel_date": "2020-08-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.18.20177451", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWGovernments, policy makers and officials around the globe are trying to mitigate the effects and progress of the COVID-19 pandemic by making decisions which will save the most lives and impose the least costs. Making these decisions needs a comprehensive understanding about the dynamics by which the disease spreads. In this work, we propose an epidemic agent-based model that simulates the spread of the disease. We show that the model is able to generate an important aspect of the pandemic: multiple waves of infection. A key point in the model description is the aspect of fear which can govern how agents behave under different conditions. We also show that the model provides an appropriate test-bed to apply different containment strategies and this work presents the results of applying two such strategies: testing, contact tracing, and travel restriction. The results show that while both strategies could result in flattening the epidemic curve and significantly reduce the maximum number of infected individuals; testing should be applied along with tracing previous contacts of the tested individuals to be effective. The results show how the curve is flattened with testing partnered with contact tracing, and the imposition of travel restrictions.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Amirarsalan Rajabi", + "author_inst": "Department of Computer Science, University of Central Florida" + }, + { + "author_name": "Alexander V. Mantzaris", + "author_inst": "Department of Statistics and Data Science, University of Central Florida" + }, + { + "author_name": "Ece C. Mutlu", + "author_inst": "Department of Industrial Engineering and Management Systems, University of Central Florida" + }, + { + "author_name": "Ozlem O. Garibay", + "author_inst": "Department of Industrial Engineering and Management Systems, University of Central Florida" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.18.20177444", "rel_title": "Environmental risk factors of airborne viral transmission: Humidity, Influenza and SARS-CoV-2 in the Netherlands", @@ -1215981,81 +1218000,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.08.20.258087", - "rel_title": "SARS-CoV-2 infection dynamics in lungs of African green monkeys", - "rel_date": "2020-08-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.20.258087", - "rel_abs": "Detailed knowledge about the dynamics of SARS-CoV-2 infection is important for unraveling the viral and host factors that contribute to COVID-19 pathogenesis. Old-World nonhuman primates recapitulate mild-moderate COVID-19 cases, thereby serving as important pathogenesis models. We compared African green monkeys inoculated with SARS-CoV-2 or inactivated virus to study the dynamics of virus replication throughout the respiratory tract. RNA sequencing of single cells from the lungs and mediastinal lymph nodes allowed a high-resolution analysis of virus replication and host responses over time. Viral replication was mainly localized to the lower respiratory tract, with evidence of replication in the pneumocytes. Macrophages were found to play a role in initiating a pro-inflammatory state in the lungs, while also interacting with infected pneumocytes. Our dataset provides a detailed view of changes in host and virus replication dynamics over the course of mild COVID-19 and serves as a valuable resource to identify therapeutic targets.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Emily Speranza", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Brandi N. Williamson", - "author_inst": "National Institues of Health" - }, - { - "author_name": "Friederike Feldmann", - "author_inst": "National Institues of Health" - }, - { - "author_name": "Gail L. Sturdevant", - "author_inst": "National Institues of Health" - }, - { - "author_name": "Lizzette Perez-Perez", - "author_inst": "National Institues of Health" - }, - { - "author_name": "Kimberly Mead-White", - "author_inst": "National Institues of Health" - }, - { - "author_name": "Brian J. Smith", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Jamie Lovaglio", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Craig Martens", - "author_inst": "National Institues of Health" - }, - { - "author_name": "Vincent Munster", - "author_inst": "NIAID" - }, - { - "author_name": "Atsushi Okumura", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Carl Shaia", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Heinz Feldmann", - "author_inst": "NIAID, NIH" - }, - { - "author_name": "Sonja M. Best", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Emmie de Wit", - "author_inst": "NIAID, NIH" - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.08.20.258376", "rel_title": "SARS-CoV-2 Quasispecies provides insight into its genetic dynamics during infection", @@ -1217107,6 +1219051,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.18.256446", + "rel_title": "Neutralizing antibody-dependent and -independent immune responses against SARS-CoV-2 in cynomolgus macaques", + "rel_date": "2020-08-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.18.256446", + "rel_abs": "Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infectious disease (COVID-19) has been threatening the world because of severe symptoms and relatively high mortality. To develop vaccines and antiviral drugs for COVID-19, an animal model of SARS-CoV-2 infection is required to evaluate the efficacy of prophylactics and therapeutics in vivo. Therefore, we examined the pathogenicity of SARS-CoV-2 in cynomolgus macaques until 28 days after virus inoculation in the present study. Cynomolgus macaques showed body temperature rises after infection and X-ray radiographic viral pneumonia was observed in one of three macaques. However, none of the macaques showed life-threatening clinical signs of disease corresponding that approximately 80% of human patients did not show a critical disease in COVID-19. A neutralizing antibody against SARS-CoV-2 and T-lymphocytes that produced interferon (IFN)-{gamma} and interleukin (IL)-2 specifically for SARS-CoV-2 N protein were detected on day 14 in the macaque that showed viral pneumonia. On the other hand, in the other macaques, in which a neutralizing antibody was not detected, T-lymphocytes that produced IFN-{gamma} specifically for SARS-CoV-2 N protein increased on day 7 to day 14 prior to an increase in the number of T-lymphocytes that produced IL-2. These results suggest that not only a neutralizing antibody but also cellular immunity augmented by IFN-{gamma} has a role in the elimination of SARS-CoV-2. Thus, because of the mild clinical signs of disease and low/no antibody responses against SARS-CoV-2 in two thirds of the macaques, cynomolgus macaques are appropriate to extrapolate human responses in vaccine and drug development.\n\nAuthor SummarySevere acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infectious disease (COVID-19) has been threatening the world. To develop vaccines and antiviral drugs for COVID-19, an animal model of SARS-CoV-2 infection is required to evaluate their efficacy in vivo. Therefore, we examined the pathogenicity of SARS-CoV-2 in a non-human primate model until 28 days after virus inoculation. Cynomolgus macaques showed a fever after infection and X-ray radiographic viral pneumonia was observed in one of three macaques. However, none of the macaques showed life-threatening symptoms. A neutralizing antibody against SARS-CoV-2 and T-lymphocytes that produced interferon (IFN)-{gamma} and interleukin (IL)-2 specifically for SARS-CoV-2 protein were detected on day 14 in the macaque that showed viral pneumonia. In the other macaques, in which a neutralizing antibody was not detected, T-lymphocytes that produced IFN-{gamma} specifically for SARS-CoV-2 N protein increased on day 7 to day 14. These results suggest that not only a neutralizing antibody but also cellular immunity augmented by IFN-{gamma} has a role in the elimination of SARS-CoV-2. Thus, because of the mild symptoms and low/no antibody responses against SARS-CoV-2 in two thirds of the macaques, cynomolgus macaques are appropriate to extrapolate human responses in vaccine and drug development.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Hirohito Ishigaki", + "author_inst": "Shiga University of Medical Science" + }, + { + "author_name": "Misako Nakayama", + "author_inst": "Shiga University of Medical Science" + }, + { + "author_name": "Yoshinori Kitagawa", + "author_inst": "Shiga University of Medical Science" + }, + { + "author_name": "Cong Thanh Nguyen", + "author_inst": "Shiga University of Medical Science" + }, + { + "author_name": "Kaori Hayashi", + "author_inst": "Shiga University of Medical Science" + }, + { + "author_name": "Masanori Shiohara", + "author_inst": "Shiga University of Medical Science" + }, + { + "author_name": "Bin Gotoh", + "author_inst": "Shiga University of Medical Science" + }, + { + "author_name": "Yasushi Itoh", + "author_inst": "Shiga University of Medical Science" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.08.18.256776", "rel_title": "SARS-CoV-2 ORF9c Is a Membrane-Associated Protein that Suppresses Antiviral Responses in Cells", @@ -1217931,53 +1219922,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.15.20175489", - "rel_title": "Colorimetric Test for Fast Detection of SARS-CoV-2 in Nasal and Throat Swabs", - "rel_date": "2020-08-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.15.20175489", - "rel_abs": "Mass testing is fundamental to face the pandemic caused by the coronavirus SARS-CoV-2 discovered at the end of 2019. To this aim, it is necessary to establish reliable, fast and cheap tools to detect viral particles in biological material so to identify the people capable to spread the infection. We demonstrate that a colorimetric biosensor based on gold nanoparticle (AuNP) interaction induced by SARS-CoV-2 lends itself as an outstanding tool for detecting viral particles in nasal and throat swabs. The extinction spectrum of a colloidal solution of multiple viral-target gold nanoparticles - AuNPs functionalized with antibodies targeting three surface proteins of SARS-CoV-2 (spike, envelope and membrane) - is redshifted in few minutes when mixed to a solution containing the viral particle. The optical density of the mixed solution measured at 560 nm was compared to the threshold cycle (Ct) of a Real Time-PCR (gold standard for detecting the presence of viruses) finding that the colorimetric method is able to detect very low viral load with a detection limit approaching that of RT-PCR. Since the method is sensitive to the infecting viral particle rather than to its RNA, the achievements reported here open new perspective not only in the context of the current and possible future pandemics, but also in microbiology as the biosensor proves itself to be a powerful though simple tool for measuring the viral particle concentration.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Bartolomeo Della Ventura", - "author_inst": "University of Naples \"Federico II\"" - }, - { - "author_name": "Michele Cennamo", - "author_inst": "University of Naples \"Federico II\"" - }, - { - "author_name": "Antonio Minopoli", - "author_inst": "University of Naples \"Federico II\"" - }, - { - "author_name": "Raffaele Campanile", - "author_inst": "University of Naples \"Federico II\"" - }, - { - "author_name": "Sergio Bolletti Censi", - "author_inst": "Cosvitec scarl" - }, - { - "author_name": "Daniela Terracciano", - "author_inst": "University of Naples \"Federico II\"" - }, - { - "author_name": "Giuseppe Portella", - "author_inst": "University of Naples \"Federico II\"" - }, - { - "author_name": "Raffaele Velotta", - "author_inst": "University of Naples \"Federico II\"" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.16.20176156", "rel_title": "Interobserver Agreement of Lung Ultrasound Findings of COVID-19", @@ -1218893,6 +1220837,49 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.08.18.255315", + "rel_title": "In-depth blood proteome profiling analysis revealed distinct functional characteristics of plasma proteins between severe and non-severe COVID-19 patients", + "rel_date": "2020-08-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.18.255315", + "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected over ten million patients worldwide. Although most coronavirus disease 2019 (COVID-19) patients have a good prognosis, some develop severe illness. Markers that define disease severity or predict clinical outcome need to be urgently developed as the mortality rate in critical cases is approximately 61.5%. In the present study, we performed indepth proteome profiling of undepleted plasma from eight COVID-19 patients. Quantitative proteomic analysis using the BoxCar method revealed that 91 out of 1,222 quantified proteins were differentially expressed depending on the severity of COVID-19. Importantly, we found 76 proteins, previously not reported, which could be novel prognostic biomarker candidates. Our plasma proteome signatures captured the host response to SARS-CoV-2 infection, thereby highlighting the role of neutrophil activation, complement activation, platelet function, and T cell suppression as well as proinflammatory factors upstream and downstream of interleukin-6, interleukin-1B, and tumor necrosis factor. Consequently, this study supports the development of blood biomarkers and potential therapeutic targets to aid clinical decision-making and subsequently improve prognosis of COVID-19.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Joonho Park", + "author_inst": "Seoul National University Hospital" + }, + { + "author_name": "Hyeyoon Kim", + "author_inst": "Seoul National University Hospital" + }, + { + "author_name": "So Yeon Kim", + "author_inst": "National Medical Center" + }, + { + "author_name": "Yeonjae Kim", + "author_inst": "National Medical Center" + }, + { + "author_name": "Jee-Soo Lee", + "author_inst": "Seoul National University Hospital" + }, + { + "author_name": "Moon-Woo Seong", + "author_inst": "Seoul National University Hospital" + }, + { + "author_name": "Dohyun Han", + "author_inst": "Seoul National University Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "systems biology" + }, { "rel_doi": "10.1101/2020.08.18.255935", "rel_title": "IFITM proteins promote SARS-CoV-2 infection in human lung cells", @@ -1219865,49 +1221852,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.15.20175851", - "rel_title": "Rapid, sensitive and high-throughput screening method for detection of SARS-CoV-2 antibodies by bio layer interferometry", - "rel_date": "2020-08-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.15.20175851", - "rel_abs": "Present pandemic scenario, there exists an unmet global need for the development of a rapid and sensitive method for the detection of SARS-CoV-2 infection. The available options for identification of SARS-CoV-2 infection are detection of viral RNA by qRT-PCR, Antigen or Antibody testing by serological methods. Even though many kits available commercially but none of them are rapid, sensitive and high throughput. OnCovid total antibody assay is a diagnostic method developed by us uses the principle of bio-layer Interferometry to detect IgM, IgA and IgG antibodies against SARS-CoV-2 antigens. This method overcomes many of the limitations normally faced in antibody detection by other methods and offers a superior platform for a rapid, sensitive and specific detection of SARS-CoV-2 infection. The test is economical, and the results can be obtained in as short as 30 seconds per test. In addition to its standalone use in early diagnosis of SARS-CoV-2, OnCovid total antibody assay can be used to therapeutic monitoring of antiviral therapies used in clinical management and to estimate the antibody titers during convalescent plasma donation.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Sudarshan Reddy Lokireddy", - "author_inst": "Oncosimis Biotech Pvt Ltd" - }, - { - "author_name": "Sridhar Rao Kunchala", - "author_inst": "Oncosimis Biotech Pvt Ltd" - }, - { - "author_name": "Ranga Pratyusha Godavarthy", - "author_inst": "Oncosimis Biotech Pvt Ltd" - }, - { - "author_name": "Venkata Sri Krishna Kona", - "author_inst": "Oncosimis Biotech Pvt Ltd" - }, - { - "author_name": "Laxmaiah Avula", - "author_inst": "ICMR-National Institute of Nutrition" - }, - { - "author_name": "Rakesh Kumar Mishra", - "author_inst": "CSIR-Centre for Cellular and Molecular Biology" - }, - { - "author_name": "Madhusudhana Rao Nalam", - "author_inst": "AIC-CCMB" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.15.20175703", "rel_title": "COVID-19 TRANSMISSION DYNAMICS IN INDIA WITH EXTENDED SEIR MODEL", @@ -1220567,6 +1222511,57 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.08.17.253682", + "rel_title": "Transcriptomic profiling of human corona virus (HCoV)-229E -infected human cells and genomic mutational analysis of HCoV-229E and SARS-CoV-2", + "rel_date": "2020-08-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.17.253682", + "rel_abs": "Human coronaviruses (HCoVs) cause mild to severe respiratory infection. Most of the common cold illnesses are caused by one of four HCoVs, namely HCoV-229E, HCoV-NL63, HCoV-HKU1 and HCoV-OC43. Several studies have applied global transcriptomic methods to understand host responses to HCoV infection, with most studies focusing on the pandemic severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome CoV (MERS-CoV) and the newly emerging SARS-CoV-2. In this study, Next Generation Sequencing was used to gain new insights into cellular transcriptomic changes elicited by alphacoronavirus HCoV-229E. HCoV-229E-infected MRC5 cells showed marked downregulation of superpathway of cholesterol biosynthesis and eIF2 signaling pathways. Moreover, upregulation of cyclins, cell cycle control of chromosomal replication, and the role of BRCA1 in DNA damage response, alongside downregulation of the cell cycle G1/S checkpoint, suggest that HCoV-229E favors S phase for viral infection. Intriguingly, a significant portion of key factors of cell innate immunity, interferon-stimulated genes (ISGs) and other transcripts of early antiviral response genes were downregulated early in HCoV-229E infection. On the other hand, early upregulation of the antiviral response factor Apolipoprotein B mRNA editing enzyme catalytic subunit 3B (APOBEC3B) was observed. APOBEC3B cytidine deaminase signature (C-to-T) was previously observed in genomic analysis of SARS-CoV-2 but not HCoV-229E. Higher levels of C-to-T mutations were found in countries with high mortality rates caused by SARS-CoV-2. APOBEC activity could be a marker for new emerging CoVs. This study will enhance our understanding of commonly circulating HCoVs and hopefully provide critical information about still-emerging coronaviruses.\n\nAuthor summaryHuman coronaviruses (HCoVs) generate respiratory tract infections. HCoV-229E is one of four known HCoV strains that circulate annually in the population for several decades. Beside these, three pandemic CoV emerged since year 2002, the Severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV) and SARS-CoV-2. These three strains attracted most attention for extensive research and less consideration has been given to the commonly infecting HCoVs. In this study we use Next generation sequencing analysis to understand global transcriptomic changes in human host cells following HCoV-229E infection. We found several cellular pathways that change during infection that involve cholesterol biosynthesis, cell cycle control, DNA replication, DNA repair, innate immune response and an interesting RNA editing enzyme which could be involve in CoVs pathogenesis.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Nehemya Friedman", + "author_inst": "Sheba Medical Center at Tel Hashomer" + }, + { + "author_name": "Jasmine Jacob-Hirsch", + "author_inst": "Sheba Medical Center at Tel Hashomer" + }, + { + "author_name": "Yaron Drori", + "author_inst": "Sheba Medical Center at Tel Hashomer" + }, + { + "author_name": "Eran Eyal", + "author_inst": "Sheba Medical Center at Tel Hashomer" + }, + { + "author_name": "Nitzan Kol", + "author_inst": "Sheba Medical Center at Tel Hashomer" + }, + { + "author_name": "Omri Nayshool", + "author_inst": "Sheba Medical Center at Tel Hashomer" + }, + { + "author_name": "Ella Mendelson", + "author_inst": "Sheba Medical Center at Tel Hashomer" + }, + { + "author_name": "Gidi Rechavi", + "author_inst": "Sheba Medical Center at Tel Hashomer" + }, + { + "author_name": "Michal Mandelboim", + "author_inst": "Sheba Medical Center" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.08.14.20174961", "rel_title": "Rates of COVID-19-related Outcomes in Cancer compared to non-Cancer Patients", @@ -1221467,29 +1223462,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.14.20175240", - "rel_title": "The limits of estimating COVID-19 intervention effects using Bayesian models", - "rel_date": "2020-08-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.14.20175240", - "rel_abs": "To limit the rapid spread of COVID-19, most governments have introduced different non-pharmaceutical interventions, which might have severe costs for society. Therefore, it is crucial to evaluate the most cost-effective interventions, using, for instance, Bayesian modelling. Such modelling efforts have deemed lockdown to account for 81% of the reduction in R0, contributing to government policies. Here, we show that these conclusions are unsupported and that policies therefore should not be based on these studies.\n\nhttps://www.eurosurveillance.org/for-authors", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Patrick Bryant", - "author_inst": "Stockholm University" - }, - { - "author_name": "Arne Elofsson", - "author_inst": "Stockholm University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.15.252437", "rel_title": "Design of a highly thermotolerant, immunogenic SARS-CoV-2 spike fragment", @@ -1222401,6 +1224373,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.13.20174482", + "rel_title": "Comparison of COVID-19 Infections Among Healthcare Workers and Non-Healthcare Workers", + "rel_date": "2020-08-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.13.20174482", + "rel_abs": "ObjectivesHealthcare workers face distinct occupational challenges that affect their personal health, especially during a pandemic. In this study we compare the characteristics and outcomes of Covid-19 patients who are and who are not healthcare workers (HCW).\n\nMethodsWe retrospectively analyzed a cohort of adult patients with known HCW status and a positive SARS-CoV-2 PCR test presenting to a large academic medical center emergency department (ED) in New York State. We routinely collect data on occupation and exposures to suspected Covid-19. The primary outcome was hospital admission. Secondary outcomes were ICU admission, need for invasive mechanical ventilation (IMV), and mortality. We compared baseline characteristics and outcomes of Covid-19 adult patients based on whether they were or were not HCW using univariable and multivariable analyses.\n\nResultsFrom March 1 2020 through June 2020, 2,842 adult patients (mean age 53+/-19 years, 53% male) with positive SARS-CoV-2 PCR tests and known HCW status visited the ED. This included 193 (6.8%) known HCWs and 2,649 (93.2%) non-HCWs. Compared with non-HCW, HCWs were younger (43 vs 53 years, P<0.001), more likely female (118/193 vs 1211/2649, P<0.001), and more likely to have a known Covid-19 exposure (161/193 vs 946/2649, P<0.001), but had fewer comorbidities. On presentation to the ED, HCW also had lower frequencies of tachypnea (12/193 vs 426/2649, P<0.01), hypoxemia (15/193 vs 564/2649, P<0.01), bilateral opacities on imaging (38/193 vs 1189/2649, P<0.001), and lymphocytopenia (6/193 vs 532/2649, P<0.01) compared to non-HCWs. Direct discharges home from the ED were more frequent in HCW 154/193: 80% vs 1275/2649: 48% p<0.001). Hospital admissions (38/193 20% vs 1264/2694 47%, P<0.001), ICU admissions (7/193 3% vs 321/2694 12%, P<0.001), need for IMV (6/193 3% vs 321/2694 12%, P<0.001) and mortality (2/193 1% vs 219/2694 8%, P<0.01) were lower than among non-HCW. After controlling for age, sex, comorbidities, presenting vital signs and radiographic imaging, HCW were less likely to be admitted (OR 0.6, 95%CI 0.3-0.9) than non HCW.\n\nConclusionsCompared with non HCW, HCW with Covid-19 were younger, had less severe illness, and were less likely to be admitted.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Rachel Kim", + "author_inst": "Stony Brook University" + }, + { + "author_name": "Sharon Nachman", + "author_inst": "Stony Brook University" + }, + { + "author_name": "Rafael Fernandes", + "author_inst": "Stony Brook University" + }, + { + "author_name": "Kristen Meyers", + "author_inst": "Stony Brook University" + }, + { + "author_name": "Maria Taylor", + "author_inst": "Stony Brook University" + }, + { + "author_name": "Debra LeBlanc", + "author_inst": "Stony Brook University" + }, + { + "author_name": "Adam Singer", + "author_inst": "Stony Brook University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.13.20174136", "rel_title": "Genomic Diversity of SARS-CoV-2 During Early Introduction into the United States National Capital Region", @@ -1223473,45 +1225488,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.14.20174888", - "rel_title": "Impact of the COVID-19 pandemic on ongoing health research: an ad hoc survey among investigators in Germany", - "rel_date": "2020-08-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.14.20174888", - "rel_abs": "ObjectivesTo gain insights into the impact of the COVID-19 pandemic on ongoing health research projects, using projects from a selected funding programme in Germany as an example.\n\nDesignOnline survey\n\nSettingLockdowns and social distancing policies impact upon clinical and public health research in various forms, especially if unrelated to COVID-19. Research institutions have reduced onsite activities, data is often collected remotely, and during the height of the crisis, clinical researchers were partially forced to abandon their projects in favour of front-line care and crisis response.\n\nParticipants120 investigators of health research projects across Germany, performed between 15 and 25 May 2020.\n\nResultsThe response rate (78%) showed that the survey generated significant interest among investigators. 85 responses were included for analysis, and the majority of investigators (93%) reported that their projects were affected by the pandemic, with many (80%) stating that data collection was not possible as planned, and they could not carry out interventions as planned (67%). Other impacts were caused by staff being unavailable, for example through child or elder care commitments or because of COVID-19 quarantine or illness. Investigators also reported that publications were delayed or not feasible at all (56%), and some experienced problems with PhD or Masters theses 18%). The majority of investigators had mitigation strategies in place such as adjustment of data collection methods using digital tools (46%) or of project implementation in general (46%), others made changes in research design or research questions (27%).\n\nConclusionsThe COVID-19 pandemic has severely impacted upon health research projects. The main challenge is now to mitigate negative effects and to improve long-term resilience in health research. The pandemic has also acted as a driver of innovation and change, for example by accelerating the use of digital methods.\n\nStrengths and limitations of this studyO_LITo our knowledge, this is the first study investigating the impact of the COVID-19 pandemic on non COVID-19 health research projects, mitigation strategies employed by investigators and needs for support.\nC_LIO_LIThe sample is representative of the projects from the \"Healthy - for a lifetime\" funding programme in Germany, which includes different types of health research projects and involves different population groups.\nC_LIO_LIWe were not able to clearly distinguish the effects on different types of projects (clinical studies, observational studies, secondary data analyses etc.), because a small number of investigators led more than one project and were not asked to report on each project individually.\nC_LIO_LIThe survey presents a snapshot of the situation in May 2020. To assess effects more widely as well as long-term impacts on projects, the survey would need to be repeated.\nC_LI", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Tanja Bratan", - "author_inst": "Fraunhofer Institute of Systems and Innovation Research" - }, - { - "author_name": "Heike Aichinger", - "author_inst": "Fraunhofer Institute of Systems and Innovation Research" - }, - { - "author_name": "Nicole Brkic", - "author_inst": "Fraunhofer Institute of Systems and Innovation Research" - }, - { - "author_name": "Jana Rueter", - "author_inst": "Medical Sociology, Department for Epidemiology and Preventive Medicine, University of Regensburg" - }, - { - "author_name": "Christian Apfelbacher", - "author_inst": "Institute of Social Medicine and Health Systems Research, Otto von Guericke University Magdeburg" - }, - { - "author_name": "Julika Loss", - "author_inst": "Medical Sociology, Department for Epidemiology and Preventive Medicine, University of Regensburg; Robert Koch Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.08.13.20174706", "rel_title": "England's Lockdown vs. Sweden's Herd Immunity: A Comparison of the Daily New COVID-19 Cases and Related Deaths Using Comparative Interrupted Time Series Analysis", @@ -1224215,6 +1226191,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.08.11.20173054", + "rel_title": "Infodemiological study of COVID-19 in Latin America and The Caribbean", + "rel_date": "2020-08-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.11.20173054", + "rel_abs": "BackgroundInfodemiology has been widely used to assess epidemics. In light of the recent pandemic, we use Google Search data to explore online interest about COVID-19 and related topics in 20 countries of Latin America and the Caribbean.\n\nMethodData from Google Trends from 2019/12/30 to 2020/04/25 regarding COVID-19 and other related topics were retrieved and correlated with official data on COVID-19 cases and with national epidemiological indicators.\n\nResultsThe Latin American and Caribbean countries with the most interest for COVID19 were Peru (100%) and Panama (98.39%). No correlation was found between this interest and national epidemiological indicators. The global and local response time were 20.2{+/-}1.2 days and 16.7{+/-}15 days, respectively. The duration of public attention was 64.8{+/-}12.5 days. The most popular topics related to COVID-19 were: the countrys situation (100 {+/-} 0) and coronavirus symptoms (36.82{+/-}16.16). Most countries showed a strong or moderated (r=0.72) significant correlation between searches related to COVID-19 and daily new cases. In addition, the highest significant lag correlation was found on day 13.35{+/-}5.76 (r=0.79).\n\nConclusionsInterest shown by Latin American and Caribbean countries for COVID-19 was high. The degree of online interest in a country does not clearly reflect the magnitude of their epidemiological indicators. The response time and the lag correlation were greater than in European and Asian countries. Little interest was found for preventive measures. Strong correlation between searches for COVID-19 and daily new cases suggests a predictive utility that should be investigated by further studies.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Carlos Jes\u00fas Arag\u00f3n-Ayala", + "author_inst": "Universidad Nacional de San Agust\u00edn de Arequipa, Arequipa, Peru" + }, + { + "author_name": "Julissa Copa-Uscamayta", + "author_inst": "Universidad Nacional de San Agust\u00edn de Arequipa, Arequipa, Peru" + }, + { + "author_name": "Luis Herrera", + "author_inst": "Universidad Nacional de San Agust\u00edn de Arequipa, Arequipa, Peru" + }, + { + "author_name": "Frank Zela-Coila", + "author_inst": "Universidad Nacional de San Agust\u00edn de Arequipa, Arequipa, Peru" + }, + { + "author_name": "Cender U Quispe-Juli", + "author_inst": "Universidad Peruana Cayetano Heredia, Lima, Peru" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.11.20172775", "rel_title": "Trends in Covid-19 risk-adjusted mortality rates in a single health system", @@ -1224991,77 +1227002,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nursing" }, - { - "rel_doi": "10.1101/2020.08.12.20173872", - "rel_title": "Severity Assessment of COVID-19 based on Clinical and Imaging Data", - "rel_date": "2020-08-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.12.20173872", - "rel_abs": "ObjectivesThis study aims to develop a machine learning approach for automated severity assessment of COVID-19 patients based on clinical and imaging data.\n\nMaterials and MethodsClinical data--demographics, signs, symptoms, comorbidities and blood test results--and chest CT scans of 346 patients from two hospitals in the Hubei province, China, were used to develop machine learning models for automated severity assessment of diagnosed COVID-19 cases. We compared the predictive power of clinical and imaging data by testing multiple machine learning models, and further explored the use of four oversampling methods to address the imbalance distribution issue. Features with the highest predictive power were identified using the SHAP framework.\n\nResultsTargeting differentiation between mild and severe cases, logistic regression models achieved the best performance on clinical features (AUC:0.848, sensitivity:0.455, specificity:0.906), imaging features (AUC:0.926, sensitivity:0.818, specificity:0.901) and the combined features (AUC:0.950, sensitivity:0.764, specificity:0.919). The SMOTE oversampling method further improved the performance of the combined features to AUC of 0.960 (sensitivity:0.845, specificity:0.929).\n\nDiscussionImaging features had the strongest impact on the model output, while a combination of clinical and imaging features yielded the best performance overall. The identified predictive features were consistent with findings from previous studies. Oversampling yielded mixed results, although it achieved the best performance in our study.\n\nConclusionsThis study indicates that clinical and imaging features can be used for automated severity assessment of COVID-19 patients and have the potential to assist with triaging COVID-19 patients and prioritizing care for patients at higher risk of severe cases.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Juan Quiroz", - "author_inst": "Centre for Health Informatics, Australian Institute of Health Innovation, Faculty of Medicine, Health and Human Sciences, Macquarie University; Centre for Big D" - }, - { - "author_name": "Youzhen Feng", - "author_inst": "Medical Imaging Centre, The First Affiliated Hospital of Jinan University, Guangzhou, China" - }, - { - "author_name": "Zhongyuan Cheng", - "author_inst": "Medical Imaging Centre, The First Affiliated Hospital of Jinan University, Guangzhou, China" - }, - { - "author_name": "Dana Rezazadegan", - "author_inst": "Centre for Health Informatics, Australian Institute of Health Innovation, Faculty of Medicine, Health and Human Sciences, Macquarie University; Department of Co" - }, - { - "author_name": "Pingkang Chen", - "author_inst": "Medical Imaging Centre, The First Affiliated Hospital of Jinan University, Guangzhou, China" - }, - { - "author_name": "Qiting Lin", - "author_inst": "Medical Imaging Centre, The First Affiliated Hospital of Jinan University, Guangzhou, China" - }, - { - "author_name": "Long Qian", - "author_inst": "Department of Biomedical Engineering, Peking University, Beijing, China" - }, - { - "author_name": "Xiaofang Liu", - "author_inst": "School of Data and Computer Science, Sun Yat-sen University, Guangzhou, China" - }, - { - "author_name": "Shlomo Berkovsky", - "author_inst": "Centre for Health Informatics, Australian Institute of Health Innovation, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australi" - }, - { - "author_name": "Enrico Coiera", - "author_inst": "Centre for Health Informatics, Australian Institute of Health Innovation, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australi" - }, - { - "author_name": "Lei Song", - "author_inst": "Department of Radiology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China" - }, - { - "author_name": "Xiaoming Qiu", - "author_inst": "Department of Radiology, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Edong Healthcare Group, Huangshi, China" - }, - { - "author_name": "Sidong Liu", - "author_inst": "Centre for Health Informatics, Australian Institute of Health Innovation, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australi" - }, - { - "author_name": "Xiangran Cai", - "author_inst": "Medical Imaging Centre, The First Affiliated Hospital of Jinan University, Guangzhou, China" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.08.10.20171728", "rel_title": "Decontamination of SARS-CoV-2 and other RNA viruses from N95 level meltblown polypropylene fabric using heat under different humidities", @@ -1225973,6 +1227913,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.08.11.20172734", + "rel_title": "Social Network Analysis of COVID-19 Transmission in Karnataka, India", + "rel_date": "2020-08-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.11.20172734", + "rel_abs": "We used social network analysis (SNA) to study the novel coronavirus (COVID-19) outbreak in Karnataka, India, and assess the potential of SNA as a tool for outbreak monitoring and control. We analyzed contact tracing data of 1147 Covid-19 positive cases (mean age 34.91 years, 61.99% aged 11-40, 742 males), anonymized and made public by the government. We used software tools Cytoscape and Gephi to create SNA graphics and determine network attributes of nodes (cases) and edges (directed links, determined by contact tracing, from source to target patients). Outdegree was 1-47 for 199 (17.35%) nodes, and betweenness 0.5-87 for 89 (7.76%) nodes. Men had higher mean outdegree and women, higher betweenness. Delhi was the exogenous source of 17.44% cases. Bangalore city had the highest caseload in the state (229, 20%), but comparatively low cluster formation. Thirty-four (2.96%) \"super-spreaders\" (outdegree[≥]5) caused 60% of the transmissions. Real-time social network visualization can allow healthcare administrators to flag evolving hotspots and pinpoint key actors in transmission. Prioritizing these areas and individuals for rigorous containment could help minimize resource outlay and potentially achieve a significant reduction in COVID-19 transmission.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Sakranaik Saraswathi", + "author_inst": "Bangalore Medical College and Research Institute, Bangalore, Karnataka, India." + }, + { + "author_name": "Amita Mukhopadhyay", + "author_inst": "Bangalore Medical College and Research Institute (former)" + }, + { + "author_name": "Hemant Shah", + "author_inst": "Independent researcher" + }, + { + "author_name": "T S Ranganath", + "author_inst": "Bangalore Medical College and Research Institute, Bangalore, Karnataka, India" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.12.20173831", "rel_title": "Temporal Dynamics of Viral Load and False Negative Rate Influence the Levels of Testing Necessary to Combat COVID19 Spread", @@ -1226709,41 +1228680,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "dentistry and oral medicine" }, - { - "rel_doi": "10.1101/2020.08.11.20173039", - "rel_title": "Local protection bubbles: an interpretation of the decrease in the velocity of coronavirus's spread in the city of Sao Paulo", - "rel_date": "2020-08-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.11.20173039", - "rel_abs": "After four months of dealing with the pandemic, the city of Sao Paulo entered a phase of relaxed social-distancing measures in July 2020, and saw its social isolation rate fall at the same time as the number of cases, deaths, and hospital bed occupation declined. We use a calibrated multi-agent model to describe these dynamics. We assert here that this phenomenon can be understood as the result of local protective bubbles formed in the citys sub-environments at the same time that there was an exhaustion of contagion networks. Both reduce the velocity of the viruss spread, causing temporary reductions in the epidemic curve, albeit in an unstable equilibrium. These local bubbles can burst anytime and anywhere due to the reintroduction of a few infected people at the same time that there is a reduction in non-pharmaceutical interventions (NPI), such as social-distancing practices. It is important to stress that this hypothesis aligns with the dynamics of the viruss spread observed so far, without needing ad hoc suppositions about natural collective immunity thresholds or heterogeneity in the populations transmission rate, which come with the risk of making mistaken predictions that may could lead to the loss of many lives. The safe way to move ahead is to continue doing all we can to avoid new infections until a vaccine is found that properly and safely creates herd immunity.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Jose Paulo Guedes Pinto", - "author_inst": "Federal University of ABC (UFABC)" - }, - { - "author_name": "Patricia Camargo Magalhaes", - "author_inst": "University of Bristol" - }, - { - "author_name": "Gerusa Maria Figueiredo", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Domingos Alves", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Diana Maritza Segura-Angel", - "author_inst": "Army Aviation School, Bogota, Colombia" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.13.20163030", "rel_title": "Clinical characteristics and Outcomes of 500 patients with COVID Pneumonia : Results from a Single center(Southend University Hospital)", @@ -1227323,6 +1229259,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.13.20173799", + "rel_title": "Clinical characteristics of COVID-19 and the model for predicting the occurrence of critically ill patients: a retrospective cohort study.", + "rel_date": "2020-08-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.13.20173799", + "rel_abs": "BackgroundThe present study aim to comprehensively report the epidemiological and clinical characteristics of the COVID-19 patients and to develop a multi-feature fusion model for predicting the critical ill probability.\n\nMethodsIt was a retrospective cohort study that incorporating the laboratory-confirmed COVID-19 patients in the Chongqing Public Health Medical Center. The prediction model was constructed with least absolute shrinkage and selection operator (LASSO) logistic regression method and the model was further tested in the validation cohort. The performance was evaluated by the receiver operating curve (ROC), calibration curve and decision curve analysis (DCA).\n\nResultsA total of 217 patients were included in the study. During the treatment, 34 patients were admitted to intensive care unit (ICU) and no developed death. A model incorporating the demographic and clinical characteristics, imaging features and laboratory findings were constructed to predict the critical ill probability and it was proved to have good calibration, discrimination ability and clinic use.\n\nConclusionsThe prevalence of critical ill was relatively high and the model may help the clinicians to identify the patients with high risk for developing the critical ill, thus to conduct timely and targeted treatment to reduce the mortality rate.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Jing Ouyang", + "author_inst": "Chongqing Public Health Medical Center, Chongqing, China" + }, + { + "author_name": "Xuefeng Shan", + "author_inst": "Department of Pharmacy, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China" + }, + { + "author_name": "Xin Wang", + "author_inst": "Department of Epidemiology and Biostatistics, First Affiliated Hospital, Army Medical University, 30 Gaotanyan Street Shapingba District, Chongqing 400038, Chin" + }, + { + "author_name": "Xue Zhang", + "author_inst": "Chongqing Public Health Medical Center, Chongqing, China" + }, + { + "author_name": "Yaling Chen", + "author_inst": "Chongqing Public Health Medical Center, Chongqing, China" + }, + { + "author_name": "Miaomiao Qi", + "author_inst": "Chongqing Public Health Medical Center, Chongqing, China" + }, + { + "author_name": "Chao Xia", + "author_inst": "Chongqing Public Health Medical Center, Chongqing, China" + }, + { + "author_name": "Dongqing Gu", + "author_inst": "Department of Epidemiology and Biostatistics, First Affiliated Hospital, Army Medical University, 30 Gaotanyan Street Shapingba District, Chongqing 400038, Chin" + }, + { + "author_name": "Yaokai Chen", + "author_inst": "Chongqing Public Health Medical Center, Chongqing, China" + }, + { + "author_name": "Ben Zhang", + "author_inst": "Department of Epidemiology and Biostatistics, First Affiliated Hospital, Army Medical University, 30 Gaotanyan Street Shapingba District, Chongqing 400038, Chin" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.11.20173179", "rel_title": "Water, Sanitation, Hygiene and Covid-19 pandemic: a global socioeconomic analysis", @@ -1228103,137 +1230094,6 @@ "type": "new results", "category": "zoology" }, - { - "rel_doi": "10.1101/2020.08.13.248872", - "rel_title": "SARS-CoV-2 manipulates the SR-B1-mediated HDL uptake pathway for its entry", - "rel_date": "2020-08-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.13.248872", - "rel_abs": "The recently emerged pathogenic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread rapidly, leading to a global COVID-19 pandemic. Binding of the viral spike protein (SARS-2-S) to cell surface receptor angiotensin-converting enzyme 2 (ACE2) mediates host cell infection. In the present study, we demonstrate that in addition to ACE2, the S1 subunit of SARS-2-S binds to HDL and that SARS-CoV-2 hijacks the SR-B1-mediated HDL uptake pathway to facilitate its entry. SR-B1 facilitates SARS-CoV-2 entry into permissive cells by augmenting virus attachment. MAb (monoclonal antibody)-mediated blocking of SARS-2-S-HDL binding and SR-B1 antagonists strongly inhibit HDL-enhanced SARS-CoV-2 infection. Notably, SR-B1 is co-expressed with ACE2 in human pulmonary and extrapulmonary tissues. These findings revealed a novel mechanism for SARS-CoV-2 entry and could provide a new target to treat SARS-CoV-2 infection.", - "rel_num_authors": 29, - "rel_authors": [ - { - "author_name": "Congwen Wei", - "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing 100071, China" - }, - { - "author_name": "Luming Wan", - "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing 100071, China" - }, - { - "author_name": "Qiulin Yan", - "author_inst": "Institute of Physical Science and Information Technology, Anhui University, Hefei 230601, China" - }, - { - "author_name": "Xiaolin Wang", - "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing 100071, China" - }, - { - "author_name": "Jun Zhang", - "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing 100071, China" - }, - { - "author_name": "Yanhong Zhang", - "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing 100071, China" - }, - { - "author_name": "Jin Sun", - "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing 100071, China" - }, - { - "author_name": "Xiaopan Yang", - "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing 100071, China" - }, - { - "author_name": "Jing Gong", - "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing 100071, China" - }, - { - "author_name": "Chen Fan", - "author_inst": "Department of Laboratory Medicine, the 960th Hospital of PLA, Jinan 250031, China" - }, - { - "author_name": "Xiaoli Yang", - "author_inst": "Department of Clinical Laboratory, the Third Medical Centre, Chinese PLA General Hospital, Beijing, P.R. China" - }, - { - "author_name": "Yufei Wang", - "author_inst": "Department of Clinical Laboratory, the Third Medical Centre, Chinese PLA General Hospital, Beijing, P.R. China" - }, - { - "author_name": "Xuejun Wang", - "author_inst": "Beijing Institute of Radiation Medicine, Academy of Military Medical Sciences (AMMS), Beijing 100071, China." - }, - { - "author_name": "Jianmin Li", - "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing 100071, China" - }, - { - "author_name": "Huan Yang", - "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing 100071, China" - }, - { - "author_name": "Huilong Li", - "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing 100071, China" - }, - { - "author_name": "Zhe Zhang", - "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing 100071, China" - }, - { - "author_name": "Rong Wang", - "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing 100071, China" - }, - { - "author_name": "Peng Du", - "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing 100071, China" - }, - { - "author_name": "Yulong Zong", - "author_inst": "Department of Laboratory Medicine, Taian City Central Hospital Branch, Taian 271000, China" - }, - { - "author_name": "Feng Yin", - "author_inst": "Department of Laboratory Medicine, Taian City Central Hospital Branch, Taian 271000, China" - }, - { - "author_name": "Wanchuan Zhang", - "author_inst": "Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang 110042, China" - }, - { - "author_name": "Yumeng Peng", - "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing 100071, China" - }, - { - "author_name": "Haotian Lin", - "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing 100071, China" - }, - { - "author_name": "Rui Zhang", - "author_inst": "Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang 110042, China" - }, - { - "author_name": "Wei Chen", - "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing 100071, China" - }, - { - "author_name": "Qi Gao", - "author_inst": "Hotgen Biotech Co., Ltd. Beijing 102600, China" - }, - { - "author_name": "Yuan Cao", - "author_inst": "Department of Laboratory Medicine, the 960th Hospital of PLA, Jinan 250031, China" - }, - { - "author_name": "Hui Zhong", - "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing 100071, China" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.08.14.251421", "rel_title": "Methylation of RNA Cap in SARS-CoV-2 captured by serial crystallography", @@ -1229021,6 +1230881,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.09.20170977", + "rel_title": "Effect of covid-19 lockdown on child protection medical assessments: a retrospective observational study in Birmingham, UK.", + "rel_date": "2020-08-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.09.20170977", + "rel_abs": "ObjectivesTo determine any change in referral patterns and outcomes in children (0-18) referred for child protection medical examination (CPME) during the covid-19 pandemic compared to previous years.\n\nDesignRetrospective observational study, analysing routinely collected clinical data from CPME reports in a rapid response to the pandemic lockdown.\n\nSettingBirmingham Community Healthcare NHS Trust, which provides all routine CPME for Birmingham, England, population 1.1 million including 288,000 children.\n\nParticipantsChildren aged under 18 years attending CPME during an 18 week period from late February to late June during the years 2018, 2019, and 2020.\n\nMain Outcome MeasuresNumbers of referrals, source of disclosure and outcomes from CPME\n\nResultsThere were 78 CPME referrals in 2018, 75 in 2019 and 47 in 2020, this was a 39.7% (95%CI 12.4-59.0) reduction in referrals from 2018 to 2020, and a 37.3% (95%CI 8.6-57.4) reduction from 2019 to 2020. There were fewer CPME referrals initiated by school staff in 2020, 12(26%) compared to 36 (47%) and 38 (52%) in 2018 and 2019 respectively. In all years 75.9% of children were known to social care prior to CPME, and 94% of CPME concluded that there were significant safeguarding concerns.\n\nConclusionsSchool closure due to covid-19 may have harmed children as child abuse has remained hidden. There needs to be either mandatory attendance at schools in future or viable alternatives found. There may be a significant increase in safeguarding referrals when schools fully re-open as children disclose the abuse they have experienced at home.\n\nArticle summary: Strengths and Limitations of the StudyO_LIThis is a highly robust study: we obtained CPME reports for 97% of CPME referrals during the study period.\nC_LIO_LIWe ensured consistency of data extraction by double reviewing every report, with further consensus discussions for the few cases that raised uncertainties.\nC_LIO_LIThe team extracting the data comprised highly experienced paediatricians with expertise in child abuse.\nC_LIO_LIOne weakness is that we only considered minor injuries from outpatient CPME, excluding those admitted to hospital, so our findings do not include those with more serious NAI, however they would be taken to hospital for treatment due to the severity of their injuries.\nC_LI", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Joanna Garstang", + "author_inst": "Birmingham Community Healthcare Trust" + }, + { + "author_name": "Geoff Debelle", + "author_inst": "Birmingham Women's and Children's NHS Foundation Trust" + }, + { + "author_name": "Indu Anand", + "author_inst": "Birmingham Community Healthcare NHS Trust" + }, + { + "author_name": "Jane Armstrong", + "author_inst": "Birmingham Community Healthcare NHS Trust" + }, + { + "author_name": "Emily Botcher", + "author_inst": "Birmingham Community Healthcare NHS Trust" + }, + { + "author_name": "Helen Chaplin", + "author_inst": "Birmingham Community Healthcare NHS Trust" + }, + { + "author_name": "Nutmeg Hallett", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Clare Morgans", + "author_inst": "Birmingham Community Healthcare NHS Trust" + }, + { + "author_name": "Malcolm Price", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Ern Ern Henna Tan", + "author_inst": "Birmingham Community Healthcare NHS Trust" + }, + { + "author_name": "Emily Tudor", + "author_inst": "Birmingham Community Healthcare NHS Trust" + }, + { + "author_name": "Julie Taylor", + "author_inst": "University of Birmingham" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2020.08.11.20168773", "rel_title": "Challenges and proposed solutions in making clinical research on COVID-19 ethical. A status quo analysis across German research ethics committees", @@ -1229865,25 +1231788,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.08.09.20171207", - "rel_title": "The Link between Poverty and COVID-19 Case and Mortality Rates in Germany", - "rel_date": "2020-08-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.09.20171207", - "rel_abs": "The effects of poverty on the case and mortality rates of Covid-19 has emerged as a controversial but understudied topic. In previous studies and reports from the UK and US evidence emerged that poverty related indicators had a significant statistical effect on case and mortality rates on district level. For Germany, it has largely been assumed that poverty is an equally relevant factor influencing the transmission rates of the outbreak mostly due to anecdotal evidence from local outbreaks in meat processing plants and reported incidents in poorer city districts. This paper addresses the lack of statistical evidence and investigates thoroughly the link between poverty related indicators and case and mortality rates of the outbreak using multivariate, multilevel regression while also considering the urban-rural divide of the country. As proxies for poverty the unemployment rate, the per capita presence of general practitioners (physicians), per capita GDP, and the rate of employees with no professional job training is evaluated in relation to the accumulated case and mortality numbers on district level taken from RKI data of June and July 2020. Interestingly, the study finds no evidence for a poverty-related effect on mortality for German districts. Furthermore, only employment in low qualification jobs approximated by the job training variable consistently affected case numbers in urban districts in the expected direction.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Felix Ettensperger", - "author_inst": "Albert-Ludwigs-University Freiburg" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.08.09.20170845", "rel_title": "Predicting the future SARS-COV-2 reproductive rate.", @@ -1230543,6 +1232447,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.08.11.20173195", + "rel_title": "The Build-Up of Droplet/Aerosols Carrying the SARS-CoV-2 Coronavirus, in Confined Spaces", + "rel_date": "2020-08-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.11.20173195", + "rel_abs": "A model of the distribution of respiratory droplets and aerosols by Lagrangian turbulent air-flow is developed and used to show how the SARS-CoV-2 Coronavirus can be dispersed by the breathing of an infected person. It is shown that the concentration of viruses in the exhaled cloud can increase to infectious levels with time, in a confined space where the air recirculates. The model is used to analyze the air-flow and SARS-CoV-2 Coronavirus build-up in a restaurant in Guangzhou, China [17, 16]. It is concluded that the outbreak of Covid-19 in the restaurant in January 2020, is due to the build-up of the airborne droplets and aerosols carrying the SARS-CoV-2 Coronavirus and could not have been prevented by standard air-conditioning.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Bjorn Birnir", + "author_inst": "University of California Santa Barbara" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.10.20170506", "rel_title": "A \"Tail\" of Two Cities: Fatality-based Modeling of COVID-19 Evolution in New York City and Cook County, IL", @@ -1231491,73 +1233414,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2020.08.10.20171348", - "rel_title": "Love during lockdown: findings from an online survey examining the impact of COVID-19 on the sexual practices of people living in Australia", - "rel_date": "2020-08-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.10.20171348", - "rel_abs": "IntroductionAustralia recorded its first case of COVID-19 in late January 2020. On 22nd March 2020, amid increasing daily case numbers, the Australian Government implemented lockdown restrictions to help flatten the curve. Our study aimed to understand the impact of lockdown restrictions on sexual and reproductive health. Here we focus on sexual practices.\n\nMethodsAn online survey was open from the 23rd April 2020 to the 11th May 2020. Participants were recruited online via social media and other networks and were asked to report on their sexual practices in 2019 and during lockdown. Logistic regression was used to calculate the difference (including 95% confidence intervals) in the proportion of sex practices between time periods.\n\nResultsOf the 1187 who commenced the survey, 965 (81.3%) completed it. Overall 70% were female and 66.3% were aged 18 to 29 years. Most (53.5%) reported less sex during lockdown than in 2019. Compared with 2019, participants were more likely to report sex with a spouse (35.3% vs 41.7%; difference=6.4%; 95%CI: 3.6, 9.2) and less likely to report sex with a girl/boyfriend (45.1% vs 41.8%; diff=-3.3%; 95%CI: -7.0, -0.4) or with casual hook-up (31.4% vs 7.8%; 95%CI:-26.9, -19.8). Solo sex activities increased, 14.6% (123/840) reported using sex toys more often and 26.0% (218/838) reported masturbating more often. Dating app use decreased during lockdown compared with 2019 (42.1% vs 27.3%; difference= -14.8%; 95%CI: -17.6, -11.9). Using dating apps for chatting/texting (89.8% vs 94.5%; diff=4.7%; 95%CI:1.0, 8.5) and for setting up virtual dates (2.6% vs 17.2%; diff=14.6%; 95%CI:10.1, 19.2) increased during lockdown.\n\nConclusionAlthough significant declines in sexual activity during lockdown were reported, people did not completely stop engaging in sexual activities during the pandemic, highlighting the importance of ensuring availability of normal sexual and reproductive health services during global emergencies.\n\nKEY MESSAGESO_LISexual activity declined among our participants during the COVID-19 lockdown restrictions in Australia, with more than half reporting having less sex than in 2019\nC_LIO_LISexual practices also changed during lockdown, with more people reporting solo sex activities like masturbating alone or using a sex toy.\nC_LIO_LIUse of dating apps also declined among our participants. Of those still using apps, we saw increased use for chatting/texting and setting up virtual dates.\nC_LI", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Jacqueline Coombe", - "author_inst": "The University of Melbourne" - }, - { - "author_name": "Fabian Kong", - "author_inst": "The University of Melbourne" - }, - { - "author_name": "Helen Bittleston", - "author_inst": "The University of Melbourne" - }, - { - "author_name": "Hennie Williams", - "author_inst": "Melbourne Sexual Health Centre & The University of Melbourne" - }, - { - "author_name": "Jane Tomnay", - "author_inst": "The University of Melbourne" - }, - { - "author_name": "Alaina Vaisey", - "author_inst": "The University of Melbourne" - }, - { - "author_name": "Sue Malta", - "author_inst": "The University of Melbourne" - }, - { - "author_name": "Jane Goller", - "author_inst": "The University of Melbourne" - }, - { - "author_name": "Meredith Temple-Smith", - "author_inst": "The University of Melbourne" - }, - { - "author_name": "Louise Bourchier", - "author_inst": "The University of Melbourne" - }, - { - "author_name": "Andrew Lau", - "author_inst": "The University of Melbourne" - }, - { - "author_name": "Eric Chow", - "author_inst": "Melbourne Sexual Health Centre, The University of Melbourne, Monash University" - }, - { - "author_name": "Jane S Hocking", - "author_inst": "The University of Melbourne" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "sexual and reproductive health" - }, { "rel_doi": "10.1101/2020.08.07.242263", "rel_title": "Worldwide tracing of mutations and the evolutionary dynamics of SARS-CoV-2", @@ -1232401,6 +1234257,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2020.08.06.20169581", + "rel_title": "The impact of the COVID-19 pandemic on rabies reemergence in Latin America: the case of Arequipa, Peru", + "rel_date": "2020-08-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.06.20169581", + "rel_abs": "Over the past decades, there has been tremendous progress towards eliminating canine rabies in Latin America. Major components of rabies prevention programs in Latin America leading to these successes have been constant and intense surveillance for rabid dogs and uninterrupted yearly mass dog vaccination campaigns. However, vital measures to control COVID-19 in Latin America have had the negative trade-off of jeopardizing these rabies elimination and prevention activities. In this paper, we aimed to assess the effect of interrupting canine rabies surveillance and mass dog vaccination campaigns on rabies trends. We built a deterministic compartment model of dog rabies dynamics parameterized for conditions found in Arequipa, Peru, where there is an ongoing dog rabies epidemic. Our model suggests that a decrease in canine vaccination coverage as well as decreased surveillance leading to an increased length of survival of infected dogs could lead to a sharp rise in canine rabies and, subsequently, human rabies risk. We examined our results over the best estimate of the basic reproductive number in Arequipa (R0 = 1.44) and a range of plausible values for R0 (1.36 - 2). The rising trend was consistent. It is very possible that COVID-19 will continue to challenge our public health departments in the short- and medium-term. Innovative strategies to conduct dog vaccination and rabies surveillance during these trying times should be considered to safeguard the achievements made in Latin America towards the elimination of dog-mediated human rabies.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Brinkley Raynor", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Elvis W. D\u00edaz", + "author_inst": "Zoonotic Disease Research Lab, One Health Unit, School of Public Health and Administration, Universidad Peruana Cayetano Heredia, Lima 15102, Peru" + }, + { + "author_name": "Julianna Shinnick", + "author_inst": "Department of Biostatistics, Epidemiology & Informatics, Perelman School of Medicine at University of Pennsylvania, Philadelphia, Pennsylvania 19104, United Sta" + }, + { + "author_name": "Edith Zegarra", + "author_inst": "Gerencia Regional de Salud de Arequipa, Ministerio de Salud, Arequipa 04002, Peru" + }, + { + "author_name": "Ynes Monroy", + "author_inst": "Gerencia Regional de Salud de Arequipa, Ministerio de Salud, Arequipa 04002, Peru" + }, + { + "author_name": "Claudia Mena", + "author_inst": "Red de Salud Arequipa Caylloma, Ministerio de Salud, Arequipa 04001, Peru" + }, + { + "author_name": "Ricardo Castillo-Neyra", + "author_inst": "Perelman School of Medicine, University of Pennsylvania" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.06.20169839", "rel_title": "Expanding COVID-19 symptom screening to retail, restaurants, and schools by preserving privacy using relaxed digital signatures", @@ -1233377,45 +1235276,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.07.20170183", - "rel_title": "COVID-19 mortality according to civilian records", - "rel_date": "2020-08-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.07.20170183", - "rel_abs": "In this short report, we bring some data-driven analyses of COVID-19 mortality in Brazil. The impact of COVID-19 is evaluated by comparing the 2019 and 2020 civilian death records. There is evidence of a considerable excess of deaths since the pandemic started with respect to the previous year. In some states, it is clear that not all excess of deaths in 2020 is due to COVID-19, but to other respiratory causes that did not present the same prevalence in the previous year. Because of this unusual behavior of respiratory deaths, we may infer the evidence of a huge amount of under-reporting deaths due to the COVID-19. The data also shows that COVID-19 has produced an excess death in all ages besides people above 90 and below 10 years. In addition, when separates by sex, data indicate a larger increase in the deaths among males than females.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Lisandro Lovisolo", - "author_inst": "Universidade do Estado do Rio de Janeiro" - }, - { - "author_name": "Diego H S Catalao", - "author_inst": "Universidade do Estado do Rio de Janeiro" - }, - { - "author_name": "Rodrigo B Burgos", - "author_inst": "Universidade do Estado do Rio de Janeiro" - }, - { - "author_name": "Malu Grave", - "author_inst": "Universidade Federal do Rio de Janeiro" - }, - { - "author_name": "Pamella Constantino-Teles", - "author_inst": "Universidade do Estado do Rio de Janeiro" - }, - { - "author_name": "Americo Cunha Jr.", - "author_inst": "Universidade do Estado do Rio de Janeiro" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.07.20170548", "rel_title": "Social Media Reveals Psychosocial Effects of the COVID-19 Pandemic", @@ -1234167,6 +1236027,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.10.20172361", + "rel_title": "Probability of elimination for COVID-19 in Aotearoa New Zealand", + "rel_date": "2020-08-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.10.20172361", + "rel_abs": "On 25th March 2020, New Zealand implemented stringent lockdown measures (Alert Level 4, in a four-level alert system) with the goal of eliminating community transmission of COVID-19. Once new cases are no longer detected over consecutive days, the probability of elimination is an important measure for informing decisions on when certain COVID-19 restrictions should be relaxed. Our model of COVID-19 spread in New Zealand estimates that after 2-3 weeks of no new reported cases, there is a 95% probability that COVID-19 has been eliminated. We assessed the sensitivity of this estimate to varying model parameters, in particular to different likelihoods of detection of clinical cases and different levels of control effectiveness. Under an optimistic scenario with high detection of clinical cases, a 95% probability of elimination is achieved after 10 consecutive days with no new reported cases, while under a more pessimistic scenario with low case detection it is achieved after 22 days.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Rachelle N Binny", + "author_inst": "Manaaki Whenua - Landcare Research" + }, + { + "author_name": "Shaun C Hendy", + "author_inst": "University of Auckland" + }, + { + "author_name": "Alex James", + "author_inst": "University of Canterbury" + }, + { + "author_name": "Audrey Lustig", + "author_inst": "Manaaki Whenua - Landcare Research" + }, + { + "author_name": "Michael J Plank", + "author_inst": "University of Canterbury" + }, + { + "author_name": "Nicholas Steyn", + "author_inst": "University of Auckland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.04.20167205", "rel_title": "Telmisartan for treatment of Covid-19 patients: an open randomized clinical trial. Preliminary report.", @@ -1235099,29 +1236998,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.08.09.243444", - "rel_title": "Identification of key genes in SARS-CoV-2 patients on bioinformatics analysis", - "rel_date": "2020-08-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.09.243444", - "rel_abs": "The COVID-19 pandemic has infected millions of people and overwhelmed many health systems globally. Our study is to identify differentially expressed genes (DEGs) and associated biological processes of COVID-19 using a bioinformatics approach to elucidate their potential pathogenesis. The gene expression profiles of the GSE152075 datasets were originally produced by using the high-throughput Illumina NextSeq 500. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses were performed to identify functional categories and biochemical pathways. GO and KEGG results suggested that several biological pathways such as \"Fatty acid metabolism\" and \"Cilium morphogenesis\" are mostly involved in the development of COVID-19. Moreover, several genes are critical for virus invasion and adhesion including FLOC, DYNLL1, FBXL3, and FBXW11 and show significant differences in COVID-19 patients. Thus, our study provides further insights into the underlying pathogenesis of COVID-19.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Hanming Gu", - "author_inst": "School of Electronic, Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, China" - }, - { - "author_name": "Gongsheng Yuan", - "author_inst": "Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.08.11.242834", "rel_title": "AT-527 is a potent in vitro replication inhibitor of SARS-CoV-2, the virus responsible for the COVID-19 pandemic", @@ -1235925,6 +1237801,249 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.10.242677", + "rel_title": "High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next generation sequencing", + "rel_date": "2020-08-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.10.242677", + "rel_abs": "The rapid emergence of coronavirus disease 2019 (COVID-19) as a global pandemic affecting millions of individuals globally has necessitated sensitive and high-throughput approaches for the diagnosis, surveillance and for determining the genetic epidemiology of SARS-CoV-2. In the present study, we used the COVIDSeq protocol, which involves multiplex-PCR, barcoding and sequencing of samples for high-throughput detection and deciphering the genetic epidemiology of SARS-CoV-2. We used the approach on 752 clinical samples in duplicates, amounting to a total of 1536 samples which could be sequenced on a single S4 sequencing flow cell on NovaSeq 6000. Our analysis suggests a high concordance between technical duplicates and a high concordance of detection of SARS-CoV-2 between the COVIDSeq as well as RT-PCR approaches. An in-depth analysis revealed a total of six samples in which COVIDSeq detected SARS-CoV-2 in high confidence which were negative in RT-PCR. Additionally, the assay could detect SARS-CoV-2 in 21 samples and 16 samples which were classified inconclusive and pan-sarbeco positive respectively suggesting that COVIDSeq could be used as a confirmatory test. The sequencing approach also enabled insights into the evolution and genetic epidemiology of the SARS-CoV-2 samples. The samples were classified into a total of 3 clades. This study reports two lineages B.1.112 and B.1.99 for the first time in India. This study also revealed 1,143 unique single nucleotide variants and added a total of 73 novel variants identified for the first time. To the best of our knowledge, this is the first report of the COVIDSeq approach for detection and genetic epidemiology of SARS-CoV-2. Our analysis suggests that COVIDSeq could be a potential high sensitivity assay for detection of SARS-CoV-2, with an additional advantage of enabling genetic epidemiology of SARS-CoV-2.", + "rel_num_authors": 57, + "rel_authors": [ + { + "author_name": "Rahul C. Bhoyar", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Abhinav Jain", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Paras Sehgal", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Mohit Kumar Divakar", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Disha Sharma", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Mohamed Imran", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Bani Jolly", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Gyan Ranjan", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Mercy Rophina", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Sumit Sharma", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Sanjay Siwach", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Kavita Pandhare", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Swayamprabha Sahoo", + "author_inst": "IMS and SUM Hospital, Siksha O Anusandhan (Deemed to be University), Kalinga Nagar, Bhubaneswar, Odisha 751003, India" + }, + { + "author_name": "Maheswata Sahoo", + "author_inst": "IMS and SUM Hospital, Siksha O Anusandhan (Deemed to be University), Kalinga Nagar, Bhubaneswar, Odisha 751003, India" + }, + { + "author_name": "Ananya Nayak", + "author_inst": "IMS and SUM Hospital, Siksha O Anusandhan (Deemed to be University), Kalinga Nagar, Bhubaneswar, Odisha 751003, India" + }, + { + "author_name": "Jatindra Nath Mohanty", + "author_inst": "IMS and SUM Hospital, Siksha O Anusandhan (Deemed to be University), Kalinga Nagar, Bhubaneswar, Odisha 751003, India" + }, + { + "author_name": "Jayashankar Das", + "author_inst": "IMS and SUM Hospital, Siksha O Anusandhan (Deemed to be University), Kalinga Nagar, Bhubaneswar, Odisha 751003, India" + }, + { + "author_name": "Sudhir Bhandari", + "author_inst": "Sawai Man Singh Medical College, Jaipur, Rajasthan 302004, India" + }, + { + "author_name": "Sandeep K Mathur", + "author_inst": "Sawai Man Singh Medical College, Jaipur, Rajasthan 302004, India" + }, + { + "author_name": "Anshul Kumar", + "author_inst": "Sawai Man Singh Medical College, Jaipur, Rajasthan 302004, India" + }, + { + "author_name": "Rahul Sahlot", + "author_inst": "Sawai Man Singh Medical College, Jaipur, Rajasthan 302004, India" + }, + { + "author_name": "Pallavali Rojarani", + "author_inst": "Department of Microbiology, Kurnool Medical College, Kurnool, A.P, India-518002" + }, + { + "author_name": "Juturu Vijaya Lakshmi", + "author_inst": "Department of Microbiology, Kurnool Medical College, Kurnool, A.P, India-518002" + }, + { + "author_name": "Araveti Surekha", + "author_inst": "Department of Microbiology, Kurnool Medical College, Kurnool, A.P, India-518002" + }, + { + "author_name": "Pulala Chandra Sekhar", + "author_inst": "Department of Microbiology, Kurnool Medical College, Kurnool, A.P, India-518002" + }, + { + "author_name": "Shelly Mahajan", + "author_inst": "Centre for Advanced Research in Imaging, Neurosciences & Genomics (CARING), Mahajan Imaging, New Delhi" + }, + { + "author_name": "Shet Masih", + "author_inst": "Centre for Advanced Research in Imaging, Neurosciences & Genomics (CARING), Mahajan Imaging, New Delhi" + }, + { + "author_name": "Pawan Singh", + "author_inst": "Centre for Advanced Research in Imaging, Neurosciences & Genomics (CARING), Mahajan Imaging, New Delhi" + }, + { + "author_name": "Vipin Kumar", + "author_inst": "Centre for Advanced Research in Imaging, Neurosciences & Genomics (CARING), Mahajan Imaging, New Delhi" + }, + { + "author_name": "Blessy Jose", + "author_inst": "Centre for Advanced Research in Imaging, Neurosciences & Genomics (CARING), Mahajan Imaging, New Delhi" + }, + { + "author_name": "Vidur Mahajan", + "author_inst": "Centre for Advanced Research in Imaging, Neurosciences & Genomics (CARING), Mahajan Imaging, New Delhi" + }, + { + "author_name": "Vivek Gupta", + "author_inst": "Government Institute of Medical Sciences, Gautam Buddh Nagar, Greater Noida, India" + }, + { + "author_name": "Rakesh Gupta", + "author_inst": "Government Institute of Medical Sciences, Gautam Buddh Nagar, Greater Noida, India" + }, + { + "author_name": "Prabhakar Arumugam", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Anjali Singh", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Ananya Nandy", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Raghavendran P.V.", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Rakesh Mohan Jha", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Anupama Kumari", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Sheetal Gandotra", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Vivek Rao", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Mohammed Faruq", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Sanjeev Kumar", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Betsy Reshma G", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Narendra G Varma", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Shuvra Shekhar Roy", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Antara Sengupta", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Sabyasachi Chattopadhyay", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Khushboo Singhal", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Shalini Pradhan", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Nishu Tyagi", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Saruchi Wadhwa", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Diksha Jha", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Salwa Naushin", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Mukta Poojary", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Vinod Scaria", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + }, + { + "author_name": "Sridhar Sivasubbu", + "author_inst": "CSIR, Institute of Genomics and Integrative Biology, Delhi, 110025, India" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.08.10.243717", "rel_title": "Comparative analyses of SARS-CoV-2 binding (IgG, IgM, IgA) and neutralizing antibodies from human serum samples", @@ -1237073,37 +1239192,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.08.06.20148288", - "rel_title": "The Epidemiology Characteristics of Positive COVID-19 patients in a Caribbean Territory.", - "rel_date": "2020-08-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.06.20148288", - "rel_abs": "BackgroundThe purpose of the study is to determine the epidemiology of COVID-19 in a Caribbean Territory by the characterisation of patients in terms of, the numbers, socio demographics and associated co-morbidities. This comparison was done between local cases and imported cases. There have been no prior studies on COVID-19 in the Caribbean and as such this paper attempts to discuss the patterns associated with COVID-19 patients in the Caribbean.\n\nMethodsThis study determined the epidemiology of COVID-19 in a Caribbean territory using retrospective data. Analysis was performed using Excel and SPSS 22.0.\n\nResultsThe majority of patients were female (61.9%) vs male (38.0%). The majority of the population were between 45 -64 yrs (43.4%) followed by above 65 at 28.8%. Cough was the most common presenting complaint at 44.9%, with fever being second 37.1%. The majority of female participants had a travel history at 61.9%, while males were 38.0 %. The occurrence of cough was high among both local cases (46.4%) and imported cases (47.6%).\n\nConclusionsThese patterns can inform clinicians and other health care workers on the unique findings associated with COVID-19 positive patients especially those in the Caribbean region", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Chavin D. Gopaul", - "author_inst": "North Central Regional Health Authority" - }, - { - "author_name": "Dale Ventour", - "author_inst": "The University of the West Indies" - }, - { - "author_name": "Michelle Trotman", - "author_inst": "North Central Regional Health Authority" - }, - { - "author_name": "Davlin Thomas", - "author_inst": "North Central Regional Health Authority" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.08.06.20162446", "rel_title": "Kinetics of viral clearance and antibody production across age groups in SARS-CoV-2 infected children", @@ -1238063,6 +1240151,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.06.20169433", + "rel_title": "The SARS-COV-2 outbreak around the Amazon rainforest: the relevance of the airborne transmission", + "rel_date": "2020-08-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.06.20169433", + "rel_abs": "BackgroundThis paper presents a global analysis of the SARS-COV-2 outbreak in Brazil.\n\nAmazonian States have a much higher contamination rate than the southern and southeastern States. So far, no explanation has been provided for this striking difference that can shed light on the airborne transmission of the virus.\n\nMinimizing airborne transmission, health authorities recommend two meters as a safe distance. However, recent experiments reveal that this can be the main form of contagion. There is a lack of theoretical explanation on how airborne transmission works.\n\nMethodsTo investigate the spread of SARS-COV-2 in different macro environments, we analyzed the daily official data on the evolution of COVID-19 in Brazil. We compared our epidemiologic results obtained in States with very different climatic characteristics, and that had adopted, almost simultaneously, similar social isolation measures. To understand the virus spread, it was necessary to calculate theoretically the movement and behavior in the air of saliva droplets.\n\nFindingsThe transmission of SARS-COV-2 is much faster in the Amazon rainforest region.\n\nOur theoretical calculations explain and support the empirical results observed in recent experiments that demonstrate the relevance of aerial transmission of the coronavirus.\n\nInterpretationAn onset of collective immunity may have been achieved with a contamination rate of about 15% of the Amazonian population. If confirmed, this result will have an essential impact on the management of the pandemic across the planet.\n\nThe airborne transmission played a decisive role in the striking difference in the evolution of the pandemic among Brazilian regions.\n\nAir humidity is the most important climatic factor in viral spreading, while usual ambient temperatures do not have strong influence.\n\nThere is no safe indoor distance for the coronavirus transmission. So, mask and eye protection are essential.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Edilson Crema", + "author_inst": "University of Sao Paulo" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.06.20169326", "rel_title": "Age disaggregation of crude excess deaths during the 2020 spring COVID-19 outbreak in Spain and Netherlands", @@ -1239031,57 +1241138,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.06.20169664", - "rel_title": "Estimating the Changing Infection Rate of COVID-19 Using Bayesian Models of Mobility", - "rel_date": "2020-08-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.06.20169664", - "rel_abs": "In order to prepare for and control the continued spread of the COVID-19 pandemic while minimizing its economic impact, the world needs to be able to estimate and predict COVID-19s spread. Unfortunately, we cannot directly observe the prevalence or growth rate of COVID-19; these must be inferred using some kind of model. We propose a hierarchical Bayesian extension to the classic susceptible-exposed-infected-removed (SEIR) compartmental model that adds compartments to account for isolation and death and allows the infection rate to vary as a function of both mobility data collected from mobile phones and a latent time-varying factor that accounts for changes in behavior not captured by mobility data. Since confirmed-case data is unreliable, we infer the models parameters conditioned on deaths data. We replace the exponential-waiting-time assumption of classic compartmental models with Erlang distributions, which allows for a more realistic model of the long lag between exposure and death. The mobility data gives us a leading indicator that can quickly detect changes in the pandemics local growth rate and forecast changes in death rates weeks ahead of time. This is an analysis of observational data, so any causal interpretations of the models inferences should be treated as suggestive at best; nonetheless, the models inferred relationship between different kinds of trips and the infection rate do suggest some possible hypotheses about what kinds of activities might contribute most to COVID-19s spread.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Luyang Liu", - "author_inst": "Google Research" - }, - { - "author_name": "Sharad Vikram", - "author_inst": "Google Research" - }, - { - "author_name": "Junpeng Lao", - "author_inst": "Google Research" - }, - { - "author_name": "Xue Ben", - "author_inst": "Google Research" - }, - { - "author_name": "Alexander D'Amour", - "author_inst": "Google Research" - }, - { - "author_name": "Shawn O'Banion", - "author_inst": "Google Research" - }, - { - "author_name": "Mark Sandler", - "author_inst": "Google Research" - }, - { - "author_name": "Rif A. Saurous", - "author_inst": "Google Research" - }, - { - "author_name": "Matthew D. Hoffman", - "author_inst": "Google Research" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.06.20169557", "rel_title": "A SEIR-like model with a time-dependent contagion factor describes the dynamics of the Covid-19 pandemic", @@ -1239833,6 +1241889,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2020.08.04.20168187", + "rel_title": "An improved methodology for estimating the prevalence of SARS-CoV-2", + "rel_date": "2020-08-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.04.20168187", + "rel_abs": "Since the identification of Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China in December 2019, there have been more than 17 million cases of the disease in 216 countries worldwide. Comparisons of prevalence estimates between different communities can inform policy decisions regarding safe travel between countries, help to assess when to implement (or remove) disease control measures and identify the risk of over-burdening healthcare providers. Estimating the true prevalence can, however, be challenging because officially reported figures are likely to be significant underestimates of the true burden of COVID-19 within a community. Previous methods for estimating the prevalence fail to incorporate differences between populations (such as younger populations having higher rates of asymptomatic cases) and so comparisons between, for example, countries, can be misleading. Here, we present an improved methodology for estimating COVID-19 prevalence. We take the reported number of cases and deaths (together with population size) as raw prevalence for the population. We then apply an age-adjustment to this which allows the age-distribution of that population to influence the case-fatality rate and the proportion of asymptomatic cases. Finally, we calculate the likely underreporting factor for the population and use this to adjust our prevalence estimate further. We use our method to estimate the prevalence for 166 countries (or the states of the United States of America, hereafter referred to as US state) where sufficient data were available. Our estimates show that as of the 30th July 2020, the top three countries with the highest estimated prevalence are Brazil (1.26%, 95% CI: 0.96 - 1.37), Kyrgyzstan (1.10%, 95% CI: 0.82 - 1.19) and Suriname (0.58%, 95% CI: 0.44 - 0.63). Brazil is predicted to have the largest proportion of all the current global cases (30.41%, 95%CI: 27.52 - 30.84), followed by the USA (14.52%, 95%CI: 14.26 - 16.34) and India (11.23%, 95%CI: 11.11 - 11.24). Amongst the US states, the highest prevalence is predicted to be in Louisiana (1.07%, 95% CI: 1.02 - 1.12), Florida (0.90%, 95% CI: 0.86 - 0.94) and Mississippi (0.77%, 95% CI: 0.74 - 0.81) whereas amongst European countries, the highest prevalence is predicted to be in Montenegro (0.47%, 95% CI: 0.42 - 0.50), Kosovo (0.35%, 95% CI: 0.29 - 0.37) and Moldova (0.28%, 95% CI: 0.23 - 0.30). Our results suggest that Kyrgyzstan (0.04 tests per predicted case), Brazil (0.04 tests per predicted case) and Suriname (0.29 tests per predicted case) have the highest underreporting out of the countries in the top 25 prevalence. In comparison, Israel (34.19 tests per predicted case), Bahrain (19.82 per predicted case) and Palestine (9.81 tests per predicted case) have the least underreporting. The results of this study may be used to understand the risk between different geographical areas and highlight regions where the prevalence of COVID-19 is increasing most rapidly. The method described is quick and easy to implement. Prevalence estimates should be updated on a regular basis to allow for rapid fluctuations in disease patterns.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Virag Patel", + "author_inst": "Animal and Plant Health Agency" + }, + { + "author_name": "Catherine McCarthy", + "author_inst": "Animal and Plant Health Agency (APHA)" + }, + { + "author_name": "Rachel A Taylor", + "author_inst": "Animal and Plant Health Agency (APHA)" + }, + { + "author_name": "Ruth Moir", + "author_inst": "Animal and Plant Health Agency (APHA)" + }, + { + "author_name": "Louise A Kelly", + "author_inst": "Animal and Plant Health Agency (APHA), University of Strathclyde" + }, + { + "author_name": "Emma L Snary", + "author_inst": "Animal and Plant Health Agency (APHA)" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.08.04.20168583", "rel_title": "COVID-19: Beliefs in misinformation in the Australian community", @@ -1240689,33 +1242784,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.04.200691", - "rel_title": "Predicted Cellular Immunity Population Coverage Gaps for SARS-CoV-2 Subunit Vaccines and their Augmentation by Compact Joint Sets", - "rel_date": "2020-08-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.04.200691", - "rel_abs": "Subunit vaccines induce immunity to a pathogen by presenting a component of the pathogen and thus inherently limit the representation of pathogen peptides for cellular immunity based memory. We find that SARS-CoV-2 subunit peptides may not be robustly displayed by the Major Histocompatibility Complex (MHC) molecules in certain individuals. We introduce an augmentation strategy for subunit vaccines that adds a small number of SARS-CoV-2 peptides to a vaccine to improve the population coverage of pathogen peptide display. Our population coverage estimates integrate clinical data on peptide immunogenicity in convalescent COVID-19 patients and machine learning predictions. We evaluate the population coverage of 9 different subunits of SARS-CoV-2, including 5 functional domains and 4 full proteins, and augment each of them to fill a predicted coverage gap.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Ge Liu", - "author_inst": "MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; MIT Electrical Engineering and Computer Science, Cambridge, MA, USA" - }, - { - "author_name": "Brandon Carter", - "author_inst": "MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; MIT Electrical Engineering and Computer Science, Cambridge, MA, USA" - }, - { - "author_name": "David K. Gifford", - "author_inst": "MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; MIT Electrical Engineering and Computer Science, Cambridge, MA, USA; MIT Biolog" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.08.05.20168930", "rel_title": "Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand", @@ -1241607,6 +1243675,85 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2020.08.05.20169128", + "rel_title": "Longitudinal analysis of clinical serology assay performance and neutralising antibody levels in COVID19 convalescents", + "rel_date": "2020-08-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.05.20169128", + "rel_abs": "ObjectivesTo investigate longitudinal trajectory of SARS-CoV-2 neutralising antibodies and the performance of serological assays in diagnosing prior infection and predicting serum neutralisation titres with time\n\nDesignRetrospective longitudinal analysis of a COVID19 case cohort.\n\nSettingNHS outpatient clinics\n\nParticipantsIndividuals with RT-PCR diagnosed SARS-CoV-2 infection that did not require hospitalization\n\nMain outcome measuresThe sensitivity with which prior infection was detected and quantitative antibody titres were assessed using four SARS-CoV-2 serologic assay platforms. Two platforms employed SARS-CoV-2 spike (S) based antigens and two employed nucleocapsid (N) based antigens. Serum neutralising antibody titres were measured using a validated pseudotyped virus SARS-CoV-2 neutralisation assay. The ability of the serological assays to predict neutralisation titres at various times after PCR diagnosis was assessed.\n\nResultsThe three of the four serological assays had sensitivities of 95 to100% at 21-40 days post PCR-diagnosis, while a fourth assay had a lower sensitivity of 85%. The relative sensitivities of the assays changed with time and the sensitivity of one assay that had an initial sensitivity of >95% declined to 85% at 61-80 post PCR diagnosis, and to 71% at 81-100 days post diagnosis. Median antibody titres decreased in one serologic assay but were maintained over the observation period in other assays. The trajectories of median antibody titres measured in serologic assays over this time period were not dependent on whether the SARS-CoV-2 N or S proteins were used as antigen source. A broad range of SARS-CoV-2 neutralising titres were evident in individual sera, that decreased over time in the majority of participants; the median neutralisation titre in the cohort decreased by 45% over 4 weeks. Each of the serological assays gave quantitative measurements of antibody titres that correlated with SARS-CoV-2 neutralisation titres, but, the S-based serological assay measurements better predicted serum neutralisation potency. The strength of correlation between serologic assay results and neutralisation titres deteriorated with time and decreases in neutralisation titres in individual participants were not well predicted by changes in antibody titres measured using serologic assays.\n\nConclusionsSARS-CoV-2 serologic assays differed in their comparative diagnostic performance over time. Different assays are more or less well suited for surveillance of populations for prior infection versus prediction of serum neutralisation potency. Continued monitoring of declining neutralisation titres during extended follow up should facilitate the establishment of appropriate serologic correlates of protection against SARS-CoV-2 reinfection.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Frauke Muecksch", + "author_inst": "Laboratory of Retrovirology, The Rockefeller University, 1230 York Avenue, New York NY 10065" + }, + { + "author_name": "Helen Wise", + "author_inst": "Royal Infirmary of Edinburgh, NHS Lothian, 51 Little France Crescent, Edinburgh EH16 4SA" + }, + { + "author_name": "Becky Batchelor", + "author_inst": "Royal Infirmary of Edinburgh, NHS Lothian, 51 Little France Crescent, Edinburgh EH16 4SA" + }, + { + "author_name": "Maria Squires", + "author_inst": "Royal Infirmary of Edinburgh, NHS Lothian, 51 Little France Crescent, Edinburgh EH16 4SA" + }, + { + "author_name": "Elizabeth Semple", + "author_inst": "Royal Infirmary of Edinburgh, NHS Lothian, 51 Little France Crescent, Edinburgh EH16 4SA" + }, + { + "author_name": "Claire Richardson", + "author_inst": "University Hospital Monklands, NHS Lanarkshire, Airdrie ML6 0JS" + }, + { + "author_name": "Jacqueline McGuire", + "author_inst": "University Hospital Monklands, NHS Lanarkshire, Airdrie ML6 0JS" + }, + { + "author_name": "Sarah Cleary", + "author_inst": "University Hospital Monklands, NHS Lanarkshire, Airdrie ML6 0JS" + }, + { + "author_name": "Elizabeth Furrie", + "author_inst": "Ninewells Hospital and Medical School, NHS Tayside, Dundee DD1 9SY" + }, + { + "author_name": "Neil Greig", + "author_inst": "Ninewells Hospital and Medical School, NHS Tayside, Dundee DD1 9SY" + }, + { + "author_name": "Gordon Hay", + "author_inst": "Ninewells Hospital and Medical School, NHS Tayside, Dundee DD1 9SY" + }, + { + "author_name": "Kate Templeton", + "author_inst": "Royal Infirmary of Edinburgh, NHS Lothian, 51 Little France Crescent, Edinburgh EH16 4SA" + }, + { + "author_name": "Julio C.C. Lorenzi", + "author_inst": "Laboratory of Molecular Immunology, The Rockefeller University, 1230 York Avenue, New York NY 10065" + }, + { + "author_name": "Theodora Hatziioannou", + "author_inst": "Laboratory of Retrovirology, The Rockefeller University, 1230 York Avenue, New York NY 10065" + }, + { + "author_name": "Sara J Jenks", + "author_inst": "NHS Lothian" + }, + { + "author_name": "Paul Bieniasz", + "author_inst": "Laboratory of Retrovirology, The Rockefeller University, 1230 York Avenue, New York NY 10065" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.05.20169078", "rel_title": "Transient dynamics of SARS-CoV-2 as England exited national lockdown", @@ -1242663,37 +1244810,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.02.232645", - "rel_title": "Host metabolic reprogramming in response to SARS-Cov-2 infection", - "rel_date": "2020-08-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.02.232645", - "rel_abs": "Understanding the pathogenesis of SARS-CoV-2 is important for developing effective treatment strategies. Viruses hijack the host metabolism to redirect the resources for their replication and survival. How SARS-CoV-2 influences the host metabolism is still unclear. In this study, we analyzed transcriptomic data obtained from different human respiratory cell lines and patient samples (Swab, PBMC, lung biopsy, BALF) to understand the metabolic alterations in response to SARS-CoV-2 infection. For this purpose, the expression pattern of metabolic genes in the human genome-scale metabolic network model Recon3D was explored. We identified metabolic genes and pathways and reporter metabolites under each SARS-CoV-2-infected condition and compared them to identify common and unique changes in the metabolism. Our analysis revealed host-dependent dysregulation of glycolysis, mitochondrial metabolism, amino acid metabolism, glutathione metabolism, polyamine synthesis, and lipid metabolism. We observed different metabolic changes that are pro- and antiviral in nature. We generated hypotheses on how antiviral metabolism can be targeted/enhanced for reducing viral titers. These warrant further exploration with more samples and in vitro studies to test predictions.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "S T R Moolamalla", - "author_inst": "Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad-500032, India" - }, - { - "author_name": "Ruchi Chauhan", - "author_inst": "Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad-500032, India" - }, - { - "author_name": "U Deva Priyakumar", - "author_inst": "Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad-500032, India" - }, - { - "author_name": "P K Vinod", - "author_inst": "Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad-500032, India" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.08.05.237651", "rel_title": "Camostat mesylate inhibits SARS-CoV-2 activation by TMPRSS2-related proteases and its metabolite GBPA exerts antiviral activity", @@ -1243629,6 +1245745,53 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.07.30.20165365", + "rel_title": "Clearing the fog: Is HCQ effective in reducing COVID-19 progression: A randomized controlled trial", + "rel_date": "2020-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.30.20165365", + "rel_abs": "ObjectiveTo analyze the efficacy of Hydroxychloroquine (HCQ) plus standard of care (SOC) compared with SOC alone in reducing disease progression in Mild COVID-19\n\nDesignA single centre, open label randomized controlled trial\n\nPlace and DurationPulmonology department, Pak emirates Military Hospital (PEMH) from 10 April 2020 to 31 May 2020.\n\nMethodologyFive hundred patients of both genders having age between 18-50 years who were PCR positive and had Mild COVID-19 were selected. Patients assigned to standard dose of HCQ (400mg 12 hourly day 1 then 200mg 12 hrly for next 4 days) plus SOC were 349 while 151 patients received SOC comprising of Vit C, Vit D, and Zinc only (control group). Primary outcome was progression of disease while secondary outcome was PCR negativity on day 7 and 14. The results were analyzed on SPSS version 23. P value <0.05 was considered significant.\n\nResultsMedian age of intervention group (34 {+/-} 11.778 years) and control group (34 {+/-} 9.813 years). Disease progressed in 16 patients, 11 (3.15%) were in intervention group as compared to 5 (3.35%) in control group, (p value = 0.865). PCR negativity in intervention and control groups were (day 7, 182 (52.1%) vs. 54 (35.7%) (p value = 0.001), (day 14, 244 (69.9%) vs. 110 (72.8%) (p value = 0.508). Consecutive PCR negativity at day 7 and 14 was observed in 240 (68.8%) in intervention group compared to 108 (71.5%) in control group. (p value = 0.231).\n\nConclusionAddition of HCQ to standard of care treatment in Mild COVID-19 neither prevents disease progression nor is it significantly associated with successive PCR negativity on day 7 and 14.\n\nTrial registrationNCT04491994\n\nEthical review of research projectThe research project titled \"Clearing the fog: Is HCQ effective in reducing COVID-19 progression\" has been reviewed by ethical review committee of Pak Emirates Military Hospital (PEMH) Rawalpindi and got legal and ethical approvals prior to initiation of the research work carried out on subject. All experiments were performed in accordance with the relevant guidelines and regulation. Grant of approval is attached as separate file.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "sultan mehmood kamran", + "author_inst": "Pak Emirates Military Hospital (PEMH) Rawalpindi" + }, + { + "author_name": "Zill e Humayun Mirza", + "author_inst": "Pak Emirates Military Hospital Rawalpindi, Pakistan" + }, + { + "author_name": "Arshad Naseem", + "author_inst": "Pak Emirates Military Hospital Rawalpindi, Pakistan" + }, + { + "author_name": "Farrukh Saeed", + "author_inst": "Pak Emirates Military Hospital Rawalpindi, Pakistan" + }, + { + "author_name": "Rizwan Azam", + "author_inst": "Pak Emirates Military Hospital Rawalpindi, Pakistan" + }, + { + "author_name": "Naqeeb Ullah", + "author_inst": "Pak Emirates Military Hospital Rawalpindi, Pakistan" + }, + { + "author_name": "Wazir Ahmad", + "author_inst": "Pak Emirates Military Hospital Rawalpindi, Pakistan" + }, + { + "author_name": "Salman Saleem", + "author_inst": "Pak Emirates Military Hospital Rawalpindi, Pakistan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.26.20154724", "rel_title": "Interim Results of a Phase II/III Multicenter Randomized Clinical Trial of AVIFAVIR in Hospitalized Patients with COVID-19", @@ -1244857,37 +1247020,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.31.20166025", - "rel_title": "Analytical Model of COVID-19 for lifting non-pharmaceutical interventions", - "rel_date": "2020-08-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.31.20166025", - "rel_abs": "In the present work, we outline a set of coarse-grain analytical models that can be used by decision-makers to bound the potential impact of the COVID-19 pandemic on specific communities with known or estimated social contact structure and to assess the effects of various non-pharmaceutical interventions on slowing the progression of disease spread. This work provides a multi-dimensional view of the problem by examining steady-state and dynamic disease spread using a network-based approach. In addition, Bayesian-based estimation procedures are used to provide a realistic assessment of the severity of outbreaks based on estimates of the average and instantaneous basic reproduction number R0.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Garry Jacyna", - "author_inst": "The MITRE Corporation" - }, - { - "author_name": "James R. Thompson", - "author_inst": "The MITRE Corporation" - }, - { - "author_name": "Matt Koehler", - "author_inst": "The MITRE Corporation" - }, - { - "author_name": "David M. Slater", - "author_inst": "The MITRE Corporation" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.31.20166066", "rel_title": "SARS-CoV-2 Infection Among Symptom-Free Healthcare Workers", @@ -1245691,6 +1247823,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "dentistry and oral medicine" }, + { + "rel_doi": "10.1101/2020.08.02.20166504", + "rel_title": "Epidemiological characteristics of SARS-COV-2 in Myanmar", + "rel_date": "2020-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.02.20166504", + "rel_abs": "Coronavirus disease (COVID-19) is an infectious disease caused by a newly discovered severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In Myanmar, first COVID-19 reported cases were identified on 23rd March 2020. There were 336 reported confirmed cases, 261 recovered and 6 deaths through 13th July 2020. The study was a retrospective case series and all COVID-19 confirmed cases from 23rd March to 13th July 2020 were included. The data series of COVID-19 cases were extracted from the daily official reports of the Ministry of Health and Sports (MOHS), Myanmar and Centers for Disease Control and Prevention (CDC), Myanmar. Among 336 confirmed cases, there were 169 cases with reported transmission events. The median serial interval was 4 days (IQR 3, 2-5) with the range of 0 - 26 days. The mean of the reproduction number was 1.44 with (95% CI = 1.30-1.60) by exponential growth method and 1.32 with (95% CI = 0.98-1.73) confident interval by maximum likelihood method. This study outlined the epidemiological characteristics and epidemic parameters of COVID-19 in Myanmar. The estimation parameters in this study can be comparable with other studies and variability of these parameters can be considered when implementing disease control strategy in Myanmar.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Aung Min Thway", + "author_inst": "Defence Services Medical Academy, Myanmar" + }, + { + "author_name": "Htun Tayza", + "author_inst": "Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand" + }, + { + "author_name": "Tun Tun Win", + "author_inst": "Defence Services Medical Academy, Myanmar" + }, + { + "author_name": "Ye Minn Tun", + "author_inst": "Health and Disease Control Unit, Myanmar" + }, + { + "author_name": "Moe Myint Aung", + "author_inst": "Health and Disease Control Unit, Myanmar" + }, + { + "author_name": "Yan Naung Win", + "author_inst": "Health and Disease Control Unit, Myanmar" + }, + { + "author_name": "Kyaw M Tun", + "author_inst": "Defence Services Medical Academy" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.01.20165142", "rel_title": "A variational model for computing the effective reproduction number of SARS-CoV-2", @@ -1246383,33 +1248558,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.01.20166447", - "rel_title": "On the temporal spreading of the SARS-CoV-2", - "rel_date": "2020-08-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.01.20166447", - "rel_abs": "The behaviour of SARS-CoV-2 virus is certainly one of the most challenging in contemporary world. Although the mathematical modelling of the virus has made relevant contributions, the unpredictable behaviour of the virus is still not fully understood. To identify some aspects of the virus elusive behaviour, we focused on the temporal characteristics of its course. We have analysed the latency trends the virus has realized worldwide, the outbreak of the hot spots, and the decreasing trends of the pandemic. We found that the spatio-temporal pandemic dynamics shows a power law distribution. As with physical systems, these changes in the pandemics course, which we have called transitional stages of contagion, highlight shared characteristics in many countries. The main results of this work is that the pandemic progression rhythms have been clearly identified for each country, providing the processes and the stages at which the virus develops, thus giving important information on the activation of containment and control measures.\n\nHighlightsO_LITemporal spreading of the novel SARS-CoV-2 is analysed all over the world, and the distribution of infected people follows a power law.\nC_LIO_LILatency, hot spots ignition, decreasing of the virus course all over the world are detected.\nC_LIO_LIAs in physical systems, the virus behaviour shows transitional stages in its evolution.\nC_LIO_LITemporal rhythms of the virus behaviour have key biological significance from the theoretical point of view, disclosing the steps of the virus evolution.\nC_LIO_LIPredictions on the contagion dynamics, for each country, for all countries may be embodied into applications, for allowing forecasting about the contagion risk.\nC_LI", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Francesca Bertacchini", - "author_inst": "Department of Mechanical, Energy and Management Engineering, University of Calabria" - }, - { - "author_name": "Eleonora Bilotta", - "author_inst": "Department of Physics, University of Calabria" - }, - { - "author_name": "Pietro S. Pantano", - "author_inst": "Department of Physics, University of Calabria" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.01.20166538", "rel_title": "Highly performing point-of-care molecular testing for SARS-CoV-2 with RNA extraction and isothermal amplification.", @@ -1246969,6 +1249117,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, + { + "rel_doi": "10.1101/2020.08.02.20166751", + "rel_title": "Gender disparities in international COVID-19 clinical trial leadership", + "rel_date": "2020-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.02.20166751", + "rel_abs": "The COVID-19 pandemic offers considerable possibilities for research and leadership that might equalize opportunity in a new field; however, our study finds instead that more than two-thirds of investigators leading COVID-19-related clinical studies are predicted to be men. These gender disparities in trial leadership during the pandemic suggest that the structural reproduction of inequalities in research has taken place once again in this new academic field. This indicates that policies are needed to facilitate the identification and implementation of strategies to correct gender bias. The active participation of women, trans and gender-nonconforming individuals are needed in research to drive scientific discovery and innovation as well as to better address health disparities.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Muge Cevik", + "author_inst": "Infection and Global Health Research, University of St Andrews" + }, + { + "author_name": "Syed Arefinul Haque", + "author_inst": "Network Science Institute, Northeastern University, Boston, Massachusetts, United States" + }, + { + "author_name": "Jennifer Manne", + "author_inst": "Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, United States" + }, + { + "author_name": "Krutika Kuppalli", + "author_inst": "Division of Infectious Diseases, Medical University of South Carolina, Charleston, South Carolina, United States" + }, + { + "author_name": "Paul E Sax", + "author_inst": "Harvard Medical School, Boston, Massachusetts, United States" + }, + { + "author_name": "Maimuna S Majumder", + "author_inst": "Boston Childrens Hospital, Harvard Medical School, Boston, MA, United States" + }, + { + "author_name": "Chloe Orkin", + "author_inst": "Blizzard Institute, Queen Mary University of London, London, United Kingdom" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.08.02.20166785", "rel_title": "The Lebanese Cohort for COVID-19; A Challenge for the ABO Blood Group System", @@ -1247997,53 +1250188,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.01.20166470", - "rel_title": "Characteristics of COVID-19 fatality cases in East Kalimantan, Indonesia", - "rel_date": "2020-08-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.01.20166470", - "rel_abs": "IntroductionCoronavirus Disease (COVID-19) is caused by SARS-CoV-2 infection. On March 2, 2020, Indonesia announced the first confirmed cases of COVID-19 infection. East Kalimantan will play an important role as the new capital of Indonesia. There is attention to the preparedness of East Kalimantan to respond to COVID-19. We report the characteristics of COVID-19 fatality cases in here.\n\nMethodsWe retrospectively analyzed the fatality cases of COVID-19 patients from the East Kalimantan Health Office information system. All patients were confirmed COVID-19 by RT-PCR examination.\n\nResultsBy July 31, 2020, 31 fatality cases of patients had been identified as having confirmed COVID-19 in East Kalimantan. The mean age of the patients was 55.1 {+/-} 9.2 years. Most of the patients were men (22 [71.0%]) with age more than 60 years old (14 [45.2%]). Balikpapan has the highest number of COVID-19 fatality cases from all regencies. Hypertension was the most comorbidities in the fatality cases of COVID-19 patients in East Kalimantan.\n\nDiscussionOlder age and comorbidities still contributed to the fatality cases of COVID-19 patients in East Kalimantan, Indonesia. Hypertension, diabetes, cardiovascular disease, and cerebrovascular disease were underlying conditions for increasing the risk of COVID-19 getting into a serious condition.\n\nConclusionActive surveillance for people older than 60 years old and having underlying diseases is needed for reducing the case fatality rate of COVID-19 in East Kalimantan.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Swandari Paramita", - "author_inst": "Mulawarman University" - }, - { - "author_name": "Ronny Isnuwardana", - "author_inst": "Mulawarman University" - }, - { - "author_name": "Krispinus Duma", - "author_inst": "Mulawarman University" - }, - { - "author_name": "Rahmat Bakhtiar", - "author_inst": "Mulawarman University" - }, - { - "author_name": "Muhammad Khairul Nuryanto", - "author_inst": "Mulawarman University" - }, - { - "author_name": "Riries Choiru Pramulia Yudia", - "author_inst": "Mulawarman University" - }, - { - "author_name": "Evi Fitriany", - "author_inst": "Mulawarman University" - }, - { - "author_name": "Meiliati Aminyoto", - "author_inst": "Mulawarman University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.03.20167395", "rel_title": "Viable SARS-CoV-2 in the air of a hospital room with COVID-19 patients", @@ -1248719,6 +1250863,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.27.20163071", + "rel_title": "Clinical Characteristics and Severity of COVID-19 Disease in Patients from Boston Area Hospitals", + "rel_date": "2020-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.27.20163071", + "rel_abs": "We summarize key demographic, clinical, and medical characteristics of patients with respect to the severity of COVID-19 disease using Electronic Health Records Data of 4,140 SARS-CoV-2 positive subjects from several large Boston Area Hospitals. We found that prior use of antihypertensive medications as well as lipid lowering and other cardiovascular drugs (such as direct oral anticoagulants and antiplatelets) all track with increased severity of COVID-19 and should be further investigated with appropriate adjustment for confounders such as age and frailty. The three most common prior comorbidities are hyperlipidemia, hypertension, and prior pneumonia, all associated with increased severity.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Hesamaddin Torabi Dashti", + "author_inst": "Division of Preventive Medicine, Brigham and Women's Hospital / Harvard Medical School" + }, + { + "author_name": "David Bates", + "author_inst": "Division of Preventive Medicine, Brigham and Women's Hospital" + }, + { + "author_name": "Julie M Fiskio", + "author_inst": "Division of Information Systems, Brigham and Women's Hospital" + }, + { + "author_name": "Elise C Roche", + "author_inst": "Division of Preventive Medicine, Brigham and Women's Hospital" + }, + { + "author_name": "Samia Mora", + "author_inst": "Division of Preventive Medicine, Brigham and Women's Hospital / Harvard Medical School" + }, + { + "author_name": "Olga Demler", + "author_inst": "Division of Preventive Medicine, Brigham and Women's Hospital / Harvard Medical School" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.04.20167890", "rel_title": "Hospital Admission Rates, Length of Stay and In-hospital Mortality for Common Acute Care Conditions in COVID-19 vs. Pre-COVID-19 Era", @@ -1249838,69 +1252021,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.08.03.235291", - "rel_title": "Lead compounds for the development of SARS-CoV-2 3CL protease inhibitors", - "rel_date": "2020-08-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.03.235291", - "rel_abs": "We report the identification of three structurally diverse compounds - compound 4, GC376, and MAC-5576 - as inhibitors of the SARS-CoV-2 3CL protease. Structures of each of these compounds in complex with the protease revealed strategies for further development, as well as general principles for designing SARS-CoV-2 3CL protease inhibitors. These compounds may therefore serve as leads for the basis of building effective SARS-CoV-2 3CL protease inhibitors.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Sho Iketani", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Farhad Forouhar", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Hengrui Liu", - "author_inst": "Columbia University" - }, - { - "author_name": "Seo Jung Hong", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Fang-Yu Lin", - "author_inst": "WuXi AppTec" - }, - { - "author_name": "Manoj S Nair", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Arie Zask", - "author_inst": "Columbia University" - }, - { - "author_name": "Yaoxing Huang", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Li Xing", - "author_inst": "WuXi AppTec" - }, - { - "author_name": "Brent R Stockwell", - "author_inst": "Columbia University" - }, - { - "author_name": "Alejandro Chavez", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "David D Ho", - "author_inst": "Columbia University Irving Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.08.04.236893", "rel_title": "Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis", @@ -1250896,6 +1253016,113 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.08.03.233718", + "rel_title": "PAN-INDIA 1000 SARS-CoV-2 RNA Genome Sequencing Reveals Important Insights into the Outbreak", + "rel_date": "2020-08-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.03.233718", + "rel_abs": "The PAN-INDIA 1000 SARS-CoV-2 RNA Genome Sequencing Consortium has achieved its initial goal of completing the sequencing of 1000 SARS-CoV-2 genomes from nasopharyngeal and oropharyngeal swabs collected from individuals testing positive for COVID-19 by Real Time PCR. The samples were collected across 10 states covering different zones within India. Given the importance of this information for public health response initiatives investigating transmission of COVID-19, the sequence data is being released in GISAID database. This information will improve our understanding on how the virus is spreading, ultimately helping to interrupt the transmission chains, prevent new cases of infection, and provide impetus to research on intervention measures. This will also provide us with information on evolution of the virus, genetic predisposition (if any) and adaptation to human hosts.\n\nOne thousand and fifty two sequences were used for phylodynamic, temporal and geographic mutation patterns and haplotype network analyses. Initial results indicate that multiple lineages of SARS-CoV-2 are circulating in India, probably introduced by travel from Europe, USA and East Asia. A2a (20A/B/C) was found to be predominant, along with few parental haplotypes 19A/B. In particular, there is a predominance of the D614G mutation, which is found to be emerging in almost all regions of the country. Additionally, mutations in important regions of the viral genome with significant geographical clustering have also been observed. The temporal haplotype diversities landscape in each region appears to be similar pan India, with haplotype diversities peaking between March-May, while by June A2a (20A/B/C) emerged as the predominant one. Within haplotypes, different states appear to have different proportions. Temporal and geographic patterns in the sequences obtained reveal interesting clustering of mutations. Some mutations are present at particularly high frequencies in one state as compared to others. The negative estimate Tajimas D (D = -2.26817) is consistent with the rapid expansion of SARS-CoV-2 population in India. Detailed mutational analysis across India to understand the gradual emergence of mutants at different regions of the country and its possible implication will help in better disease management.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Arindam Maitra", + "author_inst": "National INstitute of Biomedical Genomics" + }, + { + "author_name": "Sunil Raghav", + "author_inst": "Institute of Life Science" + }, + { + "author_name": "Ashwin Dalal", + "author_inst": "Centre for DNA Fingerprinting and Diagnostics" + }, + { + "author_name": "Farhan Ali", + "author_inst": "National Centre for Biological Sciences" + }, + { + "author_name": "Vanessa Molin Paynter", + "author_inst": "Institute for Stem Cell Science and Regenerative Medicine" + }, + { + "author_name": "Dhiraj Paul", + "author_inst": "National Centre for Cell Science" + }, + { + "author_name": "Nidhan K Biswas", + "author_inst": "National institute of Biomedical Genomics" + }, + { + "author_name": "Arup Ghosh", + "author_inst": "Institute of Life Science" + }, + { + "author_name": "Kunal Jani", + "author_inst": "National Centre for Cell Science" + }, + { + "author_name": "Sreedhar Chinnaswamy", + "author_inst": "National institute of Biomedical Genomics" + }, + { + "author_name": "Sanghamitra Pati", + "author_inst": "ICMR-Regional Centre for Medical Research" + }, + { + "author_name": "Arvind Sahu", + "author_inst": "National Centre for Cell Science" + }, + { + "author_name": "Debashis Mitra", + "author_inst": "Centre for DNA Fingerprinting and Diagnostics, National Centre for Cell Science" + }, + { + "author_name": "Manoj Kumar Bhat", + "author_inst": "National Centre for Cell Science" + }, + { + "author_name": "Satyajit Mayor", + "author_inst": "National Centre for Biological Sciences" + }, + { + "author_name": "Apurva Sarin", + "author_inst": "Institute for Stem Cell Science and Regenerative Medicine" + }, + { + "author_name": "- The PAN-INDIA 1000 SARS-CoV-2 RNA Genome Sequencing Consortium", + "author_inst": "-" + }, + { + "author_name": "Yogesh S Shouche", + "author_inst": "National Centre for Cell Science" + }, + { + "author_name": "Aswin Sai Narain Seshasayee", + "author_inst": "National Centre for Biological Sciences" + }, + { + "author_name": "Dasaradhi Palakodeti", + "author_inst": "Institute For Stem Cell Biology and Regenerative Medicine" + }, + { + "author_name": "Murali Dharan Bashyam", + "author_inst": "Centre for DNA Fingerprinting and Diagnostics (CDFD)" + }, + { + "author_name": "AJAY PARIDA", + "author_inst": "Institute of Life Sciences," + }, + { + "author_name": "Saumitra Das", + "author_inst": "National Institute of Biomedical Sciences" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.08.03.234914", "rel_title": "De novo design of picomolar SARS-CoV-2 miniprotein inhibitors", @@ -1251956,33 +1254183,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2020.07.30.20165290", - "rel_title": "COVID-19 Pandemic Severity, Lockdown Regimes, and People Mobility: Evidence from 88 Countries", - "rel_date": "2020-08-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.30.20165290", - "rel_abs": "This study empirically investigates the complex interplay between the severity of the coronavirus pandemic, mobility changes in retail and recreation, transit stations, workplaces, and residential areas, and lockdown measures in 88 countries of the word. To conduct the study, data on mobility patterns, socioeconomic and demographic characteristics of people, lockdown measures, and coronavirus pandemic were collected from multiple sources (e.g., Google, UNDP, UN, BBC, Oxford University, Worldometer). A Structural Equation Modeling (SEM) technique is used to investigate the direct and indirect effects of independent variables on dependent variables considering the intervening effects of mediators. Results show that lockdown measures have significant effects to encourage people to maintain social distancing. However, pandemic severity and socioeconomic and institutional factors have limited effects to sustain social distancing practice. The results also explain that socioeconomic and institutional factors of urbanity and modernity have significant effects on pandemic severity. Countries with a higher number of elderly people, employment in the service sector, and higher globalization trend are the worst victims of the coronavirus pandemic (e.g., USA, UK, Italy, and Spain). Social distancing measures are reasonably effective at tempering the severity of the pandemic.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Md Mokhlesur Rahman", - "author_inst": "The University of North Carolina at Charlotte" - }, - { - "author_name": "Jean-Claude Thill", - "author_inst": "The University of North Carolina at Charlotte" - }, - { - "author_name": "Kamal Chandra Paul", - "author_inst": "The University of North Carolina at Charlotte" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.07.30.20164475", "rel_title": "Projecting hospital resource utilization during a surge using parametric bootstrapping", @@ -1252850,6 +1255050,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.29.20163998", + "rel_title": "Throat wash as a source of SARS-CoV-2 RNA to monitor community spread of COVID-19.", + "rel_date": "2020-08-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.29.20163998", + "rel_abs": "BackgroundSARS-CoV-2 RNA detection with real time PCR is currently the central diagnostic tool to determine ongoing active infection. Nasopharyngeal and oral swabs are the main collection tool of biological material used as the source of viral RNA outside a hospital setting. However, limitation in swabs availability, trained health professional with proper PPE and potential risk of aerosols may hinder COVID diagnosis. Self-collection with swabs, saliva and throat wash to obtain oropharyngeal wash has been suggested as having comparable performance of regular swab. We performed throat wash (TW) based surveillance with laboratory heath workers and other employees (LHW) at a laboratory research institute.\n\nMethodsConsecutive volunteer testing of LWH and external household and close contacts were included. TW self-collection was performed in 5 mL of sterile saline that was returned to original vial after approximate 5 secs of gargle. RNA extraction and rtPCR were performed as part of routine COVID protocols using Allplex (Seegene, Korea).\n\nResultsFour hundred and twenty two volunteers, 387 (93%) LHW and 43 (7%) contacts participated in the survey. One or more positive COVID rtPCR was documented in 63 (14.9% CI95 12%-19%) individuals. No correlation was observed between with direct activities with COVID samples to positivity, with infection observed in comparable rates among different laboratory areas, administrative or supportive activities. Among 63 with detected SARS-CoV-2 RNA, 59 with clinical information, 58% reported symptoms at a median of 4 days prior to collection, most with mild disease. Over a third (38%) of asymptomatic cases developed symptoms 1-3 days after collection. Although overall CT values of TW were higher than that of contemporary swab tests from hospitalized cases, TW from symptomatic cases had comparable CTs.\n\nConclusionsThe study suggests that TW may be a valid alternative to the detection of SARS-CoV-2 RNA. The proportion of asymptomatic and pre-symptomatic cases is elevated and reinforces the need of universal precautions and frequent surveys to limit the spread of the disease.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Giselle Ibette Silva Lopez-Lopes", + "author_inst": "instituto Adolfo lutz" + }, + { + "author_name": "Cintia Mayumi Ahagon", + "author_inst": "Instituto Adolo Lutz" + }, + { + "author_name": "Margarete Aparecida Bonega", + "author_inst": "Instituto Adolfo lutz" + }, + { + "author_name": "Fabiana Pereira dos Santos", + "author_inst": "Instituto Adolfo lutz" + }, + { + "author_name": "Katia Correa de Oliveira Santos", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Audrey Cilli", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Lincoln Spinazola do Prado", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Daniela Bernardes Borges da Silva", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Nuria Borges da Luz", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Claudia Patara Saraceni", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Ana Maria Sardinha Afonso", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Maria do Carmo Timenetsky", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Luis Fernando de Macedo Brigido", + "author_inst": "Instituto Adolfo Lutz" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.29.20164681", "rel_title": "Loss expansion of SARS-CoV-2 specific immunity is a key risk factor in fatal patients with COVID-19", @@ -1253774,85 +1256041,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2020.07.30.20164988", - "rel_title": "Comparative effects of viral transport medium heat inactivation upon downstream SARS-CoV-2 detection in patient samples", - "rel_date": "2020-08-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.30.20164988", - "rel_abs": "The COVID-19 pandemic, which began in 2020 is testing economic resilience and surge capacity of healthcare providers worldwide. At time of writing, positive detection of the SARS-CoV-2 virus remains the only method for diagnosing COVID-19 infection. Rapid upscaling of national SARS-CoV-2 genome testing presented challenges: 1) Unpredictable supply chains of reagents and kits for virus inactivation, RNA extraction and PCR-detection of viral genomes 2) Rapid time to result of <24 hours is required in order to facilitate timely infection control measures. We evaluated whether alternative commercially available kits provided sensitivity and accuracy of SARS-CoV-2 genome detection comparable to those used by regional National Healthcare Services (NHS), and asked if detection was altered by heat inactivation, an approach for rapid one-step viral inactivation and RNA extraction without chemicals or kits. Using purified RNA, we found the CerTest VIASURE kit to be comparable to Altona RealStar system currently in use, and further showed that both diagnostic kits performed similarly in the BioRad CFX96 and Roche LightCycler 480 II machines. Additionally, both kits were comparable to a third alternative using a combination of Quantabio qScript 1-step qRT-PCR mix and CDC-accredited N1 and N2 primer/probes when looking specifically at borderline samples. Importantly, when using the kits in an extraction-free protocol, following heat inactivation, we saw differing results, with the combined Quantabio-CDC assay showing superior accuracy and sensitivity. In particular, detection using the CDC N2 probe following the extraction-free protocol was highly correlated to results generated with the same probe following RNA extraction and reported clinically (n=127; R2=0.9259). Our results demonstrate that sample treatment can greatly affect the downstream performance of SARS-CoV-2 diagnostic kits, with varying impact depending on the kit. We also showed that one-step heat inactivation methods could reduce time from swab receipt to outcome of test result. Combined, these findings present alternatives to the protocols in use and can serve to alleviate any arising supply chain issues at different points in the workflow, whilst accelerating testing, and reducing cost and environmental impact.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Jamie L Thompson", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Angela Downie Ruiz Velasco", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Alice Cardall", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Rebecca Tarbox", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Jaineeta Richardson", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Gemma Clarke", - "author_inst": "NUH" - }, - { - "author_name": "Michelle Lister", - "author_inst": "NUH" - }, - { - "author_name": "Hannah C Howson-Wells", - "author_inst": "NUH" - }, - { - "author_name": "Vicki M Fleming", - "author_inst": "NUH" - }, - { - "author_name": "Manjinder Khakh", - "author_inst": "Path Links Pathology" - }, - { - "author_name": "Tim Sloan", - "author_inst": "Path Links Pathology" - }, - { - "author_name": "Nichola Duckworth", - "author_inst": "Path Links Pathology" - }, - { - "author_name": "Chris Denning", - "author_inst": "University of Nottingham" - }, - { - "author_name": "C. Patrick McClure", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Andrew V Benest", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Claire H Seedhouse", - "author_inst": "University of Nottingham" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.30.20165027", "rel_title": "High rate of major drug-drug interactions of lopinavir-ritonavir for COVID-19 treatment", @@ -1254560,6 +1256748,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.29.20164020", + "rel_title": "METFORMIN USE IS ASSOCIATED WITH REDUCED MORTALITY IN A DIVERSE POPULATION WITH COVID-19 AND DIABETES", + "rel_date": "2020-07-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.29.20164020", + "rel_abs": "BACKGROUNDCoronavirus disease-2019 (COVID-19) is a growing pandemic with an increasing death toll that has been linked to various comorbidities as well as racial disparity. However, the specific characteristics of these at-risk populations are still not known and approaches to lower mortality are lacking.\n\nMETHODSWe conducted a retrospective electronic health record data analysis of 25,326 subjects tested for COVID-19 between 2/25/20 and 6/22/20 at the University of Alabama at Birmingham Hospital, a tertiary health care center in the racially diverse Southern U.S. The primary outcome was mortality in COVID-19-positive subjects and the association with subject characteristics and comorbidities was analyzed using simple and multiple linear logistic regression.\n\nRESULTSThe odds ratio of contracting COVID-19 was disproportionately high in Blacks/African- Americans (OR 2.6; 95%CI 2.19-3.10; p<0.0001) and in subjects with obesity (OR 1.93; 95%CI 1.64-2.28; p<0.0001), hypertension (OR 2.46; 95%CI 2.07-2.93; p<0.0001), and diabetes (OR 2.11; 95%CI 1.78-2.48; p<0.0001). Diabetes was also associated with a dramatic increase in mortality (OR 3.62; 95%CI 2.11-6.2; p<0.0001) and emerged as an independent risk factor in this diverse population even after correcting for age, race, sex, obesity and hypertension. Interestingly, we found that metformin treatment was independently associated with a significant reduction in mortality in subjects with diabetes and COVID-19 (OR 0.33; 95%CI 0.13-0.84; p=0.0210).\n\nCONCLUSIONThus, these results suggest that while diabetes is an independent risk factor for COVID-19- related mortality, this risk is dramatically reduced in subjects taking metformin, raising the possibility that metformin may provide a protective approach in this high risk population.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Andrew Crouse", + "author_inst": "UAB" + }, + { + "author_name": "Tiffany Grimes", + "author_inst": "UAB" + }, + { + "author_name": "Peng Li", + "author_inst": "UAB" + }, + { + "author_name": "Matthew Might", + "author_inst": "UAB" + }, + { + "author_name": "Fernando Ovalle", + "author_inst": "UAB" + }, + { + "author_name": "Anath Shalev", + "author_inst": "UAB" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "endocrinology" + }, { "rel_doi": "10.1101/2020.07.30.228023", "rel_title": "The SARS-CoV-2 Nucleocapsid phosphoprotein forms mutually exclusive condensates with RNA and the membrane-associated M protein", @@ -1255404,77 +1257631,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.07.31.20165936", - "rel_title": "High effectiveness of multimodal infection control interventions in preventing SARS-CoV-2 infections in healthcare professionals: a prospective longitudinal seroconversion study", - "rel_date": "2020-07-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.31.20165936", - "rel_abs": "ObjectiveTo assess the effectiveness of multimodal infection control interventions in the prevention of SARS-CoV-2 infections in healthcare professionals\n\nDesignSequential follow-up study\n\nSettingLargest tertiary care centre in northern Germany\n\nParticipants1253 employees of the University Medical Center Hamburg-Eppendorf were sequentially assessed for the presence of SARS-CoV-2 IgG antibodies at the beginning of the covid-19 epidemic (20 March - 9 April), one month (20 April - 8 May), and another two months later (22 June - 24 July). Of those, 1026 were healthcare workers (HCWs) of whom 292 were directly involved in the care of covid-19 patients. During the study period, infection control interventions were deployed, those included i) strict barrier nursing of all known covid-19 patients including FFP2 (N95) masks, goggles, gloves, hoods and protective gowns, ii) visitor restrictions with access control at all hospital entries, iii) mandatory wearing of disposable face masks in all clinical settings, and iv) universal RT-PCR admission screening of patients.\n\nMain Outcome MeasuresSARS-CoV-2 IgG seroconversion rate\n\nResultsAt the initial screening, ten participants displayed significant IgG antibody ratios. Another ten individuals showed seroconversion at the second time point one month later, only two further participants seroconverted during the subsequent two months. The overall SARS-CoV-2 seroprevalence in the study cohort at the last follow-up was 1.8%, the seroconversion rate dropped from 0.81% to 0.08% per month despite a longer observation period. Amongst HCWs seropositivity was increased in those directly involved in the care of patients with SARS-CoV-2 infections (3.8%, n=11) compared to other HCWs (1.4%, n=10, P=0.025). However, after the adoption of all multimodal infection control interventions seroconversions were observed in only two more HCWs, neither of whom were involved in inpatient care.\n\nConclusionMultimodal infection control and prevention interventions are highly effective in mitigating SARS-CoV-2 infections of healthcare professionals.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Thomas Theo Brehm", - "author_inst": "I. Department of Internal Medicine, University Medical Center Hamburg-Eppendorf; German Center for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borst" - }, - { - "author_name": "Dorothee Schwinge", - "author_inst": "I. Department of Internal Medicine, University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Sibylle Lampalzer", - "author_inst": "I. Department of Internal Medicine, University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Veronika Schlicker", - "author_inst": "I. Department of Internal Medicine, University Medical Center Hamburg-Eppendorf; German Center for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borst" - }, - { - "author_name": "Julia Kuechen", - "author_inst": "I. Department of Internal Medicine, University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Michelle Thompson", - "author_inst": "I. Department of Internal Medicine, University Medical Center Hamburg-Eppendorf," - }, - { - "author_name": "Felix Ullrich", - "author_inst": "I. Department of Internal Medicine, University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Samuel Huber", - "author_inst": "I. Department of Internal Medicine, University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Stefan Schmiedel", - "author_inst": "I. Department of Internal Medicine, University Medical Center Hamburg-Eppendorf; German Center for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borst" - }, - { - "author_name": "Marylyn M Addo", - "author_inst": "I. Department of Internal Medicine, University Medical Center Hamburg-Eppendorf; German Center for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borst" - }, - { - "author_name": "Marc Luetgehetmann", - "author_inst": "Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf; German Center for Infection Research (DZIF), Partner Site " - }, - { - "author_name": "Johannes K Knobloch", - "author_inst": "Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf; German Center for Infection Research (DZIF), Partner Site " - }, - { - "author_name": "Julian Schulze zur Wiesch", - "author_inst": "I. Department of Internal Medicine, University Medical Center Hamburg-Eppendorf; German Center for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borst" - }, - { - "author_name": "Ansgar W Lohse", - "author_inst": "I. Department of Internal Medicine, University Medical Center Hamburg-Eppendorf; German Center for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borst" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.31.20165829", "rel_title": "Isolation Considered Epidemiological Model for the Prediction of COVID-19 Trend in Tokyo, Japan", @@ -1256154,6 +1258310,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.29.20162917", + "rel_title": "Evidence favouring the efficacy of convalescent plasma for COVID-19 therapy", + "rel_date": "2020-07-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.29.20162917", + "rel_abs": "To determine the effect of COVID-19 convalescent plasma on mortality, we aggregated patient outcome data from randomized clinical trials, matched control, case series, and case report studies. Fixed-effects analyses demonstrated that hospitalized COVID-19 patients transfused with convalescent plasma exhibited a ~57% reduction in mortality rate (10%) compared to matched-patients receiving standard treatments (22%; OR: 0.43, P < 0.001). These data provide evidence favouring the efficacy of human convalescent plasma as a therapeutic agent in hospitalized COVID-19 patients.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Stephen A Klassen", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Jonathon Senefeld", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Patrick W Johnson", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Rickey E. Carter", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Chad C. Wiggins", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Shmuel Shoham", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Brenda J. Grossman", + "author_inst": "Washington University School of Medicine in St. Louis" + }, + { + "author_name": "Jeffrey P. Henderson", + "author_inst": "Washington University School of Medicine in St. Louis" + }, + { + "author_name": "James M. Musser", + "author_inst": "Houston Methodist Hospital" + }, + { + "author_name": "Eric Salazar", + "author_inst": "Houston Methodist Hospital" + }, + { + "author_name": "William R. Hartman", + "author_inst": "University of Wisconsin-Madison" + }, + { + "author_name": "Nicole M. Bouvier", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Sean T.H. Liu", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Liise-anne Pirofski", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Sarah E. Baker", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Noud Van Helmond", + "author_inst": "Cooper Medical School of Rowan University" + }, + { + "author_name": "R. Scott Wright", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "DeLisa Fairweather", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Katelyn A. Bruno", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Nigel S. Paneth", + "author_inst": "Michigan State University" + }, + { + "author_name": "Arturo Casadevall", + "author_inst": "Johns Hopkins School of Public Health" + }, + { + "author_name": "Michael J Joyner", + "author_inst": "Mayo Clinic" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.29.20161323", "rel_title": "Model stability of COVID-19 mortality prediction with biomarkers", @@ -1256938,29 +1259197,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.28.20164087", - "rel_title": "COVID-19: Time-Dependent Effective Reproduction Number and Sub-notification Effect Estimation Modeling", - "rel_date": "2020-07-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.28.20164087", - "rel_abs": "BackgroundSince the beginning of the COVID-19 pandemic, researchers and health authorities have sought to identify the different parameters that govern their infection and death cycles, in order to be able to make better decisions. In particular, a series of reproduction number estimation models have been presented, with different practical results.\n\nObjectiveThis article aims to present an effective and efficient model for estimating the Reproduction Number and to discuss the impacts of sub-notification on these calculations.\n\nMethodsThe concept of Moving Average Method with Initial value (MAMI) is used, as well as a model for Rt, the Reproduction Number, is derived from experimental data. The models are applied to real data and their performance is presented.\n\nResultsAnalyses on Rt and sub-notification effects for Germany, Italy, Sweden, United Kingdom, South Korea, and the State of New York are presented to show the performance of the methods here introduced.\n\nConclusionsWe show that, with relatively simple mathematical tools, it is possible to obtain reliable values for time-dependent, incubation period-independent Reproduction Numbers (Rt). We also demonstrate that the impact of sub-notification is relatively low, after the initial phase of the epidemic cycle has passed.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Eduardo Atem De Carvalho", - "author_inst": "Universidade Estadual do Norte Fluminense" - }, - { - "author_name": "Rogerio Atem De Carvalho", - "author_inst": "Instituto Federal Fluminense" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.28.20146522", "rel_title": "An Outpatient Telehealth Elective for Displaced Clinical Learners during the Coronavirus Pandemic", @@ -1257824,6 +1260060,69 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.07.29.227462", + "rel_title": "SARS-CoV-2 Spike Protein Interacts with Multiple Innate Immune Receptors", + "rel_date": "2020-07-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.29.227462", + "rel_abs": "The spike (S) glycoprotein in the envelope of SARS-CoV-2 is densely glycosylated but the functions of its glycosylation are unknown. Here we demonstrate that S is recognized in a glycan-dependent manner by multiple innate immune receptors including the mannose receptor MR/CD206, DC-SIGN/CD209, L-SIGN/CD209L, and MGL/CLEC10A/CD301. Single-cell RNA sequencing analyses indicate that such receptors are highly expressed in innate immune cells in tissues susceptible to SARS-CoV-2 infection. Binding of the above receptors to S is characterized by affinities in the picomolar range and consistent with S glycosylation analysis demonstrating a variety of N- and O-glycans as receptor ligands. These results indicate multiple routes for SARS-CoV-2 to interact with human cells and suggest alternative strategies for therapeutic intervention.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Chao Gao", + "author_inst": "Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA" + }, + { + "author_name": "Junwei Zeng", + "author_inst": "Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA" + }, + { + "author_name": "Nan Jia", + "author_inst": "Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA" + }, + { + "author_name": "Kathrin Stavenhagen", + "author_inst": "Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA" + }, + { + "author_name": "Yasuyuki Matsumoto", + "author_inst": "Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA" + }, + { + "author_name": "Hua Zhang", + "author_inst": "Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY" + }, + { + "author_name": "Adam J Hume", + "author_inst": "Department of Microbiology, Boston University School of Medicine, Boston, MA" + }, + { + "author_name": "Elke Muehlberger", + "author_inst": "National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA" + }, + { + "author_name": "Irma van Die", + "author_inst": "Department of Molecular Cell Biology and Immunology, VU University Medical Center, Amsterdam, The Netherlands" + }, + { + "author_name": "Julian Kwan", + "author_inst": "Center for Network Systems Biology, Departments of Biochemistry and Biology, Boston University, Boston, MA" + }, + { + "author_name": "Andrew Emili", + "author_inst": "Center for Network Systems Biology, Departments of Biochemistry and Biology, Boston University, Boston, MA" + }, + { + "author_name": "Richard D Cummings", + "author_inst": "Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.07.29.227785", "rel_title": "Mucin-type O-glycosylation Landscapes of SARS-CoV-2 Spike Proteins", @@ -1258696,69 +1260995,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.21.20151423", - "rel_title": "Resveratrol and Copper for treatment of severe COVID-19: an observational study (RESCU 002)", - "rel_date": "2020-07-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.21.20151423", - "rel_abs": "BackgroundTo be universally applicable in treatment of severe COVID-19, novel therapies, especially those with little toxicity and low cost, are urgently needed. We report here the use of one such therapeutic combination involving two commonly used nutraceuticals, namely resveratrol and copper in patients with this disease. This study was prompted by pre-clinical reports that sepsis-related cytokine storm and fatality in mice can be prevented by oral administration of small quantities of resveratrol and copper. Since cytokine storm and sepsis are major causes of death in severe COVID-19, we retrospectively analyzed outcomes of patients with this condition who had received resveratrol and copper.\n\nMethods & FindingsOur analysis comprised of 230 patients with severe COVID-19 requiring inhaled oxygen who were admitted in a single tertiary care hospital in Mumbai between April 1 and May 13 2020. Thirty of these patients received, in addition to standard care, resveratrol and copper at doses of 5.6 mg and 560 ng, respectively, orally, once every 6 hours, until discharge or death. These doses were based on our pre-clinical studies, and were nearly 50 times and 2000 times less, respectively, than those recommended as health supplements. A multivariable-adjusted analysis was used to model the outcome of death in these patients and evaluate factors associated with this event. A binary logistic regression analysis was used, with age, sex, presence of comorbidities and receipt of resveratrol-copper as covariates. Data were updated as of May 30 2020. The number of deaths in resveratrol-copper and standard care only groups were 7/30 (23.3%, 95% CI 8.1%-38.4%) and 89/200 (44.5%, 95% CI 37.6%-51.3%), respectively. In multivariable analysis, age >50 years [odds ratio (OR) 2.558, 95% CI 1.454-4.302, P=0.0011] and female sex (OR 1.939, 95% CI 1.079-3.482, P=0.0267) were significantly associated, while presence of co-morbidities was not significantly associated (OR 0.713, 95% CI 0.405-1.256, P=0.2421) with death. There was a trend towards reduction in death in patients receiving resveratrol-copper (OR 0.413, 95% CI 0.164-1.039, P= 0.0604).\n\nConclusionsWe provide preliminary results of a novel approach to the treatment of severe COVID-19 using a combination of small amounts of commonly used nutraceuticals, which is non-toxic and inexpensive, and therefore could be widely accessible globally. The nearly two-fold reduction in mortality with resveratrol-copper observed in our study needs to be confirmed in a randomized controlled trial.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Indraneel Mittra", - "author_inst": "Tata Memorial Centre, Mumbai, India" - }, - { - "author_name": "Rosemarie de Souza", - "author_inst": "BYL Nair Charitable Hospital, Mumbai, India" - }, - { - "author_name": "Rakesh Bhadade", - "author_inst": "BYL Nair Charitable Hospital, Mumbai, India" - }, - { - "author_name": "Tushar Madke", - "author_inst": "BYL Nair Charitable Hospital, Mumbai, India" - }, - { - "author_name": "P.D. Shankpal", - "author_inst": "BYL Nair Charitable Hospital, Mumbai, India" - }, - { - "author_name": "Mohan Joshi", - "author_inst": "BYL Nair Charitable Hospital, Mumbai, India" - }, - { - "author_name": "Burhanuddin Qayyumi", - "author_inst": "Tata Memorial Center, Mumbai, India" - }, - { - "author_name": "Atanu Bhattacharya", - "author_inst": "Tata Memorial Center, Mumbai, India" - }, - { - "author_name": "Vikram Gota", - "author_inst": "Tata Memorial Center, Mumbai, India" - }, - { - "author_name": "Sudeep Gupta", - "author_inst": "Tata Memorial Center, Mumbai, India." - }, - { - "author_name": "Pankaj Chaturvedi", - "author_inst": "Tata Memorial Center, Mumbai, India." - }, - { - "author_name": "Rajendra Badwe", - "author_inst": "Tata Memorial Centre, Mumbai, India" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.25.20161091", "rel_title": "Baseline Cardiometabolic Profiles and SARS-CoV-2 Risk in the UK Biobank", @@ -1259490,6 +1261726,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.26.20162420", + "rel_title": "Persistent heterogeneity not short-term overdispersion determines herd immunity to COVID-19", + "rel_date": "2020-07-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.26.20162420", + "rel_abs": "Epidemics generally spread through a succession of waves that reflect factors on multiple time-scales. On short time-scales, superspreading events lead to burstiness and overdispersion, while long-term persistent heterogeneity in susceptibility is expected to lead to a reduction in the infection peak and the herd immunity threshold (HIT). Here, we develop a general approach to encompass both time-scales, including time variations in individual social activity, and demonstrate how to incorporate them phenomenologically into a wide class of epidemiological models through parameterization. We derive a non-linear dependence of the effective reproduction number Re on the susceptible population fraction S. We show that a state of transient collective immunity (TCI) emerges well below the HIT during early, high-paced stages of the epidemic. However, this is a fragile state that wanes over time due to changing levels of social activity, and so the infection peak is not an indication of herd immunity: subsequent waves can and will emerge due to behavioral changes in the population, driven (e.g.) by seasonal factors. Transient and long-term levels of heterogeneity are estimated by using empirical data from the COVID-19 epidemic as well as from real-life face-to-face contact networks. These results suggest that the hardest-hit areas, such as NYC, have achieved TCI following the first wave of the epidemic, but likely remain below the long-term HIT. Thus, in contrast to some previous claims, these reqions can still experience subsequent waves.\n\nO_TEXTBOXSignificance Statement\n\nEpidemics generally spread through a succession of waves that reflect factors on multiple time-scales. Here, we develop a general approach to encompass super-spreading and population heterogeneity, and demonstrate that a fragile state of transient collective immunity (TCI) emerges well below the HIT during early, high-paced stages of the epidemic. However, this is not an indication of herd immunity: subsequent waves can and will emerge due to behavioral changes in the population, driven (e.g.) by seasonal factors. Analysis of empirical data suggests that even in locations with strong first waves of COVID-19, subsequent waves will still emerge.\n\nC_TEXTBOX", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Alexei V Tkachenko", + "author_inst": "Brookhaven National Laboratory" + }, + { + "author_name": "Sergei Maslov", + "author_inst": "University of Illinois at Urbana-Champaign" + }, + { + "author_name": "Ahmed Elbanna", + "author_inst": "University of Illinois at Urbana-Champaign" + }, + { + "author_name": "George N Wong", + "author_inst": "University of Illinois at Urbana-Champaign" + }, + { + "author_name": "Zachary J Weiner", + "author_inst": "University of Illinois at Urbana-Champaign" + }, + { + "author_name": "Nigel Goldenfeld", + "author_inst": "University of Illinois at Urbana-Champaign" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.26.20162495", "rel_title": "Impact of the COVID-19 Pandemic on the Short-term Course of Obsessive-Compulsive Disorder", @@ -1260394,177 +1262669,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.27.20162693", - "rel_title": "Seroprevalence of anti-SARS-CoV-2 IgG antibodies in Kenyan blood donors", - "rel_date": "2020-07-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.27.20162693", - "rel_abs": "BackgroundThere are no data on SARS-CoV-2 seroprevalence in Africa though the COVID-19 epidemic curve and reported mortality differ from patterns seen elsewhere. We estimated the anti-SARS-CoV-2 antibody prevalence among blood donors in Kenya.\n\nMethodsWe measured anti-SARS-CoV-2 spike IgG prevalence by ELISA on residual blood donor samples obtained between April 30 and June 16, 2020. Assay sensitivity and specificity were 83% (95% CI 59-96%) and 99.0% (95% CI 98.1-99.5%), respectively. National seroprevalence was estimated using Bayesian multilevel regression and post-stratification to account for non-random sampling with respect to age, sex and region, adjusted for assay performance.\n\nResultsComplete data were available for 3098 of 3174 donors, aged 15-64 years. By comparison with the Kenyan population, the sample over- represented males (82% versus 49%), adults aged 25-34 years (40% versus 27%) and residents of coastal Counties (49% versus 9%). Crude overall seroprevalence was 5.6% (174/3098). Population-weighted, test- adjusted national seroprevalence was 5.2% (95% CI 3.7- 7.1%). Seroprevalence was highest in the 3 largest urban Counties - Mombasa (9.3% [95% CI 6.4-13.2%)], Nairobi (8.5% [95% CI 4.9-13.5%]) and Kisumu (6.5% [95% CI 3.3-11.2%]).\n\nConclusionsWe estimate that 1 in 20 adults in Kenya had SARS-CoV-2 antibodies during the study period. By the median date of our survey, only 2093 COVID-19 cases and 71 deaths had been reported through the national screening system. This contrasts, by several orders of magnitude, with the numbers of cases and deaths reported in parts of Europe and America when seroprevalence was similar.", - "rel_num_authors": 39, - "rel_authors": [ - { - "author_name": "Sophie Uyoga", - "author_inst": "KEMRI Wellcome Trust Research Programme, Kenya" - }, - { - "author_name": "Ifedayo M.O. Adetifa", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kenya. Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, UK" - }, - { - "author_name": "Henry K. Karanja", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kenya" - }, - { - "author_name": "James Nyagwange", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kenya" - }, - { - "author_name": "James Tuju", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kenya" - }, - { - "author_name": "Perpetual Wanjiku", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kenya" - }, - { - "author_name": "Rashid Aman", - "author_inst": "Ministry of Health, Government of Kenya" - }, - { - "author_name": "Mercy Mwangangi", - "author_inst": "Ministry of Health, Government of Kenya" - }, - { - "author_name": "Patrick Amoth", - "author_inst": "Ministry of Health, Government of Kenya" - }, - { - "author_name": "Kadondi Kasera", - "author_inst": "Ministry of Health, Government of Kenya" - }, - { - "author_name": "Wangari Ng'ang'a", - "author_inst": "Presidential Policy & Strategy Unit, The Presidency, Government of Kenya" - }, - { - "author_name": "Charles Rombo", - "author_inst": "Kenya National Blood Transfusion Services" - }, - { - "author_name": "Christine K. Yegon", - "author_inst": "Kenya National Blood Transfusion Services" - }, - { - "author_name": "Khamisi Kithi", - "author_inst": "Kenya National Blood Transfusion Services" - }, - { - "author_name": "Elizabeth Odhiambo", - "author_inst": "Kenya National Blood Transfusion Services" - }, - { - "author_name": "Thomas Rotich", - "author_inst": "Kenya National Blood Transfusion Services" - }, - { - "author_name": "Irene Orgut", - "author_inst": "Kenya National Blood Transfusion Services" - }, - { - "author_name": "Sammy Kihara", - "author_inst": "Kenya National Blood Transfusion Services" - }, - { - "author_name": "Mark Otiende", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Christian Bottomley", - "author_inst": "Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, UK" - }, - { - "author_name": "Zonia N. Mupe", - "author_inst": "KEMRI-Wellcome Trust Research Programme,Kenya" - }, - { - "author_name": "Eunice W. Kagucia", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kenya" - }, - { - "author_name": "Katherine Gallagher", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kenya" - }, - { - "author_name": "Anthony Etyang", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kenya" - }, - { - "author_name": "Shirine Voller", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kenya" - }, - { - "author_name": "John Gitonga", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kenya" - }, - { - "author_name": "Daisy Mugo", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kenya" - }, - { - "author_name": "Charles N. Agoti", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kenya" - }, - { - "author_name": "Edward Otieno", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kenya" - }, - { - "author_name": "Leonard Ndwiga", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kenya" - }, - { - "author_name": "Teresa Lambe", - "author_inst": "Nuffield Department of Medicine, Oxford University, UK" - }, - { - "author_name": "Daniel Wright", - "author_inst": "Nuffield Department of Medicine, Oxford University, UK" - }, - { - "author_name": "Edwine Barasa", - "author_inst": "KEMRI-Wellcome Trust Research Programme" - }, - { - "author_name": "Benjamin Tsofa", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kenya" - }, - { - "author_name": "Philip Bejon", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kenya. Nuffield Department of Medicine, Oxford University, UK" - }, - { - "author_name": "Lynette I. Ochola-Oyier", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kenya" - }, - { - "author_name": "Ambrose Agweyu", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kenya" - }, - { - "author_name": "J. Anthony G. Scott", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kenya. Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, UK" - }, - { - "author_name": "George M Warimwe", - "author_inst": "KEMRI-Wellcome Trust Research Programme" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.27.20162123", "rel_title": "Computer-aided medical microbiology monitoring tool: a strategy to adapt to the SARS-CoV-2 epidemic and that highlights RT-PCR consistency", @@ -1261136,6 +1263240,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.07.27.20163196", + "rel_title": "Whence the next pandemic? The intersecting global geography of the animal-human interface, poor health systems and air transit centrality reveals conduits for high-impact spillover", + "rel_date": "2020-07-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.27.20163196", + "rel_abs": "The health and economic impacts of infectious disease pandemics are catastrophic as most recently manifested by coronavirus disease 2019 (COVID-19). The emerging infections that lead to substantive epidemics or pandemics are typically zoonoses that cross species boundaries at vulnerable points of animal-human interface. The sharing of space between wildlife and humans, and their domesticated animals, has dramatically increased in recent decades and is a key driver of pathogen spillover. Increasing animal-human interface has also occurred in concert with both increasing globalisation and failing health systems, resulting in a trifecta with dire implications for human and animal health. Nevertheless, to date we lack a geographical description of this trifecta that can be applied strategically to pandemic prevention. This investigation provides the first geographical quantification of the intersection of animal-human interfaces, poor human health system performance and global connectivity via the network of air travel. In so doing, this work provides a systematic, data-driven approach to classifying spillover hazard based on the distribution of animal-human interfaces while simultaneously identifying globally connected cities that are adjacent to these interfaces and which may facilitate global pathogen dissemination. We present this geography of high-impact spillover as a tool for developing targeted surveillance systems and improved health infrastructure in vulnerable areas that may present conduits for future pandemics.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Michael G Walsh", + "author_inst": "Faculty of Medicine, University of Sydney" + }, + { + "author_name": "Shailendra Sawleshwarkar", + "author_inst": "Faculty of Medicine, University of Sydney" + }, + { + "author_name": "Shah Hossain", + "author_inst": "Manipal Academy of Higher Education" + }, + { + "author_name": "Siobhan Mor", + "author_inst": "Faculty of Health and Life Sciences, University of Liverpool" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.07.27.20163188", "rel_title": "Cell-Free DNA in Blood Reveals Significant Cell, Tissue and Organ Specific injury and Predicts COVID-19 Severity", @@ -1262264,29 +1264399,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.25.20162131", - "rel_title": "A Bayesian Framework for Estimating the Risk Ratio of Hospitalization for People with Comorbidity Infected by the SARS-CoV-2 Virus", - "rel_date": "2020-07-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.25.20162131", - "rel_abs": "Estimating the hospitalization risk for people with certain comorbidities infected by the SARS-CoV-2 virus is important for developing public health policies and guidance based on risk stratification. Traditional biostatistical methods require knowing both the number of infected people who were hospitalized and the number of infected people who were not hospitalized. However, the latter may be undercounted, as it is limited to only those who were tested for viral infection. In addition, comorbidity information for people not hospitalized may not always be readily available for traditional biostatistical analyses. To overcome these limitations, we developed a Bayesian approach that only requires the observed frequency of comorbidities in COVID-19 patients in hospitals and the prevalence of comorbidities in the general population. By applying our approach to two different large-scale datasets in the U.S., our results consistently indicated that cardiovascular diseases carried the highest hospitalization risk for COVID-19 patients, followed by diabetes, chronic respiratory disease, hypertension, and obesity, respectively.\n\nSignificance StatementWe developed a novel Bayesian approach to estimate the hospitalization risk for people with comorbidities infected with the SARS-CoV-2 virus. Our results indicated that cardiovascular diseases carried the highest hospitalization risk for COVID-19 patients, followed by diabetes, chronic respiratory disease, hypertension, and obesity, respectively.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Xiang Gao", - "author_inst": "Loyola University Chicago" - }, - { - "author_name": "Qunfeng Dong", - "author_inst": "Loyola University Chicago" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.26.20158618", "rel_title": "Does sampling saliva increase detection of SARS-CoV-2 by RT-PCR? Comparing saliva with oro-nasopharyngeal swabs", @@ -1262922,6 +1265034,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.25.20161919", + "rel_title": "Impact of climatic parameters on COVID-19 pandemic progression in India: analysis and prediction", + "rel_date": "2020-07-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.25.20161919", + "rel_abs": "The COVID-19 is spreading very fast globally and various factors of it have to be analysed. The aim of this study is to analyze the effect of climatic parameters (Average Temperature (AT), Atmospheric Pressure (AP), Relative Humidity (RH), Solar Radiation (SR) and Wind Speed (WS)) on the COVID-19 epidemic during 25 March 2020 to 15 June 2020 in most affected states of India i.e. Maharashtra, Delhi and Tamilnadu. We quantitatively establish the correlation between these parameters by using Kendall & Spearman rank correlation test. The results indicate that the numbers of cases are highly correlated with the AT (r2 > 0.6, p < 0.001) in Delhi where as a moderate correlation (r2 > 0.6, p < 0.001) has been estimated for Maharashtra and Tamilnadu. Similarly, an intermediate range of correlation coefficient has been observed for other climatic parameters. A comparative study of climatic parameters in the current COVID-19 period with previous two years (2018-2019) has been carried out. Corresponding results imply a substantial trend for all three states. The range of climatic parameters have been found corresponding to maximum number of cases results as AT (25[~] 40 {degrees} C), RH (40[~]70%), AT (740[~]965 mmHg), SR (200-250 W/mt 2) and WS (.5[~]14 m/sec). Time series analysis depicts that the number of cases and mortality are increasing rapidly. COVID-19 epidemic peak has been predicted by SIR model for capital of India (New Delhi) and it would be around October 2020. The outcomes of this study will be helpful for the containment of COVID- 19 not only in India but globally.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Namrata Deyal", + "author_inst": "Department of Physics, KU, SSJ campus Almora (263601), Uttarakhand (India)" + }, + { + "author_name": "Vipin Tiwari", + "author_inst": "Department of Physics, KU, SSJ campus Almora (263601), Uttarakhand (India)" + }, + { + "author_name": "Nandan Bisht", + "author_inst": "Department of Physics, KU, SSJ campus Almora (263601), Uttarakhand (India)" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.26.20158550", "rel_title": "Association of olfactory dysfunction with hospitalization for COVID-19: a multicenter study in Kurdistan", @@ -1263838,221 +1265977,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.07.24.20161802", - "rel_title": "An effective COVID-19 response in South America: the Uruguayan Conundrum", - "rel_date": "2020-07-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.24.20161802", - "rel_abs": "BackgroundSouth America has become the new epicenter of the COVID-19 pandemic with more than 1.1M reported cases and >50,000 deaths (June 2020). Conversely, Uruguay stands out as an outlier managing this health crisis with remarkable success.\n\nMethodsWe developed a molecular diagnostic test to detect SARS-CoV-2. This methodology was transferred to research institutes, public hospitals and academic laboratories all around the country, creating a \"COVID-19 diagnostic lab network\". Uruguay also implemented active epidemiological surveillance following the \"Test, Trace and Isolate\" (TETRIS) strategy coupled to real-time genomic epidemiology.\n\nResultsThree months after the first cases were detected, the number of positive individuals reached 826 (23 deaths, 112 active cases and 691 recovered). The Uruguayan strategy was based in a close synergy established between the national health authorities and the scientific community. In turn, academia rapidly responded to develop national RT-qPCR tests. Consequently, Uruguay was able to perform [~]1,000 molecular tests per day in a matter of weeks. The \"COVID-19 diagnostic lab network\" performed more than 54% of the molecular tests in the country. This, together with real- time genomics, were instrumental to implement the TETRIS strategy, helping to contain domestic transmission of the main outbreaks registered so far.\n\nConclusionsUruguay has successfully navigated the first trimester of the COVID-19 health crisis in South America. A rapid response by the scientific community to increase testing capacity, together with national health authorities seeking out the support from the academia were fundamental to successfully contain, until now, the COVID-19 outbreak in the country.", - "rel_num_authors": 50, - "rel_authors": [ - { - "author_name": "Pilar Moreno", - "author_inst": "Institut Pasteur de Montevideo Facultad de Ciencias, Udelar" - }, - { - "author_name": "Gonzalo Andres Moratorio", - "author_inst": "Institut Pasteur de Montevideo Facultad de Ciencias, Udelar" - }, - { - "author_name": "Gregorio Iraola", - "author_inst": "Institut Pasteur de Montevideo" - }, - { - "author_name": "Alvaro Fajardo", - "author_inst": "Institut Pasteur de Montevideo Facultad de Ciencias, Udelar" - }, - { - "author_name": "Fabian Aldunate", - "author_inst": "Institut Pasteur de Montevideo Facultad de Ciencias, Udelar" - }, - { - "author_name": "Marianoel Pereira", - "author_inst": "Institut Pasteur de Montevideo Facultad de Ciencias, Udelar" - }, - { - "author_name": "Paula Perbolianachis", - "author_inst": "Institut Pasteur de Montevideo Facultad de Ciencias, Udelar" - }, - { - "author_name": "Alicia Costabile", - "author_inst": "Institut Pasteur de Montevideo Facultad de Ciencias, Udelar" - }, - { - "author_name": "Fernando Lopez-Tort", - "author_inst": "Centro Universitario Regional Norte, Udelar" - }, - { - "author_name": "Diego Simon", - "author_inst": "Institut Pasteur de Montevideo Facultad de Ciencias, Udelar" - }, - { - "author_name": "Cecilia Salazar", - "author_inst": "Institut Pasteur de Montevideo" - }, - { - "author_name": "Ignacio Ferres", - "author_inst": "Institut Pasteur de Montevideo" - }, - { - "author_name": "Florencia Diaz-Viraque", - "author_inst": "Institut Pasteur de Montevideo" - }, - { - "author_name": "Andres Abin", - "author_inst": "Institut Pasteur de Montevideo ATGen Biotech" - }, - { - "author_name": "Mariana Bresque", - "author_inst": "Institut Pasteur de Montevideo" - }, - { - "author_name": "Matias Fabregat", - "author_inst": "Institut Pasteur de Montevideo" - }, - { - "author_name": "Matias Maidana", - "author_inst": "Instituto Nacional de Investigacion Agropecuaria" - }, - { - "author_name": "Bernardina Rivera", - "author_inst": "Institut Pasteur de Montevideo Hospital Maciel" - }, - { - "author_name": "Maria Cruces", - "author_inst": "Institut Pasteur de Montevideo" - }, - { - "author_name": "Jorge Rodriguez", - "author_inst": "Institut Pasteur de Montevideo" - }, - { - "author_name": "Paola Scavone", - "author_inst": "IIBCE" - }, - { - "author_name": "Miguel Alegretti", - "author_inst": "MSP" - }, - { - "author_name": "Adriana Nabon", - "author_inst": "MSP" - }, - { - "author_name": "Gustavo Gagliano", - "author_inst": "MSP" - }, - { - "author_name": "Raquel Rosa", - "author_inst": "MSP" - }, - { - "author_name": "Eduardo Henderson", - "author_inst": "ASSE" - }, - { - "author_name": "Estela Bidegain", - "author_inst": "Hospital Maciel ASSE" - }, - { - "author_name": "Leticia Zarantonelli", - "author_inst": "Institut Pasteur de Montevideo" - }, - { - "author_name": "Claudia Piattoni", - "author_inst": "Institut Pasteur de Montevideo" - }, - { - "author_name": "Gonzalo Greif", - "author_inst": "Institut Pasteur de Montevideo" - }, - { - "author_name": "Maria Francia", - "author_inst": "Institut Pasteur de Montevideo Facultad de Medicina, Udelar" - }, - { - "author_name": "Carlos Robello", - "author_inst": "Institut Pasteur de Montevideo Facultad de Medicina, Udelar" - }, - { - "author_name": "Rosario Duran", - "author_inst": "Institut Pasteur de Montevideo IIBCE" - }, - { - "author_name": "Gustavo Brito", - "author_inst": "INIA" - }, - { - "author_name": "Victoria Bonnecarrere", - "author_inst": "INIA" - }, - { - "author_name": "Miguel Sierra", - "author_inst": "INIA" - }, - { - "author_name": "Rodney Colina", - "author_inst": "Centro Universitario Regional Norte, Udelar" - }, - { - "author_name": "Monica Marin", - "author_inst": "Facultad de Ciencias, Udelar" - }, - { - "author_name": "Juan Cristina", - "author_inst": "Facultad de Ciencias, Udelar" - }, - { - "author_name": "Ricardo Erlich", - "author_inst": "Institut Pasteur de Montevideo" - }, - { - "author_name": "Fernando Paganini", - "author_inst": "Universidad Ort" - }, - { - "author_name": "Henry Cohen", - "author_inst": "Hospital de Clinicas, Facultad de Medicina, Udelar" - }, - { - "author_name": "Rafael Radi", - "author_inst": "Facultad de Medicina, UdelaR" - }, - { - "author_name": "Luis Barbeito", - "author_inst": "Institut Pasteur de Montevideo" - }, - { - "author_name": "Jose Badano", - "author_inst": "Institut Pasteur de Montevideo" - }, - { - "author_name": "Otto Pritsch", - "author_inst": "Institut Pasteur de Montevideo Facultad de Medicina Udelar" - }, - { - "author_name": "Cecilia Fernandez", - "author_inst": "Udelar" - }, - { - "author_name": "Rodrigo Arim", - "author_inst": "Udelar" - }, - { - "author_name": "Carlos Batthyany", - "author_inst": "Institut Pasteur de Montevideo" - }, - { - "author_name": "- Interinstitutional COVID-19 Working Group", - "author_inst": "-" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.24.20051508", "rel_title": "New Insights on Excess Deaths and COVID-19", @@ -1264736,6 +1266660,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.25.20161984", + "rel_title": "Power Law in COVID-19 Cases in China", + "rel_date": "2020-07-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.25.20161984", + "rel_abs": "The novel coronavirus (COVID-19) was first identified in China in December 2019. Within a short period of time, the infectious disease has spread far and wide. This study focuses on the distribution of COVID-19 confirmed cases in China--the original epicenter of the outbreak. We show that the upper tail of COVID-19 cases in Chinese cities is well described by a power law distribution, with exponent around one in the early phases of the outbreak (when the number of cases was growing rapidly) and less than one thereafter. This finding is significant because it implies that (i) COVID-19 cases in China is heavy-tailed and disperse; (ii) a few cities account for a disproportionate share of COVID-19 cases; and (iii) the distribution generally has no finite mean or variance. We find that a proportionate random growth model predicated by Gibrats law offers a plausible explanation for the emergence of a power law in the distribution of COVID-19 cases in Chinese cities in the early phases of the outbreak.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Behzod B. Ahundjanov", + "author_inst": "University of Illionois, Chicago" + }, + { + "author_name": "Sherzod B. Akhundjanov", + "author_inst": "Utah State University" + }, + { + "author_name": "Botir B. Okhunjanov", + "author_inst": "Washington State University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.24.20161851", "rel_title": "Trends in Angiotensin Receptor Blocker Use Among those at Risk for COVID-19 Morbidity and Mortality in the United States", @@ -1265800,33 +1267751,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.07.27.223172", - "rel_title": "A-to-I RNA editing in SARS-COV-2: real or artifact?", - "rel_date": "2020-07-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.27.223172", - "rel_abs": "ADAR1-mediated deamination of adenosines in long double stranded RNAs plays an important role in modulating the innate immune response. However, recent investigations based on metatranscriptomic samples of COVID-19 patients and SARS-COV-2 infected Vero cells have recovered contrasting findings. Using RNAseq data from time course experiments of infected human cell lines and transcriptome data from Vero cells and clinical samples, we prove that A-to-G changes observed in SARS-COV-2 genomes represent genuine RNA editing events, likely mediated by ADAR1. While the A-to-I editing rate is generally low, changes are distributed along the entire viral genome, are overrepresented in exonic regions and are, in the majority of cases, nonsynonymous. The impact of RNA editing on virus-host interactions could be relevant to identify potential targets for therapeutic interventions.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Ernesto Picardi", - "author_inst": "University of Bari" - }, - { - "author_name": "Luigi Mansi", - "author_inst": "University of Bari" - }, - { - "author_name": "Graziano Pesole", - "author_inst": "University of Bari" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.07.27.223727", "rel_title": "Structure and inhibition of the SARS-CoV-2 main protease reveals strategy for developing dual inhibitors against Mpro and cathepsin L", @@ -1266610,6 +1268534,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.20.20147769", + "rel_title": "Clinical Outcomes With the Use of Prophylactic Versus Therapeutic Anticoagulation in COVID-19", + "rel_date": "2020-07-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.20.20147769", + "rel_abs": "BackgroundThis study is the first of its kind to assess the impact of preemptive therapeutic dose anticoagulation on mortality compared to prophylactic anticoagulation among COVID-19 patients. Its findings provide insight to clinicians regarding the management of COVID-19, particularly with the known prothrombotic state.\n\nResearch QuestionTo determine the impact of anticoagulation on in-hospital mortality among COVID-19 positive patients with the a priori hypothesis that there would be a lower risk of in-hospital mortality with use of preemptive therapeutic over prophylactic dose enoxaparin or heparin.\n\nStudy Design and MethodsO_ST_ABSStudy DesignC_ST_ABSRetrospective cohort study from April 1 - April 25, 2020. The date of final follow-up was June 12, 2020.\n\nSettingTwo large, acute care hospitals in Western Connecticut.\n\nParticipantFive hundred and one inpatients were identified after discharge as 18 years or older and positive for SARS-CoV-2. The final sample size included 374 patients after applying exclusion criteria. Demographic variables were collected via hospital billing inquiries, while the clinical variables were abstracted from patients medical records.\n\nExposurePreemptive enoxaparin or heparin at a therapeutic or prophylactic dose.\n\nMain OutcomIn-hospital mortality.\n\nResultsWhen comparing preemptive therapeutic to prophylactic anticoagulation through multi-variable analysis, risk of in-hospital mortality was 2.3 times greater in patients receiving preemptive therapeutic anticoagulation (95% CI = 1.0, 4.9; p = 0.04).\n\nInterpretationAn increase in in-hospital mortality was observed with preemptive therapeutic anticoagulation. Thus, in the management of COVID-19 and its complications, we recommend further research and cautious use of preemptive therapeutic over prophylactic anticoagulation.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Jishu K Motta", + "author_inst": "Danbury Hospital" + }, + { + "author_name": "Rahila O Ogunnaike", + "author_inst": "Danbury Hospital" + }, + { + "author_name": "Rutvik Shah", + "author_inst": "Danbury Hospital" + }, + { + "author_name": "Stephanie Stroever", + "author_inst": "Danbury Hospital" + }, + { + "author_name": "Harold V Cedeno", + "author_inst": "Danbury Hospital" + }, + { + "author_name": "Shyam K Thapa", + "author_inst": "Danbury Hospital" + }, + { + "author_name": "John J Chronakos", + "author_inst": "Danbury Hospital" + }, + { + "author_name": "Eric J Jimenez", + "author_inst": "Danbury Hospital" + }, + { + "author_name": "Joann Petrini", + "author_inst": "Danbury Hospital" + }, + { + "author_name": "Abhijith Hegde", + "author_inst": "Danbury Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2020.07.20.20157651", "rel_title": "A Cluster-Randomized Trial of Hydroxychloroquine as Prevention of Covid-19 Transmission and Disease", @@ -1268230,89 +1270209,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.20.20156372", - "rel_title": "Serial Profiling of SARS-CoV-2 Antigens and Antibodies in COVID-19 Patient Plasma", - "rel_date": "2020-07-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.20.20156372", - "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected millions of people worldwide. PCR tests are currently the gold standard for diagnosis of the current coronavirus disease (COVID-19) and serology tests are used to detect seroconversion in infected patients. However, there is a lack of quantitative and ultra-sensitive viral antigen tests for COVID-19. Here we show that Single Molecule Array (Simoa) assays can quantitatively detect SARS-CoV-2 spike, S1 subunit, and nucleocapsid antigens in the plasma of COVID-19 patients. Combined with Simoa anti-SARS-CoV-2 serological assays, we show correlation between production of antibodies and clearance of viral antigens from serial plasma samples from COVID-19 patients. Furthermore, we demonstrate the presence of viral antigens in blood correlates with disease severity in hospitalized COVID-19 patients. These data suggest that SARS-CoV-2 viral antigens in the blood could be a marker for severe COVID-19 cases.\n\nOne Sentence SummarySARS-CoV-2 antigens S1, spike, and nucleocapsid and anti-SARS-Cov-2 antibodies were measured in longitudinal plasma samples from COVID-19 patients using Single Molecule Array (Simoa) assays.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Alana F Ogata", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Adam M Maley", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Connie Wu", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Tal Gilboa", - "author_inst": "Harvard medical school" - }, - { - "author_name": "Maia Norman", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Roey Lazarovits", - "author_inst": "Wyss Institute" - }, - { - "author_name": "Chih-Ping Mao", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Gail Newton", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Matthew Chang", - "author_inst": "Dana-Farber Cancer Institute" - }, - { - "author_name": "Katrina Nguyen", - "author_inst": "Dana-Farber Cancer Institute" - }, - { - "author_name": "Maliwan Kamkaew", - "author_inst": "Dana-Farber Cancer Institute" - }, - { - "author_name": "Quan Zhu", - "author_inst": "Dana-Farber Cancer Institute" - }, - { - "author_name": "Travis E Gibson", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Edward Ryan", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Richelle Charles", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Wayne A Marasco", - "author_inst": "Dana-Farber Cancer Institute" - }, - { - "author_name": "David R Walt", - "author_inst": "Brigham and Women's Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.20.20155945", "rel_title": "Seroprevalence of SARS-CoV-2 IgG Antibodies in Utsunomiya City, Greater Tokyo, after first pandemic in 2020 (U-CORONA): a household- and population-based study", @@ -1269048,6 +1270944,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.22.20159590", + "rel_title": "EPICOVID19: Psychometric assessment and validation of a short diagnostic scale for a rapid Covid-19 screening based on reported symptoms", + "rel_date": "2020-07-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.22.20159590", + "rel_abs": "BackgroundConfirmed COVID-19 cases have been registered in more than two hundred countries and regions and of July 28 over 16 million cases of COVID-19, including 650805 deaths, have been reported to WHO. The number of cases changes quickly and varies depending upon which source you use to track, so in the current epidemiological context, the early recognition is critical for the rapid identification of suspected cases (with SARS-CoV-2 infection-like symptoms and signs) to be immediately subjected to quarantine measures. Although surveys are widely used for identifying COVID-19 cases, outcomes and associated risks, no validated epidemiological tool exists for surveying SARS-CoV-2 infection in the population so far.\n\nMethodsOur study is the phase II of the EPICOVID19 Italian national survey, launched in April 2020 including a national convenience sample of 201121 adults, who voluntarily filled the EPICOVID19 questionnaire. The phase II questionnaire was mailed to all subjects who underwent tests for COVID-19 by nasopharyngeal swab (NPS) and who accepted to be involved in the second phase of the study, focused on the results reported for NPS and/or serological IgG/IgM tests. We evaluated the capability of the self-reported symptoms collected through the EPICOVID19 questionnaire to discriminate the COVID-19 among symptomatic subjects, in order to identify possible cases to undergo instrumental measurements and clinical examinations. We defined a method for the identification of a total score and validated it with reference to the serological and molecular clinical diagnosis, using four standard steps: identification of critical factors, confirmation of presence of latent variable, development of optimal scoring algorithm and validation of the scoring algorithm.\n\nFindings2703 subjects [66% response rate] completed the Phase II questionnaire. Of 2703 individuals, 694 (25.7%) were NPS(+) and of these 84 (12.1% of the 694 NPS(+)) were asymptomatic. In the individuals who performed serological testing, of the 472 who did IgG(+) and 421 who did IgM(+), 22.9% and 11.6% tested positive, respectively. Among IgG(+) 1 of 108 subjects was asymptomatic (0.9%) while 5/49 subjects among IgM(+) were asymptomatic (10.2%). Compared with NPS(-), among NPS(+) subjects there was a higher rate for Fever (421 [60.7%] vs 391[19.5%]; p<0.0001), Loss of Taste and/or Smell (365 [52.6%] vs 239 [11.9%]; p<0.0001) and Cough (352 [50.7%] vs 580 [28.9%]; p<0.0001). Also for other symptoms the frequencies were significantly higher in NPS(+) subjects than in NPS(-) ones (p<0.001). Among groups with serological tests, the symptoms with higher percentages in the subjects IgG(+) were Fever (65 [60.2%] vs 43[11.8%]; p<0.0001) and Pain in muscles, bones, joints (73 [67.6%] vs 71 [19.5%]; p<0.0001). For the COVID-19 self-reported symptoms items, exploratory (proportion variance explained [89.9%]) and confirmatory factor analysis results (SMSR 0.072; RMSEA 0.052) highlights the presence of one latent variable (factor) underlying the symptoms. We define the one-factor solution as EPICOVID19 diagnostic scale and optimal score for each items was identified: Respiratory problems (1.03), Chest pain (1.07), Loss of Taste and/or Smell (0.97) and Tachycardia (palpitations) (1.05) were the most important symptoms.\n\nThe cut-off score was 2.56 (Sensitivity 76.56%; Specificity 68.24%) in NPS(+) and 2.59 (Se 80.37; Sp 80.17) in IgG(+) subjects.\n\nInterpretationWe developed a short diagnostic scale to detect subjects with symptoms potentially associated with COVID-19 among a wide population. Early recognition screening and rapid diagnosis are essential to prevent transmission and provide supportive care in a timely manner and our score supports the potential for identifying individuals who need to seek immediate clinical evaluation. Although these results are referred to the Italian pandemic period, this short diagnostic scale could be optimised and tested as a screening tool in other similar pandemic contexts.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Luca Bastiani", + "author_inst": "National Research Council, Institute of Clinical Physiology" + }, + { + "author_name": "Loredana Fortunato", + "author_inst": "National Research Council, Institute of Clinical Physiology" + }, + { + "author_name": "Stefania Pieroni", + "author_inst": "National Research Council, Institute of Clinical Physiology" + }, + { + "author_name": "Fabrizio Bianchi", + "author_inst": "National Research Council, Institute of Clinical Physiology" + }, + { + "author_name": "Fulvio Adorni", + "author_inst": "National Research Council, Institute of Biomedical Technologies" + }, + { + "author_name": "Federica Prinelli", + "author_inst": "National Research Council, Institute of Biomedical Technologies" + }, + { + "author_name": "Andrea Giacomelli", + "author_inst": "ASST-FBF-Sacco, University of Milan" + }, + { + "author_name": "Gabriele Pagani", + "author_inst": "Infectious Diseases Unit, Department of Biomedical and Clinical Sciences L.Sacco" + }, + { + "author_name": "Stefania Maggi", + "author_inst": "National Research Council, Institute of Neuroscience" + }, + { + "author_name": "Caterina Trevisan", + "author_inst": "University of Padova, Department of Medicine (DIMED)" + }, + { + "author_name": "Marianna Noale", + "author_inst": "National Research Council, Institute of Neuroscience" + }, + { + "author_name": "Nithiya Jesuthasan", + "author_inst": "National Research Council, Institute of Biomedical Technologies" + }, + { + "author_name": "Aleksandra Sojic", + "author_inst": "National Research Council, Institute of Biomedical Technologies" + }, + { + "author_name": "Carla Pettenati", + "author_inst": "National Research Council, Institute of Biomedical Technologies" + }, + { + "author_name": "Massimo Andreoni", + "author_inst": "Infectious Diseases Clinic, Department of System Medicine" + }, + { + "author_name": "Raffaele Antonelli Incalzi", + "author_inst": "Unit of Geriatrics, Department of Medicine, Biomedical Campus of Rome" + }, + { + "author_name": "Massimo Galli", + "author_inst": "Infectious Diseases Unit, Department of Biomedical and Clinical Sciences L.Sacco" + }, + { + "author_name": "Sabrina Molinaro", + "author_inst": "National Research Council, Institute of Clinical Physiology" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.22.20159806", "rel_title": "Estimating Variation of Covid-19 infection in the Population:Results from Understanding Society (UKHLS) first monthly covid-19 survey", @@ -1269876,29 +1271859,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.21.20159046", - "rel_title": "TESTING INFORMED SIR BASED EPIDEMIOLOGICAL MODEL FOR COVID-19 IN LUXEMBOURG", - "rel_date": "2020-07-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.21.20159046", - "rel_abs": "The interpretation of the number of COVID-19 cases and deaths in a country or region is strongly dependent on the number of performed tests. We developed a novel SIR based epidemiological model (SIVRT) which allows the country-specific integration of testing information and other available data. The model thereby enables a dynamic inspection of the pandemic and allows estimating key figures, like the number of overall detected and undetected COVID-19 cases and the infection fatality rate. As proof of concept, the novel SIVRT model was used to simulate the first phase of the pandemic in Luxembourg. An overall number of infections of 13.000 and an infection fatality rate of 1,3% was estimated, which is in concordance with data from population-wide testing. Furthermore based on the data as of end of May 2020 and assuming a partial deconfinement, an increase of cases is predicted from mid of July 2020 on. This is consistent with the current observed rise and shows the predictive potential of the novel SIVRT model.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Thomas Sauter", - "author_inst": "University of Luxembourg" - }, - { - "author_name": "Maria Pires Pacheco", - "author_inst": "University of Luxembourg" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.22.20158949", "rel_title": "Impact of Restrictions on Parental Presence in Neonatal Intensive Care Units Related to COVID-19", @@ -1270578,6 +1272538,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.21.20158303", + "rel_title": "Threshold analyses on rates of testing, transmission, and contact for COVID-19 control in a university setting", + "rel_date": "2020-07-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.21.20158303", + "rel_abs": "We simulated epidemic projections of a potential COVID-19 outbreak in a residential university population in the United States under varying combinations of asymptomatic tests (5% to 33% per day), transmission rates (2.5% to 14%), and contact rates (1 to 25), to identify the contact rate threshold that, if exceeded, would lead to exponential growth in infections. Using this, we extracted contact rate thresholds among non-essential workers, population size thresholds in the absence of vaccines, and vaccine coverage thresholds. We further stream-lined our analyses to transmission rates of 5 to 8%, to correspond to the reported levels of face-mask-use/physical-distancing during the 2020 pandemic.\n\nOur results suggest that, in the absence of vaccines, testing alone without reducing population size would not be sufficient to control an outbreak. If the population size is lowered to 34% (or 44%) of the actual population size to maintain contact rates at 4 (or 7) among non-essential workers, mass tests at 25% (or 33%) per day would help control an outbreak. With the availability of vaccines, the campus can be kept at full population provided at least 95% are vaccinated. If vaccines are partially available such that the coverage is lower than 95%, keeping at full population would require asymptomatic testing, either mass tests at 25% per day if vaccine coverage is at 63-79%, or mass tests at 33% per day if vaccine coverage is at 53-68%. If vaccine coverage is below 53%, to control an outbreak, in addition to mass tests at 33% per day, it would also require lowering the population size to 90%, 75%, and 60%, if vaccine coverage is at 38-53%, 23-38%, and below 23%, respectively.\n\nThreshold estimates from this study, interpolated over the range of transmission rates, can collectively help inform campus level preparedness plans for adoption of face mask/physical-distancing, testing, remote instructions, and personnel scheduling, during non-availability or partial-availability of vaccines, in the event of SARS-Cov2-type disease outbreaks.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Xinmeng Zhao", + "author_inst": "University of Massachusetts Amherst" + }, + { + "author_name": "Hanisha Anand Tatapudi", + "author_inst": "University of South Florida" + }, + { + "author_name": "George Corey", + "author_inst": "University of Massachusetts, Amherst" + }, + { + "author_name": "Chaitra Gopalappa", + "author_inst": "University of Massachusetts, Amherst" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.20.20158147", "rel_title": "Acute Shortage Ventilator", @@ -1271362,29 +1273353,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.21.20159236", - "rel_title": "We are at risk too: The disparate impacts of the pandemic on younger generations", - "rel_date": "2020-07-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.21.20159236", - "rel_abs": "BackgroundThe COVID-19 pandemic has resulted in profound global impact with high rates of morbidity and mortality. It is essential to understand the psychosocial impacts of the pandemic to identify appropriate prevention and intervention targets. Across generational groups, this study examined: (1) rates of precautions and adaptive and maladaptive health behaviours, (2) differences in levels of anxiety, and (3) rates of and changes in COVID-related concerns over time during the early outbreak of COVID-19 in Canada.\n\nMethodsWe analyzed data from two Canadian population-based datasets: the Canadian Perspective Survey Series: Impact of COVID-19 survey (N=4,627; March 29-April 3, 2020), and Crowdsourcing: Impacts of COVID-19 on Canadians - Your Mental Health (N=45,989; April 24-May 11, 2020). We categorized generational age group, participants self-reported changes in behaviours and COVID-related concerns, and a validated measure assessed anxiety symptoms.\n\nResultsThere are age differences in behavioural responses to the pandemic; adaptive health habits (e.g., exercise) were stable across groups, while maladaptive health habits (e.g., substance use) were highest among younger groups. COVID-related precautions were also highest among the younger generations, with Generation X exhibiting the highest rate of precautionary behaviour. Results also revealed that anxiety and worry are prevalent in response to the pandemic across all generations, with the highest rate of clinically significant anxiety among Millennials (36.0%). Finally, COVID-related concerns are greatest for younger generations and appear to be decreasing with time.\n\nConclusionThese early data are essential in understanding at-risk groups given the unpredictable nature of the pandemic and its potential long-term implications.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Renee El-Gabalawy", - "author_inst": "University of Manitoba" - }, - { - "author_name": "Jordana Sommer", - "author_inst": "University of Manitoba" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.07.21.20159301", "rel_title": "Prevalence and clinical correlates of COVID-19 outbreak among healthcare workers in a tertiary level hospital", @@ -1272196,6 +1274164,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.24.20161257", + "rel_title": "Distributional challenges regarding data on death and incidences during the SARS-CoV-2 pandemic up to July 2020", + "rel_date": "2020-07-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.24.20161257", + "rel_abs": "COVID-19 is a major global crisis with unpredictable consequences. Many scientists have struggled to make forecasts about its impact. Especially, appropriate preparations for a second wave are needed not to move in a costly panic mode again. It is necessary to get ideas about worst case scenarios regarding incidences, hospitalization, or use of ICU resources. They can be described in terms of extreme quantiles (95%, 99%, 99.9%) of specific distributions that supposedly formalize the data mechanism behind future observations.\n\nTherefore, distributional issues do matter. Cirillo and Taleb argue that a natural and empirically correct framework for assessing and managing real risk in pandemics is provided by extreme value theory dealing with extrema and not averages. We explore this idea in more detail.\n\nIn this paper we discuss the fat-tail patterns in the distribution of the global COVID-19 data by analyzing data from 66 countries worldwide. We also explore their relevance at a lower, regional scale perspective (national, federal state), which is in our opinion more relevant for planning measures against the epidemic spread. For this we analyze data from the German federal state of Bavaria.\n\nWe conclude that fat-tail patterns are seen in global data, possibly reflecting the respective heterogeneity between different countries regarding incidences and fatalities during the ongoing epidemic. However, the disease activity at regional level seems to be better described by classical Poisson based models. To bridge the gap between regional and global phenomena we refer to mixtures of slim-tail distributions that may create fat-tail features.\n\nEspecially in the beginning of a pandemic acting according to the \"better safe than sorry\" principle and taking extreme forecasts as the basis for the decisions might be justified. However, as the pandemic continues and control measures are partially lifted, there is a need for a careful discussion how to choose relevant distributions and their respective quantiles for future resource planning in order not to cause more harm as the pandemic itself.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Kirsi Manz", + "author_inst": "Ludwig Maximilians University Munich" + }, + { + "author_name": "Ulrich Mansmann", + "author_inst": "Ludwig Maximilians University Munich" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.23.20161240", "rel_title": "Rhythmic components of COVID-19 daily cases in various countries", @@ -1272900,33 +1274891,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.23.20161026", - "rel_title": "Lifting mobility restrictions and the induced short-term dynamics of COVID-19", - "rel_date": "2020-07-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.23.20161026", - "rel_abs": "SARS-CoV-2 has now infected 15 million people and produced more than six hundred thousand deaths around the world. Due to high transmission levels, many governments implemented social-distancing measures and confinement with different levels of required compliance to mitigate the COVID-19 epidemic. In several countries, these measures were effective, and it was possible to flatten the epidemic curve and control it. In others, this objective was not or has not been achieved. In far to many cities around the world rebounds of the epidemic are occurring or, in others, plateau-like states have appeared where high incidence rates remain constant for relatively long periods of time. Nonetheless, faced with the challenge of urgent social need to reactivate their economies, many countries have decided to lift mitigation measures at times of high incidence. In this paper, we use a mathematical model to characterize the impact of short duration transmission events within the confinement period previous but close to the epidemic peak. The model describes too, the possible consequences on the disease dynamics after mitigation measures are lifted. We use Mexico City as a case study. The results show that events of high mobility may produce either a later higher peak, a long plateau with relatively constant but high incidence or the same peak as in the original baseline epidemic curve, but with a post-peak interval of slower decay. Finally, we also show the importance of carefully timing the lifting of mitigation measures. If this occurs during a period of high incidence, then the disease transmission will rapidly increase, unless the effective contact rate keeps decreasing, which will be very difficult to achieve once the population is released.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Mario Santana-Cibrian", - "author_inst": "Universidad Nacional Autonoma de Mexico" - }, - { - "author_name": "Manuel A. Acuna-Zegarra", - "author_inst": "Universidad de Sonora" - }, - { - "author_name": "Jorge X. Velasco-Hernandez", - "author_inst": "Universidad Nacional Autonoma de Mexico" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.24.20161281", "rel_title": "Strategies to reduce the risk of SARS-CoV-2 re-introduction from international travellers", @@ -1273610,6 +1275574,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2020.07.23.20160531", + "rel_title": "Superspreaders and lockdown timing explain the power law dynamics of COVID-19", + "rel_date": "2020-07-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.23.20160531", + "rel_abs": "Infectious disease outbreaks are expected to grow exponentially in time, when left unchecked Measures such as lockdown and social distancing can drastically alter the growth dynamics of the outbreak. Indeed the 2019-2020 COVID-19 outbreak is characterized by a power law growth 1. Strikingly however, the power law exponent is different across countries 2. Here I illustrate the relationship between these two extreme scenarios, exponential and power law growth, based on the impact of superspreaders and lockdown strategies to contain the outbreak. The theory predicts an inverse relationship between the power law exponent and the speed of the lockdown that is validated by the observed COVID-19 data across different countries.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Alexei Vazquez", + "author_inst": "CRUK Beatson Institute" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.23.20160853", "rel_title": "COVID-19: A Data-Driven Mean-Field-Type Game Perspective", @@ -1274290,85 +1276273,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.07.24.20160390", - "rel_title": "A multinational e-survey on the delivery of cardiology services in Africa during the COVID-19 pandemic: what should we expect after this pandemic?", - "rel_date": "2020-07-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.24.20160390", - "rel_abs": "ObjectiveTo evaluate the impact of the COVID-19 pandemic on the delivery of cardiology services in Africa.\n\nDesignCross-sectional e-survey study.\n\nSettingAfrican countries\n\nParticipantsCardiologists\n\nPrimary and Secondary outcomes measuresThe primary outcome was the change in service delivery in African cardiology units during the on-going COVID-19 pandemic. The secondary outcomes were the satisfaction of cardiologists with regards to the workload and factors associated with this satisfaction.\n\nResultsThere was a significant reduction in working time and the number of patients consulted by week during this pandemic (p<0.001). In general, there was a decrease in the overall activities in cardiovascular care delivery. The majority of cardiology services (76.5%) and consulting programs (85%) were adjusted to the pandemic. Only half of the participants were satisfied with their workload. Reconfiguration of the consultation schedule was associated with a reduced satisfaction of participants (p=0.02).\n\nConclusionsCOVID-19 is associated with an overall reduction in cardiology services rendered in Africa. Since the cardiovascular burdens continue to increase in this part of the World and the risk of cardiovascular complications linked to SARS COV2 remains unchanged cardiology, departments in Africa should anticipate a significant surge of cardiology services demanded by patients after the COVID-19 pandemic.\n\nStrengths and limitations of this studyO_LIThe study is one of the first African studies to report the impact of the COVID-19 pandemic on the delivery of cardiology services which are very important for Africans given the high prevalence of cardiovascular diseases in this continent.\nC_LIO_LIThe multinational design of the study leading to the inclusion of 14 African countries makes the results generalizable to the entire African.\nC_LIO_LIThe cross-sectional design of the study represents a major limitation as it remains impossible to either infer causality or untangle bi-directional relationships between the reduction of the delivery in cardiology services and the pandemic or participants satisfaction.\nC_LIO_LIAlso, the e-survey was drawn in English and this might have restricted the participation by some non-English African respondents due to the language barrier. Hence, perhaps contributing to the relatively small sample size of the study.\nC_LI", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Chris Nadege Nganou-Gnindjio", - "author_inst": "FMSB-UYI" - }, - { - "author_name": "Mazou Ngou Temgoua", - "author_inst": "FMSB-UYI" - }, - { - "author_name": "Liliane Mfeukeu Kuate", - "author_inst": "FMSB-UYI" - }, - { - "author_name": "Clovis Nkoke", - "author_inst": "Internal Medicine depatment, Buea" - }, - { - "author_name": "Joel Noutakdie Tochie", - "author_inst": "FMSB-UYI" - }, - { - "author_name": "Valerie Ndobo-Kue", - "author_inst": "FMSB-UYI" - }, - { - "author_name": "Amalia Owona-Nsiaguam", - "author_inst": "FMSB-UYI" - }, - { - "author_name": "Jerome Boombhi", - "author_inst": "FMSB-UYI" - }, - { - "author_name": "Richie Kipenge", - "author_inst": "Lubumbashi University Clinics, DRCongo" - }, - { - "author_name": "Urbain Huba", - "author_inst": "University Teaching Hospital, Yalgado Ouedraogo, Burkina faso" - }, - { - "author_name": "Malick Kane", - "author_inst": "National University Teaching Hospital, Fann, Senegal" - }, - { - "author_name": "Mohamed Taha el Jirari", - "author_inst": "National University Teaching Hospital, Fann, Senegal" - }, - { - "author_name": "Sylvie Ndongo-Amougou", - "author_inst": "FMSB-UYI" - }, - { - "author_name": "Ba Hamadou", - "author_inst": "FMSB-UYI" - }, - { - "author_name": "Alain Menanga", - "author_inst": "FMSB-UYI" - }, - { - "author_name": "Samuel Kingue", - "author_inst": "FMSB-UYI" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2020.07.22.20160168", "rel_title": "Decreased incidence, virus transmission capacity, and severity of COVID-19 at altitude on the American continent", @@ -1275012,6 +1276916,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.22.20160119", + "rel_title": "Decreasing median age of COVID-19 cases in the United States: changing epidemiology or changing surveillance?", + "rel_date": "2020-07-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.22.20160119", + "rel_abs": "BackgroundUnderstanding and monitoring the demographics of SARS-CoV-2 infection can inform strategies for prevention. Surveillance monitoring has suggested that the age distribution of people infected with SARS-CoV-2 has changed since the pandemic began, but no formal analysis has been performed.\n\nMethodsRetrospective review of SARS-CoV-2 molecular testing results from a national reference laboratory was performed. Result distributions by age and positivity were compared between early period (March-April 2020) and late periods (June-July 2020) of the COVID-19 pandemic. Additionally, a sub-analysis compared changing age distributions between inpatients and outpatients.\n\nResultsThere were 277,601 test results of which 19320 (7.0%) were positive. The median age of infected people declined over time (p < 0.0005). In March-April, the median age of positive people was 40.8 years (Interquartile range (IQR): 29.0 - 54.1). In June-July, the median age of positive people was 35.8 years (IQR: 24.0 - 50.2). The positivity rate of patients under 50 increased from 6.0 to 10.6 percent and the positivity rate for those over 50 decreased from 6.3 to 5.0 percent between the early and late periods. The trend was only observed for outpatient populations.\n\nConclusionsWe confirm that there is a trend toward decreasing age among persons with laboratory- confirmed SARS-CoV-2 infection, but that these trends seem to be specific to the outpatient population. Overall, this suggests that observed age-related trends are driven by changes in testing patterns rather than true changes in the epidemiology of SARS-CoV-2 infection. This calls for caution in interpretation of routine surveillance data until testing patterns stabilize.\n\nSummaryWe used national reference laboratory data to compare ages of patients tested for SARS-CoV-2 in March/April 2020 vs. June/July. Median age declined overall, but increased for inpatients, suggesting that declining age is due to changes in surveillance, not COVID-19 epidemiology.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Dina N Greene", + "author_inst": "University of Washington, Kaiser Permanente" + }, + { + "author_name": "Michael L Jackson", + "author_inst": "Kaiser Permanente Washington" + }, + { + "author_name": "David R Hillyard", + "author_inst": "University of Utah Department of Pathology and ARUP Laboratories" + }, + { + "author_name": "Julio C Delgado", + "author_inst": "University of Utah Department of Pathology and ARUP Laboratories" + }, + { + "author_name": "Robert L Schmidt", + "author_inst": "University of Utah Department of Pathology and ARUP Laboratories" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.22.20160291", "rel_title": "The collective wisdom in the COVID-19 research: comparison and synthesis of epidemiological parameter estimates in preprints and peer-reviewed articles", @@ -1275824,77 +1277763,6 @@ "type": "new results", "category": "pathology" }, - { - "rel_doi": "10.1101/2020.07.23.208041", - "rel_title": "SARS-CoV-2 receptor Angiotensin I-Converting Enzyme type 2 is expressed in human pancreatic islet \u03b2-cells and is upregulated by inflammatory stress", - "rel_date": "2020-07-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.23.208041", - "rel_abs": "Increasing evidence demonstrated that the expression of Angiotensin I-Converting Enzyme type 2 (ACE2), is a necessary step for SARS-CoV-2 infection permissiveness. In the light of the recent data highlighting an association between COVID-19 and diabetes, a detailed analysis aimed at evaluating ACE2 expression pattern distribution in human pancreas is still lacking. Here, we took advantage of INNODIA network EUnPOD biobank collection to thoroughly analyse ACE2, both at mRNA and protein level, in multiple human pancreatic tissues and using several methodologies.\n\nUsing multiple reagents and antibodies, we showed that ACE2 is expressed in human pancreatic islets, where it is preferentially expressed in subsets of insulin producing {beta}-cells. ACE2 is also is highly expressed in pancreas microvasculature pericytes and moderately expressed in rare scattered ductal cells. By using different ACE2 antibodies we showed that a recently described short-ACE2 isoform is also prevalently expressed in human {beta}-cells.\n\nFinally, using RT-qPCR, RNA-seq and High-Content imaging screening analysis, we demonstrated that pro-inflammatory cytokines, but not palmitate, increases ACE2 expression in the {beta}-cell line EndoC-{beta}H1 and in primary human pancreatic islets.\n\nTaken together, our data indicate a potential link between SARS-CoV-2 and diabetes through putative infection of pancreatic microvasculature and/or ductal cells and/or through direct {beta}-cell virus tropism.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Daniela Fignani", - "author_inst": "Diabetes Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, Siena, Italy; Fondazione Umberto Di Mario, c/o Toscana Life Sciences, Sie" - }, - { - "author_name": "Giada Licata", - "author_inst": "Diabetes Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, Siena, Italy; Fondazione Umberto Di Mario, c/o Toscana Life Sciences, Sie" - }, - { - "author_name": "Noemi Brusco", - "author_inst": "Diabetes Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, Siena, Italy; Fondazione Umberto Di Mario, c/o Toscana Life Sciences, Sie" - }, - { - "author_name": "Laura Nigi", - "author_inst": "Diabetes Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, Siena, Italy; Fondazione Umberto Di Mario, c/o Toscana Life Sciences, Sie" - }, - { - "author_name": "Giuseppina Emanuela Grieco", - "author_inst": "Diabetes Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, Siena, Italy; Fondazione Umberto Di Mario, c/o Toscana Life Sciences, Sie" - }, - { - "author_name": "Lorella Marselli", - "author_inst": "Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy" - }, - { - "author_name": "Lut Overbergh", - "author_inst": "Clinical and Experimental Endocrinology (CEE), Katholieke Universiteit Leuven (KULEUVEN), Leuven, Belgium" - }, - { - "author_name": "Conny Gysemans", - "author_inst": "Clinical and Experimental Endocrinology (CEE), Katholieke Universiteit Leuven (KULEUVEN), Leuven, Belgium" - }, - { - "author_name": "Maikel Luis Colli", - "author_inst": "ULB Center for Diabetes Research, Medical Faculty, Universite Libre de Bruxelles, Brussels, Belgium" - }, - { - "author_name": "Piero Marchetti", - "author_inst": "Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy" - }, - { - "author_name": "Chantal Mathieu", - "author_inst": "Clinical and Experimental Endocrinology (CEE), Katholieke Universiteit Leuven (KULEUVEN), Leuven, Belgium" - }, - { - "author_name": "Decio Laks Eizirik", - "author_inst": "ULB Center for Diabetes Research, Medical Faculty, Universite Libre de Bruxelles, Brussels, Belgium" - }, - { - "author_name": "Guido Sebastiani", - "author_inst": "Diabetes Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, Siena, Italy; Fondazione Umberto Di Mario, c/o Toscana Life Sciences, Sie" - }, - { - "author_name": "Francesco Dotta", - "author_inst": "Diabetes Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, Siena, Italy; Fondazione Umberto Di Mario, c/o Toscana Life Sciences, Sie" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2020.07.22.216648", "rel_title": "Rapid in vitro assays for screening neutralizing antibodies and antivirals against SARS-CoV-2", @@ -1276562,6 +1278430,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.21.20158758", + "rel_title": "Temporal dynamics of human respiratory and gut microbiomes during the course of COVID-19 in adults", + "rel_date": "2020-07-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.21.20158758", + "rel_abs": "SARS-CoV-2 infects multiple organs including the respiratory tract and gut. Whether regional microbiomes are disturbed significantly to affect the disease progression of COVID-19 is largely unknown. To address this question, we performed cross-sectional and longitudinal analyses of throat and anal swabs from 35 COVID-19 adults and 15 controls by 16S rRNA gene sequencing. The results allowed a partitioning of patients into 3-4 categories (I-IV) with distinct microbial community types in both sites. Lower-diversity community types often appeared in the early phase of COVID-19, and synchronous fast restoration of both the respiratory and gut microbiomes from early dysbiosis towards late near-normal was observed in 6/8 mild COVID-19 adult patients despite they had a relatively slow clinical recovery. The synchronous shift of the community types was associated with significantly positive bacterial interactions between the respiratory tract and gut, possibly along the airway-gut axis. These findings reveal previously unknown interactions between respiratory and gut microbiomes, and suggest that modulations of regional microbiota might help to improve the recovery from COVID-19 in adult patients.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Rong Xu", + "author_inst": "Institut Pasteur of Shanghai, Chinese Academy of Sciences" + }, + { + "author_name": "Renfei Lu", + "author_inst": "Nantong Third Hospital Affiliated to Nantong University" + }, + { + "author_name": "Tao Zhang", + "author_inst": "Yunnan University" + }, + { + "author_name": "Qunfu Wu", + "author_inst": "Yunnan University" + }, + { + "author_name": "Weihua Cai", + "author_inst": "Nantong Third Hospital Affiliated to Nantong University" + }, + { + "author_name": "Xudong Han", + "author_inst": "Nantong Third Hospital Affiliated to Nantong University" + }, + { + "author_name": "Xia Jin", + "author_inst": "Shanghai Public Health Clinical Center" + }, + { + "author_name": "Zhigang Zhang", + "author_inst": "Yunnan University" + }, + { + "author_name": "Chiyu Zhang", + "author_inst": "Shanghai Public Health Clinical Center" + }, + { + "author_name": "Zhenzhou Wan", + "author_inst": "Medical Laboratory of Taizhou Fourth People's Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.21.20158782", "rel_title": "Real-time IP-10 measurements as a new tool for inflammation regulation within a clinical decision support protocol for managing severe COVID-19 patients", @@ -1277614,61 +1279537,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.07.22.213926", - "rel_title": "The discovery of a recombinant SARS2-like CoV strain provides insights into SARS and COVID-2019 pandemics", - "rel_date": "2020-07-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.22.213926", - "rel_abs": "In December 2019, the world awoke to a new zoonotic strain of coronavirus named severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). In the present study, we identified key recombination regions and mutation sites cross the SARS-CoV-2, SARS-CoV and SARS-like CoV clusters of betacoronavirus subgroup B. Based on the analysis of these recombination events, we proposed that the Spike protein of SARS-CoV-2 may have more than one specific receptor for its function. In addition, we reported--for the first time--a recombination event of ORF8 at the whole-gene level in a bat and ultimately determined that ORF8 enhances the viral replication. In conjunction with our previous discoveries, we found that receptor binding abilities, junction furin cleavage sites (FCSs), strong first ribosome binding sites (RBSs) and enhanced ORF8s are main factors contributing to transmission, virulence and host adaptability of CoVs. Junction FCSs and enhanced ORF8s increase the efficiencies in viral entry into cells and replication, respectively while strong first RBSs enhance the translational initiation. The strong recombination ability of CoVs integrated these factors to generate multiple recombinant strains, two of which evolved into SARS-CoV and SARS-CoV-2 by nature selection, resulting in the SARS and COVID-19 pandemics.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Xin Li", - "author_inst": "College of Life Sciences, Nankai University, Tianjin, Tianjin 300071, P.R.China" - }, - { - "author_name": "Xiufeng Jin", - "author_inst": "College of Life Sciences, Nankai University, Tianjin, Tianjin 300071, P.R.China" - }, - { - "author_name": "Shunmei Chen", - "author_inst": "Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Biomedical Engineering Research Center, Kunming Medical University, Kunming, Yunnan 650500, P.R.Ch" - }, - { - "author_name": "Liangge Wang", - "author_inst": "Taikang Xianlin Drum Tower Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu 210046, P.R.China" - }, - { - "author_name": "Tung On Yau", - "author_inst": "John Van Geest Cancer Research Centre, School of Science and Technology, Nottingham Trent University, Nottingham, NG11 8NS, United Kingdom" - }, - { - "author_name": "Jianyi Yang", - "author_inst": "School of Mathematical Sciences, Nankai University, Tianjin, Tianjin 300071, P.R.China" - }, - { - "author_name": "Zhangyong Hong", - "author_inst": "College of Life Sciences, Nankai University, Tianjin, Tianjin 300071, P.R.China" - }, - { - "author_name": "Jishou Ruan", - "author_inst": "School of Mathematical Sciences, Nankai University, Tianjin, Tianjin 300071, P.R.China" - }, - { - "author_name": "Guangyou Duan", - "author_inst": "School of Life Sciences, Qilu Normal University, Jinan, Shandong 250200, P.R.China" - }, - { - "author_name": "Shan Gao", - "author_inst": "College of Life Sciences, Nankai University, Tianjin, Tianjin 300071, P.R.China" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.07.22.216150", "rel_title": "Hydroxychloroquine-mediated inhibition of SARS-CoV-2 entry is attenuated by TMPRSS2", @@ -1278340,6 +1280208,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.18.20156307", + "rel_title": "Time between Symptom Onset, Hospitalisation and Recovery or Death: a Statistical Analysis of Different Time-Delay Distributions in Belgian COVID-19 Patients", + "rel_date": "2020-07-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.18.20156307", + "rel_abs": "BackgroundThere are different patterns in the COVID-19 outbreak in the general population and amongst nursing home patients. Different age-groups are also impacted differently. However, it remains unclear whether the time from symptom onset to diagnosis and hospitalization or the length of stay in the hospital is different for different age groups, gender, residence place or whether it is time dependent.\n\nMethodsSciensano, the Belgian Scientific Institute of Public Health, collected information on hospitalized patients with COVID-19 hospital admissions from 114 participating hospitals in Belgium. Between March 14, 2020 and June 12, 2020, a total of 14,618 COVID-19 patients were registered. The time of symptom onset, time of COVID-19 diagnosis, time of hospitalization, time of recovery or death, and length of stay in intensive care are recorded. The distributions of these different event times for different age groups are estimated accounting for interval censoring and right truncation in the observed data.\n\nResultsThe truncated and interval-censored Weibull regression model is the best model for the time between symptom onset and diagnosis/hospitalization best, whereas the length of stay in hospital is best described by a truncated and interval-censored lognormal regression model.\n\nConclusionsThe time between symptom onset and hospitalization and between symptom onset and diagnosis are very similar, with median length between symptom onset and hospitalization ranging between 3 and 10.4 days, depending on the age of the patient and whether or not the patient lives in a nursing home. Patients coming from a nursing home facility have a slightly prolonged time between symptom onset and hospitalization (i.e., 2 days). The longest delay time is observed in the age group 20-60 years old. The time from symptom onset to diagnosis follows the same trend, but on average is one day longer as compared to the time to hospitalization. The median length of stay in hospital varies between 3 and 10.4 days, with the length of stay increasing with age. However, a difference is observed between patients that recover and patients that die. While the hospital length of stay for patients that recover increases with age, we observe the longest time between hospitalization and death in the age group 20-60. And, while the hospital length of stay for patients that recover is shorter for patients living in a nursing home, the time from hospitalization to death is longer for these patients. But, over the course of the first wave, the length of stay has decreased, with a decrease in median length of stay of around 2 days.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Christel Faes", + "author_inst": "Data Science Institute (DSI), I-BioStat, Hasselt University" + }, + { + "author_name": "Steven Abrams", + "author_inst": "Data Science Institute (DSI), I-BioStat, Hasselt University & Global Health Institute (GHI), University of Antwerp" + }, + { + "author_name": "Dominique Van Beckhoven", + "author_inst": "Department of Epidemiology and public health, Sciensano" + }, + { + "author_name": "Geert Meyfroidt", + "author_inst": "Department and Laboratory of Intensive Care Medicine, UniversityHospitals Leuven and KU Leuven" + }, + { + "author_name": "Erika Vlieghe", + "author_inst": "Department of General Internal Medicine, Infectious and TropicalDiseases, University Hospital Antwerp" + }, + { + "author_name": "Niel Hens", + "author_inst": "Data Science Institute (DSI), I-BioStat, Universiteit Hasselt & Centre for Health Economics Research and Modelling of InfectiousDiseases (CHERMID" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.18.20156778", "rel_title": "COVID-19 DEATH TOLL: THE ROLE OF THE NATION'S ECONOMIC DEVELOPMENT", @@ -1279064,89 +1280971,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.07.21.212639", - "rel_title": "SARS-CoV-2 infection induces a pro-inflammatory cytokine response through cGAS-STING and NF-\u03baB", - "rel_date": "2020-07-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.21.212639", - "rel_abs": "SARS-CoV-2 is a novel virus that has rapidly spread, causing a global pandemic. In the majority of infected patients, SARS-CoV-2 leads to mild disease; however, in a significant proportion of infections, individuals develop severe symptoms that can lead to permanent lung damage or death. These severe cases are often associated with high levels of pro-inflammatory cytokines and low antiviral responses which can lead to systemic complications. We have evaluated transcriptional and cytokine secretion profiles from infected cell cultures and detected a distinct upregulation of inflammatory cytokines that parallels samples taken from infected patients. Building on these observations, we found a specific activation of NF-{kappa}B and a block of IRF3 nuclear translocation in SARS-CoV-2 infected cells. This NF-{kappa}B response is mediated by cGAS-STING activation and could be attenuated through STING targeting drugs. Our results show that SARS-CoV-2 curates a cGAS-STING mediated NF-{kappa}B driven inflammatory immune response in epithelial cells that likely contributes to inflammatory responses seen in patients and might be a target to suppress severe disease symptoms.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Christopher J Neufeldt", - "author_inst": "Heidelberg University" - }, - { - "author_name": "Berati Cerikan", - "author_inst": "Heidelberg University" - }, - { - "author_name": "Mirko Cortese", - "author_inst": "Heidelberg University" - }, - { - "author_name": "Jamie Frankish", - "author_inst": "BioMed X" - }, - { - "author_name": "Ji-Young Lee", - "author_inst": "Heidelberg University" - }, - { - "author_name": "Agnieszka Plociennikowska", - "author_inst": "Heidelberg University" - }, - { - "author_name": "Florian Heigwer", - "author_inst": "German Cancer Research Center (DKFZ)" - }, - { - "author_name": "Sebastian Joecks", - "author_inst": "Heidelberg University" - }, - { - "author_name": "Sandy S Burkart", - "author_inst": "German Cancer Research Center" - }, - { - "author_name": "David Y Zander", - "author_inst": "German Cancer Research Center" - }, - { - "author_name": "Mathieu Gendarme", - "author_inst": "BioMed X" - }, - { - "author_name": "Bachir El Debs", - "author_inst": "BioMed X" - }, - { - "author_name": "Niels Halama", - "author_inst": "German Cancer Research Center (DKFZ)" - }, - { - "author_name": "Uta Merle", - "author_inst": "University Hospital Heidelberg" - }, - { - "author_name": "Michael Boutros", - "author_inst": "German Cancer Research Center (DKFZ)" - }, - { - "author_name": "Marco Binder", - "author_inst": "German Cancer Research Center (DKFZ)" - }, - { - "author_name": "Ralf Bartenschlager", - "author_inst": "Heidelberg University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.07.20.213249", "rel_title": "Evaluation of a novel multiplexed assay for determining IgG levels and functional activity to SARS-CoV-2.", @@ -1279954,6 +1281778,89 @@ "type": "new results", "category": "zoology" }, + { + "rel_doi": "10.1101/2020.07.12.20148197", + "rel_title": "COVID-19 in patients undergoing renal replacement therapy in Scotland: findings and experience from the Scottish Renal Registry", + "rel_date": "2020-07-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.12.20148197", + "rel_abs": "IntroductionInfection with the severe acute respiratory coronavirus 2 (SARS-CoV-2) has led to a worldwide pandemic with coronavirus disease 2019 (COVID-19), the disease caused by SARS-CoV-2, overwhelming healthcare systems globally. Preliminary reports suggest a high incidence of infection and mortality with SARS-CoV-2 in patients receiving renal replacement therapy (RRT). The aims of this study are to report characteristics, rates and outcomes of all patients affected by infection with SARS-CoV-2 undergoing RRT in Scotland.\n\nMethodsStudy design was an observational cohort study. Data were linked between the Scottish Renal Registry, Health Protection Scotland and the Scottish Intensive Care Society Audit Group national data sets using a unique patient identifier (Community Health Index (CHI)) for each individual by the Public Health and Intelligence unit of Public Health, Scotland. Descriptive statistics and survival analyses were performed.\n\nResultsDuring the period 1st March 2020 to 31st May 2020, 110 patients receiving RRT tested positive for SARS-CoV-2 amounting to 2% of the prevalent RRT population. Of those affected, 87 were receiving haemodialysis or peritoneal dialysis and 24 had a renal transplant. Patients who tested positive were older and more likely to reside in more deprived postcodes. Mortality was high at 26.7% in the dialysis patients and 29.2% in the transplant patients.\n\nConclusionThe rate of detected SARS-CoV-2 in people receiving RRT in Scotland was relatively low but with a high mortality for those demonstrating infection. Although impossible to confirm, it appears that the measures taken within dialysis units coupled with the national shielding policy, have been effective in protecting this population from infection.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Samira Bell", + "author_inst": "University of Dundee" + }, + { + "author_name": "Jacqueline Campbell", + "author_inst": "Public Health Intelligence, Scotland" + }, + { + "author_name": "Jackie McDonald", + "author_inst": "Public Health Intelligence, Scotland" + }, + { + "author_name": "Chrissie Watters", + "author_inst": "Public Health Intelligence, Scotland." + }, + { + "author_name": "Katharine Buck", + "author_inst": "Victoria Hospital, Kirkcaldy" + }, + { + "author_name": "Zoe Cousland", + "author_inst": "Monklands Hospital, Airdrie" + }, + { + "author_name": "Mark Findlay", + "author_inst": "Queen Elizabeth University Hospital, Glasgow" + }, + { + "author_name": "Nazir Lone", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Wendy Metcalfe", + "author_inst": "Royal Infirmary of Edinburgh" + }, + { + "author_name": "Shona Methven", + "author_inst": "Aberdeen Royal Infirmary" + }, + { + "author_name": "Robert Peel", + "author_inst": "Raigmore Hospital, Inverness" + }, + { + "author_name": "Alison Almond", + "author_inst": "Mountainhall Treatment Centre, Dumfries" + }, + { + "author_name": "Vinod Sanu", + "author_inst": "Ninewells Hospital, Dundee" + }, + { + "author_name": "Elaine Spalding", + "author_inst": "Crosshouse Hospital, Kilmarnock." + }, + { + "author_name": "Peter Thomson", + "author_inst": "Queen Elizabeth University Hospital, Glasgow." + }, + { + "author_name": "Patrick Mark", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Jamie Traynor", + "author_inst": "Queen Elizabeth University Hospital, Glasgow" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "nephrology" + }, { "rel_doi": "10.1101/2020.07.19.20157511", "rel_title": "Bioaersols in orthopedic surgical procedures and implications for clinical practice in the times of COVID-19 pandemic: a protocol for systematic review and meta-analysis", @@ -1280858,133 +1282765,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.14.20144469", - "rel_title": "Initial experience in Mexico with convalescent plasma in COVID-19 patients with severe respiratory failure, a retrospective case series", - "rel_date": "2020-07-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.14.20144469", - "rel_abs": "IntroductionHospital mortality due to COVID-19 in Mexico is high (32%) and as of today, effective treatment options are limited. More effective treatments that shorten hospital stay and reduce mortality are needed. Initial reports for the use of convalescent plasma (CP) therapy for COVID-19 appear promising. We describe a case series of eight patients with impending respiratory failure, who underwent CP therapy.\n\nMethodsSix male and two female (ages 31 to 79) patients that were admitted to the intensive-care unit for severe COVID-19 were transfused with two doses of CP (250 mL per dose, anti-SARS-CoV-2 IgG titers > 1:100). Donors were six SARS-CoV-2 infected males who remained asymptomatic for > 7 days and were negative for two nasopharyngeal RT-PCR tests. Clinical characteristics, inflammatory and cellular injury markers, chest X-ray findings and viral loads were analyzed before and after CP administration. Viral load association to disease severity was further analyzed on a separate cohort of asymptomatic vs hospitalized patients with COVID-19.\n\nResultsEight patients with respiratory failure were successfully discharged with a median length of stay of 22.5 (IQR 18.25-29.00). After CP therapy, we observed a reduction of C-reactive protein (CRP) (median, 22.80 mg/dL vs. 1.63 mg/dL), and of procalcitonin (median, 0.27 ng/mL vs. 0.13 ng/mL). High-Sensitivity Cardiac Troponin I (hs-cTnI), Brain Natriuretic Peptide (BNP) and Lactate Dehydrogenase (LDH) were lower, and a mild reduction of pulmonary infiltrates by chest X-ray was observed. Lastly, a reduction of viral load was after CP therapy was found. (log, median [IQR], 1.2 [0.70-2.20] vs. 0.25 [0.00-1.78]). We observed no adverse effects.\n\nConclusionsCP could potentially be an effective therapeutic option for patients with severe COVID-19. Clinical benefit needs to be studied further through randomized controlled trials.", - "rel_num_authors": 28, - "rel_authors": [ - { - "author_name": "Michel F. Martinez-Resendez", - "author_inst": "Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico" - }, - { - "author_name": "Fernando Castilleja-Leal", - "author_inst": "Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico" - }, - { - "author_name": "Alejandro Torres-Quintanilla", - "author_inst": "Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico" - }, - { - "author_name": "Augusto Rojas-Martinez", - "author_inst": "Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico" - }, - { - "author_name": "Gerardo Garcia-Rivas", - "author_inst": "Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico" - }, - { - "author_name": "Rocio Ortiz-Lopez", - "author_inst": "Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico" - }, - { - "author_name": "Victor Trevino", - "author_inst": "Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico" - }, - { - "author_name": "Reynaldo Lara-Medrano", - "author_inst": "Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico" - }, - { - "author_name": "Hiram Villanueva-Lozano", - "author_inst": "Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico" - }, - { - "author_name": "Teresa Ramirez-Elizondo", - "author_inst": "Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico" - }, - { - "author_name": "Victor Sanchez-Nava", - "author_inst": "Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico" - }, - { - "author_name": "Francisco Moreno-Hoyos", - "author_inst": "Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico" - }, - { - "author_name": "Alfonso Martinez-Thomae", - "author_inst": "Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico" - }, - { - "author_name": "Martin Hernandez-Torre", - "author_inst": "Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico" - }, - { - "author_name": "Carlos Diaz-Olachea", - "author_inst": "Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico" - }, - { - "author_name": "Servando Cardona-Huerta", - "author_inst": "Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico" - }, - { - "author_name": "Sylvia de la Rosa-Pacheco", - "author_inst": "Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico" - }, - { - "author_name": "Carlos Diaz-Garza", - "author_inst": "Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico" - }, - { - "author_name": "Paola Reynoso-Lobo", - "author_inst": "Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico" - }, - { - "author_name": "Alma R. Marroquin-Escamilla", - "author_inst": "Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico" - }, - { - "author_name": "Jessica G. Herrera-Gamboa", - "author_inst": "Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico" - }, - { - "author_name": "Fatima M. Alvarado-Monroy", - "author_inst": "Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico" - }, - { - "author_name": "Claudia D. Aguayo-Millan", - "author_inst": "Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico" - }, - { - "author_name": "Francisco F. Villegas-Macedo", - "author_inst": "Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico" - }, - { - "author_name": "Jesus E. Flores-Osorio", - "author_inst": "Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico" - }, - { - "author_name": "Daniel Davila-Gonzalez", - "author_inst": "Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico" - }, - { - "author_name": "Maria E. Diaz-Sanchez", - "author_inst": "Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico" - }, - { - "author_name": "Guillermo Torre-Amione", - "author_inst": "Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.13.20146175", "rel_title": "Qing Fei Pai Du Tang, a Chinese multi-herbal medicine formulated against COVID-19, elevates the plasma levels of IL-1\u03b2, IL-18, TNF-\u03b1, and IL-8", @@ -1281656,6 +1283436,37 @@ "type": "new results", "category": "systems biology" }, + { + "rel_doi": "10.1101/2020.07.20.210534", + "rel_title": "SARS-CoV2 spike protein displays biologically significant similarities with paramyxovirus surface proteins; a bioinformatics study", + "rel_date": "2020-07-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.20.210534", + "rel_abs": "Recent emergence of SARS-CoV2 and associated COVID-19 pandemic has posed a great challenge for the scientific community. Understanding various aspects of SARS-CoV2 biology, virulence and pathogenesis as well as determinants of immune response have become a global research priority. In this study, we performed bioinformatic analyses on SAR-CoV2 protein sequences, trying to unravel biologically important similarities between this newly emerged virus with other RNA viruses. Comparing the proteome of SARS-CoV2 with major positive and negative strand ssRNA viruses showed significant homologies between SARS-CoV2 spike protein with pathogenic paramyxovirus fusion proteins. This spike-fusion homology was not limited to SARS-CoV2 and it existed for some other pathogenic coronaviruses; nonetheless, SARS-CoV2 spike-fusion homology was orders of magnitude stronger than homologies observed for other known coronaviruses. Moreover, this homology did not seem to be a consequence of general ssRNA virus phylogenetic relations. We also explored potential immunological significance of this spike-fusion homology. Spike protein epitope analysis using experimentally verified data deposited in Immune Epitope Database (IEDB) revealed that the majority of spikes T cell epitopes as well as many B cell and MHC binding epitopes map within the spike-fusion homology region. Overall, our data indicate that there might be a relation between SARS-CoV2 and paramyxoviruses at the level of their surface proteins and this relation could be of crucial immunological importance.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Ehsan Ahmadi", + "author_inst": "Tehran University of Medical Sciences" + }, + { + "author_name": "Mohammad Reza Zabihi", + "author_inst": "Tehran University of Medical Sciences" + }, + { + "author_name": "Ramin Hosseinzadeh", + "author_inst": "Tehran University of Medical Sciences" + }, + { + "author_name": "Farshid Noorbakhsh", + "author_inst": "Tehran University of Medical Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.07.19.197129", "rel_title": "Population genetic analysis of Indian SARS-CoV-2 isolates reveals a unique phylogenetic cluster", @@ -1282376,45 +1284187,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.17.20155762", - "rel_title": "Regional COVID-19 spread despite expected declines: how mitigation is hindered by spatio-temporal variation in local control measures.", - "rel_date": "2020-07-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.17.20155762", - "rel_abs": "Successful public health regimes for COVID-19 push below unity long-term global Rt -the average number of secondary cases caused by an infectious individual. Most assessments use local information. Populations differ in Rt, amongst themselves and over time. We use a SIR model for two populations to make the conceptual point that even if each locality averages Rt < 1, the overall epidemic can still grow, provided these populations have asynchronous variation in transmission, and are coupled by movement of infectious individuals. This emergent effect in pandemic dynamics instantiates \"Parrondos Paradox,\" -- an entity comprised of distinct but interacting units can behave qualitatively differently than each part on its own. For effective COVID-19 disease mitigation strategies, it is critical that infectious individuals moving among locations be identified and quarantined. This does not warrant indiscriminate prevention of movement, but rather rational, targeted testing and national coordination.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Nicholas Kortessis", - "author_inst": "University of Florida" - }, - { - "author_name": "Margaret W Simon", - "author_inst": "University of Florida" - }, - { - "author_name": "Michael Barfield", - "author_inst": "University of Florida" - }, - { - "author_name": "Gregory Glass", - "author_inst": "University of Florida" - }, - { - "author_name": "Burton H Singer", - "author_inst": "University of Florida" - }, - { - "author_name": "Robert D Holt", - "author_inst": "University of Florida" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.16.20155317", "rel_title": "Characterizing the Qatar advanced-phase SARS-CoV-2 epidemic", @@ -1283318,6 +1285090,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.16.20155580", + "rel_title": "Outcomes of Mechanically Ventilated Patients with COVID-19 Associated Respiratory Failure", + "rel_date": "2020-07-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.16.20155580", + "rel_abs": "PurposeThe outcomes of patients requiring invasive mechanical ventilation for COVID-19 remain poorly defined. We sought to determine clinical characteristics and outcomes of patients with COVID-19 managed with invasive mechanical ventilation in an appropriately resourced US health care system.\n\nMethodsOutcomes of COVID-19 infected patients requiring mechanical ventilation treated within the Inova Health System between March 5, 2020 and April 26, 2020 were evaluated through an electronic medical record review.\n\nResults1023 COVID-19 positive patients were admitted to the Inova Health System during the study period. Of these, 165 (16.1%) were managed with invasive mechanical ventilation. At the time of data censoring, 63/165 patients (38.1%) had died and 102/165 (61.8%) were still alive. Of the surviving 102 patients, 17 (10.3%) remained on mechanical ventilation, 51 (30.9%) were extubated but remained hospitalized, and 34 (20.6%) had been discharged. Deceased patients were older (median age of 66 vs. 55, p <0.0001). 75.7% of patients over 70 years old had died at the time of data analysis. Conversely, % of patients age 70 or younger were still alive at the time of data analysis. Younger age, non-Caucasian race and treatment at a tertiary care center were all associated with survivor status.\n\nConclusionMortality of patients with COVID-19 requiring invasive mechanical ventilation is high, with particularly daunting mortality seen in patients of advanced age, even in a well-resourced health care system. A substantial proportion of patients requiring invasive mechanical ventilation were not of advanced age, and this group had a reasonable chance for recovery.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Christopher King", + "author_inst": "Inova Fairfax" + }, + { + "author_name": "Dhwani Sahjwani", + "author_inst": "Inova Fairfax Hospital" + }, + { + "author_name": "A Whitney Brown", + "author_inst": "Inova Fairfax Hospital" + }, + { + "author_name": "Saad Feroz", + "author_inst": "Inova Fairfax Hospital" + }, + { + "author_name": "Paula Cameron", + "author_inst": "Inova Fairfax Hospital" + }, + { + "author_name": "Erik Osborn", + "author_inst": "Inova Fairfax Hospital" + }, + { + "author_name": "Mehul Desai", + "author_inst": "Inova Fairfax Hospital" + }, + { + "author_name": "Svetolik Djurkovic", + "author_inst": "Inova Fairfax Hospital" + }, + { + "author_name": "Aditya Kasarabada", + "author_inst": "Inova Fairfax Hospital" + }, + { + "author_name": "Rachel Hinerman", + "author_inst": "Inova Fairfax Hospital" + }, + { + "author_name": "James Lantry", + "author_inst": "Inova Fairfax Hospital" + }, + { + "author_name": "Oksana Shlobin", + "author_inst": "Inova Fairfax Hospital" + }, + { + "author_name": "Kareem Ahmad", + "author_inst": "Inova Fairfax Hospital" + }, + { + "author_name": "Vikramjit Khangoora", + "author_inst": "Inova Fairfax Hospital" + }, + { + "author_name": "Shambhu Aryal", + "author_inst": "Inova Fairfax Hospital" + }, + { + "author_name": "A Claire Collins", + "author_inst": "Inova Fairfax Hospital" + }, + { + "author_name": "Alan Speir", + "author_inst": "Inova Fairfax Hospital" + }, + { + "author_name": "Steven Nathan", + "author_inst": "Inova Fairfax Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.07.16.20155382", "rel_title": "Identifying organ dysfunction trajectory-based subphenotypes in critically ill patients with COVID-19", @@ -1284078,73 +1285937,6 @@ "type": "new results", "category": "neuroscience" }, - { - "rel_doi": "10.1101/2020.07.17.208959", - "rel_title": "Structural basis for the inhibition of the papain-like protease of SARS-CoV-2 by small molecules", - "rel_date": "2020-07-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.17.208959", - "rel_abs": "SARS-CoV-2 is the pathogen responsible for the COVID-19 pandemic. The SARS-CoV-2 papain-like cysteine protease has been implicated in virus maturation, dysregulation of host inflammation and antiviral immune responses. We showed that PLpro preferably cleaves the K48-ubiquitin linkage while also being capable of cleaving ISG15 modification. The multiple functions of PLpro render it a promising drug target. Therefore, we screened an FDA-approved drug library and also examined available inhibitors against PLpro. Inhibitor GRL0617 showed a promising IC50 of 2.1 M. The co-crystal structure of SARS-CoV-2 PLpro-C111S in complex with GRL0617 suggests that GRL0617 is a non-covalent inhibitor. NMR data indicate that GRL0617 blocks the binding of ISG15 to PLpro. The antiviral activity of GRL0617 reveal that PLpro is a promising drug target for therapeutically treating COVID-19.\n\nOne Sentence SummaryCo-crystal structure of PLpro in complex with GRL0617 reveals the druggability of PLpro for SARS-CoV-2 treatment.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Ziyang Fu", - "author_inst": "State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China;" - }, - { - "author_name": "Bin Huang", - "author_inst": "Laboratory of Structural Biology and Drug Discovery, Peking University Shenzhen Graduate SchoolState Key Laboratory of Chemical Oncogenomics, School of Chemical" - }, - { - "author_name": "Jinle Tang", - "author_inst": "State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China;" - }, - { - "author_name": "Ming Liu", - "author_inst": "State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China;" - }, - { - "author_name": "Yuxin Ye", - "author_inst": "State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China;" - }, - { - "author_name": "Zhihong Liu", - "author_inst": "State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China;" - }, - { - "author_name": "Yuxian Xiong", - "author_inst": "State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China;" - }, - { - "author_name": "Dan Cao", - "author_inst": "State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China;" - }, - { - "author_name": "Jihui Li", - "author_inst": "State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China;" - }, - { - "author_name": "Xiaogang Niu", - "author_inst": "College of Chemistry and Molecular Engineering, Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China" - }, - { - "author_name": "Huanz Zhou", - "author_inst": "Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China" - }, - { - "author_name": "Yong Juan Zhao", - "author_inst": "State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China" - }, - { - "author_name": "Hao Huang", - "author_inst": "State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China;" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.07.18.204362", "rel_title": "The landscape of SARS-CoV-2 RNA modifications", @@ -1284984,6 +1286776,137 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.14.20153320", + "rel_title": "Clinical characteristics of children and young people hospitalised with covid-19 in the United Kingdom: prospective multicentre observational cohort study", + "rel_date": "2020-07-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.14.20153320", + "rel_abs": "ObjectiveTo characterise the clinical features of children and young people admitted to hospital with laboratory-confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in the UK, and explore factors associated with admission to critical care, mortality, and development of multisystem inflammatory syndrome in children and adolescents temporarily related to covid-19 (MIS-C).\n\nDesignProspective observational cohort study with rapid data gathering and near real time analysis.\n\nSetting260 acute care hospitals in England, Wales, and Scotland between 17th January and 5th June 2020, with a minimal follow-up time of two weeks (to 19th June 2020).\n\nParticipants451 children and young people aged less than 19 years admitted to 116 hospitals and enrolled into the International Severe Acute Respiratory and emergency Infections Consortium (ISARIC) WHO Clinical Characterisation Protocol UK study with laboratory-confirmed SARS-CoV-2.\n\nMain Outcome MeasuresAdmission to critical care (high dependency or intensive care), in-hospital mortality, or meeting the WHO preliminary case definition for MIS-C.\n\nResultsMedian age was 3.9 years [interquartile range (IQR) 0.3-12.9 years], 36% (162/451) were under 12 months old, and 57% (256/450) were male. 56% (224/401) were White, 12% (49/401) South Asian and 10% (40/401) Black. 43% (195/451) had at least one recorded comorbidity. A muco-enteric cluster of symptoms was identified, closely mirroring the WHO MIS-C criteria.\n\n17% of children (72/431) were admitted to critical care. On multivariable analysis this was associated with age under one month odds ratio 5.05 (95% confidence interval 1.69 to 15.72, p=0.004), age 10 to 14 years OR 3.11 (1.21 to 8.55, p=0.022) and Black ethnicity OR 3.02 (1.30 to 6.84, p=0.008). Three young people died (0.7 %, 3/451) aged 16 to 19 years, all of whom had profound comorbidity.\n\nTwelve percent of children (36/303) met the WHO MIS-C criteria, with the first patient developing symptoms in mid-March. Those meeting MIS-C criteria were older, (median age 10.8 years ([IQR 8.4-14.1] vs 2.0 [0.2-12.6]), p<0.001) and more likely to be of non-White ethnicity (70% (23/33) vs 43% (101/237), p=0.005). Children with MIS-C were four times more likely to be admitted to critical care (61% (22/36) vs 15% (40/267, p<0.001). In addition to the WHO criteria, children with MIS-C were more likely to present with headache (45% (13/29) vs 11% (19/171), p<0.001), myalgia (39% (11/28) vs 7% (12/170), p<0.001), sore throat (37% (10/27) vs (13% (24/183, p = 0.004) and fatigue (57% (17/30) vs 31% (60/192), p =0.012) than children who did not and to have a platelet count of less than 150 x109/L (30% (10/33) vs 10% (24/232), p=0.004).\n\nConclusionsOur data confirms less severe covid-19 in children and young people than in adults and we provide additional evidence for refining the MIS-C case definition. The identification of a muco-enteric symptom cluster also raises the suggestion that MIS-C is the severe end of a spectrum of disease.\n\nStudy registrationISRCTN66726260", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Olivia V Swann", + "author_inst": "Department of Child Life and Health, University of Edinburgh, UK" + }, + { + "author_name": "Karl A Holden", + "author_inst": "Institute of Translational Medicine, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK" + }, + { + "author_name": "Lance Turtle", + "author_inst": "Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK" + }, + { + "author_name": "Louisa Pollock", + "author_inst": "Royal Hospital for Children, Glasgow, UK" + }, + { + "author_name": "Cameron J Fairfield", + "author_inst": "Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK" + }, + { + "author_name": "Thomas M Drake", + "author_inst": "Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK" + }, + { + "author_name": "Sohan Seth", + "author_inst": "Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK" + }, + { + "author_name": "Conor Egan", + "author_inst": "Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK" + }, + { + "author_name": "Hayley Hardwick", + "author_inst": "Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK" + }, + { + "author_name": "Sophie Halpin", + "author_inst": "Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK" + }, + { + "author_name": "Michelle Girvan", + "author_inst": "Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK" + }, + { + "author_name": "Chloe Donohue", + "author_inst": "Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK" + }, + { + "author_name": "Mark G Pritchard", + "author_inst": "Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, United Kingdom" + }, + { + "author_name": "Latifa Patel", + "author_inst": "Respiratory Medicine, Alder Hey Childrens Hospital, Liverpool L12 2AP, UK" + }, + { + "author_name": "Shamez Ladhani", + "author_inst": "Immunisation and Countermeasures Division, Public Health England Colindale" + }, + { + "author_name": "Louise Sigfrid", + "author_inst": "Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, United Kingdom" + }, + { + "author_name": "Ian P Sinha", + "author_inst": "Respiratory Medicine, Alder Hey Childrens Hospital, Liverpool L12 2AP, UK" + }, + { + "author_name": "Piero L Olliaro", + "author_inst": "Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, United Kingdom" + }, + { + "author_name": "Jonathan S Nguyen-Van-Tam", + "author_inst": "Division of Epidemiology and Public Health, University of Nottingham School of Medicine, Nottingham, UK" + }, + { + "author_name": "Peter W Horby", + "author_inst": "ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK" + }, + { + "author_name": "Laura Merson", + "author_inst": "ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK" + }, + { + "author_name": "Gail Carson", + "author_inst": "ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK" + }, + { + "author_name": "W Jake Dunning", + "author_inst": "National Infection Service Public Health England" + }, + { + "author_name": "Peter JM Openshaw", + "author_inst": "National Heart and Lung Institute, Imperial College London, London, UK" + }, + { + "author_name": "J Kenneth Baillie", + "author_inst": "Roslin Institute, University of Edinburgh" + }, + { + "author_name": "Ewen M Harrison", + "author_inst": "Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK" + }, + { + "author_name": "Annemarie B Docherty", + "author_inst": "Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK" + }, + { + "author_name": "Malcolm Gracie Semple", + "author_inst": "NIHR Health Protection Research Unit in Emerging and Zoonotic Infections and Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and " + }, + { + "author_name": "- ISARIC Coronavirus Clinical Characterisation Consortium (ISARIC4C) Investigators", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2020.07.15.20152967", "rel_title": "Outcome of hospitalisation for COVID-19 in patients with Interstitial Lung Disease: An international multicentre study.", @@ -1286320,25 +1288243,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.16.20155093", - "rel_title": "Computer-aided covid-19 patient screening using chest images (X-Ray and CT scans)", - "rel_date": "2020-07-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.16.20155093", - "rel_abs": "Objectivesto evaluate the performance of Artificial Intelligence (AI) methods to detect covid-19 from chest images (X-Ray and CT scans).\n\nMethodsChest CT scans and X-Ray images collected from different centers and institutions were downloaded and combined together. Images were separated by patient and 66% of the patients were used to develop and train AI image-based classifiers. Then, the AI automated classifiers were evaluated on a separate set of patients (the remaining 33% patients).\n\nResults (Chest X-Ray)Five different data sources were combined for a total of N=9,841 patients (1,733 with covid-19, 810 with bacterial tuberculosis and 7,298 healthy patients). The test sample size was N=3,528 patients. The best AI method reached an Area Under the Curve (AUC) for covid-19 detection of 99%, with a detection rate of 96.4% at 1.0% false positive rate.\n\nResults (Chest CT scans)Two different data sources were combined for a total of N=363 patients (191 having covid-19 and 172 healthy patients). The test sample size was N=121 patients. The best AI method reached an AUC for covid-19 detection of 90.9%, with a detection rate of 90.6% at 24.6% false positive rate.\n\nConclusionsComputer aided automatic covid-19 detection from chest X-ray images showed promising results to be used as screening tool during the covid-19 outbreak. The developed method may help to manage patients better in case access to PCR testing is not possible or to detect patients with symptoms missed in a first round of PCR testing. The method will be made available online (www.quantuscovid19.org). These results merit further evaluation collecting more images. We hope this study will allow us to start such collaborations.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Xavier P Burgos-Artizzu", - "author_inst": "Transmural Biotech" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2020.07.14.20153536", "rel_title": "Qualitative Changes in the SARS-CoV-2 Antibody Response in the Post-Infection Phase Impact the estimates of infections in Population-Based Seroprevalence Studies", @@ -1287066,6 +1288970,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2020.07.16.20141069", + "rel_title": "COVID-19 ANXIETY AMONG FRONTLINE NURSES: PREDICTIVE ROLE OF ORGANISATIONAL SUPPORT, PERSONAL RESILIENCE AND SOCIAL SUPPORT", + "rel_date": "2020-07-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.16.20141069", + "rel_abs": "AimThis study examines the relative influence of personal resilience, social support and organisational support in reducing COVID-19 anxiety in frontline nurses.\n\nBackgroundAnxiety related to the COVID-19 pandemic is prevalent in the nursing workforce, potentially affecting nurses well-being and work performance. Identifying factors that could help maintain mental health and reduce coronavirus-related anxiety among frontline nurses is imperative. Currently, no studies have been conducted examining the influence of personal resilience, social support and organisational support in reducing COVID-19 anxiety among nurses.\n\nMethodsThis cross-sectional study involved 325 registered nurses from the Philippines using four standardised scales.\n\nResultsOf the 325 nurses in the study, 123 (37.8%) were found to have dysfunctional levels of anxiety. Using multiple linear regression analyses, social support ({beta} = -0.142, p = 0.011), personal resilience ({beta} = -0.151, p = 0.008) and organisational support ({beta} = -0.127, p = 0.023) predicted COVID-19 anxiety. Nurse characteristics were not associated with COVID-19 anxiety.\n\nConclusionsResilient nurses and those who perceived higher organisational and social support were more likely to report lower anxiety related to COVID-19.\n\nImplication for Nursing ManagementCOVID-19 anxiety may be addressed through organisational interventions, including increasing social support, assuring adequate organisational support, providing psychological and mental support services and providing resilience-promoting and stress management interventions.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Leodoro Labrague", + "author_inst": "Sultan Qaboos University" + }, + { + "author_name": "Janet Alexis De los Santos", + "author_inst": "Visayas State University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "nursing" + }, { "rel_doi": "10.1101/2020.07.05.20146589", "rel_title": "COVID-19 national lockdown in Morocco: impacts on air quality and public health", @@ -1288154,109 +1290081,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.07.17.20155978", - "rel_title": "Broncho-alveolar inflammation in COVID-19 patients: a correlation with clinical outcome", - "rel_date": "2020-07-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.17.20155978", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rapidly reached pandemic proportions. We conducted a prospective study to assess deep lung inflammatory status in patients with moderate to severe COVID-19.\n\nDiagnostic bronchoalveolar lavage (BAL) was performed in 33 adult patients with SARS-CoV-2 infection by real-time PCR on nasopharyngeal swab admitted to the Intensive care unit (ICU) (n=28) and to the Intermediate Medicine Ward (IMW) (n=5). We analyze the differential cell count, ultrastructure of cells and Interleukin(IL)6, 8 and 10 levels.\n\nICU patients showed a marked increase in neutrophils (72%, 60-81), lower lymphocyte (8%, 4-12) and macrophages fractions (17%, 11-27) compared to IMW patients (3%, 2-17, 15%, 6-26 and 74%, 58-90, respectively) (p<0.01). Ultrastructural study from ICU patients showed viral-like particles in cytopathic mononuclear cells however extensive cytopathic damage in all cell lineages. Immunostaining with anti-viral capsid and spike antibodies specifically immunoreacted with BAL cells, mostly cytopathic ones. IL6 and IL8 were significantly higher in ICU patients than in IMW (IL6 p<0.01, IL8 p<0.0001), and also in patients who did not survive (IL6 p < 0.05, IL8 p = 0.05 vs. survivors). IL10 did not show a significant variation between groups. Dividing patients by treatment received, lower BAL concentrations of IL6 were found in patients treated with steroids as compared to those treated with tocilizumab (p<0.1) or antivirals (p<0.05).\n\nAlveolitis, associated with COVID-19, is mainly sustained by innate effectors which showed features of extensive activation. The burden of pro-inflammatory cytokines IL6 and IL8 in the broncho-alveolar environment is associated with clinical outcome.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Laura Pandolfi", - "author_inst": "Fondazione IRCCS Policlinico San Matteo" - }, - { - "author_name": "Tommaso Fossali", - "author_inst": "Division of Anaesthesiology and Intensive Care, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, University of Milan, Milan, Italy" - }, - { - "author_name": "Vanessa Frangipane", - "author_inst": "Fondazione IRCCS Policlinico San Matteo" - }, - { - "author_name": "Sara Bozzini", - "author_inst": "Fondazione IRCCS Policlinico San Matteo" - }, - { - "author_name": "Monica Morosini", - "author_inst": "Fondazione IRCCS Policlinico San Matteo" - }, - { - "author_name": "Maura D'Amato", - "author_inst": "Fondazione IRCCS Policlinico San Matteo" - }, - { - "author_name": "Sara Lettieri", - "author_inst": "University of Pavia" - }, - { - "author_name": "Mario Urtis", - "author_inst": "Fondazione IRCCS Policlinico San Matteo" - }, - { - "author_name": "Alessandro Di Toro", - "author_inst": "IRCCS Policlinico San Matteo Foundation, University of Pavia, Pavia, Italy" - }, - { - "author_name": "Laura Saracino", - "author_inst": "IRCCS Policlinico S. Matteo Foundation, Pavia, Italy" - }, - { - "author_name": "Elena Percivalle", - "author_inst": "IRCCS Policlinico S. Matteo Foundation, Pavia, Italy" - }, - { - "author_name": "Stefano Tomaselli", - "author_inst": "IRCCS Policlinico S. Matteo Foundation, Pavia, Italy" - }, - { - "author_name": "Lorenzo Cavagna", - "author_inst": "University of Pavia and IRCCS Policlinico S. Matteo Foundation, Pavia, Italy" - }, - { - "author_name": "Emanuela Cova", - "author_inst": "IRCCS Policlinico S. Matteo Foundation, Pavia, Italy" - }, - { - "author_name": "Francesco Mojoli", - "author_inst": "University of Pavia" - }, - { - "author_name": "Paola Bergomi", - "author_inst": "ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, University of Milan" - }, - { - "author_name": "davide ottolina", - "author_inst": "L. Sacco Hospital, ASST Fatebenefratelli-Sacco" - }, - { - "author_name": "Daniele Lilleri", - "author_inst": "IRCCS Policlinico San Matteo Foundation" - }, - { - "author_name": "Angelo Guido Corsico", - "author_inst": "University of Pavia and Pneumology Unit, IRCCS Policlinico S. Matteo Foundation" - }, - { - "author_name": "Eloisa Arbustini", - "author_inst": "IRCCS Policlinico San Matteo Foundation, University of Pavia" - }, - { - "author_name": "Riccardo Colombo", - "author_inst": "ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, University of Milan" - }, - { - "author_name": "Federica Meloni", - "author_inst": "University of Pavia and Pneumology Unit, IRCCS Policlinico S. Matteo Foundation" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2020.07.16.20155903", "rel_title": "Epidemiological aspects of COVID-19 disease in India during nationwide lockdown phase- An empirical data-based analysis and its implications on interrupting the transmission", @@ -1289220,6 +1291044,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.15.20154294", + "rel_title": "The impact of host resistance on cumulative mortality and the threshold of herd immunity for SARS-CoV-2", + "rel_date": "2020-07-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.15.20154294", + "rel_abs": "It is widely believed that the herd immunity threshold (HIT) required to prevent a resurgence of SARS-CoV-2 is in excess of 50% for any epidemiological setting. Here, we demonstrate that HIT may be greatly reduced if a fraction of the population is unable to transmit the virus due to innate resistance or cross-protection from exposure to seasonal coronaviruses. The drop in HIT is proportional to the fraction of the population resistant only when that fraction is effectively segregated from the general population; however, when mixing is random, the drop in HIT is more precipitous. Significant reductions in expected mortality can also be observed in settings where a fraction of the population is resistant to infection. These results help to explain the large degree of regional variation observed in seroprevalence and cumulative deaths and suggest that sufficient herd-immunity may already be in place to substantially mitigate a potential second wave.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Jose Lourenco", + "author_inst": "University of Oxford" + }, + { + "author_name": "Francesco Pinotti", + "author_inst": "University of Oxford" + }, + { + "author_name": "Craig Thompson", + "author_inst": "University of Oxford" + }, + { + "author_name": "Sunetra Gupta", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.15.20154823", "rel_title": "SARS-COV-2 THREE FORCING SEASONALITIES: POLICIES, ENVIRONMENT AND URBAN SPACES", @@ -1290000,29 +1291855,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.15.20154526", - "rel_title": "Possible fates of the dispersion of SARS-COV-2 in the Mexican context", - "rel_date": "2020-07-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.15.20154526", - "rel_abs": "The determination of the adequate time for house confinement and when social distancing restrictions should end are now two of the main challenges that any country has to face in an effective battle against. The possibility of a new outbreak of the pandemic and how to avoid it is, nowadays, one of the primary objectives of epidemiological research. In this work, we go deep in this subject by presenting an innovative compartmental model, that explicitly introduces the number of active cases, and employing it as a conceptual tool to explore the possible fates of the dispersion of SARS-COV-2 in the Mexican context. We incorporated the impact of starting, inattention, and end of restrictive social policies on the time evolution of the pandemics via time-in-run corrections to the infection rates. The magnitude and impact on the epidemic due to post-social restrictive policies are also studied. The scenarios generated by the model can help authorities to determine an adequate time and population load that may be allowed to reassume normal activities.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Ivan Santamaria-Holek", - "author_inst": "UMDI-J, Faculty of Sciences, Universidad Nacional Autonoma de Mexico" - }, - { - "author_name": "Victor Castano", - "author_inst": "Universidad Autonoma de Mexico" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.15.20154740", "rel_title": "A parsimonious model for spatial transmission and heterogeneity in the COVID-19 propagation", @@ -1290622,6 +1292454,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.15.20154518", + "rel_title": "Viral load of SARS-CoV-2 across patients and compared to other respiratory viruses", + "rel_date": "2020-07-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.15.20154518", + "rel_abs": "RT-PCRs to detect SARS-CoV-2 RNA is key to manage the COVID-19 pandemic. We analyzed SARS-CoV-2 viral loads from 22323 RT-PCR results according to samples types, gender, age, and health units. Viral load did not show any difference across age and appears to be a poor predictor of disease outcome. SARS-CoV-2 viral load showed similar high viral loads than the one observed for RSV and influenza B. The importance of viral load to predict contagiousness and to assess disease progression is discussed.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Damien Jacot", + "author_inst": "Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland" + }, + { + "author_name": "Gilbert Greub", + "author_inst": "Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland and Infectious Diseases Service, University Hospital of Lausanne, " + }, + { + "author_name": "Katia Jaton", + "author_inst": "Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland" + }, + { + "author_name": "Onya Opota", + "author_inst": "Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.14.20154005", "rel_title": "A sensitive and affordable multiplex RT-qPCR assay for SARS-CoV-2 detection", @@ -1291530,37 +1293393,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.07.13.201517", - "rel_title": "Comparative multiplexed interactomics of SARS-CoV-2 and homologous coronavirus non-structural proteins identifies unique and shared host-cell dependencies", - "rel_date": "2020-07-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.13.201517", - "rel_abs": "Human coronaviruses (hCoV) have become a threat to global health and society, as evident from the SARS outbreak in 2002 caused by SARS-CoV-1 and the most recent COVID-19 pandemic caused by SARS-CoV-2. Despite high sequence similarity between SARS-CoV-1 and -2, each strain has distinctive virulence. A better understanding of the basic molecular mechanisms mediating changes in virulence is needed. Here, we profile the virus-host protein-protein interactions of two hCoV non-structural proteins (nsps) that are critical for virus replication. We use tandem mass tag-multiplexed quantitative proteomics to sensitively compare and contrast the interactomes of nsp2 and nsp4 from three betacoronavirus strains: SARS-CoV-1, SARS-CoV-2, and hCoV-OC43 - an endemic strain associated with the common cold. This approach enables the identification of both unique and shared host cell protein binding partners and the ability to further compare the enrichment of common interactions across homologs from related strains. We identify common nsp2 interactors involved in endoplasmic reticulum (ER) Ca2+ signaling and mitochondria biogenesis. We also identifiy nsp4 interactors unique to each strain, such as E3 ubiquitin ligase complexes for SARS-CoV-1 and ER homeostasis factors for SARS-CoV-2. Common nsp4 interactors include N-linked glycosylation machinery, unfolded protein response (UPR) associated proteins, and anti-viral innate immune signaling factors. Both nsp2 and nsp4 interactors are strongly enriched in proteins localized at mitochondrial-associated ER membranes suggesting a new functional role for modulating host processes, such as calcium homeostasis, at these organelle contact sites. Our results shed light on the role these hCoV proteins play in the infection cycle, as well as host factors that may mediate the divergent pathogenesis of OC43 from SARS strains. Our mass spectrometry workflow enables rapid and robust comparisons of multiple bait proteins, which can be applied to additional viral proteins. Furthermore, the identified common interactions may present new targets for exploration by host-directed anti-viral therapeutics.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Jonathan P Davies", - "author_inst": "Vanderbilt University" - }, - { - "author_name": "Katherine M Almasy", - "author_inst": "Vanderbilt University" - }, - { - "author_name": "Eli F McDonald", - "author_inst": "Vanderbilt University" - }, - { - "author_name": "Lars Plate", - "author_inst": "Vanderbilt University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.07.13.20148668", "rel_title": "Quantifying the impacts of human mobility restriction on the spread of COVID-19: an empirical analysis from 344 cities of China", @@ -1292248,6 +1294080,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.13.20152819", + "rel_title": "Work Related and Personal Predictors of Covid 19 transmission", + "rel_date": "2020-07-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.13.20152819", + "rel_abs": "The paper provides new evidence from a survey of 2000 individuals in the US and UK related to predictors of Covid-19 transmission. Specifically, it investigates work and personal predictors of transmission experience reported by respondents using regression models to better understand possible transmission pathways and mechanisms in the community. Three themes emerge from the analysis. Firstly, transport roles and travelling practices are significant predictors of infection. Secondly, evidence from the US especially shows union membership, consultation over safety measures and the need to use public transport to get to work are also significant predictors. This is interpreted as evidence of the role of deprivation and of reactive workplace consultations. Thirdly and finally, there is some, often weaker, evidence that income, car-owership, use of a shared kitchen, university degree type, risk-aversion, extraversion and height are predictors of transmission. The comparative nature of the evidence indicates that the less uniformly stringent nature of the US lockdown provides more information about both structural and individual factors that predict transmission. The evidence about height is discussed in the context of the aerosol transmission debate. The paper concludes that both structural and individual factors must be taken into account when predicting transmission or designing effective public health measures and messages to prevent or contain transmission.\n\nJEL CodesI1 I12 I14 I18", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Paul Anand", + "author_inst": "Open University, London School of Economics, Oxford University" + }, + { + "author_name": "Heidi Allen", + "author_inst": "Columbia University" + }, + { + "author_name": "Robert Ferrer", + "author_inst": "University of Texas at San Antonio" + }, + { + "author_name": "Natalie Gold", + "author_inst": "Oxford University" + }, + { + "author_name": "Rolando Manuel Gonzales Martinez", + "author_inst": "Agder University" + }, + { + "author_name": "Evangelos Kontopantelis", + "author_inst": "University of Manchester" + }, + { + "author_name": "Melanie Krause", + "author_inst": "University College London" + }, + { + "author_name": "Francis Vergunst", + "author_inst": "University of Montreal" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.13.20152983", "rel_title": "Smart Pooling: AI-powered COVID-19 testing", @@ -1293232,53 +1295111,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.07.15.204602", - "rel_title": "Evidence of SARS-CoV2 entry protein ACE2 in the human nose and olfactory bulb", - "rel_date": "2020-07-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.15.204602", - "rel_abs": "Usually, pandemic COVID-19 disease, caused by SARS-CoV2, presents with mild respiratory symptoms such as fever, cough but frequently also with anosmia and neurological symptom. Virus-cell fusion is mediated by Angiotensin-Converting Enzyme 2 (ACE2) and Transmembrane Serine Protease 2 (TMPRSS2) with their organ expression pattern determining viral tropism. Clinical presentation suggests rapid viral dissemination to central nervous system leading frequently to severe symptoms including viral meningitis. Here, we provide a comprehensive expression landscape of ACE2 and TMPRSS2 proteins across human, post-mortem nasal and olfactory tissue. Sagittal sections through the human nose complemented with immunolabelling of respective cell types represent different anatomically defined regions including olfactory epithelium, respiratory epithelium of the nasal conchae and the paranasal sinuses along with the hardly accessible human olfactory bulb. ACE2 can be detected in the olfactory epithelium, as well as in the respiratory epithelium of the nasal septum, the nasal conchae and the paranasal sinuses. ACE2 is located in the sustentacular cells and in the glandular cells in the olfactory epithelium, as well as in the basal cells, glandular cells and epithelial cells of the respiratory epithelium. Intriguingly, ACE2 is not expressed in mature or immature olfactory receptor neurons and basal cells in the olfactory epithelium. Similarly ACE2 is not localized in the olfactory receptor neurons albeit the olfactory bulb is positive. Vice versa, TMPRSS2 can also be detected in the sustentacular cells and the glandular cells of the olfactory epithelium.\n\nOur findings provide the basic anatomical evidence for the expression of ACE2 and TMPRSS2 in the human nose, olfactory epithelium and olfactory bulb. Thus, they are substantial for future studies that aim to elucidate the symptom of SARS-CoV2 induced anosmia of via the olfactory pathway.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Moritz Klingenstein", - "author_inst": "Institute of Neuroanatomy and Developmental Biology, Eberhard Karls University Tuebingen, Tuebingen, Germany" - }, - { - "author_name": "Stefanie Klingenstein", - "author_inst": "Institute of Neuroanatomy and Developmental Biology, Eberhard Karls University Tuebingen, Tuebingen, Germany" - }, - { - "author_name": "Peter Helmut Neckel", - "author_inst": "Institute of Clinical Anatomy and Cell Analysis, Eberhard Karls University Tuebingen, Tuebingen, Germany" - }, - { - "author_name": "Andreas F Mack", - "author_inst": "Institute of Clinical Anatomy and Cell Analysis, Eberhard Karls University Tuebingen, Tuebingen, Germany" - }, - { - "author_name": "Andreas Peter Wagner", - "author_inst": "Institute of Clinical Anatomy and Cell Analysis, Eberhard Karls University Tuebingen, Tuebingen, Germany" - }, - { - "author_name": "Alexander Kleger", - "author_inst": "Department of Internal Medicine I, University Medical Center Ulm, Ulm, Germany" - }, - { - "author_name": "Stefan Liebau", - "author_inst": "Institute of Neuroanatomy and Developmental Biology, Eberhard Karls University Tuebingen, Tuebingen, Germany" - }, - { - "author_name": "Alfio Milazzo", - "author_inst": "Institute of Neuroanatomy and Developmental Biology, Eberhard Karls University Tuebingen, Tuebingen, Germany" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2020.07.15.203059", "rel_title": "The Effect Of Famotidine On SARS-CoV-2 Proteases And Virus Replication", @@ -1293986,6 +1295818,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.12.20150110", + "rel_title": "Efficacy of Chloroquine or Hydroxychloroquine in COVID-19 Patients: A Systematic Review and Meta-Analysis", + "rel_date": "2020-07-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.12.20150110", + "rel_abs": "BackgroundChloroquine (CQ) and hydroxychloroquine (HCQ) show anti-SARS-CoV-2 activity in vitro; however, clinical studies have reported conflicting results. We sought to systematically evaluate the effect of CQ and HCQ with or without azithromycin (AZ) on outcomes of COVID-19 patients.\n\nMethodsWe searched Medline, Embase, EBM Reviews, Scopus, Web of Science, preprints and grey literature up to July 7, 2020. We included studies that assessed COVID-19 patients treated with CQ or HCQ, with or without AZ. We pooled only adjusted effect estimates of mortality using a random effect model. We summarized the effect of CQ or HCQ on viral clearance and ICU admission/ mechanical ventilation.\n\nResultsOut of 1463 citations screened for eligibility, five RCTs and 14 cohort studies were included (20,263 hospitalized patients). Thirteen studies (1 RCT and 12 cohorts) with 15,938 patients examined the effect of HCQ on short term mortality. The pooled adjusted OR was 1.05 (95% CI 0.96-1.15, I2=0 %, p=0.647). Six cohort studies examined the effect of HCQ and AZ combination among 14,016 patients. The pooled adjusted OR was 0.93 (95% CI 0.79-1.11, I2=59.3%, p=0.003). Two cohort studies and three RCTs found no significant effect of HCQ on viral clearance. One RCT with 48 patients demonstrated improved viral clearance in patients treated with CQ and HCQ. Three cohort studies found that HCQ with or without AZ had no significant effect on mechanical ventilation/ ICU admission.\n\nConclusionModerate certainty evidence suggests that HCQ, with or without AZ, lacks efficacy in reducing short-term mortality in patients hospitalized with COVID-19.\n\nSummaryThis systematic review and meta-analysis showed that in-hospital treatment of COVID-19 patients with antimalarials medications failed to reduce short-term mortality and morbidity with potential harm if used in combination with azithromycin.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Zakariya Tarek Kashour", + "author_inst": "University of Alberta" + }, + { + "author_name": "Muhammad Riaz", + "author_inst": "Quaid Azam University Islamabad" + }, + { + "author_name": "Musa garbati", + "author_inst": "University of Maiduguri" + }, + { + "author_name": "Oweida Aldosary", + "author_inst": "King Fahad Medical City" + }, + { + "author_name": "Haytham Tlayjeh", + "author_inst": "King Abdulaziz Medical City" + }, + { + "author_name": "Dana Gerberi", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "M.Hassan Murad", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "M.Rizwan Sohail", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Tarek Kashour", + "author_inst": "King Saud University" + }, + { + "author_name": "Imad M Tleyjeh", + "author_inst": "King Fahad Medical City" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.12.20151084", "rel_title": "Prehospitalization Proton Pump Inhibitor (PPI) use and Clinical Outcomes in COVID-19", @@ -1294870,33 +1296757,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.23.20135442", - "rel_title": "Spectral analysis of the daily evolution of deaths due to Covid-19 in France and in the world shows a weekend effect: myth or reality?", - "rel_date": "2020-07-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.23.20135442", - "rel_abs": "BackgroundThe weekend effect has been extensively observed for different diseases and countries and recognized as a fact but without obvious causes.\n\nObjectivesIn this paper we first aimed at investigating the existence of a periodicity in the death count due to Covid-19, and second, at opening the discussion concerning the reality of this effect in this particular context.\n\nMethodsDaily statistics of deaths due to the Covid-19 pandemic were subjected to a discrete Fourier transform spectral analysis for France and the world, over the periods from March 29 to May 16, 2020 and from January 22 to May 18, 2020 respectively.\n\nResultsIn both cases, a frequency peak of one harmonic corresponding to a period of 7.11 days was observed for France and the world. In France, this weekly frequency corresponds to a decrease in deaths every Sunday, whereas for the world the systematic decrease is shifted on average by 1.5 days and corresponds to Saturday or Friday.\n\nConclusionAt the world scale and for the epidemic period we confirm the existence of a consecutive weekend effect in the context of the Covid-19 pandemic.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Andre CONSTANTINESCO", - "author_inst": "UF6237 - Preclinical Imaging Lab, Imaging Dpt Hopitaux Universitaires de Strasbourg Hopital de Hautepierre 1, Avenue Moliere, F-67098 Strasbourg Cedex, France" - }, - { - "author_name": "Vincent ISRAEL-JOST", - "author_inst": "Centre de recherche en Epidemiologie et sante des populations (CESP), Inserm/Universite Paris-Saclay, Espace ethique/AP-HP/Ile-de-France Hopital Saint Louis 1 A" - }, - { - "author_name": "Philippe CHOQUET", - "author_inst": "UF6237 - Preclinical Imaging Lab, Imaging Dpt Hopitaux Universitaires de Strasbourg Hopital de Hautepierre 1, Avenue Moliere, F-67098 Strasbourg Cedex, France" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.13.20152710", "rel_title": "Excess mortality in mental health service users during the COVID-19 pandemic described by ethnic group: South London and Maudsley data", @@ -1295664,6 +1297524,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.12.20151753", + "rel_title": "COVID-19 incidence and R decreased on the Isle of Wight after the launch of the Test, Trace, Isolate programme", + "rel_date": "2020-07-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.12.20151753", + "rel_abs": "In May 2020 the UK introduced a Test, Trace, Isolate programme in response to the COVID-19 pandemic. The programme was first rolled out on the Isle of Wight and included Version 1 of the NHS contact tracing app. We used COVID-19 daily case data to infer incidence of new infections and estimate the reproduction number R for each of 150 Upper Tier Local Authorities in England, and at the National level, before and after the launch of the programme on the Isle of Wight. We used Bayesian and Maximum-Likelihood methods to estimate R, and compared the Isle of Wight to other areas using a synthetic control method. We observed significant decreases in incidence and R on the Isle of Wight immediately after the launch. These results are robust across each of our approaches. Our results show that the sub-epidemic on the Isle of Wight was controlled significantly more effectively than the sub-epidemics of most other Upper Tier Local Authorities, changing from having the third highest reproduction number R (of 150) before the intervention to the tenth lowest afterwards. The data is not yet available to establish a causal link. However, the findings highlight the need for further research to determine the causes of this reduction, as these might translate into local and national non-pharmaceutical intervention strategies in the period before a treatment or vaccination becomes available.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Michelle Kendall", + "author_inst": "University of Oxford" + }, + { + "author_name": "Luke Milsom", + "author_inst": "University of Oxford" + }, + { + "author_name": "Lucie Abeler-Dorner", + "author_inst": "University of Oxford" + }, + { + "author_name": "Chris Wymant", + "author_inst": "University of Oxford" + }, + { + "author_name": "Luca Ferretti", + "author_inst": "University of Oxford" + }, + { + "author_name": "Mark Briers", + "author_inst": "Alan Turing Institute" + }, + { + "author_name": "Chris Holmes", + "author_inst": "University of Oxford; Alan Turing Institute" + }, + { + "author_name": "David Bonsall", + "author_inst": "University of Oxford" + }, + { + "author_name": "Johannes Abeler", + "author_inst": "University of Oxford" + }, + { + "author_name": "Christophe Fraser", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.11.20151597", "rel_title": "Effectiveness of COCOA, a COVID-19 contact notification application, in Japan", @@ -1296616,25 +1298531,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.12.20151860", - "rel_title": "Implied susceptible population size: modelling and projecting Covid19 dynamics via the SIR equations", - "rel_date": "2020-07-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.12.20151860", - "rel_abs": "The SIR differential equations in Epidemiology are re-examined in the context of Covid19, 2020. The number of recovered cases is calibrated in time. Methods for estimating all pertinent parameters are described. A notion of implied susceptible population size ISPS is introduced, as the potential target population size for which the solution to the SIR equations would yield the current number of new affected cases. Analysis is applied to the Covid19 2020 data of a number of countries, as reported by the Johns Hopkins University data repository.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Isaac Meilijson", - "author_inst": "Tel Aviv University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.13.20152512", "rel_title": "PROJECTING A MATURE EPIDEMIC: A SIMPLE TOOL WITH AN APPLICATION TO COVID-19 DEATHS", @@ -1297250,6 +1299146,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.07.20147900", + "rel_title": "Empirical non-linear modeling & forecast of global daily deaths of COVID-19 pandemic & evidence that a third wave is beginning to decay", + "rel_date": "2020-07-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.07.20147900", + "rel_abs": "ObjectivesThe present COVID-19 pandemic (C19P) is challenging our socities all over the world. In this work, based on massive health information daily updated, the C19P daily death numbers at a global level, are modelled, analyzed and forecasted.\n\nMethodsTwo empirical models are proposed to explain daily death (DD) records: a) self-similar (SS) recurrences of the global responses, and b) geometric averaging of two independent SS models for global DD records.\n\nFindingsThe detected self-similar recurrences in the global response suggest three global \"self-similar waves\" that support multi-month forecasts of the DD numbers. However, there are upper and lower-limit SS forecast DD scenarios that were jointly integrated with a geometrical average (GA) model, that support the existence of a moderated \"third wave\", with a decaying stage for the next months (July-September 2020). It appears that the \"third world\" (South America [SAM]+Asia [ASI] +Africa [AFR]), is the actual \"big player\", (following China, and Europe [EUR]+North America [NAM]) with its biggest contribution to a global \"third wave\" (W3) of C19P.\n\nConclusionThe empirical global modeling of the C19P has suggested us a possible moderated W3 scenario, with contributions mainly coming from the third world people. This moderated W3 scenario, after to be calibrated with the last weeks, has provided to stakeholders of significant data and criteria to define, sustain and support plans for the next months, based on data and self-similarities. These scenarios provide a well-based perspective on non-linear dynamics of C19P, that will complement the standard health and economic models.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Jorge Sanchez-Sesma", + "author_inst": "Independent researcher and consultant" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.12.199588", "rel_title": "Cold sensitivity of the SARS-CoV-2 spike ectodomain", @@ -1298138,97 +1300053,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.10.20150557", - "rel_title": "Neutralizing Antibody Responses in COVID-19 Convalescent Sera", - "rel_date": "2020-07-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.10.20150557", - "rel_abs": "Passive transfer of antibodies from COVID-19 convalescent patients is being used as an experimental treatment for eligible patients with SARS-CoV-2 infections. The United States Food and Drug Administrations (FDA) guidelines for convalescent plasma recommends target antibody titers of 160. We evaluated SARS-CoV-2 neutralizing antibodies in sera from recovered COVID-19 patients using plaque reduction neutralization tests (PRNT) at low (PRNT50) and high (PRNT90) stringency thresholds. We found that neutralizing activity increased with time post symptom onset (PSO), reaching a peak at 31-35 days PSO. At this point, the number of sera having neutralizing titers of at least 160 was [~]93% (PRNT50) and [~]54% (PRNT90). Sera with high SARS-CoV-2 antibody levels (>960 ELISA titers) showed maximal activity, but not all high titer sera contained neutralizing antibody at FDA recommended levels, particularly at high stringency. These results underscore the value of serum characterization for neutralization activity.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "William T Lee", - "author_inst": "Wadsworth Center/New York State Department of Health" - }, - { - "author_name": "Roxanne C Girardin", - "author_inst": "Wadsworth Center/New York State Department of Health." - }, - { - "author_name": "Alan P Dupuis II", - "author_inst": "Wadsworth Center/New York State Department of Health" - }, - { - "author_name": "Karen E Kulas", - "author_inst": "Wadsworth Center/New York State Department of Health" - }, - { - "author_name": "Anne F Payne", - "author_inst": "Wadsworth Center/New York State Department of Health" - }, - { - "author_name": "Susan J Wong", - "author_inst": "Wadsworth Center/New York State Department of Health" - }, - { - "author_name": "Suzanne Arinsburg", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Freddy T Nguyen", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Damodara Rao Mendu", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Adolfo Firpo-Betancourt", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Jeffrey Jhang", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Ania Wajnberg", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Florian Krammer", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Carlos Cordon-Cardo", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Sherlita Amler", - "author_inst": "Westchester County Department of Health" - }, - { - "author_name": "Marisa A Montecalvo", - "author_inst": "Westchester County Department of Health" - }, - { - "author_name": "Brad Hutton", - "author_inst": "New York State Department of Health" - }, - { - "author_name": "Jill Taylor", - "author_inst": "Wadsworth Center/New York State Department of Health" - }, - { - "author_name": "Kathleen A McDonough", - "author_inst": "Wadsworth Center/New York State Department of Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.10.20150540", "rel_title": "Clinical utility of targeted SARS-CoV-2 serology testing to aid the diagnosis and management of suspected missed, late or post-COVID-19 infection syndromes: results from a pilot service", @@ -1298744,6 +1300568,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.10.20151076", + "rel_title": "Association of Cancer with Risk and Mortality of COVID-19: Results from the UK Biobank", + "rel_date": "2020-07-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.10.20151076", + "rel_abs": "Although cancer has been associated with COVID-19 risk and mortality in hospital-based studies, few population-based studies have been reported. Utilizing data from the UK Biobank (UKB), a population-based prospective cohort, we formally tested the association of over 44 different types of cancer with COVID-19 infection and mortality among 7,661 subjects who were tested by June 17, 2020. Compared to non-cancer subjects, cancer subjects (N=1,521) had significantly lower overall risk for COVID-19 infection [odds ratio (OR) and 95% confidence interval (CI): 0.79 (0.68-0.92), P=2.60E-03]. However, a trend of higher risk for COVID-19 mortality was found among 256 COVID-19 positive cancer patients, especially for hematologic cancers such as non-Hodgkin lymphoma [3.82 (1.17-12.01), P=0.02]. In cancer patients, while few demographic, lifestyle, genetic and comorbidity factors predicted risk for COVID-19 infection, older age, male sex, heart disease and hypertension significantly predicted COVID-19 mortality. The lower risk for COVID-19 infection is likely due to extra caution in COVID-19 prevention and more testing among cancer patients, an encouraging finding that demonstrates the feasibility of intervention. These results, if confirmed in future releases of UKB data and other independent populations, may provide guidance for COVID-19 prevention and treatment among cancer patients.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Zhuqing Shi", + "author_inst": "NorthShore University HealthSystem" + }, + { + "author_name": "W. Kyle Resurreccion", + "author_inst": "NorthShore University HealthSystem" + }, + { + "author_name": "Chi-Hsiung Wang", + "author_inst": "NorthShore University HealthSystem" + }, + { + "author_name": "Jun Wei", + "author_inst": "NorthShore University HealthSystem" + }, + { + "author_name": "Rong Na", + "author_inst": "NorthShore University HealthSystem" + }, + { + "author_name": "S. Lilly Zheng", + "author_inst": "NorthShore University HealthSystem" + }, + { + "author_name": "Liana K. Billings", + "author_inst": "NorthShore University HealthSystem" + }, + { + "author_name": "Brian T. Helfand", + "author_inst": "NorthShore University HealthSystem" + }, + { + "author_name": "Janardan Khandekar", + "author_inst": "NorthShore University HealthSystem" + }, + { + "author_name": "Jianfeng Xu", + "author_inst": "NorthShore University HealthSystem" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.10.20150680", "rel_title": "Addition of Tocilizumab to the standard of care reduces mortality in severe COVID-19: A systematic review and meta-analysis", @@ -1299604,89 +1301483,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.10.20147942", - "rel_title": "The emergence of COVID-19 in Indonesia: analysis of predictors of infection and mortality using independent and clustered data approaches", - "rel_date": "2020-07-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.10.20147942", - "rel_abs": "BackgroundAnalyses of correlates of SARS-CoV-2 infection or mortality have usually assessed individual predictors. This study aimed to determine if patterns of combined predictors may better identify risk of infection and mortality\n\nMethodsFor the period of March 2nd to 10th 2020, the first 9 days of the COVID-19 pandemic in Indonesia, we selected all 18 confirmed cases, of which 6 died, and all 60 suspected cases, of which 1 died; and 28 putatively negative patients with pneumonia and no travel history. We recorded data for travel, contact history, symptoms, haematology, comorbidities, and chest x-ray. Hierarchical cluster analyses (HCA) and principal component analyses (PCA) identified cluster and covariance patterns for symptoms or haematology which were analysed with other predictors of infection or mortality using logistic regression.\n\nResultsFor univariate analyses, no significant association with infection was seen for fever, cough, dyspnoea, headache, runny nose, sore throat, gastrointestinal complaints (GIC), or haematology. A PCA symptom component for fever, cough, and GIC tended to increase risk of infection (OR 3.41; 95% CI 1.06-14; p=0.06), and a haematology component with elevated monocytes decreased risk (OR 0.26; 0.07-0.79; 0.027). Multivariate analysis revealed that an HCA cluster of 3-5 symptoms, typically fever, cough, headache, runny nose, sore throat but little dyspnoea and no GIC tended to reduce risk (aOR 0.048; <0.001-0.52; 0.056). In univariate analyses for death, an HCA cluster of cough, fever and dyspnoea had increased risk (OR 5.75; 1.06 - 31.3, 0.043), but no other individual predictor, cluster or component was associated. Other significant predictors of infection were age [≥] 45, international travel, contact with COVID-19 patient, and pneumonia. Diabetes and history of contact were associated with higher mortality.\n\nConclusionsCluster groups and co-variance patterns may be stronger correlates of SARS-CoV-2 infection than individual predictors. Comorbidities may warrant careful attention as would COVID-19 exposure levels.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Erlina Burhan", - "author_inst": "Department of Pulmonology and Respiratory Medicine, Faculty of Medicine, Universitas Indonesia; Persahabatan General Hospital, Jakarta, Indonesia" - }, - { - "author_name": "Ari Fahrial Syam", - "author_inst": "Department of Internal Medicine, Faculty of Medicine, Universitas Indonesia, Dr. Cipto Mangunkusumo General Hospital, Jakarta, Indonesia" - }, - { - "author_name": "Ahmad Jabir Rahyussalim", - "author_inst": "Department of Orthopedic and Traumatology, Faculty of Medicine, Universitas Indonesia, Dr. Cipto Mangunkusumo General Hospital, Jakarta, Indonesia" - }, - { - "author_name": "Prasenohadi Prasenohadi", - "author_inst": "Department of Pulmonology and Respiratory Medicine, Faculty of Medicine, Universitas Indonesia; Persahabatan General Hospital, Jakarta, Indonesia" - }, - { - "author_name": "Navy G Lolong Wulung", - "author_inst": "Persahabatan General Hospital, Jakarta, Indonesia" - }, - { - "author_name": "Agus Dwi Susanto", - "author_inst": "Department of Pulmonology and Respiratory Medicine, Faculty of Medicine, Universitas Indonesia; Persahabatan General Hospital, Jakarta, Indonesia" - }, - { - "author_name": "I Gede Ketut Sajinadiyasa", - "author_inst": "Sanglah General Hospital, Bali, Indonesia" - }, - { - "author_name": "Dewi Puspitorini", - "author_inst": "Gatot Soebroto Central Army Hospital, Jakarta, Indonesia" - }, - { - "author_name": "Dewi Lestari", - "author_inst": "Raden Mattaher District Hospital, Jambi, Indonesia" - }, - { - "author_name": "Indah Suci Widyahening", - "author_inst": "Department of Community Medicine, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia" - }, - { - "author_name": "Vivi Setiawaty", - "author_inst": "Center for Research and Development for Biomedical and Basic Health Technology, National Institute of Health Research and Development, Ministry of Health, Repub" - }, - { - "author_name": "Dwiana Ocviyanti", - "author_inst": "Department of Obstetrics and Gynaecology, Faculty of Medicine, Universitas Indonesia, Dr. Cipto Mangunkusumo General Hospital, Jakarta, Indonesia" - }, - { - "author_name": "Kartika Qonita Putri", - "author_inst": "Medical Study Program, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia" - }, - { - "author_name": "Aswin Guntara", - "author_inst": "Medical Study Program, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia" - }, - { - "author_name": "Davrina Rianda", - "author_inst": "Human Nutrition Research Center, Indonesian Medical Education and Research Center, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia" - }, - { - "author_name": "Anuraj H Shankar", - "author_inst": "Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Eijkman-Oxford Clinical Research " - }, - { - "author_name": "Rina Agustina", - "author_inst": "Human Nutrition Research Center, Indonesian Medical Education and Research Center, Faculty of Medicine, Universitas Indonesia; Department of Nutrition, Faculty " - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.10.20149773", "rel_title": "Clinical importance of reporting SARS-CoV-2 viral loads across the different stages of the COVID-19 pandemic", @@ -1300234,6 +1302030,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.07.10.20149237", + "rel_title": "Characteristics and transmission dynamics of COVID-19 in healthcare workers at a London teaching hospital", + "rel_date": "2020-07-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.10.20149237", + "rel_abs": "BackgroundHealthcare worker (HCW) associated COVID-19 is of global concern due to the potential for nosocomial spread and depletion of staff numbers. However, the literature on transmission routes and risk factors for COVID-19 in HCWs is limited.\n\nAimTo examine the characteristics and transmission dynamics of SARS-CoV-2 in HCWs in a university teaching hospital in London, UK.\n\nMethodsStaff records and virology testing results were combined to identify staff sickness and COVID-19 rates from March to April 2020. Comparisons were made with staff professional groups, department of work and ethnicity. Analysis was performed using Microsoft Excel.\n\nFindingsCOVID-19 rates in our HCWs largely rose and declined in parallel with the number of community cases. White and non-white ethnic groups among our HCWs had similar rates of infection. Clinical staff had a higher rate of laboratory-confirmed COVID-19 than non-clinical staff, but total sickness rates were similar. Doctors had the highest rate of infection, but took the fewest sickness days. Critical Care had lower rates than the Emergency Department (ED), but rates in the ED declined once all staff were advised to use Personal Protective Equipment (PPE).\n\nConclusionThese findings show that sustained transmission of SARS-CoV-2 among our hospital staff did not occur, beyond the community outbreak, even in the absence of strict infection control measures in non-clinical areas. The results also suggest that current PPE is effective when used appropriately. In addition, our findings emphasise the importance of testing both clinical and non-clinical staff groups during a pandemic.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Charlotte Zheng", + "author_inst": "Infection Care Group, St George's University Hospitals NHS Foundation Trust, London, UK" + }, + { + "author_name": "Nema Hafezi", + "author_inst": "St George's University Hospitals NHS Foundation Trust, London, UK" + }, + { + "author_name": "Victoria Cooper", + "author_inst": "Emergency Department, St George's University Hospitals NHS Foundation Trust, London, UK" + }, + { + "author_name": "Harriet Davidson", + "author_inst": "Infection Care Group, St George's University Hospitals NHS Foundation Trust, London, UK" + }, + { + "author_name": "Maximillian Habibi", + "author_inst": "South West London Pathology, St George's University Hospitals NHS Foundation Trust, London, UK" + }, + { + "author_name": "Peter Riley", + "author_inst": "Infection Care Group, St George's University Hospitals NHS Foundation Trust, London, UK" + }, + { + "author_name": "Aodhan Breathnach", + "author_inst": "Infection Care Group, St George's University Hospitals NHS Foundation Trust, London, UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.09.20149633", "rel_title": "Antibody dynamics to SARS-CoV-2 in Asymptomatic and Mild COVID-19 patients", @@ -1301302,49 +1303141,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.08.20148973", - "rel_title": "Clinical, Behavioral and Social Factors Associated with Racial Disparities in Hospitalized and Ambulatory COVID-19 Patients from an Integrated Health Care System in Georgia", - "rel_date": "2020-07-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.08.20148973", - "rel_abs": "IntroductionRacial and ethnic minorities have shouldered a disproportioned burden of coronavirus disease 2019 (COVID-19) infection to date in the US, but data on the various drivers of these disparities is limited.\n\nObjectivesTo describe the characteristics and outcomes of COVID-19 patients and explore factors associated with hospitalization risk by race.\n\nMethodsCase series of 448 consecutive patients with confirmed COVID-19 seen at Kaiser Permanente Georgia (KPGA), an integrated health care system serving the Atlanta metropolitan area, from March 3 to May 12, 2020. KPGA members with laboratory-confirmed COVID-19. Multivariable analyses for hospitalization risk also included an additional 3489 persons under investigation (PUI) with suspected infection. COVID-19 treatment and outcomes, underlying comorbidities and quality of care management metrics, socio-demographic and other individual and community-level social determinants of health (SDOH) indicators.\n\nResultsOf 448 COVID-19 positive members, 68,3% was non-Hispanic Black (n=306), 18% non-Hispanic White (n=81) and 13,7% Other race (n=61). Median age was 54 [IQR 43-63) years. Overall, 224 patients were hospitalized, median age 60 (50-69) years. Black race was a significant factor in the Confirmed + PUI, female and male models (ORs from 1.98 to 2.19). Obesity was associated with higher hospitalization odds in the confirmed, confirmed + PUI, Black and male models (ORs from 1.78 to 2.77). Chronic disease control metrics (diabetes, hypertension, hyperlipidemia) were associated with lower odds of hospitalization ranging from 48% to 35% in the confirmed + PUI and Black models. Self-reported physical inactivity was associated with 50% higher hospitalization odds in the Black and Female models. Residence in the Northeast region of Atlanta was associated with lower hospitalization odds in the Confirmed + PUI, White and female models (ORs from 0.22 to 0.64)\n\nConclusionsWe found that non-Hispanic Black KPGA members had a disproportionately higher risk of infection and, after adjusting for covariates, twice the risk of hospitalization compared to other race groups. We found no significant differences in clinical outcomes or mortality across race/ethnicity groups. In addition to age, sex and comorbidity burden, pre-pandemic self-reported exercise, metrics on quality of care and control of underlying cardio-metabolic diseases, and location of residence in Atlanta were significantly associated with hospitalization risk by race groups. Beyond well-known physiologic and clinical factors, individual and community-level social indicators and health behaviors must be considered as interventions designed to reduce COVID-19 disparities and the systemic effects of racism are implemented.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Felipe Lobelo", - "author_inst": "The Southeast Permanente Medical Group, Kaiser Permanente Georgia" - }, - { - "author_name": "Alan X Bienvenida", - "author_inst": "The Southeast Permanente Medical Group" - }, - { - "author_name": "Serena Leung", - "author_inst": "The Southeast Permanente Medical Group" - }, - { - "author_name": "Armand N Mbanya", - "author_inst": "The Southeast Permanente Medical Group" - }, - { - "author_name": "Elizabeth J. Leslie", - "author_inst": "The Southeast Permanente Medical Group" - }, - { - "author_name": "Kate E Koplan", - "author_inst": "The Southeast Permanente Medical Group" - }, - { - "author_name": "S. Ryan Shin", - "author_inst": "The Southeast Permanente Medical Group" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.08.20147371", "rel_title": "D614G Spike Variant Does Not Alter IgG, IgM, or IgA Spike Seroassay Performance", @@ -1302196,6 +1303992,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2020.07.08.20148866", + "rel_title": "Predictors of Anxiety Regarding The COVID-19 Pandemic Among Health-care Workers in a Hospital Not Assigned to Manage COVID-19 Patients in Nepal.", + "rel_date": "2020-07-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.08.20148866", + "rel_abs": "IntroductionWe studied the levels and severity of anxiety caused by COVID-19 amongst frontline health-care workers (HCWs) in a tertiary care neurological hospital in Nepal, not assigned to manage COVID-19 cases.\n\nMethodsA cross-sectional study was conducted on 100 frontline Health Care Workers (HCWs) using a 10-point subjective assessment tool, the Anxiety Level Index (ALI), and the Zung Self Rating Anxiety Score (SAS), to assess the level of anxiety regarding COVID-19.\n\nResultsOn ALI 55% of HCW were found to have marked severe anxiety (6-9), however, on SAS 44% of HCWs reported anxiety. The majority HCWs were female (n=78) with nurses forming 62% of the sample size. The mean age ({+/-}SD) was 26.8 years ({+/-} 8.17). Factors associated with significantly higher levels of anxiety regarding COVID-19 on ALI were age (p=0.002), sex (p=0.001), receiving regular COVID-19 updates via social media (p=0.011) and a high frequency of checking for COVID-19 information authenticity (p=0.039). Work experience (p=0.026) and frequency of checking for information authenticity (p=0.029) were factors found to increase SAS measured anxiety and were found to be associated with significantly higher levels of anxiety. Multivariate logistic regression analysis showed that respondents with work experience of [≤]2 years were 0.380 (95% CI 0.158 to 0.910) times less likely to have anxiety than those with work experience of [≥]2 years. Similarly, the odds of having anxiety among those who checked information authenticity less frequently was 0.377 (95% CI 0.153 to 0.931) times less than those who often did.\n\nConclusionThe COVID-19 outbreak has caused a substantial impact on the mental health of frontline HCWs in a hospital not assigned to manage COVID-19 patients. Length of time of worked in healthcare and the frequency of checking for COVID-19-related information were significant predictors of anxiety.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Lekhjung Thapa", + "author_inst": "UDM-NINAS, Neuro and Allied Clinic" + }, + { + "author_name": "Aparna Ghimire", + "author_inst": "BPKIHS" + }, + { + "author_name": "Sulochana Ghimire", + "author_inst": "UCNS" + }, + { + "author_name": "Nooma Sharma", + "author_inst": "PAHS" + }, + { + "author_name": "Shakti Shrestha", + "author_inst": "Neuro and Allied Clinic" + }, + { + "author_name": "Medha Devkota", + "author_inst": "Portsmouth Hospitals NHS Trust" + }, + { + "author_name": "Suman Bhattarai", + "author_inst": "UDM-NINAS" + }, + { + "author_name": "Anzil Maharjan", + "author_inst": "UDM-NINAS" + }, + { + "author_name": "Subash Lohani", + "author_inst": "UDM-NINAS" + }, + { + "author_name": "Subash Phuyal", + "author_inst": "UDM-NINAS" + }, + { + "author_name": "Prathiba Maharjan", + "author_inst": "UDM-NINAS" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.07.08.20148171", "rel_title": "Sleep quality, mental health and circadian rhythms during COVID lockdown: Results from the SleepQuest Study", @@ -1303216,61 +1305071,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.07.09.196337", - "rel_title": "Discovery of clinically approved drugs capable of inhibiting SARS-CoV-2 in vitro infection using a phenotypic screening strategy and network-analysis to predict their potential to treat covid-19", - "rel_date": "2020-07-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.09.196337", - "rel_abs": "The disease caused by SARS-CoV2, covid-19, rapidly spreads worldwide, causing the greatest threat to global public health in the last 100 years. This scenario has become catastrophic as there are no approved vaccines to prevent the disease, and the main measures to contain the virus transmission are confinement and social distancing. One priority strategy is based on drug repurposing by pursuing antiviral chemotherapy that can control transmission and prevent complications associated with covid-19. With this aim, we performed a high content screening assay for the discovery of anti-SARS-CoV-2 compounds. From the 65 screened compounds, we have found four drugs capable to selectively inhibit SARS-CoV-2 in vitro infection: brequinar, abiraterone acetate, neomycin, and the extract of Hedera helix. Brequinar and abiraterone acetate had higher inhibition potency against SARS-CoV-2 than neomycin and Hedera helix extract, respectively. Drugs with reported antiviral activity and in clinical trials for covid-19, chloroquine, ivermectin, and nitazoxanide, were also included in the screening, and the last two were found to be non-selective. We used a data mining approach to build drug-host molecules-biological function-disease networks to show in a holistic way how each compound is interconnected with host node molecules and virus infection, replication, inflammatory response, and cell apoptosis. In summary, the present manuscript identified four drugs with active inhibition effect on SARS-CoV-2 in vitro infection, and by network analysis, we provided new insights and starting points for the clinical evaluation and repurposing process to treat SARS-CoV-2 infection.\n\nSummary sentenceDiscovery of drug repurposing candidates, inhibitors of SARS-CoV-2 infection in vitro, using a phenotypic screening strategy and network analysis.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Douglas Ferreira Sales-Medina", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Ludmila Rodrigues Pinto Ferreira", - "author_inst": "Universidade Federal de Minas Gerais" - }, - { - "author_name": "Lavinia M. D. Romera", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Karolina R Goncalves", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Rafael V. C. Guido", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Gilles Courtemanche", - "author_inst": "Bioaster" - }, - { - "author_name": "Marcos S. Buckeridge", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Edison Luiz Durigon", - "author_inst": "Universidade de Sao Paulo Instituto de Ciencias Biomedicas" - }, - { - "author_name": "Carolina B. Moraes", - "author_inst": "Universidade Federal de Sao Paulo" - }, - { - "author_name": "Lucio Freitas Junior", - "author_inst": "Universidade de Sao Paulo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.07.10.197889", "rel_title": "A drug repurposing screen identifies hepatitis C antivirals as inhibitors of the SARS-CoV-2 main protease.", @@ -1304130,6 +1305930,29 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.07.08.20148767", + "rel_title": "Epidemiological model for the inhomogeneous spatial spreading of COVID-19 and other diseases", + "rel_date": "2020-07-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.08.20148767", + "rel_abs": "We suggest a mathematical model for the spread of an infectious disease in human population, with particular attention to the COVID-19. Common epidemiological models, e.g., the well-known susceptible-exposed-infectious-recovered (SEIR) model, implicitly assume fast mixing of the population relative to the local infection rate, similar to the regime applicable to many chemical reactions. However, in human populations, especially under different levels of quarantine conditions, this assumption is likely to fail. We develop a continuous spatial model that includes five different populations, in which the infectious population is split into latent (or pre-symptomatic) and symptomatic. Based on nearest-neighbor infection kinetics, we arrive into a \"reaction-diffusion\" model. Our model accounts for front propagation of the infectious population domains under partial quarantine conditions, which is present on top of the common local infection process. Importantly, we also account for the variable geographic density of the population, that can strongly enhance or suppress infection spreading. Our results demonstrate how infected domains spread outward from epicenters/hotspots, leading to different regimes of sub-exponential (quasi linear or power-law) growth. Moreover, we show how weakly infected regions surrounding a densely populated area can cause rapid migration of the infection towards the center of the populated area. Predicted heat-maps show remarkable similarity to recently media released heat-maps. We further demonstrate how localized strong quarantine conditions can prevent the spreading of the disease from an epicenter/hotspot, significantly reducing the number of infected people. Application of our model in different countries, using actual demographic data and infectious disease parameters, can provide a useful predictive tool for the authorities, in particular, for planning strong lockdown measures in localizes areas.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Yoav Tsori", + "author_inst": "Ben-Gurion University of the Negev" + }, + { + "author_name": "Rony Granek", + "author_inst": "Ben-Gurion University of the Negev" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.08.20148700", "rel_title": "G6PD Deficiency Overrepresented Among Pediatric COVID-19 Cases in One Saudi Children Hospital", @@ -1305445,93 +1307268,6 @@ "type": "new results", "category": "developmental biology" }, - { - "rel_doi": "10.1101/2020.07.09.195040", - "rel_title": "Screening and testing for a suitable untransfected cell line for SARS-CoV-2 studies", - "rel_date": "2020-07-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.09.195040", - "rel_abs": "At present, the novel pandemic coronavirus SARS-CoV-2 is a major global threat to human health and hence demands united research activities at different levels. Finding appropriate cell systems for drug screening and testing molecular interactions of the virus with the host cell is mandatory for drug development and understanding the mechanisms of viral entry and replication. For this, we selected human cell lines represented in the Cancer Cell Line Encyclopedia (CCLE) based on RNA-seq data determined transcript levels of ACE2 and TMPRSS2, two membrane proteins that have been identified to aid SARS-CoV-2 entry into the host cell. mRNA and protein expression of these host factors were verified via RQ-PCR and western blot. We then tested permissiveness of these cell lines towards SARS-CoV-2 infection, cytopathic effect, and viral replication finding limited correlation between receptor expression and infectability. One of the candidate cancer cell lines, the human colon cancer cell line CL-14, tested positive for SARS-CoV-2 infection. Our data argue that SARS-CoV-2 in vitro infection models need careful selection and validation since ACE2/TMPRSS2 receptor expression on its own does not guarantee permissiveness to the virus.\n\nAuthor summaryIn the midst of the pandemic outbreak of corona-virus SARS-CoV-2 therapeutics for disease treatment are still to be tested and the virus-host-interactions are to be elucidated. Drug testing and viral studies are commonly conducted with genetically manipulated cells. In order to find a cell model system without genetic modification we screened human cell lines for two proteins known to facilitate entry of SARS-CoV-2. We confirmed and quantified permissiveness of current cell line infection models, but dismissed a number of receptor-positive cell lines that did not support viral replication. Importantly, ACE2/TMPRSS2 co-expression seems to be necessary for viral entry but is not sufficient to predict permissiveness of various cancer cell lines. Moreover, the expression of specific splice variants and the absence of missense mutations of the host factors might hint on successful infection and virus replication of the cell lines.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Claudia Pommerenke", - "author_inst": "Leibniz Institut - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH" - }, - { - "author_name": "Ulfert Rand", - "author_inst": "Helmholtz-Zentrum fur Infektionsforschung GmbH" - }, - { - "author_name": "Stefan Nagel", - "author_inst": "Leibniz Institut - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH" - }, - { - "author_name": "Margarete Zaborski", - "author_inst": "Leibniz Institut - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH" - }, - { - "author_name": "Vivien Hauer", - "author_inst": "Leibniz Institut - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH" - }, - { - "author_name": "Maren Kaufmann", - "author_inst": "Leibniz Institut - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH" - }, - { - "author_name": "Corinna Meyer", - "author_inst": "Leibniz Institut - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH" - }, - { - "author_name": "Sabine A. Denkmann", - "author_inst": "Leibniz Institut - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH" - }, - { - "author_name": "Peggy Riese", - "author_inst": "Helmholtz-Zentrum fur Infektionsforschung GmbH" - }, - { - "author_name": "Kathrin Eschke", - "author_inst": "Helmholtz-Zentrum fur Infektionsforschung GmbH" - }, - { - "author_name": "Yeonsu Kim", - "author_inst": "Helmholtz-Zentrum fur Infektionsforschung GmbH" - }, - { - "author_name": "Zeljka Macak Safranko", - "author_inst": "Klinika za Infektivne Bolesti Dr Fran Mihaljevic" - }, - { - "author_name": "Ivan-Christian Kurolt", - "author_inst": "Klinika za Infektivne Bolesti Dr Fran Mihaljevic" - }, - { - "author_name": "Alemka Markotic", - "author_inst": "Klinika za Infektivne Bolesti Dr Fran Mihaljevic" - }, - { - "author_name": "Linda Brunotte", - "author_inst": "Medical University M\u00fcnster" - }, - { - "author_name": "Stephan Ludwig", - "author_inst": "Medical University M\u00fcnster" - }, - { - "author_name": "Luka Cicin-Sain", - "author_inst": "Helmholtz-Zentrum fur Infektionsforschung GmbH" - }, - { - "author_name": "Laura Steenpa\u00df", - "author_inst": "Leibniz Institut - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2020.07.09.193680", "rel_title": "Dual nature of human ACE2 glycosylation in binding to SARS-CoV-2 spike", @@ -1306435,6 +1308171,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.07.20147983", + "rel_title": "High excess mortality during the COVID-19 outbreak in Stockholm Region areas with young and socially vulnerable populations", + "rel_date": "2020-07-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.07.20147983", + "rel_abs": "BackgroundWe aimed to describe the distribution of excess mortality (EM) during the first weeks of the COVID-19 outbreak in the Stockholm Region, Sweden, according to individual age and sex, and the sociodemographic context\n\nMethodsWeekly all-cause mortality data were obtained from Statistics Sweden for the period 01/01/2015 to 17/05/2020. EM during the first 20 weeks of 2020 was estimated by comparing observed mortality rates with expected mortality rates during the five previous years (N=2,379,792). EM variation by socioeconomic status (tertiles of income, education, Swedish-born, gainful employment) and age distribution (share of 70+ year-old persons) was explored based on Demographic Statistics Area (DeSO) data.\n\nFindingsAn EM was first detected during the week of March 23-29 2020. During the peaking week of the epidemic (6-12 April 2020), an EM of 160% was observed: 211% in 80+ year-old women; 179% in 80+ year-old men. During the same week, the highest EM was observed for DeSOs with lowest income (171%), lowest education (162%), lowest share of Swedish-born (178%), and lowest share of gainfully employed (174%). There was a 1.2 to 1.7-fold increase in EM between those areas with a higher vs. lower proportion of young people.\n\nInterpretationLiving in areas with lower socioeconomic status and younger populations is linked to COVID-19 EM. These conditions might have facilitated the viral spread. Our findings add to the well-known biological vulnerability linked to increasing age, the relevance of the sociodemographic context when estimating the individual risk to COVID-19.\n\nFundingNone.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Amaia Calderon-Larranaga", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Davide L Vetrano", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Debora Rizzuto", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Tom Bellander", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Laura Fratiglioni", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Serhiy Dekhtyar", + "author_inst": "Karolinska Institutet" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.05.20140343", "rel_title": "The COVID-19 mortality effects of underlying health conditions in India: a modelling study", @@ -1307415,49 +1309190,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2020.07.07.20148510", - "rel_title": "Modeling reductions in SARS-CoV-2 transmission and hospital burden achieved by prioritizing testing using a clinical prediction rule", - "rel_date": "2020-07-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.07.20148510", - "rel_abs": "Prompt identification of cases is critical for slowing the spread of COVID-19. However, many areas have faced diagnostic testing shortages, requiring difficult decisions to be made regarding who receives a test, without knowing the implications of those decisions on population-level transmission dynamics. Clinical prediction rules (CPRs) are commonly used tools to guide clinical decisions. We used data from electronic health records to develop a parsimonious 5-variable CPR to identify those who are most likely to test positive, and found that its application to prioritize testing increases the proportion of those testing positive in settings of limited testing capacity. To consider the implications of these gains in daily case detection on the population level, we incorporated testing using the CPR into a compartmentalized disease transmission model. We found that prioritized testing led to a delayed and lowered infection peak (i.e. \"flattens the curve\"), with the greatest impact at lower values of the effective reproductive number (such as with concurrent social distancing measures), and when higher proportions of infectious persons seek testing. Additionally, prioritized testing resulted in reductions in overall infections as well as hospital and intensive care unit (ICU) burden. In conclusion, we present a novel approach to evidence-based allocation of limited diagnostic capacity, to achieve public health goals for COVID-19.\n\nOne Sentence SummaryA clinical prediction rule to prioritize SARS-CoV-2 testing improves daily case detection, flattens and delays the curve, and reduces hospital burden.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Jody R Reimer", - "author_inst": "University of Utah" - }, - { - "author_name": "Sharia M Ahmed", - "author_inst": "University of Utah" - }, - { - "author_name": "Benjamin Brintz", - "author_inst": "University of Utah" - }, - { - "author_name": "Rashmee U Shah", - "author_inst": "University of Utah" - }, - { - "author_name": "Lindsay T Keegan", - "author_inst": "University of Utah" - }, - { - "author_name": "Matthew J Ferrari", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Daniel T Leung", - "author_inst": "University of Utah" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.06.20147199", "rel_title": "Ranking the effectiveness of worldwide COVID-19 government interventions", @@ -1308269,6 +1310001,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.06.20147348", + "rel_title": "Community prevalence of SARS-CoV-2 in England: Results from the ONS Coronavirus Infection Survey Pilot", + "rel_date": "2020-07-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.06.20147348", + "rel_abs": "ObjectiveTo estimate the percentage of individuals infected with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) over time in the community in England and to quantify risk factors.\n\nDesignRepeated cross-sectional surveys of population-representative households with longitudinal follow-up if consent given.\n\nSettingEngland\n\nParticipants34,992 Individuals aged 2 years and over from 16,722 private residential households. Data were collected in a pilot phase of the survey between 26 April and 28 June 2020.\n\nMain outcome measuresPercentage of individuals in the community testing positive for SARS-CoV-2 RNA using throat and nose swabs. Individuals were asked about any symptoms and potential risk factors.\n\nResultsThe percentage of people in private-residential households testing positive for SARS-CoV-2 reduced from 0.32% (95% credible interval (CrI) 0.19% to 0.52%) on 26 April to 0.08% (95% CrI 0.05% to 0.12%) on 28 June, although the prevalence stabilised near the end of the pilot. Factors associated with an increased risk of testing positive included having a job with direct patient contact (relative exposure (RE) 4.06, 95% CrI 2.42 to 6.77)), working outside the home (RE 2.49, 95% CrI 1.39 to 4.45), and having had contact with a hospital (RE 2.20, 95% CrI 1.09 to 4.16 for having been to a hospital individually and RE 1.95, 95% CrI 0.81 to 4.09 for a household member having been to a hospital). In 133 visits where individuals tested positive, 82 (61%, 95% CrI 53% to 69%) reported no symptoms, stably over time.\n\nConclusionThe percentage of SARS-CoV-2 positive individuals declined between 26 April and 28 June 2020. Positive tests commonly occurred without symptoms being reported. Working outside your home was an important risk factor, indicating that continued monitoring for SARS-CoV-2 in the community will be essential for early detection of increases in infections following return to work and other relaxations of control measures.\n\nWhat is already known on this topic- Unprecedented control measures, such as national lockdowns, have been widely implemented to contain the spread of SARS-CoV-2.\n- Previous mass surveillance has been based on data sources such as hospital admission, deaths or self-reported symptoms that do not measure community prevalence of virus directly.\n- Decisions regarding the continued need for social distancing measures in the overall population, specific subgroups and geographic areas heavily rely on accurate and up-to-date information about the number of people and risk factors for testing positive.\n\n\nWhat this study adds- The percentage of individuals from the general community in England testing positive for SARS-CoV-2 clearly declined between 26 April and 28 June 2020 from around one in three 300 to around one in a thousand.\n- Risk factors for testing positive included having a job with direct patient contact, having had (indirect) contact with a hospital in the past 2 weeks, and working outside your home.\n- Positive tests commonly occurred without symptoms being reported and the percentage of individuals with a positive test that reported no symptoms was stable over time.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Koen B Pouwels", + "author_inst": "University of Oxford" + }, + { + "author_name": "Thomas House", + "author_inst": "University of Manchester" + }, + { + "author_name": "Julie V Robotham", + "author_inst": "Public Health England" + }, + { + "author_name": "Paul Birrell", + "author_inst": "Public Health England" + }, + { + "author_name": "Andrew B Gelman", + "author_inst": "Columbia University" + }, + { + "author_name": "Nikola Bowers", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Ian Boreham", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Heledd Thomas", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "James Lewis", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Iain Bell", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "John I Bell", + "author_inst": "University of Oxford" + }, + { + "author_name": "John Newton", + "author_inst": "Public Health England" + }, + { + "author_name": "Jeremy Farrar", + "author_inst": "Wellcome Trust" + }, + { + "author_name": "Ian Diamond", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Pete Benton", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Sarah Walker", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.06.20147272", "rel_title": "Reopening universities during the COVID-19 pandemic: A testing strategy to minimize active cases and delay outbreaks", @@ -1308953,33 +1310764,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.07.03.20145755", - "rel_title": "WHO-INTEGRATE COVID framework Version 1.0: Criteria and considerations to guide evidence-informed decision-making on non-pharmacological interventions targeting COVID-19", - "rel_date": "2020-07-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.03.20145755", - "rel_abs": "1IntroductionDecision-making on matters of public health and health policy requires the balancing of numerous, often conflicting factors. However, a broad societal discourse and a participatory decision-making process on the criteria underpinning the decision was often not feasible within the time constraints imposed on by the SARS-CoV-2 pandemic. While evidence-to-decision frameworks are not able or intended to replace stakeholder participation, they can serve as a tool to approach relevancy and comprehensiveness of the criteria considered.\n\nObjectiveTo develop a decision-making framework adapted to the challenges of decision-making on national and sub-national level implementation of non-pharmacological interventions (NPIs) measures to contain the global SARS-CoV-2 pandemic.\n\nMethodsWe employed the \"best-fit\" framework synthesis technique and used the WHO-INTEGRATE framework Version 1.0 as a starting point. In a first phase adapted the framework through brainstorming exercises and application to exemplary case studies (e.g. school reopening). In a second phase we conducted a content analysis of comprehensive strategy documents intended to guide policymakers on the phasing out of applied lockdown measures in Germany. Based on factors and criteria identified in this process, we adapted previous framework versions into the WICID (WHO-INTEGRATE COVID-19) framework Version 1.0.\n\nResultsTwelve comprehensive strategy documents were included in the content analysis. The revised WICID framework consists of eleven criteria, supported by 48 aspects, the metacriterion quality of evidence and embraces a complexity and systems-perspective. The criteria cover implications for the health of individuals and populations due to and beyond COVID-19, infringement on liberties and fundamental human rights, acceptability and equity considerations, societal, environmental, and economic implications, as well as resource and feasibility considerations.\n\nDiscussionIn a third phase, the proposed framework will be expanded through a comprehensive document analysis focusing on key-stakeholder groups across the society. The WICID framework can be a tool to support comprehensive evidence-informed decision-making processes.\n\n2 Key-questionsO_ST_ABSWhat is already known?C_ST_ABSAd-hoc Decision-making on matters of public health and health policy such as non-pharmaceutical interventions to contain the global SARS-CoV-2 pandemic, requires decision-makers to balance numerous and often conflicting criteria. Insufficient consideration of relevant factors reduces acceptance and can limit the effectiveness of the intervention.\n\nWhat are the new findings?Based on a content-analysis of comprehensive strategy documents, we newly developed WICID framework provides of 11+1 criteria informed by 47 aspects which are intended to support decision-makers in the balancing act of identifying and considering criteria of relevance.\n\nWhat do the new findings imply?The usage of the WICID evidence-to-decision framework can support decision-makers and expert committees in making more balanced decision, even if not all voices of relevant stakeholders could be included in the process due to time constraints imposed by the rapid progress of the pandemic.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Jan M Stratil", - "author_inst": "Institute for Medical Information Processing, Biometry, and Epidemiology IBE, LMU Munich, Marchioninistr. 17, 81377 Munich and Pettenkofer School of Public" - }, - { - "author_name": "Maike Voss", - "author_inst": "German Institute for International and Security Affairs (SWP), Global Issues Division, Berlin, Germany" - }, - { - "author_name": "Laura Arnold", - "author_inst": "Academy of Public Health Services, Kanzlerstrasse 4, 40472 Duesseldorf, Germany" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.07.07.191247", "rel_title": "Alignment of virus-host protein-protein interaction networks by integer linear programming: SARS-CoV-2", @@ -1309583,6 +1311367,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.04.20143123", + "rel_title": "Implementing a Negative Pressure Isolation Space within a Skilled Nursing Facility to Control SARS-CoV-2 Transmission", + "rel_date": "2020-07-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.04.20143123", + "rel_abs": "BackgroundIsolation space must be expanded during pandemics involving airborne transmission. Little to no work has been done to establish optimal design strategies and implementation plans to ease surge capacity and expand isolation capacity over long periods in congregate living facilities. The COVID-19 pandemic has an airborne transmission component and requires isolation, which is difficult to accomplish in skilled nursing facilities.\n\nPurposeIn this study we designed, implemented, and validated an isolation space at a skilled nursing facility in Lancaster, PA. The overall goal was to minimize disease transmission between residents and staff within the facility.\n\nBasic ProceduresWe created an isolation space by modifying an existing HVAC system of the SNF. We measured pressure on-site and performed computational fluid dynamics and Lagrangian particle-based modeling to test containment and possible transmission extent given the isolation space is considered negative rather than individual rooms.\n\nMain FindingsPressure data shows the isolation space maintained an average hourly value of (standard deviation) -2.3 Pa (0.12 Pa) pressure differential between it and the external hallway connected to the rest of the facility. No transmission of SARS-CoV-2 between residents isolated to the space occurred, nor did any transmission to the staff or other residents occur. The isolation space was successfully implemented and, as of writing, continues to be operational through the pandemic.\n\nHighlightsO_LINegative pressure isolation space is an effective method to meet needed surge capacity during the COVID-19 pandemic and future pandemics\nC_LIO_LIPlanning for how and where to rapidly create a negative pressure isolation space is needed in congregate living areas such as skilled nursing facilities\nC_LIO_LIThis demonstration shows the feasibility of using low-cost and in-house systems to quickly create negative pressure within a skilled nursing facility hallway and to maintain these conditions, minimizing disease transmission between residents and staff\nC_LI", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Shelly Miller", + "author_inst": "University of Colorado Boulder" + }, + { + "author_name": "Debanjan Mukherjee", + "author_inst": "University of Colorado Boulder" + }, + { + "author_name": "Joseph Wilson", + "author_inst": "University of Colorado Boulder" + }, + { + "author_name": "Nicholas Clements", + "author_inst": "Well Living Lab, Rochester, Minnesota" + }, + { + "author_name": "Cedric Steiner", + "author_inst": "Eastern University, St. Davids, Pennsylvania" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.02.20145375", "rel_title": "Risk Factors for Mortality of COVID-19 Patients", @@ -1310183,65 +1312002,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.07.20147926", - "rel_title": "Causally Associations of Blood Lipids Levels with COVID-19 Risk: Mendelian Randomization Study", - "rel_date": "2020-07-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.07.20147926", - "rel_abs": "BackgroundCoronavirus disease 2019 (COVID-19) is a global pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2). It has been found that coronary artery disease (CAD) is a comorbid condition for COVID-19. As the risk factors of CAD, whether blood lipids levels are causally related to increasing susceptibility and severity of COVID-19 is still unknown.\n\nDesignWe performed two-sample Mendelian Randomization (MR) analyses to explore whether dyslipidemia, low density lipoprotein cholesterol (LDL-c), high density lipoprotein cholesterol (HDL-c), triglyceride (TG) and total cholesterol (TC) were causally related to COVID-19 risk and severity. The GWAS summary data of blood lipids involving in 188,578 individuals and dyslipidemia in a total of 53,991 individuals were used as exposures, respectively. Two COVID-19 GWASs including 1,221 infected patients and 1,610 severe patients defined as respiratory failure were employed as outcomes. Based on the MR estimates, we further carried out gene-based and gene-set analysis to explain the potential mechanism for causal effect.\n\nResultsThe MR results showed that dyslipidemia was casually associated with the susceptibility of COVID-19 and induced 27% higher odds for COVID-19 infection (MR-IVW OR = 1.27, 95% CI: 1.08 to 1.49, p-value = 3.18 x 10-3). Moreover, the increasing level of blood TC will raise 14 % higher odds for the susceptibility of COVID-19 (MR-IVW OR = 1.14, 95% CI: 1.04 to 1.25, p-value = 5.07 x 10-3). Gene-based analysis identified that ABO gene was associated with TC and the gene-set analysis found that immune processes were involved in the risk effect of TC.\n\nConclusionsWe obtained three conclusions: 1) Dyslipidemia is casually associated with the susceptibility of COVID-19; 2) TC is a risk factor for the susceptibility of COVID-19; 3) The different susceptibility of COVID-19 in specific blood group may be partly explained by the TC concentration in diverse ABO blood groups.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Kun Zhang", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Yan Guo", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Zhuo-Xin Wang", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Jing-Miao Ding", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Shi Yao", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Hao Chen", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Dong-Lin Zhu", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Kun Zhang", - "author_inst": "Honghui Hospital" - }, - { - "author_name": "Wei Huang", - "author_inst": "Honghui Hospital" - }, - { - "author_name": "Shan-Shan Dong", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Tie-Lin Yang", - "author_inst": "Xi'an Jiaotong University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.06.20147843", "rel_title": "The usefulness of SARS-CoV-2 test positive proportion as a surveillance tool", @@ -1310797,6 +1312557,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.06.27.20134932", + "rel_title": "Has the Indian lockdown averted deaths?", + "rel_date": "2020-07-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.27.20134932", + "rel_abs": "Within the context of SEIR models, we consider a lockdown that is both imposed and lifted at an early stage of an epidemic. We show that, in these models, although such a lockdown may delay deaths, it eventually does not avert a significant number of fatalities. Therefore, in these models, the efficacy of a lockdown cannot be gauged by simply comparing figures for the deaths at the end of the lockdown with the projected figure for deaths by the same date without the lockdown. We provide a simple but robust heuristic argument to explain why this conclusion should generalize to more elaborate compartmental models. We qualitatively discuss some important effects of a lockdown, which go beyond the scope of simple models, but could cause it to increase or decrease an epidemics final toll. Given the significance of these effects in India, and the limitations of currently available data, we conclude that simple epidemiological models cannot be used to reliably quantify the impact of the Indian lockdown on fatalities caused by the COVID-19 pandemic.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Suvrat Raju", + "author_inst": "International Centre for Theoretical Sciences" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.04.20142752", "rel_title": "Mapping Systemic Inflammation and Antibody Responses in Multisystem Inflammatory Syndrome in Children (MIS-C)", @@ -1311605,49 +1313384,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2020.07.03.20143628", - "rel_title": "Prevalence of HIV in patients hospitalized for COVID-19 and associated outcomes: a systematic review and meta-analysis", - "rel_date": "2020-07-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.03.20143628", - "rel_abs": "ObjectiveTo conduct a systematic review and meta-analysis of the prevalence of HIV in patients hospitalized for COVID-19 and delineating clinical outcomes including mortality.\n\nDesign/MethodsMEDLINE, SCOPUS, OVID, and Cochrane Library databases and medrxiv.org were searched from January 1st, 2020, to June 15th, 2020. Data were extracted from studies reporting the prevalence of HIV among hospitalized COVID-19 patients and their clinical outcomes.\n\nAnalyses were performed using random-effects models on log-transformed proportions and risk ratio estimates, and heterogeneity was quantified.\n\nResultsA total of 144,795 hospitalized COVID-19 patients were identified from 14 studies in North America, Europe, and Asia. Median age was 55 years, and 66% were male. The pooled prevalence of HIV in COVID-19 patients was 1.22% [95% confidence interval (CI): 0.61%-2.43%)] translating to a 2-fold increase compared to the respective local-level pooled HIV prevalence in the general population of 0.65% (95% CI: 0.48%-0.89%). When stratified by country, the pooled HIV prevalence among COVID-19 patients in United States (1.43%, 95% CI: 0.98%-2.07%) was significantly higher compared to Spain (0.26%, 95% CI: 0.23%-0.29%) but was not different from China (0.99%, 95% CI: 0.25%-3.85%). The pooled mortality rate in HIV-positive patients hospitalized for COVID-19 was 14.1% (95% CI: 5.78%-30.50%) and was substantially higher in the United States compared to other countries.\n\nConclusionsThe prevalence of HIV among COVID-19 patients appeared higher than the general population, suggesting a greater susceptibility to COVID-19 for PLWH. The pooled mortality rate is high, but the rates vary significantly across countries.\n\nSuggested ReviewersNelson Sewankambo, MD, PhD\n\nMakerere University College of Health Sciences\n\nOpposed Reviewers", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Paddy Ssentongo", - "author_inst": "Penn State College of Medicine" - }, - { - "author_name": "Emily S Heilbrunn", - "author_inst": "Penn State College of Medicine" - }, - { - "author_name": "Anna E Ssentongo", - "author_inst": "Penn State College of Medicine" - }, - { - "author_name": "Shailesh Advani", - "author_inst": "Georgetown University School of Medicine" - }, - { - "author_name": "Vernon M Chinchilli", - "author_inst": "Penn State College of Medicine" - }, - { - "author_name": "Jonathan J Nunez", - "author_inst": "Penn State College of Medicine" - }, - { - "author_name": "Ping Du", - "author_inst": "Penn State College of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "hiv aids" - }, { "rel_doi": "10.1101/2020.07.04.20146381", "rel_title": "Chloroquine and Hydroxychloroquine for the treatment of COVID-19: A Systematic Review and Meta-analysis", @@ -1312251,6 +1313987,41 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.07.06.189944", + "rel_title": "Mutational signatures and heterogeneous host response revealed via large-scale characterization of SARS-CoV-2 genomic diversity", + "rel_date": "2020-07-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.06.189944", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWTo dissect the mechanisms underlying the inflation of variants in the SARS-CoV-2 genome, we present one of the largest up-to-date analyses of intra-host genomic diversity, which reveals that most samples present heterogeneous genomic architectures, due to the interplay between host-related mutational processes and transmission dynamics.\n\nThe deconvolution of the set of intra-host minor variants unveils the existence of non overlapping mutational signatures related to specific nucleotide substitutions, which prove that distinct hosts respond differently to SARS-CoV-2 infections, and which are likely ruled by APOBEC, Reactive Oxygen Species (ROS) and ADAR.\n\nThanks to a corrected-for-signatures dN/dS analysis we demonstrate that the mutational processes underlying such signatures are affected by purifying selection, with important exceptions. In fact, several mutations linked to low-rate mutational processes appear to transit to clonality in the population, eventually leading to the definition of new clonal genotypes and to a statistically significant increase of overall genomic diversity.\n\nImportantly, the analysis of the phylogenetic model shows the presence of multiple homoplasies, due to mutational hotspots, phantom mutations or positive selection, and supports the hypothesis of transmission of minor variants during infections. Overall, the results of this study pave the way for the integrated characterization of intra-host genomic diversity and clinical outcome of SARS-CoV-2 hosts.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Alex Graudenzi", + "author_inst": "Inst. of Molecular Bioimaging and Physiology, Consiglio Nazionale delle Ricerche (IBFM-CNR), Segrate, Milan, Italy" + }, + { + "author_name": "Davide Maspero", + "author_inst": "Dept. of Informatics, Systems and Communication, Univ. of Milan-Bicocca, Milan, Italy" + }, + { + "author_name": "Fabrizio Angaroni", + "author_inst": "Dept. of Informatics, Systems and Communication, Univ. of Milan-Bicocca, Milan, Italy" + }, + { + "author_name": "Rocco Piazza", + "author_inst": "Dept. of Medicine and Surgery, Univ. of Milan-Bicocca, Monza, Italy" + }, + { + "author_name": "Daniele Ramazzotti", + "author_inst": "Dept. of Medicine and Surgery, Univ. of Milan-Bicocca, Monza, Italy" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "genetics" + }, { "rel_doi": "10.1101/2020.07.06.190348", "rel_title": "SARS-CoV-2 contributes to altering the post-transcriptional regulatory networks across human tissues by sponging RNA binding proteins and micro-RNAs", @@ -1312911,45 +1314682,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.07.03.184846", - "rel_title": "The potential role of miR-21-3p in coronavirus-host interplay", - "rel_date": "2020-07-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.03.184846", - "rel_abs": "ABSTRACTHost miRNAs are known as important regulators of virus replication and pathogenesis. They can interact with various viruses by several possible mechanisms including direct binding the viral RNA. Identification of human miRNAs involved in coronavirus-host interplay is becoming important due to the ongoing COVID-19 pandemic. In this work we performed computational prediction of high-confidence direct interactions between miRNAs and seven human coronavirus RNAs. In order to uncover the entire miRNA-virus interplay we further analyzed lungs miRNome of SARS-CoV infected mice using publicly available miRNA sequencing data. We found that miRNA miR-21-3p has the largest probability of binding the human coronavirus RNAs and being dramatically up-regulated in mouse lungs during infection induced by SARS-CoV. Further bioinformatic analysis of binding sites revealed high conservativity of miR-21-3p binding regions within RNAs of human coronaviruses and their strains.Competing Interest StatementThe authors have declared no competing interest.View Full Text", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Stepan Nersisyan", - "author_inst": "Higher School of Economics" - }, - { - "author_name": "Narek Engibaryan", - "author_inst": "Higher School of Economics" - }, - { - "author_name": "Aleksandra Gorbonos", - "author_inst": "Higher School of Economics" - }, - { - "author_name": "Ksenia Kirdey", - "author_inst": "Higher School of Economics" - }, - { - "author_name": "Alexey Makhonin", - "author_inst": "Higher School of Economics" - }, - { - "author_name": "Alexander Tonevitsky", - "author_inst": "Higher School of Economics" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.07.04.187989", "rel_title": "A pH-dependent switch mediates conformational masking of SARS-CoV-2 spike", @@ -1313629,6 +1315361,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.02.20145151", + "rel_title": "Association of SARS-CoV-2 Genomic Load with COVID-19 Patient Outcomes", + "rel_date": "2020-07-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.02.20145151", + "rel_abs": "RationaleThe Infectious Diseases Society of America has identified the use of SARS-CoV-2 genomic load for prognostication purposes as a key research question.\n\nObjectivesWe explored the SARS-CoV-2 genomic load as a risk factor for adverse patient outcomes.\n\nMethodsA retrospective cohort study among adult patients admitted to the hospital between March 31st to April 10th, 2020 with COVID-19 pneumonia was conducted. We segregated patients into 3 genomic load groups: low (Cycle threshold (Ct) [≥]35), intermediate (250.25ng/ml. Primary outcomes included antibiotic consumption, mortality, intensive care admission and length of hospital stay.\n\nResults368 patients met the inclusion criteria; 218 (59%) had a negative PCT and 150 (41%) positive. At 48 hours post-diagnosis, 73 (33%) of those with a negative PCT were receiving antimicrobials compared to 126 (84%) with a positive PCT (p<0.001), with a corresponding reduction in antimicrobial usage over 28 days (median DDD of 3.0 vs 6.8 (p<0.001); median DOT 2 vs 5 days (p<0.001) between the negative and positive PCT groups.) In the negative PCT group, there were fewer deaths (62 (28%) vs. 54 (36%), (p=0.021)) and critical care admissions (19 (9%) vs. 28 (19%), (p=0.007)) than in the positive PCT group. Median length of hospital stay was 8.7 and 9 days in the negative and positive PCT groups respectively.\n\nConclusionsProcalcitonin is a valuable tool in the assessment of patients with SARS-CoV-2 infection, safely reducing the potential burden of unnecessary antibiotic usage.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Emma Jane Williams", + "author_inst": "Sheffield Teaching Hospitals NHS Foundation Trust" + }, + { + "author_name": "Luke Mair", + "author_inst": "Sheffield Teaching Hospitals NHS Foundation Trust" + }, + { + "author_name": "Thushan I. de Silva", + "author_inst": "Sheffield Teaching Hospitals NHS Foundation Trust" + }, + { + "author_name": "Dan J. Green", + "author_inst": "School of Health and Related Research (ScHARR), University of Sheffield" + }, + { + "author_name": "Philip House", + "author_inst": "Sheffield Teaching Hospitals NHS Foundation Trust" + }, + { + "author_name": "Kay Cawthron", + "author_inst": "Sheffield Teaching Hospitals NHS Foundation Trust" + }, + { + "author_name": "Christopher Gillies", + "author_inst": "Sheffield Teaching Hospitals NHS Foundation Trust" + }, + { + "author_name": "James Wigfull", + "author_inst": "Sheffield Teaching Hospitals NHS Foundation Trust" + }, + { + "author_name": "Helena Parsons", + "author_inst": "Sheffield Teaching Hospitals NHS Foundation Trust" + }, + { + "author_name": "David G. Partridge", + "author_inst": "Sheffield Teaching Hospitals NHS Foundation Trust" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.02.184481", "rel_title": "Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission", @@ -1318951,189 +1320774,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.06.29.20142430", - "rel_title": "Standard operating procedures for SARS-CoV-2 detection by a clinical diagnostic RT-LAMP assay", - "rel_date": "2020-07-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.29.20142430", - "rel_abs": "The ongoing pandemic of SARS-CoV-2 calls for rapid and cost-effective methods to accurately identify infected individuals. The vast majority of patient samples is assessed for viral RNA presence by RT-qPCR. Our biomedical research institute, in collaboration between partner hospitals and an accredited clinical diagnostic laboratory, established a diagnostic testing pipeline that has reported on more than 40,000 RT-qPCR results since its commencement at the beginning of April 2020. However, due to ongoing demand and competition for critical resources, alternative testing strategies were sought. In this work, we present a clinically-validated standard operating procedure (SOP) for high-throughput SARS-CoV-2 detection by RT-LAMP in 25 minutes that is robust, reliable, repeatable, sensitive, specific, and inexpensive.", - "rel_num_authors": 42, - "rel_authors": [ - { - "author_name": "Michael D. Buck", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Enzo Z. Poirier", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Ana Cardoso", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Bruno Frederico", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Johnathan Canton", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Sam Barrell", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Rupert Beale", - "author_inst": "The Francis Crick Institute; University College London" - }, - { - "author_name": "Richard Byrne", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Simon Caidan", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Margaret Crawford", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Laura Cubitt", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Steve Gamblin", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Sonia Gandhi", - "author_inst": "The Francis Crick Institute; University College London; University College London Hospitals, NHS Foundation Trust" - }, - { - "author_name": "Robert Goldstone", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Paul R. Grant", - "author_inst": "Health Service Laboratories" - }, - { - "author_name": "Kiran Gulati", - "author_inst": "New England Biolabs" - }, - { - "author_name": "Steve Hindmarsh", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Michael Howell", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Michael Hubank", - "author_inst": "The Royal Marsden Hospital; The Institute of Cancer Research" - }, - { - "author_name": "Rachael Instrell", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Ming Jiang", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "George Kassiotis", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Wei-Ting Lu", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "James I. MacRae", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Iana Martini", - "author_inst": "The Royal Free Hospital" - }, - { - "author_name": "Davin Miller", - "author_inst": "New England Biolabs" - }, - { - "author_name": "David Moore", - "author_inst": "University College London; University College London Hospitals, NHS Foundation Trust" - }, - { - "author_name": "Eleni Nastouli", - "author_inst": "University College London Hospitals, NHS Foundation Trust; University College London GOS Institute of Child Health" - }, - { - "author_name": "Jerome Nicod", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Luke Nightingale", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Jessica Olsen", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Amin Oomatia", - "author_inst": "The Royal Free Hospital" - }, - { - "author_name": "Nicola O'Reilly", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Anett Rideg", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Ok-Ryul Song", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Amy Strange", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Charles Swanton", - "author_inst": "The Francis Crick Institute; University College London; University College London Hospitals, NHS Foundation Trust" - }, - { - "author_name": "Samra Turajlic", - "author_inst": "The Francis Crick Institute; The Royal Marsden Hospital" - }, - { - "author_name": "Philip A. Walker", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Mary Wu", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Caetano Reis e Sousa", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "- Crick COVID-19 Consortium", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2020.06.29.20141978", "rel_title": "Pseudo-Likelihood Based Logistic Regression for Estimating COVID-19 Infection and Case Fatality Rates by Gender, Race, and Age in California", @@ -1319981,6 +1321621,41 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.06.24.20133249", + "rel_title": "Real-world Experience with Favipiravir for Treatment of COVID-19 in Thailand: Results from a Multi-center Observational Study", + "rel_date": "2020-07-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.24.20133249", + "rel_abs": "SYNOPSISO_ST_ABSBackgroundC_ST_ABSFavipiravir is a broad-spectrum oral antiviral agent that shows in vitro activity against SARS-CoV-2. Presently, data on the effectiveness and optimal dosage of favipiravir for treating COVID-19 is limited.\n\nMethodsWe conducted a retrospective observational study of hospitalized adult patients with COVID-19 at five tertiary care hospitals in Thailand. We reviewed patient charts to obtain all necessary data.\n\nResultsAmong 247 COVID-19 patients, 63 (23.0%) received [≥]1 dose of favipiravir. Of these, 27.0% required an O2-nasal cannula, 9.5% required non-invasive ventilation and/or high-flow O2-therapy, and 6.4% required invasive mechanical ventilation and/or ECMO. The median baseline NEWS2 score was 5(0-16). The Day-7 clinical improvement rate [95%CI] was 66.7%[53.7-78.0%] in all patients, 92.5%[75.7%-99.1%] in patients who did not require O2-supplementation, and 47.2%[0.4%-64.5%] in patients who required O2-supplementation. No life-threatening adverse events were identified. The 28-day mortality rate was 4.8%.\n\nMultivariate analysis revealed three poor prognostic factors for Day-7 clinical improvement [odds ratio (95%CI); p-value]: older age [0.94 (0.89-0.99); p=0.04], higher baseline NEWS2 score [0.64 (0.47-0.88); p=0.006], and lower favipiravir loading dose ([≤]45 mg/kg/day) [0.04 (0.005-0.4); p=0.006].\n\nConclusionsOur study reports the promising effectiveness of favipiravir for treating COVID-19 patients. In addition to older age and a high baseline NEWS2 score, a low loading dose of favipiravir ([≤]45 mg/kg/day) was also identified as a poor prognostic factor for early clinical improvement. Further studies to explore the optimal dose and the optimal timing of drug initiation for favipiravir should be performed.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Pinyo Rattanaumpawan", + "author_inst": "Faculty of Medicine Siriraj Hospital, Mahidol University" + }, + { + "author_name": "Supunnee Jirajariyavej", + "author_inst": "Taksin Hospital" + }, + { + "author_name": "Kanokorn Lerdlamyong", + "author_inst": "Vachira Phuket Hospital" + }, + { + "author_name": "Nattawan Palavutitotai", + "author_inst": "Lerdsin Hospital" + }, + { + "author_name": "Jatuporn Saiyarin", + "author_inst": "Central Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.30.20142877", "rel_title": "Quantifying the impact of US state non-pharmaceutical interventions on COVID-19 transmission", @@ -1320973,53 +1322648,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.06.30.179663", - "rel_title": "Genetic variants in TMPRSS2 and Structure of SARS-CoV-2 spike glycoprotein and TMPRSS2 complex", - "rel_date": "2020-06-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.30.179663", - "rel_abs": "SARS-CoV-2, a highly transmittable pathogen has infected over 3.8 million people around the globe. The spike glycoprotein of SARS-CoV-2 engages host ACE2 for adhesion, TMPRSS2 for activation and entry. With the aid of whole-exome sequencing, we report a variant rs12329760 in TMPRSS2 gene and its mutant V160M, which might impede viral entry. Furthermore, we identified TMPRSS2 cleavage sites in S2 domain of spike glycoprotein and report the structure of TMPRSS2 in complex with spike glycoprotein. We also report the structures of protease inhibitors in complex with TMPRSS2, which could hamper the interaction with spike protein. These findings advance our understanding on the role of TMPRSS2 and in the development of potential therapeutics.Competing Interest StatementThe authors have declared no competing interest.View Full Text", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Ravikanth Vishnubhotla", - "author_inst": "Institute of Translational Research, Department of Genomics and Molecular Biology, Asian Institute of Gastroenterology and AIG Hospitals, Gachibowli, Hyderabad " - }, - { - "author_name": "Naveen Vankadari", - "author_inst": "Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia." - }, - { - "author_name": "Vijayasarathy Ketavarapu", - "author_inst": "Institute of Translational Research, Department of Genomics and Molecular Biology, Asian Institute of Gastroenterology and AIG Hospitals, Gachibowli, Hyderabad " - }, - { - "author_name": "Ramars Amanchy", - "author_inst": "Division of Applied Biology, CSIR-IICT (Indian Institute of Chemical Technology), Ministry of Science and Technology (GOI), Hyderabad 500007, Telangana, India" - }, - { - "author_name": "Steffie Avanthi", - "author_inst": "Institute of Translational Research, Department of Genomics and Molecular Biology, Asian Institute of Gastroenterology and AIG Hospitals, Gachibowli, Hyderabad " - }, - { - "author_name": "Govardhan Bale", - "author_inst": "Institute of Translational Research, Department of Genomics and Molecular Biology, Asian Institute of Gastroenterology and AIG Hospitals, Gachibowli, Hyderabad " - }, - { - "author_name": "Duvvur Nageshwar Reddy", - "author_inst": "Institute of Translational Research, Department of Genomics and Molecular Biology, Asian Institute of Gastroenterology and AIG Hospitals, Gachibowli, Hyderabad " - }, - { - "author_name": "Mitnala Sasikala", - "author_inst": "AIG Hospitals" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "genetics" - }, { "rel_doi": "10.1101/2020.06.30.178897", "rel_title": "A glycan cluster on the SARS-CoV-2 spike ectodomain is recognized by Fab-dimerized glycan-reactive antibodies", @@ -1321903,6 +1323531,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, + { + "rel_doi": "10.1101/2020.06.29.20142703", + "rel_title": "Evidence for structural protein damage and membrane lipid remodeling in red blood cells from COVID-19 patients", + "rel_date": "2020-06-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.29.20142703", + "rel_abs": "The SARS-CoV-2 beta coronavirus is the etiological driver of COVID-19 disease, which is primarily characterized by shortness of breath, persistent dry cough, and fever. Because they transport oxygen, red blood cells (RBCs) may play a role in the severity of hypoxemia in COVID-19 patients.\n\nThe present study combines state-of-the-art metabolomics, proteomics, and lipidomics approaches to investigate the impact of COVID-19 on RBCs from 23 healthy subjects and 29 molecularly-diagnosed COVID-19 patients. RBCs from COVID-19 patients had increased levels of glycolytic intermediates, accompanied by oxidation and fragmentation of ankyrin, spectrin beta, and the N-terminal cytosolic domain of band 3 (AE1). Significantly altered lipid metabolism was also observed, especially short and medium chain saturated fatty acids, acyl-carnitines, and sphingolipids. Nonetheless, there were no alterations of clinical hematological parameters, such as RBC count, hematocrit, and mean corpuscular hemoglobin concentration, with only minor increases in mean corpuscular volume. Taken together, these results suggest a significant impact of SARS-CoV-2 infection on RBC structural membrane homeostasis at the protein and lipid levels. Increases in RBC glycolytic metabolites are consistent with a theoretically improved capacity of hemoglobin to off-load oxygen as a function of allosteric modulation by high-energy phosphate compounds, perhaps to counteract COVID-19-induced hypoxia. Conversely, because the N-terminus of AE1 stabilizes deoxyhemoglobin and finely tunes oxygen off-loading, RBCs from COVID-19 patients may be incapable of responding to environmental variations in hemoglobin oxygen saturation when traveling from the lungs to peripheral capillaries and, as such, may have a compromised capacity to transport and deliver oxygen.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC=\"FIGDIR/small/20142703v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (46K):\norg.highwire.dtl.DTLVardef@16db0d2org.highwire.dtl.DTLVardef@73b808org.highwire.dtl.DTLVardef@1374ee5org.highwire.dtl.DTLVardef@1cbbc8_HPS_FORMAT_FIGEXP M_FIG C_FIG Key PointsO_LICOVID-19 promotes oxidation and fragmentation of membrane proteins, including the N-term of band 3\nC_LIO_LIRBCs from COVID-19 patients are characterized by increases in glycolysis and altered lipidomes\nC_LIO_LICOVID-19 impacts two critical mechanisms that finely tune red cell membranes and hemoglobin oxygen affinity\nC_LI", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Tiffany Thomas", + "author_inst": "Columbia University, New York, NY, USA" + }, + { + "author_name": "Davide Stefanoni", + "author_inst": "University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, USA" + }, + { + "author_name": "Monika Dzieciatkowska", + "author_inst": "University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, USA" + }, + { + "author_name": "Aaron Issaian", + "author_inst": "University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, USA" + }, + { + "author_name": "Travis Nemkov", + "author_inst": "University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, USA" + }, + { + "author_name": "Ryan C Hill", + "author_inst": "University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, USA" + }, + { + "author_name": "Richard O Francis", + "author_inst": "Columbia University, New York, NY, USA" + }, + { + "author_name": "Krystalyn E Hudson", + "author_inst": "Columbia University, New York, NY, USA" + }, + { + "author_name": "Paul W Buehler", + "author_inst": "University of Maryland, Baltimore, MD, USA" + }, + { + "author_name": "James C Zimring", + "author_inst": "University of Virginia, Charlottesville, VA, USA" + }, + { + "author_name": "Eldad A Hod", + "author_inst": "Columbia University, New York, NY, USA" + }, + { + "author_name": "Kirk C Hansen", + "author_inst": "University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, USA" + }, + { + "author_name": "Steven L Spitalnik", + "author_inst": "Columbia University, New York, NY, USA" + }, + { + "author_name": "Angelo D'Alessandro", + "author_inst": "University of Colorado Denver - Anschutz Medical Campus" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "hematology" + }, { "rel_doi": "10.1101/2020.06.29.20142661", "rel_title": "COVID-19, smoking, vaping and quitting: A representative population survey in England", @@ -1322975,37 +1324674,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.06.21.20128181", - "rel_title": "Face Masks Considerably Reduce Covid-19 Cases in Germany", - "rel_date": "2020-06-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.21.20128181", - "rel_abs": "We use the synthetic control method to analyze the effect of face masks on the spread of Covid-19 in Germany. Our identification approach exploits regional variation in the point in time when face masks became compulsory. Depending on the region we analyse, we find that face masks reduced the cumulative number of registered Covid-19 cases between 2.3% and 13% over a period of 10 days after they became compulsory. Assessing the credibility of the various estimates, we conclude that face masks reduce the daily growth rate of reported infections by around 40%.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Timo Mitze", - "author_inst": "University of Southern Denmark" - }, - { - "author_name": "Reinhold Kosfeld", - "author_inst": "University of Kassel" - }, - { - "author_name": "Johannes Rode", - "author_inst": "TU Darmstadt" - }, - { - "author_name": "Klaus W\u00e4lde", - "author_inst": "Johannes Gutenberg-University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2020.06.25.20137935", "rel_title": "Blood parameters measured on admission as predictors of outcome for COVID-19; a prospective UK cohort study", @@ -1323893,6 +1325561,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.06.27.20141614", + "rel_title": "Beta regression with spatio-temporal effects as a tool for hospital impact analysis of initial phase epidemics: the case of COVID-19 in Spain", + "rel_date": "2020-06-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.27.20141614", + "rel_abs": "COVID-19 has put an extraordinary strain on medical staff around the world, but also on hospital facilities and the global capacity of national healthcare systems. In this paper, Beta regression is introduced as a tool to analyze the rate of hospitalization and the proportion of Intensive Care Unit admissions over both hospitalized and diagnosed patients, with the aim of explaining as well as predicting, and thus allowing to better anticipate, the impact on hospital resources during an early-phase epidemic. This is applied to the initial phase COVID-19 pandemic in Spain and its different regions from 20-Feb to 08-Apr of 2020. Spatial and temporal factors are included in the Beta distribution through a precision factor. The model reveals the importance of the lagged data of hospital occupation, as well as the rate of recovered patients. Excellent agreement is found for next-day predictions, while even for multiple-day predictions (up to 12 days), robust results are obtained in most cases in spite of the limited reliability and consistency of the data.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Gil Jannes", + "author_inst": "Complutense University of Madrid" + }, + { + "author_name": "Jesus Barreal", + "author_inst": "Complutense University of Madrid" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2020.06.29.20142364", "rel_title": "Estimation of COVID-19 dynamics in the different states of the United States using Time-Series Clustering", @@ -1324837,153 +1326528,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.06.28.20141929", - "rel_title": "Outcomes and Cardiovascular Comorbidities in a Predominantly African-American Population with COVID-19", - "rel_date": "2020-06-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.28.20141929", - "rel_abs": "ImportanceRacial disparities in COVID-19 outcomes have been amplified during this pandemic and reports on outcomes in African-American (AA) populations, known to have higher rates of cardiovascular (CV) comorbidities, remain limited.\n\nObjectiveTo examine prevalence of comorbidities, rates of hospitalization and survival, and incidence of CV manifestations of COVID-19 in a predominantly AA population in south metropolitan Chicago.\n\nDesign, Setting, ParticipantsThis was an observational cohort study of COVID-19 patients encountered from March 16 to April 16, 2020 at the University of Chicago. Deidentified data were obtained from an institutional data warehouse. Group comparisons and logistic regression modeling based on baseline demographics, clinical characteristics, laboratory and diagnostic testing was performed.\n\nExposuresCOVID-19 was diagnosed by nasopharyngeal swab testing and clinical management was at the discretion of treating physicians.\n\nMain Outcomes and MeasuresPrimary outcomes were hospitalization and in-hospital mortality, and secondary outcomes included incident CV manifestations of COVID-19 in the context of overall cardiology service utilization.\n\nResultsDuring the 30 day study period, 1008 patients tested positive for COVID-19 and 689 had available encounter data. Of these, 596 (87%) were AA and 356 (52%) were hospitalized, of which 319 (90%) were AA. Age > 60 years, tobacco use, BMI >40 kg/m2, diabetes mellitus (DM), insulin use, hypertension, chronic kidney disease, coronary artery disease (CAD), and atrial fibrillation (AF) were more common in hospitalized patients. Age > 60 years, tobacco use, CAD, and AF were associated with greater risk of in-hospital mortality along with several elevated initial laboratory markers including troponin, NT-proBNP, blood urea nitrogen, and ferritin. Despite this, cardiac manifestations of COVID-19 were uncommon, coincident with a 69% decrease in cardiology service utilization. For hospitalized patients, median length of stay was 6.2 days (3.4-11.9 days) and mortality was 13%. AA patients were more commonly hospitalized, but without increased mortality.\n\nConclusions and RelevanceIn this AA-predominant experience from south metropolitan Chicago, CV comorbidities and chronic diseases were highly prevalent and associated with increased hospitalization and mortality. Insulin-requiring DM and CKD emerged as novel predictors for hospitalization. Despite the highest rate of comorbidities reported to date, CV manifestations of COVID-19 and mortality were relatively low. The unexpectedly low rate of mortality merits further study.\n\nKEY POINTSO_ST_ABSQuestionsC_ST_ABSWhat comorbidities are present in African Americans (AA) with COVID-19 and what are the associations with subsequent hospitalization and mortality? What is the incidence of COVID-19-associated cardiac manifestations requiring cardiology service utilization?\n\nFindingsIn this observational cohort study that included 689 patients with COVID-19 from south metropolitan Chicago (87% AA), cardiovascular (CV) comorbidities were highly prevalent and more common in those that required hospitalization. In addition to AA, age > 60 years, tobacco use, BMI >40 kg/m2, diabetes mellitus, hypertension, chronic kidney disease, coronary artery disease (CAD), and atrial fibrillation (AF) were more common in those hospitalized. Age > 60 years, tobacco use, CAD, and AF were associated with in-hospital mortality. Despite this, cardiac manifestations of COVID-19 were uncommon, and cardiology service utilization was low. In-hospital mortality was 13%. AA patients were more commonly hospitalized, but without increased mortality.\n\nMeaningIn a predominantly AA population with COVID-19 at a major academic hospital located in south metropolitan Chicago, CV comorbidities were common and were risk factors for hospitalization and death. Although the highest rates of comorbidities to date were present in this cohort, mortality was relatively low and merits further study.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Ann B. Nguyen", - "author_inst": "University of Chicago Medicine" - }, - { - "author_name": "Gaurav A. Upadhyay", - "author_inst": "University of Chicago Medicine" - }, - { - "author_name": "Ben Chung", - "author_inst": "University of Chicago Medicine" - }, - { - "author_name": "Bryan Smith", - "author_inst": "University of Chicago Medicine" - }, - { - "author_name": "Stephanie A. Besser", - "author_inst": "University of Chicago Medicine" - }, - { - "author_name": "Julie A. Johnson", - "author_inst": "University of Chicago Medicine" - }, - { - "author_name": "John Blair", - "author_inst": "University of Chicago Medicine" - }, - { - "author_name": "R. Parker Ward", - "author_inst": "University of Chicago Medicine" - }, - { - "author_name": "Jeanne DeCara", - "author_inst": "University of Chicago Medicine" - }, - { - "author_name": "Tamar Polonsky", - "author_inst": "University of Chicago Medicine" - }, - { - "author_name": "Amit R. Patel", - "author_inst": "University of Chicago Medicine" - }, - { - "author_name": "Jonathan Grinstein", - "author_inst": "University of Chicago Medicine" - }, - { - "author_name": "Luise Holzhauser", - "author_inst": "University of Chicago Medicine" - }, - { - "author_name": "Rohan Kalathiya", - "author_inst": "University of Chicago Medicine" - }, - { - "author_name": "Atman P. Shah", - "author_inst": "University of Chicago Medicine" - }, - { - "author_name": "Jonathan Paul", - "author_inst": "University of Chicago Medicine" - }, - { - "author_name": "Sandeep Nathan", - "author_inst": "University of Chicago Medicine" - }, - { - "author_name": "James Liao", - "author_inst": "University of Chicago Medicine" - }, - { - "author_name": "Roberto M. Lang", - "author_inst": "University of Chicago Medicine" - }, - { - "author_name": "Krysta Wolfe", - "author_inst": "University of Chicago Medicine" - }, - { - "author_name": "Ayodeji Adegunsoye", - "author_inst": "University of Chicago Medicine" - }, - { - "author_name": "David Wu", - "author_inst": "University of Chicago Medicine" - }, - { - "author_name": "Bhakti Patel", - "author_inst": "University of Chicago Medicine" - }, - { - "author_name": "Monica E. Peek", - "author_inst": "University of Chicago Medicined" - }, - { - "author_name": "Doriane Miller", - "author_inst": "University of Chicago Medicine" - }, - { - "author_name": "Dinesh J. Kurian", - "author_inst": "University of Chicago Medicine" - }, - { - "author_name": "Stephen R. Estime", - "author_inst": "University of Chicago Medicine" - }, - { - "author_name": "Allison Dalton", - "author_inst": "University of Chicago Medicine" - }, - { - "author_name": "Avery Tung", - "author_inst": "University of Chicago Medicine" - }, - { - "author_name": "Michael F. O'Connor", - "author_inst": "University of Chicago Medicine" - }, - { - "author_name": "John P. Kress", - "author_inst": "University of Chicago Medicine" - }, - { - "author_name": "Francis J. Alenghat", - "author_inst": "University of Chicago Medicine" - }, - { - "author_name": "Roderick Tung", - "author_inst": "University of Chicago Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.28.20141994", "rel_title": "Impact of the Novel Coronavirus Disease (COVID-19) on Treatment Adherence and Sleep Duration in Obstructive Sleep Apnea Patients Treated with Positive Airway Pressure", @@ -1325535,6 +1327079,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.28.20142141", + "rel_title": "The Influence of Time-Limited Immunity on a COVID-19 Epidemic: A Simulation Study", + "rel_date": "2020-06-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.28.20142141", + "rel_abs": "A series of spreadsheet simulations using SEIS, SEIR, and SEIRS models showed that different durations of effective immunity could have important consequences for the prevalence of an epidemic disease with COVID-19 characteristics. Immunity that lasted four weeks, twelve weeks, six months, one year, and two years was tested with pathogen R0 values of 1.5, 2.3, and 3.0. Shorter durations of immunity resulted in oscillations in disease prevalence. Immunity that lasted from three months to two years produced recurrent disease outbreaks triggered by the expiration of immunity. If immunity \"faded out\" gradually instead of persisting at full effectiveness to the end of the immune period, the recurrent outbreaks became more frequent. The duration of effective immunity is an important consideration in the epidemiology of a disease like COVID-19.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Robert Joseph Kosinski", + "author_inst": "retired from Clemson University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.28.20141986", "rel_title": "Protocol for the development and evaluation of a tool for predicting risk of short-term adverse outcomes due to COVID-19 in the general UK population", @@ -1326311,49 +1327874,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.06.26.174672", - "rel_title": "Role of Anti-SARS-CoV-2 antibodies in different cohorts: Can they provide clues for appropriate patient triaging?", - "rel_date": "2020-06-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.26.174672", - "rel_abs": "The emergence of coronavirus disease 2019 (COVID-19) has become a major global health crisis. Currently, diagnosis is based on molecular techniques, which detect the viral nucleic acids when present at detectable levels. The serum IgG response against SARS-CoV-2 was examined by using an ELISA-based assay. Serum samples, along with nasopharyngeal specimens were collected from various cohorts and analyzed by ELISA and rRT-PCR, respectively. A total of 167 serum samples were tested for serum IgG antibodies against SARS-CoV-2 in outpatient cohorts, 15 (8.9%) were positive by rRT-PCR and the remaining 152 (91%) were negative. We used these data to generate two different assay cutoffs for serum IgG assay and investigated percent concordance with rRT-PCR test results. The emergency department data revealed, out of 151 nasopharyngeal swabs, 4 (2.6%) were positive by rRT-PCR and 18 (11.9%) were positive for serum IgG assay. Among the 18 patients that were positive for serum IgG, 13 (72.2%) exhibited 1-3 symptoms of COVID-19 and 5 (27.7%) patients did not present with any COVID-19 related symptoms, per CDC criteria. All 4 (100%) patients that were positive by rRT-PCR had symptoms of COVID-19 disease. A longitudinal study from the inpatient population suggested there was a sharp increase in the serum IgG titers in 5 patients, a moderate increase in 1 patient and a plateau in 3 patients. Sero-prevalence of COVID-19 disease in pre-procedure patients was 5.5%. Our findings suggest serological tests can be used for appropriate patient triaging when performed as an adjunct to existing molecular testing.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Manohar B Mutnal", - "author_inst": "Baylor Scott and White Medical Center" - }, - { - "author_name": "Amin A Mohammad", - "author_inst": "Baylor Scott and White Health Medical Center" - }, - { - "author_name": "Alejandro C. Arroliga", - "author_inst": "Baylor Scott and White Medical Center / Texas A&M University" - }, - { - "author_name": "Yinan Hua", - "author_inst": "Baylor Scott and White Health Medical Center" - }, - { - "author_name": "Liping Wang", - "author_inst": "Baylor Scott and White Health Medical Center" - }, - { - "author_name": "William Koss", - "author_inst": "Baylor Scott and White Health Medical Center" - }, - { - "author_name": "Arundhati Rao", - "author_inst": "Baylor Scott and White Healthcare" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.06.28.175802", "rel_title": "Whole-Genome Sequences of the Severe Acute Respiratory Syndrome Coronavirus-2 obtained from Romanian patients between March and June of 2020", @@ -1327093,6 +1328613,33 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.06.26.20141242", + "rel_title": "Memory-Dependent Model for the Dynamics of COVID-19 Pandemic", + "rel_date": "2020-06-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.26.20141242", + "rel_abs": "COVID-19 pandemic has impacted people all across the world. As a result, there has been a collective effort to monitor, predict, and control the spread of this disease. Among this effort is the development of mathematical models that could capture accurately the available data and simulate closely the futuristic scenarios. In this paper, a fractional-order memory-dependent model for simulating the spread of COVID-19 is proposed. In this model, the impact of governmental action and public perception are incorporated as part of the time-varying transmission rate. The model simulation is performed using the two-step generalized exponential time-differencing method and tested for data from Wuhan, China. The mean-square errors demonstrate the merit of the fractional-order model and provide a good estimate of the optimal order.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Khaled M Furati", + "author_inst": "King Fahd University of Petroleum and Minerals" + }, + { + "author_name": "Ibrahim O. Sarumi", + "author_inst": "King Fahd University of Petroleum & Minerals" + }, + { + "author_name": "Abdul Q.M. Khaliq", + "author_inst": "Middle Tennessee State University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.26.20141150", "rel_title": "Social media and smartphone app use predicts maintenance of physical activity during Covid-19 enforced isolation in psychiatric outpatients", @@ -1327837,65 +1329384,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.06.25.20140392", - "rel_title": "Lung Ultrasound Findings in Patients Hospitalized with Covid-19", - "rel_date": "2020-06-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.25.20140392", - "rel_abs": "IntroductionPoint-of-care ultrasound (POCUS) has the potential to transform healthcare delivery in the era of COVID-19 with its diagnostic and therapeutic expediency. It can be performed by clinicians already at the bedside, which permits an immediate and augmented assessment of a patient. Although lung ultrasound can be used to accurately diagnose a variety of disease states such as pneumothorax, pleural effusions, pneumonia and interstitial lung disease2, there are limited reports on the sonographic manifestations of COVID-19. There is an urgent need to identify alternative diagnostic modalities that can be immediately employed at the bedside of COVID-19 patients.\n\nMethodsThis study was conducted at two medical centers in the United States from 3/21/2020-6/01/2020. Any adult who was hospitalized with COVID-19 (based on symptomatology and a confirmatory RT-PCR for SARS-CoV-2) and received a pulmonary POCUS examination was included. Providers were instructed to use a 12-zone scanning protocol for pulmonary views and save 6 second clips of each lung zone. This study utilized several POCUS devices, including Butterfly IQ, Vave, Lumify, and Sonosite. The collected images were interpreted by the study researchers based on a consensus document developed by the study authors and previously accepted definitions of lung POCUS findings.\n\nResultsA total of 22 eligible patients who received 36 lung scans were included in our study. Eleven (50%) patients experienced clinical deterioration (defined as either ICU admission, invasive mechanical ventilation, or death within 28 days from the initial symptom onset). Among the 36 lung scans collected, only 3 (8%) were classified as normal. The remaining scans had the following abnormalities: presence of B-lines (n=32, 89%), consolidations (n=20, 56%), pleural thickening (n=17, 47%), and pleural effusion (n=4, 11%). Out of 20 scans with consolidations, 14 (70%) were subpleural and 5 (25%) were translobar. A-lines were present in 26 (72%) of patients, although they were only observed in the majority of the collected lung zones in 5 (14%) of patients. Ultrasound findings were stratified by time from symptom onset to the scan based on the following time periods: early (0-6 days), middle (7-13 days), and late (14-28 days). B-lines appeared early after symptom onset and persisted well into the late disease course. In contrast, pleural thickening increased in frequency over time (early: 25%, middle: 47%, late: 67%). Subpleural consolidations also appeared in higher frequency later in the disease course (early: 13%, middle 42%, late: 56%).\n\nDiscussioncertain lung ultrasound findings may be common in Covid-19, while others may appear later in the disease course or only occur in patients who experience clinical deterioration. Future efforts should investigate the predictive utility of consolidations, pleural thickening and B-lines for clinical deterioration and compare them to traditional radiological studies such as X-rays or CTs.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Andre D Kumar", - "author_inst": "Stanford University" - }, - { - "author_name": "Sukyung Chung", - "author_inst": "Stanford University" - }, - { - "author_name": "Youyou Duanmu", - "author_inst": "Stanford University" - }, - { - "author_name": "Sally Graglia", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Farhan Lalani", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Kavita Gandhi", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Viveta Lobo", - "author_inst": "Stanford University" - }, - { - "author_name": "Trevor Jensen", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Yingjie Weng", - "author_inst": "Stanford University" - }, - { - "author_name": "Jeffrey Nahn", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "John Kugler", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.26.20139063", "rel_title": "Sex, age, and hospitalization drive antibody responses in a COVID-19 convalescent plasma donor population", @@ -1328607,6 +1330095,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2020.06.24.20139121", + "rel_title": "Exploring Causal relationship between risk factors and vulnerability to COVID-19Cases of Italy, Spain, France, Greece, Portugal, Morocco and South Africa", + "rel_date": "2020-06-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.24.20139121", + "rel_abs": "Even though the infection rate of COVID-19 is very high as of today 31 May: 5,819,962 confirmed cases worldwide, the death rate is only about 6.23%, 362,786 deaths as for the same date. Furthermore, the rate of total infected cases is extremely different from one country to another as well as for the rate of mortality. Therefore, there may be some factors that possibly amplify the rate of infection from one country to another as well as for the rate of mortality due to COVID-19. In the literature, we have found multiple identified risk factors responsible for vulnerability to COVID19, we have chosen pertinent key risk factors for our study: Median-age, age>65 years old, weight, population density, diabetics, International arrivals, median temperature between March and May.\n\nObjectiveWe aim to find correlation between the identified risk factors and vulnerability to COVID-19 in seven different countries from Europe and Africa: Most affected countries Italy, Spain, France, moderately affected: Portugal, and less affected countries: Greece, Morocco and South Africa.\n\nData sourcesWHO, Worldometers, Ourworldindata\n\nPopulationall reported COVID-19 total in-hospital infected and death cases in Italy, Spain, France, Portugal, Greece, Morocco, and South Africa.\n\nTime period15th March 2020 to 15th May 2020\n\nMethodsWe used Multiple linear regression in our approach to modeling the relationship between the dependent variable (DV): vulnerability to COVID19 (which we presented by number of totals in-hospital infected cases per million for each country) and the independent variables (IV) scores: median age, aged 65+, population density, international arrivals, BMI, diabetes prevalence, and temperature. We used SPSS software to generate multiple linear regression; Pearson correlation factor: r, ANOVA table, Coefficients table, as well as bar charts and scatter plots.\n\nThe multiple linear regression equation of our study model is: O_FD O_INLINEFIG[Formula 1]C_INLINEFIGM_FD(1)C_FD\n\nWhere:\n\nY: Predicted score on total cases per million or Vulnerability to COVID19; a: intercept; b1: regression coefficient or weight for median age; X1: median age; b2: regression coefficient or weight for population density; X2: population density; b3: regression coefficient or weight for international arrivals; X3: international arrivals in millions; b4: regression coefficient or weight average temperature; X4: average temperature in Celsius; b5: regression coefficient or weight for BMI; X5: BMI Body Mass Index in Kg/m; b6: regression coefficient or weight for diabetes prevalence percentage; X6: diabetes prevalence percentage; B7: regression coefficient or weight for aged 65+; X7: aged 65+ percentage\n\nResultsTill 15th May 2020 There were in Spain: 229540 total infected cases and 27321 total death attributed to COVID-19, France: 141356 total cases and 27425 total deaths, Italy: 223096 total cases and 31368 total deaths, Portugal: 28319 total cases and 1184 total deaths, Greece: 2770 total cases and 156 total deaths, Morocco: 6607 total cases and 190 total deaths, and South Africa: 12739 total cases and 238 total deaths. In summary after full adjustment, total death cases were strongly associated with total infected cases for the population of all the seven chosen countries combined: correlation factor r= 0.921 with a P-value= .000: P<0.05 (Sig.(2-tailed). Population density was significantly correlated with total infected cases for all the seven countries combined: r= 0.478 with a P-value= .000: P<0.05. the median age was moderately associated with infected cases: r= 0.563 with P<0.05. However, diabetes prevalence was less associated with infected cases: r= 0.146 with P<0.05. International exposure was significantly associated with infected cases: r= 0.609 with P<0.05. Median temperature was negatively correlated with total infected cases in the seven countries combined.\n\nConclusionsWe have quantified a range of risk factors for infection and death from COVID-19, in seven highly, moderate and less affected countries, in a large correlation-regression study. People from countries with high international exposure, high population density, are at markedly risk of getting infected such as France, Spain, and Italy. Moreover, people from countries with high median age are at increased risk of in-hospital death from COVID19. Furthermore, by conducting multiple linear regression analysis we have found that the overall regression model is significant (as shown in the tables). 66.2% (r2=.662) of the vulnerability is explained by the model which includes all predictor variables or risk factors.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC=\"FIGDIR/small/20139121v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (56K):\norg.highwire.dtl.DTLVardef@bde5b4org.highwire.dtl.DTLVardef@133ac9aorg.highwire.dtl.DTLVardef@188c58aorg.highwire.dtl.DTLVardef@611a13_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "ABDLEGHANI YOUMNI", + "author_inst": "MUNDIAPOLIS UNIVERSITY" + }, + { + "author_name": "MBAREK CHAYKH", + "author_inst": "Mundiapolis University Casablanca" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.06.23.20138370", "rel_title": "Novel coronavirus (COVID-19) Outbreak in Iraq: The First Wave and Future Scenario", @@ -1329367,85 +1330878,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, - { - "rel_doi": "10.1101/2020.06.24.20139436", - "rel_title": "Characterization of a novel, low-cost, scalable vaporized hydrogen peroxide system for sterilization of N95 respirators and other COVID-19 related personal protective equipment.", - "rel_date": "2020-06-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.24.20139436", - "rel_abs": "Due to the virulence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogen responsible for the respiratory disease termed COVID-19, there has been a significant increase in demand for surgical masks and N95 respirators in medical clinics as well as within communities operating during the COVID-19 epidemic. Thus, community members, business owners, and even medical personnel have resorted to alternative methods for sterilizing face coverings and N95 respirators for reuse. While significant work has shown that vaporized hydrogen peroxide (VHP) can be used to sterilize N95 respirators, the cost and installation time for these sterilization systems limit their accessibility. To this end, we have designed and constructed a novel, cost-effective, and scalable VHP system that can be used to sterilize N95 respirators and other face coverings for clinical and community applications. N95 respirators inoculated with P22 bacteriophage showed a greater than 6-log10 reduction in viral load when sterilized in the VHP system for one 60-minute cycle. Further, N95 respirators treated with 20 cycles in this VHP system showed comparable filtration efficiency to untreated N95 respirators in a 50 to 200 nanometer particulate challenge filtration test. While a 23% average increase in water droplet roll-off time was observed for N95 respirators treated with 5 cycles in the sterilization, no breakdown in fluid resistance was detected. These data suggest that our VHP system is effective in sterilizing N95 respirators and other polypropylene masks for reuse. Relating to the present epidemic, deployment of this system reduces the risk of COVID-19 community transmission while conserving monetary resources otherwise spent on the continuous purchase of disposable N95 respirators and other face coverings. In summary, this novel, scientifically validated sterilization system can be easily built at a low cost and implemented in a wide range of settings.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Nikhil Dave", - "author_inst": "Arizona State University" - }, - { - "author_name": "Katie Sue Pascavis", - "author_inst": "Arizona State University" - }, - { - "author_name": "John M Patterson", - "author_inst": "Arizona State University" - }, - { - "author_name": "David W Wallace", - "author_inst": "Arizona State University" - }, - { - "author_name": "Abhik Chowdhury", - "author_inst": "Arizona State University" - }, - { - "author_name": "Morteza Abbaszadegan", - "author_inst": "Arizona State University" - }, - { - "author_name": "Absar Alum", - "author_inst": "Arizona State University" - }, - { - "author_name": "Pierre Herckes", - "author_inst": "Arizona State University" - }, - { - "author_name": "Zhaobo Zhang", - "author_inst": "Arizona State University" - }, - { - "author_name": "Michael Kozicki", - "author_inst": "Arizona State University" - }, - { - "author_name": "Erica Forzani", - "author_inst": "Arizona State University" - }, - { - "author_name": "Sabrina Jimena Mora", - "author_inst": "Arizona State University" - }, - { - "author_name": "Josh Chang", - "author_inst": "Arizona State University" - }, - { - "author_name": "Clinton Ewell", - "author_inst": "Arizona State University" - }, - { - "author_name": "Tyler Smith", - "author_inst": "Arizona State University" - }, - { - "author_name": "Mark Naufel", - "author_inst": "Arizona State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2020.06.24.20134783", "rel_title": "Analytical and Clinical Validation for RT-qPCR detection of SARS-CoV-2 without RNA extraction", @@ -1330045,6 +1331477,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.24.20139501", + "rel_title": "A direct RT-qPCR approach to test large numbers of individuals for SARS-CoV-2", + "rel_date": "2020-06-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.24.20139501", + "rel_abs": "SARS-CoV-2 causes substantial morbidity and mortality in elderly and immunocompromised individuals, particularly in retirement homes, where transmission from asymptomatic staff and visitors may introduce the infection. Here we present a cheap and fast approach to detect SARS-CoV-2 in single or pooled gargle lavages (\"mouthwashes\"). With this approach, we test all staff at a nursing home daily over a period of three weeks in order to reduce the risk that the infection penetrates the facility. This or similar approaches could be implemented to protect hospitals, nursing homes and other institutions in this and future viral epidemics.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Tomislav Maricic", + "author_inst": "Max Planck Institute for Evolutionary Anthropology" + }, + { + "author_name": "Olaf Nickel", + "author_inst": "Hospital St. Georg" + }, + { + "author_name": "Ayinuer Aximu-Petri", + "author_inst": "Max Planck Institute for Evolutionary Anthropology" + }, + { + "author_name": "Elena Essel", + "author_inst": "Max Planck Institute for Evolutionary Anthropology" + }, + { + "author_name": "Marie Gansauge", + "author_inst": "Max Planck Institute for Evolutionary Anthropology" + }, + { + "author_name": "Philipp Kanis", + "author_inst": "Max Planck Institute for Evolutionary Anthropology" + }, + { + "author_name": "Dominik Macak", + "author_inst": "Max Planck Institute for Evolutionary Anthropology" + }, + { + "author_name": "Stephan Riesenberg", + "author_inst": "Max Planck Institute for Evolutionary Anthropology" + }, + { + "author_name": "Lukas Bokelmann", + "author_inst": "Max Planck Institute for Evolutionary Anthropology" + }, + { + "author_name": "Hugo Zeberg", + "author_inst": "Max Planck Institute for Evolutionary Anthropology" + }, + { + "author_name": "Matthias Meyer", + "author_inst": "Max Planck Institute for Evolutionary Anthropology" + }, + { + "author_name": "Stephan Borte", + "author_inst": "Hospital St. Georg" + }, + { + "author_name": "Svante Paabo", + "author_inst": "Max Planck Institute for Evolutionary Anthropology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.25.20137323", "rel_title": "Factors Associated with Hospitalization and Disease Severity in a Racially and Ethnically Diverse Population of COVID-19 Patients", @@ -1330769,93 +1332268,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.06.26.173476", - "rel_title": "In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges", - "rel_date": "2020-06-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.26.173476", - "rel_abs": "The spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is required for cell entry and is the major focus for vaccine development. We combine cryo electron tomography, subtomogram averaging and molecular dynamics simulations to structurally analyze S in situ. Compared to recombinant S, the viral S is more heavily glycosylated and occurs predominantly in a closed pre-fusion conformation. We show that the stalk domain of S contains three hinges that give the globular domain unexpected orientational freedom. We propose that the hinges allow S to scan the host cell surface, shielded from antibodies by an extensive glycan coat. The structure of native S contributes to our understanding of SARS-CoV-2 infection and the development of safe vaccines. The large scale tomography data set of SARS-CoV-2 used for this study is therefore sufficient to resolve structural features to below 5 [A]ngstrom, and is publicly available at EMPIAR-10453.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Beata Turo\u0148ov\u00e1", - "author_inst": "European Molecular Biology Laboratory" - }, - { - "author_name": "Mateusz Sikora", - "author_inst": "Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany" - }, - { - "author_name": "Christoph Sch\u00fcrmann", - "author_inst": "Division of Veterinary Medicine, Paul Ehrlich Institute, Paul Ehrlich Strasse 51-59, 63225 Langen, Germany." - }, - { - "author_name": "Wim J. H. Hagen", - "author_inst": "European Molecular Biology Laboratory, Structural and Computational Biology" - }, - { - "author_name": "Sonja Welsch", - "author_inst": "Central electron microscopy facility, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany." - }, - { - "author_name": "Florian E. C. Blanc", - "author_inst": "Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany" - }, - { - "author_name": "S\u00f6ren von B\u00fclow", - "author_inst": "Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany" - }, - { - "author_name": "Michael Gecht", - "author_inst": "Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany" - }, - { - "author_name": "Katrin Bagola", - "author_inst": "Division of Immunology, Paul Ehrlich Institute, Paul Ehrlich Strasse 51-59, 63225 Langen, Germany." - }, - { - "author_name": "Cindy H\u00f6rner", - "author_inst": "Division of Veterinary Medicine, Paul Ehrlich Institute, Paul Ehrlich Strasse 51-59, 63225 Langen, Germany. German Center for Infection Research, Giessen-Marbur" - }, - { - "author_name": "Ger van Zandbergen", - "author_inst": "Division of Immunology, Paul Ehrlich Institute, Paul Ehrlich Strasse 51-59, 63225 Langen, Germany; Institute for Immunology, University Medical Center, Johannes" - }, - { - "author_name": "Shyamal Mosalaganti", - "author_inst": "European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstr. 1, Germany; Department of Molecular Sociology, Max Planck Institu" - }, - { - "author_name": "Andre Schwarz", - "author_inst": "European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstr. 1, Germany" - }, - { - "author_name": "Roberto Covino", - "author_inst": "Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany; Frankfurt Institute for Advance" - }, - { - "author_name": "Michael D. M\u00fchlebach", - "author_inst": "Division of Veterinary Medicine, Paul Ehrlich Institute, Paul Ehrlich Strasse 51-59, 63225 Langen, Germany; German Center for Infection Research, Giessen-Marbur" - }, - { - "author_name": "Gerhard Hummer", - "author_inst": "Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany; Institute of Biophysics, Goethe" - }, - { - "author_name": "Jacomine Krijnse Locker", - "author_inst": "Electron Microscopy of Pathogens Unit, Paul Ehrlich Institute, Paul Ehrlich Strasse 51-59, 63225 Langen, Germany." - }, - { - "author_name": "Martin Beck", - "author_inst": "European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstr. 1, Germany; Department of Molecular Sociology, Max Planck Institu" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2020.06.26.171033", "rel_title": "Evaluation of K18-hACE2 mice as a model of SARS-CoV-2 infection", @@ -1331579,6 +1332991,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.26.173567", + "rel_title": "Adhesive Contact Between Cylindrical (Ebola) and Spherical (SARS-CoV-2) Viral Particles and a Cell Membrane", + "rel_date": "2020-06-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.26.173567", + "rel_abs": "A critical event during the process of cell infection by a viral particle is attachment, which is driven by adhesive interactions and resisted by bending and tension. The biophysics of this process has been studied extensively but the additional role of externally applied force or displacement has generally been neglected. In this work we study the adhesive force-displacement response of viral particles against a cell membrane. We have built two models: one in which the viral particle is cylindrical (say, representative of filamentous virus such as Ebola) and another in which it is spherical (such as SARS-CoV-2 and Zika). Our interest is in initial adhesion, in which case deformations are small and the mathematical model for the system can be simplified considerably. The parameters that characterize the process combine into two dimensionless groups that represent normalized membrane bending stiffness and tension. In the limit where bending dominates, for sufficiently large values of normalized bending stiffness, there is no adhesion between viral particles and the cell membrane without applied force. (The zero-external-force contact width and pull-off force are both zero.) For large values of normalized membrane tension, the adhesion between virus and cell membrane is weak but stable. (The contact width at zero external force has a small value.) Our results for pull-off force and zero force contact width help to quantify conditions that could aid the development of therapies based on denying the virus entry into the cell by blocking its initial adhesion.Competing Interest StatementThe authors have declared no competing interest.View Full Text", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Jiajun Wang", + "author_inst": "Lehigh University" + }, + { + "author_name": "Nicole Fortoul", + "author_inst": "Lehigh University" + }, + { + "author_name": "X. Frank Zhang", + "author_inst": "Lehigh University" + }, + { + "author_name": "Anand Jagota", + "author_inst": "Lehigh University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2020.06.26.152520", "rel_title": "Ag nanoparticles-based antimicrobial polycotton fabrics to prevent the transmission and spread of SARS-CoV-2", @@ -1332259,57 +1333702,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, - { - "rel_doi": "10.1101/2020.06.22.20137505", - "rel_title": "An analysis of COVID-19 article dissemination by Twitter compared to citation rates", - "rel_date": "2020-06-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.22.20137505", - "rel_abs": "BackgroundThe COVID-19 pandemic has resulted in over 1,000,000 cases across 181 countries worldwide. The global impact of COVID-19 has resulted in a surge of related research. Researchers have turned to social media platforms, namely Twitter, to disseminate their articles. The online database Altmetric is a tool which tracks the social media metrics of articles and is complementary to traditional, citation-based metrics. Citation-based metrics may fail to portray dissemination accurately, due to the lengthy publication process. Altmetrics are not subject to this time-lag, suggesting that they may be an effective marker of research dissemination during the COVID-19 pandemic.\n\nObjectivesTo assess the dissemination of COVID-19 articles as measured by Twitter dissemination, compared to traditional citation-based metrics, and determine article characteristics associated with tweet rates.\n\nMethodsCOVID-19 articles obtained from LitCovid published between January 1st to March 18th, 2020 were screened for inclusion. The following article characteristics were extracted independently, in single: Topic (General Info, Mechanism, Diagnosis, Transmission, Treatment, Prevention, Case Report, and Epidemic Forecasting), open access status (open access and subscription-based), continent of corresponding author (Asia, Australia, Africa, North America, South America, and Europe), tweets, and citations. A sign test was used to compare the tweet rate and citation rate per day. A negative binomial regression analysis was conducted to evaluate the association between tweet rate and article characteristics of interest.\n\nResults1328 articles were included in the analysis. Tweet rates were found to be significantly higher than citation rates for COVID-19 articles, with a median tweet rate of 1.09 (IQR 6.83) tweets per day and median citation rate of 0.00 (IQR 0.00) citations per day, resulting in a median of differences of 1.09 (95% CI 0.86-1.33, P < .001). 2018 journal impact factors were positively correlated with tweet rate (P < .001). The topics Diagnosis (P = .01), Transmission (P < .001), Treatment (P = .01), and Epidemic Forecasting (P < .001) were positively correlated with tweet rate, relative to Case Report. The following continents of the corresponding author were negatively correlated with tweet rate, Africa (P < .001), Australia (P = .03), and South America (P < .001), relative to Asia. Open access journals were negatively correlated with tweet rate, relative to subscription-based journals (P < .001).\n\nConclusionsCOVID-19 articles had significantly higher tweets rates compared to citation rates. This study further identified article characteristics that are correlated with the dissemination of articles on Twitter, such as 2018 journal impact factor, continent of the corresponding author, topic, and open access status. This highlights the importance of altmetrics in periods of rapidly expanding research, such as the COVID-19 pandemic to localize highly disseminated articles.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Nicholas Fabiano", - "author_inst": "University of Ottawa" - }, - { - "author_name": "Zachary Hallgrimson", - "author_inst": "University of Ottawa" - }, - { - "author_name": "Sakib Kazi", - "author_inst": "University of Ottawa" - }, - { - "author_name": "Jean-Paul Salameh", - "author_inst": "Ottawa Hospital Research Institute" - }, - { - "author_name": "Stanley Wong", - "author_inst": "University of Ottawa" - }, - { - "author_name": "Abrar Kazi", - "author_inst": "Carleton University" - }, - { - "author_name": "Rudy R Unni", - "author_inst": "University of Ottawa" - }, - { - "author_name": "Ross Prager", - "author_inst": "University of Ottawa" - }, - { - "author_name": "Matthew DF McInnes", - "author_inst": "University of Ottawa & Ottawa Hospital Research Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.06.22.20136309", "rel_title": "Surveillance testing of SARS-CoV-2", @@ -1332924,6 +1334316,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.06.24.20138198", + "rel_title": "The remaining unknowns: A determination of the current research priorities for COVID-19 by the global health research community", + "rel_date": "2020-06-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.24.20138198", + "rel_abs": "IntroductionIn March 2020 the World Health Organisation (WHO) released a Global Research Roadmap in an effort to coordinate and accelerate the global research response to combat COVID-19 based on deliberations of 400 experts across the world. Three months on, the disease and our understanding have both evolved significantly. As we now tackle a pandemic in very different contexts and with increased knowledge, we sought to build on the work of the WHO to gain a more current and global perspective on these initial priorities.\n\nMethodsWe undertook a mixed methods study seeking the views of the global research community to i) assess which of the early WHO roadmap priorities are still most pressing; ii) understand whether they are still valid in different settings, regions or countries; and iii) identify any new emerging priorities.\n\nResultsThematic analysis of the significant body of combined data shows the WHO roadmap is globally relevant, however, new important priorities have emerged, in particular, pertinent to low and lower-middle income countries (less resourced countries), where health systems are under significant competing pressures. We also found a shift from prioritising vaccine and therapeutic development towards a focus on assessing the effectiveness, risks, benefits and trust in the variety of public health interventions and measures. Our findings also provide insight into temporal nature of these research priorities, highlighting the urgency of research that can only be undertaken within the period of virus transmission, as well as other important research questions but which can be answered outside the transmission period. Both types of studies are key to help combat this pandemic but also importantly to ensure we are better prepared for the future.\n\nConclusionWe hope these findings will help guide decision making across the broad research system including the multi-lateral partners, research funders, public health practitioners, clinicians and civil society.\n\nSummary boxO_ST_ABSWhat is already known?C_ST_ABSThe WHO produced a roadmap that set out the research priorities following a meeting in February, just before COVID-19 was declared a Pandemic. Now, at this point in the evolution of this novel disease across the world, and almost 6 months later, it is important to assess whether these priorities remain and if research teams in all countries across the globe agree that these are the most important question that need to be tackled within their health care setting and communities, both to mitigate this outbreak and to learn for next time.\n\nWhat are the new findings?Over 3,000 healthcare workers and researchers contributed to this research and their data tells us that across the globe there has been a shift in priorities and new questions have emerged, particularly from low-resourced settings. For example, there is a strong call for evidence on the relative effectiveness and optimal implementation of public health interventions in varied global settings, for social science studies to guide how to gain public trust and mitigate myths, to understand the impact on already present diseases within communities, and to explore the ethics of research within a pandemic.\n\nWhat do the new findings imply?The WHO roadmap is globally relevant, however, our findings also provide insight into the temporal nature of these research priorities, highlighting the urgency of research that can only be undertaken within the period of virus transmission, as well as other important research questions but which can be answered outside the transmission period. Both types of studies are key to help combat this pandemic but also importantly to ensure we are better prepared for the future.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Alice Norton", + "author_inst": "UK Collaborative on Development Research" + }, + { + "author_name": "Arancha De La Horra Gozalo", + "author_inst": "Centre for Tropical Medicine and Global Health" + }, + { + "author_name": "Nicole Feune de Colombi", + "author_inst": "Centre for Tropical Medicine and Global Health" + }, + { + "author_name": "Moses Alobo", + "author_inst": "African Academy of Science" + }, + { + "author_name": "Juliete Mutheu Asego", + "author_inst": "African Academy of Science" + }, + { + "author_name": "Zainab Al-Rawni", + "author_inst": "Centre for Tropical Medicine and Global Health" + }, + { + "author_name": "Emila Antonio", + "author_inst": "UK Collaborative on Development Research" + }, + { + "author_name": "James Parker", + "author_inst": "Centre for Tropical Medicine and Global Health" + }, + { + "author_name": "Wayne Mwangi", + "author_inst": "African Academy of Science" + }, + { + "author_name": "Colette Adhiambo", + "author_inst": "African Academy of Science" + }, + { + "author_name": "Kevin Marsh", + "author_inst": "African Academy of Science" + }, + { + "author_name": "Marta Tufet Bayona", + "author_inst": "UK Collaborative on Development Research" + }, + { + "author_name": "Peter Piot", + "author_inst": "UK Collaborative on Development Research" + }, + { + "author_name": "Trudie A. Lang", + "author_inst": "Centre for Tropical Medicine and Global Health" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.06.24.20138313", "rel_title": "Practical recommendations for staying physically active during the COVID-19 pandemic: A systematic literature review", @@ -1333876,25 +1335339,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.06.24.169144", - "rel_title": "Integration of viral transcriptome sequencing with structure and sequence motifs predicts novel regulatory elements in SARS-CoV-2", - "rel_date": "2020-06-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.24.169144", - "rel_abs": "In the last twenty years, three separate coronaviruses have left their typical animal hosts and became human pathogens. An area of research interest is coronavirus transcription regulation that uses an RNA-RNA mediated template-switching mechanism. It is not known how different transcriptional stoichiometries of each viral gene are generated. Analysis of SARS-CoV-2 RNA sequencing data from whole RNA transcriptomes identified TRS dependent and independent transcripts. Integration of transcripts and 5-UTR sequence motifs identified that the pentaloop and the stem-loop 3 were also located upstream of spliced genes. TRS independent transcripts were detected as likely non-polyadenylated. Additionally, a novel conserved sequence motif was discovered at either end of the TRS independent splice junctions. While similar both SARS viruses generated similar TRS independent transcripts they were more abundant in SARS-CoV-2. TRS independent gene regulation requires investigation to determine its relationship to viral pathogenicity.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Brian J. Cox", - "author_inst": "University of Toronto" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genetics" - }, { "rel_doi": "10.1101/2020.06.23.20138321", "rel_title": "Point prevalence of SARS-CoV-2 and infection fatality rate in Orleans and Jefferson Parish, Louisiana, May 9-15, 2020", @@ -1334557,6 +1336001,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, + { + "rel_doi": "10.1101/2020.06.23.20138479", + "rel_title": "How Previous Epidemics Enable Timelier COVID-19 Responses: A Cross-Sectional Study Using Organizational Memory Theory", + "rel_date": "2020-06-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.23.20138479", + "rel_abs": "IntroductionThere has been little systematic exploration of what affects timeliness of epidemic response, despite the potential for earlier responses to be more effective. Speculations have circulated that exposure to major epidemics helped health systems respond more quickly to COVID-19. This study leverages organizational memory theory to test whether health systems with any, more severe, more recent exposure to major epidemics enacted timelier COVID-19 policy responses.\n\nMethodsA dataset was constructed cataloguing 846 policies across 178 health systems in total, 37 of which had major epidemics within the last twenty years. Hypothesis testing used OLS regressions with WHO region fixed effects, controlling for several health system expenditure and political variables.\n\nResultsResults show that exposure to any major epidemics was significantly associated with providing earlier response in any category or for surveillance / response, distancing, and international travel policies when tested alone or with total number of cases. The effect was about six to ten days earlier response. The significance was largely nullified with additional independent variables. Both total cases and years since previous epidemics showed no statistical significance.\n\nConclusionThis study suggests that health systems may learn from past major epidemics. Policymakers ought to institutionalize lessons from COVID-19. Future studies can examine specific generalizable lessons and whether timelier responses correlated with lower health and economic impacts.\n\nWhat is already known about this subject?There has been little systematic exploration into what affects the timeliness of response to epidemics. For COVID-19, there has been speculation that previous exposure to major epidemics may have spurred timelier responses.\n\nWhat are the new findings?Applying organizational memory theory, this study identified policy response timeliness to COVID-19 was significantly associated with any past exposure to major epidemics within the last 20 years.\n\nWhat are the recommendations for policy and practice?The fact that any exposure to past epidemics is significantly associated with timelier responses suggest that health systems do learn from past mistakes. Institutionalizing the learnings through more permanent policies. Once COVID-19 fades, health systems may wish to revitalize the organizational memory through various exercises.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Sian Hsiang-Te Tsuei", + "author_inst": "Harvard T H Chan School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2020.06.24.20138818", "rel_title": "Transmission of Respiratory Infectious Diseases between Neighboring Cities using Agent-based Model and Compartmental Model", @@ -1335233,37 +1336696,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.06.20.20099010", - "rel_title": "Compassionate Use of Opaganib For Patients with Severe COVID-19", - "rel_date": "2020-06-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.20.20099010", - "rel_abs": "BackgroundOpaganib is a selective sphingosine-kinase (SK)-2 inhibitor with anti-inflammatory and anti-viral properties.\n\nMethodsWe provided opaganib on a compassionate-use basis to patients with severe COVID-19. Patients who required oxygen support via high-flow nasal cannula (HFNC) were offered the treatment. For comparison, we used a control group with same-sex, same-severity patients.\n\nResultsSeven patients received at least one dose of opaganib since April 2, 2020. One patient, who received both hydroxychloroquine and azithromycin, developed diarrhea and all his medications were stopped. This was the only adverse effect possibly related to opaganib. A second patient was weaned of oxygen and discharged after receiving two doses of opaganib. Therefore, five patients were included in this analysis. Baseline characteristics were not significantly different between cases and controls. Patients treated with opaganib had significantly faster increase in lymphocyte count. All other clinical outcomes had a non-statistically significant trend in favor of the treatment group: median time to weaning from HFNC was 10 and 15 days in cases vs. controls (HR= 0.3, 95% CI: 0.07-1.7, p=0.2), time to ambient air was 13 vs.14.5 days (HR=0.4, 95% CI: 0.15-1.5), none of the cases required mechanical ventilation compared with 33% of controls.\n\nConclusionIn this small cohort of severe COVID-19 patients, opaganib was safe and well tolerated with improvement in both clinical and laboratory parameters in all treated patients. The efficacy of opaganib for COVID-19 infection should be further tested in randomized placebo-controlled trials.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Ramzi Kurd", - "author_inst": "Shaare-Zedek Medical center" - }, - { - "author_name": "Eli Ben-Chetrit", - "author_inst": "Shaare-Zedek Medical Center" - }, - { - "author_name": "Hani Karameh", - "author_inst": "Shaare-Zedek medical Center" - }, - { - "author_name": "Maskit Bar-Meir", - "author_inst": "Shaare-Zedek Medical center" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.22.20131573", "rel_title": "Organisms causing secondary pneumonias in COVID-19 patients at 5 UK ICUs as detected with the FilmArray test", @@ -1335859,6 +1337291,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.21.20136622", + "rel_title": "The role of pre-existing chronic disease in cardiac complications from SARS-CoV-2 infection: A systematic review and meta-analysis", + "rel_date": "2020-06-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.21.20136622", + "rel_abs": "ImportanceSARS-CoV-2 is associated with multiple direct and indirect effects to the heart. It is not yet well defined whether patient groups at increased risk of severe respiratory disease due to SARS-CoV-2 infection also experience a heightened incidence of cardiac complications.\n\nObjectiveWe sought to analyse the role of pre-existing chronic disease (chronic respiratory illness, cardiovascular disease (CVD), hypertension and diabetes mellitus) in the development of cardiac complications from SARS-CoV-2.\n\nData SourcesWe retrospectively investigated published (including pre-prints), publicly released, de-identified, data made available between Dec 1, 2019, and May 11, 2020. Information was accessed from PubMed, Embase, medRxiv and SSRN.\n\nStudy Selection379 full-text articles were reviewed and 321 excluded for lack of original research, irrelevance to outcome, inappropriate cohort, or small patient numbers (case reports of <10 patients). Data were extracted from two studies and the remaining 56 contacted to request appropriate data, to which three responded with data contributions. A final of five studies were included.\n\nData Extraction and SynthesisThis systematic review was conducted based on PRISMA and MOOSE statements. Included studies were critically appraised using Newcastle Ottawa Quality Assessment Scale (NOS). Data were extracted independently by multiple observers. A fixed-effects model was selected for the meta-analysis based on relatively low heterogeneity between the studies (I 2<50%).\n\nMain Outcome and MeasuresCardiac complications were determined via blood levels of cardiac biomarkers above the 99th percentile of the upper reference limit, abnormalities in electrocardiography, and/or abnormalities in echocardiography.\n\nResultsSARS-CoV-2-infected patients who developed cardiac complications were, on average, 10 years older than those that did not. Pooled analyses showed the development of cardiac complications from SARS-CoV-2 was significantly increased in patients with underlying chronic respiratory illness (OR 2.88[1.45,5.71]), CVD (OR 5.12[3.09,8.48]), hypertension (OR 4.37[2.99,6.39]) and diabetes mellitus (OR 2.61[1.67,4.09]).\n\nConclusions and RelevanceOlder age and pre-existing chronic respiratory illness, CVD, hypertension, and diabetes mellitus may represent prognostic factors for the development of additional cardiac complications in COVID-19, highlighting the need for a multidisciplinary approach to chronic disease patient management and providing justification for a larger scale observational study.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Jane E Sinclair", + "author_inst": "School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia" + }, + { + "author_name": "Yanshan Zhu", + "author_inst": "School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia" + }, + { + "author_name": "Gang Xu", + "author_inst": "Guangzhou First People's Hospital, Guangzhou, Guangdong, China" + }, + { + "author_name": "Wei Ma", + "author_inst": "Department of Geriatric Medicine, Guangzhou First People's Hospital, and School of Medicine, South China University of Technology, Guangzhou, Guangdong, China" + }, + { + "author_name": "Haiyan Shi", + "author_inst": "Department of Respiratory Medicine, Guangzhou Eighth People's Hospital, Guangzhou, Guangdong, China" + }, + { + "author_name": "Kun-Long Ma", + "author_inst": "Yongchuan Hospital of Chongqing Medical University, Yongchuan, Chongqing, China" + }, + { + "author_name": "Chun-Feng Cao", + "author_inst": "Yongchuan Hospital of Chongqing Medical University, Yongchuan, Chongqing, China" + }, + { + "author_name": "Ling-Xi Kong", + "author_inst": "Yongchuan Hospital of Chongqing Medical University, Yongchuan, Chongqing, China" + }, + { + "author_name": "Ke-Qiang Wan", + "author_inst": "Yongchuan Hospital of Chongqing Medical University, Yongchuan, Chongqing, China" + }, + { + "author_name": "Juan Liao", + "author_inst": "Yongchuan Hospital of Chongqing Medical University, Yongchuan, Chongqing, China" + }, + { + "author_name": "Hai-Qiang Wang", + "author_inst": "Institute of Integrative Medicine, Shaanxi University of Chinese Medicine, Xi'an Shaanxi Province, China" + }, + { + "author_name": "Matt Arentz", + "author_inst": "Department of Global Health, University of Washington, Seattle, Washington, U.S.A" + }, + { + "author_name": "Meredith Redd", + "author_inst": "Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia" + }, + { + "author_name": "Linda A Gallo", + "author_inst": "School of Biomedical Sciences, The University of Queensland, Brisbane, Australia" + }, + { + "author_name": "Kirsty R Short", + "author_inst": "School of Chemistry and Molecular Biosciences, and School of Public Health, The University of Queensland, Brisbane, Australia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.21.20136903", "rel_title": "Low serum 25-hydroxyvitamin D (25D) levels in patients hospitalised with COVID-19 are associated with greater disease severity: results of a local audit of practice.", @@ -1336603,49 +1338110,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.22.20137489", - "rel_title": "The impact of asymptomatic COVID-19 infections on future pandemic waves", - "rel_date": "2020-06-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.22.20137489", - "rel_abs": "Letter textThe prevalence of asymptomatic COVID-19 infections is largely unknown and may determine the course of future pandemic waves and the effectiveness of interventions. Using an epidemiological model fit to COVID-19 hospitalization counts from New York City, New York and Austin, Texas, we found that the undocumented attack rate in the first pandemic wave depends on the proportion of asymptomatic infections but not on the infectiousness of such individuals. Based on a recent report that 22.7% of New Yorkers are seropositive for SARS-CoV-2, we estimate that 56% (95% CI: 53-59%) of COVID-19 infections are asymptomatic. Given uncertainty in the case hospitalization rate, however, the asymptomatic proportion could be as low as 20% or as high as 80%. We find that at most 1.26% of the Austin population was infected by April 27, 2020 and conclude that immunity from undetected infections is unlikely to slow future pandemic spread in most US cities in the summer of 2020.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Spencer J Fox", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Remy Pasco", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Mauricio Tec", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Zhanwei Du", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Michael Lachmann", - "author_inst": "Santa Fe Institute" - }, - { - "author_name": "James Scott", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Lauren Ancel Meyers", - "author_inst": "The University of Texas at Austin, Santa Fe Institute" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.22.20137299", "rel_title": "Vitamin D insufficiency and deficiency and mortality from respiratory diseases in a cohort of older adults: potential for limiting the death toll during and beyond the COVID-19 pandemic", @@ -1337337,6 +1338801,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.22.20137646", + "rel_title": "SARS-CoV-2 exposure, symptoms and seroprevalence in health care workers", + "rel_date": "2020-06-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.22.20137646", + "rel_abs": "BackgroundSARS-CoV-2 may pose an occupational health risk to health care workers, but the prevalence of infections in this population is unknown. We examined the seroprevalence of SARS-CoV-2 antibodies among health care workers at a large acute care hospital in Stockholm, Sweden. We determined correlations between seroprevalence, self-reported symptoms and occupational exposure to SARS-CoV-2.\n\nMethods and findingsAll employees at Danderyd Hospital (n=4375) were invited to participate in a cross-sectional study. 2149 employees from all hospital departments were enrolled in the study between April 14th and May 8th 2020. Study participants completed a questionnaire consisting of symptoms compatible with SARS-CoV-2 infection since January 2020 and occupational exposure to patients infected with SARS-CoV-2. IgG antibodies against SARS-CoV-2 were analyzed using a multiplex assay evaluated to have 99.4% sensitivity and 99.1% specificity. The over-all seroprevalence among 2149 participants was 19.1% (n=410). There was no difference in age or sex between seropositive and seronegative participants. The symptoms with the strongest correlation to seroprevalence were anosmia and ageusia, with odds ratios of 28.4 (p=2.02*10^-120) and 19.2 (p=1.67*10^-99) respectively. Seroprevalence was strongly associated with patient-related work (OR 2.9, p=4.24*10^-8), covid-19 patient contact (OR 1.43, p=0.003), and occupation as assisting nurse (OR 3.67, p=2.16*10^-9).\n\nConclusionThese results demonstrate that anosmia and ageusia should be included in screening guidance and in the recommendations of self-isolation to reduce further spread of SARS-CoV-2. The results furthermore imply an occupational health risk for SARS-CoV-2 infection among hospital workers. Continued measures are warranted to assure healthcare worker safety and reduce transmission from health care settings to the community during the covid-19 outbreak.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Ann-Sofie Rudberg", + "author_inst": "Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "Sebastian Havervall", + "author_inst": "Department of Clinical Sciences, Danderyd Hospital, Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "Anna Manberg", + "author_inst": "Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden" + }, + { + "author_name": "August Jernbom Falk", + "author_inst": "Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden" + }, + { + "author_name": "Katherina Aguilera", + "author_inst": "Department of Clinical Sciences, Karolinska Institutet, Danderyd Hospital, Stockholm, Sweden" + }, + { + "author_name": "Henry Ng", + "author_inst": "Department of Medical Cell Biology, Uppsala University, SciLifeLab, Uppsala, Sweden" + }, + { + "author_name": "Lena Gabrielsson", + "author_inst": "Department of Clinical Sciences, Karolinska Institutet, Danderyd Hospital, Stockholm, Sweden" + }, + { + "author_name": "Ann-Christin Salomonsson", + "author_inst": "Department of Clinical Sciences, Karolinska Institutet, Danderyd Hospital, Stockholm, Sweden" + }, + { + "author_name": "Leo Hanke", + "author_inst": "Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "Benjamin Murell", + "author_inst": "Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "Gerald McInerney", + "author_inst": "Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "Jennie Olofsson", + "author_inst": "Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden" + }, + { + "author_name": "Eni Andersson", + "author_inst": "Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden" + }, + { + "author_name": "Cecilia Hellstrom", + "author_inst": "Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden" + }, + { + "author_name": "Shaghayegh Bayati", + "author_inst": "Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden" + }, + { + "author_name": "Sofia Bergstrom", + "author_inst": "Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden" + }, + { + "author_name": "Elisa Pin", + "author_inst": "Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden" + }, + { + "author_name": "Ronald Sjoberg", + "author_inst": "Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden" + }, + { + "author_name": "Hanna Tegel", + "author_inst": "Division of Protein Technology, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden" + }, + { + "author_name": "My Hedhammar", + "author_inst": "Division of Protein Technology, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden" + }, + { + "author_name": "Mia Phillipson", + "author_inst": "Department of Medical Cell Biology, Uppsala University, SciLifeLab, Uppsala, Sweden" + }, + { + "author_name": "Peter Nilsson", + "author_inst": "Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden" + }, + { + "author_name": "Sophia Hober", + "author_inst": "Division of Protein Technology, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden" + }, + { + "author_name": "Charlotte Thalin", + "author_inst": "Department of clinical medicine, Danderyd Hospital, Karolinska Institutet, Stockholm, Sweden" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.22.20137588", "rel_title": "The impact of COVID-19 non-pharmaceutical interventions on the future dynamics of endemic infections", @@ -1338001,53 +1339576,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.06.23.164947", - "rel_title": "A graph-based approach identifies dynamic H-bond communication networks in spike protein S of SARS-CoV-2", - "rel_date": "2020-06-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.23.164947", - "rel_abs": "Corona virus spike protein S is a large homo-trimeric protein embedded in the membrane of the virion particle. Protein S binds to angiotensin-converting-enzyme 2, ACE2, of the host cell, followed by proteolysis of the spike protein, drastic protein conformational change with exposure of the fusion peptide of the virus, and entry of the virion into the host cell. The structural elements that govern conformational plasticity of the spike protein are largely unknown. Here, we present a methodology that relies upon graph and centrality analyses, augmented by bioinformatics, to identify and characterize large H-bond clusters in protein structures. We apply this methodology to protein S ectodomain and find that, in the closed conformation, the three protomers of protein S bring the same contribution to an extensive central network of H-bonds, has a relatively large H-bond cluster at the receptor binding domain, and a cluster near a protease cleavage site. Markedly different H-bonding at these three clusters in open and pre-fusion conformations suggest dynamic H-bond clusters could facilitate structural plasticity and selection of a protein S protomer for binding to the host receptor, and proteolytic cleavage. From analyses of spike protein sequences we identify patches of histidine and carboxylate groups that could be involved in transient proton binding.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Konstantine Karathanou", - "author_inst": "Freie Universitaet Berlin, Department of Physics, Theoretical Molecular Biophysics" - }, - { - "author_name": "Michalis Lazaratos", - "author_inst": "Freie Universitaet Berlin, Department of Physics, Theoretical Molecular Biophysics Group" - }, - { - "author_name": "Eva Bertalan", - "author_inst": "Freie Universitaet Berlin, Department of Physics, Theoretical Molecular Biophysics" - }, - { - "author_name": "Malte Siemers", - "author_inst": "Freie Universitaet Berlin, Department of Physics, Theoretical Molecular Biophysics Group" - }, - { - "author_name": "Krzysztof Buzar", - "author_inst": "Freie Universitaet Berlin, Department of Physics, Theoretical Molecular Biophysics Group" - }, - { - "author_name": "Gebhard F.X. Schertler", - "author_inst": "Paul Scherrer Institut, Department of Biology and Chemistry, Laboratory of Biomolecular Research, and ETH Zuerich, Department of Biology" - }, - { - "author_name": "Coral del Val", - "author_inst": "University of Granada, Department of Computer Science and Artificial Intelligence, Instituto de Investigacion Biosanitaria ibs. Granada, and Andalusian Research" - }, - { - "author_name": "Ana-Nicoleta Bondar", - "author_inst": "Freie Universitaet Berlin, Department of Physics, Theoretical Molecular Biophysics Group" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.06.23.165415", "rel_title": "Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2", @@ -1338847,6 +1340375,69 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.06.22.165464", + "rel_title": "Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study.", + "rel_date": "2020-06-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.22.165464", + "rel_abs": "Spatiotemporal bias in genome sequence sampling can severely confound phylogeographic inference based on discrete trait ancestral reconstruction. This has impeded our ability to accurately track the emergence and spread of SARS-CoV-2, the virus responsible for the COVID-19 pandemic. Despite the availability of unprecedented numbers of SARS-CoV-2 genomes on a global scale, evolutionary reconstructions are hindered by the slow accumulation of sequence divergence over its relatively short transmission history. When confronted with these issues, incorporating additional contextual data may critically inform phylodynamic reconstructions. Here, we present a new approach to integrate individual travel history data in Bayesian phylogeographic inference and apply it to the early spread of SARS-CoV-2, while also including global air transportation data. We demonstrate that including travel history data for each SARS-CoV-2 genome yields more realistic reconstructions of virus spread, particularly when travelers from undersampled locations are included to mitigate sampling bias. We further explore methods to ameliorate the impact of sampling bias by augmenting the phylogeographic analysis with lineages from undersampled locations in the analyses. Our reconstructions reinforce specific transmission hypotheses suggested by the inclusion of travel history data, but also suggest alternative routes of virus migration that are plausible within the epidemiological context but are not apparent with current sampling efforts. Although further research is needed to fully examine the performance of our travel-aware phylogeographic analyses with unsampled diversity and to further improve them, they represent multiple new avenues for directly addressing the colossal issue of sample bias in phylogeographic inference.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Philippe Lemey", + "author_inst": "KU Leuven" + }, + { + "author_name": "Samuel Hong", + "author_inst": "KU Leuven" + }, + { + "author_name": "Verity Hill", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Guy Baele", + "author_inst": "KU Leuven" + }, + { + "author_name": "Chiara Poletto", + "author_inst": "INSERM" + }, + { + "author_name": "Vittoria Colizza", + "author_inst": "INSERM" + }, + { + "author_name": "John T McCrone", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Kristian G Andersen", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Michael Worobey", + "author_inst": "University of Arizona" + }, + { + "author_name": "Martha I Nelson", + "author_inst": "Fogarty International Center" + }, + { + "author_name": "Andrew Rambaut", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Marc A. Suchard", + "author_inst": "David Geffen School of Medicine at UCLA" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2020.06.22.165035", "rel_title": "Oral epithelial expression of angiotensin converting enzyme-2: Implications for COVID-19 diagnosis and prognosis.", @@ -1339635,53 +1341226,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "dentistry and oral medicine" }, - { - "rel_doi": "10.1101/2020.06.20.20136242", - "rel_title": "Comparison of primer-probe sets among different master mixes for laboratory screening of Severe Acute Respiratory Syndrome - Coronavirus 2 (SARS-CoV-2)", - "rel_date": "2020-06-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.20.20136242", - "rel_abs": "BackgroundThere is a shortage of chemical reagents for severe acute respiratory syndrome - coronavirus 2 (SARS-CoV-2) diagnosis and a surge of SARS-CoV-2cases, especially in limited-resource settings. Therefore, the combination of an optimal assay kit is necessary.\n\nMethodsWe compared the ability to screen SARS-CoV-2 among three primer-probe sets in two different master mixes, Invitrogen SuperScript III One-Step RT-PCR and LightCycler Multiplex RNA Virus Master.\n\nResultsThe assay with TIB-Molbiol, IDT, and Phu Sa sets for LightCycler Multiplex RNA Virus Master or Invitrogen SuperScript III One-Step RT-PCR showed positive results from a single reaction of triplicate in the three days of 4.8 copies per reaction. R-squared and amplification efficiency were 0.97 and ranged from 107 to 108%, respectively.\n\nConclusionsOur findings indicated that TIB-Molbiol, IDT, and Phu Sa primer-probe sets could be beneficial for the laboratory screening of SARS-CoV-2 by RT-qPCR assay of E gene. There is a need to consider the combination of these reagent sets as a new strategy to increase the testing capacity of screening programs for COVID-19.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Cuong Quoc Hoang", - "author_inst": "Pasteur Institute HCMC" - }, - { - "author_name": "Hai Duc Nguyen", - "author_inst": "Pasteur Institute" - }, - { - "author_name": "Linh Thuy Hoang", - "author_inst": "Pasteur Institue HCMC" - }, - { - "author_name": "Anh Hoang Nguyen", - "author_inst": "Pasteur institute HCMC" - }, - { - "author_name": "Hieu Trung Nguyen", - "author_inst": "Pasteur Institute HCMC" - }, - { - "author_name": "Thang Minh Cao", - "author_inst": "PI HCMC" - }, - { - "author_name": "Thao Thi Thanh Nguyen", - "author_inst": "PI HCMC" - }, - { - "author_name": "Lan Trong Phan", - "author_inst": "PI HCMC" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "emergency medicine" - }, { "rel_doi": "10.1101/2020.06.20.20135764", "rel_title": "Comparison of COVID-19 case and death counts in the United States reported by four online trackers: January 22-May 31, 2020", @@ -1340153,6 +1341697,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.18.20135111", + "rel_title": "Are men who smoke at higher risk for a more severe case of COVID-19 than women who smoke? A Systematic Review", + "rel_date": "2020-06-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.18.20135111", + "rel_abs": "BackgroundThe novelty of the Covid-19 pandemic is reflected in the lack of literature available for the impact of smoking on the intensity of the COVID-19 clinical manifestations. Our study tries to address this gap.\n\nMethodSix cohorts from China were analysed and a crude odds ratio was manually calculated.\n\nResultsPatients with a smoking history were approximately 2 times (95% CI= 1.036-1.883) as likely to suffer from severe clinical manifestations of COVID-19 compared to patients without a smoking history. A higher percentage of males suffer more severe symptoms of COVID-19 in comparison to females, but this could be associated with the gender specific smoking trends observed in China.\n\nConclusionThe gender specific smoking trends could be associated with the increased severity of COVID-19 disease manifestations in the male population.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Aoife Rodgers", + "author_inst": "University College Cork" + }, + { + "author_name": "Emilie Kruke Indreberg", + "author_inst": "University College Cork" + }, + { + "author_name": "Lenah Alfallaj", + "author_inst": "University College Cork" + }, + { + "author_name": "Manasi Nadkarni", + "author_inst": "University College Cork" + }, + { + "author_name": "Zubair Kabir", + "author_inst": "University College Cork" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.06.22.20137273", "rel_title": "Effect of Dexamethasone in Hospitalized Patients with COVID-19: Preliminary Report", @@ -1341192,113 +1342771,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.20.137687", - "rel_title": "SARS-CoV-2 infection of African green monkeys results in mild respiratory disease discernible by PET/CT imaging and prolonged shedding of infectious virus from both respiratory and gastrointestinal tracts", - "rel_date": "2020-06-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.20.137687", - "rel_abs": "Vaccines are urgently needed to combat the global coronavirus disease 2019 (COVID-19) pandemic, and testing of candidate vaccines in an appropriate non-human primate (NHP) model is a critical step in the process. Infection of African green monkeys (AGM) with a low passage human isolate of SARS-CoV-2 by aerosol or mucosal exposure resulted in mild clinical infection with a transient decrease in lung tidal volume. Imaging with human clinical-grade 18F-fluoro-2-deoxy-D-glucose positron emission tomography (18F-FDG PET) co-registered with computed tomography (CT) revealed pulmonary lesions at 4 days post-infection (dpi) that resolved over time. Infectious virus was shed from both respiratory and gastrointestinal (GI) tracts in all animals in a biphasic manner, first between 2-7 dpi followed by a recrudescence at 14-21 dpi. Viral RNA (vRNA) was found throughout both respiratory and gastrointestinal systems at necropsy with higher levels of vRNA found within the GI tract tissues. All animals seroconverted simultaneously for IgM and IgG, which has also been documented in human COVID-19 cases. Young AGM represent an excellent species to study mild/subclinical COVID-19 disease and have shed light on unknown aspects of long-term virus shedding. They are ideally suited for preclinical evaluation of candidate vaccines and therapeutic interventions.\n\nOne Sentence SummarySubclinical infection of African green monkeys infected with SARS-CoV-2 results in prolonged shedding of infectious virus from both respiratory and gastrointestinal tracts.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Amy L Hartman", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Shamkumar Nambulli", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Cynthia M. McMillen", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Alexander G White", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Natasha Tilston-Lunel", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Joseph R. Albe", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Emily L. Cottle", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Matthew D Dunn", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Lonnie James Frye", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Theron H. Gilliland", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Emily L Olsen", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Madeline M Schwarz", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Jaime A. Tomko", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Reagan C. Walker", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Mengying Xia", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Matthew S Hartman", - "author_inst": "Allegheny Health Network" - }, - { - "author_name": "Edwin Klein", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Charles Scanga", - "author_inst": "University of Pittsburgh School of Medicine" - }, - { - "author_name": "JoAnne L. Flynn", - "author_inst": "University of Pittsburgh School of Medicine" - }, - { - "author_name": "William B. Klimstra", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Anita K. McElroy", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Douglas S. Reed", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "W. Paul Duprex", - "author_inst": "University of Pittsburgh School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.06.20.163162", "rel_title": "An Analysis of SARS-CoV-2 Using ViReport", @@ -1342002,6 +1343474,65 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.06.19.20135749", + "rel_title": "COVID-19 and first trimester spontaneous abortion: a case-control study of 225 pregnant patients", + "rel_date": "2020-06-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.19.20135749", + "rel_abs": "BackgroundEvidence for the impact of COVID-19 during the second and the third trimester of pregnancy is limited to a relatively small series, while data on the first trimester are scant. With this study we evaluated COVID-19 infection as a risk factor for spontaneous abortion in first trimester of pregnancy.\n\nMethodsBetween February 22 and May 21, 2020, we conducted a case-control study at S. Anna Hospital, Turin, among first trimester pregnant women, paired for last menstruation. The cumulative incidence of COVID-19 was compared between women with spontaneous abortion (case group, n=100) and those with ongoing pregnancy (control group, n=125). Current or past infection was determined by detection of SARS-CoV-2 from nasopharingeal swab and SARS- CoV-2 IgG/IgM antibodies in blood sample. Patient demographics, COVID-19-related symptoms, and the main risk factors for abortion were collected.\n\nFindingsTwenty-three (10.2%) of the 225 women tested positive for COVID-19 infection. There was no difference in the cumulative incidence of COVID-19 between the cases (11/100, 11%) and the controls (12/125, 9.6%) (p=0.73). Logistic regression analysis confirmed that COVID-19 was not an independent predictor of abortion (1.28 confidence interval 0.53-3.08).\n\nInterpretationCOVID-19 infection during the first trimester of pregnancy does not appear to predispose to abortion; its cumulative incidence did not differ from that of women with ongoing pregnancy.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Stefano Cosma", + "author_inst": "Gynecology and Obstetrics 1, Department of Surgical Sciences, City of Health and Science, University of Turin, Turin, Italy" + }, + { + "author_name": "Andrea Carosso", + "author_inst": "Gynecology and Obstetrics 1, Department of Surgical Sciences, City of Health and Science, University of Turin, Turin, Italy" + }, + { + "author_name": "Jessica Cusato", + "author_inst": "Laboratory of Clinical Pharmacology and Pharmacogenetics, Amedeo di Savoia Hospital, Department of Medical Sciences, University of Turin, Turin, Italy" + }, + { + "author_name": "Fulvio Borella", + "author_inst": "Gynecology and Obstetrics 1, Department of Surgical Sciences, City of Health and Science, University of Turin, Turin, Italy" + }, + { + "author_name": "Marco Carosso", + "author_inst": "Gynecology and Obstetrics 1, Department of Surgical Sciences, City of Health and Science, University of Turin, Turin, Italy" + }, + { + "author_name": "Marialuisa Bovetti", + "author_inst": "Gynecology and Obstetrics 1, Department of Surgical Sciences, City of Health and Science, University of Turin, Turin, Italy" + }, + { + "author_name": "Claudia Filippini", + "author_inst": "Department of Surgical Sciences, City of Health and Science, University of Turin, Turin, Italy" + }, + { + "author_name": "Antonio D'Avolio", + "author_inst": "Unit of Infectious Diseases, Amedeo di Savoia Hospital, Department of Medical Sciences, University of Turin, Turin, Italy" + }, + { + "author_name": "Valeria Ghisetti", + "author_inst": "Laboratory of Microbiology and Virology, Amedeo di Savoia Hospital, ASL Citta' di Torino, Turin, Italy" + }, + { + "author_name": "Giovanni Di Perri", + "author_inst": "Unit of Infectious Diseases, Amedeo di Savoia Hospital, Department of Medical Sciences, University of Turin, Turin, Italy" + }, + { + "author_name": "Chiara Benedetto", + "author_inst": "Gynecology and Obstetrics 1, Department of Surgical Sciences, City of Health and Science, University of Turin, Turin, Italy" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "obstetrics and gynecology" + }, { "rel_doi": "10.1101/2020.06.19.20135723", "rel_title": "Clinical Sensitivity and Interpretation of PCR and Serological COVID-19 Diagnostics for Patients Presenting to the Hospital", @@ -1342906,29 +1344437,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.19.20135269", - "rel_title": "Affected medical services in Iwate prefecture in the absence of a COVID-19 outbreak", - "rel_date": "2020-06-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.19.20135269", - "rel_abs": "The Japanese government has declared a national emergency and travel entry ban since the coronavirus disease 2019 (COVID-19) pandemic began. As of June 19, 2020, there have been no confirmed cases of COVID-19 in Iwate. Here, we analyzed the excess deaths as well as the number of patients and medical earnings due to the pandemic from prefectural hospitals located in one of the least-affected areas in Japan. From January to March 2020, the excess death rates per month were not significantly higher than the past-year average. Compared to January 2020, the numbers of both outpatients and inpatients in April 2020 showed a 5.2% and 6.1% decrease, respectively. Accordingly, the amount of medical earnings of both outpatients and inpatients in April 2020 showed a 3.0% and 6.3% decrease, respectively. Present analysis demonstrated that there were no excess deaths due to \"unidentified\" COVID-19 infections in Iwate; however, hospital budgetary management has been affected by the social restrictions. Regardless of COVID-19 infection spread, it may be difficult to maintain daily medical services if such low service activity continues in the existing hospitals. Additional longitudinal studies will be necessary to evaluate the effects of social restrictions on hospital management, but the true demand of regional medical services may emerge after this outbreak.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Noriyuki Sasaki", - "author_inst": "Iwate Medical University" - }, - { - "author_name": "Satoshi S Nishizuka", - "author_inst": "Iwate Medical University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.19.20135483", "rel_title": "Epidemiological Risk Factors Associated with Death and Severe Disease in Patients Suffering From COVID-19: A Comprehensive Systematic Review and Meta-analysis", @@ -1343556,6 +1345064,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.06.18.20134668", + "rel_title": "Twitter activity about treatments during the COVID-19 pandemic: case studies of remdesivir, hydroxychloroquine, and convalescent plasma.", + "rel_date": "2020-06-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.18.20134668", + "rel_abs": "Since the COVID-19 pandemic started, the public has been eager for news about promising treatments, and social media has played a large role in information dissemination. In this paper, our objectives are to characterize the public discussion of treatments on Twitter, and demonstrate the utility of these discussions for public health surveillance. We pulled tweets related to three promising COVID-19 treatments (hydroxychloroquine, remdesivir and convalescent plasma), between the dates of February 28th and May 22nd using the Twitter public API. We characterize treatment tweet trends over this time period. Most major tweet/retweet/sentiment trends correlated to public announcement made by the white house and/or to new clinical trial evidence about treatments. Most of the websites people shared in treatment-related tweets were non-scientific media sources that leaned conservative. Hydroxychloroquine was the most discussed treatment on Twitter, and over 10% of hydroxychloroquine tweets mentioned an adverse drug reaction. There is a gap between the public attention/discussion around COVID-19 treatments and their evidence. Twitter data can and should be used for public health surveillance during this pandemic, as it is informative for monitoring adverse drug reactions, especially as many people avoid going to hospitals/doctors.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Tymor Carpenter Hamamsy", + "author_inst": "New York University" + }, + { + "author_name": "Richard Bonneau", + "author_inst": "New York University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.06.18.20134627", "rel_title": "Kidney function on admission predicts in-hospital mortality in COVID-19", @@ -1344356,37 +1345887,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.19.162529", - "rel_title": "The enzymatic activity of the nsp14 exoribonuclease is critical for replication of Middle East respiratory syndrome-coronavirus", - "rel_date": "2020-06-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.19.162529", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWCoronaviruses (CoVs) stand out for their large RNA genome and complex RNA-synthesizing machinery comprising 16 nonstructural proteins (nsps). The bifunctional nsp14 contains an N-terminal 3-to-5 exoribonuclease (ExoN) and a C-terminal N7-methyltransferase (N7-MTase) domain. While the latter presumably operates during viral mRNA capping, ExoN is thought to mediate proofreading during genome replication. In line with such a role, ExoN-knockout mutants of mouse hepatitis virus (MHV) and severe acute respiratory syndrome coronavirus (SARS-CoV) were previously found to have a crippled but viable hypermutation phenotype. Remarkably, using an identical reverse genetics approach, an extensive mutagenesis study revealed the corresponding ExoN-knockout mutants of another betacoronavirus, Middle East respiratory syndrome coronavirus (MERS-CoV), to be non-viable. This is in agreement with observations previously made for alpha- and gammacoronaviruses. Only a single MERS-CoV ExoN active site mutant could be recovered, likely because the introduced D191E substitution is highly conservative in nature. For 11 other MERS-CoV ExoN active site mutants, not a trace of RNA synthesis could be detected, unless - in some cases - reversion had first occurred. Subsequently, we expressed and purified recombinant MERS-CoV nsp14 and established in vitro assays for both its ExoN and N7-MTase activities. All ExoN knockout mutations that were lethal when tested via reverse genetics were found to severely decrease ExoN activity, while not affecting N7-MTase activity. Our study thus reveals an additional function for MERS-CoV nsp14 ExoN, which apparently is critical for primary viral RNA synthesis, thus differentiating it from the proofreading activity thought to boost long-term replication fidelity in MHV and SARS-CoV.\n\nIO_SCPLOWMPORTANCEC_SCPLOWThe bifunctional nsp14 subunit of the coronavirus replicase contains 3-to-5 exoribonuclease (ExoN) and N7-methyltransferase (N7-MTase) domains. For the betacoronaviruses MHV and SARS-CoV, the ExoN domain was reported to promote the fidelity of genome replication, presumably by mediating some form of proofreading. For these viruses, ExoN knockout mutants are alive while displaying an increased mutation frequency. Strikingly, we now established that the equivalent knockout mutants of MERS-CoV ExoN are non-viable and completely deficient in RNA synthesis, thus revealing an additional and more critical function of ExoN in coronavirus replication. Both enzymatic activities of (recombinant) MERS-CoV nsp14 were evaluated using newly developed in vitro assays that can be used to characterize these key replicative enzymes in more detail and explore their potential as target for antiviral drug development.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Natacha S. Ogando", - "author_inst": "Leiden University Medical Center" - }, - { - "author_name": "Jessika Zevenhoven-Dobbe", - "author_inst": "Leiden University Medical Center" - }, - { - "author_name": "Clara C Posthuma", - "author_inst": "Department of Medical Microbiology; Leiden University Medical Center" - }, - { - "author_name": "Eric J. Snijder", - "author_inst": "Leiden University Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.06.18.20134510", "rel_title": "PROGNOSTIC FACTORS IN SPANISH COVID-19 PATIENTS: A CASE SERIES FROM BARCELONA", @@ -1345542,6 +1347042,69 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.06.17.20133892", + "rel_title": "Routine laboratory blood tests predict SARS-CoV-2 infection using machine learning", + "rel_date": "2020-06-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.17.20133892", + "rel_abs": "BackgroundAccurate diagnostic strategies to rapidly identify SARS-CoV-2 positive individuals for management of patient care and protection of health care personnel are urgently needed. The predominant diagnostic test is viral RNA detection by RT-PCR from nasopharyngeal swabs specimens, however the results are not promptly obtainable in all patient care locations. Routine laboratory testing, in contrast, is readily available with a turn-around time (TAT) usually within 1-2 hours.\n\nMethodWe developed a machine learning model incorporating patient demographic features (age, sex, race) with 27 routine laboratory tests to predict an individuals SARS-CoV-2 infection status. Laboratory test results obtained within two days before the release of SARS-CoV-2-RT-PCR result were used to train a gradient boosted decision tree (GBDT) model from 3,356 SARS-CoV-2 RT-PCR tested patients (1,402 positive and 1,954 negative) evaluated at a metropolitan hospital.\n\nResultsThe model achieved an area under the receiver operating characteristic curve (AUC) of 0.854 (95% CI: 0.829-0.878). Application of this model to an independent patient dataset from a separate hospital resulted in a comparable AUC (0.838), validating the generalization of its use. Moreover, our model predicted initial SARS-CoV-2 RT-PCR positivity in 66% individuals whose RT-PCR result changed from negative to positive within two days.\n\nConclusionThis model employing routine laboratory test results offers opportunities for early and rapid identification of high-risk SARS-CoV-2 infected patients before their RT-PCR results are available. It may play an important role in assisting the identification of SARS-COV-2 infected patients in areas where RT-PCR testing is not accessible due to financial or supply constraints.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "He Sarina Yang", + "author_inst": "Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA; New York-Presbyterian Hospital, Weill Cornell Medicine, New York, NY" + }, + { + "author_name": "Yu Hou", + "author_inst": "Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA" + }, + { + "author_name": "Ljiljana V Vasovic", + "author_inst": "Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA; New York-Presbyterian Hospital, Lower Manhattan Hospital, New York, " + }, + { + "author_name": "Peter Steel", + "author_inst": "Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA; Department of Emergency Medicine, Weill Cornell Medicine, New York, " + }, + { + "author_name": "Amy Chadburn", + "author_inst": "Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA; New York-Presbyterian Hospital, Weill Cornell Medicine, New York, NY" + }, + { + "author_name": "Sabrina E Racine-Brzostek", + "author_inst": "Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA; New York-Presbyterian Hospital, Weill Cornell Medicine, New York, NY" + }, + { + "author_name": "Priya Velu", + "author_inst": "Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA; New York-Presbyterian Hospital, Weill Cornell Medicine, New York, NY" + }, + { + "author_name": "Melissa Cushing", + "author_inst": "Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA; New York-Presbyterian Hospital, Weill Cornell Medicine, New York, NY" + }, + { + "author_name": "Massimo Loda", + "author_inst": "Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA; New York-Presbyterian Hospital, Weill Cornell Medicine, New York, NY" + }, + { + "author_name": "Rainu Kaushal", + "author_inst": "Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA; New York-Presbyterian Hospital, Weill Cornell Medicine, New York, NY, US" + }, + { + "author_name": "Zhen Zhao", + "author_inst": "Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA; New York-Presbyterian Hospital, Weill Cornell Medicine, New York, NY" + }, + { + "author_name": "Fei Wang", + "author_inst": "Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.15.20132407", "rel_title": "Comparative efficacy and safety of pharmacological interventions for the treatment of COVID-19: A systematic review and network meta-analysis of confounder-adjusted 20212 hospitalized patients", @@ -1346702,85 +1348265,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.06.19.160606", - "rel_title": "Phylogenetic pattern of SARS-CoV-2 from COVID-19 patients from Bosnia and Herzegovina: lessons learned to optimize future molecular and epidemiological approaches", - "rel_date": "2020-06-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.19.160606", - "rel_abs": "Whole Genome Sequence of four samples from COVID-19 outbreaks was done in two laboratories in Bosnia and Herzegovina (Veterinary Faculty Sarajevo and Alea Genetic Center). All four BiH sequences cluster mainly with European ones (Italy, Austria, France, Sweden, Cyprus, England). The constructed phylogenetic tree indicates probable multiple independent introduction events. The success of future containment measures concernig new introductions will be highly challenging for country due to the significant proportion of BH population living abroad.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Teufik Goletic", - "author_inst": "Veterinary faculty of University of Sarajevo, Zmaja od Bosne 90, 71000 Sarajevo, Bosnia and Herzegovina" - }, - { - "author_name": "Rijad Konjhodzic", - "author_inst": "ALEA Genetic Center, Olovska 67, 71000 Sarajevo, Bosnia and Herzegovina" - }, - { - "author_name": "Nihad Fejzic", - "author_inst": "Veterinary faculty of University of Sarajevo, Zmaja od Bosne 90, 71000 Sarajevo, Bosnia and Herzegovina" - }, - { - "author_name": "Sejla Goletic", - "author_inst": "Veterinary faculty of University of Sarajevo, Zmaja od Bosne 90, 71000 Sarajevo, Bosnia and Herzegovina" - }, - { - "author_name": "Toni Eterovic", - "author_inst": "Veterinary faculty of University of Sarajevo, Zmaja od Bosne 90, 71000 Sarajevo, Bosnia and Herzegovina" - }, - { - "author_name": "Adis Softic", - "author_inst": "Veterinary faculty of University of Sarajevo, Zmaja od Bosne 90, 71000 Sarajevo, Bosnia and Herzegovina" - }, - { - "author_name": "Aida Kustura", - "author_inst": "Veterinary faculty of University of Sarajevo, Zmaja od Bosne 90, 71000 Sarajevo, Bosnia and Herzegovina" - }, - { - "author_name": "Lana Salihefendic", - "author_inst": "ALEA Genetic Center, Olovska 67, 71000 Sarajevo, Bosnia and Herzegovina" - }, - { - "author_name": "Maja Ostojic", - "author_inst": "University Clinical Hospital of Mostar, Bijeli Brijeg b.b., 88000 Mostar, Bosnia and Herzegovina" - }, - { - "author_name": "Maja Travar", - "author_inst": "University Clinical Centre of the Republic of Srpska, Dvanaest beba bb, 78000 Banja Luka, Bosnia and Herzegovina" - }, - { - "author_name": "Visnja Mrdjen", - "author_inst": "University Clinical Centre of the Republic of Srpska, Dvanaest beba bb, 78000 Banja Luka, Bosnia and Herzegovina" - }, - { - "author_name": "Nijaz Tihic", - "author_inst": "University Clinical Center Tuzla, Ulica Profesora doktora Ibre Pasica, 75000 Tuzla, Bosnia and Herzegovina" - }, - { - "author_name": "Sead Jazic", - "author_inst": "General Hospital \"Abdulah Nakas\", Kranjceviceva 12, 71000 Sarajevo, Bosnia and Herzegovina" - }, - { - "author_name": "Sanjin Musa", - "author_inst": "Institute for Public Health of Federation of Bosnia and Herzegovina, Marsala Tita 9, 71000 Sarajevo, Bosnia and Herzegovina" - }, - { - "author_name": "Damir Marjanovic", - "author_inst": "Center for Applied Bioanthropology, Institute for Anthropological Researches, Gajeva ulica 32, 10 000 Zagreb, Croatia" - }, - { - "author_name": "Mirsada Hukic", - "author_inst": "The Academy of Science and Arts of Bosnia and Herzegovina, Bistrik 7, 71000 Sarajevo, Bosnia and Herzegovina" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genetics" - }, { "rel_doi": "10.1101/2020.06.19.159053", "rel_title": "Antiviral treatment of SARS-CoV-2-infected hamsters reveals a weak effect of favipiravir and a complete lack of effect for hydroxychloroquine", @@ -1347468,6 +1348952,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.16.20130278", + "rel_title": "The effect of the COVID-19 induced lockdown on nutrition, health and lifestyle patterns among adults in Zimbabwe", + "rel_date": "2020-06-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.16.20130278", + "rel_abs": "BackgroundThe 2019 coronavirus disease (COVID-19) is a global public health emergency resulting in lockdowns, associated diet and lifestyle changes and constraint public health delivery.\n\nObjectiveTo investigate the impacts of the COVID-19 induced lockdown in Zimbabwe on nutrition, physical activity, alcohol consumption and smoking among Zimbabwean population aged [≥]18years.\n\nMethodsA cross-sectional online survey was conducted using a structured questionnaire to collect information on demographics (age, gender, place of residence, current employment), food system dimensions, diet and physical activity patterns, stress and anxiety, body image perceptions, lifestyle behaviours like smoking, alcohol intake, screen time, and ease of access to health services. The study obtained ethical clearance from the Medical Research Council of Zimbabwe (MRCZ/B/1920).\n\nResultsThe participants (n=507) were mostly female (63.0%) between the ages of 31-40 years (48.1%) and had tertiary education (91.3%). The lockdown resulted in increase in food prices (94.8%) and decrease in availability of nutritious foods (64%). Most (62.5%) of the participants reported a reduction in their physical activity levels. The prevalence of Generalised Anxiety Disorder (GAD) was 40.4% and mostly affecting females [63.5%, P=0.909), 31-40 years age group (49.6%, P=0.886). Based on the BMI-based Silhouette Matching Test (BMI-SMT) 44.5% gained weight, 24.3% lost weight and 31.2% did not have weight change. The paired samples T test showed that there was a significant increase in perceived body weight (P<0.001). More than half (59.6%) reported having difficulties accessing medicinal drugs and 37.8% growth monitoring services.\n\nConclusionsThe lockdown period was associated with increase in food prices, decrease in dietary diversification, elevated stress, disrupted diet and consumption patterns. There were low levels of physical activity and perceived weight gained during the lockdown period, thus increasing the risk of overweight and obesity. Further studies incorporating participants of different socio-economic status are warranted to get more conclusive results.\n\nWhat this paper adds?O_LIFirst diet and lifestyle survey in Zimbabwe documenting negative effects of lockdown on the urban elite on diets and lifestyles;\nC_LIO_LIThe COVID-19 induced lockdown was associated with elevated anxiety, disruptions of food supply chains and consumption patterns;\nC_LIO_LIMost of the participants were less active and gained weight in the lockdown period, thus increasing the risk of overweight and obesity an emerging risk factor for severe COVID-19 complications.\nC_LI", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Tonderayi M Matsungo", + "author_inst": "Department of Nutrition, Dietetics and Food Sciences, University of Zimbabwe, P O Box MP 167, Mt Pleasant, Harare, Zimbabwe" + }, + { + "author_name": "Prosper Chopera", + "author_inst": "Department of Nutrition, Dietetics and Food Sciences, University of Zimbabwe, P O Box MP 167, Mt Pleasant, Harare, Zimbabwe" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "nutrition" + }, { "rel_doi": "10.1101/2020.06.16.20131243", "rel_title": "SARS-CoV-2 qRT-PCR Ct value distribution in Japan and possible utility of rapid antigen testing kit", @@ -1348228,57 +1349735,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, - { - "rel_doi": "10.1101/2020.06.15.20131391", - "rel_title": "Identification of immunodominant linear epitopes from SARS-CoV-2 patient plasma", - "rel_date": "2020-06-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.15.20131391", - "rel_abs": "A novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) is the source of a current pandemic (COVID-19) with devastating consequences in public health and economic stability. Using a peptide array to map the antibody response of plasma from healing patients, we identified immunodominant linear epitopes corresponding to key proteolytic sites on the spike protein.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Lluc Farrera", - "author_inst": "University of Geneva" - }, - { - "author_name": "Jean-Pierre Daguer", - "author_inst": "University of Geneva" - }, - { - "author_name": "Sofia Barluenga", - "author_inst": "University of Geneva" - }, - { - "author_name": "Patrick Raoul Cohen", - "author_inst": "University of Geneva" - }, - { - "author_name": "Sabrina Pagano", - "author_inst": "University of Geneva" - }, - { - "author_name": "Sabine Yerly", - "author_inst": "University of Geneva" - }, - { - "author_name": "Laurent Kaiser", - "author_inst": "University of Geneva Hospitals" - }, - { - "author_name": "Nicolas Vuilleumier", - "author_inst": "University of Geneva" - }, - { - "author_name": "Nicolas Winssinger", - "author_inst": "University of Geneva" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.17.20133967", "rel_title": "Investigation of Compatibility of SARS-CoV-2 RT-PCR Kits Containing Different Gene Targets During COVID-19 Pandemic", @@ -1348874,6 +1350330,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.17.20133389", + "rel_title": "A novel comprehensive metric to assess COVID-19 testing outcomes: Effects of geography, government, and policy response", + "rel_date": "2020-06-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.17.20133389", + "rel_abs": "Testing and case identification are key strategies in controlling the COVID-19 pandemic. Contact tracing and isolation are only possible if cases have been identified. The effectiveness of testing must be tracked, but a single comprehensive metric is not available to assess testing effectiveness, and no timely estimates of case detection rate are available globally, making inter-country comparisons difficult. The purpose of this paper was to propose a single, comprehensive metric, called the COVID-19 Testing Index (CovTI) scaled from 0 to 100, that incorporated several testing metrics. The index was based on case-fatality rate, test positivity rate, active cases, and an estimate of the detection rate. It used parsimonious modeling to estimate the true total number of COVID-19 cases based on deaths, testing, health system capacity, and government transparency. Publicly reported data from 188 countries and territories were included in the index. Estimates of detection rates aligned with previous estimates in literature (R2=0.97). As of June 3, 2020, the states with the highest CovTI included Iceland, Australia, New Zealand, Hong Kong, and Thailand, and some island nations. Globally, CovTI increased from April 20 [Formula] to June 3 [Formula] but declined in ca. 10% of countries. Bivariate analyses showed the average in countries with open public testing policies (59.7, 95% CI 55.6-63.8) were significantly higher than countries with no testing policy (30.2, 95% CI 18.1-42.3) (p<0.0001). A multiple linear regression model assessed the association of independent grouping variables with CovTI. Open public testing and extensive contact tracing were shown to significantly increase CovTI, after adjusting for extrinsic factors, including geographic isolation and centralized forms of government. This tool may be useful for policymakers to assess testing effectiveness, inform decisions, and identify model countries. It may also serve as a tool for researchers in analyses by combining it with other databases.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Anthony C Kuster", + "author_inst": "Faculty of Public Health, Khon Kaen University, Khon Kaen, Thailand" + }, + { + "author_name": "Hans J Overgaard", + "author_inst": "Faculty of Science and Technology, Norwegian University of Life Sciences, Norway" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.17.20133702", "rel_title": "Statistical Issues and Lessons Learned from COVID-19 Clinical Trials with Lopinavir-Ritonavir and Remdesivir", @@ -1349774,61 +1351253,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.17.20133348", - "rel_title": "Perceived Challenges of COVID-19 Infection Prevention and Control Preparedness: A Multinational Survey", - "rel_date": "2020-06-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.17.20133348", - "rel_abs": "ObjectivesImplementation of effective infection prevention and control (IPC) measures is needed to support global capacity building to limit transmission of coronavirus disease 2019 (COVID-19) and mitigate its impact on health systems. We assessed the perceptions of healthcare workers on the current global IPC preparedness measures for COVID-19.\n\nMethodsA cross-sectional survey using an electronic survey was circulated between February 26, 2020, and March 20, 2020, to IPC professionals during COVID-19 pandemic. The survey addressed the presence of COVID-19 guidelines as well as specific IPC preparedness activities in response to the outbreak.\n\nFindingsIn total, 339 IPC professionals spanning 63 countries in all 6 World Health Organization (WHO) regions, mostly from tertiary care centres participated. Of all participants, 66{middle dot}6% were aware of the existence of national guidelines to prevent COVID-19. A shortage of PPE supplies was reported by 48% (ranging from 64{middle dot}2% in low-income countries to 27{middle dot}4% in high-income countries); 41{middle dot}5% of respondents considered that the media had an impact on guideline development and 63{middle dot}6% believed that guidelines were based on maximum security rather than on evidence-based analyses. 58{middle dot}5% and 72{middle dot}7% of participants believed that healthcare facilities and community settings respectively were not sufficiently prepared.\n\nConclusionResults revealed lack of guidelines and concerns over insufficient PPE supply in both high- and low-income countries. Our findings should alert national health authorities to ramp up the implementation of IPC measures and focus on long-term preparedness and readiness for future pandemics, likely requiring government funds rather than reliance on healthcare institutions.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "ERMIRA TARTARI", - "author_inst": "University of Malta" - }, - { - "author_name": "Joost Hopman", - "author_inst": "Radboud University Medical Center, Nijmegen, The Netherlands" - }, - { - "author_name": "Benedetta Allegranzi", - "author_inst": "World Health Organziation" - }, - { - "author_name": "Bin Gao", - "author_inst": "Tianjin 4th Centre Hospital" - }, - { - "author_name": "Andreas Widmer", - "author_inst": "University Hospital Basel" - }, - { - "author_name": "Vincent Chi-Chung Cheng", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Shuk Ching Wong", - "author_inst": "Queen Mary Hospital, Hong Kong" - }, - { - "author_name": "Kalisvar Marimuthu", - "author_inst": "Tan Tock Seng Hospital, Singapore" - }, - { - "author_name": "Folasade Ogunsola", - "author_inst": "College of Medicine of the University of Lagos, Nigeria" - }, - { - "author_name": "Andreas Voss", - "author_inst": "Radboud University Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.17.20133520", "rel_title": "Effect of evacuation of Japanese residents from Wuhan, China, on preventing transmission of novel coronavirus infection: a modelling study", @@ -1350644,6 +1352068,77 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.06.17.158121", + "rel_title": "The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA", + "rel_date": "2020-06-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.17.158121", + "rel_abs": "The SARS-CoV-2 nucleocapsid (N) protein is an abundant RNA binding protein critical for viral genome packaging, yet the molecular details that underlie this process are poorly understood. Here we combine single-molecule spectroscopy with all-atom simulations to uncover the molecular details that contribute to N protein function. N protein contains three dynamic disordered regions that house putative transiently-helical binding motifs. The two folded domains interact minimally such that full-length N protein is a flexible and multivalent RNA binding protein. N protein also undergoes liquid-liquid phase separation when mixed with RNA, and polymer theory predicts that the same multivalent interactions that drive phase separation also engender RNA compaction. We offer a simple symmetry-breaking model that provides a plausible route through which single-genome condensation preferentially occurs over phase separation, suggesting that phase separation offers a convenient macroscopic readout of a key nanoscopic interaction.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Jasmine Cubuk", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Jhullian J Alston", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "J. Jeremias Incicco", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Sukrit Singh", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Melissa D Stuchell-Brereton", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Michael D Ward", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Maxwell I Zimmerman", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Neha Vithani", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Daniel Griffith", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Jason A Wagoner", + "author_inst": "Stony Brook University" + }, + { + "author_name": "Gregory R Bowman", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Kathleen B Hall", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Andrea Soranno", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Alex S Holehouse", + "author_inst": "Washington University School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2020.06.17.156471", "rel_title": "The SARS-CoV-2 Spike protein has a broad tropism for mammalian ACE2 proteins", @@ -1351604,101 +1353099,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.06.15.20129411", - "rel_title": "Early impacts of the COVID-19 pandemic on mental health care and on people with mental health conditions: framework synthesis of international experiences and responses", - "rel_date": "2020-06-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.15.20129411", - "rel_abs": "PurposeThe COVID-19 pandemic has many potential impacts on people with mental health conditions and on mental health care, including direct consequences of infection, effects of infection control measures and subsequent societal changes. We aimed to map early impacts of the pandemic on people with pre-existing mental health conditions and services they use, and to identify individual and service-level strategies adopted to manage these.\n\nMethodsWe searched for relevant material in the public domain published before 30 April 2020, including papers in scientific and professional journals, published first person accounts, media articles, and publications by governments, charities and professional associations. Search languages were English, French, German, Italian, Spanish, and Mandarin Chinese. Relevant content was retrieved and summarised via a rapid qualitative framework synthesis approach.\n\nResultsWe found 872 eligible sources from 29 countries. Most documented observations and experiences rather than reporting research data. We found many reports of deteriorations in symptoms, and of impacts of loneliness and social isolation and of lack of access to services and resources, but sometimes also of resilience, effective self-management and peer support. Immediate service challenges related to controlling infection, especially in inpatient and residential settings, and establishing remote working, especially in the community. We summarise reports of swiftly implemented adaptations and innovations, but also of pressing ethical challenges and concerns for the future.\n\nConclusionOur analysis captures the range of stakeholder perspectives and experiences publicly reported in the early stages of the COVID-19 pandemic in several countries. We identify potential foci for service planning and research.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Luke Sheridan Rains", - "author_inst": "University College London" - }, - { - "author_name": "Sonia Johnson", - "author_inst": "University College London" - }, - { - "author_name": "Phoebe Barnett", - "author_inst": "University College London" - }, - { - "author_name": "Thomas Steare", - "author_inst": "University College London" - }, - { - "author_name": "Justin J Needle", - "author_inst": "City University of London" - }, - { - "author_name": "Sarah Carr", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Billie Lever Taylor", - "author_inst": "University College London" - }, - { - "author_name": "Francesca Bentivegna", - "author_inst": "University College London" - }, - { - "author_name": "Julian Edbrooke-Childs", - "author_inst": "University College London" - }, - { - "author_name": "Hannah Rachel Scott", - "author_inst": "University College London" - }, - { - "author_name": "Jessica Rees", - "author_inst": "University College London" - }, - { - "author_name": "Prisha Shah", - "author_inst": "University College London" - }, - { - "author_name": "Jo Lomani", - "author_inst": "St George's, University of London" - }, - { - "author_name": "Beverley Chipp", - "author_inst": "University College London" - }, - { - "author_name": "Nick Barber", - "author_inst": "University College London" - }, - { - "author_name": "Zainab Dedat", - "author_inst": "University College London" - }, - { - "author_name": "Sian Oram", - "author_inst": "Kings College London" - }, - { - "author_name": "Nicola Morant", - "author_inst": "University College London" - }, - { - "author_name": "Alan Simpson", - "author_inst": "Kings College London" - }, - { - "author_name": "- COVID-19 Mental Health Policy Research Unit Group", - "author_inst": "-" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.06.15.20131748", "rel_title": "Clinical, immunological and virological characterization of COVID-19 patients that test re-positive for SARS-CoV-2 by RT-PCR", @@ -1352458,6 +1353858,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.15.20131607", + "rel_title": "Prothrombotic antiphospholipid antibodies in COVID-19", + "rel_date": "2020-06-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.15.20131607", + "rel_abs": "Patients with coronavirus disease 19 (COVID-19) are at high risk for thrombotic arterial and venous occlusions. At the same time, lung histopathology often reveals fibrin-based occlusion of small vessels in patients who succumb to the disease. Antiphospholipid syndrome (APS) is an acquired and potentially life-threatening thrombophilia in which patients develop pathogenic autoantibodies (aPL) targeting phospholipids and phospholipid-binding proteins. Small case series have recently detected aPL in patients with COVID-19. Here, we measured eight types of aPL (anticardiolipin IgG/IgM/IgA, anti-beta-2 glycoprotein I IgG/IgM/IgA, and anti-phosphatidylserine/prothrombin (PS/PT) IgG/IgM) in the sera of 172 patients hospitalized with COVID-19. We detected anticardiolipin IgM antibodies in 23%, anti-PS/PT IgG in 24%, and anti-PS/PT IgM in 18%. Any aPL was present in 52% of patients using the manufacturers threshold and in 30% using a more stringent cutoff ([≥]40 units). Higher levels of aPL were associated with neutrophil hyperactivity (including the release of neutrophil extracellular traps/NETs), higher platelet count, more severe respiratory disease, and lower glomerular filtration rates. Similar to patients with known and longstanding APS, IgG fractions isolated from patients with COVID-19 promoted NET release from control neutrophils. Furthermore, injection of these COVID-19 IgG fractions into mice accelerated venous thrombosis. Taken together, these studies suggest that a significant percentage of patients with COVID-19 become at least transiently positive for aPL and that these aPL are potentially pathogenic.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Yu Zuo", + "author_inst": "University of Michigan" + }, + { + "author_name": "Shanea K. Estes", + "author_inst": "University of Michigan" + }, + { + "author_name": "Ramadan A. Ali", + "author_inst": "University of Michigan" + }, + { + "author_name": "Alex A. Gandhi", + "author_inst": "University of Michigan" + }, + { + "author_name": "Srilakshmi Yalavarthi", + "author_inst": "University of Michigan" + }, + { + "author_name": "Hui Shi", + "author_inst": "University of Michigan" + }, + { + "author_name": "Gautam Sule", + "author_inst": "University of Michigan" + }, + { + "author_name": "Kelsey Gockman", + "author_inst": "University of Michigan" + }, + { + "author_name": "Jacqueline A. Madison", + "author_inst": "University of Michigan" + }, + { + "author_name": "Melanie Zuo", + "author_inst": "University of Michigan" + }, + { + "author_name": "Vinita Yadav", + "author_inst": "University of Michigan" + }, + { + "author_name": "Jintao Wang", + "author_inst": "NIH-NHLBI" + }, + { + "author_name": "Wrenn Woodard", + "author_inst": "University of Michigan" + }, + { + "author_name": "Sean P. Lezak", + "author_inst": "University of Michigan" + }, + { + "author_name": "Njira L. Lugogo", + "author_inst": "University of Michigan" + }, + { + "author_name": "Stephanie A. Smith", + "author_inst": "University of Michigan" + }, + { + "author_name": "James H. Morrissey", + "author_inst": "University of Michigan" + }, + { + "author_name": "Yogendra Kanthi", + "author_inst": "NIH-NHLBI" + }, + { + "author_name": "Jason S. Knight", + "author_inst": "University of Michigan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.15.20131706", "rel_title": "Deregulated cellular circuits driving immunoglobulins and complement consumption associate with the severity of COVID-19", @@ -1353314,65 +1354805,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2020.06.17.155689", - "rel_title": "Holder Pasteurization Inactivates SARS-CoV-2 in Human Breast Milk", - "rel_date": "2020-06-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.17.155689", - "rel_abs": "SARS-CoV-2 RNA has been detected in the human breast milk of infected mothers, raising concerns regarding the safety of breastfeeding upon infection. We here show that holder pasteurization inactivates SARS-CoV-2 and provides an alternative and safe option for infected mothers to continue feeding breast milk to their infants.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Carina Conzelmann", - "author_inst": "Institute of Molecular Virology, Ulm University Medical Center" - }, - { - "author_name": "Ruediger Gross", - "author_inst": "Institute of Molecular Virology, Ulm University Medical Center" - }, - { - "author_name": "Toni Luise Meister", - "author_inst": "Department of Molecular and Medical Virology, Ruhr University Bochum" - }, - { - "author_name": "Daniel Todt", - "author_inst": "Department of Molecular and Medical Virology, Ruhr University Bochum" - }, - { - "author_name": "Adalbert Krawczyk", - "author_inst": "Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University of Duisburg-Essen" - }, - { - "author_name": "Ulf Dittmer", - "author_inst": "Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University of Duisburg-Essen" - }, - { - "author_name": "Steffen Stenger", - "author_inst": "Institute for Microbiology and Hygiene, Ulm University Medical Center" - }, - { - "author_name": "Jan Muench", - "author_inst": "Institute of Molecular Virology, Ulm University Medical Center" - }, - { - "author_name": "Eike Steinmann", - "author_inst": "Department of Molecular and Medical Virology, Ruhr University Bochum" - }, - { - "author_name": "Janis A Mueller", - "author_inst": "Institute of Molecular Virology, Ulm University Medical Center" - }, - { - "author_name": "Stephanie Pfaender", - "author_inst": "Department of Molecular and Medical Virology, Ruhr University Bochum" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.06.16.155580", "rel_title": "High-Accuracy Multiplexed SARS-CoV-2 Antibody Assay with Avidity and Saliva Capability on a Nano-Plasmonic Platform", @@ -1353980,6 +1355412,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.06.13.20130146", + "rel_title": "Are health indicators able to describe the ability to cope of Health Systems with COVID-19 epidemic?", + "rel_date": "2020-06-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.13.20130146", + "rel_abs": "The Coronavirus Disease 19 epidemic is an infectious disease which was declared as a pandemic and hit all the Countries, all over the world, from the beginning of the year 2020.\n\nDespite the emergency vigilance plans, in all the Countries, Health Systems experienced a different ratio of lethality, admissions to intensive care units and managing quarantine of positive patients.\n\nThe aim of this study is to investigate if some health indicators might have been useful to understand the capacity of Italian National Health Service to manage the COVID 19 epidemic.\n\nWe will compare data in two different Italian regions in the Northern part of Italy (Lombardy and Veneto) with the national data to understand if different health strategies might be significant to explain different patterns of COVID 19 epidemic in Italy.\n\nThe two regions have two different health policies to face CoViD-2019 epidemic.\n\nTo face epidemic like this one the answer should be outside hospitals but this means to have general practitioners well-trained and enough healthcare personnel working outside hospitals.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Silvana Castaldi", + "author_inst": "Department of Biomedical Sciences for Health University of Milan, Italy and Fondazione IRCCS Ca Granda Ospedale Maggiore di Milano, Italy" + }, + { + "author_name": "Ester Luconi", + "author_inst": "Fondazione IRCCS Ca Granda Ospedale Maggiore di Milano, Italy" + }, + { + "author_name": "Bruno Alessandro Rivieccio", + "author_inst": "Niguarda Hospital AREU Regional Emergency Service Agency, Milano, Italy" + }, + { + "author_name": "Patrizia Boracchi", + "author_inst": "Department of Clinical Sciences and Community Health & DSRC, University of Milan, Italy" + }, + { + "author_name": "Giuseppe Marano", + "author_inst": "Department of Clinical Sciences and Community Health & DSRC, University of Milan, Italy" + }, + { + "author_name": "Elena Pariani", + "author_inst": "Department of Biomedical Sciences for Health University of Milan, Italy and Fondazione IRCCS Ca Granda Ospedale Maggiore di Milano, Italy" + }, + { + "author_name": "Luisa Romano'", + "author_inst": "Department of Biomedical Sciences for Health University of Milan, Italy and Fondazione IRCCS Ca Granda Ospedale Maggiore di Milano, Italy" + }, + { + "author_name": "Francesco Auxilia", + "author_inst": "Department of Biomedical Sciences for Health University of Milan, Italy" + }, + { + "author_name": "Federica Nicolussi", + "author_inst": "Department of Economics, Management and Quantitative Methods & DSRC, University of Milan, Italy" + }, + { + "author_name": "Alessandra Micheletti", + "author_inst": "Department of Environmental Science and Policy, University of Milan, Italy" + }, + { + "author_name": "Giancarlo Manzi", + "author_inst": "Department of Economics, Management and Quantitative Methods & DSRC, University of Milan, Italy" + }, + { + "author_name": "Silvia Salini", + "author_inst": "Department of Economics, Management and Quantitative Methods & DSRC, University of Milan, Italy" + }, + { + "author_name": "Massimo Galli", + "author_inst": "Department of Biomedical and Clinical Sciences \"L. Sacco\", University of Milan, Italy" + }, + { + "author_name": "Elia Mario Biganzoli", + "author_inst": "Department of Clinical Sciences and Community Health & DSRC, University of Milan, Italy" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.06.13.20130211", "rel_title": "Risk and severity of COVID-19 and ABO blood group in transcatheter aortic valve patients", @@ -1354820,25 +1356323,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.13.20130070", - "rel_title": "Cohen's kappa statistics as a convenient means to identify accurate SARS-CoV-2 rapid antibody tests", - "rel_date": "2020-06-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.13.20130070", - "rel_abs": "There are many available rapid antibody tests, but the performance of such tests remains unclear. Moreover, it is difficult to compare among the various devices regarding their sensitivity & specificity.\n\nIn order to compare the performance of such devices, we used Cohen kappa statistics to assess the level of agreement between RT-PCR and rapid antibody tests. In doing this study, we considered the term of validity after symptom-onset to compare two tests. It takes more than a week to produce antibodies in the body, and RT-PCR thus gives negative result in the convalescent period. On ELISA data from the literature kappa statistics was calculated as 1.0 beyond 10 days after symptom-onset. By taking these factors into consideration, we evaluated agreement with samples collected beyond 10 days of symptom-onset during the active period.\n\nWe calculated the data from 9 devices, and the kappa statistics for English data were calculated as 0.64 on average. The same finding was 0.75 for Chinese data. These results corresponded with the values from sensitivity & specificity of their reports. Both reports had no details about the collection procedures. Kappa statistics might become even more accurate, if samples could be restricted to ones collected beyond 10 days. Regarding the data from our hospital, the kappa statistics was 0.97 when restricted to samples collected beyond 10 days, which thus showed excellent agreement.\n\nBy using kappa statistics, the performances of rapid antibody tests can be shown as one figure, so that their comparison becomes easy to carry out.\n\nHighlights{blacksquare} Using kappa statistics, agreement between PCR and ELISA was perfect from the data beyond 10 days of symptom-onset.\n{blacksquare}The results of kappa statistics corresponded with the values from sensitivity & specificity of the English and the Chinese literatures.\n{blacksquare}Kappa statistics was calculated as 0.97 from the data beyond 10 days of symptom-onset, and sensitivity & specificity were 95.2% and 100% in our hospital.\n{blacksquare}Kappa statistics is a convenient means to identify accurate rapid antibody tests.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Harukazu Iseki", - "author_inst": "Sagamihara Kyodo Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.15.20130344", "rel_title": "Utility of Lung Ultrasound in COVID-19: A Systematic Scoping Review", @@ -1355310,6 +1356794,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.14.20130823", + "rel_title": "Publish or perish: Reporting Characteristics of Peer-reviewed publications, pre-prints and registered studies on the COVID-19 pandemic", + "rel_date": "2020-06-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.14.20130823", + "rel_abs": "BackgroundThe COVID-19 pandemic has resulted in a mass of academic papers being published in a very brief span of time. Our aim was to compare the amount and reporting characteristics of COVID-19 related peer-reviewed and pre-prints publications. We also investigated the amount of ongoing trials and systematic reviews.\n\nMethods and findingsA cross-sectional study of publications covering the COVID-19 pandemic time frame, up to May 20, 2020 was conducted. PubMed with appropriate combinations of Medical Subject Headings and COVID-19 section of MedRxiv and BioRxiv archives were searched. We examined Clinicaltrial.gov, Chinese Clinical Trial Registry, EU Register and 15 other trial registers as well as the international prospective register of systematic reviews (PROSPERO). Characteristics of each publication source were extracted. Regression analyses and Z tests were used to analyze publication trends over the weeks and compare their relative proportions.\n\nWe found 3635 peer-reviewed publications and 3805 pre-prints, of which 8.6% (n=329) were published in indexed journals. Peer-reviewed and pre-print publications amount both increased significantly over time (p<0.001). Case reports (peer-reviewed: 6% vs pre-prints: 0.9%, p<0.001) and letters (17.4% vs 0.5%, p<0.001) accounted for a greater share of the peer-reviewed compared to pre-print publications. In turn, randomized controlled trials (0.22% vs 0.63% p<0.001) and systematic reviews (0.08% vs 5%) accounted for a significantly greater share of the pre-print publications. Clinicaltrials.gov, Chinese Clinical Trial Registry and EU register included 57.9%, 49.5 % and 98.9% trials mostly still \"recruiting\". PROSPERO amounted to 962 systematic review protocols.\n\nConclusionPre-prints were slightly more prevalent than peer-reviewed publications, yet both are growing. To fill the void given by the absence of published primary studies, immediate opinions (i.e., letters) has virulently been published in PubMed. However, preprints has been promoted as rapid responses to give direct and promptly access at scientific findings in this pandemic.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Silvia Gianola", + "author_inst": "IRCCS Istituto Ortopedico Galeazzi" + }, + { + "author_name": "Tiago S Jesus", + "author_inst": "Global Health and Tropical Medicine (GHTM), WHO Collaborating Centre for Health Workforce Policy and Planning, Institute of Hygiene and Tropical Medicine - NOVA" + }, + { + "author_name": "Silvia Bargeri", + "author_inst": "Universita' Vita-Salute San Raffaele" + }, + { + "author_name": "Greta Castellini", + "author_inst": "IRCCS Istituto Ortopedico Galeazzi" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.13.20130658", "rel_title": "Global and local mobility as a barometer for COVID-19 dynamics", @@ -1356130,81 +1357645,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.14.20131045", - "rel_title": "Clinical characteristics of Coronavirus Disease 2019 (COVID-19) patients in Kuwait", - "rel_date": "2020-06-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.14.20131045", - "rel_abs": "This is a retrospective single-center study of 417 consecutive patients with coronavirus disease 2019 (COVID-19) admitted to Jaber Al-Ahmad Hospital in Kuwait between February 24, 2020 and May 24, 2020. In total, 39.3% of patients were asymptomatic, 41% were symptomatic with mild/moderate symptoms, 5.3% were admitted to the intensive care unit (ICU) and recovered, and 14.4% died. The mean age of death cases was 54.20 years ({+/-} 11.09). Comorbidities were more prevalent in patients who died compared with others. Key findings include abnormal levels of markers assicated with infection, inflammation, abnormal blood clotting, heart problems and kidney problems in patients with severe form of the disease and poor putcome. We report a rapidly deteriorating estimated glomerular filtration rate (eGFR) in deaths during ICU stay with kidney injury complications reported in 65% of deaths (p < 0.05). Our dynamic profiling of eGFR in ICU highlights the potential role of renal markers in forecasting disease outcome that could perhaps identify patients at risk of poor outcome.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Abdullah Alshukry", - "author_inst": "Department of Otolaryngology & Head and Neck Surgery, Jaber Al-Ahmad Hospital, Ministry of Health, Kuwait" - }, - { - "author_name": "Hamad Ali", - "author_inst": "Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Health Sciences Center (HSC), Kuwait University, Kuwait" - }, - { - "author_name": "Yaseen Ali", - "author_inst": "Department of Otolaryngology & Head and Neck Surgery, Jaber Al-Ahmad Hospital, Ministry of Health, Kuwait" - }, - { - "author_name": "Talal Al-Taweel", - "author_inst": "Gastroenterology Unit, Department of Internal Medicine, Jaber Al-Ahmad Hospital, Ministry of Health, Kuwait." - }, - { - "author_name": "Mohamed Abu-farha", - "author_inst": "Dasman Diabetes Institute (DDI), Dasman, Kuwait" - }, - { - "author_name": "Jehad AbuBaker", - "author_inst": "Dasman Diabetes Institute (DDI), Dasman, Kuwait" - }, - { - "author_name": "Sriraman Devarajan", - "author_inst": "Dasman Diabetes Institute (DDI), Dasman, Kuwait" - }, - { - "author_name": "Ali A. Dashti", - "author_inst": "Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Health Sciences Center (HSC), Kuwait University, Kuwait" - }, - { - "author_name": "Ali Bandar", - "author_inst": "Department of Anesthesia and Intensive Care, Jaber Al-Ahmad Hospital, Ministry of Health, Kuwait" - }, - { - "author_name": "Hessah Taleb", - "author_inst": "Department of Pediatric Emergency, Jaber Al-Ahmad Hospital, Ministry of Health, Kuwait" - }, - { - "author_name": "Abdullah Al Bader", - "author_inst": "Department of Otolaryngology & Head and Neck Surgery, Jaber Al-Ahmad Hospital, Ministry of Health, Kuwait" - }, - { - "author_name": "Nasser Y. Aly", - "author_inst": "Department of Preventive Health, Jaber Al-Ahmad Hospital, Ministry of Health, Kuwait" - }, - { - "author_name": "Ebaa Al-Ozairi", - "author_inst": "Dasman Diabetes Institute (DDI), Dasman, Kuwait" - }, - { - "author_name": "Fahd Al-Mulla", - "author_inst": "Dasman Diabetes Institute (DDI), Dasman, Kuwait" - }, - { - "author_name": "Mohammad Bu Abbas", - "author_inst": "Department of Otolaryngology & Head and Neck Surgery, Jaber Al-Ahmad Hospital, Ministry of Health, Kuwait" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.14.20130955", "rel_title": "Critical Complications of COVID-19: A systematic Review and Meta-Analysis study", @@ -1356836,6 +1358276,153 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2020.06.14.20131169", + "rel_title": "Hypokalemia in Patients with COVID-19", + "rel_date": "2020-06-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.14.20131169", + "rel_abs": "Patients with COVID-19 may experience multiple conditions (e.g., fever, hyperventilation, anorexia, gastroenteritis, acid-base disorder) that may cause electrolyte imbalances. Hypokalemia is a concerning electrolyte disorder that may increase the susceptibility to various kinds of arrhythmia. This study aimed to estimate prevalence, risk factors and outcome of hypokalemia in a cohort of non-critically ill patients. A retrospective analysis was conducted on 290 hospitalized patients with confirmed COVID-19 infection at the tertiary teaching hospital of Modena, Italy.\n\nHypokalemia (<3.5 mEq/L) was detected in 119 patients (41%). The decrease of serum potassium level was of mild entity (3-3.4 mEq/L) and occurred in association with hypocalcemia (P=0.001) and lower level of serum magnesium (P=0.028) compared to normokaliemic patients. Urine K: creatinine ratio, measured in a small subset of patients (n=45; 36.1%), showed an increase of urinary potassium excretion in the majority of the cases (95.5%). Causes of kaliuria were diuretic therapy (53.4%) and corticosteroids (23.3%). In the remaining patients, urinary potassium loss was associated with normal serum magnesium, low sodium excretion (FENa< 1%) and metabolic alkalosis. Risk factors for hypokalemia were female gender (P=0.002; HR 0.41, 95%CI 0.23-0.73) and diuretic therapy (P=0.027; HR 1.94, 95%CI 1.08-3.48). Hypokalemia, adjusted for sex, age and SOFA score, resulted not associated with ICU admission (P=0.131, 95% CI 0.228-1.212) and in-hospital mortality (P=0.474; 95% CI 0,170-1,324) in our cohort of patients.\n\nHypokalemia is a frequent disorder in COVID-19 patients and urinary potassium loss may be the main cause of hypokalemia. The disorder was mild in the majority of the patients and was unrelated to poor outcomes. Nevertheless, hypokalemic patients required potassium supplements to dampen the risk of arrhythmias.", + "rel_num_authors": 33, + "rel_authors": [ + { + "author_name": "Gaetano Alfano", + "author_inst": "University of Modena and Reggio Emilia" + }, + { + "author_name": "Annachiara Ferrari", + "author_inst": "Policlinico di Modena" + }, + { + "author_name": "Francesco Fontana", + "author_inst": "Policlinco di Modena" + }, + { + "author_name": "Rossella Perrone", + "author_inst": "Policlinico di Modena" + }, + { + "author_name": "Giacomo Mori", + "author_inst": "Policlinco di Modena" + }, + { + "author_name": "Elisabetta Ascione", + "author_inst": "Policlinico di Modena" + }, + { + "author_name": "Magistroni Riccardo", + "author_inst": "Policlinico di Modena" + }, + { + "author_name": "Giulia Venturi", + "author_inst": "Policlinico di Modena" + }, + { + "author_name": "Simone Pederzoli", + "author_inst": "Policlinico di Modena" + }, + { + "author_name": "Gianluca Margiotta", + "author_inst": "Policlinico di Modena" + }, + { + "author_name": "Marilina Romeo", + "author_inst": "Policlinico di Modena" + }, + { + "author_name": "Francesca Piccinini", + "author_inst": "Policlinico di Modena" + }, + { + "author_name": "Giacomo Franceschi", + "author_inst": "Policlinico di Modena" + }, + { + "author_name": "Sara Volpi", + "author_inst": "Policlinico di Modena" + }, + { + "author_name": "Matteo Faltoni", + "author_inst": "Policlinico di Modena" + }, + { + "author_name": "Giacomo Ciusa", + "author_inst": "Policlinico di Modena" + }, + { + "author_name": "Erica Bacca", + "author_inst": "Policlinico di Modena" + }, + { + "author_name": "Marco Tutone", + "author_inst": "Policlinico di Modena" + }, + { + "author_name": "Alessandro Raimondi", + "author_inst": "Policlinico di Modena" + }, + { + "author_name": "marianna menozzi", + "author_inst": "Policlinico di Modena" + }, + { + "author_name": "Erica Franceschini", + "author_inst": "Policlinico di Modena" + }, + { + "author_name": "Gianluca Cuomo", + "author_inst": "Policlinico di Modena" + }, + { + "author_name": "Gabriella Orlando", + "author_inst": "Policlinico di Modena" + }, + { + "author_name": "Antonella Santoro", + "author_inst": "Policlinico di Modena" + }, + { + "author_name": "Margherita Di Gaetano", + "author_inst": "Policlinico di Modena" + }, + { + "author_name": "Cinzia Puzzolante", + "author_inst": "Policlinico di Modena" + }, + { + "author_name": "Federica Carli", + "author_inst": "Policlinico di Modena" + }, + { + "author_name": "Andrea Bedini", + "author_inst": "Policlinico di Modena" + }, + { + "author_name": "Jovana Milic", + "author_inst": "Policlinico di Modena" + }, + { + "author_name": "Marianna Meschiari", + "author_inst": "Policlinico di Modena" + }, + { + "author_name": "Cristina Mussini", + "author_inst": "Policlinico di Modena" + }, + { + "author_name": "Gianni Cappelli", + "author_inst": "Policlinico di Modena" + }, + { + "author_name": "Giovanni Guaraldi", + "author_inst": "Policlinico di Modena" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "nephrology" + }, { "rel_doi": "10.1101/2020.06.14.20131128", "rel_title": "Innate immune signaling in the olfactory epithelium reduces odorant receptor levels: modeling transient smell loss in COVID-19 patients", @@ -1357784,53 +1359371,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.06.15.153387", - "rel_title": "The Integrin Binding Peptide, ATN-161, as a Novel Therapy for SARS-CoV-2 Infection", - "rel_date": "2020-06-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.15.153387", - "rel_abs": "Many efforts to design and screen therapeutics for severe acute respiratory syndrome coronavirus (SARS-CoV-2) have focused on inhibiting viral cell entry by disrupting ACE2 binding with the SARS-CoV-2 spike protein. This work focuses on inhibiting SARS-CoV-2 entry through a hypothesized 5{beta}1 integrin-based mechanism, and indicates that inhibiting the spike protein interaction with 5{beta}1 integrin (+/- ACE2), and the interaction between 5{beta}1 integrin and ACE2 using a molecule ATN-161 represents a promising approach to treat COVID-19.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Brandon Beddingfield", - "author_inst": "Tulane University" - }, - { - "author_name": "Naoki Iwanaga", - "author_inst": "Tulane University" - }, - { - "author_name": "Prem P Chapagain", - "author_inst": "Florida International University" - }, - { - "author_name": "Wenshu Zheng", - "author_inst": "Tulane University" - }, - { - "author_name": "Chad J Roy", - "author_inst": "Tulane University School of Medicine" - }, - { - "author_name": "Tony Y Hu", - "author_inst": "Tulane University" - }, - { - "author_name": "Jay Kolls", - "author_inst": "Tulane School of Medicine" - }, - { - "author_name": "Gregory Bix", - "author_inst": "Tulane University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.06.15.134403", "rel_title": "AGE IS ASSOCIATED WITH INCREASED EXPRESSION OF PATTERN RECOGNITION RECEPTOR GENES AND ACE2, THE RECEPTOR FOR SARS-COV-2: IMPLICATIONS FOR THE EPIDEMIOLOGY OF COVID-19 DISEASE", @@ -1358582,6 +1360122,73 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.06.14.150862", + "rel_title": "An enzyme-based immunodetection assay to quantify SARS-CoV-2 infection", + "rel_date": "2020-06-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.14.150862", + "rel_abs": "SARS-CoV-2 is a novel pandemic coronavirus that caused a global health and economic crisis. The development of efficient drugs and vaccines against COVID-19 requires detailed knowledge about SARS-CoV-2 biology. Several techniques to detect SARS-CoV-2 infection have been established, mainly based on counting infected cells by staining plaques or foci, or by quantifying the viral genome by PCR. These methods are laborious, time-consuming and expensive and therefore not suitable for a high sample throughput or rapid diagnostics. We here report a novel enzyme-based immunodetection assay that directly quantifies the amount of de novo synthesized viral spike protein within fixed and permeabilized cells. This in-cell ELISA enables a rapid and quantitative detection of SARS-CoV-2 infection in microtiter format, regardless of the virus isolate or target cell culture. It follows the established method of performing ELISA assays and does not require expensive instrumentation. Utilization of the in-cell ELISA allows to e.g. determine TCID50 of virus stocks, antiviral efficiencies (IC50 values) of drugs or neutralizing activity of sera. Thus, the in-cell spike ELISA represents a promising alternative to study SARS-CoV-2 infection and inhibition and may facilitate future research.\n\nHighlightsO_LIDetermination of SARS-CoV-2 infection by enzymatically quantifying the expression of viral spike protein in bulk cell cultures\nC_LIO_LITargeting a highly conserved region in the S2 subunit of the S protein allows broad detection of several SARS-CoV-2 isolates in different cell lines\nC_LIO_LIScreening of antivirals in microtiter format and determining the antiviral activity as inhibitory concentrations 50 (IC50)\nC_LI", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Carina Conzelmann", + "author_inst": "Institute of Molecular Virology, Ulm University Medical Center" + }, + { + "author_name": "Andrea Gilg", + "author_inst": "Institute of Molecular Virology, Ulm University Medical Center" + }, + { + "author_name": "Ruediger Gross", + "author_inst": "Institute of Molecular Virology, Ulm University Medical Center" + }, + { + "author_name": "Desiree Schuetz", + "author_inst": "Institute of Molecular Virology, Ulm University Medical Center" + }, + { + "author_name": "Nico Preising", + "author_inst": "Core Facility Functional Peptidomics, Ulm University Medical Center" + }, + { + "author_name": "Ludger Staendker", + "author_inst": "Core Facility Functional Peptidomics, Ulm University Medical Center" + }, + { + "author_name": "Bernd Jahrsdoerfer", + "author_inst": "Institute for Transfusion Medicine, Ulm University" + }, + { + "author_name": "Hubert Schrezenmeier", + "author_inst": "Institute for Transfusion Medicine, Ulm University" + }, + { + "author_name": "Konstantin MJ Sparrer", + "author_inst": "Institute of Molecular Virology, Ulm University Medical Center" + }, + { + "author_name": "Thomas Stamminger", + "author_inst": "Institute of Virology, Ulm University Medical Center" + }, + { + "author_name": "Steffen Stenger", + "author_inst": "Institute of Medical Microbiology and Hygiene, Ulm University Medical Center" + }, + { + "author_name": "Jan Muench", + "author_inst": "Institute of Molecular Virology, Ulm University Medical Center" + }, + { + "author_name": "Janis A Mueller", + "author_inst": "Institute of Molecular Virology, Ulm University Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.06.14.150607", "rel_title": "Characterization of the SARS-CoV-2 S Protein: Biophysical, Biochemical, Structural, and Antigenic Analysis", @@ -1359506,93 +1361113,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.12.20129221", - "rel_title": "Assessment of spread of SARS-CoV-2 by RT-PCR and concomitant serology in children in a region heavily affected by COVID-19 pandemic", - "rel_date": "2020-06-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.12.20129221", - "rel_abs": "BackgroundSeveral studies indicated that children seem to be less frequently infected with SARS-CoV-2 and potentially less contagious. To examine the spread of SARS-CoV-2 we combined both RT-PCR testing and serology in children in the most affected region in France, during the COVID-19 epidemic.\n\nMethodsFrom April 14, 2020 to May 12, 2020, we conducted a cross-sectional prospective, multicenter study. Healthy controls and pauci-symptomatic children from birth to age 15 years were enrolled by 27 ambulatory pediatricians. A nasopharyngeal swab was taken for detection of SARS-CoV-2 by RT-PCR and a microsample of blood for micro-method serology.\n\nResultsAmong the 605 children, 322 (53.2%) were asymptomatic and 283 (46.8%) symptomatic. RT-PCR testing and serology were positive for 11 (1.8%) and 65 (10.7%) of all children, respectively. Only 3 children were RT-PCR-positive without any antibody response have been detected. The frequency of positivity on RT-PCR for SARS-CoV-2 was significantly higher in children with positive serology than those with a negative one (12.3% vs 0.6%, p<0.001). Contact with a person with proven COVID-19 increased the odds of positivity on RT-PCR (OR 7.8, 95% confidence interval [1.5; 40.7]) and serology (15.1 [6.6;34.6]).\n\nConclusionIn area heavily affected by COVID-19, after the peak of the first epidemic wave and during the lockdown, the rate of children with positive SARS-CoV-2 RT-PCR was very low (1.8%), but the rate of positive on serology was higher (10.7%). Most of PCR positive children had at the same time positive serology.\n\nWhat is already known on this topic?- As compared with adults, children seem to be less frequently infected with SARS-CoV-2 and potentially less contagious according to several studies.\n- Most of the studies were based on RT-PCR SARS-CoV-2 testing, without antibody assays.\n\n\nWhat this study adds?- This study combining RT-PCR and serologic testing, assessed the spread of SARS-CoV-2 infection in children in area heavily affected by COVID-19 pandemic.\n- Among a large cohort of children (>600), 11 (1.8%) were positive on RT-PCR for SARS-CoV-2 and 65 (10.7%) were positive on serology.\n- The only factor affecting positivity of RT-PCR for SARS-CoV-2 or serology was the household contact COVID-19.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Robert Cohen", - "author_inst": "ACTIV" - }, - { - "author_name": "Camille Jung", - "author_inst": "CRC CHI Creteil" - }, - { - "author_name": "Naim Ouldali", - "author_inst": "ACTIV" - }, - { - "author_name": "Aurelie Sellam", - "author_inst": "ACTIV" - }, - { - "author_name": "Christophe Batard", - "author_inst": "ACTIV" - }, - { - "author_name": "Fabienne Cahn-Sellem", - "author_inst": "AFPA" - }, - { - "author_name": "Annie Elbez", - "author_inst": "ACTIV" - }, - { - "author_name": "Alain Wollner", - "author_inst": "ACTIV" - }, - { - "author_name": "Olivier Romain", - "author_inst": "ACTIV" - }, - { - "author_name": "Francois Corrard", - "author_inst": "ACTIV" - }, - { - "author_name": "Said Aberrane", - "author_inst": "CHI Creteil" - }, - { - "author_name": "Nathalie Soismier", - "author_inst": "CHI Creteil" - }, - { - "author_name": "Rita Creidy", - "author_inst": "CHI Creteil" - }, - { - "author_name": "Mounira Smati-Lafarge", - "author_inst": "CHI Creteil" - }, - { - "author_name": "Odile Launay", - "author_inst": "Cochin hospital" - }, - { - "author_name": "Stephane Bechet", - "author_inst": "ACTIV" - }, - { - "author_name": "Emmanuelle Varon", - "author_inst": "CHI Creteil" - }, - { - "author_name": "Corinne Levy", - "author_inst": "ACTIV" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2020.06.13.20122762", "rel_title": "Global research trend in the treatment of the new Coronavirus diseases (COVID-19) : bibliometric analysis.", @@ -1360452,6 +1361972,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.06.12.20129643", + "rel_title": "Improving effectiveness of different deep learning-based models for detecting COVID-19 from computed tomography (CT) images", + "rel_date": "2020-06-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.12.20129643", + "rel_abs": "Computerized Tomography (CT) has a prognostic role in the early diagnosis of COVID-19 due to it gives both fast and accurate results. This is very important to help decision making of clinicians for quick isolation and appropriate patient treatment. In this study, we combine methods such as segmentation, data augmentation and the generative adversarial network (GAN) to improve the effectiveness of learning models. We obtain the best performance with 99% accuracy for lung segmentation. Using the above improvements we get the highest rates in terms of accuracy (99.8%), precision (99.8%), recall (99.8%), f1-score (99.8%) and roc acu (99.9979%) with deep learning methods in this paper. Also we compare popular deep learning-based frameworks such as VGG16, VGG19, Xception, ResNet50, ResNet50V2, DenseNet121, DenseNet169, InceptionV3 and InceptionResNetV2 for automatic COVID-19 classification. The DenseNet169 amongst deep convolutional neural networks achieves the best performance with 99.8% accuracy. The second-best learner is InceptionResNetV2 with accuracy of 99.65%. The third-best learner is Xception and InceptionV3 with accuracy of 99.60%.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Erdi Acar", + "author_inst": "Canakkale Onsekiz Mart University" + }, + { + "author_name": "Engin \u015eAH\u0130N", + "author_inst": "Canakkale Onsekiz Mart University" + }, + { + "author_name": "\u0130hsan Yilmaz", + "author_inst": "Canakkale Onsekiz Mart University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.06.12.20129460", "rel_title": "Cross-reactivity of neutralizing antibody and its correlation with circulating T follicular cells in recovered COVID-19 individuals", @@ -1360984,37 +1362531,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.06.13.149591", - "rel_title": "Coronavirus genomes carry the signatures of their habitats", - "rel_date": "2020-06-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.13.149591", - "rel_abs": "Coronaviruses such as SARS-CoV-2 regularly infect host tissues that express antiviral proteins (AVPs) in abundance. Understanding how they evolve to adapt or evade host immune responses is important in the effort to control the spread of COVID-19. Two AVPs that may shape viral genomes are the zinc finger antiviral protein (ZAP) and the apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3 protein (APOBEC3). The former binds to CpG dinucleotides to facilitate the degradation of viral transcripts while the latter deaminates C into U residues leading to dysfunctional transcripts. We tested the hypothesis that both APOBEC3 and ZAP may act as primary selective pressures that shape the genome of an infecting coronavirus by considering a comprehensive number of publicly available genomes for seven coronaviruses (SARS-CoV-2, SARS-CoV, MERS, Bovine CoV, Murine MHV, Porcine HEV, and Canine CoV). We show that coronaviruses that regularly infect tissues with abundant AVPs have CpG-deficient and U-rich genomes; whereas viruses that do not infect tissues with abundant AVPs do not share these sequence hallmarks. In SARS-CoV-2, CpG is most deficient in the S protein region to evaded ZAP-mediated antiviral defense during cell entry. Furthermore, over four months of SARS-CoV-2 evolutionary history, we observed a marked increase in C to U substitutions in the 5 UTR and ORF1ab regions. This suggests that the two regions could be under constant C to U deamination by APOBEC3. The evolutionary pressures exerted by host immune systems onto viral genomes may motivate novel strategies for SARS-CoV-2 vaccine development.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Yulong Wei", - "author_inst": "University of Ottawa" - }, - { - "author_name": "Jordan R. Silke", - "author_inst": "University of Ottawa" - }, - { - "author_name": "Parisa Aris", - "author_inst": "University of Ottawa" - }, - { - "author_name": "Xuhua Xia", - "author_inst": "University of Ottawa; Ottawa Institute of Systems Biology" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.06.12.149377", "rel_title": "WHOLE-GENOME SEQUENCING AND DE NOVO ASSEMBLY OF A 2019 NOVEL CORONAVIRUS (SARS-COV-2) STRAIN ISOLATED IN VIETNAM", @@ -1361838,6 +1363354,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.13.20130013", + "rel_title": "Impacts of regional climate on the COVID-19 pandemic", + "rel_date": "2020-06-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.13.20130013", + "rel_abs": "The COVID-19 pandemic had led to 500000 confirmed death by June 30, 2020. We combined the number of monthly confirmed new cases and deaths with latitude, temperature, humidity, rainfall, and sunshine ultraviolet (UV) to explore the climate impacts on COVID-19 fatality in 88 countries. There was a significant decrease in overall case-fatality rate in May and June (from 8.17% to 4.99% and 3.22%). The fatality in temperate marine regions was the highest (11.13%). The fatality was 5.71% in high latitudes ([≥]30{degrees}) but only 3.73% in low latitudes (<30{degrees}). The fatality was 6.76% in cold regions (<20{degrees}C) but only 3.90% in hot regions ([≥]20{degrees}C). The fatality was 5.87% in rainy regions ([≥]40mm) but only 3.33% in rainless regions (<40mm). The fatality was 6.57% in cloudy regions (<50) but only 3.86% in sunny regions ([≥]50). Traveling to hot sunny regions without pollution is a strategy for risk reduction.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Minneng Wen", + "author_inst": "Peking University Shenzhen Graduate School" + }, + { + "author_name": "Liyuan Chen", + "author_inst": "Peking University Shenzhen Graduate School" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.13.20130096", "rel_title": "Nearly Perfect Forecasting of the Total COVID-19 Cases in India: A Numerical Approach", @@ -1362418,65 +1363957,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2020.06.10.20123398", - "rel_title": "Evaluation of Sample Pooling for Screening of SARS-CoV-2", - "rel_date": "2020-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.10.20123398", - "rel_abs": "BackgroundThe coronavirus disease (COVID-19) pandemic has revealed the global public health importance of robust diagnostic testing. To overcome the challenge of nucleic acid (NA) extraction and testing kit availability efficient method is urgently needed.\n\nObjectivesTo establish an efficient, time and resource-saving and cost-effective methods, and to propose an ad hoc pooling approach for mass screening of SARS-CoV-2\n\nMethodsDirect clinical sample and NA pooling approach was used for the standard reverse transcriptase polymerase chain reaction (RT-PCR) test of the SARS CoV-2 targeting the envelop (E) and open reading frame (ORF1ab) genomic region of the virus. In this approach, experimental pools were created using SARS CoV-2 positive clinical samples spiked with up to 9 negative samples prior to NA extraction step to have a final extraction volume of 200 L (maximum dilution factor of 10). Viral NA was also subsequently extracted from each pool and tested using the SARS CoV-2 RT-PCR assay.\n\nResultsWe found that a single positive sample can be amplified and detected in pools of up to 7 samples depending on the ct value of the original sample, corresponding to high, medium, and low SARS CoV-2 viral copies/reaction. However, to minimize false negativity of the assay with pooling strategies and with unknown false negativity rate of the assay under validation, we recommend poling of 4 in 1 using the standard protocols of the assay, reagents and equipment. The predictive algorithm indicated a pooling ratio of 4 in 1 was expected to retain accuracy of the test irrespective of the ct value (relative RNA copy number) of the sample spiked and result in a 237% increase in testing efficiency.\n\nConclusionsThe approaches showed its concept in easily customized and resource-saving manner and would allow expanding of current screening capacities and enable the expansion of detection in the community.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Andargachew Mulu", - "author_inst": "Armauer Hansen Research Institute" - }, - { - "author_name": "Dawit Hailu Alemayehu", - "author_inst": "Armauer Hansen Research Institute" - }, - { - "author_name": "Fekadu Alemu", - "author_inst": "Armauer Hansen Research Institute" - }, - { - "author_name": "Dessalegn Abeje Tefera", - "author_inst": "Armauer Hansen Research Institute" - }, - { - "author_name": "Sinknesh Wolde", - "author_inst": "Armauer Hansen Research Institute" - }, - { - "author_name": "Gebeyehu Aseffa", - "author_inst": "Armauer Hansen Research Institute" - }, - { - "author_name": "Tamrayehu Seyoum", - "author_inst": "Armauer Hansen Research Institute" - }, - { - "author_name": "Meseret Habtamu", - "author_inst": "Armauer Hansen Research Institute" - }, - { - "author_name": "Alemseged Abdissa", - "author_inst": "Armauer Hansen Research Institute" - }, - { - "author_name": "Abebe Genetu Bayih", - "author_inst": "Armauer Hansen Research Institute" - }, - { - "author_name": "Getachew Tesfaye Beyene", - "author_inst": "Armauer Hansen Research Institute" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2020.06.05.20123299", "rel_title": "Early administration of lopinavir/ritonavir plus hydroxychloroquine does not alter the clinical course of SARS-CoV-2 infection: a retrospective cohort study.", @@ -1363088,6 +1364568,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.11.20125799", + "rel_title": "The arrival and spread of SARS-CoV2 in Colombia", + "rel_date": "2020-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20125799", + "rel_abs": "We performed phylogenomic analysis of severe acute respiratory syndrome coronavirus-2 (SARS-CoV2) from 88 infected individuals across different regions of Colombia. Eleven different lineages were detected, suggesting multiple introduction events. Pangolin lineages B.1 and B.1.5 were the most frequent, with B.1 being associated with prior travel to high-risk areas.\n\nArticle Summary LineWe sequenced 88 genomes of SARS-CoV2 from Colombia finding 11 lineages and eight different introduction events", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Juan David Ramirez", + "author_inst": "Universidad del Rosario" + }, + { + "author_name": "Carolina Florez", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Marina Munoz", + "author_inst": "Universidad del Rosario" + }, + { + "author_name": "Carolina Hernandez", + "author_inst": "Universidad del Rosario" + }, + { + "author_name": "Adriana Castillo", + "author_inst": "Universidad del Rosario" + }, + { + "author_name": "Sergio Gomez", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Angelica Rico", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Lisseth Pardo", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Esther C Barros", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Sergio Castaneda", + "author_inst": "Universidad del Rosario" + }, + { + "author_name": "Nathalia Ballesteros", + "author_inst": "Universidad del Rosario" + }, + { + "author_name": "David Martinez", + "author_inst": "Universidad del Rosario" + }, + { + "author_name": "Laura Vega", + "author_inst": "Universidad del Rosario" + }, + { + "author_name": "Jesus Jaimes", + "author_inst": "Universidad del Rosario" + }, + { + "author_name": "Lissa Cruz-Saavedra", + "author_inst": "Universidad del Rosario" + }, + { + "author_name": "Luz H Patino", + "author_inst": "Universidad del Rosario" + }, + { + "author_name": "Anibal Teheran", + "author_inst": "Fundacion Universitaria Juan N Corpas" + }, + { + "author_name": "Ana Gonzalez-Reiche", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Matthew Hernandez", + "author_inst": "Icahn School of Medicina at Mount Sinai" + }, + { + "author_name": "Emilia Sordillo", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Viviana Simon", + "author_inst": "Icahn School of Medicine" + }, + { + "author_name": "Harm van Bakel", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Alberto Paniz-Mondolfi", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.09.20125286", "rel_title": "Clinical characteristics and factors associated with admission to intensive care units inhospitalized COVID-19 patients in Lyon University Hospitals, France", @@ -1363760,29 +1365347,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.09.20127118", - "rel_title": "A systematic review on the levels of antibodies in COVID-19 virus exposed but negative newborns: a possible vertical transmission of IgG/ IgM", - "rel_date": "2020-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.09.20127118", - "rel_abs": "BackgroundCurrently, there is no doubt on human-to-human transmission of Coronavirus Disease 2019 (COVID-19). Now, the debates remain on whether, vertical transmission of Severe Respiratory Syndrome Virus 2 (SARS-CoV-2) and antibodies against the virus do exist. We therefore, conducted a systematic review to determine the immunoglobulin G and M (IgG/IgM) levels among infants born to mothers with COVID-19.\n\nMethodsThe systematic search was done using PubMed/MEDLINE and Google Scholar database. The research included studies on IgG/ IgM against SARS-CoV-2 among infants born to mother with COVID-19 published in English from December 1, 2019 onwards. Data were extracted by two independent authors in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA-P) guidelines. We synthesized a narrative from eligible studies and performed two tailed non-parametric Mann-Whitney test to determine and compare the median IgG/IgM levels.\n\nResultsIn total, 486 abstracts were screened and 63 full-text articles were assessed. Of 63 articles, 6 met the inclusion criteria for qualitative analysis. Two articles were included in quantitative analysis of anti-SARS-CoV-2 IgG/ IgM levels. The median antibody levels was 75.49AU/mL (range: 7.25AU/mL-140.32AU/mL) and for 3.79AU/mL (range: 0.16AU/mL-45.83AU/mL) (P = 0.0041) for anti-SARS-CoV-2 IgG and IgM, respectively.\n\nConclusionThere were high levels of IgG but low IgM against SARS-CoV-2 (using <10 AU/mL as a reference range) among COVID-19 virus exposed but negative newborns. This review suggest a possible natural passive immunity (IgG/ IgM) against COVID-19 virus.\n\nImpactA systematic review of infants born to mothers with COVID-19 was conducted to characterize the magnitude of antibodies generated against SARS-CoV-2 among infants who were vertically exposed to the virus. These findings were necessary to inform the ongoing vaccine development and research on the background natural passive immunity among COVID-19 exposed newborns. Furthermore, evidence are revealing the possibility of vertical transmission of anti-SARS-CoV-2 IgG/ IgM among the exposed newborns who tested negative for the virus.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "George M. Bwire", - "author_inst": "Muhimbili University of Health and Allied Sciences" - }, - { - "author_name": "Belinda J. Njiro", - "author_inst": "Muhimbili University of Health and Allied Sciences" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.11.20127027", "rel_title": "Modelling the impact of reducing control measures on the COVID-19 pandemic in a low transmission setting", @@ -1364494,6 +1366058,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.06.10.20115543", + "rel_title": "Evaluation of 30-day mortality for 500 patients undergoing non-emergency surgery in a COVID-19 cold site within a multicentre regional surgical network during the COVID-19 pandemic", + "rel_date": "2020-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.10.20115543", + "rel_abs": "BackgroundTwo million non-emergency surgeries are being cancelled globally every week due to the COVID-19 pandemic, which will have a major impact on patients and healthcare systems.\n\nObjectiveTo determine whether it is feasible and safe to continue non-emergency surgery in the COVID-19 pandemic\n\nDesign, setting and participantsThis is a cohort study of 500 consecutive patients undergoing non-emergency surgery in a dedicated COVID-19 cold site following the first case of COVID-19 that was reported in the institution. The study was carried out during the peak of the pandemic in the United Kingdom, which currently has one of the highest number of cases and deaths from COVID-19 globally.\n\nWe set up a hub-and-spoke surgical network amongst 14 National Health Service institutions during the pandemic. The hub was a cancer centre, which was converted into a COVID-19 cold site, performing urological, thoracic, gynaecological and general surgical operations.\n\nOutcomesThe primary outcome was 30-day mortality from COVID-19. Secondary outcomes included all-cause mortality and post-operative complications at 30-days.\n\nResults500 patients underwent surgery with median age 62.5 (IQR 51-71). 65% were male and 60% had a known diagnosis of cancer. 44% of surgeries were performed with robotic or laparoscopic assistance and 61% were considered complex or major operations.\n\nNone of the 500 patients undergoing surgery died from COVID-19 at 30-days. 30-day allcause mortality was 3/500 (1%). 10 (2%) patients were diagnosed with COVID-19, 4 (1%) with confirmed laboratory diagnosis and 6 (1%) with probable COVID-19. 33/500 (7%) of patients developed Clavien-Dindo grade 3 or higher complications, with 1/33 (3%) occurring in a patient with COVID-19.\n\nConclusionIt is safe to continue non-emergency surgery during the COVID-19 pandemic with appropriate service reconfiguration.\n\nPatient summaryNo patients died from COVID-19 when undergoing non-emergency surgery during the pandemic in one of the worst affected world regions.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Veeru Kasivisvanathan", + "author_inst": "University College London" + }, + { + "author_name": "Jamie Lindsay", + "author_inst": "University College London Hospital NHS Foundation Trust" + }, + { + "author_name": "Sara Rakhshani-moghadam", + "author_inst": "University College London Hospital NHS Foundation Trust" + }, + { + "author_name": "Ahmed Elhamshary", + "author_inst": "University College London Hospital NHS Foundation Trust" + }, + { + "author_name": "Konstantinos Kapriniotis", + "author_inst": "University College London Hospital NHS Foundation Trust" + }, + { + "author_name": "Georgios Kazantzis", + "author_inst": "University College London Hospital NHS Foundation Trust" + }, + { + "author_name": "Bilal Syed", + "author_inst": "University College London Hospital NHS Foundation Trust" + }, + { + "author_name": "John Hines", + "author_inst": "University College London Hospital NHS Foundation Trust" + }, + { + "author_name": "Axel Bex", + "author_inst": "Royal Free Hospital NHS Foundation Trust" + }, + { + "author_name": "Daniel Heffernan Ho", + "author_inst": "University College London Hospital NHS Foundation Trust" + }, + { + "author_name": "Martin Hayward", + "author_inst": "University College London Hospital NHS Foundation Trust" + }, + { + "author_name": "Chetan Bhan", + "author_inst": "Whittington Health NHS Trust" + }, + { + "author_name": "Nicola MacDonald", + "author_inst": "University College London Hospital NHS Foundation Trust" + }, + { + "author_name": "Simon Clarke", + "author_inst": "University College London Hospital NHS Foundation Trust" + }, + { + "author_name": "David Walker", + "author_inst": "University College London" + }, + { + "author_name": "Geoff Bellingan", + "author_inst": "University College London Hospital NHS Foundation Trust" + }, + { + "author_name": "James Moore", + "author_inst": "NHS England and NHS Improvement" + }, + { + "author_name": "Jennifer Rohn", + "author_inst": "University College London" + }, + { + "author_name": "Asif Muneer", + "author_inst": "University College London Hospital NHS Foundation Trust" + }, + { + "author_name": "Lois Roberts", + "author_inst": "University College London Hospital NHS Foundation Trust" + }, + { + "author_name": "Fares Haddad", + "author_inst": "University College London" + }, + { + "author_name": "John D Kelly", + "author_inst": "University College London" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "surgery" + }, { "rel_doi": "10.1101/2020.06.11.20127415", "rel_title": "Even one metre seems generous. A reanalysis of data in: Chu et al. (2020) Physical distancing, face masks, and eye protection to prevent person-to-person transmission of SARS-CoV-2 and COVID-19.", @@ -1365234,33 +1366901,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "sports medicine" }, - { - "rel_doi": "10.1101/2020.06.10.20127753", - "rel_title": "Self-reported changes in energy balance behaviors during COVID-19 related home confinement: A Cross-Sectional Study", - "rel_date": "2020-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.10.20127753", - "rel_abs": "BackgroundThe COVID-19 pandemic has caused people to shelter-at-home for an extended period, resulting in a sudden rise in unstructured time. This unexpected disruption in everyday life has raised concerns about weight management, especially in high-risk populations of women and individuals with overweight and obesity. This study aimed to investigate the changes in behaviors that may impact energy intake and/or energy expenditure in U.S. adults during the home confinement.\n\nMethodsCross-sectional data from 1,779 adults were collected using an online Qualtrics survey between April 24th and May 4th, 2020. Self-reported data on demographics, eating behaviors, physical activity, sleep, screen time, takeout food intake, and food purchasing behaviors were collected. Chi-Square analyses were conducted to evaluate differences in the percent of participants reporting increasing, decreasing, or staying the same in each health behavior since the COVID-19 outbreak in their area. Each analysis was followed by comparing whether increases or decreases were more likely for each health behavior. Similar comparisons were made between male and female participants and between body mass index (BMI) categories.\n\nResultsWe observed an increase in the intake of both healthy and energy-dense unhealthy foods and snacks during the home confinement. Participants also reported increases in sedentary activities and decrease in physical activity, alcohol intake, and consumption of takeout meals during this time. In women, several behavioral changes support greater energy intake and less energy expenditure than men. No clear difference in patterns was observed across BMI status.\n\nConclusionAcute changes in behaviors underscore the significance of a sudden increase in unstructured time at home on potential weight gain. Our findings support the need to implement and support measures that promote strategies to maintain body weight and establish a methodology to collect body weight data at multiple time points to longitudinally assess the dynamic relationship between behaviors and body weight change.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Surabhi Bhutani", - "author_inst": "San Diego State University, San Diego, California, USA" - }, - { - "author_name": "Jamie A Cooper", - "author_inst": "University of Georgia, Athens, Georgia, USA" - }, - { - "author_name": "Michelle R Vandellen", - "author_inst": "University of Georgia, Athens, Georgia, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "nutrition" - }, { "rel_doi": "10.1101/2020.06.11.20128033", "rel_title": "Angiotensin-converting enzyme (ACE1, ACE2) gene variants are associated with COVID19 severity depending on the hypertension status.", @@ -1365864,6 +1367504,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.11.20128439", + "rel_title": "The male excess in case-fatality rates for COVID-19. A meta-analytic study of the age-related differences and consistency over six countries", + "rel_date": "2020-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20128439", + "rel_abs": "BackgroundEarly in the COVID-19 pandemic, it was noted that males seemed to be more affected than females. We examined the magnitude and consistency of the sex differences in age-specific case-fatality rates (CFRs) in six countries.\n\nMethodsData on the cases and deaths from COVID-19, by sex and age group, were extracted from the published reports from Denmark, England, Israel, Italy, Spain, and the United States. Age-specific CFRs were computed for males and females separately. The ratio of the male to female CFRs were computed and meta-analytic methods were used to obtained pooled estimates of the male to female ratio of the CFRs over the six countries, for seven age-groups.\n\nFindingsThe CFRs were consistently higher in males at all ages. The differences were greater in the younger age groups. The pooled M:F CFR ratios were 2.53, 2.92, 2.57, 1.83, 1.57, 1.58 and 1.48 for ages 0-39, 40-49, 50-59, 60-69, 70-79, 80-89 and 90+. There was remarkable consistency between countries in the magnitude of the M:F CFRs, in each age group. In meta-regression, age group explained almost all the heterogeneity in the CFR ratios.\n\nConclusionsThe sex differences in the CFRs are intriguing and are compatible with the male dominance in the incidence rates of many infectious diseases. For COVID-19, factors such as sex differences in the prevalence of underlying diseases may play a part in the CFR differences. However, the greater severity of the disease in males, particularly at younger ages, may be part of the disease mechanism and should be explored further.\n\nFundingNo funding was provided for this study. The authors declare no conflict of interests", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Manfred S Green", + "author_inst": "University of Haifa" + }, + { + "author_name": "Naama Swartz", + "author_inst": "University of Haifa" + }, + { + "author_name": "Dorit Nitzan", + "author_inst": "World Health Organization, European Region" + }, + { + "author_name": "Victoria Peer", + "author_inst": "University of Haifa" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.10.20128025", "rel_title": "Mortality Attributed to COVID-19 in High-Altitude Populations", @@ -1366600,29 +1368271,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.11.20129023", - "rel_title": "How far Covid19 virus spread can be curbed byrelaxing lockdown in different stages? -A study inIndian scenario", - "rel_date": "2020-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20129023", - "rel_abs": "After the emergence of the first cases in Wuhan, China, the novel coronavirus (2019-nCoV) infection has rapidly spread out to other provinces, neighboring countries and finally has become a global terror. It is indeed a matter of serious concern to study the transmission dynamics of this virus. The potential and severity of an outbreak and providing critical information for identifying the type of disease interventions and intensity can be well understood by the unknown basic reproduction number. A stochastic model can be used to estimate this number with possible safeguard on uncertainties. It is essential to assess how the expensive, resource-intensive measures can contribute to the prevention and control of the 2019-nCoV infection and how long they should be maintained. A short-term forecast of incidences are often of high priority. The challenge is to forecast unseen \"future\" simulated data for three different scenarios at some time points. We estimate current levels of transmissibility, over variable time points under different levels of interventions and use that to forecast near-future incidence. The forecasted values of incidence can be used for determining the near future mortality also.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Arindom Chakraborty", - "author_inst": "Visva-Bharati University" - }, - { - "author_name": "Kalyan Das", - "author_inst": "Indian Institute of Technology Bombay" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.11.20128272", "rel_title": "Estimating the Effect and Cost-Effectiveness of Facemasks in Reducing the Spread of the Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2) in Uganda", @@ -1367618,6 +1369266,41 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.06.11.145425", + "rel_title": "Machine Learning Maps Research Needs in COVID-19 Literature", + "rel_date": "2020-06-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.11.145425", + "rel_abs": "SummaryManually assessing the scope of the thousands of publications on the COVID-19 (coronavirus disease 2019) pandemic is an overwhelming task. Shortcuts through metadata analysis (e.g., keywords) assume that studies are properly tagged. However, machine learning approaches can rapidly survey the actual text of coronavirus abstracts to identify research overlap between COVID-19 and other coronavirus diseases, research hotspots, and areas warranting exploration. We propose a fast, scalable, and reusable framework to parse novel disease literature. When applied to the COVID-19 Open Research Dataset (CORD-19), dimensionality reduction suggested that COVID-19 studies to date are primarily clinical-, modeling- or field-based, in contrast to the vast quantity of laboratory-driven research for other (non-COVID-19) coronavirus diseases. Topic modeling also indicated that COVID-19 publications have thus far focused primarily on public health, outbreak reporting, clinical care, and testing for coronaviruses, as opposed to the more limited number focused on basic microbiology, including pathogenesis and transmission.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Anhvinh L Doanvo", + "author_inst": "Washington, D.C." + }, + { + "author_name": "Xiaolu Qian", + "author_inst": "University of Washington" + }, + { + "author_name": "Divya Ramjee", + "author_inst": "Department of Justice, Law & Criminology, American University" + }, + { + "author_name": "Helen Piontkivska", + "author_inst": "Department of Biological Sciences, Kent State University" + }, + { + "author_name": "Angel N Desai", + "author_inst": "International Society for Infectious Diseases" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "scientific communication and education" + }, { "rel_doi": "10.1101/2020.06.11.147199", "rel_title": "Specific viral RNA drives the SARS CoV-2 nucleocapsid to phase separate", @@ -1368706,37 +1370389,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, - { - "rel_doi": "10.1101/2020.06.09.20126417", - "rel_title": "Identification of SARS-CoV-2 in wastewater in Japan by multiple molecular assays-implication for wastewater-based epidemiology (WBE)", - "rel_date": "2020-06-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.09.20126417", - "rel_abs": "Presence of SARS-coronavirus-2 (SARS-CoV-2) in wastewater sample has been documented in several countries. Wastewater-based epidemiology (WBE) is potentially effective for early warning of COVID-19 outbreak. The purpose of this study was to verify the detection limit of WBE for COVID-19. In total, 27 influent wastewater samples were collected from four wastewater treatment plants in Ishikawa and Toyama prefectures in Japan. During the study period, numbers of the confirmed COVID-19 cases in these prefectures increased from almost 0 to around 20 per 100,000 peoples. SARS-CoV-2 RNA in the samples were identified by several PCR-based assays. Among the 27 samples, 7 were positive for SARS-CoV-2 by at least one out of the three quantitative RT-PCR assays. These samples were also positive by RT-nested PCR assays. The detection frequency became higher when the number of total confirmed SARS-CoV-2 cases in 100,000 peoples became above 10 in each prefecture. However, SARS-CoV-2 could also be detected with a low frequency when the number was below 1.0. Considering that the number of the confirmed cases does not necessarily reflect the actual prevalence of the infection at the time point, data on the relationship between the number of infection cases and concentration in wastewater needs to be accumulated further.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Akihiko Hata", - "author_inst": "Faculty of Engineering, Toyama Prefectural University" - }, - { - "author_name": "Ryo Honda", - "author_inst": "Faculty of Geosciences and Civil Engineering, Kanazawa University" - }, - { - "author_name": "Hiroe Hara-Yamamura", - "author_inst": "Faculty of Geosciences and Civil Engineering, Kanazawa University" - }, - { - "author_name": "Yuno Meuchi", - "author_inst": "Faculty of Engineering, Toyama Prefectural University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.09.20126581", "rel_title": "Assessment of Experiences of Preventive Measures Practice including Vaccination History and Health Education among Umrah Pilgrims in Saudi Arabia, 1440H-2019", @@ -1369376,6 +1371028,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2020.06.09.20125690", + "rel_title": "Proteomic Profiling in Biracial Cohorts Implicates DC-SIGN as a Mediator of Genetic Risk in COVID-19", + "rel_date": "2020-06-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.09.20125690", + "rel_abs": "Brief SummaryCOVID-19 is one of the most consequential pandemics in the last century, yet the biological mechanisms that confer disease risk are incompletely understood. Further, heterogeneity in disease outcomes is influenced by race, though the relative contributions of structural/social and genetic factors remain unclear.1,2 Very recent unpublished work has identified two genetic risk loci that confer greater risk for respiratory failure in COVID-19: the ABO locus and the 3p21.31 locus.3 To understand how these loci might confer risk and whether this differs by race, we utilized proteomic profiling and genetic information from three cohorts including black and white participants to identify proteins influenced by these loci. We observed that variants in the ABO locus are associated with levels of CD209/DC-SIGN, a known binding protein for SARS-CoV and other viruses,4 as well as multiple inflammatory and thrombotic proteins, while the 3p21.31 locus is associated with levels of CXCL16, a known inflammatory chemokine.5 Thus, integration of genetic information and proteomic profiling in biracial cohorts highlights putative mechanisms for genetic risk in COVID-19 disease.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Daniel H. Katz", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Usman A. Tahir", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Debby Ngo", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Mark D. Benson", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Alexander G. Bick", + "author_inst": "Broad Institute of Harvard and MIT" + }, + { + "author_name": "Akhil Pampana", + "author_inst": "Broad Institute of Harvard and MIT" + }, + { + "author_name": "Yan Gao", + "author_inst": "University of Mississippi Medical Center" + }, + { + "author_name": "Michelle J. Keyes", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Adolfo Correa", + "author_inst": "University of Mississippi Medical Center" + }, + { + "author_name": "Sumita Sinha", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Dongxiao Shen", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Qiong Yang", + "author_inst": "Boston University School of Public Health" + }, + { + "author_name": "Jeremy M. Robbins", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Zsu-Zsu Chen", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Daniel E. Cruz", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Bennet Peterson", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Pradeep Natarajan", + "author_inst": "Broad Institute of Harvard and MIT" + }, + { + "author_name": "Ramachandran S. Vasan", + "author_inst": "Boston University School of Medicine" + }, + { + "author_name": "Gustav Smith", + "author_inst": "Lund University" + }, + { + "author_name": "Thomas J. Wang", + "author_inst": "University of Texas Southwestern Medical Center" + }, + { + "author_name": "Robert E. Gerszten", + "author_inst": "Beth Israel Deaconess Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.09.20126334", "rel_title": "Modeling the Transmission of Respiratory Infectious Diseases in Mass Transportation Systems", @@ -1370128,45 +1371879,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2020.06.10.145292", - "rel_title": "COVID-19 Variants Database: A repository for Human SARS-CoV-2 Polymorphism Data", - "rel_date": "2020-06-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.10.145292", - "rel_abs": "COVID-19 is a newly communicable disease with a catastrophe outbreak that affects all over the world. We retrieved about 8,781 nucleotide fragments and complete genomes of SARS-CoV-2 reported from sixty-four countries. The CoV-2 reference genome was obtained from the National Genomics Data Center (NGDC), GISAID, and NCBI Genbank. All the sequences were aligned against reference genomes using Clustal Omega and variants were called using in-house built Python script. We intend to establish a user-friendly online resource to visualize the variants in the viral genome along with the Primer Infopedia. After analyzing and filtering the data globally, it was made available to the public. The detail of data available to the public includes mutations from 5688 SARS-CoV-2 sequences curated from 91 regions. This database incorporated 39920 mutations over 3990 unique positions. According to the translational impact, these mutations include 11829 synonymous mutations including 681 synonymous frameshifts and 21701 nonsynonymous mutations including 10 nonsynonymous frameshifts. Development of SARS-CoV-2 mutation genome browsers is a fundamental step obliging towards the virus surveillance, viral detection, and development of vaccine and therapeutic drugs. The SARS-COV-2 mutation browser is available at http://covid-19.dnageography.com.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Allah Rakha", - "author_inst": "Department of Forensic Sciences, University of Health Sciences Lahore, 54610, Pakistan" - }, - { - "author_name": "Haroon Rasheed", - "author_inst": "Department of Forensic Sciences, University of Health Sciences Lahore, 54610, Pakistan" - }, - { - "author_name": "Zunaira Batool", - "author_inst": "Department of Forensic Sciences, University of Health Sciences Lahore, 54610, Pakistan" - }, - { - "author_name": "Javed Akram", - "author_inst": "Department of Forensic Sciences, University of Health Sciences Lahore, 54610, Pakistan" - }, - { - "author_name": "Atif Adnan", - "author_inst": "China Medical University" - }, - { - "author_name": "Jiang Du", - "author_inst": "China Medical University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.06.11.145920", "rel_title": "SARS-CoV-2 mRNA Vaccine Development Enabled by Prototype Pathogen Preparedness", @@ -1371202,6 +1372914,69 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.06.09.142372", + "rel_title": "One-Step Rapid Quantification of SARS-CoV-2 Virus Particles via Low-Cost Nanoplasmonic Sensors in Generic Microplate Reader and Point-of-Care Device", + "rel_date": "2020-06-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.09.142372", + "rel_abs": "The spread of SARS-CoV-2 virus in the ongoing global pandemics has led to infections of millions of people and losses of many lives. The rapid, accurate and convenient SARS-CoV-2 virus detection is crucial for controlling and stopping the pandemics. Diagnosis of patients in the early stage infection are so far limited to viral nucleic acid or antigen detection in human nasopharyngeal swab or saliva samples. Here we developed a method for rapid and direct optical measurement of SARS-CoV-2 virus particles in one step nearly without any sample preparation using a spike protein specific nanoplasmonic resonance sensor. We demonstrate that we can detect as few as 30 virus particles in one step within 15 minutes and can quantify the virus concentration linearly in the range of 103 vp/ml to 106 vp/ml. Measurements shown on both generic microplate reader and a handheld smartphone connected device suggest that our low-cost and rapid detection method may be adopted quickly under both regular clinical environment and resource-limited settings.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Liping Huang", + "author_inst": "Huazhong University of Science and Technology" + }, + { + "author_name": "Longfei Ding", + "author_inst": "Shanghai Public Health Clinical Center" + }, + { + "author_name": "Jun Zhou", + "author_inst": "Wuhan Xinxin Semiconductor Manufacturing Co. Ltd" + }, + { + "author_name": "Shuiliang Chen", + "author_inst": "Taiwan Semiconductor Manufacturing Co." + }, + { + "author_name": "Fang Chen", + "author_inst": "Taiwan Semiconductor Manufacturing Co." + }, + { + "author_name": "Chen Zhao", + "author_inst": "Shanghai Public Health Clinical Center" + }, + { + "author_name": "Yiyi Zhang", + "author_inst": "Huazhong University of Science and Technology" + }, + { + "author_name": "Jianqing Xu", + "author_inst": "Shanghai Public Health Clinical Center" + }, + { + "author_name": "Wenjun Hu", + "author_inst": "Huazhong University of Science and Technology" + }, + { + "author_name": "Jiansong Ji", + "author_inst": "Lishui Central Hospital, Zhejiang University" + }, + { + "author_name": "Hao Xu", + "author_inst": "Liangzhun (Shanghai) Industrial Co. Ltd" + }, + { + "author_name": "Gang L. Liu", + "author_inst": "Huazhong University of Science and Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2020.06.09.142315", "rel_title": "Designed peptides as potential fusion inhibitors against SARA-CoV-2 coronavirus infection", @@ -1371898,33 +1373673,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.08.20125914", - "rel_title": "Intimate Partner Violence Victimization and Perpetration among U.S. Adults during COVID-19: A Brief Report", - "rel_date": "2020-06-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.08.20125914", - "rel_abs": "ImportanceAnecdotal evidence such as increased calls to domestic violence (DV) hotlines across the globe suggest that there may be an increase of IPV prevalence in association with the COVID-19 outbreak; however, no study has investigated this phenomenon empirically.\n\nObjectiveTo evaluate the association between COVID-19 related conditions and recent use or experience of IPV (since the pandemic outbreak in the U.S).\n\nDesign, Setting, and ParticipantsThis cross-sectional study analyzed data collected online from a sample of noninstitutionalized adults (age 18+) in the U.S. (N=2,045). More than half of the sample self-identified as being in an intimate relationship at the time of the study.\n\nMain Outcomes and MeasuresA four-item tool was used to assess IPV perpetration and victimization since the outbreak of COVID-19. The rapid tool inquired about two forms of IPV, psychological and physical. Participants self-reported demographic data and recent health histories, including COVID-19 tests results, related symptoms and degree of personal social distancing. We hypothesized that COVID-19 related factors would increase risks of IPV.\n\nResultsIn this study, self-reported COVID-19 impacted respondents had an increased risk of IPV victimization and perpetration. Among those who reported having symptoms consistent with coronavirus, but were denied access to testing, psychological IPV victimization was 3 times greater than those who did not (Exp[B] =3.15, [1.19, 2.29] p <.05). For participants who reported testing positive to COVID-19, the odds of using psychological IPV (Exp[B] =3.24, [1.18, 8.89] p <.05) and physical IPV (Exp[B]=3.02, [1.12, 8.17] p <.05) against an intimate partner increased by more than 3 times.\n\nConclusions and RelevancePatient education and community outreach/health care system initiatives focused on IPV risk behaviors may help reduce the potential development of IPV. Continued surveillance is imperative to improve health and well-being along with effective intervention development and implementation.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Maxine Davis", - "author_inst": "University of Texas at Arlington" - }, - { - "author_name": "Ohad Gilbar", - "author_inst": "University of Texas at Arlington" - }, - { - "author_name": "Diana Padilla-Medina", - "author_inst": "University of Texas at Arlington" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.06.08.20125401", "rel_title": "Examine the impact of weather and ambient air pollutant parameters on daily case of COVID-19 in India.", @@ -1372720,6 +1374468,161 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.06.20123414", + "rel_title": "Sex differences in immune responses to SARS-CoV-2 that underlie disease outcomes", + "rel_date": "2020-06-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.06.20123414", + "rel_abs": "A growing body of evidence indicates sex differences in the clinical outcomes of coronavirus disease 2019 (COVID-19)1-4. However, whether immune responses against SARS-CoV-2 differ between sexes, and whether such differences explain male susceptibility to COVID-19, is currently unknown. In this study, we examined sex differences in viral loads, SARS-CoV-2-specific antibody titers, plasma cytokines, as well as blood cell phenotyping in COVID-19 patients. By focusing our analysis on patients with mild to moderate disease who had not received immunomodulatory medications, our results revealed that male patients had higher plasma levels of innate immune cytokines and chemokines including IL-8, IL-18, and CCL5, along with more robust induction of non-classical monocytes. In contrast, female patients mounted significantly more robust T cell activation than male patients during SARS-CoV-2 infection, which was sustained in old age. Importantly, we found that a poor T cell response negatively correlated with patients age and was predictive of worse disease outcome in male patients, but not in female patients. Conversely, higher innate immune cytokines in female patients associated with worse disease progression, but not in male patients. These findings reveal a possible explanation underlying observed sex biases in COVID-19, and provide important basis for the development of sex-based approach to the treatment and care of men and women with COVID-19.", + "rel_num_authors": 35, + "rel_authors": [ + { + "author_name": "Takehiro Takahashi", + "author_inst": "Yale University" + }, + { + "author_name": "Patrick Wong", + "author_inst": "Yale University" + }, + { + "author_name": "Mallory Ellingson", + "author_inst": "Yale University" + }, + { + "author_name": "Carolina Lucas", + "author_inst": "Yale University" + }, + { + "author_name": "Jon Klein", + "author_inst": "Yale University" + }, + { + "author_name": "Benjamin Israelow", + "author_inst": "Yale University" + }, + { + "author_name": "Julio Silva", + "author_inst": "Yale University" + }, + { + "author_name": "Jieun Oh", + "author_inst": "Yale University" + }, + { + "author_name": "Tianyang Mao", + "author_inst": "Yale University" + }, + { + "author_name": "Maria Tokuyama", + "author_inst": "Yale University" + }, + { + "author_name": "Peiwen Lu", + "author_inst": "Yale University" + }, + { + "author_name": "Arvind Venkataraman", + "author_inst": "Yale University" + }, + { + "author_name": "Annsea Park", + "author_inst": "Yale University" + }, + { + "author_name": "Feimei Liu", + "author_inst": "Yale University" + }, + { + "author_name": "Amit Meir", + "author_inst": "Yale University" + }, + { + "author_name": "Jonathan Sun", + "author_inst": "Yale University" + }, + { + "author_name": "Eric Wang", + "author_inst": "Yale University" + }, + { + "author_name": "Anne Louise Wyllie", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Chantal B.F. Vogels", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Rebecca Earnest", + "author_inst": "Yale University" + }, + { + "author_name": "Sarah Lapidus", + "author_inst": "Yale University" + }, + { + "author_name": "Isabel Ott", + "author_inst": "Yale University" + }, + { + "author_name": "Adam Moore", + "author_inst": "Yale University" + }, + { + "author_name": "Arnau Casanovas", + "author_inst": "Yale University" + }, + { + "author_name": "Charles Dela Cruz", + "author_inst": "Yale University" + }, + { + "author_name": "John Fournier", + "author_inst": "Yale University" + }, + { + "author_name": "Camila Odio", + "author_inst": "Yale University" + }, + { + "author_name": "Shelli Farhadian", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Nathan Grubaugh", + "author_inst": "Yale University" + }, + { + "author_name": "Wade Schulz", + "author_inst": "Yale University" + }, + { + "author_name": "Albert Ko", + "author_inst": "Yale University School of Public Health" + }, + { + "author_name": "Aaron Ring", + "author_inst": "Yale University" + }, + { + "author_name": "Saad Omer", + "author_inst": "Yale University" + }, + { + "author_name": "Akiko Iwasaki", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "- Yale IMPACT research team", + "author_inst": "-" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.08.138990", "rel_title": "Relationship between Anti-Spike Protein Antibody Titers and SARS-CoV-2 In Vitro Virus Neutralization in Convalescent Plasma", @@ -1373971,73 +1375874,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.06.20122341", - "rel_title": "Effect of tocilizumab in hospitalized patients with severe pneumonia COVID-19: a cohort study", - "rel_date": "2020-06-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.06.20122341", - "rel_abs": "BackgroundTocilizumab, a drug targeting interleukin-6 administrated in the right timeframe may be beneficial in coronavirus-disease-2019 (COVID-19). We aimed to assess its benefit, drawing from observations in compassionately treated patients.\n\nMethodsIn a retrospective case-control study, treatment effect (tocilizumab 400mg, single-dose) was assessed using three statistical methods: propensity-score matching, Cox multivariable survival and inverse probability score weighting (IPSW) analyses. Were included all patients hospitalized with COVID-19, who presented severity criteria with SpO2[≤]96% despite O2-support [≥]6L/min for more than 6 hours. Were excluded patients in critical care medicine department and those under invasive mechanical ventilation. Primary outcome was a composite of mortality and ventilation, with a maximum follow-up of 28 days.\n\nResults246 patients were included (106 treated by tocilizumab). They were 67.6 {+/-}15.3 years-old, with 95 (38.5%) women. Delay between first symptoms and inclusion was 8.4 {+/-}4.5 days. Overall, 105 (42.7%) patients presented the primary outcome, with 71 (28.9%) deaths during the 28-days follow-up. Propensity-score-matched 84 pairs of comparable patients. In the matched cohort (n = 168), tocilizumab was associated with fewer primary outcomes (hazard ratio (HR) = 0.49 (95% confidence interval (95CI) = 0.3-0.81), p-value = 0.005). These results were similar in the overall cohort (n = 246), with Cox multivariable analysis yielding a protective association between tocilizumab and primary outcome (adjusted HR = 0.26 (95CI = 0.135-0.51, p = 0.0001), confirmed by IPSW analysis (p<0.0001). Analyses on mortality with 28-days follow-up yielded similar results.\n\nConclusionIn this retrospective study, tocilizumab single-dose was associated with improved survival without mechanical ventilation in patients with severe COVID-19.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Benjamin Rossi", - "author_inst": "Hopital Robert Ballanger" - }, - { - "author_name": "Lee S Nguyen", - "author_inst": "Sorbonne Universite" - }, - { - "author_name": "Philippe Zimmermann", - "author_inst": "Hopital Robert Ballanger" - }, - { - "author_name": "Faiza Boucenna", - "author_inst": "Hopital Robert Ballanger" - }, - { - "author_name": "Louise Baucher", - "author_inst": "Hopital Robert Ballanger" - }, - { - "author_name": "Louis Dubret", - "author_inst": "Hopital Robert Ballanger" - }, - { - "author_name": "Helene Guillot", - "author_inst": "Hopital Robert Ballanger" - }, - { - "author_name": "Marie-anne Bouldouyre", - "author_inst": "Hopital Robert Ballanger" - }, - { - "author_name": "Yves Allenbach", - "author_inst": "Sorbonne Universite - APHP - Groupe Hospitalie Pitie Salpetriere" - }, - { - "author_name": "Joe-Elie Salem", - "author_inst": "Sorbonne Universite" - }, - { - "author_name": "Paul Barsoum", - "author_inst": "Hopital Robert Ballanger" - }, - { - "author_name": "Arezki Oufella", - "author_inst": "HopitalRobert Ballanger" - }, - { - "author_name": "Helene Gros", - "author_inst": "Hopital Robert Ballanger" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.08.20110437", "rel_title": "SARS-CoV-2 placental infection and inflammation leading to fetal distress and neonatal multi-organ failure in an asymptomatic woman", @@ -1374681,6 +1376517,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, + { + "rel_doi": "10.1101/2020.06.08.20125310", + "rel_title": "Shedding of infectious virus in hospitalized patients with coronavirus disease-2019 (COVID-19): duration and key determinants", + "rel_date": "2020-06-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.08.20125310", + "rel_abs": "BackgroundLong-term shedding of viral RNA in COVID-19 prevents timely discharge from the hospital or de-escalation of infection prevention and control practices. Key questions are the duration and determinants of infectious virus shedding. We assessed these questions using virus cultures of respiratory tract samples from hospitalized COVID-19 patients as a proxy for infectious virus shedding.\n\nMethodsClinical and virological data were obtained from 129 hospitalized COVID-19 patients (89 intensive care, 40 medium care). Generalized estimating equations were used to identify if viral RNA load, detection of viral subgenomic RNA, serum neutralizing antibody response, duration of symptoms, or immunocompromised status were predictive for a positive virus culture.\n\nFindingsInfectious virus shedding was detected in 23 of the 129 patients (17,8%). The median duration of shedding was 8 days post onset of symptoms (IQR 5 - 11) and the probability of detecting infectious virus dropped below 5% after 15,2 days post onset of symptoms (95% confidence interval (CI) 13,4 - 17,2). Multivariate analyses identified viral loads above 7 log10 RNA copies/mL (odds ratio [OR]; CI 14,7 (3,57-58,1; p<0,001) as independently associated with isolation of infectious SARS-CoV-2 from the respiratory tract. A serum neutralizing antibody titre of at least 1:20 (OR of 0,01 (CI 0,003-0,08; p<0,001) was independently associated with non-infectious SARS-CoV-2.\n\nInterpretationInfection prevention and control guidelines should take into account that patients with severe or critical COVID-19 may shed infectious virus for longer periods of time compared to what has been reported for in patients with mild COVID-19. Infectious virus shedding drops to undetectable levels below a viral RNA load threshold and once serum neutralizing antibodies are present, which warrants the use of quantitative viral RNA load assays and serological assays in test-based strategies to discontinue or de-escalate infection prevention and control precautions.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed, bioRxiv, and medRxiv for articles that reported on shedding of infectious virus in COVID-19 patients using the search terms (\"coronavirus\" OR \"SARS\" OR \"SARS-CoV-2\" OR \"COVID-19\") AND (\"shedding\" OR \"infectivity\" OR \"infectious\" OR \"virus culture\") with no language or time restrictions. A detailed study on nine patients with mild COVID-19 reported that infectious virus could not be isolated after more than eight days of symptoms. The probability of isolating infectious virus was less than 5% when viral loads dropped below 6,51 Log10 RNA copies/mL. Similar results were obtained with a larger diagnostic sample set, but that study did not report on clinical parameters such as disease severity. Finally there is a report of a single patient shedding infectious virus up to 18 days after onset of symptoms. No published works were found on the shedding of infectious virus in patients with severe or critical COVID-19, and no published works were found on factors independently associated with shedding of infectious virus.\n\nAdded value of this studyWe assessed the duration and determinants of infectious virus shedding in 129 patients with severe or critical COVID-19. The duration of infectious virus shedding ranged from 0 to 20 days post onset of symptoms (median 8 days, IQR 5 - 11). The probability of detecting infectious virus dropped below 5% after 15,2 days post onset of symptoms (95% confidence interval (CI) 13,4 - 17,2). Viral loads above 7 log10 RNA copies/mL were independently associated with detection of infectious SARS-CoV-2 from the respiratory tract (odds ratio [OR]; CI 14,7 (3,57-58,1; p<0,001). A serum neutralizing antibody titre of at least 1:20 (OR of 0,01 (CI 0,003-0,08; p<0,001) was independently associated with non-infectious SARS-CoV-2.\n\nImplications of all the available evidenceInfection prevention and control guidelines should take into account that patients with severe or critical COVID-19 may shed infectious virus for longer periods of time compared to what has been reported for in patients with mild COVID-19. Quantitative viral RNA load assays and serological assays should be used for test-based strategies to discontinue or de-escalate infection prevention and control precautions.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Jeroen J.A. van Kampen", + "author_inst": "Erasmus MC" + }, + { + "author_name": "David A.M.C. van de Vijver", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Pieter L.A. Fraaij", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Bart L. Haagmans", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Mart M. Lamers", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Nisreen Okba", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Johannes P.C. van den Akker", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Henrik Endeman", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Diederik A.M.P.J. Gommers", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Jan J. Cornelissen", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Rogier A.S. Hoek", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Menno M. van der Eerden", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Dennis A. Hesselink", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Herold J. Metselaar", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Annelies Verbon", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Jurriaan E.M. de Steenwinkel", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Georgina I. Aron", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Eric C.M. van Gorp", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Sander van Boheemen", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Jolanda C. Voermans", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Charles A.B. Boucher", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Richard Molenkamp", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Marion P.G. Koopmans", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Corine Geurtsvankessel", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Annemiek A. van der Eijk", + "author_inst": "Erasmus MC" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.07.20125047", "rel_title": "Survival and predictors of deaths of patients hospitalized due to COVID-19 from a retrospective and multicenter cohort study in Brazil", @@ -1375601,61 +1377552,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "geriatric medicine" }, - { - "rel_doi": "10.1101/2020.05.29.20109199", - "rel_title": "Therapeutic effectiveness of interferon-alpha2b against COVID-19: the Cuban experience", - "rel_date": "2020-06-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.29.20109199", - "rel_abs": "BackgroundEffective therapies are needed to control the SARS-Cov-2 infection pandemic and reduce mortality associated with COVID-19. Several clinical studies have provided evidence for the antiviral effects of type I interferons (IFNs) in patients with respiratory coronaviruses. This study assessed the therapeutic efficacy of IFN-2b in patients infected with SARS-CoV-2 during the first month after the outbreak began in Cuba.\n\nMethodThis multicenter prospective observational study was conducted in 16 hospitals in 8 Cuban provinces. Participants were patients with confirmed SARS-CoV-2 infection detected from throat swab specimens by real time RT-PCR who gave informed consent and had no contraindications for IFN treatment. Patients received therapy as per the Cuban COVID protocol, that included a combination of oral antivirals (lopinavir/ritonavir and chloroquine) with intramuscular administration of IFN-2b (Heberon(R) Alpha R, Center for Genetic Engineering and Biotechnology, Havana), 3 times per week, for 2 weeks. The primary endpoint was the proportion of patients discharged from hospital (without clinical and radiological symptoms and non-detectable virus by RT-PCR). The secondary endpoint was the case fatality rate (CFR), defined as the number of confirmed deaths divided by the number of confirmed cases.\n\nResultsFrom March 11th to April 14th, 814 patients were confirmed SARS-CoV-2 positive in Cuba, 761 (93.4%) were treated with Heberon(R) Alpha R and 53 received the approved protocol without IFN treatment. The proportion of fully recovered patients was higher in the IFN-treated compared with non-IFN treated group (95.4% vs 26.1%, p<0.01). The CFR for all patients was 2.95%, and for those patients who received IFN-2b the CFR was reduce to 0.92. The estimated global CFR is 6.34% and 4.05% for the Americas reported by WHO and PAHO, respectively. In this study, 82 patients (10.1%) required intensive care and, of these, 42 (5.5%) were treated with IFN.\n\nConclusionsThis report provides preliminary evidence for the therapeutic effectiveness of IFN-2b for COVID-19 and suggests that the use of Heberon(R) Alpha R may contribute to complete recovery.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Ricardo Pereda", - "author_inst": "Medical college of Havana. Havana city, Cuba" - }, - { - "author_name": "Daniel Gonzalez", - "author_inst": "Medical college of Havana. Havana city, Cuba" - }, - { - "author_name": "Hubert Rivero", - "author_inst": "Medical college of Havana. Havana city, Cuba" - }, - { - "author_name": "Juan Rivero", - "author_inst": "Medical college of Havana. Havana city, Cuba" - }, - { - "author_name": "Albadio Perez", - "author_inst": "Medical college of Havana. Havana city, Cuba" - }, - { - "author_name": "Lizet del Rosario Lopez", - "author_inst": "Medical college of Havana. Havana city, Cuba" - }, - { - "author_name": "Natacha Mezquia", - "author_inst": "Medical college of Havana. Havana city, Cuba" - }, - { - "author_name": "Rafael Venegas", - "author_inst": "Medical college of Havana. Havana city, Cuba" - }, - { - "author_name": "Julio Betancourt", - "author_inst": "Medical college of Villa Clara. Santa Clara city, Cuba" - }, - { - "author_name": "Rodolfo Dominguez", - "author_inst": "Medical college of Camaguey. Camaguey city, Cuba" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.08.20125211", "rel_title": "Estimating weekly excess mortality at subnational level in Italy during the COVID-19 pandemic", @@ -1376167,6 +1378063,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.03.20121210", + "rel_title": "The Current COVID-19 Spread Pattern in India", + "rel_date": "2020-06-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.03.20121210", + "rel_abs": "In this article, we are going to show how to find out short term forecasts of the total number of COVID-19 cases in India in an easy way. Initially the spread of the disease was observably slow in India. Since the first week of May a highly nonlinear pattern has started to take shape. It can be observed that currently in India the spread pattern is nearly exponential. It can be seen further that the number of cases is still continuing to grow very fast. Therefore, instead of going for rigorous time series analysis, we may opt for looking at the data from a recent date downwards, and short term forecasts based on simple numerical analytical methods can be made accordingly.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Hemanta Kumar Baruah", + "author_inst": "The Assam Royal Global University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.05.20109637", "rel_title": "Rapid implementation of SARS-CoV-2 emergency use authorization RT-PCR testing and experience at an academic medical institution", @@ -1376891,37 +1378806,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "ophthalmology" }, - { - "rel_doi": "10.1101/2020.06.06.20124065", - "rel_title": "Enforced inactivity in the elderly and diabetes risk: initial estimates of the burden of an unintended consequence of COVID-19 lockdown", - "rel_date": "2020-06-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.06.20124065", - "rel_abs": "BackgroundOlder adults and those with underlying health conditions were advised to stay at home to help reduce the spread of COVID-19 however little advice on regular physical activity was given to those at risk. We modelled the effects of enforced inactivity on diabetes burden using published evidence.\n\nMethodsUsing Health Survey for England data, we estimated the prevalence of pre-diabetes and physical activity in adults aged 70 and older. The number of new diabetes cases directly attributed to lockdown were calculated using population attributable risk. Unit cost estimates of the additional burden on primary care and the cost of complications to secondary care were taken from the literature.\n\nResultsFrom 9 million older ([≥]70yrs) people living in England, 2.1 million could be defined as pre-diabetic (glycated haemoglobin 42<48 mmol/mol). The estimated population attributable fraction (0.281) (assuming relative risk of diabetes from inactivity=3.3, 40% physically active) would give rise to 392,948 new cases of diabetes which we argue are directly attributed to a prolonged period of lockdown. We estimate that the cost of screening and testing these patients in primary care ({pound}35m), their subsequent treatment and management ({pound}229m), and complications ({pound}909m) would equate to an additional {pound}1.17bn to the health care system.\n\nConclusionsInactivity related to lockdown in previously active older adults may contribute up to {pound}1.17b in additional healthcare costs through a potential increase in diabetes. Clear advice about the importance of physical activity may reduce this potential economic burden during global pandemics.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Courtney Kipps", - "author_inst": "UCL" - }, - { - "author_name": "Mark Hamer", - "author_inst": "UCL" - }, - { - "author_name": "Neil Hill", - "author_inst": "Imperial College London" - }, - { - "author_name": "Paula Lorgelly", - "author_inst": "UCL" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2020.06.03.20120832", "rel_title": "A how-to-guide to building a robust SARS-CoV-2 testing program at a university-based health system", @@ -1377885,6 +1379769,81 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.06.08.138826", + "rel_title": "SARS-CoV-2-specific T cells exhibit unique features characterized by robust helper function, lack of terminal differentiation, and high proliferative potential", + "rel_date": "2020-06-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.08.138826", + "rel_abs": "Convalescing COVID-19 patients mount robust T cell responses against SARS-CoV-2, suggesting an important role for T cells in viral clearance. To date, the phenotypes of SARS-CoV-2-specific T cells remain poorly defined. Using 38-parameter CyTOF, we phenotyped longitudinal specimens of SARS-CoV-2-specific CD4+ and CD8+ T cells from nine individuals who recovered from mild COVID-19. SARS-CoV-2-specific CD4+ T cells were exclusively Th1 cells, and predominantly Tcm with phenotypic features of robust helper function. SARS-CoV-2-specific CD8+ T cells were predominantly Temra cells in a state of less terminal differentiation than most Temra cells. Subsets of SARS-CoV-2-specific T cells express CD127, can homeostatically proliferate, and can persist for over two months. Our results suggest that long-lived and robust T cell immunity is generated following natural SARS-CoV-2 infection, and support an important role for SARS-CoV-2-specific T cells in host control of COVID-19.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Jason Neidleman", + "author_inst": "University of California, San Francisco; and Gladstone Institutes" + }, + { + "author_name": "Xiaoyu Luo", + "author_inst": "Gladstone Institutes" + }, + { + "author_name": "Julie Frouard", + "author_inst": "University of California, San Francisco; and Gladstone Institutes" + }, + { + "author_name": "Guorui Xie", + "author_inst": "University of California, San Francisco; and Gladstone Institutes" + }, + { + "author_name": "Gurjot Gill", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Ellen S. Stein", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Matthew McGregor", + "author_inst": "University of California, San Francisco; and Gladstone Institutes" + }, + { + "author_name": "Tongcui Ma", + "author_inst": "University of California, San Francisco; and Gladstone Institutes" + }, + { + "author_name": "Ashley George", + "author_inst": "University of California, San Francisco; and Gladstone Institutes" + }, + { + "author_name": "Astrid Kosters", + "author_inst": "Emory University" + }, + { + "author_name": "Warner C. Greene", + "author_inst": "Gladstone Institutes" + }, + { + "author_name": "Joshua Vasquez", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Eliver Ghosn", + "author_inst": "Emory University" + }, + { + "author_name": "Sulggi Lee", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Nadia R. Roan", + "author_inst": "University of California, San Francisco; and Gladstone Institutes" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.06.08.140236", "rel_title": "Effective Inhibition of SARS-CoV-2 Entry by Heparin and Enoxaparin Derivatives", @@ -1378777,25 +1380736,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.05.20123539", - "rel_title": "A shred of evidence that BCG vaccine may protect against COVID-19: Comparing cohorts in Spain and Italy", - "rel_date": "2020-06-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.05.20123539", - "rel_abs": "IntroductionThere is evidence that the BCG vaccine against tuberculosis also helps prevent other diseases - perhaps including COVD-19. Spain had a program for universal BCG vaccination until 1981.\n\nObjectiveTo see whether cohorts born when Spain had a program of universal BCG vaccination had lower rates of confirmed cases of COVID-19 and mortality (relative to similar cohorts in Italy).\n\nMethodsWe compare COVID-19 mortality and confirmed cases for those born roughly a decade before and after 1981. We compare the outcomes to the same age cohorts in Italy, which never had universal BCG vaccination.\n\nResultsThe Spanish cohort that received BCG had a relative risk of 0.962 of having a confirmed case of COVID-19. This risk is statistically significantly below unity (95% CI 0.952 to 0.972, P< 0.001). There is also suggestive evidence the BCG cohort in Spain had lower mortality (relative risk 0.929, CI 0.850 to 1.01, P = 0.11). The small sample size makes this test underpowered.\n\nConclusionThese suggestive results provide a shred of evidence that BCG vaccinations help protect against COVID. I outline many limitations to this study and point how better data can help be more convincing.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "David I. Levine", - "author_inst": "University of California, Berkeley" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.06.20123919", "rel_title": "Covid-19 Seroprevalence rate in healthy blood donors from a community under strict lockdown measures", @@ -1379283,6 +1381223,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.06.05.20123026", + "rel_title": "Losing ground at the wrong time: Trends in self-reported influenza vaccination uptake in Switzerland, Heath Survey 2007-2017", + "rel_date": "2020-06-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.05.20123026", + "rel_abs": "ObjectivesWe studied time trends in seasonal influenza vaccination and associations with socioeconomic and health-related determinants in Switzerland, overall and in people aged [≥] 65 years.\n\nDesignThree cross-sectional surveys.\n\nParticipantsIndividuals who participated in the Swiss Health Surveys 2007, 2012, and 2017. We calculated the proportion reporting influenza vaccination in the last 12 months, and performed multivariable logistic regression analyses.\n\nResultsThe proportion of reporting a history of influenza vaccination overall was 31.9% (95% confidence intervals [95% CI] 31.4-32.4); and dropped from 34.5% in 2007 to 28.8% in 2017. The uptake of vaccination within the past 12 months was 16% in 2007 and similar in 2012 and 2017 (around 14%). In people with chronic disease, uptake dropped from 43.8% in 2007 to 37.1% in 2012 and to 31.6% in 2017 (p<0.001). In people aged [≥] 65 years, uptake dropped from 47.8% in 2007 to 38.5% in 2012 to 36.2% in 2017 (p<0.001). Similarly, a decrease in vaccine uptake was seen in people with poor self-reported health status (39.4%, 33.1%, and 27.0%). In logistic regression, self-reported vaccination coverage decreased in the 65 to 75 years old (adjusted odds ratio (aOR) aOR 0.56, 95% Cl 0.48-0.66 between 2007 and 2012; aOR 0.89, 95% CI 0.77-1.03). Uptake was positively associated with the [≥] 65 age group, living in French-speaking and urban areas, history of smoking, bad self-reported health status, private/semiprivate health insurance, having a medical profession, and having any underlying chronic disease. Use of any alternative medicine therapy was negatively associated with influenza vaccination (aOR 0.72, 95% CI 0.67-0.80).\n\nConclusionInfluenza vaccination coverage was low in older and chronically ill persons. Significant efforts are required in preparing for the flu season 2020/21 to reduce the double burden of COVID-19 and seasonal influenza. These efforts should include campaigns but also novel approaches using social media.\n\nStrengths and limitations of this studyO_LIData analysis of the Swiss Health Survey 2007, 2012, and 2017 focussing on influenza vaccine uptake overall and in the age group [≥]65 years in Switzerland.\nC_LIO_LIThe Swiss Health Survey is a nationwide, representative survey that is repeated every five years using the same methodology.\nC_LIO_LIAnalyses were weighted and adjusted for a wide range of important cofactors.\nC_LIO_LIWe calculated percent of people reporting having been vaccinated and associations between vaccination status and socio-demographic and health-related factors.\nC_LIO_LIInfluenza vaccination status is self-reported in the Swiss Health Survey and the reliability of the data not ascertained.\nC_LI", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Kathrin Zuercher", + "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland" + }, + { + "author_name": "Marcel Zwahlen", + "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland" + }, + { + "author_name": "Claudia Berlin", + "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland" + }, + { + "author_name": "Matthias Egger", + "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland" + }, + { + "author_name": "Lukas Fenner", + "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.06.04.20122838", "rel_title": "ENVIRONMENTAL SAFETY EVALUATION OF THE PROTECTION AND ISOLATION SYSTEM FOR PATIENTS WITH COVID-19.", @@ -1380043,37 +1382018,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.05.28.20116012", - "rel_title": "Cremation based estimates suggest significant under- and delayed reporting of COVID-19 epidemic data in Wuhan and China", - "rel_date": "2020-06-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.28.20116012", - "rel_abs": "BackgroundChinas COVID-19 statistics fall outside of recognized and accepted medical norms. Here we estimated the incidence, death and starting time of the COVID-19 outbreak in Wuhan and China based on cremation related information.\n\nMethodsData sources included literature on COVID-19 in China, official Chinese government figures, state-run and non state-run media reports. Our estimates are based on investigative media reports of crematory operations in Wuhan, which is considered as a common data end point to life. A range of estimates is presented by an exponential growth rate model from lockdown (Jan 23,2020) until the intervention started to show effects, which was estimated 14.5 days after lockdown.\n\nResultsFor the cumulative infections and total deaths, under different assumptions of case fatality rates (from 2.5% to 10%) and doubling time 6.4 days, the estimates projected on February 7, 2020 in Wuhan range from 305,000 to 1,272,000 for infections and from 6,811 to 7,223 for deaths - on the order of at least 10 times the official figures (13,603 and 545). The implied starting time of the outbreak is October 2019. The estimates of cumulative deaths, based on both funeral urns distribution and continuous full capacity operation of cremation services up to March 23, 2020, give results around 36,000, more than 10 times of the official death toll of 2,524.\n\nConclusionsOur study indicates a significant under-reporting in Chinese official data on the COVID-19 epidemic in Wuhan in early February, the critical time for response to the COVID-19 pandemic.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Mai He", - "author_inst": "Washington University in St. Louis School of Medicine" - }, - { - "author_name": "Li Li", - "author_inst": "AT&T, Bedminster, NJ 07921, USA" - }, - { - "author_name": "Louis P Dehner", - "author_inst": "Washington University in St. Louis School of Medicine, Department of Pathology & Immunology" - }, - { - "author_name": "Lucia Dunn", - "author_inst": "Department of Economics, The Ohio State University, Columbus, OH 43210, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.03.20121558", "rel_title": "Multicenter point-prevalence evaluation of the utilization and safety of drug therapies for COVID-19", @@ -1380853,6 +1382797,197 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.06.02.20119735", + "rel_title": "A CRISPR-Cas12a-based specific enhancer for more sensitive detection of SARS-CoV-2 infection", + "rel_date": "2020-06-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.02.20119735", + "rel_abs": "High Ct-values falling in the grey zone are frequently encountered in SARS-CoV-2 detection by real-time reverse transcription PCR (rRT-PCR) and have brought urgent challenges in diagnosis of samples with low viral load. Based on the single-stranded DNA reporter trans-cleavage activity by Cas12a upon target DNA recognition, we create a Specific Enhancer for detection of PCR-amplified Nucleic Acids (SENA) to confirm SARS-CoV-2 detection through specifically targeting its rRT-PCR amplicons. SENA is highly sensitive, with its limit of detection being at least 2 copies/reaction lower than that of the corresponding rRT-PCR, and highly specific, which identifies both false-negative and false-positive cases in clinic applications. SENA provides effective confirmation for nucleic acid amplification-based molecular diagnosis, and may immediately eliminate the uncertainty problems of rRT-PCR in SARS-CoV-2 clinic detection.\n\nOne Sentence SummaryCRISPR-Cas12a-based COVID-19 diagnosis.", + "rel_num_authors": 44, + "rel_authors": [ + { + "author_name": "Weiren Huang", + "author_inst": "Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University" + }, + { + "author_name": "Lei Yu", + "author_inst": "Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University" + }, + { + "author_name": "Donghua Wen", + "author_inst": "Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200123, China" + }, + { + "author_name": "Dong Wei", + "author_inst": "Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China" + }, + { + "author_name": "Yangyang Sun", + "author_inst": "Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University" + }, + { + "author_name": "Huailong Zhao", + "author_inst": "Jinan Center for Disease Control and Prevention, Jinan, Shandong 250021, China" + }, + { + "author_name": "Yu Ye", + "author_inst": "Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China" + }, + { + "author_name": "Wei Chen", + "author_inst": "Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University" + }, + { + "author_name": "Yongqiang Zhu", + "author_inst": "Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, China" + }, + { + "author_name": "Lijun Wang", + "author_inst": "Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, China" + }, + { + "author_name": "Li Wang", + "author_inst": "Jinan Infectious Diseases Hospital of Shandong University, Jinan, Shandong 250021, China" + }, + { + "author_name": "Wenjuan Wu", + "author_inst": "Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine" + }, + { + "author_name": "Qianqian Zhao", + "author_inst": "Medical Research & Laboratory Diagnostic Center, Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong 250013, China" + }, + { + "author_name": "Yong Xu", + "author_inst": "Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University" + }, + { + "author_name": "Dayong Gu", + "author_inst": "Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University" + }, + { + "author_name": "Guohui Nie", + "author_inst": "Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University" + }, + { + "author_name": "Dongyi Zhu", + "author_inst": "Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200123, China" + }, + { + "author_name": "Zhongliang Guo", + "author_inst": "Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200123, China" + }, + { + "author_name": "Xiaoling Ma", + "author_inst": "The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China" + }, + { + "author_name": "Liman Niu", + "author_inst": "Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University" + }, + { + "author_name": "Yikun Huang", + "author_inst": "Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University" + }, + { + "author_name": "Yuchen Liu", + "author_inst": "Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University" + }, + { + "author_name": "Bo Peng", + "author_inst": "Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China" + }, + { + "author_name": "Renli Zhang", + "author_inst": "Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China" + }, + { + "author_name": "Xiuming Zhang", + "author_inst": "Shenzhen Sixth People's Hospital (Nanshan Hospital), Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen 518052, China" + }, + { + "author_name": "Dechang Li", + "author_inst": "Yuebei Second People's Hospital, Shaoguan, Guangdong 512000, China" + }, + { + "author_name": "Yang Liu", + "author_inst": "Shanghai Institute of Quality Inspection and Technical Research/National Quality Supervision and Inspection Center for Food Products (Shanghai), Shanghai 200233" + }, + { + "author_name": "Guoliang Yang", + "author_inst": "Jinan Center for Disease Control and Prevention, Jinan, Shandong 250021, China" + }, + { + "author_name": "Lanzheng Liu", + "author_inst": "Jinan Center for Disease Control and Prevention, Jinan, Shandong 250021, China" + }, + { + "author_name": "Yunying Zhou", + "author_inst": "Medical Research & Laboratory Diagnostic Center, Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong 250013, China" + }, + { + "author_name": "Yunshan Wang", + "author_inst": "Medical Research & Laboratory Diagnostic Center, Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong 250013, China" + }, + { + "author_name": "Tieying Hou", + "author_inst": "Laboratory of Medicine, Provincial People's Hospital, Guangdong Academy of Medical Sciences Guangzhou, Guangdong 510080, China" + }, + { + "author_name": "Qiuping Gao", + "author_inst": "Tolo Biotechnology Company Limited, Shanghai 200233, China" + }, + { + "author_name": "Wujiao Li", + "author_inst": "Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University" + }, + { + "author_name": "Shuo Chen", + "author_inst": "Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China" + }, + { + "author_name": "Xuejiao Hu", + "author_inst": "Laboratory of Medicine, Provincial People's Hospital, Guangdong Academy of Medical Sciences Guangzhou, Guangdong 510080, China" + }, + { + "author_name": "Mei Han", + "author_inst": "Public Health Medical Centre of Chongqing Municipality, Chongqing 400036, China" + }, + { + "author_name": "Huajun Zheng", + "author_inst": "Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, China" + }, + { + "author_name": "Jianping Wen", + "author_inst": "The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China" + }, + { + "author_name": "Zhiming Cai", + "author_inst": "Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University" + }, + { + "author_name": "Xinxin Zhang", + "author_inst": "Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China" + }, + { + "author_name": "Fei Song", + "author_inst": "Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University" + }, + { + "author_name": "Guoping Zhao", + "author_inst": "CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Sh" + }, + { + "author_name": "Jin Wang", + "author_inst": "College of Life Sciences, Shanghai Normal University, Shanghai 200234, China" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.03.20119818", "rel_title": "Suppressive myeloid cells are a hallmark of severe COVID-19", @@ -1381773,25 +1383908,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, - { - "rel_doi": "10.1101/2020.06.03.20120667", - "rel_title": "County-Level Proportions of Black and Hispanic populations, and Socioeconomic Characteristics in Association with Confirmed COVID-19 Cases and Deaths in the United States", - "rel_date": "2020-06-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.03.20120667", - "rel_abs": "ObjectivesThe objective of this study was to investigate potential county-level disparities among racial/ethnic and economic groups in COVID-19 burden which was measured using confirmed cases and deaths in 100,000 population.\n\nDesignSecondary data analysis using county-level data for 3,142 US counties was conducted in 2020. Hierarchical linear regression and concentration curve analyses were performed. The association of COVID-19 cases and deaths was examined separately by sociodemographic and economic characteristics of the county population. American Community Survey (ACS) 5-year estimates (2014-2018), Area Health Resources File (AHRF) 2018-2019, and 2020 COVID-19 data from Johns Hopkins University were used in this study.\n\nResultsAfter adjusting for covariates, US counties with a higher proportion of black population, and a higher proportion of adults with less than high school diploma had disproportionately higher COVID-19 cases and deaths ({beta}>0, p<0.05). A higher proportion of the Hispanic population was associated with higher confirmed cases ({beta}= 1.03, 95% CI= 0.57-1.5), and higher housing cost to household income ratio was associated with higher deaths ({beta}= 3.74, 95% CI= 2.14-5.37). This observed disparities can potentially aggravate the existing health disparities among these population groups.\n\nConclusionsIdentification of disproportionately impacted population groups can pave the way towards narrowing the disparity gaps and guide policymakers and stakeholders in designing and implementing population group-specific interventions to mitigate the negative consequences of COVID-19 pandemic.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Ahmad Khanijahani", - "author_inst": "Duquesne University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.06.03.20120196", "rel_title": "Limiting Spread of COVID-19 in Ghana: Compliance audit of selected transportation stations in the Greater Accra region of Ghana", @@ -1382503,6 +1384619,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2020.06.03.20121459", + "rel_title": "Modelling daily infections with Covid-19 in Germany, France, and Sweden with a trend line based on day-to-day reproduction rates", + "rel_date": "2020-06-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.03.20121459", + "rel_abs": "The number of persons daily infected with Covid-19 as a function of time is fitted with a trend line based on an iterative power law (n = [1/4]) with a day-to-day reproduction rate modelled with a polyline. From the trend line, an effective reproduction rate Reff of Covid-19 is calculated. In all three states, Reff decreases in the initial phase to one indicating that there is no exponential growth. In Sweden, a steady state with Reff around 1 and a high daily infection rates. In Germany, Reff = 1 is reached before public and private life is restricted. With these restrictions, Reff is reduced further to 0.87 (CI95 [0.83.; 0.91]) after 40 days so that, speculatively estimated, 9500 premature fatalities within two months may have been avoided. In France, it seems that only strongly restricting private life sends Reff down to 1 and further down to about 0.7 (CI95 [0.3; 1.1]) after 45 days. With Reff permanently below 1, an exponential decline of the number of daily infections is observed in Germany and France.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Dieter Mergel", + "author_inst": "University of Duisburg-Essen" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.03.20120691", "rel_title": "Modeling COVID-19 dynamics in Illinois under non-pharmaceutical interventions", @@ -1383147,49 +1385282,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.03.20121574", - "rel_title": "Predicting individual risk for COVID19 complications using EMR data", - "rel_date": "2020-06-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.03.20121574", - "rel_abs": "BackgroundThe global pandemic of COVID-19 has challenged healthcare organizations and caused numerous deaths and hospitalizations worldwide. The need for data-based decision support tools for many aspects of controlling and treating the disease is evident but has been hampered by the scarcity of real-world reliable data. Here we describe two approaches: a. the use of an existing EMR-based model for predicting complications due to influenza combined with available epidemiological data to create a model that identifies individuals at high risk to develop complications due to COVID-19 and b. a preliminary model that is trained using existing real world COVID-19 data.\n\nMethodsWe have utilized the computerized data of Maccabi Healthcare Services a 2.3 million member state-mandated health organization in Israel. The age and sex matched matrix used for training the XGBoost ILI-based model included, circa 690,000 rows and 900 features. The available dataset for COVID-based model included a total 2137 SARS-CoV-2 positive individuals who were either not hospitalized (n = 1658), or hospitalized and marked as mild (n = 332), or as having moderate (n = 83) or severe (n = 64) complications.\n\nFindingsThe AUC of our models and the priors on the 2137 COVID-19 patients for predicting moderate and severe complications as cases and all other as controls, the AUC for the ILI-based model was 0.852[0.824-0.879] for the COVID19-based model - 0.872[0.847-0.879].\n\nInterpretationThese models can effectively identify patients at high-risk for complication, thus allowing optimization of resources and more focused follow up and early triage these patients if once symptoms worsen.\n\nFundingThere was no funding for this study\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe have search PubMed for coronavirus[MeSH Major Topic] AND the following MeSH terms: risk score, predictive analytics, algorithm, predictive analytics. Only few studies were found on predictive analytics for developing COVID19 complications using real-world data. Many of the relevant works were based on self-reported information and are therefore difficult to implement at large scale and without patient or physician participation.\n\nAdded value of this studyWe have described two models for assessing risk of COVID-19 complications and mortality, based on EMR data. One model was derived by combining a machine-learning model for influenza-complications with epidemiological data for age and sex dependent mortality rates due to COVID-19. The other was directly derived from initial COVID-19 complications data.\n\nImplications of all the available evidenceThe developed models may effectively identify patients at high-risk for developing COVID19 complications. Implementing such models into operational data systems may support COVID-19 care workflows and assist in triaging patients.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Yaron Kinar", - "author_inst": "Medial EarlySign, Hod Hasharon, Israel" - }, - { - "author_name": "Alon Lanyado", - "author_inst": "Medial EarlySign, Hod Hasharon, Israel" - }, - { - "author_name": "Avi Shoshan", - "author_inst": "Medial EarlySign, Hod Hasharon, Israel" - }, - { - "author_name": "Rachel Yesharim", - "author_inst": "Medial EarlySign, Hod Hasharon, Israel" - }, - { - "author_name": "Tamar Domany", - "author_inst": "Medial EarlySign, Hod Hasharon, Israel" - }, - { - "author_name": "Varda Shalev", - "author_inst": "KSM Kahn - Sagol -. Maccabi Research & Innovation Institute" - }, - { - "author_name": "Gabriel Chodcik", - "author_inst": "Maccabitech Maccabi Institute for Research & Innovation" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.04.20121673", "rel_title": "Dynamics of COVID-19 under social distancing measures are driven by transmission network structure", @@ -1384201,6 +1386293,169 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.06.04.135046", + "rel_title": "An OpenData portal to share COVID-19 drug repurposing data in real time", + "rel_date": "2020-06-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.04.135046", + "rel_abs": "The National Center for Advancing Translational Sciences (NCATS) has developed an online open science data portal for its COVID-19 drug repurposing campaign - named OpenData - with the goal of making data across a range of SARS-CoV-2 related assays available in real-time. The assays developed cover a wide spectrum of the SARS-CoV-2 life cycle, including both viral and human (host) targets. In total, over 10,000 compounds are being tested in full concentration-response ranges from across multiple annotated small molecule libraries, including approved drug, repurposing candidates and experimental therapeutics designed to modulate a wide range of cellular targets. The goal is to support research scientists, clinical investigators and public health officials through open data sharing and analysis tools to expedite the development of SARS-CoV-2 interventions, and to prioritize promising compounds and repurposed drugs for further development in treating COVID-19.", + "rel_num_authors": 37, + "rel_authors": [ + { + "author_name": "Kyle R. Brimacombe", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Tongan Zhao", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Richard T Eastman", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Xin Hu", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Ke Wang", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Mark Backus", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Bolormaa Baljinnyam", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Catherine Z. Chen", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Lu Chen", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Tara Eicher", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Marc Ferrer", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Ying Fu", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Kirill Gorshkov", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Hui Guo", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Quinlin M Hanson", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Zina Itkin", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Stephen C Kales", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Carleen Klumpp-Thomas", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Emily M Lee", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Sam Michael", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Tim Mierzwa", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Andrew Patt", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Manisha Pradhan", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Alex Renn", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Paul Shinn", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Jonathan H Shrimp", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Amit Viraktamath", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Kelli M Wilson", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Miao Xu", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Alexey V Zakharov", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Wei Zhu", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Wei Zheng", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Anton Simeonov", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Ewy A Math\u00e9", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Donald C Lo", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Matthew D Hall", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + }, + { + "author_name": "Min Shen", + "author_inst": "National Center for Advancing Translational Sciences, NIH" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.06.04.135608", "rel_title": "Design of a Novel Multiplex Real Time RT-PCR Assay for SARS-CoV-2 Detection", @@ -1385152,53 +1387407,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.04.20122507", - "rel_title": "Impaired glucose metabolism in patients with diabetes, prediabetes and obesity is associated with severe Covid-19", - "rel_date": "2020-06-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.04.20122507", - "rel_abs": "BackgroundIdentification of risk factors of severe Covid-19 is critical for improving therapies and understanding SARS-CoV-2 pathogenesis.\n\nMethodsWe analyzed 184 patients hospitalized for Covid-19 in Livingston, New Jersey for clinical characteristics associated with severe disease.\n\nResultsThe majority of Covid-19 patients had diabetes mellitus (DM) (62.0%), Pre-DM (23.9%) with elevated FBG, or a BMI > 30 with normal HbA1C (4.3%). SARS-CoV-2 infection was associated with new and persistent hyperglycemia in 29 patients, including several with normal HbA1C levels. Forty-four patients required intubation, which occurred significantly more often in patients with DM as compared to non-diabetics.\n\nConclusionsSevere Covid-19 occurs in the presence of impaired glucose metabolism in patients with SARS-CoV-2 infection. The association of dysregulated glucose metabolism and severe Covid-19 suggests a previously unrecognized manifestation of primary SARS-CoV-2 infection. Exploration of pathways by which SARS-CoV-2 impacts glucose metabolism is critical for understanding disease pathogenesis and developing therapies.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Stephen Smith", - "author_inst": "Smith Center for Infectious Diseases and Urban Health" - }, - { - "author_name": "Avinash Boppana", - "author_inst": "Smith Center for Infectious Diseases and Urban Health" - }, - { - "author_name": "Julie A Traupman", - "author_inst": "Smith Center for Infectious Diseases and Urban Health" - }, - { - "author_name": "Enrique Unson", - "author_inst": "Smith Center for Infectious Diseases and Urban Health" - }, - { - "author_name": "Daniel A Maddock", - "author_inst": "Smith Center for Infectious Diseases and Urban Health" - }, - { - "author_name": "Kathy Y Chao", - "author_inst": "Smith Center for Infectious Diseases and Urban Health" - }, - { - "author_name": "David P Dobesh", - "author_inst": "Saint Barnabas Medical Center" - }, - { - "author_name": "Ruth I Connor", - "author_inst": "Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.03.20117994", "rel_title": "Ozone therapy for patients with SARS-COV-2 pneumonia: a single-center prospective cohort study", @@ -1385746,6 +1387954,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.05.135806", + "rel_title": "A novel in-cell ELISA assay allows rapid and automated quantification of SARS-CoV-2 to analyse neutralizing antibodies and antiviral compounds", + "rel_date": "2020-06-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.05.135806", + "rel_abs": "The coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently the most pressing medical and socioeconomic challenge. Constituting important correlates of protection, determination of virus-neutralizing antibodies (NAbs) is indispensable for convalescent plasma selection, vaccine candidate evaluation, and immunity certificates. In contrast to standard serology ELISAs, plaque reduction neutralization tests (PRNTs) are laborious, time-consuming, expensive, and restricted to specialized laboratories. To replace microscopic counting-based SARS-CoV-2 PRNTs by a novel assay exempt from genetically modified viruses, which are inapplicable in most diagnostics departments, we established a simple, rapid, and automated SARS-CoV-2 neutralization assay employing an in-cell ELISA (icELISA) approach.\n\nAfter optimization of various parameters such as virus-specific antibodies, cell lines, virus doses, and duration of infection, SARS-CoV-2-infected cells became amenable as direct antigen source for quantitative icELISA. Using commercially available nucleocapsid protein-specific antibodies, viral infection could easily be quantified in human and highly permissive Vero E6 cells by icELISA. Antiviral agents such as human sera containing NAbs or antiviral interferons dose-dependently reduced the SARS-CoV-2-specific signal. Applying increased infectious doses, the icNT was superior to PRNT in discriminating convalescent sera with high from those with intermediate neutralizing capacities.\n\nThe SARS-CoV-2 icELISA test allows rapid (<48h in total, read-out in seconds) and automated quantification of virus infection in cell culture to evaluate the efficacy of NAbs as well as antiviral drugs, using reagents and equipment present in most routine diagnostics departments. We propose the icELISA and the icNT for COVID-19 research and diagnostics.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Lara Schoeler", + "author_inst": "Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany" + }, + { + "author_name": "Vu Thuy Khanh Le-Trilling", + "author_inst": "Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany" + }, + { + "author_name": "Mareike Eilbrecht", + "author_inst": "Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany" + }, + { + "author_name": "Denise Mennerich", + "author_inst": "Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany" + }, + { + "author_name": "Olympia E. Anastasiou", + "author_inst": "Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany" + }, + { + "author_name": "Adalbert Krawczyk", + "author_inst": "Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University of Duisburg-Essen, Essen, Germany" + }, + { + "author_name": "Anke Herrmann", + "author_inst": "Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany" + }, + { + "author_name": "Ulf Dittmer", + "author_inst": "Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany" + }, + { + "author_name": "Mirko Trilling", + "author_inst": "Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.06.05.134114", "rel_title": "Neuropilin-1 is a host factor for SARS-CoV-2 infection", @@ -1386714,33 +1388973,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.03.20120923", - "rel_title": "Trajectories of depression and anxiety during enforced isolation due to COVID-19: longitudinal analyses of 59,318 adults in the UK with and without diagnosed mental illness", - "rel_date": "2020-06-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.03.20120923", - "rel_abs": "BackgroundThere is currently major concern about the impact of the global COVID-19 outbreak on mental health. A number of studies suggest that mental health deteriorated in many countries prior to and during enforced isolation (\"lockdown\"), but it remains unknown how mental health has changed week by week over the course of the COVID-19 pandemic.\n\nAimsThis study explored trajectories of anxiety and depression over the 20 weeks after lockdown was announced using data from England, and compared the growth trajectories by individual characteristics.\n\nMethodsData from 36,520 adults in the UCL COVID -19 Social Study (a well-stratified panel study weighted to population proportions collecting data weekly during the COVID-19 pandemic) were analysed from 23/03/2020-09/08/2020. Latent growth models were fitted accounting for socio-demographic and health covariates.\n\nResults22.6% of the sample had scores indicating moderate-severe anxiety, and 25.1% indicating moderate-severe depressive symptoms. Anxiety and depression levels both declined across the first 20 weeks following the introduction of lockdown in the England. The fastest decreases were seen across the strict lockdown period, with symptoms plateauing as further lockdown easing measures were introduced. Being female or younger, having lower educational attainment, lower income or pre-existing mental health conditions, and living alone or with children were all risk factors for higher levels of anxiety and depression at the start of lockdown. Many of these inequalities in experiences were reduced as lockdown continued, but differences were still evident 20 weeks after the start of lockdown.\n\nConclusionsAs countries face potential future lockdowns, these data suggest that the highest levels of depression and anxiety are in the early stages of lockdown but decline fairly rapidly as individuals adapt to circumstances. They also suggest the importance of supporting individuals in the lead-up to lockdown measures being brought in to try and reduce distress and highlight that emotionally vulnerable groups have remained at risk throughout lockdown and its aftermath.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSData from representative cohort studies have highlighted the substantial impact of the COVID-19 pandemic on levels of depression, anxiety and mental distress, showing increases in average scores of symptoms of psychological distress from before to during the pandemic as well as a rise in the proportion of people experiencing clinically significant levels of mental illness. But it remains unknown how mental health has changed week by week over the course of the COVID-19 pandemic.\n\nAdded value of this studyThis study finds that anxiety and depression levels both declined across the first 20 weeks following the introduction of lockdown in the England. The fastest decreases were seen across the strict lockdown period, with symptoms plateauing as further lockdown easing measures were introduced. Specific risk factors for poorer trajectories of mental health during the pandemic are identified.\n\nImplications of all the available evidenceThis study is the first globally to look longitudinally at trajectories of anxiety and depression across the COVID-19 pandemic. Overall, these findings suggest that the highest levels of depression and anxiety in England were in the early stages of lockdown but declined fairly rapidly following the introduction of lockdown. Many known risk factors for poorer mental health were apparent at the start of lockdown, but some groups experienced faster improvements in symptoms, thereby reducing the differences over time. Nevertheless, many inequalities in mental health experiences did remain and emotionally vulnerable groups have remained at risk throughout lockdown and its aftermath. This has implications for planning and support for individuals during potential future waves of the virus.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Daisy Fancourt", - "author_inst": "University College London" - }, - { - "author_name": "Andrew Steptoe", - "author_inst": "University College London" - }, - { - "author_name": "Feifei Bu", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.06.02.20120790", "rel_title": "Assessing capacity to social distance and neighborhood-level health disparities during the COVID-19 pandemic", @@ -1387496,6 +1389728,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.02.20120501", + "rel_title": "Climatic influence on the magnitude of COVID-19 outbreak: a stochastic model-based global analysis", + "rel_date": "2020-06-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.02.20120501", + "rel_abs": "This study examines the association between community transmission of COVID-19 cases and climatic predictors, considering travel information and annual parasite index across the three climatic zones, i.e., tropical, subtropical, and temperate. A Boosted Regression Tree model has been employed to understand the association between the COVID-19 cases. The results show that average temperature and average relative humidity are the major contributors in explaining the differentials of COVID-19 transmission in temperate and subtropical regions whereas the mean diurnal temperature range and temperature seasonality are the most significant determinants in tropical regions. The average temperature is the most influential factor affecting the number of COVID-19 cases in France, Turkey, the US, the UK, and Germany, and the cases decrease sharply above 10{degrees}C. Among the tropical countries, India found to be most affected by mean diurnal temperature, and Brazil fazed by temperature seasonality. Most of the temperate countries like France, USA, Turkey, UK, and Germany with an average temperature between 5-12{degrees}C had high number of COVID-19 cases. The findings are expected to add to the ongoing debates on the influence of climatic factors influencing the number of COVID-19 cases and could help researchers and policymakers to make appropriate decisions for preventing the spread.\n\nHighlightsO_LIAnalyzed influence of climatic & bioclimatic factors on the spread of COVID-19\nC_LIO_LIFirst to analyze COVID-19 cases in 228 cities globally across three climatic zones\nC_LIO_LITemperature & humidity influenced COVID-19 cases in temperate & sub-tropics\nC_LIO_LIMean diurnal temperature & temperature seasonality had effects in tropics\nC_LIO_LILow temperature elicits COVID-19 cases in France, Turkey, the US, the UK, & Germany\nC_LI\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC=\"FIGDIR/small/20120501v1_figG1.gif\" ALT=\"Figure 1\">\nView larger version (30K):\norg.highwire.dtl.DTLVardef@7082daorg.highwire.dtl.DTLVardef@9ee185org.highwire.dtl.DTLVardef@e7f692org.highwire.dtl.DTLVardef@ecefcf_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Malay Pramanik", + "author_inst": "Asian Institute of Technology" + }, + { + "author_name": "Koushik Chowdhury", + "author_inst": "Indian Institute of Technology Kharagpur" + }, + { + "author_name": "Md Juel Rana", + "author_inst": "International Institute for Population Sciences" + }, + { + "author_name": "Praffulit Bisht", + "author_inst": "Jawaharlal Nehru University" + }, + { + "author_name": "Raghunath Pal", + "author_inst": "Jawaharlal Nehru University" + }, + { + "author_name": "Sylvia Szabo", + "author_inst": "Asian Institute of Technology" + }, + { + "author_name": "Indrajit Pal", + "author_inst": "Asian Institute of Technology" + }, + { + "author_name": "Bhagirath Behera", + "author_inst": "Indian Institute of Technology Kharagpur" + }, + { + "author_name": "Qiuhua Liang", + "author_inst": "Loughborough University" + }, + { + "author_name": "Sabu S. Padmadas", + "author_inst": "University of Southampton" + }, + { + "author_name": "Parmeshwar Udmale", + "author_inst": "Asian Institute of Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.02.20120311", "rel_title": "Are adversities and worries during the COVID-19 pandemic related to sleep quality? Longitudinal analyses of 45,000 UK adults", @@ -1388092,37 +1390383,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.05.30.20117796", - "rel_title": "A Statistical Model for Quantifying the Needed Duration of Social Distancing for the COVID-19 Pandemic", - "rel_date": "2020-06-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.30.20117796", - "rel_abs": "Understanding the effectiveness of strategies such as social distancing is a central question in attempts to control the COVID-19 pandemic. A key unknown in social distancing strategies is the duration of time for which such strategies are needed. Answering this question requires an accurate model of the transmission trajectory. A challenge in fitting such a model is the limited COVID-19 case data available from a given location. To overcome this challenge, we propose fitting a model of SARS-CoV-2 transmission jointly across multiple locations. We apply the model to COVID-19 case data from Spain, UK, Germany, France, Denmark, and New York to estimate the distribution for the time needed for social distancing to end to range from May 2020 to July 2021 (95% credible interval), where the median date is October, 2020. Our method is not specific to COVID-19, and it can also be applied to future pandemics.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Nadav Rakocz", - "author_inst": "University of California Los Angeles" - }, - { - "author_name": "Boyang Fu", - "author_inst": "University of California Los Angeles" - }, - { - "author_name": "Eran Halperin", - "author_inst": "University of California Los Angeles" - }, - { - "author_name": "Sriram Sankararaman", - "author_inst": "University of California Los Angeles" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.05.31.20118497", "rel_title": "Prevalence, clinical characteristics and treatment outcomes of HIV and SARS-CoV-2 co-infection: a systematic review and meta-analysis", @@ -1388642,6 +1390902,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.31.20117986", + "rel_title": "How Efficient Can Non-Professional MasksSuppress COVID-19 Pandemic?", + "rel_date": "2020-06-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.31.20117986", + "rel_abs": "The coronavirus disease 2019 (COVID-19) pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which can be transmitted via respiratory secretions. Since there are currently no specific therapeutics or vaccines available against the SARS-CoV-2, the commen non-pharmaceutical interventions (NPIs) are still the main measures to curb the COVID-19 epidemic. Face mask wearing is one important measure to suppress the pandemic. In order to know how efficient is face mask wearing in reducing the pandemic even with low efficiency non-professional face masks, we exploit physical abstraction to model the non-professional face masks made from cotton woven fabrics and characterize them by a parameter virus penetration rate (VPR){gamma} . Monte Carlo simulations exhibit that the effective reproduction number R of COVID-19 or similar pandemics can be approximately reduced by factor{gamma} 4 with respect to the basic reproduction number R0, if the face masks with 70% < {gamma} < 90% are universally applied for the entire network. Furthermore, thought experiments and practical exploitation examples in country-level and city-level are enumerated and discussed to support our discovery in this study and indicate that the outbreak of a COVID-19 like pandemic can be even suppressed by the low efficiency non-professional face masks.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Yejian Chen", + "author_inst": "Bell Laboratories, Nokia" + }, + { + "author_name": "Meng Dong", + "author_inst": "Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology and University of Tuebingen" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.30.20117523", "rel_title": "Missing clinical trial data: the knowledge gap in the safety of potential COVID-19 drugs", @@ -1389450,45 +1391733,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.06.01.20118893", - "rel_title": "The COVID-19 Pandemic in Africa: Predictions using the SIR Model Indicate the Cases are Falling", - "rel_date": "2020-06-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.01.20118893", - "rel_abs": "Since the earliest reports of the Coronavirus disease - 2019 (COVID-19) in Wuhan, China in December 2019, the disease has rapidly spread worldwide, attaining pandemic levels in early March 2020. However, the spread of COVID-19 has differed in the African setting compared to countries on other continents. To predict the spread of COVID-19 in Africa and within each country on the continent, we applied a Susceptible-Infectious-Recovered mathematical model. Here, our results show that, overall, Africa is currently (July 24, 2020) at the peak of the COVID-19 pandemic, after which we predict the number of cases would begin to fall in August 2020. Furthermore, we predict that the ending phase of the pandemic would be in Late-November 2020 and that decreasing cases of COVID-19 infections would be detected until around August 2021 and September 2021. Our results also reveal that of the 51 countries with reported COVID-19 cases, only eight, including Algeria, Morocco and Zambia, are likely to report higher monthly COVID-19 cases in the coming months of 2020 than those reported in the previous months. Overall, at the end of this pandemic, we predict that approximately 2,201,849 (about 1,451,567 future cases) individuals in Africa would have been infected with the COVID-19 virus. Here, our predictions are data-driven and based on the previously observed trends in the spread of the COVID-19 pandemic. Shifts in the population dynamics and/or changes in the infectiousness of the COVID-19 virus may require new forecasts of the disease spread.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Musalula Sinkala", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Panji Nkhoma", - "author_inst": "University of Zambia" - }, - { - "author_name": "Mildred Zulu", - "author_inst": "University of Zambia" - }, - { - "author_name": "Doris Kafita", - "author_inst": "University of Zambia" - }, - { - "author_name": "Rabecca Tembo", - "author_inst": "University of Zambia" - }, - { - "author_name": "Victor Daka", - "author_inst": "Copperbelt University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.31.20118372", "rel_title": "Modelling Singapore COVID-19 pandemic with a SEIR multiplex network model", @@ -1389928,6 +1392172,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.31.20118380", + "rel_title": "Sensitivity and specifity of prediction models based on gustatory disorders in diagnosing COVID-19 patients: a case-control study.", + "rel_date": "2020-06-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.31.20118380", + "rel_abs": "Objectiveto quantitatively assess disturbances of sweet, sour and salty and bitter tastes in a group of young, asymptomatic or oligosymptomatic COVID-19 patients; establish a reliable, sensitive and specific test that can diagnose COVID-19 on the basis of taste disorders and publish the results according to STARD 2015 statement (Standards for Reporting Diagnostic Accuracy).\n\nDesigncase-control study\n\nSettingisolated rooms in the Central Clinical Hospital of the Ministry of the Interior and Administration in Warsaw (which had been transformed into an infectious hospital) and a dormitory in one of Warsaw universities.\n\nParticipants52 SARS-CoV-2 positive (51 men, mean age 21.7 years) and 36 negative students (34 men, mean age 20.8 years).\n\nMain outcome measuresa gustatory function assessment (sweet, salty, sour and bitter taste), with flavour concentrations established previously in healthy subjects was conducted for all subjects. Each participant received one tasteless reference and nine flavour tablets with sucrose concentrations of 40, 80 and 106.4 mg/ml; NaCl at 13.5, 17 and 27 mg/ml; ascorbic acid at 6.25 and 12.5 mg/ml and grapefruit extract at 40 mg/ml.\n\nResultsthe only taste that was impaired significantly more frequently in COVID-19 patients was the sweet taste at the lowest flavour concentration (40 mg/ml, p = 0.002). Different screening and diagnostic models were constructed using the examined variables. The highest accuracy screening test consisted of the positive result of a three-question questionnaire (self-reported loss of taste, self-reported loss of smell, or fever within the last month (positive if at least one present) and/or ageusia of sweet taste at a sucrose concentration of 40 mg/ml. The sensitivity of the model was 94% with a specificity of 55%. The highest accuracy diagnostic test consisted of ageusia of sweet taste at a sucrose concentration of 106.4 mg/ml or/and ageusia of salty taste at an NaCl concentration of 13.5 or 17 mg/ml. The specificity of the test was found to be 100%, and the sensitivity was 34%.\n\nConclusionas the most effective way of controlling the present pandemic involves testing the wider population for symptomatic, oligosymptomatic and asymptomatic carriers of SARSCoV-2 and isolating or hospitalising infected subjects, in the present study, an inexpensive, simple, fast and sensitive (94%) screening test that can be used for such a purpose is proposed. In addition, a specific (100%) diagnostic test that could be used to refer patients to quarantine in the case of limited availability of genetic or serological tests is proposed.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Kamil Adamczyk", + "author_inst": "Central Clinical Hospital of the Ministry of the Interior and Administration in Warsaw, Poland" + }, + { + "author_name": "Michal Herman", + "author_inst": "Central Clinical Hospital of the Ministry of the Interior and Administration in Warsaw, Poland" + }, + { + "author_name": "Janusz Fraczek", + "author_inst": "Central Clinical Hospital of the Ministry of the Interior and Administration in Warsaw, Poland" + }, + { + "author_name": "Robert Piec", + "author_inst": "Main School of Fire Service, Warsaw, Poland" + }, + { + "author_name": "Barbara Szykula-Piec", + "author_inst": "Main School of Fire Service, Warsaw, Poland" + }, + { + "author_name": "Artur Zaczynski", + "author_inst": "Central Clinical Hospital of the Ministry of the Interior and Administration in Warsaw, Poland" + }, + { + "author_name": "Rafal Wojtowicz", + "author_inst": "Central Clinical Hospital of the Ministry of the Interior and Administration in Warsaw, Poland" + }, + { + "author_name": "Krzysztof Bojanowski", + "author_inst": "Central Clinical Hospital of the Ministry of the Interior and Administration in Warsaw, Poland" + }, + { + "author_name": "Ewa Rusyan", + "author_inst": "Warsaw Medical University, Warsaw, Poland" + }, + { + "author_name": "Zbigniew Krol", + "author_inst": "Central Clinical Hospital of the Ministry of the Interior and Administration in Warsaw, Poland" + }, + { + "author_name": "Waldemar Wierzba", + "author_inst": "Central Clinical Hospital of the Ministry of the Interior and Administration in Warsaw, Poland, UHE Satellite Campus in Warsaw, University of Humanities and Eco" + }, + { + "author_name": "Edward Franek", + "author_inst": "Central Clinical Hospital of the Ministry of the Interior and Administration in Warsaw; Mossakowski Clinical Research Centre, Polish Academy of Sciences, Warsa" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.01.20119198", "rel_title": "Evaluation of symptomatic patient saliva as a sample type for the Abbott ID NOW COVID-19 assay", @@ -1390592,49 +1392899,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.01.20086025", - "rel_title": "Age differences in clinical features and outcomes in patients with COVID-19, Jiangsu, China: a retrospective, multi-center cohort study", - "rel_date": "2020-06-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.01.20086025", - "rel_abs": "ObjectivesTo determine the age-specific clinical presentations and incidence of adverse outcomes among patients with COVID-19 in Jiangsu, China.\n\nDesign and settingThis is a retrospective, multi-center cohort study performed at twenty-four hospitals in Jiangsu, China.\n\nParticipantsFrom January 10 to March 15, 2020, 625 patients with COVID-19 were involved.\n\nResultsOf the 625 patients (median age, 46 years; 329 [52.6%] males), 37 (5.9%) were children (18 years or less), 261 (40%) young adults (19-44 years), 248 (39.7%) middle-aged adults (45-64 years), and 79 (12.6%) elderly (65 years or more). The incidence of hypertension, coronary heart disease, chronic obstructive pulmonary disease, and diabetes comorbidities increased with age (trend test, P <.0001, P = 0.0003, P <.0001, and P <.0001 respectively). Fever, cough, and shortness of breath occurred more commonly among older patients, especially the elderly, compared to children (Chi-square test, P = 0.0008, 0.0146, and 0.0282, respectively). The quadrant score and pulmonary opacity score increased with age (trend test, both P <.0001). Older patients had significantly more abnormal values in many laboratory parameters than younger patients. Elderly patients contributed the highest proportion of severe or critically-ill cases (33.0%, Chi-square test P < 0.001), intensive care unit (ICU) (35.4%, Chi-square test P < 0.001), and respiratory failure (31.6%, Chi-square test P = 0.0266), and longest hospital stay (21 days, ANOVA-test P < 0.001).\n\nConclusionsElderly ([≥]65) patients with COVID-19 had the highest risk of severe or critical illness, intensive care use, respiratory failure, and the longest hospital stay, which may be due partly to that they had higher incidence of comorbidities and poor immune responses to COVID-19.\n\nStrengths and limitations of this studyThe cohort consists of almost all COVID-19 patients in Jiangsu province with a population over 80 million and its results should be representative of the patient population in the whole province and with a wide range of disease severity, therefore the results are subject to less selection bias.\n\nThe study includes imported and local cases and could study patients with different types of exposures.\n\nThe relative short follow-up time and a very small proportion of patients who remained in hospital after the 14-day follow-up period yield incomplete estimates for disease severity and clinical outcomes.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Huanyuan Luo", - "author_inst": "Liverpool School of Tropical Medicine (LSTM)" - }, - { - "author_name": "Songqiao Liu", - "author_inst": "Southeast University Zhongda Hospital" - }, - { - "author_name": "Yuancheng Wang", - "author_inst": "Southeast University Zhongda Hospital" - }, - { - "author_name": "Penelope A. Phillips-Howard", - "author_inst": "Liverpool School of Tropical Medicine" - }, - { - "author_name": "Yi Yang", - "author_inst": "Southeast University Zhongda Hospital" - }, - { - "author_name": "Shenghong Ju", - "author_inst": "Southeast University Zhongda Hospital" - }, - { - "author_name": "Duolao Wang", - "author_inst": "Liverpool School of Tropical Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.29.20109090", "rel_title": "Determinants of self-reported symptoms and testing for COVID-19 in Canada using a nationally representative survey", @@ -1391146,6 +1393410,149 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.29.20109785", + "rel_title": "Endotoxemia and circulating bacteriome in severe COVID-19 patients", + "rel_date": "2020-06-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.29.20109785", + "rel_abs": "PurposeWhen severe, COVID-19 shares many clinical features with bacterial sepsis. Yet, secondary bacterial infection is uncommon. However, as epithelium are injured and barrier function is lost, bacterial products entering the circulation might contribute to the pathophysiology of COVID-19.\n\nMethodsWe studied 19 adults, severely ill patients with COVID-19 infection, who were admitted to King Chulalongkorn Memorial Hospital, Bangkok, Thailand, between 13th March and 17th April 2020. Blood samples on day 1, 3, and 7 of enrollment were analyzed for endotoxin activity assay (EAA), (1[->]3)-{beta}-D-Glucan (BG), and 16S rRNA gene sequencing to determine the circulating bacteriome.\n\nResultsOf the 19 patients, 14 were in intensive care and 10 patients received mechanical ventilation. We found 8 patients with high EAA ([≥] 0.6) and about half of the patients had high serum BG levels which tended to be higher in later in the illness. Although only 1 patient had a positive blood culture, 18 of 19 patients were positive for 16S rRNA gene amplification. Proteobacteria was the most abundant phylum. The diversity of bacterial genera was decreased overtime.\n\nConclusionsBacterial DNA and toxins were discovered in virtual all severely ill COVID-19 pneumonia patients. This raises a previously unrecognized concern for significant contribution of bacterial products in the pathogenesis of this disease", + "rel_num_authors": 32, + "rel_authors": [ + { + "author_name": "Phatadon Sirivongrangson", + "author_inst": "Excellence Center for Critical Care Nephrology, King Chulalongkorn Memorial Hospital, Bangkok, Thailand" + }, + { + "author_name": "Win Kulvichit", + "author_inst": "Excellence Center for Critical Care Nephrology, King Chulalongkorn Memorial Hospital, Bangkok, Thailand" + }, + { + "author_name": "Sunchai Payungporn", + "author_inst": "Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" + }, + { + "author_name": "Trairak Pisitkun", + "author_inst": "Center of Excellence in Systems Biology, Chulalongkorn University (CUSB), Bangkok 10330 Thailand" + }, + { + "author_name": "Ariya Chindamporn", + "author_inst": "Department of Microbiology, Chulalongkorn University, Bangkok, Thailand" + }, + { + "author_name": "Sadudee Peerapornratana", + "author_inst": "Department of Laboratory Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand" + }, + { + "author_name": "Prapaporn Pisitkun", + "author_inst": "Division of Allergy Immunology and Rheumatology, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand." + }, + { + "author_name": "Suwalak Chitcharoen", + "author_inst": "Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand" + }, + { + "author_name": "Vorthon Sawaswong", + "author_inst": "Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand" + }, + { + "author_name": "Navaporn Worasilchai", + "author_inst": "Department of Microbiology, Chulalongkorn University, Bangkok, Thailand" + }, + { + "author_name": "Sarinya Kampunya", + "author_inst": "Center of Excellence in Systems Biology, Chulalongkorn University (CUSB), Bangkok 10330 Thailand." + }, + { + "author_name": "Opass Putcharoen", + "author_inst": "Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand" + }, + { + "author_name": "Thammasak Tawitsri", + "author_inst": "Deparment of Anesthesiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand" + }, + { + "author_name": "Nophol Leelayuwatanakul", + "author_inst": "Division of Pulmonary and Critical Care, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand" + }, + { + "author_name": "Napplika Kongpolprom", + "author_inst": "Division of Pulmonary and Critical Care, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand" + }, + { + "author_name": "Vorakamol Phoophiboon", + "author_inst": "Division of Pulmonary and Critical Care, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand" + }, + { + "author_name": "Thitiwat Sriprasart", + "author_inst": "Division of Pulmonary and Critical Care, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand" + }, + { + "author_name": "Rujipat Samransamruajkit", + "author_inst": "Critical Care Excellence Center, King Chulalongkorn Memorial Hospital and Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thai" + }, + { + "author_name": "Somkanya Tungsanga", + "author_inst": "Division of Nephrology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand" + }, + { + "author_name": "Kanitha Tiankanon", + "author_inst": "Division of Nephrology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand" + }, + { + "author_name": "Nuttha Lumlertgul", + "author_inst": "Excellence Center for Critical Care Nephrology, King Chulalongkorn Memorial Hospital, Bangkok, Thailand" + }, + { + "author_name": "Asada Leelahavanichkul", + "author_inst": "Center of Excellence in Immunology and Immune-Mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand" + }, + { + "author_name": "Tueboon Sriphojanart", + "author_inst": "Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand." + }, + { + "author_name": "Terapong Tantawichien", + "author_inst": "Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand" + }, + { + "author_name": "Usa Thisyakorn", + "author_inst": "Tropical Medicine Cluster, Chulalongkorn University, Bangkok, Thailand" + }, + { + "author_name": "Chintana Chirathaworn", + "author_inst": "Department of Microbiology, Chulalongkorn University, Bangkok, Thailand" + }, + { + "author_name": "Kearkiat Praditpornsilpa", + "author_inst": "Division of Nephrology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand" + }, + { + "author_name": "Kriang Tungsanga", + "author_inst": "Division of Nephrology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand" + }, + { + "author_name": "Somchai Eiam-Ong", + "author_inst": "Division of Nephrology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand" + }, + { + "author_name": "Visith Sitprija", + "author_inst": "Queen Saovabha Memorial Institute, Thai Red Cross Society, Bangkok, Thailand" + }, + { + "author_name": "John A. Kellum", + "author_inst": "Center for Critical Care Nephrology, The CRISMA Center, Department of Critical Care Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA" + }, + { + "author_name": "Nattachai Srisawat", + "author_inst": "Excellence Center for Critical Care Nephrology, King Chulalongkorn Memorial Hospital, Bangkok, Thailand" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.05.30.20107888", "rel_title": "Machine learning in predicting respiratory failure in patients with COVID-19 pneumonia - challenges, strengths, and opportunities in a global health emergency", @@ -1392118,81 +1394525,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.02.20119909", - "rel_title": "Monocyte class switch and hyperinflammation characterise severe COVID-19 in type 2 diabetes", - "rel_date": "2020-06-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.02.20119909", - "rel_abs": "BackgroundEarly in the COVID-19 pandemic type 2 diabetes (T2D) was marked as a risk factor of severe disease and mortality. Inflammation is central to the aetiology of both conditions where variations in immune responses have the potential to mitigate or aggravate disease course. Identifying at risk groups based on immuno-inflammatory signatures is valuable in directing personalised care and developing potential targets for precision therapy.\n\nMethodsThis study characterised immunophenotypic variation associated with COVID-19 severity in type 2 diabetes. Broad-spectrum immunophenotyping quantified 15 leukocyte populations in peripheral circulation from a cohort of 45 hospitalised COVID-19 patients with and without type 2 diabetes.\n\nResultsMorphological anomalies in the monocyte pool, monocytopenia specific to quiescent monocytes, and a decreased frequency of cytotoxic lymphocytes were associated with severe COVID-19 in patients with type 2 diabetes requiring intensive care. An aggravated inflammatory gene expression profile, reminiscent of the type-1 interferon pathway, underlaid the immunophenotype associated with severe disease in T2D.\n\nConclusionShifts in T-cell and monocyte dynamics underpin a maladaptive response to SARSCoV-2. These alterations may impact type-1 interferon signalling which is the likely source of the hyperinflammation that increases voracity of COVID-19. These findings allow the identification of type 2 diabetic patients at risk of severe disease as well as providing evidence that the type-1 interferon pathway may be an actionable therapeutic target for future studies.\n\nTrial registrationNCT02671864\n\nFundingFrench National Agency of Research (ANR); European Foundation for the study of diabetes (EFSD); European Research Council (ERC); Francophone Society for Diabetes (SFD)\n\nBrief summaryMaladapted monocyte responses including class switch, morphological anomalies and systemic hyperinflammation put patients with type 2 diabetes at higher risk of severe COVID-19\n\nGRAPHICAL ABSTRACT\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=177 SRC=\"FIGDIR/small/20119909v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (35K):\norg.highwire.dtl.DTLVardef@725aeeorg.highwire.dtl.DTLVardef@1afd714org.highwire.dtl.DTLVardef@1518dfforg.highwire.dtl.DTLVardef@1416627_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Fawaz ALZAID", - "author_inst": "INSERM, Sorbonne Universite, Cordeliers Research Centre" - }, - { - "author_name": "Jean-Baptiste Julla", - "author_inst": "INSERM CRC / Hopital Lariboisiere - APHP" - }, - { - "author_name": "Marc Diedisheim", - "author_inst": "INSERM-CRC / Hopital Cochin" - }, - { - "author_name": "Charline Potier", - "author_inst": "INSERM-CRC" - }, - { - "author_name": "Louis Potier", - "author_inst": "Hopital Bichat - APHP" - }, - { - "author_name": "Gilberto Velho", - "author_inst": "INSERM-CRC" - }, - { - "author_name": "Benedicte Gaborit", - "author_inst": "Aix Marseille University, INSERM, INRA, C2VN, Marseille, France. Endocrinology, Metabolic Diseases and Nutrition Department, Assistance Publique Hopitaux de Mar" - }, - { - "author_name": "Philippe Manivet", - "author_inst": "Centre de Ressources Biologique -biobank Lariboisiere-, BB-0033-00064. APHP.Nord, Universite de Paris, Paris Diderot. Hopital Lariboisiere, Paris 10, France." - }, - { - "author_name": "Stephane Germain", - "author_inst": "Center for Interdisciplinary Research in Biology (CIRB), College de France - Centre National de la Recherche Scientifique (CNRS), Institut National de la Sante " - }, - { - "author_name": "Tiphaine Vidal-Trecan", - "author_inst": "Department of Diabetes, Clinical Investigation Centre (CIC-9504), Lariboisiere Hospital, Assistance Publique - Hopitaux de Paris, Paris, France" - }, - { - "author_name": "Ronan Roussel", - "author_inst": "Department of Diabetology, Endocrinology and Nutrition, Bichat Hospital" - }, - { - "author_name": "Jean-Pierre Riveline", - "author_inst": "Department of Diabetes, Clinical Investigation Centre (CIC-9504), Lariboisiere Hospital, Assistance Publique - Hopitaux de Paris, Paris, France" - }, - { - "author_name": "Elise Dalmas", - "author_inst": "INSERM-CRC" - }, - { - "author_name": "Nicolas Venteclef", - "author_inst": "INSERM-CRC" - }, - { - "author_name": "Jean-Francois Gautier", - "author_inst": "Department of Diabetes, Clinical Investigation Centre (CIC-9504), Lariboisiere Hospital, Assistance Publique - Hopitaux de Paris, Paris, France" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "endocrinology" - }, { "rel_doi": "10.1101/2020.06.02.20120022", "rel_title": "Hand Washing Compliance and COVID-19: A Non-Participatory Observational Study among Hospital Visitors", @@ -1392856,6 +1395188,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.01.20119800", + "rel_title": "The SARS-CoV-2 pandemic course in Saudi Arabia: A dynamic epidemiological model", + "rel_date": "2020-06-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.01.20119800", + "rel_abs": "ObjectiveSaudi Arabia ranks second in the number of coronavirus disease 2019 (COVID-19) cases in the Eastern Mediterranean region. It houses the two most sacred religious places for Muslims: Mecca and Medina. It is important to know what the trend in case numbers will be in the next 4-6 months, especially during the Hajj pilgrimage season.\n\nMethodsEpidemiological data on COVID-19 were obtained from the Saudi Arabian Ministry of Health, the World Health Organization, and the Humanitarian Data Exchange. A susceptible-exposed-infectious-recovered (SEIR) prediction model was constructed to predict the trend in COVID-19 in Saudi Arabia in the next 6 months.\n\nFindingsThe model predicts that the number of active cases will peak by 20 May 2020. The cumulative infected cases are predicted to reach 59,663 at that time. The total number of infected individuals is estimated reach to 102,647 by the end of the pandemic.\n\nConclusionOur estimates show that by the time the Hajj season commences in Saudi Arabia, the pandemic will be in the midst of its deceleration phase (phase 3). This information will likely be useful to policymakers in their management of the outbreak.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Abdullah Murhaf Al-Khani", + "author_inst": "Sulaiman Al Rajhi University" + }, + { + "author_name": "Mohamed Abdelghafour Khalifa", + "author_inst": "Sulaiman Al Rajhi University" + }, + { + "author_name": "Abdulrahman AlMazrou", + "author_inst": "Sulaiman Al Rajhi University" + }, + { + "author_name": "Nazmus Saquib", + "author_inst": "Sulaiman Al Rajhi University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.29.20113571", "rel_title": "A Time-Dependent SEIRD Model for Forecasting the COVID-19 Transmission Dynamics", @@ -1394332,61 +1396695,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.28.20115220", - "rel_title": "Direct diagnostic testing of SARS-CoV-2 without the need for prior RNA extraction.", - "rel_date": "2020-06-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.28.20115220", - "rel_abs": "The COVID-19 pandemic has resulted in an urgent global need for rapid, point-of-care diagnostic testing. Existing methods for nucleic acid amplification testing (NAAT) require an RNA extraction step prior to amplification of the viral RNA. This step necessitates the use of a centralized laboratory or complex and costly proprietary cartridges and equipment, and thereby prevents low-cost, scalable, point-of-care testing. We report the development of a highly sensitive and robust, easy-to-implement, SARS-CoV-2 test that utilizes isothermal amplification and can be run directly on viral transport media following a nasopharyngeal swab without the need for prior RNA extraction. Our assay provides visual results in 30 min with 85% sensitivity, 100% specificity, and a limit of detection (LoD) of 2.5 copies/l, and can be run using a simple heat block.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Shan Wei", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Esther Kohl", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Alexandre Djandji", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Stephanie Morgan", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Susan Whittier", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Mahesh Mansukhani", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Eldad Hod", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Mary D'Alton", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Yousin Suh", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Zev Williams", - "author_inst": "Columbia University Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.01.20119461", "rel_title": "Covid-19 testing strategies and lockdowns: the European closed curves, analysed by ``skew-normal'' distributions, the forecasts for the UK, Sweden, and the USA, and the ongoing outbreak in Brazil.", @@ -1394982,6 +1397290,57 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2020.06.02.130484", + "rel_title": "HiDRA-seq: High-Throughput SARS-CoV-2 Detection by RNA Barcoding and Amplicon Sequencing", + "rel_date": "2020-06-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.02.130484", + "rel_abs": "The recent outbreak of a new coronavirus that causes a Severe Acute Respiratory Syndrome in humans (SARS-CoV-2) has developed into a global pandemic with over 6 million reported cases and more than 375,000 deaths worldwide. Many countries have faced a shortage of diagnostic kits as well as a lack of infrastructure to perform necessary testing. Due to these limiting factors, only patients showing symptoms indicating infection were subjected to testing, whilst asymptomatic individuals, who are widely believed to be responsible for the fast dispersion of the virus, were largely omitted from the testing regimes. The inability to implement high throughput diagnostic and contact tracing strategies has forced many countries to institute lockdowns with severe economic and social consequences. The World Health Organization (WHO) has encouraged affected countries to increase testing capabilities to identify new cases, allow for a well-controlled lifting of lockdown measures, and prepare for future outbreaks. Here, we propose HiDRA-seq, a rapidly implementable, high throughput, and scalable solution that uses NGS lab infrastructure and reagents for population-scale SARS-CoV-2 testing. This method is based on the use of indexed oligo-dT primers to generate barcoded cDNA from a large number of patient samples. From this, highly multiplexed NGS libraries are prepared targeting SARS-CoV-2 specific regions and sequenced. The low amount of sequencing data required for diagnosis allows the combination of thousands of samples in a sequencing run, while reducing the cost to approximately 2 CHF/EUR/USD per RNA sample. Here, we describe in detail the first version of the protocol, which can be further improved in the future to increase its sensitivity and to identify other respiratory viruses or analyze individual genetic features associated with disease progression.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Emilio Yanguez", + "author_inst": "Functional Genomics Center Zurich (ETH/UZH)" + }, + { + "author_name": "Griffin White", + "author_inst": "Functional Genomics Center Zurich (ETH/UZH)" + }, + { + "author_name": "Susanne Kreutzer", + "author_inst": "Functional Genomics Center Zurich (ETH/UZH)" + }, + { + "author_name": "Lennart Opitz", + "author_inst": "Functional Genomics Center Zurich (ETH/UZH)" + }, + { + "author_name": "Lucy Poveda", + "author_inst": "Functional Genomics Center Zurich (ETH/UZH)" + }, + { + "author_name": "Timothy Sykes", + "author_inst": "Functional Genomics Center Zurich (ETH/UZH)" + }, + { + "author_name": "Maria Domenica Moccia", + "author_inst": "Functional Genomics Center Zurich (ETH/UZH)" + }, + { + "author_name": "Catharine Aquino", + "author_inst": "Functional Genomics Center Zurich (ETH/UZH)" + }, + { + "author_name": "Ralph Schlapbach", + "author_inst": "Functional Genomics Center Zurich (ETH/UZH)" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.06.02.129312", "rel_title": "System Dynamics Modeling Of Within-Host Viral Kinetics Of Coronavirus (SARS CoV-2)", @@ -1395798,101 +1398157,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.30.20033407", - "rel_title": "Safety of Breastfeeding in Mothers with SARS-CoV-2 Infection", - "rel_date": "2020-06-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.30.20033407", - "rel_abs": "BackgroundThe outbreak of Coronavirus Disease 2019 (COVID-19) is threatening a surging number of populations worldwide, including women in breastfeeding period. Limited evidence is available concerning breastfeeding in women with COVID-19.\n\nMethodsTwenty-three pregnant women and puerperae were enrolled in the study. To evaluate the effect of breastfeeding on SARS-CoV-2 transmission, the presence of SARS-CoV-2, IgG and IgM in breast milk, maternal blood and infant blood were assessed. Feeding patterns were also recorded in follow-up.\n\nResultsNo positive detection for SARS-CoV-2 of neonates was found. All breast milk samples were negative for the detection of SARS-CoV-2. The presence of IgM of SARS-CoV-2 in breast milk was correlated with maternal blood. The results of IgG detection for SARS-CoV-2 were negative in all breast milk samples. All the infants were in healthy condition while six of them were fed with whole or partial breast milk. Eight infants received antibody test for SARS-CoV-2 in one month after birth and the results were all negative.\n\nConclusionFindings from this small number of cases suggest that there is currently no evidence for mother-to-child transmission via breast feeding in women with COVID-19 in the third trimester and puerperium.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Qingqing Luo", - "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Lan Chen", - "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Dujuan Yao", - "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Jianwen Zhu", - "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Xiangzhi Zeng", - "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Lin Xia", - "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Min Wu", - "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Lin Lin", - "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Zhishan Jin", - "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Qingmiao Zhang", - "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Dilu Feng", - "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Shihuan Yu", - "author_inst": "2.First Affiliated Hospital, Harbin Medical University, Harbin, China" - }, - { - "author_name": "Bo Song", - "author_inst": "Forth Affiliated Hospital, Harbin Medical University, Harbin, China" - }, - { - "author_name": "Wanlin Zhang", - "author_inst": "Reproductive Center, Tangdu Hospital, Fourth Military Medical University" - }, - { - "author_name": "Hongbo Wang", - "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Yanfang Zhang", - "author_inst": "State Key Laboratory of Virology, National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China" - }, - { - "author_name": "Zhengyuan Su", - "author_inst": "State Key Laboratory of Virology, National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China" - }, - { - "author_name": "Minhua Luo", - "author_inst": "6.State Key Laboratory of Virology, Chinese Academy of Sciences Center for Excellence in Brain Science and Intelligence Technology, Wuhan Institute of Virology," - }, - { - "author_name": "Xuan Jiang", - "author_inst": "The Joint Center of Translational Precision Medicine, Guangzhou Institute of Pediatrics, Guangzhou Women and Children Medical Center, Guangzhou, China" - }, - { - "author_name": "Hui Chen", - "author_inst": "Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.29.20086645", "rel_title": "Characteristics and Outcomes of COVID-19 Patients in New York City's Public Hospital System", @@ -1396456,6 +1398720,41 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2020.05.31.124966", + "rel_title": "coronapp: a Web Application to Annotate and Monitor SARS-CoV-2 Mutations", + "rel_date": "2020-06-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.31.124966", + "rel_abs": "The avalanche of genomic data generated from the SARS-CoV-2 virus requires the development of tools to detect and monitor its mutations across the world. Here, we present a webtool, coronapp, dedicated to easily processing user-provided SARS-CoV-2 genomic sequences and visualizing current worldwide status of SARS-CoV-2 mutations.\n\nThe webtool allows users to highlight mutations and categorize them by frequency, country, genomic location and effect on protein sequences, and to monitor their presence in the population over time.\n\nThe tool is available at http://giorgilab.unibo.it/coronapp/ for the worldwide dataset and at http://giorgilab.unibo.it/coronannotator/ for the annotation of user-provided sequences. The full code is freely shared at https://github.com/federicogiorgi/giorgilab/tree/master/coronapp\n\nData Availability StatementThe data that support the findings of this study derive from the GISAID consortium and are openly available in Github, in Rdata format for the R environment, in files results.rda and metadata.rda, at the following link: https://github.com/federicogiorgi/giorgilab/tree/master/coronapp/data", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Daniele Mercatelli", + "author_inst": "Department of Pharmacy and Biotechnology, University of Bologna" + }, + { + "author_name": "Luca Triboli", + "author_inst": "Department of Pharmacy and Biotechnology, University of Bologna" + }, + { + "author_name": "Eleonora Fornasari", + "author_inst": "Department of Pharmacy and Biotechnology, University of Bologna" + }, + { + "author_name": "Forest Ray", + "author_inst": "Department of Systems Biology, Columbia University Medical Center, New York City, 10032, United States" + }, + { + "author_name": "Federico M Giorgi", + "author_inst": "University of Bologna" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.05.31.126524", "rel_title": "A Scalable Topical Vectored Vaccine Candidate Against SARS-CoV-2", @@ -1397291,41 +1399590,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.28.20115642", - "rel_title": "Spread of COVID-19 through Georgia, USA. Near-term projections and impacts of social distancing via a metapopulation model", - "rel_date": "2020-05-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.28.20115642", - "rel_abs": "Epidemiological forecasts of COVID-19 spread at the country and/or state level have helped shape public health interventions. However, such models leave a scale-gap between the spatial resolution of actionable information (i.e. the county or city level) and that of modeled viral spread. States and nations are not spatially homogeneous and different areas may vary in disease risk and severity. For example, COVID-19 has age-stratified risk. Similarly, ICU units, PPE and other vital equipment are not equally distributed within states. Here, we implement a county-level epidemiological framework to assess and forecast COVID-19 spread through Georgia, where 1,933 people have died from COVID-19 and 44,638 cases have been documented as of May 27, 2020. We find that county-level forecasts trained on heterogeneity due to clustered events can continue to predict epidemic spread over multiweek periods, potentially serving efforts to prepare medical resources, manage supply chains, and develop targeted public health interventions. We find that the premature removal of physical (social) distancing could lead to rapid increases in cases or the emergence of sustained plateaus of elevated fatalities.\n\nHighlightsO_LIContact heterogeneity and age-structured risk is represented in a metapopulation model.\nC_LIO_LIThe metapopulation model can be used in the near-term to make joint predictions on cases, hospitalizations, and fatalities at county levels.\nC_LIO_LIIn Georgia, a long-term plateauing epidemic, rather than a distinctive epidemic peak, is possible.\nC_LI", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Stephen J Beckett", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Marian Dominguez-Mirazo", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Seolha Lee", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Clio Andris", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Joshua S Weitz", - "author_inst": "Georgia Institute of Technology" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.28.20115626", "rel_title": "Investigating spatiotemporal patterns of the COVID-19 in Sao Paulo State, Brazil", @@ -1398021,6 +1400285,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.28.20115659", + "rel_title": "Future scenarios for the SARS-CoV-2 epidemic in Switzerland: an age-structured model", + "rel_date": "2020-05-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.28.20115659", + "rel_abs": "The recent lifting of COVID-19 related restrictions in Switzerland causes uncertainty about the future of the epidemic. We developed a compartmental model for SARS-CoV-2 transmission in Switzerland and projected the course of the epidemic until the end of year 2020 under various scenarios. The model was age-structured with three categories, children (0-17), adults (18-64) and seniors (65- years). Lifting all restrictions according to the plans disclosed by the Swiss federal authorities by mid-May resulted in a rapid rebound in the epidemic, with the peak expected in July. Measures equivalent to at least 90% reduction in all contacts were able to eradicate the epidemic; 56% reduction in contacts could keep the intensive care unit occupancy under the critical level, and delay the next wave until October. Scenarios where strong contact reductions were only applied in selected age groups could not suppress the epidemic, increasing the risk of a next wave in July, and another stronger wave in September. Future interventions need to cover all age groups to keep the SARS-CoV-2 epidemic under control.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Janne Estill", + "author_inst": "University of Geneva" + }, + { + "author_name": "Plamenna Venkova-Marchevska", + "author_inst": "University of Geneva" + }, + { + "author_name": "Maroussia Roelens", + "author_inst": "University of Geneva" + }, + { + "author_name": "Erol Orel", + "author_inst": "University of Geneva" + }, + { + "author_name": "Alexander Temerev", + "author_inst": "University of Geneva" + }, + { + "author_name": "Antoine Flahault", + "author_inst": "University of Geneva" + }, + { + "author_name": "Olivia Keiser", + "author_inst": "University of Geneva" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.28.20115667", "rel_title": "Targeted Immunosuppression Distinguishes COVID-19 from Influenza in Moderate and Severe Disease", @@ -1399073,49 +1401380,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.28.20116087", - "rel_title": "Association of Poor Housing Conditions with COVID-19 Incidence and Mortality Across US Counties", - "rel_date": "2020-05-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.28.20116087", - "rel_abs": "ObjectivePoor housing conditions have been linked with worse health outcomes and infectious spread in communities but its relationship with incidence and mortality of COVID-19 is unknown. Therefore, we undertook this study to determine the association between poor housing condition and COVID-19 incidence and mortality in US counties.\n\nMethodsWe conducted cross-sectional analysis of county-level data from the US Centers for Disease Control, US Census Bureau and John Hopkins Coronavirus Resource Center for 3141 US counties. The exposure of interest was percentage of households with poor housing conditions (one or more of: overcrowding, high housing cost, incomplete kitchen facilities, or incomplete plumbing facilities). Outcomes were incidence rate ratios (IRR) and mortality rate ratios (MRR) of COVID-19 across US counties through 4/21/2020. Multilevel generalized linear modeling was utilized with adjustment for population density and county characteristics including demographics, income, education, prevalence of medical comorbidities, access to healthcare insurance and emergency rooms, and state-level COVID-19 test density.\n\nResultsAcross 3135 US counties, the mean percentage of households with poor housing conditions was 14.2% (range 2.7% to 60.2%). The mean (SD) incidence and mortality of COVID-19 were 255.68 (2877.03) cases and 13.90 (272.22) deaths per county, respectively. In the fully adjusted models, with each 5% increase in percent households with poor housing conditions, there was a 50% higher risk of COVID-19 incidence (IRR 1.50, 95% CI: 1.38 - 1.62) and a 42% higher risk of COVID-19 mortality (MRR 1.42, 95% CI: 1.25 - 1.61). Results remained similar using earlier timepoints (3/31/2020 and 4/10/2020).\n\nConclusions and RelevanceCounties with a higher percentage of households with poor housing had higher incidence of, and mortality associated with, COVID-19. These findings suggest targeted health policies to support individuals living in poor housing conditions should be considered in further efforts to mitigate adverse outcomes associated with COVID-19.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Khansa Ahmad", - "author_inst": "Brown University" - }, - { - "author_name": "Sebhat Erqou", - "author_inst": "Brown University" - }, - { - "author_name": "Nishant Shah", - "author_inst": "Brown University" - }, - { - "author_name": "Umair Nazir", - "author_inst": "Brown University" - }, - { - "author_name": "Alan Morrison", - "author_inst": "Brown University" - }, - { - "author_name": "Gaurav Choudhary", - "author_inst": "Brown University" - }, - { - "author_name": "Wen-Chih Wu", - "author_inst": "Brown University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.28.20116129", "rel_title": "The effectiveness and perceived burden of nonpharmaceutical interventions against COVID-19 transmission: a modelling study with 41 countries", @@ -1399663,6 +1401927,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.29.20116426", + "rel_title": "SARS-CoV-2 PCR and antibody testing for an entire rural community: methods and feasibility of high-throughput testing procedures", + "rel_date": "2020-05-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.29.20116426", + "rel_abs": "High-volume, community-wide ascertainment of SARS-CoV-2 prevalence by PCR and antibody testing was successfully performed using a community-led, drive-through model with strong operational support, well-trained testing units, and an effective technical platform", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Ayesha Appa", + "author_inst": "University of California San Francisco; Zuckerberg San Francisco General Hospital" + }, + { + "author_name": "Gabriel Chamie", + "author_inst": "University of California San Francisco; Zuckerberg San Francisco General Hospital" + }, + { + "author_name": "Aenor Sawyer", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Kimberly Baltzell", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Kathryn Dippel", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Salu Ribeiro", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Elias Duarte", + "author_inst": "University of California San Francisco; Zuckerberg San Francisco General Hospital" + }, + { + "author_name": "Joanna Vinden", + "author_inst": "University of California San Francisco; Zuckerberg San Francisco General Hospital" + }, + { + "author_name": "CLIAHUB Consortium", + "author_inst": "Chan Zuckerberg Biohub; University of California San Francisco" + }, + { + "author_name": "Jonathan Kramer-Feldman", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Shahryar Rahdari", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Doug MacIntosh", + "author_inst": "San Francisco State University" + }, + { + "author_name": "Katherine Nicholson", + "author_inst": "San Francisco State University" + }, + { + "author_name": "Jonathan Im", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Diane Havlir", + "author_inst": "University of California San Francisco; Zuckerberg San Francisco General Hospital" + }, + { + "author_name": "Bryan Greenhouse", + "author_inst": "University of California San Francisco; Zuckerberg San Francisco General Hospital" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.29.20117176", "rel_title": "Investigation of subsequent and co-infections associated with SARS-CoV-2 (COVID-19) in hospitalized patients", @@ -1400383,33 +1402726,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, - { - "rel_doi": "10.1101/2020.05.27.20115139", - "rel_title": "Causal Impact of Masks, Policies, Behavior on Early Covid-19 Pandemic in the U.S.", - "rel_date": "2020-05-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.27.20115139", - "rel_abs": "The paper evaluates the dynamic impact of various policies adopted by US states on the growth rates of confirmed Covid-19 cases and deaths as well as social distancing behavior measured by Google Mobility Reports, where we take into consideration peoples voluntarily behavioral response to new information of transmission risks in a causal structural model framework. Our analysis finds that both policies and information on transmission risks are important determinants of Covid-19 cases and deaths and shows that a change in policies explains a large fraction of observed changes in social distancing behavior. Our main counterfactual experiments suggest that nationally mandating face masks for employees early in the pandemic could have reduced the weekly growth rate of cases and deaths by more than 10 percentage points in late April and could have led to as much as 19 to 47 percent less deaths nationally by the end of May, which roughly translates into 19 to 47 thousand saved lives. We also find that, without stay-at-home orders, cases would have been larger by 6 to 63 percent and without business closures, cases would have been larger by 17 to 78 percent. We find considerable uncertainty over the effects of school closures due to lack of cross-sectional variation; we could not robustly rule out either large or small effects. Overall, substantial declines in growth rates are attributable to private behavioral response, but policies played an important role as well. We also carry out sensitivity analyses to find neighborhoods of the models under which the results hold robustly: the results on mask policies appear to be much more robust than the results on business closures and stay-at-home orders. Finally, we stress that our study is observational and therefore should be interpreted with great caution. From a completely agnostic point of view, our findings uncover predictive effects (association) of observed policies and behavioral changes on future health outcomes, controlling for informational and other confounding variables.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Victor Chernozhukov", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Hiroyuki Kasahara", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Paul Schrimpf", - "author_inst": "University of British Columbia" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2020.05.27.20115329", "rel_title": "Did the National lockdown lock COVID-19 down in India, and reduce pressure on health infrastructure?", @@ -1400965,6 +1403281,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.27.20114744", + "rel_title": "Factors affecting healthcare workers' compliance with social and behavioural infection control measures during emerging infectious disease outbreaks: Rapid evidence review.", + "rel_date": "2020-05-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.27.20114744", + "rel_abs": "The 2019-2020 outbreak of novel coronavirus has raised concerns about nosocomial transmission; that is, transmission within healthcare settings. Research from previous outbreaks of emerging infectious diseases suggests a major cause of nosocomial transmission is healthcare professionals poor compliance with recommended personal protective behaviours. This rapid evidence review explored existing literature on emerging infectious disease outbreaks to identify factors associated with compliance with social and behavioural infection control measures among healthcare staff. 56 papers were reviewed and several positive associations were found: Staff working in emergency or intensive care settings appeared more likely to comply with recommendations than those in other settings, and there was some evidence that contact with confirmed cases could improve compliance. There was some evidence that staff with higher levels of anxiety and higher concern about the risk of infection were more likely to comply with recommended behaviour, and that monitoring from superiors could improve compliance. Several negative associations were also found. Observed non-compliance of colleagues could hinder compliance. Staff identified many barriers to compliance related to personal protective equipment, including availability; perceived difficulty and effectiveness; inconvenience; discomfort; and a negative impact on patient care. There appeared to be many issues regarding the communication and ease of understanding of infection control guidance. Based on the results of this review we recommend provision of training and education tailored for different occupational roles within the healthcare setting; managerial staff leading by example; ensuring adequate resources for infection control; and timely provision of practical evidence-based infection control guidelines.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Samantha K Brooks", + "author_inst": "King's College London" + }, + { + "author_name": "Neil Greenberg", + "author_inst": "King's College London" + }, + { + "author_name": "Simon Wessely", + "author_inst": "King's College London" + }, + { + "author_name": "G James Rubin", + "author_inst": "King's College London" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.27.20114272", "rel_title": "How did governmental interventions affect the spread of COVID-19 in European countries?", @@ -1401525,77 +1403872,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.27.20114322", - "rel_title": "Study protocol for COvid-19 Vascular sERvice (COVER) study: The impact of the COVID-19 pandemic on the provision, practice and outcomes of vascular surgery", - "rel_date": "2020-05-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.27.20114322", - "rel_abs": "BackgroundThe novel Coronavirus Disease 2019 (COVID-19) pandemic is having a profound impact on global healthcare. Shortages in staff, operating theatre space and intensive care beds has led to a significant reduction in the provision of surgical care. Even vascular surgery, often insulated from resource scarcity due to its status as an urgent specialty, has limited capacity due to the pandemic. Furthermore, many vascular surgical patients are elderly with multiple comorbidities putting them at increased risk of COVID-19 and its complications. There is an urgent need to investigate the impact on patients presenting to vascular surgeons during the COVID-19 pandemic.\n\nMethods and AnalysisThe COvid-19 Vascular sERvice (COVER) study has been designed to investigate the worldwide impact of the COVID-19 pandemic on vascular surgery, at both service provision and individual patient level. COVER is running as a collaborative study through the Vascular and Endovascular Research Network (VERN) with the support of numerous national (Vascular Society of Great Britain and Ireland, British Society of Endovascular Therapy, British Society of Interventional Radiology, Rouleaux Club) and an evolving number of international organisations (Vascupedia, SingVasc, Audible Bleeding (USA), Australian and New Zealand Vascular Trials Network (ANZVTN)). The study has 3 Tiers: Tier 1 is a survey of vascular surgeons to capture longitudinal changes to the provision of vascular services within their hospital; Tier 2 captures data on vascular and endovascular procedures performed during the pandemic; and Tier 3 will capture any deviations to patient management strategies from prepandemic best practice. Data submission and collection will be electronic using online survey tools (Tier 1: SurveyMonkey(R) for service provision data) and encrypted data capture forms (Tiers 2 and 3: REDCap(R) for patient level data). Tier 1 data will undergo real-time serial analysis to determine longitudinal changes in practice, with country-specific analyses also performed. The analysis of Tier 2 and Tier 3 data will occur on completion of the study as per the prespecified statistical analysis plan.\n\nEthical ApprovalEthical approval from the UK Health Research Authority has been obtained for Tiers 2 and 3 (20/NW/0196 Liverpool Central). Participating centres in the UK will be required to seek local research and development approval. Non-UK centres will need to obtain a research ethics committee or institutional review board approvals in accordance with national and/or local requirements.\n\nISRCTN: 80453162 (https://doi.org/10.1186/ISRCTN80453162)\n\nEthical Approval: 20/NW/0196 Liverpool Central, IRAS: 282224", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "- Vascular and Endovascular Research Network", - "author_inst": "" - }, - { - "author_name": "Ruth A Benson", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Dave C Bosanquet", - "author_inst": "Royal Gwent Hospital, Wales" - }, - { - "author_name": "Sandip Nandhra", - "author_inst": "Newcastle University Northern Vascular Centre" - }, - { - "author_name": "Joseph Shalhoub", - "author_inst": "Department of Surgery & Cancer, Imperial College London" - }, - { - "author_name": "Athanasios Saratzis", - "author_inst": "University of Leicester Department of Cardiovascular Sciences" - }, - { - "author_name": "Rachel Forsythe", - "author_inst": "Royal Infirmary, Edinburgh" - }, - { - "author_name": "Sarah Onida", - "author_inst": "Department of Surgery and Cancer, Imperial College London" - }, - { - "author_name": "George Dovell", - "author_inst": "University of Bristol" - }, - { - "author_name": "Louise Hitchman", - "author_inst": "York Medical School" - }, - { - "author_name": "Nikesh Dattani", - "author_inst": "Queen Elizabeth Hospital, Birmingham" - }, - { - "author_name": "Ryan Preece", - "author_inst": "Cheltenham General Hospital" - }, - { - "author_name": "Graeme K Ambler", - "author_inst": "University of Bristol" - }, - { - "author_name": "Christopher Imray", - "author_inst": "University Hospital Coventry and Warwickshire" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "surgery" - }, { "rel_doi": "10.1101/2020.05.27.20114827", "rel_title": "COVID-19 in Multiple Sclerosis Patients and Risk Factors for Severe Infection", @@ -1402139,6 +1404415,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.29.20116731", + "rel_title": "SARS-CoV-2 SEROPREVALENCE AMONG ALL WORKERS IN A TEACHING HOSPITAL IN SPAIN: UNMASKING THE RISK.", + "rel_date": "2020-05-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.29.20116731", + "rel_abs": "BackgroundHealth-care workers (HCW) are at increased risk for SARS-CoV-2 infection, but few studies have evaluated prevalence of antibodies against SARS-CoV-2 among them.\n\nObjectiveTo determine the seroprevalence against SARS-CoV-2 in all HCW.\n\nMethodsCross-sectional study (April 14th- 27th, 2020) of all HCW at Hospital Universitario Fundacion Alcorcon, a second level teaching hospital in Madrid, Spain. SARS-CoV-2 IgG was measured by ELISA. HCW were classified by professional category, working area, and risk for SARS-CoV-2 exposure.\n\nResultsAmong 2919 HCW, 2590 (90.5%) were evaluated. Mean age was 43.8 years (SD 11.1) and 73.9% were females. Globally, 818 (31.6%) workers were IgG positive, with no differences for age, sex or previous diseases. Among them, 48.5% did not report previous symptoms. Seropositivity was more frequent in high (33.1%) and medium (33.8%) than in low-risk areas (25.8%, p = 0.007), but no difference was found for hospitalization areas attending COVID-19 and non-COVID-19 patients (35.5 vs 38.3% p = NS). HCW with a previous SARS-CoV2 PCR positive test were IgG seropositive in 90.8%. By multivariate logistic regression analysis, seropositivity was associated with being physicians (OR 2.37, CI95% 1.61-3.49), nurses (OR 1.67, CI95% 1.14-2.46), or nurse- assistants (OR 1.84, CI95% 1.24-2.73), HCW working at COVID-19 hospitalization areas (OR 1.71, CI95% 1.22-2.40), non-COVID-19 hospitalization areas (OR 1.88, CI95% 1.30-2.73), and at the Emergency Room (OR 1.51, CI95% 1.01-2.27)\n\nConclusionsSeroprevalence uncovered a high rate of infection previously unnoticed among HCW. Patients not suspected of having COVID-19 as well as asymptomatic HCW may be a relevant source for nosocomial SARS-CoV-2 transmission.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Isabel Galan", + "author_inst": "Hospital Universitario Fundacion Alcorcon" + }, + { + "author_name": "Maria Velasco", + "author_inst": "Hospital Universitario Fundacion Alcorcon" + }, + { + "author_name": "M Luisa Casas", + "author_inst": "Hospital Universitario Fundacion Alcorcon" + }, + { + "author_name": "M Jose Goyanes", + "author_inst": "Hospital Universitario Fundacion Alcorcon" + }, + { + "author_name": "Gil Rodriguez-Caravaca", + "author_inst": "Hospital Universitario Fundacion Alcorcon" + }, + { + "author_name": "Juan E Losa", + "author_inst": "Hospital Universitario Fundacion Alcorcon" + }, + { + "author_name": "Carmen Noguera", + "author_inst": "Hospital Universitario Fundacion Alcorcon" + }, + { + "author_name": "Virgilio Castilla", + "author_inst": "Hospital Universitario Fundacion Alcorcon" + }, + { + "author_name": "- Working Group Alcorcon COVID-19 investigators", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.29.20116723", "rel_title": "A simple Stochastic model for the SARS-CoV-2 Epidemic curve", @@ -1402879,29 +1405206,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.26.20114140", - "rel_title": "Mental health outcomes and associations during the coronavirus disease 2019 pandemic: A cross-sectional survey of the US general population", - "rel_date": "2020-05-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.26.20114140", - "rel_abs": "Pandemic coronavirus disease 2019 (COVID-19) may lead to significant mental health stresses, potentially with modifiable risk factors. To determine the presence of and magnitude of associations between baseline associations and anxiety and depression in the US general population, we performed an internet-based cross-sectional survey of an age-, sex-, and race-stratified representative sample from the US general population. Degrees of anxiety, depression, and loneliness were assessed using the 7-item Generalized Anxiety Disorder scale (GAD-7), the 9-item Patient Health Questionnaire (PHQ-9), and the 8-item UCLA Loneliness Scale, respectively. Unadjusted and multivariable logistic regression analyses were performed to determine associations with baseline demographic characteristics. A total of 1,005 finished surveys were returned of the 1,020 started, yielding a completion rate of 98.5% in the survey panel. The mean (SD) age of respondents was 45 (16), and 494 (48.8%) were male. Baseline demographic data were similar between those that were (n=663, 66.2%) and were not (n=339, 33.8%) under a shelter in place/ stay at home order, with the exception of sex and geographic location. Overall, 264 subjects (26.8%) met criteria for an anxiety disorder based on a GAD-7 cutoff of 10; a cutoff of 7 yielded 416 subjects (41.4%) meeting clinical criteria for anxiety. On multivariable analysis, male sex (OR 0.65, 95% CI [0.49, 0.87]) and living in a larger home (OR 0.46, 95% CI [0.24, 0.88]) were associated with a decreased odds of meeting anxiety criteria. Rural location (OR 1.39, 95% CI [1.03, 1.89]), loneliness (OR 4.92, 95% CI [3.18, 7.62]), and history of hospitalization (OR 2.04, 95% CI [1.38, 3.03]), were associated with increased odds of meeting anxiety criteria. 232 subjects (23.6%) met criteria for clinical depression. On multivariable analysis, male sex (OR 0.71, 95% CI [0.53, 0.95]), increased time outdoors (OR 0.51, 95% CI [0.29, 0.92]), and living in a larger home (OR 0.35, 95% CI [0.18, 0.69]), were associated with decreased odds of meeting depression criteria. Having lost a job (OR 1.64, 95% CI [1.05, 2.54]), loneliness (OR 10.42, 95% CI [6.26, 17.36]), and history of hospitalization (OR 2.42, 95% CI [1.62, 3.62]), were associated with an increased odds of meeting depression criteria. Income, media consumption, and religiosity were not associated with mental health outcomes. Anxiety and depression are common in the US general population in the context of the COVID-19 pandemic, and are associated with potentially modifiable factors.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Bella Nichole Kantor", - "author_inst": "Harvard University" - }, - { - "author_name": "Jonathan Kantor", - "author_inst": "University of Pennsylvania Perelman School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.26.20114082", "rel_title": "High Resolution CHEST CT(HRCT) Evaluation in Patients Hospitalized with COVID-19 Infection", @@ -1403501,6 +1405805,33 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2020.05.27.120105", + "rel_title": "Analysis of Rapidly Emerging Variants in Structured Regions of the SARS-CoV-2 Genome", + "rel_date": "2020-05-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.27.120105", + "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has motivated a widespread effort to understand its epidemiology and pathogenic mechanisms. Modern high-throughput sequencing technology has led to the deposition of vast numbers of SARS-CoV-2 genome sequences in curated repositories, which have been useful in mapping the spread of the virus around the globe. They also provide a unique opportunity to observe virus evolution in real time. Here, we evaluate two cohorts of SARS-CoV-2 genomic sequences to identify rapidly emerging variants within structured cis-regulatory elements of the SARS-CoV-2 genome. Overall, twenty variants are present at a minor allele frequency of at least 0.5%. Several enhance the stability of Stem Loop 1 in the 5UTR, including a set of co-occurring variants that extend its length. One appears to modulate the stability of the frameshifting pseudoknot between ORF1a and ORF1b, and another perturbs a bi-stable molecular switch in the 3UTR. Finally, five variants destabilize structured elements within the 3UTR hypervariable region, including the S2M stem loop, raising questions as to the functional relevance of these structures in viral replication. Two of the most abundant variants appear to be caused by RNA editing, suggesting host-viral defense contributes to SARS-CoV-2 genome heterogeneity. This analysis has implications for the development of therapeutics that target viral cis-regulatory RNA structures or sequences, as rapidly emerging variations in these regions could lead to drug resistance.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Sean P. Ryder", + "author_inst": "University of Massachusetts Medical School" + }, + { + "author_name": "Brittany R Morgan", + "author_inst": "University of Massachusetts Medical School" + }, + { + "author_name": "Francesca Massi", + "author_inst": "University of Massachusetts Medical School" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.05.28.122143", "rel_title": "Phylogenetic clustering of the Indian SARS-CoV-2 genomes reveals the presence of distinct clades of viral haplotypes among states", @@ -1404409,25 +1406740,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.25.20112532", - "rel_title": "Six Scenarios for non-medical interventions in the SARS-CoV-2 epidemic", - "rel_date": "2020-05-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.25.20112532", - "rel_abs": "We investigate six scenarios spanning main parts of the decision space of non-medical interventions against the CoV-2 epidemic in Germany. Based on the notion of interventions-lifting we classify and evaluate the scenarios by five attributes (indicators): amount of interventions-lifting, death numbers, Public Health Care capacity, population immunity, peak dates of infections. For quantitative reasoning we use a simulated modified SEIR-model calibrated with actual data. We identify margins for intervention-liftings wrt. 13.05.2020 and discuss the relation to the effective reproduction number with a 6d-generation time. We show that, in order to constrain death numbers comparable to a strong Influenza epidemic, there is only a small corridor of 16% of possible liftings, with an additional 4% margin contributed by automated contact tracing. We show also that there is a much broader corridor of 50%+18%, though not overloading critical Public Health Care capacity, implying high death numbers.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Peter Kempf", - "author_inst": "None" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.26.20113340", "rel_title": "To isolate, or not to isolate: a theoretical framework for disease control via contact tracing", @@ -1404943,6 +1407255,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.27.118893", + "rel_title": "Mouse model of SARS-CoV-2 reveals inflammatory role of type I interferon signaling", + "rel_date": "2020-05-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.27.118893", + "rel_abs": "Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-Cov-2) has caused over 5,000,000 cases of Coronavirus disease (COVID-19) with significant fatality rate.1-3 Due to the urgency of this global pandemic, numerous therapeutic and vaccine trials have begun without customary safety and efficacy studies.4 Laboratory mice have been the stalwart of these types of studies; however, they do not support infection by SARS-CoV-2 due to the inability of its spike (S) protein to engage the mouse ortholog of its human entry receptor angiotensin-converting enzyme 2 (hACE2). While hACE2 transgenic mice support infection and pathogenesis,5 these mice are currently limited in availability and are restricted to a single genetic background. Here we report the development of a mouse model of SARS-CoV-2 based on adeno associated virus (AAV)-mediated expression of hACE2. These mice support viral replication and antibody production and exhibit pathologic findings found in COVID-19 patients as well as non-human primate models. Moreover, we show that type I interferons are unable to control SARS-CoV2 replication and drive pathologic responses. Thus, the hACE2-AAV mouse model enables rapid deployment for in-depth analysis following robust SARS-CoV-2 infection with authentic patient-derived virus in mice of diverse genetic backgrounds. This represents a much-needed platform for rapidly testing prophylactic and therapeutic strategies to combat COVID-19.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Benjamin Goldman-Israelow", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Eric Song", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Tianyang Mao", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Peiwen Lu", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Amit Meir", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Feimei Liu", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Mia Madel Alfajaro", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Jin Wei", + "author_inst": "Yale University" + }, + { + "author_name": "Huiping Dong", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Robert Homer", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Aaron Ring", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Craig B Wilen", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Akiko Iwasaki", + "author_inst": "Yale University School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.05.26.117549", "rel_title": "Development and validation of IMMUNO-COV: a high-throughput clinical assay for detecting antibodies that neutralize SARS-CoV-2", @@ -1405855,69 +1408234,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.26.20113480", - "rel_title": "Frailty and mortality in hospitalized older adults with COVID-19: retrospective observational study", - "rel_date": "2020-05-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.26.20113480", - "rel_abs": "BackgroundOlder adults with coronavirus disease 2019 (COVID-19) face an increased risk of adverse health outcomes including mortality. Ethical guidelines consider allocation of limited resources based on likelihood of survival, frilty, co-morbidities and age. However, the association of frailty with clinical outcomes in older COVID-19 patients remains unclear.\n\nObjectivesTo determine the association between frailty and short-term mortality in older adults hospitalized for COVID-19.\n\nDesignRetrospective single-center observational study.\n\nSetting and participantsN = 81 patients with COVID-19 confirmed by reverse-transcriptase polymerase chain reaction (RT-PCR), at the Geriatrics department of Imelda general hospital, Belgium.\n\nMeasurementsFrailty was graded according to the Rockwood Clinical Frailty Scale (CFS). Demographic, biochemical and radiological variables, co-morbidities, symptoms and treatment were extracted from electronic medical records.\n\nResultsParticipants (N = 48 women, 59%) had a median age of 85 years (range 65-97 years), median CFS score of 7 (range 2 - 9), and 42 (52%) were long-term care residents. Within six weeks, eighteen patients died. Mortality was significantly but weakly associated with age (Spearman r = 0.241, P = 0.03) and CFS score (r = 0.282, P = 0.011), baseline lactate dehydrogenase (LDH) (r = 0.301, P = 0.009), lymphocyte count (r = -0.262, P = 0.02) and RT-PCR Ct value (r = -0.285, P = 0.015). Mortality was not associated with long-term care residence, dementia, delirium or polypharmacy. In multivariable logistic regression analyses, CFS, LDH and RT-PCR Ct values (but not age) remained independently associated with mortality. Both age and frailty had poor specificity to predict survival. A multivariable model combining age, CFS, LDH and viral load significantly predicted survival.\n\nConclusions and implicationsAlthough their prognosis is worse, even the oldest and most severely frail patients may benefit from hospitalization for COVID-19, if sufficient resources are available.\n\nBRIEF SUMMARYOutcomes of frail older adults hospitalized for COVID-19, particularly long-term care residents, remain unclear. In this retrospective cohort, frailty predicted mortality independently of age or established biomarkers.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Robert De Smet", - "author_inst": "Imelda Hospital, Bonheiden, Belgium" - }, - { - "author_name": "Bea Mellaerts", - "author_inst": "Imelda Hospital, Bonheiden, Belgium" - }, - { - "author_name": "Hannelore Vandewinckele", - "author_inst": "Imelda Hospital, Bonheiden, Belgium" - }, - { - "author_name": "Peter Lybeert", - "author_inst": "Imelda Hospital, Bonheiden, Belgium" - }, - { - "author_name": "Eric Frans", - "author_inst": "Imelda Hospital, Bonheiden, Belgium" - }, - { - "author_name": "Sara Ombelet", - "author_inst": "Imelda Hospital, Bonheiden, Belgium" - }, - { - "author_name": "Wim Lemahieu", - "author_inst": "Imelda Hospital, Bonheiden, Belgium" - }, - { - "author_name": "Rolf Symons", - "author_inst": "Imelda Hospital, Bonheiden, Belgium" - }, - { - "author_name": "Erwin Ho", - "author_inst": "Imelda Hospital, Bonheiden, Belgium" - }, - { - "author_name": "Johan Frans", - "author_inst": "Imelda Hospital, Bonheiden, Belgium" - }, - { - "author_name": "Annick Smismans", - "author_inst": "Imelda Hospital, Bonheiden, Belgium" - }, - { - "author_name": "Michael R Laurent", - "author_inst": "Imelda Hospital, Bonheiden, Belgium" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "geriatric medicine" - }, { "rel_doi": "10.1101/2020.05.25.20112664", "rel_title": "For-profit nursing homes and the risk of COVID-19 outbreaks and resident deaths in Ontario, Canada", @@ -1406685,6 +1409001,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.25.20105213", + "rel_title": "Evaluating the burden of COVID-19 on hospital resources in Bahia, Brazil: A modelling-based analysis of 14.8 million individuals", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.25.20105213", + "rel_abs": "Here we present a general compartment model with a time-varying transmission rate to describe the dynamics of the COVID-19 epidemic, parameterized with the demographics of Bahia, a state in northeast Brazil. The dynamics of the model are influenced by the number of asymptomatic cases, hospitalization requirements and mortality due to the disease. A locally-informed model was determined using actual hospitalization records. Together with cases and casualty data, optimized estimates for model parameters were obtained within a metaheuristic framework based on Particle Swarm Optimization. Our strategy is supported by a statistical sensitivity analysis on the model parameters, adequate to properly account for the simulated scenarios. First, we evaluated the effect of previously enforced interventions on the transmission rate. Then, we studied its effects on the number of deaths as well as hospitalization requirements, considering the state as a whole. Special attention is given to the impact of asymptomatic individuals on the dynamic of COVID-19 transmission, as these were estimated to contribute to a 68% increase in the basic reproductive number. Finally, we delineated scenarios that can set guides to protect the health care system, particularly by keeping demand below total bed occupancy. Our results underscore the challenges related to maintaining a fully capable health infrastructure during the ongoing COVID-19 pandemic, specially in a low-resource setting such as the one focused in this work. The evidences produced by our modelling-based analysis show that decreasing the transmission rate is paramount to success in maintaining health resources availability, but that current local efforts, leading to a 38% decrease in the transmission rate, are still insufficient to prevent its collapse at peak demand. Carefully planned and timely applied interventions, that result in stark decreases in transmission rate, were found to be the most effective in preventing hospital bed shortages for the longest periods.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Juliane Fonseca Oliveira", + "author_inst": "Center of Data and Knowledge Integration for Health, Instituto Goncalo Moniz, Fundacao Oswaldo Cruz" + }, + { + "author_name": "Daniel C. P. Jorge", + "author_inst": "Instituto de Fisica, Universidade Federal da Bahia, Salvador, Bahia, Brazi" + }, + { + "author_name": "Rafael V. Veiga", + "author_inst": "enter of Data and Knowledge Integration for Health (CIDACS), Instituto Goncalo Moniz, Fundacao Oswaldo Cruz, Salvador, Bahia, Brazil" + }, + { + "author_name": "Moreno S. Rodrigues", + "author_inst": "Fundacao Oswaldo Cruz, Porto Velho, Rondonia, Brazil" + }, + { + "author_name": "Matheus F. Torquato", + "author_inst": "College of Engineering, Swansea University, Swansea, Wales, United Kingdom" + }, + { + "author_name": "Nivea B. da Silva", + "author_inst": "Instituto de Matematica e Estatistica, Universidade Federal da Bahia, Salvador, Bahia, Brazil" + }, + { + "author_name": "Rosemeire L. Fiaconne", + "author_inst": "Instituto de Matematica e Estatistica, Universidade Federal da Bahia, Salvador, Bahia, Brazil" + }, + { + "author_name": "Caio P. Castro", + "author_inst": "Instituto de Fisica, Universidade Federal da Bahia, Salvador, Bahia, Brazi" + }, + { + "author_name": "Aureliano S. S. Paiva", + "author_inst": "Center of Data and Knowledge Integration for Health (CIDACS), Instituto Goncalo Moniz, Fundacao Oswaldo Cruz, Salvador, Bahia, Brazil" + }, + { + "author_name": "Luciana L. Cardim", + "author_inst": "Center of Data and Knowledge Integration for Health (CIDACS), Instituto Goncalo Moniz, Fundacao Oswaldo Cruz, Salvador, Bahia, Brazil" + }, + { + "author_name": "Alan A. S. Amad", + "author_inst": "College of Engineering, Swansea University, Swansea, Wales, United Kingdom" + }, + { + "author_name": "Ernesto A. B. F. Lima", + "author_inst": "Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, Texas, United States of America" + }, + { + "author_name": "Diego S. Souza", + "author_inst": "Center of Data and Knowledge Integration for Health (CIDACS), Instituto Goncalo Moniz, Fundacao Oswaldo Cruz, Salvador, Bahia, Brazil" + }, + { + "author_name": "Suani T. R. Pinho", + "author_inst": "Instituto de Fisica, Universidade Federal da Bahia, Salvador, Bahia, Brazi" + }, + { + "author_name": "Pablo I. P. Ramos", + "author_inst": "Center of Data and Knowledge Integration for Health (CIDACS), Instituto Goncalo Moniz, Fundacao Oswaldo Cruz, Salvador, Bahia, Brazil" + }, + { + "author_name": "Roberto F. S. Andrade", + "author_inst": "Center of Data and Knowledge Integration for Health (CIDACS), Instituto Goncalo Moniz, Fundacao Oswaldo Cruz, Salvador, Bahia, Brazil" + }, + { + "author_name": "Rede CoVida Modelling Task-force", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.24.20103648", "rel_title": "Ataxia as a presenting manifestation of COVID -19: Report of a single case", @@ -1407457,29 +1409856,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.23.20105643", - "rel_title": "Is there hope for the Hajj? Using the SIR Model to Forecast COVID-19 Progression in the City of Makkah", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.23.20105643", - "rel_abs": "BackgroundThe Hajj is the largest annual gathering in the world, and it is a very important event for every Muslim. Makkah annually receives three million pilgrims who perform Hajj. Although precautionary measures have been taken in Saudi Arabia to slow down the spread of COVID-19, such as locking down the most affected cities, practicing social distancing, and applying the infection-control precautions, the number of cases has increased. The total confirmed number of cases in Makkah was 10,709 with 127 deaths as of May 16, 2020.\n\nAims of the studyForecasting the COVID-19 progression in the city of Makkah will help the policymakers decide if the Hajj will be able to operate this year. Thus, to see a clear picture of the fight against COVID-19 for the economy and healthcare industry in Saudi Arabia, specifically in Makkah, the SIR model will predict COVID-19 progression in the city of Makkah.\n\nMethodThe Susceptible, Infected, and Recovered (SIR) model has been used to track the transmission dynamics and growth among the city of Makkah. The growth index was calculated, according to the data from March 16 until May 9. The estimated vital epidemiological parameters, such as forecasting works and transmission rates, were done.\n\nResultThe data showed an interesting result about the peak of the disease progression. It is projected to occur around the 12th day after running the model. According to the model, the peak time will be around the 22nd of May. Then, the number of cases will start to decrease.\n\nConclusionUsing the SIR model, the result predicts the disease progression peak and an estimated end of COVID-19 in the city of Makkah to help the policymakers decide if the Hajj will be able to operate this year.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Alaa F Mujallad", - "author_inst": "University of Jeddah" - }, - { - "author_name": "haitham khoj", - "author_inst": "king Abdulaziz university" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.21.20106500", "rel_title": "The estimated impact of the COVID-19 epidemic in the general population of France", @@ -1408243,6 +1410619,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.19.20106336", + "rel_title": "ROBUST COVID-19-RELATED CONDITION CLASSIFICATION NETWORK", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.19.20106336", + "rel_abs": "COVID-19 can exponentially precipitate life-threatening emergencies as witnessed during the recent spreading of a novel coronavirus infection which can rapidly evolve into lung collapse and respiratory distress (among other various severe clinical conditions). Our study evaluates the performance of a tailor-designed deep convolutional network on the tasks of early detection and localization of radiological signs associated to COVID-19 on frontal chest X-rays. We also asses the frameworks capacity in differentiating the above-mentioned signs, which are usually confused with the more usual common bacterial and viral pneumonias. Open-source chest X-ray images categorized as Normal, Non-COVID-19 and COVID-19 pneumonias were downloaded from the NIH (n=2,259), RSNA (n=600) and HM Hospitales (n=2,307). Our algorithmic framework was able to precisely detect the images with COVID19-related radiological findings (mean Accuracy: 90.5%; Sensitivity: 80.6%; Specificity: 98.0%), whilst correctly categorizing images deemed as Non-COVID-19 pneumonias (mean Accuracy: 88.4%; Sensitivity: 93.3%; Specificity: 92.0%) and normal chest X-rays (mean Accuracy 92.1%; Sensitivity: 91.8%; Specificity: 94.3%). The associated results show that our AI framework is able to classify COVID-19 accurately, making of it a potential tool to improve the diagnostic performance across primary-care centres and, to grant priority to a subset of algorithmic selected images for urgent follow-on expert review. This would sensibly accelerate diagnosis in remote locations, reduce the bottleneck on specialized centres, and/or help to alleviate the needs on situations of scarcity in the availability of molecular tests.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Maximiliano Lucius", + "author_inst": "Topazium Artificial Intelligence" + }, + { + "author_name": "Martin Belvisi", + "author_inst": "Topazium Artificial Intelligence" + }, + { + "author_name": "Carlos Maria Galmarini", + "author_inst": "Topazium Artificial Intelligence" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2020.05.19.20107045", "rel_title": "Strict Physical Distancing May Be More Efficient: A Mathematical Argument for Making Lockdowns Count", @@ -1408991,57 +1411394,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.20.20107607", - "rel_title": "Chansu Injection Improves the Respiratory Function of Severe COVID-19 Patients", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.20.20107607", - "rel_abs": "Chansu and its major active constituent of bufalin have been reported to have broad-spectrum antiviral effects. This study aims to assess the efficacy of Chansu injection in treating patients with severe COVID-19. The patients diagnosed as severe or critical COVID-19 in The First Peoples Hospital of Jiangxia District, Wuhan, China from February 5 to March 5, 2020 were randomly allocated in a 1:1 ratio to receive general treatment plus Chansu injection or only general treatment as the control group. The treatment course was 7 days. The changes of PaO2/FiO2 and ROX index indicating respiratory function, the white blood cell (WBC) count, peripheral blood mononuclear lymphocyte (PBML) count, respiratory support step-down time (RSST), and safety indicators for the 7th day were retrospectively analyzed. After 7 days treatment, the oxygenation index was improved in 20 of 21 patients (95.2%) in the treatment group, as compared with 13 of 19 patients (68.4%) in the control group. The PaO2/FiO2 and ROX indices in the treatment group (mean, 226.27{+/-}67.35 and 14.01{+/-}3.99 respectively) were significantly higher than the control group (mean, 143.23{+/-}51.29 and 9.64{+/-}5.54 respectively). The RSST was 1 day shorter in the treatment group than the control group. Multivariate regression analysis suggested that Chansu injection contributed the most to the outcome of PaO2/FiO2. No obvious adverse effects were observed. Preliminary data showed that Chansu injection had apparent efficacy in treating patients with severe COVID-19.\n\nSignificance StatementPatients with severe COVID-19 usually have dyspnea and/or hypoxemia one week after the onset of symptoms, and can quickly progress to acute respiratory distress syndrome, septic shock, metabolic acidosis that is difficult to correct, coagulation dysfunction and multiple organs failure. Chansu injection, a widely used drug in clinical cancer and chronic hepatitis B therapy in China, can improve the respiratory function and shorten the respiratory support step-down time with 1 day in patients with severe COVID-19. These preliminary findings raise the possibility that Chansu injection may be helpful in the treatment of patients with severe COVID-19.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Fen Hu", - "author_inst": "The First People's Hospital of Jiangxia District, Wuhan, 430033, China" - }, - { - "author_name": "Jiao Chen", - "author_inst": "Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, China" - }, - { - "author_name": "Hao Chen", - "author_inst": "Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, China" - }, - { - "author_name": "Jin Zhu", - "author_inst": "Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, China" - }, - { - "author_name": "Chen Wang", - "author_inst": "Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, China" - }, - { - "author_name": "Haibin Ni", - "author_inst": "Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, China" - }, - { - "author_name": "Jianming Cheng", - "author_inst": "Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, China" - }, - { - "author_name": "Peng Cao", - "author_inst": "Nanjing University of Chinese Medicine" - }, - { - "author_name": "Xingxing Hu", - "author_inst": "Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, China" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.24.20111765", "rel_title": "Age, gender and COVID-19 infections", @@ -1409621,6 +1411973,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.22.20109777", + "rel_title": "A benchmark of online COVID-19 symptom checkers", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.22.20109777", + "rel_abs": "BackgroundA large number of online COVID-19 symptom checkers and chatbots have been developed but anecdotal evidence suggests that their conclusions are highly variable. To our knowledge, no study has evaluated the accuracy of COVID-19 symptom checkers in a statistically rigorous manner.\n\nMethodsIn this paper, we evaluate 10 different COVID-19 symptom checkers screening 50 COVID-19 case reports alongside 410 non-COVID-19 control cases.\n\nResultsWe find that the number of correctly assessed cases varies considerably between different symptom checkers, with Symptoma (F1=0.92, MCC=0.85) showing the overall best performance followed by Infermedica (F1=0.80, MCC=0.61).", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Nicolas Munsch", + "author_inst": "Symptoma" + }, + { + "author_name": "Alistair Martin", + "author_inst": "Symptoma" + }, + { + "author_name": "Stefanie Gruarin", + "author_inst": "Symptoma" + }, + { + "author_name": "Jama Nateqi", + "author_inst": "Symptoma" + }, + { + "author_name": "Isselmou Abdarahmane", + "author_inst": "Symptoma" + }, + { + "author_name": "Rafael Weingartner-Ortner", + "author_inst": "Symptoma" + }, + { + "author_name": "Bernhard Knapp", + "author_inst": "Symptoma" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.05.24.20111633", "rel_title": "Pitting the Gumbel and logistic growth models against one another to model COVID-19 spread", @@ -1410449,101 +1412844,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.22.20109934", - "rel_title": "Organizing Pneumonia of COVID-19: Time-dependent Evolution and Outcome in CT Findings", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.22.20109934", - "rel_abs": "ObjectiveAs a pandemic, a most-common pattern resembled organizing pneumonia (OP) has been identified by CT findings in novel coronavirus disease (COVID-19). We aimed to delineate the evolution of CT findings and outcome in OP of COVID-19.\n\nMaterials and Methods106 COVID-19 patients with OP based on CT findings were retrospectively included and categorized into non-severe (mild/common) and severe (severe/critical) groups. CT features including lobar distribution, presence of ground glass opacities (GGO), consolidation, linear opacities and total severity CT score were evaluated at three time intervals from symptom-onset to CT scan (day 0-7, day 8-14, day>14). Discharge or adverse outcome (admission to ICU or death), and pulmonary sequelae (complete absorption or lesion residuals) on CT after discharge were analyzed based on the CT features at different time interval.\n\nResults79(74.5%) patients were non-severe and 103(97.2%) were discharged at median day 25 (range, day 8-50) after symptom-onset. Of 67 patients with revisit CT at 2-4 weeks after discharge, 20(29.9%) had complete absorption of lesions at median day 38 (range, day 30-53) after symptom-onset. Significant differences between complete absorption and residuals groups were found in percentages of consolidation (1.5% vs. 13.8%, P=0.010), number of involved lobe >3 (40.0% vs. 72.5%, P=0.030), CT score >4 (20.0% vs. 65.0%, P=0.010) at day 8-14.\n\nConclusionsMost OP cases had good prognosis. Approximately one-third of cases had complete absorption of lesions during 1-2 months after symptom-onset while those with increased frequency of consolidation, number of involved lobe>3, and CT score >4 at week 2 after symptom-onset may indicate lesion residuals on CT.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Yan Wang", - "author_inst": "The First Affiliated Hospital of Xi'an Jiaotong University" - }, - { - "author_name": "Chao Jin", - "author_inst": "The First Affiliated Hospital of Xi'an Jiaotong University" - }, - { - "author_name": "Carol C. Wu", - "author_inst": "University of Texas M.D. Anderson Cancer Center" - }, - { - "author_name": "Huifang Zhao", - "author_inst": "The First Affiliated Hospital of Xi'an Jiaotong University" - }, - { - "author_name": "Ting Liang", - "author_inst": "The First Affiliated Hospital of Xi'an Jiaotong University" - }, - { - "author_name": "Zhe Liu", - "author_inst": "The First Affiliated Hospital of Xi'an Jiaotong University" - }, - { - "author_name": "Zhijie Jian", - "author_inst": "The First Affiliated Hospital of Xi'an Jiaotong University" - }, - { - "author_name": "Runqing Li", - "author_inst": "The First Affiliated Hospital of Xi'an Jiaotong University" - }, - { - "author_name": "Zekun Wang", - "author_inst": "The Eighth Hospital of Xi.an" - }, - { - "author_name": "Fen Li", - "author_inst": "The Eighth Hospital of Xi.an" - }, - { - "author_name": "Jie Zhou", - "author_inst": "Xi.an Chest Hospital" - }, - { - "author_name": "Shubao Cai", - "author_inst": "Xi.an Chest Hospital" - }, - { - "author_name": "Yang Liu", - "author_inst": "The First Affiliated Hospital of Xi.an Jiaotong University" - }, - { - "author_name": "Hao Li", - "author_inst": "The First Affiliated Hospital of Xi.an Jiaotong University" - }, - { - "author_name": "Zhongyi Li", - "author_inst": "Wuhan No.9 Hospital" - }, - { - "author_name": "Yukun Liang", - "author_inst": "Ankang Center Hospital" - }, - { - "author_name": "Heping Zhou", - "author_inst": "Ankang Center Hospital" - }, - { - "author_name": "Xibin Wang", - "author_inst": "Hanzhong Center Hospital" - }, - { - "author_name": "Zhuanqin Ren", - "author_inst": "Baoji Center Hospital" - }, - { - "author_name": "Jian Yang", - "author_inst": "The First Affiliated Hospital of Xi'an Jiaotong University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2020.05.23.20111419", "rel_title": "Visualizing the invisible: The effect of asymptomatic transmission on the outbreak dynamics of COVID-19", @@ -1411195,6 +1413495,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.24.20111971", + "rel_title": "Clinical characteristics of patients hospitalized with COVID-19 in Spain: results from the SEMI-COVID-19 Network.", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.24.20111971", + "rel_abs": "BackgroundSpain has been one of the countries most affected by the COVID-19 pandemic.\n\nObjectiveTo create a registry of patients with COVID-19 hospitalized in Spain in order to improve our knowledge of the clinical, diagnostic, therapeutic, and prognostic aspects of this disease.\n\nMethodsA multicentre retrospective cohort study, including consecutive patients hospitalized with confirmed COVID-19 throughout Spain. Epidemiological and clinical data, additional tests at admission and at seven days, treatments administered, and progress at 30 days of hospitalization were collected from electronic medical records.\n\nResultsUp to April 30th 2020, 6,424 patients from 109 hospitals were included. Their median age was 69.1 years (range: 18-102 years) and 56.9% were male. Prevalences of hypertension, dyslipidemia, and diabetes mellitus were 50.2%, 39.7%, and 18.7%, respectively. The most frequent symptoms were fever (86.2%) and cough (76.5%). High values of ferritin (72.4%), lactate dehydrogenase (70.2%), and D-dimer (61.5%), as well as lymphopenia (52.6%), were frequent. The most used antiviral drugs were hydroxychloroquine (85.7%) and lopinavir/ritonavir (62.4%). 31.5% developed respiratory distress. Overall mortality rate was 21.1%, with a marked increase with age (50-59 years: 4.2%, 60-69 years: 9.1%, 70-79 years: 21.4%, 80-89 years: 42.5%, [≥] 90 years: 51.1%).\n\nConclusionsThe SEMI-COVID-19 Network provides data on the clinical characteristics of patients with COVID-19 hospitalized in Spain. Patients with COVID-19 hospitalized in Spain are mostly severe cases, as one in three patients developed respiratory distress and one in five patients died. These findings confirm a close relationship between advanced age and mortality.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Jos\u00e9 Manuel Casas Rojo", + "author_inst": "Internal Medicine Department, Infanta Cristina University Hospital, Parla (Madrid), Spain" + }, + { + "author_name": "Juan Miguel Ant\u00f3n Santos", + "author_inst": "Internal Medicine Department, Infanta Cristina University Hospital, Parla (Madrid), Spain" + }, + { + "author_name": "Jes\u00fas Mill\u00e1n N\u00fa\u00f1ez-Cort\u00e9s", + "author_inst": "Internal Medicine Department, Gregorio Mara\u00f1\u00f3n University Hospital, Madrid, Spain" + }, + { + "author_name": "Carlos Lumbreras Bermejo", + "author_inst": "Internal Medicine Department, 12 de Octubre University Hospital, Madrid, Spain" + }, + { + "author_name": "Jos\u00e9 Manuel Ramos Rinc\u00f3n", + "author_inst": "Internal Medicine Department, General University Hospital of Alicante, Alicante Institute for Health and Biomedical Research (ISABIAL), Miguel Hern\u00e1ndez de Elch" + }, + { + "author_name": "Emilia Roy-Vallejo", + "author_inst": "Internal Medicine Department, La Princesa University Hospital, Madrid, Spain" + }, + { + "author_name": "Arturo Artero Mora", + "author_inst": "Internal Medicine Department. Dr. Peset University Hospital, Valencia. University of Valencia, Spain" + }, + { + "author_name": "Francisco Arnalich Fern\u00e1ndez", + "author_inst": "Internal Medicine Department. La Paz University Hospital, Madrid, Spain" + }, + { + "author_name": "Jos\u00e9 Miguel Garc\u00eda Bru\u00f1\u00e9n", + "author_inst": "Internal Medicine Department. Miguel Servet University Hospital, Zaragoza, Spain" + }, + { + "author_name": "Juan Antonio Vargas N\u00fa\u00f1ez", + "author_inst": "Internal Medicine Department. Puerta de Hierro University Hospital, Majadahonda (Madrid), Spain" + }, + { + "author_name": "Santiago J Freire Castro", + "author_inst": "Internal Medicine Department. A Coru\u00f1a University Hospital, A Coru\u00f1a, Spain" + }, + { + "author_name": "Luis Manzano", + "author_inst": "Internal Medicine Department. Ram\u00f3n y Cajal University Hospital. University of Alcal\u00e1, IRYCIS. Madrid, Spain" + }, + { + "author_name": "Isabel Perales Fraile", + "author_inst": "Internal Medicine Department. Infanta Sof\u00eda University Hospital, San Sebasti\u00e1n de los Reyes (Madrid), Spain" + }, + { + "author_name": "Anxela Crestelo Vieitez", + "author_inst": "Internal Medicine Department. Royo Villanova Hospital, Zaragoza, Spain" + }, + { + "author_name": "Francesc Puchades", + "author_inst": "Internal Medicine Department. Valencia General University Hospital, Valencia, Spain" + }, + { + "author_name": "Enrique Rodilla", + "author_inst": "Internal Medicine Department. Sagunto Hospital, Sagunto (Valencia), Universidad Cardenal Herrera-CEU, CEU Universities, Spain" + }, + { + "author_name": "Marta Nataya Sol\u00eds Marqu\u00ednez", + "author_inst": "Internal Medicine Department. San Agustin University Hospital, Avil\u00e9s (Asturias), Spain" + }, + { + "author_name": "David Bonet Tur", + "author_inst": "Internal Medicine Department. San Juan de Alicante University Hospital, Alicante, Spain" + }, + { + "author_name": "Mar\u00eda del Pilar Fidalgo Moreno", + "author_inst": "Internal Medicine Department. Henares University Hospital, Coslada (Madrid), Spain" + }, + { + "author_name": "Eva M Fonseca Aizpuru", + "author_inst": "Internal Medicine Department. Cabue\u00f1es University Hospital, Gij\u00f3n (Asturias), Spain" + }, + { + "author_name": "Franscisco Javier Carrasco S\u00e1nchez", + "author_inst": "Internal Medicine Department. Juan Ram\u00f3n Jim\u00e9nez University Hospital, Huelva, Spain" + }, + { + "author_name": "Elisa Rabad\u00e1n Pejenaute", + "author_inst": "Internal Medicine Department. San Pedro Hospital, Logro\u00f1o, Spain" + }, + { + "author_name": "Manuel Rubio-Rivas", + "author_inst": "Internal Medicine Department. Bellvitge University Hospital, L'Hospitalet de Llobregat (Barcelona), Spain" + }, + { + "author_name": "Jos\u00e9 David Torres Pe\u0144a", + "author_inst": "Lipids and Atherosclerosis Unit, Department of Internal Medicine, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sof&a University Hospital," + }, + { + "author_name": "Ricardo G\u00f3mez Huelgas", + "author_inst": "Internal Medicine Department, Regional University Hospital of M\u00e1laga, Biomedical Research Institute of M\u00e1laga (IBIMA), University of M\u00e1laga (UMA), M\u00e1laga, Spain" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.24.20112300", "rel_title": "COVID-19 serology at population scale: SARS-CoV-2-specific antibody responses in saliva", @@ -1412047,25 +1414462,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.23.20110908", - "rel_title": "Incubation period of COVID-19 in the live-house cluster of accurately known infection events and delay time from symptom onset of public reporting observed in cases in Osaka, Japan", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.23.20110908", - "rel_abs": "The incubation period of an infectious disease is very important for control of the disease but estimating the period is not easy because the date of infection is not easy to identify. Accurate incubation period distribution by examining cases in the cluster generated in \"live-houses\" in Osaka, Japan with known infection events is reported. The distribution of the latent period is also estimated. The modes of incubation and latent periods of COVID-19 in Japan are 4.1 days and 3.3 days, respectively. The mode of the delay time from the onset to reporting is estimated to be 4.7 days, telling that the effects of interventions show up in the number of infections two weeks later after the measures.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Toshihisa Tomie", - "author_inst": "Changchun University of Science and Technology" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.25.20112466", "rel_title": "Bayesian Network Analysis of Covid-19 data reveals higher Infection Prevalence Rates and lower Fatality Rates than widely reported", @@ -1412545,6 +1414941,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.22.20104679", + "rel_title": "COVIDTrach; the outcomes of mechanically ventilated COVID-19 patients undergoing tracheostomy in the UK: Interim Report 22nd May 2020", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.22.20104679", + "rel_abs": "COVIDTrach is a UK multidisciplinary collaborative project that aims to evaluate the outcomes of tracheostomy in COVID-19 patients. An invitation to participate in an online survey tool (REDCap) was disseminated to all UK NHS departments involved in tracheostomy in mechanically ventilated COVID-19 patients. Fifty-two percent (n=219/465) of patients who had undergone tracheostomy and were still alive, had been successfully weaned from mechanical ventilation at the point of completing the survey. The all cause in-hospital mortality following tracheostomy was 12% (n=62/530), with 3% of these (n=2/62) due to tracheostomy related complications and the remaining deaths due to COVID-19 related complications. Amongst 400 cases submitting data two weeks after the tracheostomy, no instance of COVID-19 infection amongst operators was recorded. This interim report highlights early outcomes following tracheostomy in mechanically ventilated COVID-19 patients. Future reporting from COVIDTrach will include more detailed analysis at later timepoints using comparator groups in order to provide a more comprehensive assessment of tracheostomy in COVID-19.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "COVIDTrach", + "author_inst": "" + }, + { + "author_name": "Nick JI Hamilton", + "author_inst": "University College London Hospitals NHS Foundation Trust" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.05.19.20107326", "rel_title": "The effect of multiple interventions to balance healthcare demand for controlling COVID-19 outbreaks: a modelling study", @@ -1413201,65 +1415620,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, - { - "rel_doi": "10.1101/2020.05.25.115600", - "rel_title": "Generation of human bronchial organoids for SARS-CoV-2 research", - "rel_date": "2020-05-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.25.115600", - "rel_abs": "Coronavirus disease 2019 (COVID-19) is a disease that causes fatal disorders including severe pneumonia. To develop a therapeutic drug for COVID-19, a model that can reproduce the viral life cycle and evaluate the drug efficacy of anti-viral drugs is essential. In this study, we established a method to generate human bronchial organoids (hBO) from commercially available cryopreserved human bronchial epithelial cells and examined whether they could be used as a model for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) research. Our hBO contain basal, club, ciliated, and goblet cells. Angiotensin-converting enzyme 2 (ACE2), which is a receptor for SARS-CoV-2, and transmembrane serine proteinase 2 (TMPRSS2), which is an essential serine protease for priming spike (S) protein of SARS-CoV-2, were highly expressed. After SARS-CoV-2 infection, not only the intracellular viral genome, but also progeny virus, cytotoxicity, pyknotic cells, and moderate increases of the type I interferon signal could be observed. Treatment with camostat, an inhibitor of TMPRSS2, reduced the viral copy number to 2% of the control group. Furthermore, the gene expression profile in SARS-CoV-2-infected hBO was obtained by performing RNA-seq analysis. In conclusion, we succeeded in generating hBO that can be used for SARS-CoV-2 research and COVID-19 drug discovery.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC=\"FIGDIR/small/115600v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (99K):\norg.highwire.dtl.DTLVardef@13a6908org.highwire.dtl.DTLVardef@1c59300org.highwire.dtl.DTLVardef@362167org.highwire.dtl.DTLVardef@1cb31ed_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Tatsuya Suzuki", - "author_inst": "Research Institute for Microbial Diseases, Osaka University" - }, - { - "author_name": "Yumi Ito", - "author_inst": "Research Institute for Microbial Diseases, Osaka University" - }, - { - "author_name": "Yusuke Sakai", - "author_inst": "Joint Faculty of Veterinary Medicine, Yamaguchi University" - }, - { - "author_name": "Akatsuki Saito", - "author_inst": "Faculty of Agriculture, University of Miyazaki" - }, - { - "author_name": "Daisuke Okuzaki", - "author_inst": "Osaka University Research Institute for Microbial Diseases" - }, - { - "author_name": "Daisuke Motooka", - "author_inst": "Osaka University Research Institute for Microbial Diseases" - }, - { - "author_name": "Shohei Minami", - "author_inst": "Research Institute for Microbial Diseases, Osaka University" - }, - { - "author_name": "Takeshi Kobayashi", - "author_inst": "Research Institute for Microbial Diseases, Osaka University" - }, - { - "author_name": "Takuya Yamamoto", - "author_inst": "Center for iPS Cell Research and Application (CiRA), Kyoto University" - }, - { - "author_name": "Toru Okamoto", - "author_inst": "Research Institute for Microbial Diseases, Osaka University" - }, - { - "author_name": "Kazuo Takayama", - "author_inst": "Kyoto University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2020.05.24.20111013", "rel_title": "Noninvasive respiratory support in acute hypoxemicrespiratory failure associated with COVID-19 and other viralinfections", @@ -1413939,6 +1416299,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.20.20108399", + "rel_title": "Inflammation Level Severity and Death in Patients With COVID-19: A Rapid Systematic Review and Meta-Analysis", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.20.20108399", + "rel_abs": "BackgroundAn association among the use of angiotensin-converting-enzyme(ACE) inhibitors and angiotensin-receptor blockers(ARBs) with the clinical outcomes of coronavirus disease 2019 (COVID-19) is unclear.\n\nMethodsPubMed, EMBASE, and the preprint databases MedRxiv and BioRxiv were searched for relevant studies that assessed the association among inflammation level, application of ACEI/ARB, infection severity and death in patients with COVID-19. Odd risks(OR) and 95% confidence interval (CI) were combined using random-effects or fixed models depending on heterogeneity.\n\nResultsEleven studies were included with a total of 33,483 patients. Our review showed ACEI/ARB therapy might be associated with the reduced inflammatory factor (interleukin-6) and elevated level of immune cells(CD3, CD8). Meta-analysis showed no significant increase in the risk of COVID-19 infection(OR:0.95, 95%CI:0.89-1.05) in patients receiving ACEI/ARB therapy, and ACEI/ARB therapy was associated with a decreased risk of severe COVID-19 (OR:0.75, 95%CI: 0.59-0.96) and mortality (OR:0.52, 95%CI: 0.35-0.79). Subgroup analyses showed that, among the general population, application of ACEI/ARB therapy was associated with reduced risks of all-cause death(OR:0.31, 95%CI: 0.13-0.75), and the risk of severe COVID-19(OR:0.79, 95%CI: 0.60-1.05) infection and COVID-19 infection(OR:0.85, 95% CI: 0.66-1.08) were not increased. Among patients with hypertension, the use of an ACEI/ARB was associated with a lower severity of COVID-19(OR:0.73, 95%CI: 0.51-1.03) and lower mortality(OR:0.57, 95%CI: 0.37-0.87), without evidence of an increased risk of COVID-19 infection(OR:1.00, 95%CI: 0.90-1.12).\n\nConclusionOn the basis of the available evidence, this is the first meta-analysis showed that, in general population, the use of ACEI/ARB therapy was safe without an increased risk of COVID-19 infection and with a decreasing trend of severe COVID-19 infection and lower mortality. In patients with hypertension, the use of ACEI/ARB therapy should be encouraged, without increased risk of COVID-19 inflection, and better prognosis (a decreasing trends of severe COVID-19 and reduced all-cause death). Overall, ACEI/ARB therapy should be continued in patients who are at risk for, or have COVID-19, either in general population or hypertension patients. Our results need to be interpreted with caution considering the potential for residual confounders, and more well-designed studies that control the clinical confounders are necessary to confirm our findings.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Xiao Liu", + "author_inst": "Cardiovascular Department, the Second Affiliated Hospital of Nanchang University" + }, + { + "author_name": "Chuyan Long", + "author_inst": "Cardiovascular Department, the Second Affiliated Hospital of Nanchang University" + }, + { + "author_name": "Qinmei Xiong", + "author_inst": "Cardiovascular Department, the Second Affiliated Hospital of Nanchang University" + }, + { + "author_name": "Jianyong Ma", + "author_inst": "Cardiovascular Department, the Second Affiliated Hospital of Nanchang University" + }, + { + "author_name": "Chen Chen", + "author_inst": "Cardiovascular Department, the Second Affiliated Hospital of Nanchang University" + }, + { + "author_name": "Yuhao Su", + "author_inst": "Cardiovascular Department, the Second Affiliated Hospital of Nanchang University" + }, + { + "author_name": "Kui Hong", + "author_inst": "Cardiovascular Department, the Second Affiliated Hospital of Nanchang University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2020.05.26.117069", "rel_title": "SARS-CoV-2 genome evolution exposes early human adaptations", @@ -1414711,41 +1417114,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.22.20110148", - "rel_title": "The lower COVID-19 related mortality and incidence rates in Eastern European countries are associated with delayed start of community circulation", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.22.20110148", - "rel_abs": "BackgroundThe purpose of this analysis was to assess the variations in COVID-19 related mortality and incidence rates in relation to the time differences in the commencement of virus circulation and containment measures in different countries of the European Region.\n\nMethodsThe data for the current analysis (N=50 countries) were retrieved from the John Hopkins University dataset on the 7th of May 2020, with countries as study units. A piecewise regression analysis was conducted with mortality and cumulative incidence rates introduced as dependent variables and time interval (days from the 22nd of January to the date when 100 first cases were reported) as the main predictor. The country average life expectancy at birth was statistically adjusted for in the regression model.\n\nResultsMortality and incidence were strongly and inversely intercorrelated with days from January 22, respectively -0.83 (p<.0001) and -0.73 (p<.0001). Adjusting for average life expectancy, between days 33 to 50 from the 22th of the January, the average mortality rate decreased by 30.4/million per day (95% CI: 23.2, 37.1, p<0.0001). During interval 51 to 73 days, the change in mortality was no longer statistically significant but still showed a decreasing trend. A similar relationship with time interval was found in incidence. Life expectancy was not associated with mortality rate.\n\nConclusionCountries in Europe which observed the earliest COVID-19 circulation, suffered the worst consequences in terms of health outcomes, specifically mortality. The drastic social isolation measures, undertaken especially in Eastern European countries, where community circulation started after March 11th, may have been timely. This may explain their significantly lower COVID-related mortality compared with the Western European countries.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Alban Ylli", - "author_inst": "Institute of Public Health; Univeresity of Medicine" - }, - { - "author_name": "Yan Yan Wu", - "author_inst": "Office of Public Health Studies, University of Honolulu at Manoa, Honolulu, Hawaii, USA" - }, - { - "author_name": "Genc Burazeri", - "author_inst": "Department of International Health, School CAPHRI (Care and Public Health Research Institute), Maastricht University, Maastricht, The Netherlands; Department of" - }, - { - "author_name": "Catherine M. Pirkle", - "author_inst": "Office of Public Health Studies, University of Honolulu at Manoa, Honolulu, Hawaii, USA" - }, - { - "author_name": "Tetine Sentell", - "author_inst": "Office of Public Health Studies, University of Honolulu at Manoa, Honolulu, Hawaii, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.25.20100438", "rel_title": "Drug treatments affecting ACE2 in COVID-19 infection: a systematic review protocol", @@ -1415213,6 +1417581,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.20.20107854", + "rel_title": "Spread dynamics of SARS-CoV-2 epidemic in China: a phylogenetic analysis", + "rel_date": "2020-05-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.20.20107854", + "rel_abs": "BackgroundSince December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused a pandemic and infected millions of people. As the first country proclaimed the SARS-CoV-2 outbreak, China implemented travel ban measure, and curbed the epidemic quickly. We performed a phylogenetic analysis to reveal the spread dynamics detail of SARS-CoV-2 in China and the impact of travel ban on SARS-CoV-2.\n\nMethodFocusing on SARS-CoV-2 sequences collected from China in public database released as of March 31, 2020, we performed a Bayesian inference phylogenetic analyses to estimate the effective population size (Ne) curve of SARS-CoV-2 epidemic. Furthermore, we displayed the geographic spread mode of SARS-CoV-2 among different China regions by using Bayesian stochastic search variable selection (BSSVS) method.\n\nResultsThe most recent common ancestor (tMRCA) of SARS-CoV-2 in China was traced back to December 9, 2019. According the Ne estimation and geographic spread reconstruction, January 25, 2020 was considered as the crucial time point during the SARS-CoV-2 epidemic in China,which was 2 days after the travel ban implemented. On the point, the tendency of viral population size changed from ascending to decreasing, and the cross-regional spread paths were blocked.\n\nConclusionsTravel ban is an effective measure to intervene in the spread of SARS-CoV-2, It is necessary to continue efforts in research for prevention and control measures.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Hong Guohu", + "author_inst": "Department of Infectious Disease, Guizhou Provincial People's Hospital" + }, + { + "author_name": "Guan Qing", + "author_inst": "Department of Dermatology, The First People's Hospital of Guiyang" + }, + { + "author_name": "Mao Qing", + "author_inst": "Department of Infectious Disease, The first hospital affiliated to Army Medical University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.21.20107581", "rel_title": "Prevalence of SARS-CoV-2 infection among asymptomatic healthcare workers in greater Houston: a cross-sectional analysis of surveillance data from a large healthcare system", @@ -1416029,213 +1418424,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.19.20107482", - "rel_title": "SARS-CoV-2 seroprevalence and neutralizing activity in donor and patient blood from the San Francisco Bay Area", - "rel_date": "2020-05-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.19.20107482", - "rel_abs": "We report very low SARS-CoV-2 seroprevalence in two San Francisco Bay Area populations. Seropositivity was 0.26% in 387 hospitalized patients admitted for non-respiratory indications and 0.1% in 1,000 blood donors. We additionally describe the longitudinal dynamics of immunoglobulin-G, immunoglobulin-M, and in vitro neutralizing antibody titers in COVID-19 patients. Neutralizing antibodies rise in tandem with immunoglobulin levels following symptom onset, exhibiting median time to seroconversion within one day of each other, and there is >93% positive percent agreement between detection of immunoglobulin-G and neutralizing titers.", - "rel_num_authors": 48, - "rel_authors": [ - { - "author_name": "Dianna Ng", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Gregory Goldgof", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Brian Shy", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Andrew Levine", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Joanna Balcerek", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Sagar P Bapat", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "John Prostko", - "author_inst": "Abbott Laboratories" - }, - { - "author_name": "Mary Rodgers", - "author_inst": "Abbott Laboratories" - }, - { - "author_name": "Kelly Coller", - "author_inst": "Abbott Laboratories" - }, - { - "author_name": "Sandra Pearce", - "author_inst": "Abbott Laboratories" - }, - { - "author_name": "Sergej Franz", - "author_inst": "Vitalant Research Institute" - }, - { - "author_name": "Li Du", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Mars Stone", - "author_inst": "Vitalant Research Institute" - }, - { - "author_name": "Satish Pillai", - "author_inst": "Vitalant Research Institute" - }, - { - "author_name": "Alicia Sotomayor-Gonzalez", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Venice Servellita", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Claudia Sanchez-San Martin", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Andrea Granados", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Dustin R Glasner", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Lucy M Han", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Kent Truong", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Naomi Akagi", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "David N Nguyen", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Neil Neumann", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Daniel Qazi", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Elaine Hsu", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Wei Gu", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Yale A Santos", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Brian Custer", - "author_inst": "Vitalant Research Institute" - }, - { - "author_name": "Valerie Green", - "author_inst": "Creative Testing Solutions" - }, - { - "author_name": "Phillip Williamson", - "author_inst": "Creative Testing Solutions" - }, - { - "author_name": "Nancy K Hills", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Chuanyi M Lu", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Jeffrey D. Whitman", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Susan Stramer", - "author_inst": "American Red Cross" - }, - { - "author_name": "Candace Wang", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Kevin Reyes", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Jill Hakim", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Kirk Sujishi", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Fariba Alazzeh", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Lori Pharm", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Ching-Ying Oon", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Steve Miller", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Theodore Kurtz", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "John Hackett Jr.", - "author_inst": "Abbott Laboratories" - }, - { - "author_name": "Graham Simmons", - "author_inst": "Vitalant Research Institute" - }, - { - "author_name": "Michael P Busch", - "author_inst": "Vitalant Research Institute" - }, - { - "author_name": "Charles Y Chiu", - "author_inst": "University of California, San Francisco" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.21.20109280", "rel_title": "Standardization of enzyme-linked immunosorbent assays for serosurveys of the SARS-CoV-2 pandemic using clinical and at-home blood sampling", @@ -1416855,6 +1419043,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.25.20112763", + "rel_title": "In-depth phenotyping of human peripheral blood mononuclear cells in convalescent COVID-19 patients following a mild versus severe disease course", + "rel_date": "2020-05-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.25.20112763", + "rel_abs": "BackgroundCovid-19, the disease caused by infection with SARS-CoV-2, has developed to a pandemic causing more than 239, 000 deaths worldwide as of 6th May according to the World Health Organization (WHO). It presents with a highly variable disease course ranging from a large proportion of asymptomatic cases to severe respiratory failure in 17-29% of cases even in the absence of apparent comorbidities 1, 2. This implies a diverse host immune response to SARS-CoV-2. The immunological characteristics underlying these divergent disease courses, however, still remain elusive. While insights into abrogations of innate immunity begin to emerge, adaptive immune responses towards SARS-CoV-2 are poorly investigated, although they serve as immune signatures of protection and vaccine responses. We therefore set out to characterize immune signatures of convalescent COVID-19 patients stratified according to their disease severity.\n\nMethodsWe performed high-dimensional flow cytometric profiling of peripheral blood mononuclear cells of convalescent COVID-19 patients who we stratified according to their disease severity by a physician-assisted questionnaire based assessment of COVID-19 symptoms.\n\nResultsSurprisingly, we did not observe any difference in the relative proportions of any major immune cell type in convalescent patients presenting with different severity of COVID-19 disease except for a reduction in monocytes. The frequency of Tnaive T cells was significantly reduced in CD4+ and CD8+ T cells, whereas other T cell differentiations states (TCM, TEM, TEMRA) remained relatively unaffected by COVID-19 severity as assessed approximately two weeks after infection.\n\nConclusionsIn our COVID-19 patient cohort, which is characterized by absence of comorbidities and therapeutic interventions other than symptomatic antipyretics, the immunophenotype is similar irrespective of a highly variable disease severity. Convalescence is therefore associated with a rather uniform immune signature. Abrogations, which were previously identified in the innate and adaptive immune compartment of COVID-19 patients should be scrutinized for direct associations with a preconditioned immune system shaped and made vulnerable for SARS-CoV-2 by preexisting comorbidities.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Chang-Feng Chu", + "author_inst": "Technical University of Munich" + }, + { + "author_name": "Florian Sabath", + "author_inst": "Technical University of Munich" + }, + { + "author_name": "Shan Sun", + "author_inst": "Technical University of Munich" + }, + { + "author_name": "Ying-Yin Chao", + "author_inst": "Technical University of Munich" + }, + { + "author_name": "Christina E. Zielinski", + "author_inst": "Technical University of Munich" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.24.20111914", "rel_title": "The spectrum of COVID-19-associated dermatologic manifestations: an international registry of 716 patients from 31 countries", @@ -1417603,149 +1419826,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.21.20109207", - "rel_title": "Hydroxychloroquine and Tocilizumab Therapy in COVID-19 Patients - An Observational Study", - "rel_date": "2020-05-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.21.20109207", - "rel_abs": "BackgroundHydroxychloroquine has been touted as a COVID-19 treatment. Tocilizumab, an inhibitor of IL-6, has been proposed as a treatment of critically ill patients.\n\nObjectiveTo describe the association between mortality and hydroxychloroquine or tocilizumab therapy among hospitalized COVID-19 patients.\n\nDesignRetrospective observational cohort study of electronic health records Setting: 13-hospital network spanning the state of New Jersey.\n\nParticipantsPatients hospitalized between March 1, 2020 and April 22, 2020 with positive polymerase chain reaction results for SARS-CoV-2. Follow up was through May 5, 2020.\n\nMain OutcomesThe primary outcome was death.\n\nResultsAmong 2512 hospitalized patients with COVID-19 there have been 547 deaths (22%), 1539 (61%) discharges and 426 (17%) remain hospitalized. 1914 (76%) received at least one dose of hydroxychloroquine and 1473 (59%) received hydroxychloroquine with azithromycin. After adjusting for imbalances via propensity modeling, compared to receiving neither drug, there were no significant differences in associated mortality for patients receiving any hydroxychloroquine during the hospitalization (HR, 0.99 [95% CI, 0.80-1.22]), hydroxychloroquine alone (HR, 1.02 [95% CI, 0.83-1.27]), or hydroxychloroquine with azithromycin (HR, 0.98 [95% CI, 0.75-1.28]). The 30-day unadjusted mortality for patients receiving hydroxychloroquine alone, azithromycin alone, the combination or neither drug was 25%, 20%, 18%, and 20%, respectively. Among 547 evaluable ICU patients, including 134 receiving tocilizumab in the ICU, an exploratory analysis found a trend towards an improved survival association with tocilizumab treatment (adjusted HR, 0.76 [95% CI, 0.57-1.00]), with 30 day unadjusted mortality with and without tocilizumab of 46% versus 56%.\n\nConclusionsThis observational cohort study suggests hydroxychloroquine, either alone or in combination with azithromycin, was not associated with a survival benefit among hospitalized COVID-19 patients. Tocilizumab demonstrated a trend association towards reduced mortality among ICU patients. Our findings are limited to hospitalized patients and must be interpreted with caution while awaiting results of randomized trials.\n\nTrial RegistrationClinicaltrials.gov Identifier: NCT04347993", - "rel_num_authors": 32, - "rel_authors": [ - { - "author_name": "Andrew Ip", - "author_inst": "Division of Outcomes and Value Research, John Theurer Cancer Center at Hackensack University Medical Center" - }, - { - "author_name": "Donald A Berry", - "author_inst": "Berry Consultants, LLC" - }, - { - "author_name": "Eric Hansen", - "author_inst": "COTA" - }, - { - "author_name": "Andre H Goy", - "author_inst": "John Theurer Cancer Center at Hackensack University Medical Center" - }, - { - "author_name": "Andrew L Pecora", - "author_inst": "John Theurer Cancer Center at Hackensack University Medical Center" - }, - { - "author_name": "Brittany A Sinclaire", - "author_inst": "John Theurer Cancer Center at Hackensack University Medical Center" - }, - { - "author_name": "Urszula Bednarz", - "author_inst": "John Theurer Cancer Center at Hackensack University Medical Center" - }, - { - "author_name": "Michael Marafelias", - "author_inst": "John Theurer Cancer Center at Hackensack University Medical Center" - }, - { - "author_name": "Scott M Berry", - "author_inst": "Berry Consultants, LLC" - }, - { - "author_name": "Nicholas S Berry", - "author_inst": "Berry Consultants, LLC" - }, - { - "author_name": "Shivam Mathura", - "author_inst": "COTA" - }, - { - "author_name": "Ihor S Sawczuk", - "author_inst": "Hackensack Meridian Health, and Hackensack Meridian School of Medicine at Seton Hall University" - }, - { - "author_name": "Noa Biran", - "author_inst": "John Theurer Cancer Center at Hackensack University Medical Center" - }, - { - "author_name": "Ronaldo C Go", - "author_inst": "Hackensack Meridian Health, and Hackensack Meridian School of Medicine at Seton Hall University" - }, - { - "author_name": "Steven Sperber", - "author_inst": "Hackensack Meridian Health, and Hackensack Meridian School of Medicine at Seton Hall University" - }, - { - "author_name": "Julia A Piwoz", - "author_inst": "Hackensack Meridian Health, and Hackensack Meridian School of Medicine at Seton Hall University" - }, - { - "author_name": "Bindu Balani", - "author_inst": "Hackensack Meridian Health, and Hackensack Meridian School of Medicine at Seton Hall University" - }, - { - "author_name": "Cristina Cicogna", - "author_inst": "Hackensack Meridian Health, and Hackensack Meridian School of Medicine at Seton Hall University" - }, - { - "author_name": "Rani Sebti", - "author_inst": "Hackensack Meridian Health, and Hackensack Meridian School of Medicine at Seton Hall University" - }, - { - "author_name": "Jason Zuckerman", - "author_inst": "Hackensack Meridian Health, and Hackensack Meridian School of Medicine at Seton Hall University" - }, - { - "author_name": "Keith M Rose", - "author_inst": "Hackensack Meridian Health, and Hackensack Meridian School of Medicine at Seton Hall University" - }, - { - "author_name": "Lisa Tank", - "author_inst": "Hackensack Meridian Health, and Hackensack Meridian School of Medicine at Seton Hall University" - }, - { - "author_name": "Laurie Jacobs", - "author_inst": "Hackensack Meridian Health, and Hackensack Meridian School of Medicine at Seton Hall University" - }, - { - "author_name": "Jason Korcak", - "author_inst": "Hackensack Meridian Health, and Hackensack Meridian School of Medicine at Seton Hall University" - }, - { - "author_name": "Sarah L Timmapuri", - "author_inst": "Hackensack Meridian Health, and Hackensack Meridian School of Medicine at Seton Hall University" - }, - { - "author_name": "Joseph P Underwood III", - "author_inst": "Hackensack Meridian Health, and Hackensack Meridian School of Medicine at Seton Hall University" - }, - { - "author_name": "Gregory Sugalski", - "author_inst": "Hackensack Meridian Health, and Hackensack Meridian School of Medicine at Seton Hall University" - }, - { - "author_name": "Carol Barsky", - "author_inst": "Hackensack Meridian Health, and Hackensack Meridian School of Medicine at Seton Hall University" - }, - { - "author_name": "Daniel W Varga", - "author_inst": "Hackensack Meridian Health, and Hackensack Meridian School of Medicine at Seton Hall University" - }, - { - "author_name": "Arif Asif", - "author_inst": "Hackensack Meridian Health, and Hackensack Meridian School of Medicine at Seton Hall University" - }, - { - "author_name": "Joseph C Landolfi", - "author_inst": "Hackensack Meridian Health, and Hackensack Meridian School of Medicine at Seton Hall University" - }, - { - "author_name": "Stuart L Goldberg", - "author_inst": "Division of Outcomes and Value Research, John Theurer Cancer Center at Hackensack University Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.22.20109991", "rel_title": "Is there an airborne component to the transmission of COVID-19? : a quantitative analysis study", @@ -1418405,6 +1420485,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.23.111385", + "rel_title": "COVIDep: A web-based platform for real-time reporting of vaccine target recommendations for SARS-CoV-2", + "rel_date": "2020-05-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.23.111385", + "rel_abs": "We introduce COVIDep (https://COVIDep.ust.hk), a web-based platform that provides immune target recommendations for guiding SARS-CoV-2 vaccine development. COVIDep implements a protocol that pools together publicly-available genetic data for SARS-CoV-2 and epitope data for SARS-CoV to identify B cell and T cell epitopes that present potential immune targets for SARS-CoV-2. Correspondences between outputs of COVIDep and immune responses recorded in COVID-19 patients and preclinical vaccine trials are also indicated. The platform is user-friendly, flexible, and based on up-to-date data. It may help guide vaccine designs and associated experimental studies for SARS-CoV-2.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Syed Faraz Ahmed", + "author_inst": "The Hong Kong University of Science and Technology" + }, + { + "author_name": "Ahmed A. Quadeer", + "author_inst": "The Hong Kong University of Science and Technology" + }, + { + "author_name": "Matthew R. McKay", + "author_inst": "The Hong Kong University of Science and Technology" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.05.24.111823", "rel_title": "The ORF8 Protein of SARS-CoV-2 Mediates Immune Evasion through Potently Downregulating MHC-I", @@ -1419061,61 +1421168,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.21.20108696", - "rel_title": "Hospital admissions in inflammatory rheumatic diseases during the COVID-19 pandemic: incidence and role of disease modifying agents", - "rel_date": "2020-05-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.21.20108696", - "rel_abs": "BackgroundIn this pandemic, it is essential for rheumatologist and patients to know the relationship between COVID-19 and inflammatory rheumatic diseases (IRD). We want to assess the role of targeted synthetic or biologic disease modifying antirheumatic drugs (ts/bDMARDs) and other variables in the development of moderate-severe COVID-19 disease in IRD.\n\nMethodsAn observational longitudinal study was conducted (1stMar to 15thApr 2020). All patients from the rheumatology outpatient clinic from a hospital in Madrid with a medical diagnosis of IRD were included. Main outcome: hospital admission related to COVID-19. Independent variable: ts/bDMARDs. Covariates: sociodemographic, comorbidities, type of IRD diagnosis, glucocorticoids, NSAIDs and conventional synthetic DMARDs (csDMARDs). Incidence rate (IR) of hospital admission related to COVID-19, was expressed per 1,000 patients-month. Cox multivariate regression analysis was run to examine the influence of ts/bDMARDs and other covariates on IR.\n\nResults3,591 IRD patients were included (5,896 patients-month). Concerning csDMARDs, methotrexate was the most used followed by antimalarial. 802 patients were on ts/bDMARDs, mainly anti-TNF agents, and rituximab. Hospital admissions related to COVID-19 occurred in 54 patients (1.36%) with an IR of 9.15 [95%CI: 7-11.9]. In the multivariate analysis, older, male gender, presence of comorbidities and specific systemic autoimmune conditions (Sjoegren, polychondritis, Raynaud and mixed connective tissue disease) had more risk of hospital admissions regardless other factors. Exposition to ts/bDMARDs did not achieve statistical signification. Use of glucocorticoids, NSAIDs, and csDMARDs dropped from the final model.\n\nConclusionThis study provides additional evidence in IRD patients regarding susceptibility to moderate-severe infection related to COVID-19.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Benjamin Fernandez-Gutierrez", - "author_inst": "Hospital Clinico San Carlos" - }, - { - "author_name": "Leticia Leon", - "author_inst": "Hospital Clinico San Carlos. IdISSC" - }, - { - "author_name": "Alfredo Madrid", - "author_inst": "Hospital Clinico San Carlos. IdISSC" - }, - { - "author_name": "Luis Rodriguez-Rodriguez", - "author_inst": "Hospital Clinico San Carlos. IdISSC" - }, - { - "author_name": "Dalifer Freites", - "author_inst": "Hospital Clinico San Carlos. IdISSC" - }, - { - "author_name": "Judit Font", - "author_inst": "Hospital Clinico San Carlos" - }, - { - "author_name": "Arkaitz Mucientes", - "author_inst": "Hospital Clinico San Carlos. IdISSC" - }, - { - "author_name": "Jose Ignacio Colomer", - "author_inst": "Hospital Clinico San Carlos. IdISSC" - }, - { - "author_name": "Juan Angel Jover", - "author_inst": "Hospital Clinico San Carlos. Universidad Complutense Madrid" - }, - { - "author_name": "Lydia Abasolo", - "author_inst": "Hospital Clinico San Carlos. IdISSC" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "rheumatology" - }, { "rel_doi": "10.1101/2020.05.20.20108530", "rel_title": "Development and clinical application of a rapid and sensitive loop-mediated isothermalamplification test for SARS-CoV-2 infection", @@ -1419619,6 +1421671,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.21.20109116", + "rel_title": "Improved measurement of racial/ethnic disparities in COVID-19 mortality in the United States", + "rel_date": "2020-05-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.21.20109116", + "rel_abs": "Different estimation methods produce diverging accounts of racial/ethnic disparities in COVID-19 mortality in the United States. The CDCs decision to present the racial/ethnic distribution of COVID-19 deaths at the state level alongside re-weighted racial/ethnic population distributions--in effect, a geographic adjustment--makes it seem that Whites have the highest death rates. Age adjustment procedures used by others, including the New York City Department of Health and Mental Hygiene, lead to the opposite conclusion that Blacks and Hispanics are dying from COVID-19 at higher rates than Whites. In this paper, we use indirect standardization methods to adjust per-capita death rates for both age and geography simultaneously, avoiding the one-sided adjustment procedures currently in use. Using CDC data, we find age-and-place-adjusted COVID-19 death rates are 80% higher for Blacks and more than 50% higher for Hispanics, relative to Whites, on a national level, while there is almost no disparity for Asians. State-specific estimates show wide variation in mortality disparities. Comparison with non-epidemic mortality reveals potential roles for pre-existing health disparities and differential rates of infection and care.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Joshua Robert Goldstein", + "author_inst": "Department of Demography, University of California, Berkeley" + }, + { + "author_name": "Serge Atherwood", + "author_inst": "Department of Demography, University of California, Berkeley" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.21.20108753", "rel_title": "Forecasting trajectories of an emerging epidemic with mathematical modeling in an online dashboard: The case of COVID-19", @@ -1420743,53 +1422818,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2020.05.21.20108936", - "rel_title": "Risk Factors for COVID-19 versus non-COVID-19 related in-hospital and community deaths by Local Authority District in Great Britain", - "rel_date": "2020-05-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.21.20108936", - "rel_abs": "ObjectivesTo undertake a preliminary hypothesis-generating analysis exploring putative risk factors for coronavirus diseae 2019 (COVID-19) population-adjusted deaths, compared with non-COVID-19 related deaths, at a local authority district (LAD) level in hospital, care homes and at home.\n\nDesignEcological retrospective cohort study\n\nSettingLocal authority districts (LADs) in England, Scotland and Wales (Great Britain (GB)).\n\nParticipantsAll LAD deaths registered by week 16 of 2020.\n\nMain Outcome MeasuresDeath registration where COVID-19 is mentioned as a contributing factor per 100,000 people in all settings, and in i) cares homes, ii) hospitals or iii) home only, in comparison to non-COVID-19 related deaths.\n\nResultsAcross GB by week 16 of 2020, 20,684 deaths had been registered mentioning COVID-19, equivalent to 25.6 per 100,000 people. Significant risk factors for LAD COVID-19 death in comparison to non-COVID-19 related death were air pollution and proportion of the population who were female. Significant protective factors were higher air temperature and proportion of the population who were ex-smokers. Conversely, for all COVID-19 unrelated deaths in comparison to COVID-19 deaths, higher rates of communal living, higher population rates of chronic kidney disease, chronic obstructive pulmonary disease, cerebrovascular disease deaths under 75 and dementia were predictive of death, whereas, higher rates of flight passengers was protective. Looking at individual setttings, the most notable findings in care homes was Scotland being a significant risk factor for COVID-19 related deaths compared to England. For hospital setting, the proportion of the population who were from black and Asian minority ethnic (BAME) groups significantly predicted COVID-19 related death.\n\nConclusionsThis is the first study within GB to assess COVID-19 related deaths in comparison to COVID-19 unrelated deaths across hospital, care homes and home combined. As an ecological study, the results cannot be directly extrapolated to individuals. However, the analysis may be informative for public health policy and protective measures. From our hypothesis-generating analysis, we propose that air pollution is a significant risk factor and high temperature a significant protective factor for COVID-19 related deaths. These factors cannot readily be modelled at an individual level. Scottish local authorities and local authorities with a higher proportion of individuals of BAME origin are potential risk factors for COVID-19 related deaths in care homes and in hospitals, respectively. Altogether, this analysis shows the benefits of access to high quality open data for public information, public health policy and further research.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Samuel Paul Leighton", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Danielle Jane Leighton", - "author_inst": "University of Glasgow" - }, - { - "author_name": "James Herron", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Rachel Upthegrove", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Jonathan Cavanagh", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Georgios Gkoutos", - "author_inst": "University of Birmingham & Associate Director of Health Data Research UK" - }, - { - "author_name": "Breda Cullen", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Pavan K Mallikarjun", - "author_inst": "University of Birmingham" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.22.20109892", "rel_title": "Occupation and risk of COVID-19: prospective cohort study of 120,621 UK Biobank participants", @@ -1421401,6 +1423429,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.21.20109181", + "rel_title": "Quantification of SARS-CoV-2 and cross-assembly phage (crAssphage) from wastewater to monitor coronavirus transmission within communities", + "rel_date": "2020-05-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.21.20109181", + "rel_abs": "Wastewater surveillance of SARS-CoV-2 has become an attractive tool for combating the spread of COVID-19 by assessing the presence or levels of the virus shed in a population. However, the methods to quantify viral RNA and to link those quantities to the level of infection within the community vary. In this study, we sought to identify and optimize scalable methods for recovery of viral nucleic acids from wastewater and attempted to use a constitutive member of the gut virome, human-specific crAssphage, to help account for unknown levels of SARS-CoV-2 decay and dilution in the wastewater infrastructure. Results suggest that ultracentrifugation of a small volume of wastewater through a 50% sucrose cushion followed by total nucleic acid extraction yielded quantifiable virus in an area with a modest number of COVID-19 cases. Further, the ratio of log10(SARS-CoV-2):log10(crAssphage) appears to be associated with the cumulative incidence of COVID-19 in the Syracuse, NY area. In areas where ultracentrifuges are available, these methods may be used to link SARS-CoV-2 quantities in wastewater to levels of transmission within communities with sewer service.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Hyatt Green", + "author_inst": "SUNY-ESF" + }, + { + "author_name": "Maxwell Wilder", + "author_inst": "SUNY-ESF" + }, + { + "author_name": "Frank A. Middleton", + "author_inst": "SUNY-Upstate Medical University" + }, + { + "author_name": "Mary Collins", + "author_inst": "SUNY-ESF" + }, + { + "author_name": "Ariana Fenty", + "author_inst": "SUNY-ESF" + }, + { + "author_name": "Karen Gentile", + "author_inst": "SUNY-Upstate Medical University" + }, + { + "author_name": "Brittany Kmush", + "author_inst": "Syracuse University" + }, + { + "author_name": "Teng Zeng", + "author_inst": "Syracuse University" + }, + { + "author_name": "David Aaron Larsen", + "author_inst": "Syracuse University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.22.20109942", "rel_title": "Clustering method for spread pattern analysis of corona-virus (COVID-19) infection in Iran", @@ -1422065,29 +1424144,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2020.05.18.20106112", - "rel_title": "Going by the Numbers : Learning and Modeling COVID-19 Disease Dynamics", - "rel_date": "2020-05-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.18.20106112", - "rel_abs": "The COrona VIrus Disease (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) has resulted in a challenging number of infections and deaths worldwide. In order to combat the pandemic, several countries worldwide enforced mitigation measures in the forms of lockdowns, social distancing and disinfection measures. In an effort to understand the dynamics of this disease, we propose a Long Short Term Memory (LSTM) based model. We train our model on nearly four months of cumulative COVID-19 cases and deaths. Our model can be adjusted based on the parameters in order to provide predictions as needed. We provide results at both the country and county levels. We also perform a quantitative comparison of mitigation measures in various counties in the United States based on the rate of difference of a short and long window parameter of the proposed LSTM model. The analyses provided by our model can provide valuable insights based on the trends in the rate of infections and deaths. This can also be of help for countries and counties deciding on mitigation and reopening strategies. We believe that the results obtained from the proposed method will contribute to societal benefits for a current global concern.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Sayantani Basu", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Roy H. Campbell", - "author_inst": "University of Illinois at Urbana-Champaign" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.05.18.20105882", "rel_title": "Efficient Prevalence Estimation and Population Screening for SARS-CoV-2", @@ -1422803,6 +1424859,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.20.20104257", + "rel_title": "Trends of SARS-CoV-2 infection worldwide: Role of population density, age structure, and climate on transmission and case fatality", + "rel_date": "2020-05-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.20.20104257", + "rel_abs": "IntroductionThe highly heterogenous disease transmission pattern of COVID-19 suggests that the pandemic maybe driven by complex factors, which may include habitat suitability, region specific human mobility, and transmission related to susceptibility. The purpose of this study was to examine the effects of different spatial and demographic factors on COVID-19 transmission and case fatality worldwide.\n\nMethodsWe assessed SARS-CoV-2 virus transmission and COVID-19 related fatalities in 50 countries in all continents of the globe. Data from the COVID-19 data repository of the Johns Hopkins Center for Systems Science and Engineering, the European center for disease control and prevention, and the World Health Organization were used to obtain the daily number of cases and organize incidence data. Disease spread was assessed using the reproduction number of the disease across the sampled countries. R statistical softwares R0 package was used to estimate the reproduction number of the COVID19 using the exponential growth method. After computing the reproductive number of each country in the study, a multiple linear regression model was fitted using R0 value as dependent variable, and latitude and population density as an independent variable. Disease severity was analyzed using the case fatality ratio of COVID-19. The proportion of deaths were meta-analyzed using the R statistical softwares metaphor package, using random effect inverse variance weighting to come up with the case fatality ratio.\n\nResultsWe found no statistically significant association between disease spread and latitude or population density. The regression model analysis that accounted for age, population density and latitude showed that age distribution remains an important driver shaping the current distribution of COVID-19 cases. The relative frequency of people above 65 years old was positively correlated with the cumulative numbers of COVID-19 cases as well as case fatality ratio in each country. The multiple linear regression model fitted between CFR and the three major covariates showed that, the demographic distribution of the sampled countries is strongly associated with the case fatality ratio. Correlation with proportion of populations over 65 years old is concordant with the previous findings relationship between case fatality ratio and patient age.\n\nConclusionThis analysis provides important information that can inform the decisions of local and global health authorities. Particularly, as our study confirms that death and severity of COVID19 are associated with age, in countries with the biggest outbreaks, strategies must be employed to ensure that high-risk groups, such as old people received adequate protection from COVID-19.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Tewodros B Endailalu", + "author_inst": "Clinton Health Access Initiative" + }, + { + "author_name": "Fitsum W Hadgu", + "author_inst": "Clinton Health Access Initiative" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.19.20105999", "rel_title": "SARS-CoV-2 RNA concentrations in primary municipal sewage sludge as a leading indicator of COVID-19 outbreak dynamics", @@ -1423759,45 +1425838,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.18.20099325", - "rel_title": "The \"Double Eights Mask Brace\" Improves the Fit and Protection and Protection of a Basic Surgical Mask Amidst Covid-19 Pandemic", - "rel_date": "2020-05-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.18.20099325", - "rel_abs": "Study ObjectiveThe COVID-19 pandemic has resulted in widespread shortages in personal protective equipment, including N95 respirators. While basic surgical facemasks are more commonly available, their efficacy is limited due primarily to their poor face seal. This pilot study examined the impact of a rubber band mask brace on a basic surgical mask, as determined by quantitative fit testing.\n\nMethodsSubjects wearing a basic surgical facemask and the rubber band mask brace underwent quantitative fit testing using machinery designed to certify N95 mask fit. Subjects were tested with the brace anchored behind their eyes, with a paperclip behind the head, and on the side knobs of their face shields. The primary outcome measure was whether the subject passed the quantitative fit test at or above the OSHA verified standard for N95 masks.\n\nResultsSubjects (n=11) were 54.5% female, with a median height of 70 inches (IQR 68-74), weight of 170 lbs (IQR 145-215) and BMI of 24.6 (IQR 22.2-27.2), and encompassing 5 distinct N95 mask fit types. We found that 45%, 100% and 100% of subjects passed the quantitative fit test when the brace was anchored behind the ears, with a paperclip and on a face shield respectively.\n\nConclusionOf the 11 subjects included in the analysis, across a range of body habitus and N95 mask fit types, all passed the quantitative fit test when the mask brace was anchored on either face shield or with a paperclip. This data suggests the brace would offer an improved margin of safety when worn with a basic surgical mask.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Daniel P Runde", - "author_inst": "University of Iowa Hospitals and Clinics, Department of Emergency Medicine" - }, - { - "author_name": "Karisa Harland", - "author_inst": "University of Iowa College of Public Health, Department of Epidemiology" - }, - { - "author_name": "Paul Van Heukelom", - "author_inst": "University of Iowa Hospitals and Clinics, Department of Emergency Medicine" - }, - { - "author_name": "Brett Faine", - "author_inst": "Iowa College of Pharmacy, Department of Pharmacy Practice and Science," - }, - { - "author_name": "Patrick OShaughnessy", - "author_inst": "University of Iowa College of Public Health, Department of Occupational and Environmental Health" - }, - { - "author_name": "Nicholas Mohr", - "author_inst": "University of Iowa Hospitals and Clinics, Department of Emergency Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.18.20066902", "rel_title": "Doxycycline and Hydroxychloroquine as Treatment for High-Risk COVID-19 Patients: Experience from Case Series of 54 Patients in Long-Term Care Facilities", @@ -1424489,6 +1426529,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.19.20103150", + "rel_title": "Detection of SARS-CoV-2 from raw patient samples by coupled high temperature reverse transcription and amplification", + "rel_date": "2020-05-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.19.20103150", + "rel_abs": "The SARS-CoV-2 beta coronavirus is spreading globally with unprecedented consequences for modern societies. The early detection of infected individuals is a prerequisite for all strategies aiming to contain the virus. Currently, purification of RNA from patient samples followed by RT-PCR is the gold standard to assess the presence of this single-strand RNA virus. However, these procedures are time consuming, require continuous supply of specialized reagents, and are prohibitively expensive in resource-poor settings. Here, we report an improved nucleic-acid-based approach to detect SARS-CoV-2, which alleviates the need to purify RNA, reduces handling steps, minimizes costs, and allows evaluation by non-specialized equipment. The use of unprocessed swap samples and the ability to detect as little as three viral genome equivalents is enabled by employing a heat-stable RNA- and DNA-dependent DNA polymerase, which performs the double task of stringent reverse transcription of RNA at elevated temperatures as well as PCR amplification of a SARS-CoV-2 specific target gene. As results are obtained within 2 hours and can be read-out by a hand-held LED-screen, this novel protocol will be of particular importance for large-scale virus surveillance in economically constrained settings.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Johannes W.P. Kuiper", + "author_inst": "University of Konstanz" + }, + { + "author_name": "Timo Baade", + "author_inst": "University of Konstanz" + }, + { + "author_name": "Marcel Kremer", + "author_inst": "Labor Brunner Konstanz" + }, + { + "author_name": "Ramon Kranaster", + "author_inst": "myPOLS" + }, + { + "author_name": "Linda Irmisch", + "author_inst": "Klinikum Konstanz" + }, + { + "author_name": "Marcus Schuchmann", + "author_inst": "Klinikum Konstanz" + }, + { + "author_name": "Johannes Zander", + "author_inst": "Labor Brunner Konstanz" + }, + { + "author_name": "Andreas Marx", + "author_inst": "University of Konstanz" + }, + { + "author_name": "Christof R Hauck", + "author_inst": "University of Konstanz" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.17.20101063", "rel_title": "Hospital-acquired infective endocarditis during Covid-19 pandemic", @@ -1425345,65 +1427436,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.20.20103804", - "rel_title": "Comorbidities, clinical signs and symptoms, laboratory findings, imaging features, treatment strategies, and outcomes in adult and pediatric patients with COVID-19: A systematic review and meta-analysis", - "rel_date": "2020-05-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.20.20103804", - "rel_abs": "IntroductionSince December 2019, a novel coronavirus (SARS-CoV-2) has triggered a world-wide pandemic with an enormous medical, societal, and economic toll. Thus, our aim was to gather all available information regarding comorbidities, clinical signs and symptoms, outcomes, laboratory findings, imaging features, and treatments in patients with coronavirus disease 2019 (COVID-19).\n\nMethodsEMBASE, PubMed/ Medline, Scopus, and Web of Science were searched for studies published in any language between December 1st, 2019 and March 28th. Original studies were included if the exposure of interest was an infection with SARS-CoV-2 or confirmed COVID-19. The primary outcome was the risk ratio of comorbidities, clinical signs and symptoms, imaging features, treatments, outcomes, and complications associated with COVID-19 morbidity and mortality. We performed random-effects pairwise meta-analyses for proportions and relative risks, I2, Tau2, and Cochrane Q, sensitivity analyses, and assessed publication bias.\n\nResults148 met the inclusion criteria for the systematic review and meta-analysis with 12149 patients (5739 female) and a median age was 47.0 [35.0-64.6]. 617 patients died from COVID-19 and its complication, while 297 patients were reported as asymptomatic. Older age (SMD: 1.25 [0.78-1.72]; p < 0.001), being male (RR = 1.32 [1.13-1.54], p = 0.005) and pre-existing comorbidity (RR = 1.69 [1.48-1.94]; p < 0.001) were identified as risk factors of in-hospital mortality. The heterogeneity between studies varied substantially (I2; range: 1.5-98.2%). Publication bias was only found in eight studies (Eggers test: p < 0.05).\n\nConclusionsOur meta-analyses revealed important risk factors that are associated with severity and mortality of COVID-19.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Catherine Ruth Jutzeler", - "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland" - }, - { - "author_name": "Lucie Bourguignon", - "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland" - }, - { - "author_name": "Caroline V. Weis", - "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland" - }, - { - "author_name": "Bobo Tong", - "author_inst": "International Collaboration on Repair Discoveries (ICORD), University of British Columbia, Vancouver, Canada" - }, - { - "author_name": "Cyrus Wong", - "author_inst": "Simon Fraser University, Vancouver, Canada" - }, - { - "author_name": "Bastian Rieck", - "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland" - }, - { - "author_name": "Hans Pargger", - "author_inst": "Intensive Care Unit, University Hospital Basel, University Basel, Basel, Switzerland" - }, - { - "author_name": "Sarah Tschudin-Sutter", - "author_inst": "Division of Infectious Diseases & Hospital Epidemiology, University Hospital Basel and University of Basel, Switzerland" - }, - { - "author_name": "Adrian Egli", - "author_inst": "Division of Clinical Bacteriology & Mycology, University Hospital Basel, Basel, Switzerland" - }, - { - "author_name": "Karsten Borgwardt", - "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland" - }, - { - "author_name": "Matthias Walter", - "author_inst": "Swiss Paraplegic Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.18.20105296", "rel_title": "Do COVID-19 patients admitted to the ICU require anti-Pneumocystis jirovecii prophylaxis?", @@ -1426107,6 +1428139,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2020.05.18.20105577", + "rel_title": "A Machine Learning Solution Framework for Combatting COVID-19 in Smart Cities from Multiple Dimensions", + "rel_date": "2020-05-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.18.20105577", + "rel_abs": "The spread of COVID-19 across the world continues as efforts are being made from multi-dimension to curtail its spread and provide treatment. The COVID-19 triggered partial and full lockdown across the globe in an effort to prevent its spread. COVID-19 causes serious fatalities with United States of America recording over 3,000 deaths within 24 hours, the highest in the world for a single day and as of October 2020 has recorded a total of 270,642 death toll. In this paper, we present a novel framework which intelligently combines machine learning models and internet of things (IoT) technology specific in combatting COVID-19 in smart cities. The purpose of the study is to promote the interoperability of machine learning algorithms with IoT technology in interacting with a population and its environment with the aim of curtailing COVID-19. Furthermore, the study also investigates and discusses some solution frameworks, which can generate, capture, store and analyze data using machine learning algorithms. These algorithms are able to detect, prevent, and trace the spread of COVID-19, and provide better understanding of the virus in smart cities. Similarly, the study outlined case studies on the application of machine learning to help in the fight against COVID-19 in hospitals across the world. The framework proposed in the study is a comprehensive presentation on the major components needed for an integration of machine learning approach with other AI-based solutions. Finally, the machine learning framework presented in this study has the potential to help national healthcare systems in curtailing the COVID-19 pandemic in smart cities. In addition, the proposed framework is poised as a point for generating research interests which will yield outcomes capable of been integrated to form an improved framework.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Absalom E Ezugwu", + "author_inst": "University of KwaZulu-Natal" + }, + { + "author_name": "Ibrahim Abaker Targio Hashem", + "author_inst": "Future Technology Research Center, National Yunlin University of Science and Technology, Taiwan" + }, + { + "author_name": "Mohammed A. Al-Garadi", + "author_inst": "Emory University, Atlanta, USA" + }, + { + "author_name": "Idris N. Abdullahi", + "author_inst": "Ahmadu Bello University, Zaria, Nigeria" + }, + { + "author_name": "Olumuyiwa Otegbeye", + "author_inst": "University of KwaZulu-Natal" + }, + { + "author_name": "Amit K Shukla", + "author_inst": "University of Rennes 1, France" + }, + { + "author_name": "Haruna Chiroma", + "author_inst": "Future Technology Research Center, National Yunlin University of Science and Technology, Taiwan" + }, + { + "author_name": "Olaide N Oyelade", + "author_inst": "School of Computer Science, University of KwaZulu-Natal, Pietermaritzburg, KwaZulu-Natal South Africa" + }, + { + "author_name": "Mubarak Almutari", + "author_inst": "College of Computer Science, University of Hafr Al Batin, Saudi Arabia" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.05.17.20104810", "rel_title": "Prediction of the coronavirus epidemic prevalence inquarantine conditions based on an approximate calculation model", @@ -1426843,65 +1428926,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.05.18.20105775", - "rel_title": "Lung ultrasound findings in patients with novel SARS-CoV2", - "rel_date": "2020-05-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.18.20105775", - "rel_abs": "BackgroundOver 2 million people worldwide have been infected with Severe Acute Respiratory Distress Syndrome Corona Virus 2 (SARS CoV2). Lung ultrasound has been proposed to diagnose and it. However, little is known about ultrasound findings in these patients. Our aim is to present an overview of lung ultrasound characteristics in critically ill patients with SARS CoV2 pneumonia overall and in relation to the duration of symptoms and clinical parameters.\n\nMethodsOn the Intensive Care Unit of two academic hospitals, adult patients who tested positive for SARS-CoV2 were included. Images were analyzed for pleural line characteristics, number and appearance of B-lines, BLUE-profiles (Bedside Lung Ultrasound in Emergency), pathology in the PLAPS (Postero Lateral Alveolar and Pleural Syndrome) point and a LUS-score (lung ultrasound). The primary outcomes were frequencies, percentages and differences in lung ultrasound findings overall and between short ([≤]14 days) and long (>14 days) duration of symptoms and their correlation with clinical parameters.\n\nResultsIn this pilot observational study, 61 patients were included with 75 examinations for analysis. The most prevalent ultrasound findings were decreased lung sliding (36%), thickening of the pleural line (42%) and a C-profile per view (37%). Patients with \"long\" duration of symptoms presented more frequently with a thickened and irregular pleural line (21% (32) vs 9% (11), p=.01), C-profile per patient (47% (18) vs. 25% (8), p=.01) and pleural effusion (19% (14) vs 5% (3), p=.02) compared to patients with short duration of symptoms. Lung ultrasound findings did not correlate with P/F ratio, fluid balance or dynamic compliance, with the exception of the LUS-score and dynamic compliance (R2=0.27, p=.02).\n\nConclusionSARS CoV2 results in significant ultrasound changes, with decreased lung sliding, thickening of the pleural line and a C-profile being the most observed. With time, a thickened and irregular pleural line, C-profile and pleural effusion become more common findings.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Mark Evert Haaksma", - "author_inst": "Amsterdam UMC, location VUmc" - }, - { - "author_name": "Micah L.A. Heldeweg", - "author_inst": "Amsterdam UMC, location VUmc" - }, - { - "author_name": "Jorge E. Lopez Matta", - "author_inst": "Leiden University Medical Center" - }, - { - "author_name": "Jasper Martijn Smit", - "author_inst": "Amsterdam UMC, location VUmc" - }, - { - "author_name": "Jessica D. van Trigt", - "author_inst": "Amsterdam UMC, location VUmc" - }, - { - "author_name": "Jip Suzanne Nooitgedacht", - "author_inst": "Amsterdam UMC, location VUmc" - }, - { - "author_name": "Carlos V. Elzo Kraemer", - "author_inst": "Leiden University Medical Center" - }, - { - "author_name": "Armand R.J. Girbes", - "author_inst": "Amsterdam UMC, location VUmc" - }, - { - "author_name": "Leo M.A. Heunks", - "author_inst": "Amsterdam UMC, location VUmc" - }, - { - "author_name": "David J. van Westerloo", - "author_inst": "Leiden University Medical Center" - }, - { - "author_name": "Pieter R. Tuinman", - "author_inst": "Amsterdam UMC, location VUmc" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.05.17.20105023", "rel_title": "Prevalence of facemask use among general public when visiting wet market during Covid-19 pandemic: An observational study.", @@ -1427585,6 +1429609,73 @@ "type": "new results", "category": "systems biology" }, + { + "rel_doi": "10.1101/2020.05.19.20107078", + "rel_title": "Dreaming during the Covid-19 pandemic: Computational assessment of dream reports reveals mental suffering associated with negative feelings and contagion fear", + "rel_date": "2020-05-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.19.20107078", + "rel_abs": "Neuroscience and psychology agree that dreaming helps to cope with negative emotions and learn from experience. The current global threat related to the COVID-19 pandemic led to widespread social isolation. Does dreaming change and/or reflect mental suffering? To address these questions, we applied natural language processing tools to study 239 dream reports from 67 individuals either before the Covid-19 outbreak or during March-April, 2020, when quarantine was imposed in Brazil following the pandemic announcement by the WHO. Pandemic dreams showed a higher proportion of anger and sadness words, and higher average semantic similarities to the terms \"contamination\" and \"cleanness\". These features were associated with mental suffering related to social isolation, as they explained 39% of the variance in PANSS negative subscale (p=0.0092). These results corroborate the hypothesis that pandemic dreams reflect mental suffering, fear of contagion, and important changes in daily habits.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Natalia B Mota", + "author_inst": "Federal University of Rio Grande do Norte" + }, + { + "author_name": "Janaina Weissheimer", + "author_inst": "Federal University of Rio Grande do Norte" + }, + { + "author_name": "Marina Ribeiro", + "author_inst": "Federal University of Rio Grande do Norte" + }, + { + "author_name": "Mizziara De Paiva", + "author_inst": "Federal University of Rio Grande do Norte" + }, + { + "author_name": "Juliana D'Avila", + "author_inst": "Federal University of Rio Grande do Norte" + }, + { + "author_name": "Gabriela Simabucuru", + "author_inst": "Federal University of Rio Grande do Norte" + }, + { + "author_name": "Monica F Chaves", + "author_inst": "Pontificia Universidade Catolica do Rio de Janeiro" + }, + { + "author_name": "Lucas Cecchi", + "author_inst": "Federal University of Rio Grande do Norte" + }, + { + "author_name": "Jaime Cirne", + "author_inst": "Federal University of Rio Grande do Norte" + }, + { + "author_name": "Guillermo Cecchi", + "author_inst": "IBM T.J. Watson Research Center" + }, + { + "author_name": "Cilene Rodrigues", + "author_inst": "Pontificia Universidade Catolica do Rio de Janeiro" + }, + { + "author_name": "Mauro Copelli", + "author_inst": "Federal University of Pernambuco" + }, + { + "author_name": "Sidarta Ribeiro", + "author_inst": "Federal University of Rio Grande do Norte" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.05.19.20106971", "rel_title": "Cancer immunotherapy does not increase the risk of death by COVID-19 in melanoma patients", @@ -1428297,33 +1430388,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.16.20104182", - "rel_title": "COVID-19 Infection Forecasting based on Deep Learning in Iran", - "rel_date": "2020-05-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.16.20104182", - "rel_abs": "Since December 2019 coronavirus disease (COVID-19) is outbreak from China and infected more than 4,666,000 people and caused thousands of deaths. Unfortunately, the infection numbers and deaths are still increasing rapidly which has put the world on the catastrophic abyss edge. Application of artificial intelligence and spatiotemporal distribution techniques can play a key role to infection forecasting in national and province levels in many countries. As methodology, the presented study employs long short-term memory-based deep for time series forecasting, the confirmed cases in both national and province levels, in Iran. The data were collected from February 19, to March 22, 2020 in provincial level and from February 19, to May 13, 2020 in national level by nationally recognised sources. For justification, we use the recurrent neural network, seasonal autoregressive integrated moving average, Holt winters exponential smoothing, and moving averages approaches. Furthermore, the mean absolute error, mean squared error, and mean absolute percentage error metrics are used as evaluation factors with associate the trend analysis. The results of our experiments show that the LSTM model is performed better than the other methods on the collected COVID-19 dataset in Iran.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Mehdi Azarafza", - "author_inst": "University of Tabriz" - }, - { - "author_name": "Mohammad Azarafza", - "author_inst": "University of Isfahan" - }, - { - "author_name": "Jafar Tanha", - "author_inst": "University of Tabriz" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.17.20104356", "rel_title": "COVID-19 Propagation and Mortality in a Two-Part Population", @@ -1428715,6 +1430779,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.05.14.20102202", + "rel_title": "COVID-19 in Uganda: Predicting the impact of the disease and public health response on disease burden", + "rel_date": "2020-05-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.14.20102202", + "rel_abs": "ObjectiveCOVID-19 transmission and the public health lock-down response are now established in sub-Saharan Africa, including Uganda. Population structure and prior morbidities differ markedly between these countries from those where outbreaks were previously established. We predicted the relative impact of COVID-19 and the response in Uganda to understand whether the benefits could be outweighed by the costs.\n\nDesign and settingAge-based COVID-19 mortality data from China were applied to the population structures of Uganda and countries with previously established outbreaks, comparing theoretical mortality and disability-adjusted life years (DALYs) lost. Based on recent Ugandan data and theoretical scenarios of programme deterioration, we predicted potential additional disease burden for HIV/AIDS, malaria and maternal mortality.\n\nMain outcome measuresDALYs lost and mortality.\n\nResultsBased on population age structure alone Uganda is predicted to have a relatively low COVID-19 burden compared to equivalent transmission in China and Western countries, with mortality and DALYs lost predicted to be 12% and 19% that of Italy. Scenarios of lockdown impact predict HIV/AIDS and malaria equivalent to or higher than that of an extensive COVID-19 outbreak. Emerging HIV/AIDS and maternal mortality data indicate that such deterioration could be occurring.\n\nConclusionsThe results predict a relatively low COVID-19 impact on Uganda associated with its young population, with a high risk of negative impact on non-COVID-19 disease burden from a prolonged lockdown response. The results are likely to reflect the situation in other sub-Saharan populations, underlining the importance of tailoring COVID-19 responses to population structure and potential disease vulnerabilities.\n\nTransparency statementThe lead author affirms that the manuscript is an honest, accurate, and transparent account of the study being reported; that no important aspects of the study have been omitted; and that there are no discrepancies from the study as originally planned.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "David Bell", + "author_inst": "Independent consultant, Issaquah, WA, USA" + }, + { + "author_name": "Kristian Schultz Hansen", + "author_inst": "Department of Public Health and Centre for Health Economics and Policy, University of Copenhagen, Oster Farimagsgade 5A, 1014 Copenhagen K, Denmark" + }, + { + "author_name": "Agnes N Kiragga", + "author_inst": "Infectious Diseases Institute, School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda" + }, + { + "author_name": "Andrew Kambugu", + "author_inst": "Infectious Diseases Institute, School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda" + }, + { + "author_name": "John Kissa", + "author_inst": "Uganda Ministry of Health - Division of Health Information, Kampala, Uganda" + }, + { + "author_name": "Anthony K Mbonye", + "author_inst": "School of Public Health, College of Health Sciences, Makerere University, Kampala, Uganda" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.16.20103796", "rel_title": "Asymptomatic COVID-19 Have Longer Treatment Cycle Than Moderate Type of Confirmed Patients", @@ -1429835,33 +1431938,6 @@ "type": "new results", "category": "physiology" }, - { - "rel_doi": "10.1101/2020.05.14.20101360", - "rel_title": "Who is lonely in lockdown? Cross-cohort analyses of predictors of loneliness before and during the COVID-19 pandemic", - "rel_date": "2020-05-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.14.20101360", - "rel_abs": "BackgroundThere are concerns internationally that lockdown measures taken during the COVID-19 pandemic could lead to a rise in loneliness. As loneliness is recognised as a major public health concern, it is therefore vital that research considers the impact of the current COVID-19 pandemic on loneliness in order to provide necessary support. But it remains unclear who is lonely in lockdown?\n\nMethodsThis study compared socio-demographic predictors of loneliness before and during the COVID-19 pandemic using cross-cohort analyses of data from UK adults captured before the pandemic (UK Household Longitudinal Study, n=31,064) and during the pandemic (UCL COVID-19 Social Study, n=60,341).\n\nResultsRisk factors for loneliness were near identical prior to and during the pandemic. Young adults, women, people with lower education or income, the economically inactive, people living alone, and urban residents had a higher risk of being lonely. Some people who were already at risk for being lonely (e.g. young adults aged 18-30, people with low household income, and adults living alone) experienced a heightened risk during the COVID-19 pandemic compared to prior to COVID-19 emerging. Further, being a student emerged as a higher risk factor during lockdown than usual.\n\nConclusionsFindings suggest that interventions to reduce or prevent loneliness during COVID-19 should be targeted at those socio-demographic groups already identified as high-risk in previous research. These groups are likely not just to experience loneliness during the pandemic but to have an even higher risk than normal of experiencing loneliness relative to low-risk groups.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Feifei Bu", - "author_inst": "University College London" - }, - { - "author_name": "Andrew Steptoe", - "author_inst": "University College London" - }, - { - "author_name": "Daisy Fancourt", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.05.14.20102475", "rel_title": "COVID-19; Systematic and literature review of transmission, case definitions, clinical management and clinical trials.", @@ -1430385,6 +1432461,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.15.20102863", + "rel_title": "Estimating the cost-of-illness associated with the COVID-19 outbreak in China from January to March 2020", + "rel_date": "2020-05-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.15.20102863", + "rel_abs": "BackgroundCOVID-19, an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), swept through China in 2019-2020, with over 80,000 confirmed cases reported by end of March 2020. This study estimates the economic burden of COVID-19 in 31 provincial-level administrative regions in China between January and March 2020.\n\nMethodsThe healthcare and societal cost of COVID-19 was estimated using bottom-up approach. The main cost components included identification, diagnosis and treatment of COVID-19, compulsory quarantine and productivity losses for all affected residents in China during the study period. Input data were obtained from government reports, clinical guidelines, and other published literature. The primary outcomes were total health and societal costs. Costs were reported in both RMB and USD (2019 value).\n\nOutcomesThe total estimated healthcare and societal cost associated with the outbreak is 4.26 billion RMB (0.62 billion USD) and 2,647 billion RMB (383 billion USD), respectively. The main components of routine healthcare costs are inpatient care (41.0%) and medicines (30.9%). The main component of societal costs is productivity losses (99.8%). Hubei province incurred the highest healthcare cost (83.2%) whilst Guangdong province incurred the highest societal cost (14.6%).\n\nInterpretationThis review highlights a large economic burden of the recent COVID-19 outbreak in China. These findings will aid policy makers in making informed decisions about prevention and control measures for COVID-19.\n\nFundingThe author(s) received no financial support for the research, authorship, and/or publication of this article.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched MEDLINE, EMBASE and Global Health on April 4th, 2020, using key words and medical subject headings including (\"coronavirus\" OR \"SARS-CoV-2\" OR \"COVID-19\") AND (\"cost\" OR \"Economics\" OR \"resource\" OR \"productivity loss\"). No restrictions on language or publication dates were applied. Our search did not identify any studies which reported the cost of COVID-19. Cost of severe acute respiratory syndrome (SARS), which is an infectious disease caused by another type of coronavirus - the SARS coronavirus - has been assessed by seven studies. The reported healthcare cost of managing SARS per case ranged from $4,151 USD in mainland China to $362,700 USD in Canada. The total healthcare cost and societal cost of the 2013 SARS outbreak in China took up 0.20% and 1.05% of Chinas GDP, respectively. The global cost of SARS was estimated to be US $40 billion, the majority of which was caused by reduced consumer demand for goods and services due to fear associated with SARS. Two studies reported a reduction in total healthcare resource use during the peak of the SARS epidemic in Taiwan, due to peoples fears of SARS.\n\nAdded value of this studyTo our knowledge, this study presents the first cost-of-illness study of COVID-19. The main cost components considered include identification, diagnosis, treatment and follow-up of COVID-19, compulsory quarantine and productivity loss for all affected residents in China during the study period. The total societal cost of COVID-19 was estimated to be 383 billion US dollars, which is equivalent to 2.7% of Chinas gross domestic product (GDP) in 2019. Healthcare costs accounted for only 0.2% of societal cost for COVID-19, while productivity losses accounted for 99.8%. The majority of productivity losses (99.7%) were attributable to people who were not considered to have had COVID-19 but experienced lost working time due to the government policies in controlling population movement.\n\nImplications of all the available evidenceOur findings suggest that the cost of COVID-19 is much larger than the cost of SARS or MERS. Productivity losses far exceeded the healthcare cost of managing COVID-19 patients. Future research is urgently required on the cost-effectiveness of different control measures of COVID-19 (e.g. policies regarding reducing working days, travel restrictions, quarantine and isolation), and development of interventions which can help to maintain the productivity of healthy population during the pandemic.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Huajie Jin", + "author_inst": "King's College London" + }, + { + "author_name": "Haiyin Wang", + "author_inst": "Shanghai Health Development Research Centre, Shanghai, P.R. China" + }, + { + "author_name": "Xiao Li", + "author_inst": "Centre for Health Economics Research & Modelling Infectious Diseases, University of Antwerp, Antwerp, Belgium" + }, + { + "author_name": "Weiwei Zheng", + "author_inst": "Key Laboratory of Public Health Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fudan University, Shanghai" + }, + { + "author_name": "Shanke Ye", + "author_inst": "Department of Infectious Disease, Shanghai Public Health Clinical Center, Shanghai, P.R. China." + }, + { + "author_name": "Sheng Zhang", + "author_inst": "Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China." + }, + { + "author_name": "Jiahui Zhou", + "author_inst": "School of Population and Global Health, The University of Western Australia, Perth, Australia." + }, + { + "author_name": "Mark Pennington", + "author_inst": "King's College London" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.16.20102947", "rel_title": "Performance of progressive and adaptive COVID-19 exit strategies: a stress test analysis for managing intensive care unit rates", @@ -1430925,25 +1433048,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, - { - "rel_doi": "10.1101/2020.05.16.20103895", - "rel_title": "Time series forecasting of COVID-19 confirmed cases with ARIMA model in the South East Asian countries of India and Thailand: a comparative case study", - "rel_date": "2020-05-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.16.20103895", - "rel_abs": "BackgroundAs economic burden makes it increasingly difficult for countries to continue imposing control measures, it is vital for countries to make predictions using time series forecasting before making decisions on lifting the restrictions.\n\nAimSince apparent differences were noted in the disease transmission between the two South East Asian countries of India and Thailand, the study aims to draw comparative account of the progression of COVID 19 in near future between these two countries.\n\nMethodsThe study used data of COVID 19 confirmed cases in India and Thailand from WHO COVID 19 situation reports during the time period between 25th March, 2020 and 14th May, 2020. After determination of stationarity in the data and differencing, observation of autocorrelation function (ACF) and partial autocorrelation function (PACF), Auto Regressive Integrated Moving Average (ARIMA) (2,2,1) model was used to forecast the COVID 19 confirmed cases in both these countries for two weeks (i.e. 28th May, 2020). IBM SPSS version 20.0 software was used for data analysis.\n\nResultsThe study demonstrated a possible increasing trend in number of COVID 19 cases in India in the coming two weeks with an estimated point forecast of 1,28,772 (95% CI 115023-142520) by 28th May, 2020. A stationary phase was forecasted for Thailand with a difference of only 43 cases between 14th May (the last case of input data) and 28th May.\n\nConclusionThe time series forecasting employed in the present study warrants thorough preparation on part of the Indian health care system and authorities and calls for caution with regard to decisions made on lifting the control measures. The difference in the time series forecasting between these two South East Asian countries also highlights the need for strengthening of public health systems.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Viswa Chaitanya Chandu", - "author_inst": "SIBAR Institute of Dental Sciences" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.15.20103473", "rel_title": "Development and validation of chest CT-based imaging biomarkers for early stage COVID-19 screening", @@ -1431679,6 +1433783,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.15.20099465", + "rel_title": "Monitoring and predicting SARS-CoV-2 epidemic in France after deconfinement using a multiscale age-stratified rate model", + "rel_date": "2020-05-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.15.20099465", + "rel_abs": "The entire world and France were strongly impacted by the SARS-COV-2 epidemic. Finding appropriate measures that effectively contain the spread of the epidemic without putting a too severe pressure on social and economic life is a major challenge for modern predictive approaches. To assess the impact of confinement (March 17th till May 11th) and deconfinement, we develop a novel rate model to monitor and predict the spread of the epidemic and its impact on the health care system. The model accounts for age-dependent interactions between population groups and predicts consequences for various infection categories such as number of infected, hospitalized, load of intensive care units (ICU), number of death, recovered from hospitalization and more. We use online health care data for the five most infected regions of France to calibrate the model. At day of deconfinement (May 11th), we find that 13% (around 4.8M) of the population is infected in the five most affected regions of France (extrapolating to 5.8M for France). The model predicts that if the reproduction number R0 is reduced by at least a factor of 2.5-3 for all age groups after deconfinement, which could be achieved by wearing masks and social distancing, a significant second peak can be prevented. However, if the reduction in R0 for the age group 0-25 would be less and below 2 (e.g. due to school openings), a second peak with ICU saturation is unavoidable. In that context, we argue that testing should be focused on children, but without tracing it will nevertheless have only a very limited impact on reducing the spread.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Juergen Reingruber", + "author_inst": "Ecole Normale Superieure" + }, + { + "author_name": "Andrea Papale", + "author_inst": "ENS" + }, + { + "author_name": "David holcman", + "author_inst": "ENS" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.13.20100222", "rel_title": "Silent Disease and Loss of Taste and Smell are Common Manifestations of SARS-COV-2 Infection in a Quarantine Facility: First report from Saudi Arabia", @@ -1432519,25 +1434650,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.13.20100628", - "rel_title": "When strong mitigation against a pandemic backfires", - "rel_date": "2020-05-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.13.20100628", - "rel_abs": "I introduce social feasibility constraints in a SIR epidemiological model: at any point in time, the ability of a social planner to impose mitigation measures is limited, but it is increasing in the proportion of infected individuals. When considering threshold policies with constant levels of mitigation for a time period, the overall fatality rate in the population is non-monotonic in the levels of mitigation: higher levels of mitigation can increase the overall fatality rate. Intuitively, strong mitigation at a point in time can undermine the social feasibility of future mitigation. O_QD\"When the economists talk the trade-off talk, lots of epidemiologists (and others) find it morally reprehensible when people are dying.\"\n\nNoah Feldman, Bloomberg, April 2 2020.\n\nC_QD", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Pierre Chaigneau", - "author_inst": "Queen's University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.15.20101097", "rel_title": "Predictors of COVID-19 incidence, mortality, and epidemic growth rate at the country level", @@ -1433041,6 +1435153,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.14.20101725", + "rel_title": "COVID-19 Epidemic Forecast in Different States of India using SIR Model", + "rel_date": "2020-05-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.14.20101725", + "rel_abs": "(May 14, 2020)\n\nThe epidemiological data up to 12th May 2020 for India and its 24 states has been used to predict COVID-19 outbreak within classical SIR (Susceptible-Infected-Recovered) model. The basic reproduction number R0 of India is calculated to be 1.15, whereas for various states it ranges from 1.03 in Uttarakhand to 7.92 in Bihar. The statistical parameters for most of the states indicates the high significance of the predicted results. It is estimated that the epidemic curve flattening in India will start from the first week of July and epidemic may end in the third week of October with final epidemic size [~]1,75,000. The epidemic in Kerala is in final phase and is expected to end by first week of June. Among Indian states, Maharashtra is severely affected where the ending phase of epidemic may occur in the second week of September with epidemic size of [~]55,000. The model indicates that the fast growth of infection in Punjab is from 27th April 2020 to 2nd June 2020, thereafter, curve flattening will start and the epidemic is expected to finished by the first week of July with the estimated number of [~]3300 infected people. The epidemic size of COVID-19 outbreak in Delhi, West Bengal, Gujrat, Tamil Nadu and Odisha can reach as large as 24,000, 18,000, 16,000, 13,000 and 11,000, respectively, however, these estimations may be invalid if large fluctuation of data occurs in coming days.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Mukesh Jakhar", + "author_inst": "Central University of Punjab" + }, + { + "author_name": "P K Ahluwalia", + "author_inst": "Himachal Pradesh University" + }, + { + "author_name": "Ashok Kumar", + "author_inst": "Central University of Punjab" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.14.20101691", "rel_title": "Blacks/African Americans are 5 Times More Likely to Develop COVID-19: Spatial Modeling of New York City ZIP Code-level Testing Results", @@ -1433633,49 +1435772,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.14.097295", - "rel_title": "High speed large scale automated isolation of SARS-CoV-2 from clinical samples using miniaturized co-culture coupled with high content screening", - "rel_date": "2020-05-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.14.097295", - "rel_abs": "SARS-CoV-2, a novel coronavirus infecting humans, is responsible for the current COVID-19 global pandemic. If several strains could be isolated worldwide, especially for in-vitro drug susceptibility testing and vaccine development, few laboratories routinely isolate SARS-CoV-2. This is due to the fact that the current co-culture strategy is highly time consuming and requires working in a biosafety level 3 laboratory. In this work, we present a new strategy based on high content screening automated microscopy (HCS) allowing large scale isolation of SARS-CoV-2 from clinical samples in 1 week. A randomized panel of 104 samples, including 72 tested positive by RT-PCR and 32 tested negative, were processed with our HCS procedure and were compared to the classical isolation procedure. Isolation rate was 43 % with both strategies on RT-PCR positive samples, and was correlated with the initial RNA viral load in the samples, where we obtained a positivity threshold of 27 Ct. Co-culture delays were shorter with HCS strategy, where 80 % of the positive samples were recovered by the third day of co-culture, as compared to only 25 % with the classic strategy. Moreover, only the HCS strategy allowed us to recover all the positive elements after 1 week of co-culture. This system allows rapid and automated screening of clinical samples with minimal operator work load, thus reducing the risks of contamination.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Rania Francis", - "author_inst": "Aix-Marseille University" - }, - { - "author_name": "Marion Le Bideau", - "author_inst": "IHU Mediterranee Infection" - }, - { - "author_name": "Priscilla Jardot", - "author_inst": "Aix-Marseille University" - }, - { - "author_name": "Clio Grimaldier", - "author_inst": "AP-HM" - }, - { - "author_name": "Didier Raoult", - "author_inst": "Aix-Marseille Univ, IRD, APHM, MEPHI, IHU-M\u00e9diterran\u00e9e Infection, Marseille, France" - }, - { - "author_name": "Jacques Yaacoub Bou Khalil", - "author_inst": "Aix-Marseille University" - }, - { - "author_name": "Bernard La Scola", - "author_inst": "Aix-Marseille University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.05.12.20099572", "rel_title": "COVID-19 Pandemic: Is Chronic Inflammation a Major Cause of Death?", @@ -1434343,6 +1436439,93 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.05.18.099234", + "rel_title": "Multi-Antigenic Virus-like Particle of SARS CoV-2 produced in Saccharomyces cerevisiae as a vaccine candidate", + "rel_date": "2020-05-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.18.099234", + "rel_abs": "Spike, Envelope and Membrane proteins from the SARS CoV-2 virus surface coat are important vaccine targets. We hereby report recombinant co-expression of the three proteins (Spike, Envelope and Membrane) in a engineered Saccharomyces cerevisiae platform (D-Crypt) and their self-assembly as Virus-like particle (VLP). This design as a multi-antigenic VLP for SARS CoV-2 has the potential to be a scalable vaccine candidate. The VLP is confirmed by transmission electron microscopy (TEM) images of the SARS CoV-2, along with supportive HPLC, Dynamic Light Scattering (DLS) and allied analytical data. The images clearly outline the presence of a \"Corona\" like morphology, and uniform size distribution.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Kajal Arora", + "author_inst": "Premas Biotech Private Limited" + }, + { + "author_name": "Ruchir Rastogi", + "author_inst": "Premas Biotech Private Limited" + }, + { + "author_name": "Nupur Mehrotra Arora", + "author_inst": "Premas Biotech Private Limited" + }, + { + "author_name": "Deepak Parashar", + "author_inst": "Premas Biotech Private Limited" + }, + { + "author_name": "Jeny Paliwal", + "author_inst": "Premas Biotech Private Limited" + }, + { + "author_name": "Aelia Naqvi", + "author_inst": "Premas Biotech Private Limited" + }, + { + "author_name": "Apoorva Srivastava", + "author_inst": "Premas Biotech Private Limited" + }, + { + "author_name": "Sudhir K Singh", + "author_inst": "Premas Biotech Private Limited" + }, + { + "author_name": "Sriganesh Kalyanaraman", + "author_inst": "Premas Biotech Private Limited" + }, + { + "author_name": "Swaroop Potdar", + "author_inst": "Premas Biotech Private Limited" + }, + { + "author_name": "Devanand Kumar", + "author_inst": "Premas Biotech Private Limited" + }, + { + "author_name": "Vidya Bhushan Arya", + "author_inst": "Premas Biotech Private Limited" + }, + { + "author_name": "Sarthi Bansal", + "author_inst": "Premas Biotech Private Limited" + }, + { + "author_name": "Satabdi Rautray", + "author_inst": "Premas Biotech Private Limited" + }, + { + "author_name": "Indrajeet Singh", + "author_inst": "Premas Biotech Private Limited" + }, + { + "author_name": "Pankaj Surendra Fengade", + "author_inst": "Premas Biotech Private Limited" + }, + { + "author_name": "Bibekanand Kumar", + "author_inst": "Premas Biotech Private Limited" + }, + { + "author_name": "Prabuddha K Kundu", + "author_inst": "Premas Biotech Private Limited" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.05.19.104117", "rel_title": "Human IgG cell neutralizing monoclonal antibodies block SARS-CoV-2 infection", @@ -1435415,73 +1437598,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.05.14.20091843", - "rel_title": "A Novel Cohorting and Isolation Strategy for Suspected COVID-19 Cases during a Pandemic", - "rel_date": "2020-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.14.20091843", - "rel_abs": "IntroductionThe COVID-19 pandemic presents a significant infection prevention and control challenge. The admission of large numbers of patients with suspected COVID-19 disease risks overwhelming the capacity to protect other patients from exposure. The delay between clinical suspicion and confirmatory testing adds to the complexity of the problem.\n\nMethodsWe implemented a triage tool aimed at minimising hospital acquired COVID-19 particularly to patients at risk of severe disease. Patients were allocated to triage categories defined by likelihood of COVID-19 and risk of a poor outcome. Category A (low-likelihood; high-risk), B (high-likelihood; high-risk), C (high-likelihood; low-risk) and D (low-likelihood; low-risk). This determined the order of priority for isolation in single-occupancy rooms with Category A the highest. Patients in other groups were cohorted when isolation capacity was limited with additional interventions to reduce transmission.\n\nResults93 patients were evaluated with 79 (85%) receiving a COVID-19 diagnosis during their admission. Of those without a COVID-19 diagnosis: 10 were initially triaged to Category A; 0 to B; 1 to C and 4 to D. All high risk patients requiring isolation were, therefore, admitted to single-occupancy rooms and protected from exposure. 28 (30%) suspected COVID-19 patients were evaluated to be low risk (groups C & D) and eligible for cohorting. No symptomatic hospital acquired infections were detected in the cohorted patients.\n\nDiscussionApplication of a clinical triage tool to guide isolation and cohorting decisions may reduce the risk of hospital acquired transmission of COVID-19 especially to individuals at the greatest of risk of severe disease.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Benjamin Patterson", - "author_inst": "Department of Clinical Microbiology, University College London" - }, - { - "author_name": "Michael Marks", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Gemma Martinez-Garcia", - "author_inst": "Division of Infection, University College London" - }, - { - "author_name": "Gabriella Bidwell", - "author_inst": "Hospital for Tropical Diseases, University College London" - }, - { - "author_name": "Akish Luintel", - "author_inst": "Hospital for Tropical Diseases, University College London" - }, - { - "author_name": "Dalia Ludwig", - "author_inst": "Department of Acute Medicine, University College London" - }, - { - "author_name": "Tom Parks", - "author_inst": "Hospital for Tropical Diseases, University College London" - }, - { - "author_name": "Philip Gothard", - "author_inst": "Hospital for Tropical Diseases, University College London" - }, - { - "author_name": "Rik Thomas", - "author_inst": "Intensive Care, University College London" - }, - { - "author_name": "Sarah Logan", - "author_inst": "Hospital for Tropical Diseases, University College London" - }, - { - "author_name": "Karen Shaw", - "author_inst": "Division of Infection, University College London" - }, - { - "author_name": "Neil Stone", - "author_inst": "Hospital for Tropical Diseases, University College London" - }, - { - "author_name": "Mike Brown", - "author_inst": "Hospital for Tropical Diseases, University College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.12.20091744", "rel_title": "Substantial underestimation of SARS-CoV-2 infection in the United States due to incomplete testing and imperfect test accuracy", @@ -1436225,6 +1438341,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.14.20094821", + "rel_title": "Transmission of aerosols through pristine and reprocessed N95 respirators", + "rel_date": "2020-05-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.14.20094821", + "rel_abs": "During the Covid-19 pandemic, pristine and reprocessed N95 respirators are crucial equipment towards limiting nosocomial infections. The NIOSH test certifying the N95 rating, however, poorly simulates aerosols in healthcare settings, limiting our understanding of the exposure risk for healthcare workers wearing these masks, especially reprocessed ones. We used experimental conditions that simulated the sizes, densities and airflow properties of infectious aerosols in healthcare settings. We analyzed the penetration and leakage of aerosols through pristine and reprocessed N95 respirators. Seven reprocessing methods were investigated. Our findings suggest that pristine and properly reprocessed N95 respirators effectively limit exposure to infectious aerosols, but that care must be taken to avoid the elucidated degradation mechanisms and limit noncompliant wear.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Paul Z Chen", + "author_inst": "University of Toronto" + }, + { + "author_name": "Aldrich Ngan", + "author_inst": "University of Toronto" + }, + { + "author_name": "Niclas Manson", + "author_inst": "Hospital for Sick Children" + }, + { + "author_name": "Jason T Maynes", + "author_inst": "Hospital for Sick Children" + }, + { + "author_name": "Gregory H Borschel", + "author_inst": "Hospital for Sick Children" + }, + { + "author_name": "Ori D Rotstein", + "author_inst": "St. Michael's Hospital" + }, + { + "author_name": "Frank X Gu", + "author_inst": "University of Toronto" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.14.20094144", "rel_title": "Sarilumab use in severe SARS-CoV-2 pneumonia", @@ -1437333,57 +1439492,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.14.20102558", - "rel_title": "ALTERED MOLECULAR PATHWAYS OBSERVED IN NASO-OROPHARYNGEAL SAMPLES OF SARS-CoV-2 PATIENTS", - "rel_date": "2020-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.14.20102558", - "rel_abs": "BackgroundCOVID-19 or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) appeared throughout the World and currently affected more than 3.6 million people and caused the death of around 252,000 people. The novel strain of the coronavirus disease is transmittable at a devastating rate with a high rate of severe hospitalization even more so for the elderly population. Currently around 50,000 patients are in a seriously critical situation. Although 1.2 million patients recovered from the disease there are still more than 2.1 Million active cases. Naso-oro-pharyngeal swab samples as the first step towards detecting suspected infection of SARS-CoV-2 provides a non-invasive method for PCR testing at a high confidence rate. Furthermore, proteomics analysis of PCR positive and negative nasooropharyngeal samples provides information on the molecular level which highlights disease pathology.\n\nMethodSamples from 15 PCR positive cases and 15 PCR negative cases were analyzed with nanoLC-MS/MS to identify the differentially expressed proteins.\n\nResultsProteomic analyses identified 207 proteins across the sample set and 17 of them were statistically significant. Protein-protein interaction analyses emphasized pathways like Neutrophil degranulation, Innate Immune System, Antimicrobial Peptides.\n\nConclusionNeutrophil Elastase (ELANE), Azurocidin (AZU1), Myeloperoxidase (MPO), Myeloblastin (PRTN3), Cathepsin G (CTSG) and Transcobalamine-1 (TCN1) were found to be significantly altered in naso-oropharyngeal samples of SARS-CoV-2 patients. The identified proteins are linked to alteration in the innate immune system specifically via neutrophil degranulation and NETosis.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Emel Akgun", - "author_inst": "ACIBADEM MEHMET ALI AYDINLAR UNIVERSITY" - }, - { - "author_name": "Mete B Tuzuner", - "author_inst": "ACIBADEM LABMED CLINICAL LABORATORIES R&D CENTER" - }, - { - "author_name": "Betul Sahin", - "author_inst": "ACIBADEM LABMED CLINICAL LABORATORIES R&D CENTER" - }, - { - "author_name": "Meltem Kilercik", - "author_inst": "ACIBADEM MEHMET ALI AYDINLAR UNIVERSITY" - }, - { - "author_name": "Canan Kulah", - "author_inst": "ACIBADEM LABMED CLINICAL LABORATORIES" - }, - { - "author_name": "Hacer N Cakiroglu", - "author_inst": "ACIBADEM LABMED CLINICAL LABORATORIES" - }, - { - "author_name": "Mustafa Serteser", - "author_inst": "ACIBADEM MEHMET ALI AYDINLAR UNIVERSITY" - }, - { - "author_name": "Ibrahim Unsal", - "author_inst": "ACIBADEM LABMED CLINICAL LABORATORIES" - }, - { - "author_name": "Ahmet T Baykal", - "author_inst": "Acibadem Mehmet Ali Aydinlar University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.15.20094920", "rel_title": "The Presence of COVID-19 in Urine: A Systematic Review and Meta-analysis of the Literature", @@ -1437891,6 +1439999,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.11.20095851", + "rel_title": "Internet-based tool for visualizing county and state level COVID-19 trends in the United States.", + "rel_date": "2020-05-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20095851", + "rel_abs": "The novel COVID-19 outbreak started in 2019 in Wuhan China and quickly spread to at least 185 countries. We developed an interactive web application that allows users to visualize the spread of COVID-19 in the Unites States at state and county levels. This tool allows visualization of how the virus spreads over time and how state-wide efforts to reduce transmissions have affected the curve in local areas. The downloadable application data allows users to conduct additional analyses. We demonstrate exemplars of trend analyses comparing the daily infection and death rates before and after safer at home orders were implemented per state. The goal was to develop a COVID-19 tracking tool that informs users about the spread of the virus to enable them to make informed decisions after better understanding the presented data.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Stefan Hinz", + "author_inst": "City of Hope" + }, + { + "author_name": "Mudaser M Basam", + "author_inst": "City of Hope" + }, + { + "author_name": "Kristina Y Aguilera", + "author_inst": "UCLA" + }, + { + "author_name": "Mark LaBarge", + "author_inst": "Beckman Research Institute at City of Hope" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.14.20102210", "rel_title": "Mental wellbeing in the Bangladeshi healthy population during nationwide lockdown over COVID-19: an online cross-sectional survey", @@ -1438595,33 +1440734,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.11.20098525", - "rel_title": "A Proposed Randomized, Double Blind, Placebo Controlled Study Evaluating Doxycycline for the Prevention of COVID-19 Infection and Disease In Healthcare Workers with Ongoing High Risk Exposure to COVID-19", - "rel_date": "2020-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20098525", - "rel_abs": "This paper proposes both a rationale and potential study design for evaluation of low dose doxycycline (20mg BID) for the prevention of COVID-19 infection in exposed health care workers. More generally, it provides a potential study design blueprint to other investigators for any interventional COVID-19 study looking to evaluate interventions for prevention or treatment of COVID-19 infection. This specific study described is a randomized, double blind, placebo controlled study to evaluate the efficacy and safety of doxycycline for the prevention of COVID-19 infection and disease in healthcare workers with ongoing high risk exposure to COVID-19. This study would consist of a 50-day Treatment Period (Day 0-Day 50), followed by an End of Study Visit, approximately 30 days after completion of study drug dosing. Initially, for approximately the first 4 to 6 weeks, an initial open-label arm would be enrolled with up to 1938 subjects who will be assigned to take 20mg doxycycline BID. In the double blind, placebo controlled arms approximately 3,692 participants would be randomized to either doxycycline or placebo for 50 days.\n\nDoxycycline is a rational candidate drug to be evaluated for repurposing against SARS-CoV-2. Doxycycline is a generally safe tetracycline derivative that has been available for decades, most commonly dosed at 100mg BID to treat bacterial infections. However, in addition to its antimicrobial properties, doxycycline (and more generally tetracycline derivatives) may have a role as an effective anti-viral agent and as an anti-inflammatory drug. Early studies indicate potential efficacy of minocycline against respiratory syncytial virus (RSV) [12], and doxycycline against Dengue and Chikungunya infection[9, 10]. In addition, doxycycline is known or proposed to target several pathways that regulate viral replication. [13, 14, 15]. Doxycycline is a particularly attractive candidate as a COVID-19 prophylactic given it has been used in clinical practice for decades and maintains an excellent safety profile as demonstrated in multiple clinical studies. Any effective prophylaxis for COVID-19 should be able to demonstrate high efficacy at preventing infection and/or lowering severity of disease.\n\nEqually important, it should demonstrate this efficacy at dosing levels that are highly unlikely to precipitate any untoward severe side effects. Doxycycline has been selected based on its ability to: 1) inhibit metalloproteinases (MMPs), implicated in initial viral entry into the cell as well as in acute respiratory distress syndrome (ARDS) associated with severe COVID-19 infection [13, 16]; 2) potential to inhibit Papain-like proteinase (PLpro) responsible for proteolytic cleavage of the replicase polyprotein to release non-structural proteins 1, 2 & 3 (Nsp1, Nsp2 and Nsp3) all essential for viral replication. [19]; 3) potential to inhibit 3C-like main protease (3CLpro) or Nsp5 which is cleaved from the polyproteins causes further cleavage of Nsp4-16 and mediates maturation of Nsps which is essential in the virus lifecycle. [19]; 4) act as an ionophore help transport Zinc intracellularly, increasing cellular concentrations of Zinc to inhibit viral replication. [6, 15]; 5) inhibit Nf-kB which may lower inflammatory response to COVID-19 infection, and lower risk of viral entry due to decreasing DPP4 cell surface receptor. [20, 21]; 6) inhibits (specifically low-dose doxycycline) expression of CD147/EMMPRIN that may be necessary for SARS-CoV-2 entry into T lymphocytes [22, 23].", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Paul A Yates", - "author_inst": "University of Virginia" - }, - { - "author_name": "Ashton M Leone", - "author_inst": "University of Virginia" - }, - { - "author_name": "Elias Reichel", - "author_inst": "Tufts University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.11.20098590", "rel_title": "High sensitivity CDC EUA SARS-CoV-2 kit-based End Point-PCR assay.", @@ -1439137,6 +1441249,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.12.20098954", + "rel_title": "Covid-19 Detection using CNN Transfer Learning from X-ray Images", + "rel_date": "2020-05-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.12.20098954", + "rel_abs": "The Covid-19 first occurs in Wuhan, China in December 2019. After that the virus spread all around the world and at the time of writing this paper the total number of confirmed cases are above 4.7 million with over 315000 deaths. Machine learning algorithms built on radiography images can be used as a decision support mechanism to aid radiologists to speed up the diagnostic process. The aim of this work is to conduct a critical analysis to investigate the applicability of convolutional neural networks (CNNs) for the purpose of COVID-19 detection in chest X-ray images and highlight the issues of using CNN directly on the whole image. To achieve this task, we first use 12-off-the-shelf CNN architectures in transfer learning mode on 3 publicly available chest X-ray databases together with proposing a shallow CNN architecture in which we train it from scratch. Chest X-ray images fed into CNN models without any preprocessing to follow the many of researches using chest X-rays in this manner. Next, a qualitative investigation performed to inspect the decisions made by CNNs using a technique known as class activation maps (CAM). Using CAMs, one can map the activations contributed most to the decision of CNNs back to the original image to visualize the most discriminating regions on the input image.\n\nWe conclude that CNN decisions should not be taken into consideration, despite their high classification accuracy, until clinicians can visually inspect, and approve, the region(s) of the input image used by CNNs that lead to its prediction.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Taban Majeed", + "author_inst": "Salahaddin University" + }, + { + "author_name": "Rasber Rashid", + "author_inst": "Koya University" + }, + { + "author_name": "Dashti Ali", + "author_inst": "Independent Researcher" + }, + { + "author_name": "Aras Asaad", + "author_inst": "Oxford Drug Design" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2020.05.14.20102327", "rel_title": "Is the Current N95 Respirator Filtration Efficiency Test Sufficient for Evaluating Protection Against Submicrometer Particles Containing SARS-CoV-2?", @@ -1439885,61 +1442028,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.05.17.100537", - "rel_title": "Binding of the SARS-CoV-2 Spike Protein to Glycans", - "rel_date": "2020-05-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.17.100537", - "rel_abs": "The pandemic of SARS-CoV-2 has caused a high number of deaths in the world. To combat it, it is necessary to develop a better understanding of how the virus infects host cells. Infection normally starts with the attachment of the virus to cell-surface glycans like heparan sulfate (HS) and sialic acid-containing oligosaccharides. In this study, we examined and compared the binding of the subunits and spike (S) proteins of SARS-CoV-2 and SARS-CoV, MERS-CoV to these glycans. Our results revealed that the S proteins and subunits can bind to HS in a sulfation-dependent manner, the length of HS is not a critical factor for the binding, and no binding with sialic acid residues was detected. Overall, this work suggests that HS binding may be a general mechanism for the attachment of these coronaviruses to host cells, and supports the potential importance of HS in infection and in the development of antiviral agents against these viruses.Competing Interest StatementThe authors have declared no competing interest.View Full Text", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Wei Hao", - "author_inst": "Chinese Academy of Medical Sciences and Peking Union Medical College" - }, - { - "author_name": "Bo Ma", - "author_inst": "Chinese Academy of Medical Sciences and Peking Union Medical College" - }, - { - "author_name": "Ziheng Li", - "author_inst": "Chinese Academy of Medical Sciences and Peking Union Medical College" - }, - { - "author_name": "Xiaoyu Wang", - "author_inst": "Chinese Academy of Medical Sciences and Peking Union Medical College" - }, - { - "author_name": "Xiaopan Gao", - "author_inst": "Chinese Academy of Medical Sciences and Peking Union Medical College" - }, - { - "author_name": "Yaohao Li", - "author_inst": "University of Colorado" - }, - { - "author_name": "Bo Qin", - "author_inst": "Chinese Academy of Medical Sciences and Peking Union Medical College" - }, - { - "author_name": "Shiying Shang", - "author_inst": "School of Pharmaceutical Sciences, Tsinghua University" - }, - { - "author_name": "Sheng Cui", - "author_inst": "Chinese Academy of Medical Sciences and Peking Union Medical College" - }, - { - "author_name": "Zhongping Tan", - "author_inst": "Chinese Academy of Medical Sciences and Peking Union Medical College" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.05.16.100206", "rel_title": "Epitope-Based Peptide Vaccine Against Severe Acute Respiratory Syndrome-Coronavirus-2 Nucleocapsid Protein: An in silico Approach", @@ -1440519,6 +1442607,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.12.20099721", + "rel_title": "Relaxing lockdown measures in epidemic outbreaks using selective socio-economic containment with uncertainty", + "rel_date": "2020-05-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.12.20099721", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWAfter the introduction of drastic containment measures aimed at stopping the epidemic contagion from SARS-CoV2, many governments have adopted a strategy based on a periodic relaxation of such measures in the face of a severe economic crisis caused by lockdowns. Assessing the impact of such openings in relation to the risk of a resumption of the spread of the disease is an extremely difficult problem due to the many unknowns concerning the actual number of people infected, the actual reproduction number and infection fatality rate of the disease. In this work, starting from a compartmental model with a social structure and stochastic inputs, we derive models with multiple feedback controls depending on the social activities that allow to assess the impact of a selective relaxation of the containment measures in the presence of uncertain data. Specific contact patterns in the home, work, school and other locations have been considered. Results from different scenarios concerning the first wave of the epidemic in some major countries, including Germany, France, Italy, Spain, the United Kingdom and the United States, are presented and discussed.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Giacomo Albi", + "author_inst": "University of Verona" + }, + { + "author_name": "Lorenzo Pareschi", + "author_inst": "University of Ferrara" + }, + { + "author_name": "Mattia Zanella", + "author_inst": "University of Pavia" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.12.20099473", "rel_title": "Country differences in hospitalisation, length of stay and admission to Intensive Care Units due to SARS-CoV-2 infection: a rapid review of available literature", @@ -1441199,29 +1443314,6 @@ "type": "new results", "category": "genetics" }, - { - "rel_doi": "10.1101/2020.05.15.098947", - "rel_title": "Implications of SARS-CoV-2 mutations for genomic RNA structure and host microRNA targeting", - "rel_date": "2020-05-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.15.098947", - "rel_abs": "The SARS-CoV-2 virus is a recently-emerged zoonotic pathogen already well adapted to transmission and replication in humans. Although the mutation rate is limited, recently introduced mutations in SARS-CoV-2 have the potential to alter viral fitness. In addition to amino acid changes, mutations could affect RNA secondary structure critical to viral life cycle, or interfere with sequences targeted by host miRNAs. We have analysed subsets of genomes from SARS-CoV-2 isolates from around the globe and show that several mutations introduce changes in Watson-Crick pairing, with resultant changes in predicted secondary structure. Filtering to targets matching miRNAs expressed in SARS-CoV-2 permissive host cells, we identified twelve separate target sequences in the SARS-CoV-2 genome; eight of these targets have been lost through conserved mutations. A genomic site targeted by the highly abundant miR-197-5p, overexpressed in patients with cardiovascular disease, is lost by a conserved mutation. Our results are compatible with a model that SARS-CoV-2 replication within the human host could be constrained by host miRNA defence. The impact of these and further mutations on secondary structures, miRNA targets or potential splice sites offers a new context in which to view future SARS-CoV-2 evolution, and a potential platform for engineered viral attenuation and antigen presentation.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Ali Hosseini Rad", - "author_inst": "University of Otago" - }, - { - "author_name": "Alexander Donald McLellan", - "author_inst": "University of Otago, Dunedin, NZ" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2020.05.12.20099374", "rel_title": "Factors linked to changes in mental health outcomes among Brazilians in quarantine due to COVID-19", @@ -1441717,6 +1443809,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2020.05.13.20101139", + "rel_title": "Triaging of Respiratory Protective Equipment on the assumed risk of SARS-CoV-2 aerosol exposure in patient-facing healthcare workers delivering secondary care: a rapid review", + "rel_date": "2020-05-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.13.20101139", + "rel_abs": "BACKGROUNDO_ST_ABSObjectivesC_ST_ABS\"In patient-facing healthcare workers delivering secondary care, what is the evidence behind UK Government PPE Guidance on surgical masks versus respirators for SARS-CoV-2 protection?\"\n\nMETHODSTwo independent reviewers searched MEDLINE, Google Scholar and grey literature 11th - 30th April 2020. Studies published on any date containing primary data comparing surgical facemasks and respirators specific to SARS-CoV-2, and studies underpinning government PPE guidance, were included. Appraisal was performed using CASP checklists. Results were synthesised by comparison of findings and appraisals.\n\nRESULTSIn all three laboratory studies of 14 different respirators and 12 surgical facemasks, respirators were significantly more effective than facemasks in protection factors, reduction factors, filter penetrations, and total inspiratory leakages at differing particle sizes, mean inspiratory flows, and breathing rates. Tests included live viruses and inert particles on dummies and humans.\n\nIn six clinical studies, 6,502 participants, there was no consistent definition of \"exposure\" to determine the efficacy of RPE. It is difficult to define \"safe\". The only statistically significant result found continuous use of respirators more effective in clinical respiratory illness compared to targeted use or surgical facemask.\n\nCONCLUSIONSThere is a paucity of evidence on the comparison of FRSMs and respirators specific to SARS-CoV-2, and poor-quality evidence in other contexts. Indirectness results in extrapolation of non-SARS-CoV-2 specific data to guide UK Government PPE guidance. The appropriateness of this is unknown given the uncertainty over the transmission of SARS-CoV-2. O_LIThe evidence base for UK Government PPE guidelines is not based on SARS-CoV-2 and requires generalisation from low-quality evidence of other pathogens/particles.\nC_LIO_LIThere is a paucity of high-quality evidence regarding the efficacy of RPE specific to SARS-CoV-2.\nC_LIO_LIHMGs PPE guidelines are underpinned by the assumption of droplet transmission of SARS-CoV-2.\nC_LI\n\nTriaging the use of FFP3 respirators might increase the risk of COVID-19 faced by some.\n\nFUNDINGThis review was unfunded and unsponsored.\n\nARTICLE SUMMARYO_ST_ABSStrengths and limitations of this studyC_ST_ABSStrengthsO_LIThis article does not aim to prove an intervention as more effective than a comparator. It identifies a paucity of evidence on respiratory protective equipment specific to SARS-CoV-2.\nC_LIO_LIThe results of this study will allow for future study with a real and tangible effect towards the wellbeing of healthcare workers nationwide, and perhaps internationally.\nC_LIO_LIThis article has an exceptionally broad range- from infection control, to public health, to biomechanical engineering, to industry. Its extensive reach would allow for citations from several disciplines.\nC_LI\n\nLimitationsO_LIThis study reviews evidence specific to a novel virus. Naturally, there is a paucity of specific evidence.\nC_LI", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Prashanth Ramaraj", + "author_inst": "Major Trauma Centre, St Mary's Hospital, Imperial College Healthcare Trust" + }, + { + "author_name": "Jonathan Thomas Super", + "author_inst": "Major Trauma Centre, St Mary's Hospital, Imperial College Healthcare Trust" + }, + { + "author_name": "Ruben Doyle", + "author_inst": "Department of Engineering, Imperial College London" + }, + { + "author_name": "Christopher Aylwin", + "author_inst": "St Mary's Hospital, Imperial College Healthcare Trust" + }, + { + "author_name": "Shehan Hettiaratchy", + "author_inst": "Major Trauma Centre, St Mary's Hospital, Imperial College Healthcare Trust" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2020.05.13.20100131", "rel_title": "Fast and accurate diagnostics from highly multiplexed sequencing assays", @@ -1442645,29 +1444772,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.15.20103325", - "rel_title": "Modeling Tempo of COVID-19 Pandemic in India and Significance of Lockdown", - "rel_date": "2020-05-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.15.20103325", - "rel_abs": "A very special type of pneumonic disease that generated the COVID-19 pandemic was first identified in Wuhan, China in December 2019 and is spreading all over the world. The ongoing outbreak presents a challenge for data scientists to model COVID-19, when the epidemiological characteristics of the COVID-19 are yet to be fully explained. The uncertainty around the COVID-19 with no vaccine and effective medicine available until today create additional pressure on the epidemiologists and policy makers. In such a crucial situation, it is very important to predict infected cases to support prevention of the disease and aid in the preparation of healthcare service. In this paper, we have tried to understand the spreading capability of COVID-19 in India taking into account of the lockdown period. The numbers of confirmed cases are increased in India and states in the past few weeks. A differential equation based simple model has been used to understand the pattern of COVID-19 in India and some states. Our findings suggest that the physical distancing and lockdown strategies implemented in India are successfully reducing the spread and that the tempo of pandemic growth has slowed in recent days.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Brijesh P Singh", - "author_inst": "Banaras Hindu University, Varanasi INDIA" - }, - { - "author_name": "Gunjan Singh", - "author_inst": "Amity University, Lucknow" - } - ], - "version": "1", - "license": "cc0_ng", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.13.20101345", "rel_title": "COVID-19 in Spain: age, Interleukin-6, C Reactive Protein and lymphocytes as key clues from a multicentre retrospective study", @@ -1443443,6 +1445547,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.13.20087734", + "rel_title": "Nebulized in-line endotracheal dornase alfa and albuterol administered to mechanically ventilated COVID-19 patients: A case series", + "rel_date": "2020-05-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.13.20087734", + "rel_abs": "BackgroundMechanically ventilated patients with coronavirus disease 2019 (COVID-19) have a mortality of 24-53%, in part due to distal mucopurulent secretions interfering with ventilation. Dornase alfa is recombinant human DNase 1 and digests DNA in mucoid sputum. Nebulized dornase alfa is FDA-approved for cystic fibrosis treatment. DNA from neutrophil extracellular traps (NETs) contributes to the viscosity of mucopurulent secretions. NETs are found in the serum of patients with severe COVID-19, and targeting NETs reduces mortality in animal models of acute respiratory distress syndrome (ARDS). Thus, dornase alfa may be beneficial to patients with severe COVID-19--acting as a mucolytic and targeting NETs. However, delivery of nebulized drugs can aerosolize SARS-CoV-2, which causes COVID-19, increasing the infection risk for staff. Here, we report a single center case series where dornase alfa was administered through an in-line nebulizer system to minimize risk of virus aerosolization.\n\nMethodsDemographic, clinical data, and outcomes were collected from the electronic medical records of five mechanically ventilated patients with COVID-19--including three requiring veno-venous extracorporeal membrane oxygenation (VV-ECMO)--treated with nebulized in-line endotracheal dornase alfa co-administered with albuterol (used to increase delivery to the alveoli), between March 31 and April 24, 2020. Data on tolerability and responses, including longitudinal values capturing respiratory function and inflammatory status, were analyzed.\n\nResultsFollowing nebulized in-line administration of dornase alfa with albuterol, the fraction of inspired oxygen requirements was reduced for all five patients. All patients remain alive and two patients have been discharged from the intensive care unit. No drug associated toxicities were identified.\n\nConclusionsThe results presented in this case series suggest that dornase alfa will be well-tolerated by critically ill patients with COVID-19. Clinical trials are required to formally test the dosing, safety, and efficacy of dornase alfa in COVID-19, and two have recently been registered (NCT04359654 and NCT04355364). With this case series, we hope to contribute to the development of management approaches for critically ill patients with COVID-19.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Andrew G. Weber", + "author_inst": "Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Northwell Health" + }, + { + "author_name": "Alice S Chau", + "author_inst": "Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington and the Center for Immunity and Immunotherapies, Seattle Children'" + }, + { + "author_name": "Mikala Egeblad", + "author_inst": "Cold Spring Harbor Laboratory" + }, + { + "author_name": "Betsy J Barnes", + "author_inst": "Center for Autoimmune, Musculoskeletal and Hematopoietic Diseases, The Feinstein Institutes for Medical Research and the Departments of Molecular Medicine and P" + }, + { + "author_name": "Tobias Janowitz", + "author_inst": "Cancer Center, Cold Spring Harbor Laboratory and Northwell Health Cancer Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.05.11.20089714", "rel_title": "Pre-existing Cardiovascular Disease in United States Population at High Risk for Severe COVID-19 Infection", @@ -1444242,97 +1446381,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.11.20096263", - "rel_title": "Reappearance of Effector T Cells Predicts Successful Recovery from COVID-19", - "rel_date": "2020-05-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20096263", - "rel_abs": "BackgroundElucidating the role of T cell responses in COVID-19 is of utmost importance to understand the clearance of SARS-CoV-2 infection.\n\nMethods30 hospitalized COVID-19 patients and 60 age- and gender-matched healthy controls (HC) participated in this study. We used two comprehensive 11-color flow cytometric panels conforming to Good Laboratory Practice and approved for clinical diagnostics.\n\nFindingsAbsolute numbers of lymphocyte subsets were differentially decreased in COVID-19 patients according to clinical severity. In severe disease (SD) patients, all lymphocyte subsets were reduced, whilst in mild disease (MD) NK, NKT and {gamma}{delta} T cells were at the level of HC. Additionally, we provide evidence of T cell activation in MD but not SD, when compared to HC. Follow up samples revealed a marked increase in effector T cells and memory subsets in convalescing but not in non-convalescing patients.\n\nInterpretationOur data suggest that activation and expansion of innate and adaptive lymphocytes play a major role in COVID-19. Additionally, recovery is associated with formation of T cell memory as suggested by the missing formation of effector and central memory T cells in SD but not in MD. Understanding T cell-responses in the context of clinical severity might serve as foundation to overcome the lack of effective anti-viral immune response in severely affected COVID-19 patients and can offer prognostic value as biomarker for disease outcome and control.\n\nFundingFunded by German Research Foundation, Excellence Strategy - EXC 2155 \"RESIST\"-Project ID39087428, and DFG-SFB900/3-Project ID158989968, grants SFB900-B3 to R.F., SFB900-B8 to I P. and C.K.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Ivan Odak", - "author_inst": "Institute of Immunology, Hannover Medical School, Germany" - }, - { - "author_name": "Joana Barros-Martins", - "author_inst": "Institute of Immunology, Hannover Medical School, Germany" - }, - { - "author_name": "Berislav Bosnjak", - "author_inst": "Institute of Immunology, Hannover Medical School, Germany" - }, - { - "author_name": "Klaus Stahl", - "author_inst": "Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Germany" - }, - { - "author_name": "Sascha David", - "author_inst": "Department of Nephrology and Hypertension, Hannover Medical School, Germany" - }, - { - "author_name": "Olaf Wiesner", - "author_inst": "Department of Pneumology and German Center of Lung Research (DZL), Hannover Medical School, Germany" - }, - { - "author_name": "Markus Busch", - "author_inst": "Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Germany" - }, - { - "author_name": "Marius M Hoeper", - "author_inst": "Department of Pneumology and German Center of Lung Research (DZL), Hannover Medical School, Germany" - }, - { - "author_name": "Isabell Pink", - "author_inst": "Department of Pneumology and German Center of Lung Research (DZL), Hannover Medical School, Germany" - }, - { - "author_name": "Tobias Welte", - "author_inst": "Department of Pneumology and German Center of Lung Research (DZL), Hannover Medical School, Germany" - }, - { - "author_name": "Markus Cornberg", - "author_inst": "Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Germany; Centre for Individualised Infection Medicine (CiiM), Hannover, G" - }, - { - "author_name": "Matthias Stoll", - "author_inst": "Department of Rheumatology and Immunology, Hannover Medical School, Germany" - }, - { - "author_name": "Lilia Goudeva", - "author_inst": "Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Germany" - }, - { - "author_name": "Rainer Blasczyk", - "author_inst": "Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Germany" - }, - { - "author_name": "Arnold Ganser", - "author_inst": "Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Germany" - }, - { - "author_name": "Immo Prinz", - "author_inst": "Institute of Immunology, Hannover Medical School, Germany; Centre for Individualised Infection Medicine (CiiM), Hannover, Germany; Cluster of Excellence RESIST " - }, - { - "author_name": "Reinhold Foerster", - "author_inst": "Institute of Immunology, Hannover Medical School, Germany; Centre for Individualised Infection Medicine (CiiM), Hannover, Germany; Cluster of Excellence RESIST " - }, - { - "author_name": "Christian Koenecke", - "author_inst": "Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Germany; Centre for Individualised Infection Medicine (Ci" - }, - { - "author_name": "Christian R Schultze-Florey", - "author_inst": "Institute of Immunology, Hannover Medical School, Germany; Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.11.20093096", "rel_title": "Risk factors for clinical progression in patients with COVID-19: a retrospective study of electronic health record data in the United Kingdom", @@ -1444904,6 +1446952,189 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.11.20093732", + "rel_title": "Assisting Scalable Diagnosis Automatically via CT Images in the Combat against COVID-19", + "rel_date": "2020-05-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20093732", + "rel_abs": "Introductory paragraphThe pandemic of coronavirus Disease 2019 (COVID-19) caused enormous loss of life globally. 1-3 Case identification is critical. The reference method is using real-time reverse transcription PCR (rRT-PCR) assays, with limitations that may curb its prompt large-scale application. COVID-19 manifests with chest computed tomography (CT) abnormalities, some even before the onset of symptoms. We tested the hypothesis that application of deep learning (DL) to the 3D CT images could help identify COVID-19 infections. Using the data from 920 COVID-19 and 1,073 non-COVID-19 pneumonia patients, we developed a modified DenseNet-264 model, COVIDNet, to classify CT images to either class. When tested on an independent set of 233 COVID-19 and 289 non-COVID-19 patients. COVIDNet achieved an accuracy rate of 94.3% and an area under the curve (AUC) of 0.98. Application of DL to CT images may improve both the efficiency and capacity of case detection and long-term surveillance.", + "rel_num_authors": 42, + "rel_authors": [ + { + "author_name": "Bohan Liu", + "author_inst": "1.Key Laboratory of Ministry of Industry and Information Technology of Biomedical Engineering and Translational Medicine, Chinese PLA General Hospital; 2.Transl" + }, + { + "author_name": "Pan Liu", + "author_inst": "1.Key Laboratory of Ministry of Industry and Information Technology of Biomedical Engineering and Translational Medicine; 2.Translational Medical Research Cente" + }, + { + "author_name": "Lutao Dai", + "author_inst": "Faculty of Business and Economics, The University of Hong Kong" + }, + { + "author_name": "Yanlin Yang", + "author_inst": "Department of Critical Care Medicine, Beijing Tiantan Hospital" + }, + { + "author_name": "Peng Xie", + "author_inst": "Department of Medical Imaging, Suizhou Hospital, Hubei University of Medicine (Suizhou Central Hospital)" + }, + { + "author_name": "Yiqing Tan", + "author_inst": "Department of Radiology, Wuhan Third Hospital, Tongren Hospital of Wuhan University" + }, + { + "author_name": "Jicheng Du", + "author_inst": "Department of Radiology, WenZhou Central Hospital" + }, + { + "author_name": "Wei Shan", + "author_inst": "Department of Neurology, Beijing Tiantan Hospital, Capital Medical University" + }, + { + "author_name": "Chenghui Zhao", + "author_inst": "1.Key Laboratory of Ministry of Industry and Information Technology of Biomedical Engineering and Translational Medicine, Chinese PLA General Hospital; 2.Transl" + }, + { + "author_name": "Qin Zhong", + "author_inst": "1.Key Laboratory of Ministry of Industry and Information Technology of Biomedical Engineering and Translational Medicine, Chinese PLA General Hospital; 2.Transl" + }, + { + "author_name": "Xixiang Lin", + "author_inst": "1.Key Laboratory of Ministry of Industry and Information Technology of Biomedical Engineering and Translational Medicine, Chinese PLA General Hospital; 2.Transl" + }, + { + "author_name": "Xizhou Guan", + "author_inst": "Pulmonary and Critical Care Medicine, Chinese PLA General Hospital" + }, + { + "author_name": "Ning Xing", + "author_inst": "Department of Radiology, Chinese PLA General Hospital" + }, + { + "author_name": "Yuhui Sun", + "author_inst": "1.Key Laboratory of Ministry of Industry and Information Technology of Biomedical Engineering and Translational Medicine, Chinese PLA General Hospital; 2.Transl" + }, + { + "author_name": "Wenjun Wang", + "author_inst": "1.Key Laboratory of Ministry of Industry and Information Technology of Biomedical Engineering and Translational Medicine, Chinese PLA General Hospital; 2.Transl" + }, + { + "author_name": "Zhibing Zhang", + "author_inst": "Department of Radiology, Xiantao First People's Hospital affiliated to Yangtze University" + }, + { + "author_name": "Xia Fu", + "author_inst": "Department of Radiology, The First People's Hospital of Jiangxia District" + }, + { + "author_name": "Yanqing Fan", + "author_inst": "Department of Radiology, Wuhan Jinyintan Hospital" + }, + { + "author_name": "Meifang Li", + "author_inst": "Department of Medical Imaging, Affiliated Hospital of Putian University" + }, + { + "author_name": "Na Zhang", + "author_inst": "Department of Radiology, Chengdu Public Health Clinical Medical Center" + }, + { + "author_name": "Lin Li", + "author_inst": "1.Department of Radiology, Wuhan Huangpi People's Hospital; 2.Jianghan University Affiliated Huangpi People's Hospital" + }, + { + "author_name": "Yaou Liu", + "author_inst": "Department of Radiology, Beijing Tiantan Hospital, Capital Medical University" + }, + { + "author_name": "Lin Xu", + "author_inst": "Department of Medical Imaging Center, Dazhou Central Hospital" + }, + { + "author_name": "Jingbo Du", + "author_inst": "Department of Radiology, Beijing Daxing District People's Hospital (Capital Medical University Daxing Teaching Hospital)" + }, + { + "author_name": "Zhenhua Zhao", + "author_inst": "Department of Radiology, Shaoxing People's Hospital (The First Affiliated Hospital of Shaoxing University)" + }, + { + "author_name": "Xuelong Hu", + "author_inst": "Department of Radiology, The People's Hospital of Zigui" + }, + { + "author_name": "Weipeng Fan", + "author_inst": "Department of Medical Imaging, Anshan Central Hospital" + }, + { + "author_name": "Rongpin Wang", + "author_inst": "Department of Medical Imaging, Guizhou Provincial People's Hospital" + }, + { + "author_name": "Chongchong Wu", + "author_inst": "Department of Radiology, Chinese PLA General Hospital" + }, + { + "author_name": "Yongkang Nie", + "author_inst": "Department of Radiology, Chinese PLA General Hospital" + }, + { + "author_name": "Liuquan Cheng", + "author_inst": "Department of Radiology, Chinese PLA General Hospital" + }, + { + "author_name": "Lin Ma", + "author_inst": "Department of Radiology, Chinese PLA General Hospital" + }, + { + "author_name": "Zongren Li", + "author_inst": "1.Key Laboratory of Ministry of Industry and Information Technology of Biomedical Engineering and Translational Medicine, Chinese PLA General Hospital; 2.Transl" + }, + { + "author_name": "Qian Jia", + "author_inst": "1.Key Laboratory of Ministry of Industry and Information Technology of Biomedical Engineering and Translational Medicine, Chinese PLA General Hospital; 2.Transl" + }, + { + "author_name": "Minchao Liu", + "author_inst": "Department of Computer Application and Management, Chinese PLA General Hospital" + }, + { + "author_name": "Huayuan Guo", + "author_inst": "Department of Computer Application and Management, Chinese PLA General Hospital" + }, + { + "author_name": "Gao Huang", + "author_inst": "Department of automation, Tsinghua University" + }, + { + "author_name": "Haipeng Shen", + "author_inst": "1.Faculty of Business and Economics, The University of Hong Kong; 2.China National Clinical Research Center for Neurological Diseases, Center for Bigdata Analyt" + }, + { + "author_name": "Weimin An", + "author_inst": "Department of Radiology, 5th Medical Center, Chinese PLA General Hospital" + }, + { + "author_name": "Hao Li", + "author_inst": "China National Clinical Research Center for Neurological Diseases, Center for Bigdata Analytics and Artificial Intelligence" + }, + { + "author_name": "Jianxin Zhou", + "author_inst": "Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University" + }, + { + "author_name": "Kunlun He", + "author_inst": "1.Key Laboratory of Ministry of Industry and Information Technology of Biomedical Engineering and Translational Medicine, Chinese PLA General Hospital; 2.Transl" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2020.05.09.20096842", "rel_title": "Impact of COVID-19 infection on maternal and neonatal outcomes: a review of 287 pregnancies", @@ -1445768,209 +1447999,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.05.14.095414", - "rel_title": "Pre-existing and de novo humoral immunity to SARS-CoV-2 in humans", - "rel_date": "2020-05-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.14.095414", - "rel_abs": "Several related human coronaviruses (HCoVs) are endemic in the human population, causing mild respiratory infections1. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the etiologic agent of Coronavirus disease 2019 (COVID-19), is a recent zoonotic infection that has quickly reached pandemic proportions2,3. Zoonotic introduction of novel coronaviruses is thought to occur in the absence of pre-existing immunity in the target human population. Using diverse assays for detection of antibodies reactive with the SARS-CoV-2 spike (S) glycoprotein, we demonstrate the presence of pre-existing humoral immunity in uninfected and unexposed humans to the new coronavirus. SARS-CoV-2 S-reactive antibodies were readily detectable by a sensitive flow cytometry-based method in SARS-CoV-2-uninfected individuals and were particularly prevalent in children and adolescents. These were predominantly of the IgG class and targeted the S2 subunit. In contrast, SARS-CoV-2 infection induced higher titres of SARS-CoV-2 S-reactive IgG antibodies, targeting both the S1 and S2 subunits, as well as concomitant IgM and IgA antibodies, lasting throughout the observation period of 6 weeks since symptoms onset. SARS-CoV-2-uninfected donor sera also variably reacted with SARS-CoV-2 S and nucleoprotein (N), but not with the S1 subunit or the receptor binding domain (RBD) of S on standard enzyme immunoassays. Notably, SARS-CoV-2-uninfected donor sera exhibited specific neutralising activity against SARS-CoV-2 and SARS-CoV-2 S pseudotypes, according to levels of SARS-CoV-2 S-binding IgG and with efficiencies comparable to those of COVID-19 patient sera. Distinguishing pre-existing and de novo antibody responses to SARS-CoV-2 will be critical for our understanding of susceptibility to and the natural course of SARS-CoV-2 infection.", - "rel_num_authors": 47, - "rel_authors": [ - { - "author_name": "Kevin W Ng", - "author_inst": "Francis Crick Institute" - }, - { - "author_name": "Nikhil Faulkner", - "author_inst": "Francis Crick Institute" - }, - { - "author_name": "Georgina Cornish", - "author_inst": "Francis Crick Institute" - }, - { - "author_name": "Annachiara Rosa", - "author_inst": "Francis Crick Institute" - }, - { - "author_name": "Ruth Harvey", - "author_inst": "Francis Crick Institute" - }, - { - "author_name": "Saira Hussain", - "author_inst": "Francis Crick Institute" - }, - { - "author_name": "Rachel Ulferts", - "author_inst": "Francis Crick Institute" - }, - { - "author_name": "Christopher Earl", - "author_inst": "Francis Crick Institute" - }, - { - "author_name": "Antoni Wrobel", - "author_inst": "Francis Crick Institute" - }, - { - "author_name": "Donald Benton", - "author_inst": "Francis Crick Institute" - }, - { - "author_name": "Chloe Roustan", - "author_inst": "Francis Crick Institute" - }, - { - "author_name": "William Bolland", - "author_inst": "Francis Crick Institute" - }, - { - "author_name": "Rachael Thompson", - "author_inst": "Francis Crick Institute" - }, - { - "author_name": "Ana Agua-Doce", - "author_inst": "Francis Crick Institute" - }, - { - "author_name": "Philip Hobson", - "author_inst": "Francis Crick Institute" - }, - { - "author_name": "Judith Heaney", - "author_inst": "University College London Hospitals NHS Trust" - }, - { - "author_name": "Hannah Rickman", - "author_inst": "University College London Hospitals NHS Trust" - }, - { - "author_name": "Stavroula Paraskevopoulou", - "author_inst": "University College London Hospitals NHS Trust" - }, - { - "author_name": "Catherine F Houlihan", - "author_inst": "University College London Hospitals NHS Trust; Division of Infection and Immunity, University College London" - }, - { - "author_name": "Kirsty Thomson", - "author_inst": "University College London Hospitals NHS Trust" - }, - { - "author_name": "Emilie Sanchez", - "author_inst": "University College London Hospitals NHS Trust" - }, - { - "author_name": "David Brealey", - "author_inst": "University College London Hospitals NHS Trust" - }, - { - "author_name": "Gee Yen Shin", - "author_inst": "University College London Hospitals NHS Trust" - }, - { - "author_name": "Moira J Spyer", - "author_inst": "University College London Hospitals NHS Trust; Department of Population, Policy and Practice, Great Ormond Street Institute for Child Health, University College" - }, - { - "author_name": "Dhira Joshi", - "author_inst": "Francis Crick Institute" - }, - { - "author_name": "Philip A Walker", - "author_inst": "Francis Crick Institute" - }, - { - "author_name": "Svend Kjaer", - "author_inst": "Francis Crick Institute" - }, - { - "author_name": "Andrew Riddell", - "author_inst": "Francis Crick Institute" - }, - { - "author_name": "Catherine Moore", - "author_inst": "Public Health Wales, University Hospital of Wales" - }, - { - "author_name": "Bethany R Jebson", - "author_inst": "UCL Great Ormond Street Institute for Child Health" - }, - { - "author_name": "Lucy R Marshall", - "author_inst": "UCL Great Ormond Street Institute for Child Health" - }, - { - "author_name": "Meredyth G Wilkinson", - "author_inst": "UCL Great Ormond Street Institute for Child Health" - }, - { - "author_name": "Elizabeth C Rosser", - "author_inst": "UCL Great Ormond Street Hospital Centre for Rheumatology Research; Division of Medicine, UCL" - }, - { - "author_name": "Anna Radziszewska", - "author_inst": "UCL Great Ormond Street Hospital Centre for Rheumatology Research; Division of Medicine, UCL" - }, - { - "author_name": "Hannah Peckham", - "author_inst": "UCL Great Ormond Street Hospital Centre for Rheumatology Research; Division of Medicine, UCL" - }, - { - "author_name": "Coziana Ciurtin", - "author_inst": "UCL Great Ormond Street Hospital Centre for Rheumatology Research; Division of Medicine, UCL" - }, - { - "author_name": "Lucy R Wedderburn", - "author_inst": "UCL Great Ormond Street Hospital Centre for Rheumatology Research; UCL Great Ormond Street Institute for Child Health; Division of Medicine, UCL" - }, - { - "author_name": "Rupert Beale", - "author_inst": "Francis Crick Institute" - }, - { - "author_name": "Charles Swanton", - "author_inst": "Francis Crick Institute" - }, - { - "author_name": "Sonia Gandhi", - "author_inst": "Francis Crick Institute" - }, - { - "author_name": "Brigitta Stockinger", - "author_inst": "Francis Crick Institute" - }, - { - "author_name": "John McCauley", - "author_inst": "Francis Crick Institute" - }, - { - "author_name": "Steve Gamblin", - "author_inst": "Francis Crick Institute" - }, - { - "author_name": "Laura E McCoy", - "author_inst": "Division of Infection and Immunity, University College London" - }, - { - "author_name": "Peter Cherepanov", - "author_inst": "Francis Crick Institute" - }, - { - "author_name": "Eleni Nastouli", - "author_inst": "University College London Hospitals NHS Trust; Department of Population, Policy and Practice, Great Ormond Street Institute for Child Health, University College" - }, - { - "author_name": "George Kassiotis", - "author_inst": "Francis Crick Institute; Department of Medicine, Imperial College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.05.14.090332", "rel_title": "Distribution of ACE2, CD147, cyclophilins, CD26 and other SARS-CoV-2 associated molecules in human tissues and immune cells in health and disease", @@ -1446950,6 +1448978,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.11.20098087", + "rel_title": "Monitoring and Tracking the Evolution of a Viral Epidemic Through Nonlinear Kalman Filtering: Application to the Covid-19 Case", + "rel_date": "2020-05-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20098087", + "rel_abs": "This work presents a novel methodology for systematically processing the time series that report the number of positive, recovered and deceased cases from a viral epidemic, such as Covid-19. The main objective is to unveil the evolution of the number of real infected people, and consequently to predict the peak of the epidemic and subsequent evolution. For this purpose, an original nonlinear model relating the raw data with the time-varying geometric ratio of infected people is elaborated, and a Kalman Filter is used to estimate the involved state variables. A hypothetical simulated case is used to show the adequacy and limitations of the proposed method. Then, several countries, including China, South Korea, Italy, Spain, UK and the USA, are tested to illustrate its behavior when real-life data are processed. The results obtained clearly show the beneficial effect of the social distancing measures adopted worldwide, confirming that the Covid-19 epidemic peak is left behind in those countries where the outbreak started earlier, and anticipating when the peak will take place in the remaining countries.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Antonio Gomez-Exposito", + "author_inst": "University of Seville" + }, + { + "author_name": "Jose A. Rosendo-Macias", + "author_inst": "University of Seville" + }, + { + "author_name": "Miguel A. Gonzalez-Cagigal", + "author_inst": "University of Seville" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.11.20098145", "rel_title": "Early estimation of the risk factors for hospitalisation and mortality by COVID-19 in Mexico", @@ -1447738,49 +1449793,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.05.11.20097980", - "rel_title": "Proposed Clinical Indicators for Efficient Screening and Testing for COVID-19 Infection from Classification and Regression Trees (CART) Analysis", - "rel_date": "2020-05-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20097980", - "rel_abs": "BackgroundThe introduction and rapid transmission of SARS CoV2 in the United States resulted in implementation of methods to assess, mitigate and contain the resulting COVID-19 disease based on limited knowledge. Screening for testing has been based on symptoms typically observed in inpatients, yet outpatient symptom complexes may differ.\n\nMethodsClassification and regression trees (CART) recursive partitioning created a decision tree classifying enrollees into laboratory-confirmed cases and non-cases. Demographic and symptom data from patients ages 18-87 years who were enrolled from March 29-April 26, 2020 were included. Presence or absence of SARSCoV2 was the target variable.\n\nResultsOf 736 tested, 55 were positive for SARS-CoV2. Cases significantly more often reported chills, loss of taste/smell, diarrhea, fever, nausea/vomiting and contact with a COVID-19 case, but less frequently reported shortness of breath and sore throat. A 7-terminal node tree with a sensitivity of 96% and specificity of 53%, and an AUC of 78% was developed. The positive predictive value for this tree was 14% while the negative predictive value was 99%. Almost half (44%) of the participants could be ruled out as likely non-cases without testing.\n\nDiscussionAmong those referred for testing, negative responses to three questions could classify about half of tested persons with low risk for SARS-CoV2 and would save limited testing resources. These questions are: was the patient in contact with a COVID-19 case? Has the patient experienced 1) a loss of taste or smell; or 2) nausea or vomiting? The outpatient symptoms of COVID-19 appear to be broader than the well-known inpatient syndrome.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Richard K Zimmerman", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Mary Patricia Nowalk", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Todd Bear", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Rachel Taber", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Theresa M Sax", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Heather Eng", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Goundappa K Balasubramani", - "author_inst": "University of Pittsburgh" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.11.20097923", "rel_title": "Comparative analyses revealed reduced spread of COVID-19 in malaria endemic countries", @@ -1448300,6 +1450312,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.12.20099754", + "rel_title": "Laboratory validation of an RNA/DNA hybrid tagmentation based mNGS workflow on SARS-CoV-2 and other respiratory RNA viruses detection", + "rel_date": "2020-05-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.12.20099754", + "rel_abs": "BackgroundAcute respiratory infection (ARI) caused by RNA viruses is still one of the main diseases all over the world such as SARS-CoV-2 and Influenza A virus. mNGS was a powerful tool for ethological diagnosis. But there were some challenges during mNGS implementation in clinical settings such as time-consuming manipulation and lack of comprehensive analytical validation.\n\nMethodsWe set up CATCH that was a mNGS method based on RNA and DNA hybrid tagmentation via Tn5 transposon. Seven respiratory RNA viruses and three subtypes of Influenza A virus had been used to test CATCHs capabilities of detection and semiquantification. Analytical performance of SARS-CoV-2 and Influenza A virus had been determined with reference standards. We compared accuracy of CATCH with quantitative real time PCR by using clinical 98 samples from 64 COVID-19 patients.\n\nResultsWe minimized the library preparation process to 3 hours and handling time to 35 minutes. Duplicate filtered RPM of 7 respiratory viruses and 3 Influenza A virus subtypes were highly correlated with viral concentration (r=0.60, p<0.001, Spearman correlation test). LOD of SARS-CoV-2 was 39.2 copies/test and of Influenza A virus was 278.1 copies/mL Comparing with qR-TPCR, the overall accuracy of CATCH was 91.4%. Sensitivity was 84.5% and specificity was 100%. Meanwhile, there were significant difference of microbial profile in oropharyngeal swabs among critical, moderate patients and healthy controls (p<0.001, PERMANOVA test).\n\nConclusionAlthough further optimization is needed before CATCH can be rolled out as a routine diagnostic test, we highlight the potential impact of it advancing molecular diagnostics for respiratory pathogens.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Feili Wei", + "author_inst": "Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China; Beijing Precision Medicine and Transformation Engi" + }, + { + "author_name": "Yanhua Yu", + "author_inst": "Clinical Laboratory Center, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China" + }, + { + "author_name": "Zhongjie Hu", + "author_inst": "Department of Critical Care Medicine of Liver Disease, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China" + }, + { + "author_name": "Rui Wang", + "author_inst": "Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China" + }, + { + "author_name": "Xianghua Guo", + "author_inst": "Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China; Beijing Precision Medicine and Transformation Engi" + }, + { + "author_name": "Haiying Jin", + "author_inst": "Clinical Laboratory Center, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China" + }, + { + "author_name": "Shan Guo", + "author_inst": "Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China; Beijing Precision Medicine and Transformation Engi" + }, + { + "author_name": "Yabo Ouyang", + "author_inst": "Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China; Beijing Precision Medicine and Transformation Engi" + }, + { + "author_name": "Ying Shi", + "author_inst": "Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China; Beijing Precision Medicine and Transformation Engi" + }, + { + "author_name": "Ronghua Jin", + "author_inst": "Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China; Beijing Precision Medicine and Transformation Engi" + }, + { + "author_name": "Dexi Chen", + "author_inst": "Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China; Beijing Precision Medicine and Transformation Engi" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.11.20097709", "rel_title": "Systemic corticosteroids show no benefit in severe and critical COVID-19 patients in Wuhan, China: A retrospective cohort study", @@ -1449116,113 +1451187,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.08.20095935", - "rel_title": "Defining the Pandemic at the State Level: Sequence-Based Epidemiology of the SARS-CoV-2 virus by the Arizona COVID-19 Genomics Union (ACGU)", - "rel_date": "2020-05-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.08.20095935", - "rel_abs": "In December of 2019, a novel coronavirus, SARS-CoV-2, emerged in the city of Wuhan, China causing severe morbidity and mortality. Since then, the virus has swept across the globe causing millions of confirmed infections and hundreds of thousands of deaths. To better understand the nature of the pandemic and the introduction and spread of the virus in Arizona, we sequenced viral genomes from clinical samples tested at the TGen North Clinical Laboratory, provided to us by the Arizona Department of Health Services, and at Arizona State University and the University of Arizona, collected as part of community surveillance projects. Phylogenetic analysis of 79 genomes we generated from across Arizona revealed a minimum of 9 distinct introductions throughout February and March. We show that >80% of our sequences descend from clades that were initially circulating widely in Europe but have since dominated the outbreak in the United States. In addition, we show that the first reported case of community transmission in Arizona descended from the Washington state outbreak that was discovered in late February. Notably, none of the observed transmission clusters are epidemiologically linked to the original travel-related cases in the state, suggesting successful early isolation and quarantine. Finally, we use molecular clock analyses to demonstrate a lack of identifiable, widespread cryptic transmission in Arizona prior to the middle of February 2020.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Jason T Ladner", - "author_inst": "Northern Arizona University" - }, - { - "author_name": "Brendan B Larsen", - "author_inst": "University of Arizona" - }, - { - "author_name": "Jolene R Bowers", - "author_inst": "Translational Genomics Research Institute" - }, - { - "author_name": "Crystal M Hepp", - "author_inst": "Northern Arizona University" - }, - { - "author_name": "Evan Bolyen", - "author_inst": "Northern Arizona University" - }, - { - "author_name": "Megan Folkerts", - "author_inst": "Translational Genomics Research Institute" - }, - { - "author_name": "Krystal Sheridan", - "author_inst": "Northern Arizona University" - }, - { - "author_name": "Ashlyn Pfeiffer", - "author_inst": "Translational Genomics Research Institute" - }, - { - "author_name": "Hayley Yaglom", - "author_inst": "Translational Genomics Research Institute" - }, - { - "author_name": "Darrin Lemmer", - "author_inst": "Translational Genomics Research Institute" - }, - { - "author_name": "Jason W Sahl", - "author_inst": "Northern Arizona University" - }, - { - "author_name": "Emily A Kaelin", - "author_inst": "Arizona State University" - }, - { - "author_name": "Rabia Maqsood", - "author_inst": "Arizona State University" - }, - { - "author_name": "Nicholas A Bokulich", - "author_inst": "Northern Arizona University" - }, - { - "author_name": "Grace Quirk", - "author_inst": "University of Arizona" - }, - { - "author_name": "Thomas D Watt", - "author_inst": "University of Arizona" - }, - { - "author_name": "Kenneth Komatsu", - "author_inst": "Arizona Department of Health Services" - }, - { - "author_name": "Victor Waddell", - "author_inst": "Arizona Department of Health Services" - }, - { - "author_name": "Efrem S Lim", - "author_inst": "Arizona State University" - }, - { - "author_name": "J. Gregory Caporaso", - "author_inst": "Northern Arizona University" - }, - { - "author_name": "David M Engelthaler", - "author_inst": "Translational Genomics Research Institute" - }, - { - "author_name": "Michael Worobey", - "author_inst": "University of Arizona" - }, - { - "author_name": "Paul Keim", - "author_inst": "Northern Arizona University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.09.20091447", "rel_title": "Rapid response flow cytometric assay for the detection of antibody responses to SARS-CoV-2", @@ -1449906,6 +1451870,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.08.20096024", + "rel_title": "SARS-CoV-2 activates lung epithelia cell proinflammatory signaling and leads to immune dysregulation in COVID-19 patients by single-cell sequencing", + "rel_date": "2020-05-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.08.20096024", + "rel_abs": "ObjectiveThe outbreak of Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 infection has become a global health emergency. We aim to decipher SARS-CoV-2 infected cell types, the consequent host immune response and their interplay in the lung of COVID-19 patients.\n\nDesignWe analyzed single-cell RNA sequencing (scRNA-seq) data of lung samples from 17 subjects (6 severe COVID-19 patients, 3 mild patients who recovered and 8 healthy controls). The expression of SARS-CoV-2 receptors (ACE2 and TMPRSS2) was examined among different cell types in the lung. The immune cells infiltration patterns, their gene expression profiles, and the interplay of immune cells and SARS-CoV-2 target cells were further investigated.\n\nResultsCompared to healthy controls, the overall ACE2 (receptor of SARS-CoV-2) expression was significantly higher in lung epithelial cells of COVID-19 patients, in particular in ciliated cell, club cell and basal cell. Comparative transcriptome analysis of these lung epithelial cells of COVID-19 patients and healthy controls identified that SARS-CoV-2 infection activated pro-inflammatory signaling including interferon pathway and cytokine signaling. Moreover, we identified dysregulation of immune response in patients with COVID-19. In severe COVID-19 patients, significantly higher neutrophil, but lower T and NK cells in lung were observed along with markedly increased cytokines (CCL2, CCL3, CCL4, CCL7, CCL3L1 and CCL4L2) compared with healthy controls as well as mild patients who recovered. The cytotoxic phenotypes were shown in lung T and NK cells of severe patients as evidenced by enhanced O_SCPLOWIFNC_SCPLOW{gamma}, Granulysin, Granzyme B and Perforin expression. Moreover, SARS-CoV-2 infection altered the community interplay of lung epithelial cells and immune cells: the interaction between epithelial cells with macrophage, T and NK cell was stronger, but their interaction with neutrophils was lost in COVID-19 patients compared to healthy controls.\n\nConclusionsSARS-CoV-2 infection activates pro-inflammatory signaling in lung epithelial cells expressing ACE2 and causes dysregulation of immune response to release more pro-inflammatory cytokines. Moreover, SARS-CoV-2 infection breaks the interplay of lung epithelial cells and immune cells.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Huarong Chen", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Weixin Liu", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Dabin Liu", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Liuyang Zhao", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Jun Yu", + "author_inst": "The Chinese University of Hong Kong" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.09.20096032", "rel_title": "A Novel Box for Aerosol and Droplet Guarding and Evacuation in Respiratory Infection (BADGER): A Potential Mitigating Strategy for the COVID-19 Pandemic and Future Outbreaks", @@ -1450546,33 +1452545,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.09.20096560", - "rel_title": "COVID-Classifier: An efficient machine learning model to assist in the diagnosis of COVID-19 infection in chest x-ray images", - "rel_date": "2020-05-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.09.20096560", - "rel_abs": "Chest-X ray (CXR) radiography can be used as a first-line triage process for non-COVID-19 patients with pneumonia. However, the similarity between features of CXR images of COVID-19 and pneumonia caused by other infections make the differential diagnosis by radiologists challenging. We hypothesized that machine learning-based classifiers can reliably distinguish the CXR images of COVID-19 patients from other forms of pneumonia. We used a dimensionality reduction method to generate a set of optimal features of CXR images to build an efficient machine learning classifier that can distinguish COVID-19 cases from non-COVID-19 cases with high accuracy and sensitivity. By using global features of the whole CXR images, we were able to successfully implement our classifier using a relatively small dataset of CXR images. We propose that our COVID-Classifier can be used in conjunction with other tests for optimal allocation of hospital resources by rapid triage of non-COVID-19 cases.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Abolfazl Zargari Khuzani", - "author_inst": "Department of Electrical and Computer Engineering, University of California, Santa Cruz, Santa Cruz, CA abzargar@ucsc.edu" - }, - { - "author_name": "Morteza Heidari", - "author_inst": "School of Electrical and Computer Engineering, The University of Oklahoma, Norman, OK" - }, - { - "author_name": "Ali Shariati", - "author_inst": "Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2020.05.08.20096040", "rel_title": "COVID-19 and Acute Kidney Injury requiring Kidney Replacement Therapy: A Bad Prognostic Sign.", @@ -1451168,6 +1453140,49 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.05.12.20092270", + "rel_title": "Planning phase-2 for the endoscopic units in Northern Italy after COVID-19 lockdown: an exit strategy with a lot of critical issues and a few opportunities.", + "rel_date": "2020-05-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.12.20092270", + "rel_abs": "Background and aimsRestarting activity in Endoscopic Departments (ED) after COVID-19 lockdown raises critical issues. This survey investigates strategies and uncertainties on resumption of elective activity.\n\nMethodsDirectors of 55 EDs in Northern Italy received a questionnaire focusing on the impact of pandemic on activity and organization and on the resources available at re-opening. A section was devoted to gather forecasts and proposals on the return path to normality.\n\nResultsAll centres had reduced their activities of at least 50% of the pre-COVID-19 period. A rate of endoscopists (13.6%), nurses (25.2%), and health assistants (14%) were not available since infected, or relocated to other departments. One third of endoscopic rooms were converted to COVID-19 care. Two third had the waiting or the recovery areas too small for distancing. A dedicated pathway for infected patients could not be guaranteed in 20% of EDs. Only one third of EDs judged realistic to completely restore a pre-crisis workload by the next months. Optimizing appropriateness of procedures, closer interaction with GPs and triaging patients with telemedicine were the proposals to re-open EDs.\n\nConclusionsThe critical issues while re-opening EDs calls for reducing the workload in the endoscopy units through appropriate rescheduling of procedures.\n\nFundingNone", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Gianpiero Manes", + "author_inst": "ASST Rhodense, Milano, Italy" + }, + { + "author_name": "alessandro Repici", + "author_inst": "Humanitas" + }, + { + "author_name": "Franco Radaelli", + "author_inst": "Valduce Hospital" + }, + { + "author_name": "Simone Saibeni", + "author_inst": "ASST Rhodense" + }, + { + "author_name": "Cristina Bezzio", + "author_inst": "ASST Rhodense" + }, + { + "author_name": "Matteo Colombo", + "author_inst": "Humanitas" + }, + { + "author_name": "Fabio Pace", + "author_inst": "Seriate Hospital" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "gastroenterology" + }, { "rel_doi": "10.1101/2020.05.11.089862", "rel_title": "Evaluation of the EUROIMMUN Anti-SARS-CoV-2 ELISA Assay for detection of IgA and IgG antibodies", @@ -1452140,49 +1454155,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rehabilitation medicine and physical therapy" }, - { - "rel_doi": "10.1101/2020.05.08.20095364", - "rel_title": "Capsid integrity quantitative PCR to determine virus infectivity in environmental and food applications; a systematic review", - "rel_date": "2020-05-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.08.20095364", - "rel_abs": "Capsid-integrity quantitative PCR (qPCR), a molecular detection method for infectious viruses combining azo-dye pretreatment with qPCR, has been widely used in recent years; however, variations in pretreatment conditions for various virus types can limit the efficacy of specific protocols. By identifying and critically synthesizing forty-two recent peer-reviewed studies employing capsid-integrity qPCR for viruses in the last decade (2009 to 2019) in the fields of food safety and environmental virology, we aimed to establish recommendations for the detection of infectious viruses. Intercalating dyes are effective measures of viability in PCR assays provided the viral capsid is damaged; viruses that have been inactivated by other causes, such as loss of attachment or genomic damage, are less well detected using this approach. Although optimizing specific protocols for each virus is recommended, we identify a framework for general assay conditions. These include concentrations of ethidium monoazide, propidium monoazide or its derivates between 10 and 200 {micro}M; incubation on ice or at room temperature (20 - 25{degrees}C) for 5 to 120 min; and dye activation using LED or high light (500 - 800 Watts) exposure for periods ranging from 5 to 20 min. These simple steps can benefit the investigation of infectious virus transmission in routine (water) monitoring settings and during viral outbreaks such as the current COVID-19 pandemic or endemic diseases like dengue fever.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=96 SRC=\"FIGDIR/small/20095364v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (28K):\norg.highwire.dtl.DTLVardef@12f34b5org.highwire.dtl.DTLVardef@2d7a8forg.highwire.dtl.DTLVardef@1c951c3org.highwire.dtl.DTLVardef@16f7df_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Mats Leifels", - "author_inst": "Singapore Centre for Life Science Engineering, Nanyang Technological University, Nanyang Technological University (NTU), Singapore" - }, - { - "author_name": "Cheng Dan", - "author_inst": "Singapore Centre for Life Science Engineering, Nanyang Technological University, Nanyang Technological University (NTU), Singapore" - }, - { - "author_name": "Emanuele Sozzi", - "author_inst": "Gillings School of Global Public Health, Department of Environmental Science and Engineering, University of North Carolina at Chapel Hill, NC, USA" - }, - { - "author_name": "David C Shoults", - "author_inst": "Civil and Resource Engineering, Dalhousie University, Halifax, Nova Scotia, Canada" - }, - { - "author_name": "Stefan Wuertz", - "author_inst": "School of Civil and Environmental Engineering and Singapore Centre for Life Sciences Engineering, Nanyang Technological University (NTU), Singapore" - }, - { - "author_name": "Skorn Mongkolsuk", - "author_inst": "Research Laboratory of Biotechnology, Chulabhorn Research Institute and Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education," - }, - { - "author_name": "Kwanrawee Sirikanchana", - "author_inst": "Research Laboratory of Biotechnology, Chulabhorn Research Institute and Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education," - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2020.05.07.20094748", "rel_title": "COVID-19 Outbreak, Social Response, and Early Economic Effects: A Global VAR Analysis of Cross-Country Interdependencies", @@ -1452750,6 +1454722,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "anesthesia" }, + { + "rel_doi": "10.1101/2020.05.08.20095133", + "rel_title": "A two-wave epidemiological model of COVID-19 outbreaks using MS-Excel(R)", + "rel_date": "2020-05-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.08.20095133", + "rel_abs": "The emergence of the coronavirus SARS-CoV-2 has raised a global issue and a pandemic disease outbreak, COVID-19, was declared by the World Health Organization on March 12th, 2020. The new virus is rapidly spreading in humans and cases of severe acute respiratory syndromes are being reported worldwide. Health authority advisors and governments from small towns to large countries need to quickly manage and deal with growing epidemiological data on a daily basis. In this work, current available data from reported cases and deaths over time were analyzed and treated. Lethality has been calculated by finding linearization of death cases against reported ones, using a time-delayed data transposition. A two-wave statistical model, 2WM, based on the superposition of normal distributions was used to fit current data and to estimate the evolution of infections and deaths, using Microsoft(R) Excel. The model showed good agreement even for apparent single wave behavior in some countries and can easily be extended to any number of waves. A gamma distribution was used as a risk function to estimate death probability from patient admission to reported death. Evolution of fatality cases over time can then be estimated from the model with reasonable accuracy. Data from South Korea, China, Australia, Germany, Italy and Spain were used to validate the model. Data from The United States, United Kingdom and Brazil were used to study the epidemiology as the pandemic progresses. Additionally, the 2WM was applied to world data and to the Brazilian state of Santa Catarina. The model was implemented in MS-Excel, a popular and easy to use analytical tool. A template spreadsheet is provided as supplementary material. Constant lethality can be determined from the initial stage of the pandemic wave. Values ranged from 1.7% to 15.3%, depending on the degree of possible sub notification cases. Even for places with low testing, a linear relationship can be found. The two-wave model can be fine-tuned to properly adjust the data. The second wave pattern was estimated according to the first wave parameter. The accuracy for estimating COVID-19 evolution was compared to the classic SIR model with good agreement. According to the model, based on current trends, health protocols and policies, approximately 10,000,000 cases and 860,000 deaths will be recorded worldwide. Approximately 99% of that number would be reached by the end of July 2020 given constant conditions.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Agenor De Noni Jr.", + "author_inst": "Federal University of Santa Catarina" + }, + { + "author_name": "Bernando Araldi da Silva", + "author_inst": "Federal University of Santa Catarina" + }, + { + "author_name": "Felipe Dal-Pizzol", + "author_inst": "University of the Extreme South of Santa Catarina" + }, + { + "author_name": "Luismar Marques Porto", + "author_inst": "Federal University of Santa Catarina" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.08.20095505", "rel_title": "Significant Relaxation of SARS-CoV-2-Targeted Non-Pharmaceutical Interventions Will Result in Profound Mortality: A New York State Modelling Study", @@ -1453502,97 +1455505,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.05.12.091298", - "rel_title": "Characterization of neutralizing antibodies from a SARS-CoV-2 infected individual", - "rel_date": "2020-05-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.12.091298", - "rel_abs": "B cells specific for the SARS-CoV-2 S envelope glycoprotein spike were isolated from a COVID-19-infected subject using a stabilized spike-derived ectodomain (S2P) twenty-one days post-infection. Forty-four S2P-specific monoclonal antibodies were generated, three of which bound to the receptor binding domain (RBD). The antibodies were minimally mutated from germline and were derived from different B cell lineages. Only two antibodies displayed neutralizing activity against SARS-CoV-2 pseudo-virus. The most potent antibody bound the RBD in a manner that prevented binding to the ACE2 receptor, while the other bound outside the RBD. Our study indicates that the majority of antibodies against the viral envelope spike that were generated during the first weeks of COVID-19 infection are non-neutralizing and target epitopes outside the RBD. Antibodies that disrupt the SARS-CoV-2 spike-ACE2 interaction can potently neutralize the virus without undergoing extensive maturation. Such antibodies have potential preventive/therapeutic potential and can serve as templates for vaccine-design.\n\nIN BRIEFSARS-CoV-2 infection leads to expansion of diverse B cells clones against the viral spike glycoprotein (S). The antibodies bind S with high affinity despite being minimally mutated. Thus, the development of neutralizing antibody responses by vaccination will require the activation of certain naive B cells without requiring extensive somatic mutation.\n\nHighlightsO_LIAnalysis of early B cell response to SARS-CoV-2 spike protein\nC_LIO_LIMost antibodies target non-neutralizing epitopes\nC_LIO_LIPotent neutralizing mAb blocks the interaction of the S protein with ACE2\nC_LIO_LINeutralizing antibodies are minimally mutated\nC_LI", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Emily Seydoux", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Leah J Homad", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Anna J MacCamy", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Katherine R Parks", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Nicholas K Hurlburt", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Madeleine F Jennewein", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Nicolas R Akins", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Andrew B Stuart", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Yu-Hsin Wan", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Junli Feng", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Rachael Nelson", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Suruchi Singh", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Kristen W Cohen", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Julie M McElrath", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Janet A Englund", - "author_inst": "University of Washington" - }, - { - "author_name": "Helen Y Chu", - "author_inst": "University of Washington" - }, - { - "author_name": "Marie Pancera", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Andrew T McGuire", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Leonidas Stamatatos", - "author_inst": "Fred Hutchinson Cancer Research Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.05.11.089896", "rel_title": "Performance of the rapid Nucleic Acid Amplification by Abbott ID NOW COVID-19 in nasopharyngeal swabs transported in viral media and dry nasal swabs, in a New York City academic institution", @@ -1454271,6 +1456183,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.08.20089268", + "rel_title": "Characteristics and outcomes of pregnant women hospitalised with confirmed SARS-CoV-2 infection in the UK: a national cohort study using the UK Obstetric Surveillance System (UKOSS)", + "rel_date": "2020-05-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.08.20089268", + "rel_abs": "ObjectiveTo describe a national cohort of pregnant women hospitalised with SARS-CoV-2 infection in the UK, identify factors associated with infection and describe outcomes, including transmission of infection, for mother and infant.\n\nDesignProspective national population-based cohort study using the UK Obstetric Surveillance System (UKOSS).\n\nSettingAll 194 obstetric units in the UK\n\nParticipants427 pregnant women admitted to hospital with confirmed Sars-CoV-2 infection between 01/03/2020 and 14/04/2020. 694 comparison women who gave birth between 01/11/2017 and 31/10/2018.\n\nMain outcome measuresIncidence of maternal hospitalisation, infant infection. Rates of maternal death, level 3 critical care unit admission, preterm birth, stillbirth, early neonatal death, perinatal death; odds ratios for infected versus comparison women.\n\nResultsEstimated incidence of hospitalisation with confirmed SARS-CoV-2 in pregnancy 4.9 per 1000 maternities (95%CI 4.5-5.4). The median gestation at symptom onset was 34 weeks (IQR 29-38). Black or other minority ethnicity (aOR 4.49, 95%CI 3.37-6.00), older maternal age (aOR 1.35, 95%CI 1.01-1.81 comparing women aged 35+ with those aged 30-34), overweight and obesity (aORs 1.91, 95%CI 1.37-2.68 and 2.20, 95%CI 1.56-3.10 respectively compared to women with a BMI<25kg/m2) and pre-existing comorbidities (aOR 1.52, 95%CI 1.12-2.06) were associated with admission with SARS-CoV-2 during pregnancy. 247 women (58%) gave birth or had a pregnancy loss; 180 (73%) gave birth at term. 40 (9%) hospitalised women required respiratory support. Twelve infants (5%) tested positive for SARS-CoV-2 RNA, six of these infants within the first 12 hours after birth.\n\nConclusionsThe majority of pregnant women hospitalised with SARS-CoV-2 were in the late second or third trimester, supporting guidance for continued social distancing measures in later pregnancy. Most had good outcomes and transmission of SARS-CoV-2 to infants was uncommon. The strong association between admission with infection and black or minority ethnicity requires urgent investigation and explanation.\n\nStudy RegistrationISRCTN 40092247", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Marian Knight", + "author_inst": "University of Oxford" + }, + { + "author_name": "Kathryn Bunch", + "author_inst": "University of Oxford" + }, + { + "author_name": "Nicola Vousden", + "author_inst": "Kings College London" + }, + { + "author_name": "Edward Morris", + "author_inst": "Norfolk and Norwich University Hospital" + }, + { + "author_name": "Nigel Simpson", + "author_inst": "University of Leeds" + }, + { + "author_name": "Christopher Gale", + "author_inst": "Imperial College London" + }, + { + "author_name": "Patrick O'Brien", + "author_inst": "University College Hospital London" + }, + { + "author_name": "Maria Quigley", + "author_inst": "University of Oxford" + }, + { + "author_name": "Peter Brocklehurst", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Jennifer J Kurinczuk", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "obstetrics and gynecology" + }, { "rel_doi": "10.1101/2020.05.07.20093831", "rel_title": "Systematic Review and Meta-analysis of the Effectiveness and Safety of Hydroxychloroquine in COVID-19.", @@ -1454951,49 +1456918,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.07.20093898", - "rel_title": "Remdesivir in treatment of COVID-19: A systematic benefit-risk assessment", - "rel_date": "2020-05-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.07.20093898", - "rel_abs": "BackgroundThere is a need to identify effective, safe treatments for COVID-19 (coronavirus disease) rapidly, given the current, ongoing pandemic. A systematic benefit-risk assessment was designed and conducted to strengthen the ongoing understanding of the benefit-risk balance for remdesivir in COVID-19 treatment by using a structured method which uses all available data.\n\nMethodsThe Benefit-Risk Action Team (BRAT) framework was used to assess the overall benefit-risk of the use of remdesivir as a treatment for COVID-19 compared to standard of care, placebo or other treatments. We searched PubMed,Google Scholar and government agency websites to identify literature reporting clinical outcomes in patients taking remdesivir for COVID-19. A value tree was constructed and key benefits and risks were ranked by two clinicians in order of considered importance.\n\nResultsSeveral key benefits and risks for use of remdesivir in COVID-19 compared to placebo have been identified. In one trial, the benefit of time to clinical improvement was not statistically significant (21 vs 23 days, HR=1.23, 95% CI: 0.87, 1.75), although the study was underpowered. In another trial, a shorter time to recovery in patients treated with remdesivir was observed (11 vs 15 days), with non-significant reduced mortality risk (8% vs 12%). Risk data were only available from one trial. This trial reported fewer serious adverse events in patients taking remdesivir (18%) comparted to the placebo group (26%), however more patients in the remdesivir group discontinued treatment as a result of an adverse event compared to those patients receiving placebo (12% vs 5%).\n\nConclusionsPreliminary clinical trial results suggest a favourable benefit-risk profile for remdesivir compared to placebo, however there is limited safety data available at the current time. The current framework summarises the key anticipated benefits and risks for which further data are needed. Ongoing clinical trial data can be incorporated into the framework when available to provide an updated benefit-risk assessment.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Miranda Davies", - "author_inst": "Drug Safety Research Unit, Southampton, UK" - }, - { - "author_name": "Vicki Osborne", - "author_inst": "Drug Safety Research Unit, Southampton, UK" - }, - { - "author_name": "Samantha Lane", - "author_inst": "Drug Safety Research Unit, Southampton, UK" - }, - { - "author_name": "Debabrata Roy", - "author_inst": "Drug Safety Research Unit, Southampton, UK" - }, - { - "author_name": "Sandeep Dhanda", - "author_inst": "Drug Safety Research Unit, Southampton, UK" - }, - { - "author_name": "Alison Evans", - "author_inst": "Drug Safety Research Unit, Southampton, UK" - }, - { - "author_name": "Saad AW Shakir", - "author_inst": "Drug Safety Research Unit, Southampton, UK" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.08.20095117", "rel_title": "CORRELATION BETWEEN CHEST COMPUTED TOMOGRAPHY AND LUNG ULTRASONOGRAPHY IN PATIENTS WITH CORONAVIRUS DISEASE 2019 (COVID-19)", @@ -1455805,6 +1457729,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2020.05.06.20092981", + "rel_title": "How many COVID-19 cases could have been prevented in the US if its interventions were as effective as those in China and South Korea?", + "rel_date": "2020-05-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20092981", + "rel_abs": "The COVID-19 [1] pandemic has forced governments to take measures to contain the spread of the disease [2]; however, the effects have varied significantly from one country to another contingent on governments responses. Countries that have flattened their coronavirus curves prove that interventions can bring COVID-19 under control. These achievements hold lessons, such as the strict social distancing and coordinated efforts of all government levels in China and massive testing in South Korea, for other countries battling the coronavirus around the world. In this work, we attempt to estimate how many COVID-19 cases could have been prevented in the United States (US) when compared with the USs actual number of cases assuming that on a certain date, the US took China-like or South Korea-like interventions and that these interventions would have been as effective in the US as in China and South Korea. We found that if that date was at the early stage of the outbreak (March 10), more than 99% (1.15 million) fewer infected cases could be expected by the end of the epidemic. This number decreases to 66.03% and 73.06% fewer infected cases with the China-like scenario and the South Korea-like scenario, respectively, if actions were taken on April 1, highlighting the need to respond quickly and effectively to fight the virus. Furthermore, we found that although interventions in both China and South Korea allowed the COVID-19 outbreak to be managed, the epidemic could still oscillate without strict large-scale lockdown measures, as shown in South Korea. Our results demonstrate that early effective interventions can save considerably more people from infection and provide a worldwide alert regard the need for swift response.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Kai Liu", + "author_inst": "Beijing Normal University" + }, + { + "author_name": "Yukun Song", + "author_inst": "Beijing Normal University" + }, + { + "author_name": "Menghui Li", + "author_inst": "Beijing Institute of Science and Technology Information" + }, + { + "author_name": "Zhesi Shen", + "author_inst": "National Science Library" + }, + { + "author_name": "Ming Wang", + "author_inst": "Beijing Normal University" + }, + { + "author_name": "Jinshan Wu", + "author_inst": "Beijing Normal University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.07.20092775", "rel_title": "Monitoring the Covid-19 epidemics in Italy from mortality data", @@ -1456605,29 +1458568,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.08.20095869", - "rel_title": "Prediction of 2019-nCov in Italy based on PSO and inversion analysis", - "rel_date": "2020-05-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.08.20095869", - "rel_abs": "Novel coronavirus (2019-nCov) has swept the world, and all of the world have been harmful. This article makes prediction and suggestions for the Italy. Up to March 11, 2020, 2019-nCov thoroughly broke out in Italy with over 10,000 confirmed cases notwithstanding the gradually block of the country since March 9, 2020. Estimation of possible infection population and prospective suggestion of handling spread based on exist data are of crucial importance. Considering of the biology parameters obtained based on Chinese clinical data in Wuhan, other scholars work and real spread feature of 2019-nCov in Italy, we built a more applicable model called SEIJR with log-normal distributed time delay to forecast the trend of spreading. Adopting Particle Swarm Optimization (PSO), we estimated the early period average spreading velocity (0) and conducted inversion analysis of time point (T0) when the virus first hit the Italy. Based on fixed 0 and T0, we then obtained the average spreading velocity 1 after the lock by PSO. For the aim of offering expeditious advice, we generated the prediction trends with different which we considered would be helpful in addressing the infection. Not only solved the complex, nondifferentiable equation of epidemic model, our research also performs well in inversion analysis based on PSO which conveys informative outcomes for further discussion on precatious action. To conclude, the first day of spread is around February 1, 2020 with the early period average spreading velocity 0=0.330 which is higher than most cities in China except Wuhan. After locking the country and attaching great attention to public precaution, the 1 sharply descended to 0.278, indicting the effectiveness of these measures. Furthermore, in order to cope the disease before mid-April, take actions to control the under 0.25 is necessary. Code can be freely downloaded from https://github.com/Summerwork/2019-nCov-Prediction.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Siyi Sun", - "author_inst": "Science and Technology University, Beijing" - }, - { - "author_name": "Yangping Zheng", - "author_inst": "Sichuan University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.05.20091611", "rel_title": "The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing.", @@ -1457543,6 +1459483,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.07.20094334", + "rel_title": "Assessing the Intervention's Effectiveness and Health System Efficiency During COVID-19 Crisis using A Signal-to-Noise Ratio Index", + "rel_date": "2020-05-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.07.20094334", + "rel_abs": "During COVID-19 nearly everyone around the globe was monitoring the situation on a daily, if not hourly, basis by tracking a set of numbers that were reported by different institutions through multiple platforms: either official, or informal. Irrespective of the sources from which the data was pulled, many researchers, reporters and professionals made the effort to represent the data in different ways in an effort to explain: what happened, what was happening, and what might happen; with the hope of seeing a sign of slowing down the spread of the virus (SARS-CoV-2). A subset of these reported numbers included: the confirmed cases, number of deaths, number of recovered cases along with the number of tests being carried out by each country. Each of these numbers (metrics) was able to reveal only one side of the reality ignoring the messages that might come from other metrics (numbers). Focusing only on one single metric to reflect on the situation opened the doors for emergent opinions, theories speculations, and even confusion among the professionals before the public. In fact, all of these efforts to explain and describe the situation through the same available numbers did not manage to see clearly or shed the light on the performance and the efficiency of the countrys health system in dealing with the ongoing COVID-19 outbreak. It was evident that none of these numbers could reconstruct the full picture about the virus spread behavior nor about the capability and capacity of the health system in dealing with the pandemic. A combined metric should have been developed to best reflect the performance of the health system during the crisis. In this paper, a signal to noise ratio like index, snr was introduced in an attempt to evaluate the efficiency of the health system as well as the effectiveness of the interventions taken by the stakeholders in an effort to control the virus spread during any health-related crisis. Using this proposed index (snr), it was possible to carry out a data-driven comparison among different countries in their efforts of dealing with the crisis. The primary focus of this study was to assess the interventions effectiveness by the decision makers along with the health systems efficiency of the countries that experienced a relatively high pressure and stress on their systems. In this study, 19 countries were selected based on predefined criteria that included: (1) the reported total confirmed cases should exceed 5,000, and (2) the total confirmed cases per 1 million people should exceed 200, at the time this study was concluded.\n\nAccording to the proposed snr index, the findings showed that Germany and South Korea were ahead of the game, by far, compared to other countries such as the USA, Spain, Italy, Belgium, Netherlands, and UK. Some other countries, such as Canada, Austria, Switzerland managed to slightly pivot their interventions at a later stage in effective manners according to the snr index. The study explains the foundation, and the underlying calculations of the proposed snr index. Moreover, the study shows how reliably the snr index measures the interventions effectiveness and health systems efficiency during the crisis or during any health related crisis.\n\nAn additional, yet interesting finding from this study, was that the snr curve showed a persistent four episode (segment) structure or pattern during the pandemic. This finding could suggest a benchmark of the expected pattern of the fight against the virus spread during the pandemic that could offer a significant tool, or approach, for the decision makers.\n\nFinally, it is worth mentioning that the implementation of this proposed index is only valid and meaningful during a crisis. In a none crisis time, the required data to calculate the snr index is not available and rather mathematically misleading.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Khaled Wahba", + "author_inst": "Algoma university" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.07.20094326", "rel_title": "Chloroquine and hydroxychloroquine effectiveness in human subjects during coronavirus: a systematic review", @@ -1458371,29 +1460330,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.08.20095059", - "rel_title": "Age-stratified model of the COVID-19 epidemic to analyze the impact of relaxing lockdown measures: nowcasting and forecasting for Switzerland", - "rel_date": "2020-05-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.08.20095059", - "rel_abs": "Compartmental models enable the analysis and prediction of an epidemic including the number of infected, hospitalized and deceased individuals in a population. They allow for computational case studies on non-pharmaceutical interventions thereby providing an important basis for policy makers. While research is ongoing on the transmission dynamics of the SARS-CoV-2 coronavirus, it is important to come up with epidemic models that can describe the main stages of the progression of the associated COVID-19 respiratory disease. We propose an age-stratified discrete compartment model as an alternative to differential equation based S-I-R type of models. The model captures the highly age-dependent progression of COVID-19 and is able to describe the day-by-day advancement of an infected individual in a modern health care system. The fully-identified model for Switzerland not only predicts the overall histories of the number of infected, hospitalized and deceased, but also the corresponding age-distributions. The model-based analysis of the outbreak reveals an average infection fatality ratio of 0.4% with a pronounced maximum of 9.5% for those aged [≥]80 years. The predictions for different scenarios of relaxing the soft lockdown indicate a low risk of overloading the hospitals through a second wave of infections. However, there is a hidden risk of a significant increase in the total fatalities (by up to 200%) in case schools reopen with insufficient containment measures in place.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Fadoua Balabdaoui", - "author_inst": "ETH Zurich" - }, - { - "author_name": "Dirk Mohr", - "author_inst": "Swiss Federal Institute of Technology" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.07.20094078", "rel_title": "Time-Resolving the COVID-19 Outbreak using frequency domain analysis", @@ -1459069,6 +1461005,61 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.05.11.088112", + "rel_title": "Evidence for strong mutation bias towards, and selection against, T/U content in SARS-CoV2: implications for attenuated vaccine design.", + "rel_date": "2020-05-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.11.088112", + "rel_abs": "Large-scale re-engineering of synonymous sites is a promising strategy to generate attenuated viruses for vaccines. Attenuation typically relies on de-optimisation of codon pairs and maximization of CpG dinculeotide frequencies. So as to formulate evolutionarily-informed attenuation strategies, that aim to force nucleotide usage against the estimated direction favoured by selection, here we examine available whole-genome sequences of SARS-CoV2 to infer patterns of mutation and selection on synonymous sites. Analysis of mutational profiles indicates a strong mutation bias towards T with concomitant selection against T. Accounting for dinucleotide effects reinforces this conclusion, observed TT content being a quarter of that expected under neutrality. A significantly different mutational profile at CDS sites that are not 4-fold degenerate is consistent with contemporaneous selection against T mutations more widely. Although selection against CpG dinucleotides is expected to drive synonymous site G+C content below mutational equilibrium, observed G+C content is slightly above equilibrium, possibly because of selection for higher expression. Consistent with gene-specific selection against CpG dinucleotides, we observe systematic differences of CpG content between SARS-CoV2 genes. We propose an evolutionarily informed gene-bespoke approach to attenuation that, unusually, seeks to increase usage of the already most common synonymous codons. Comparable analysis of H1N1 and Ebola finds that GC3 deviated from neutral equilibrium is not a universal feature, cautioning against generalization of results.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Alan M Rice", + "author_inst": "The Milner Centre for Evolution, University of Bath" + }, + { + "author_name": "Atahualpa Castillo Morales", + "author_inst": "The Milner Centre for Evolution, University of Bath" + }, + { + "author_name": "Alexander T Ho", + "author_inst": "The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath" + }, + { + "author_name": "Christine Mordstein", + "author_inst": "The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath" + }, + { + "author_name": "Stefanie M\u00fchlhausen", + "author_inst": "The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath" + }, + { + "author_name": "Samir Watson", + "author_inst": "Aarhus University" + }, + { + "author_name": "Laura Cano", + "author_inst": "MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, The University of Edinburgh" + }, + { + "author_name": "Bethan Young", + "author_inst": "MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, The University of Edinburgh" + }, + { + "author_name": "Grzegorz Kudla", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Laurence D. Hurst", + "author_inst": "The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2020.05.11.088781", "rel_title": "Structural insight into the putative role of Novel Coronavirus-2 E protein in viral infection via in silico approach: a potential target for LAV development and other therapeutic strategies", @@ -1459653,29 +1461644,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "dentistry and oral medicine" }, - { - "rel_doi": "10.1101/2020.05.06.20093039", - "rel_title": "Mobility Reduction and Covid-19 Transmission Rates", - "rel_date": "2020-05-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20093039", - "rel_abs": "Assessing the contribution of mobility declines to the control of Covid-19 diffusion is an urgent challenge of global import. We analyze the temporal correlation between transmission rates and societal mobility levels using daily mobility data from Google and Apple in an international panel of 99 countries and a panel of all states in the United States. Reduced form regression estimates that flexibly control for time trends suggest that a 10 percentage point reduction in mobility is associated with a 0.04-0.07 reduction in the value of the effective reproduction number, R(t), depending on geographical region and modelling choice. According to these estimates, to avoid the critical value of R = 1, easing mobility restrictions may have to be limited or delayed until other non-mobility related preventative measures reduce R to a level of approximately 0.7 in Europe, 0.75 in Asia, and 0.8 in the United States. Given gaps in data availability and inference challenges, these estimates should be interpreted with caution.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Nittai K Bergman", - "author_inst": "Tel Aviv University" - }, - { - "author_name": "Ram Fishman", - "author_inst": "Tel Aviv University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.05.20092015", "rel_title": "Smoking Prevalence is Low in Symptomatic Patients Admitted for COVID-19.", @@ -1460327,6 +1462295,189 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2020.05.06.20089573", + "rel_title": "Recurrence of SARS-CoV-2 PCR positivity in COVID-19 patients: a single center experience and potential implications", + "rel_date": "2020-05-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20089573", + "rel_abs": "IMPORTANCEHow to appropriately care for patients who become PCR-negative for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still not known. Patients who have recovered from coronavirus disease 2019 (COVID-19) could profoundly impact the health care system if a subset were to be PCR-positive again with reactivated SARS-CoV-2.\n\nOBJECTIVETo characterize a single center COVID-19 cohort with and without recurrence of PCR positivity, and develop an algorithm to identify patients at high risk of retest positivity after discharge to inform health care policy and case management decision-making.\n\nDESIGN, SETTING, AND PARTICIPANTSA cohort of 414 patients with confirmed SARS-CoV-2 infection, at The Second Affiliated Hospital of Southern University of Science and Technology in Shenzhen, China from January 11 to April 23, 2020.\n\nEXPOSURESPolymerase chain reaction (PCR) and IgM-IgG antibody confirmed SARS-CoV-2 infection.\n\nMAIN OUTCOMES AND MEASURESUnivariable and multivariable statistical analysis of the clinical, laboratory, radiologic image, medical treatment, and clinical course of admission/quarantine/readmission data to develop an algorithm to predict patients at risk of recurrence of PCR positivity.\n\nRESULTS16.7% (95CI: 13.0%-20.3%) patients retest PCR positive 1 to 3 times after discharge, despite being in strict quarantine. The driving factors in the recurrence prediction model included: age, BMI; lowest levels of the blood laboratory tests during hospitalization for cholinesterase, fibrinogen, albumin, prealbumin, calcium, eGFR, creatinine; highest levels of the blood laboratory tests during hospitalization for total bilirubin, lactate dehydrogenase, alkaline phosphatase; the first test results during hospitalization for partial pressure of oxygen, white blood cell and lymphocyte counts, blood procalcitonin; and the first test episodic Ct value and the lowest Ct value of the nasopharyngeal swab RT PCR results. Area under the ROC curve is 0.786.\n\nCONCLUSIONS AND RELEVANCEThis case series provides clinical characteristics of COVID-19 patients with recurrent PCR positivity, despite strict quarantine, at a 16.7% rate. Use of a recurrence prediction algorithm may identify patients at high risk of PCR retest positivity of SARS-CoV-2 and help modify COVID-19 case management and health policy approaches.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSWhat are the characteristics, clinical presentations, and outcomes of COVID-19 patients with PCR retest positivity after resolution of the initial infection and consecutive negative tests? Can we identify recovered patients, prior to discharge, at risk of the recurrence of SARS-CoV-2 PCR positivity?\n\nFindingsIn this series of 414 COVID-19 inpatients discharged to a designated quarantine center, 69 retest positive (13 with 2 readmissions, and 3 with 3 readmissions). A multivariable model was developed to predict the risk of the recurrence of SARS-CoV-2 PCR positivity.\n\nMeaningRate and timing of the recurrence of PCR positivity following strict quarantine were characterized. Our prediction algorithm may have implications for COVID-19 clinical treatment, patient management, and health policy.", + "rel_num_authors": 42, + "rel_authors": [ + { + "author_name": "Jia Huang", + "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" + }, + { + "author_name": "Le Zheng", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Zhen Li", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Shiying Hao", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Fangfan Ye", + "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" + }, + { + "author_name": "Jun Chen", + "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" + }, + { + "author_name": "Xiaoming Yao", + "author_inst": "West China Hospital of Sichuan University" + }, + { + "author_name": "Jiayu Liao", + "author_inst": "University of California at Riverside" + }, + { + "author_name": "Song Wang", + "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" + }, + { + "author_name": "Manfei Zeng", + "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" + }, + { + "author_name": "Liping Qiu", + "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" + }, + { + "author_name": "Fanlan Cen", + "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" + }, + { + "author_name": "Yajing Huang", + "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" + }, + { + "author_name": "Tengfei Zhu", + "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" + }, + { + "author_name": "Zehui Xu", + "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" + }, + { + "author_name": "Manhua Ye", + "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" + }, + { + "author_name": "Yang Yang", + "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" + }, + { + "author_name": "Guowei Wang", + "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" + }, + { + "author_name": "Jinxiu Li", + "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" + }, + { + "author_name": "Lifei Wang", + "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" + }, + { + "author_name": "Jiuxin Qu", + "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" + }, + { + "author_name": "Jing Yuan", + "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" + }, + { + "author_name": "Wei Zheng", + "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" + }, + { + "author_name": "Zheng Zhang", + "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" + }, + { + "author_name": "Chunyang Li", + "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" + }, + { + "author_name": "John C Whitin", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Lu Tian", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Henry Chubb", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "KuoYuan Hwa", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Hayley A Gans", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Scott R Ceresnak", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Wei Zhang", + "author_inst": "West China Hospital of Sichuan University" + }, + { + "author_name": "Ying Lu", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Yvonne A Maldonado", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Harvey J Cohen", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Doff B McElhinney", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Karl G Sylvester", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Qing He", + "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" + }, + { + "author_name": "Zhaoqin Wang", + "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" + }, + { + "author_name": "Yingxia Liu", + "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" + }, + { + "author_name": "Lei Liu", + "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" + }, + { + "author_name": "Xuefeng B Ling", + "author_inst": "Stanford University School of Medicine" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.06.20093351", "rel_title": "Age-adjusted associations between comorbidity and outcomes of COVID-19: a review of the evidence", @@ -1461291,33 +1463442,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.05.05.20070946", - "rel_title": "Clinical onset serial interval and diagnostic serial interval of SARS-CoV-2/COVID-19 in South Korea", - "rel_date": "2020-05-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20070946", - "rel_abs": "BACKGROUNDThe clinical onset serial interval is often used as a proxy for the transmission serial interval of an infectious disease. For SARS-CoV-2/COVID-19, data on clinical onset serial intervals is limited, since symptom onset dates are not routinely recorded and do not exist in asymptomatic carriers.\n\nMETHODSWe define the diagnostic serial interval as the time between the diagnosis dates of the infector and infectee. Based on the DS4C project data on SARS-CoV-2/COVID-19 in South Korea, we estimate the means of the diagnostic serial interval, the clinical onset serial interval and the difference between the two. We use the balanced cluster bootstrap method to construct 95\n\nRESULTSThe mean of the diagnostic serial interval was estimated to be 3.63 days (95\n\nCONCLUSIONSThe relatively short diagnostic serial intervals of SARS-CoV-2/COVID-19 in South Korea are likely due to the countrys extensive efforts towards contact tracing. We suggest the mean diagnostic serial interval as a new indicator for the effectiveness of a countrys contact tracing as part of the epidemic surveillance.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Sofia Kyonhi Mettler", - "author_inst": "1. Swiss Federal Institute of Technology, Department of Mathematics, Seminar for Statistics; 2. University of Zurich, Faculty of Medicine" - }, - { - "author_name": "Jihoo Kim", - "author_inst": "Hanyang University" - }, - { - "author_name": "Marloes H. Maathuis", - "author_inst": "Swiss Federal Institute of Technology, Department of Mathematics, Seminar for Statistics" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.06.20069302", "rel_title": "Optimal upper respiratory tract sampling time for novel coronavirus pneumonia suspects", @@ -1462037,6 +1464161,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.05.20091942", + "rel_title": "A Computational Model for Estimating the Evolution of COVID-19 in Rondenia-Brazil", + "rel_date": "2020-05-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20091942", + "rel_abs": "In this work, the modified SEIR model was proposed to account separately for the tested and isolated cases, with severe and critical symptoms, from those not tested, with mild and moderate symptoms. Two parameters were estimated and evaluated for the cases registered in Rondonia, Brazil, between March 20 and April 22. The basic reproduction rate did not remain constant during the period, showing eventual variations due to social behavior. The results show that an increase in the proportion of testing to about 56% provided a significant decrease in confirmed cases, for the expansion of tested cases beyond the current testing criterion (20%) would help to identify and isolate also mild and moderate cases, generally referred to as asymptomatic.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Tito Dias Junior", + "author_inst": "Federal Police of Brazil" + }, + { + "author_name": "Camila Bueno Machado", + "author_inst": "Asa Norte Regional Hospital, Brasilia, Brazil" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.05.20092130", "rel_title": "Phasic containment of COVID-19 in substantially affected states of India", @@ -1462773,29 +1464920,6 @@ "type": "new results", "category": "scientific communication and education" }, - { - "rel_doi": "10.1101/2020.05.02.20088971", - "rel_title": "Contribution to COVID-19 spread modelling: A physical phenomenological dissipative formalism", - "rel_date": "2020-05-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.02.20088971", - "rel_abs": "In this study, we propose an evolution law of COVID-19 transmission based first on a representation of population by a domain part of an infinite ordered lattice in which epidemic evolution is represented by a wave like free spread starting from a first case as an epicentre. Free energy of spread on a given day is defined equal to the natural logarithm of the number of infected cases. Dissipation of propagation is obtained using a postulated form of free energy built using thermodynamics of irreversible processes in analogy to isotherm wave propagation in solids and elastic damage behaviour of materials. The proposed expression of daily free energy rate leads to dissipation of propagation introducing a parameter quantifying measures taking by governments to restrict transmission. Entropy daily rate representing disorder produced in the initial system is also explicitly defined. In this context, a simple law of evolution of infected cases as function of time is given in an iterative form. The model predicts different effects on peak of infected cases Imax and epidemic period, including effects of population size N, effects of measures taking to restrict spread, effects of population density and effect of a parameter T similar to absolute temperature in thermodynamics. Different effects are presented first. The model is than applied to epidemic spread in Tunisia and compared with data registered since the report of the first confirmed case on Mar 2, 2020. It is shown that the low epidemic size in Tunisia is essentially due to a low population density and relatively strict restriction measures including lockdown and quarantine.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Oualid Limam", - "author_inst": "University of Tunis El Manar, ENIT" - }, - { - "author_name": "Mohamed Limam", - "author_inst": "Laboratory of medical biology, Regional Hospital of Sidi Bouzid, Tunisia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.02.20088989", "rel_title": "Estimation of Transmission Potential and Severity of COVID-19 in Romania and Pakistan", @@ -1463447,6 +1465571,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.04.20091298", + "rel_title": "COVID-19 is rapidly changing: Examining public perceptions and behaviors in response to this evolving pandemic", + "rel_date": "2020-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.04.20091298", + "rel_abs": "BackgroundSince the emergence of SARS-CoV-2, the virus that causes coronavirus disease (COVID-19) in late 2019, communities have been required to rapidly adopt community mitigation strategies rarely used before, or only in limited settings. This study aimed to examine the attitudes and beliefs of Australian adults towards the COVID-19 pandemic, and willingness and capacity to engage with these mitigation measures. In addition, we aimed to explore the psychosocial and demographic factors that are associated with adoption of recommended hygiene-related and avoidance-related behaviors.\n\nMethodsA national cross-sectional online survey of 1420 Australian adults (18 years and older) was undertaken between the 18 and 24 March 2020. The statistical analysis of the data included univariate and multivariate logistic regression analysis.\n\nFindingsThe survey of 1420 respondents found 50% (710) of respondents felt COVID-19 would somewhat affect their health if infected and 19% perceived their level of risk as high or very high. 84{middle dot}9% had performed [≥]1 of the three recommended hygiene-related behaviors and 93{middle dot}4% performed [≥]1 of six avoidance-related behaviors over the last one month. Adopting avoidance behaviors was associated with trust in government/authorities (aOR: 5{middle dot}5, 95% CI 3-9{middle dot}0), higher perceived rating of effectiveness of behaviors (aOR: 4{middle dot}3, 95% CI: 2{middle dot}8-6{middle dot}9) and higher levels of perceived ability to adopt social distancing strategies (aOR: 1{middle dot}8, 95% CI 1{middle dot}1-3{middle dot}0).\n\nInterpretationIn the last two months, members of the public have been inundated with messages about hygiene and social (physical) distancing. However, our results indicate that a continued focus on supporting community understanding of the rationale for these strategies, as well as instilling community confidence in their ability to adopt or sustain the recommendations is needed.\n\nFundingNone", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Holly Seale", + "author_inst": "University of New South Wales" + }, + { + "author_name": "Anita E Heywood", + "author_inst": "University of New South Wales" + }, + { + "author_name": "Julie Leask", + "author_inst": "University of Sydney" + }, + { + "author_name": "Meru Steel", + "author_inst": "The Australian National University" + }, + { + "author_name": "Susan Thomas", + "author_inst": "University of Newcastle" + }, + { + "author_name": "David N Durrheim", + "author_inst": "University of Newcastle" + }, + { + "author_name": "Katarzyna Bolsewicz", + "author_inst": "University of Newcastle" + }, + { + "author_name": "Rajneesh Kaur", + "author_inst": "University of Sydney" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.04.20091017", "rel_title": "Effects of home confinement on mental health and lifestyle behaviours during the COVID-19 outbreak: Insight from the \"ECLB-COVID19\" multi countries survey", @@ -1464559,117 +1466730,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.05.20091355", - "rel_title": "Longitudinal peripheral blood transcriptional analysis of COVID-19 patients captures disease progression and reveals potential biomarkers", - "rel_date": "2020-05-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20091355", - "rel_abs": "COVID-19, caused by SARS-CoV-2, is an acute self-resolving disease in most of the patients, but some patients can develop a severe illness or even death. To characterize the host responses and identify potential biomarkers during disease progression, we performed a longitudinal transcriptome analysis for peripheral blood mononuclear cells (PBMCs) collected from 4 COVID-19 patients at 4 different time points from symptom onset to recovery. We found that PBMCs at different COVID-19 disease stages exhibited unique transcriptome characteristics. SARS-CoV-2 infection dysregulated innate immunity especially type I interferon response as well as the disturbed release of inflammatory cytokines and lipid mediators, and an aberrant increase of low-density neutrophils may cause tissue damage. Activation of cell death, exhaustion and migratory pathways may lead to the reduction of lymphocytes and dysfunction of adaptive immunity. COVID-19 induced hypoxia may exacerbate disorders in blood coagulation. Based on our analysis, we proposed a set of potential biomarkers for monitoring disease progression and predicting the risk of severity.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Qihong Yan", - "author_inst": "Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences" - }, - { - "author_name": "Pingchao Li", - "author_inst": "Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences" - }, - { - "author_name": "Xianmiao Ye", - "author_inst": "Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences" - }, - { - "author_name": "Xiaohan Huang", - "author_inst": "Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences" - }, - { - "author_name": "Xiaoneng Mo", - "author_inst": "Guangzhou Eighth People Hospital, Guangzhou Medical University" - }, - { - "author_name": "Qian Wang", - "author_inst": "Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences" - }, - { - "author_name": "Yudi Zhang", - "author_inst": "Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences" - }, - { - "author_name": "Kun Luo", - "author_inst": "Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences" - }, - { - "author_name": "Zhaoming Chen", - "author_inst": "Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences" - }, - { - "author_name": "Jia Luo", - "author_inst": "Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences" - }, - { - "author_name": "Xuefeng Niu", - "author_inst": "Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University" - }, - { - "author_name": "Ying Feng", - "author_inst": "Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University" - }, - { - "author_name": "Tianxing Ji", - "author_inst": "Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University" - }, - { - "author_name": "Bo Feng", - "author_inst": "Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University" - }, - { - "author_name": "Jinlin Wang", - "author_inst": "Guangzhou Eighth People Hospital, Guangzhou Medical University" - }, - { - "author_name": "Feng Li", - "author_inst": "Guangzhou Eighth People Hospital, Guangzhou Medical University" - }, - { - "author_name": "Fuchun Zhang", - "author_inst": "Guangzhou Eighth People Hospital, Guangzhou Medical University" - }, - { - "author_name": "Fang Li", - "author_inst": "Guangzhou Eighth People Hospital, Guangzhou Medical University" - }, - { - "author_name": "Jianhua Wang", - "author_inst": "Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences" - }, - { - "author_name": "Liqiang Feng", - "author_inst": "Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences" - }, - { - "author_name": "Zhilong Chen", - "author_inst": "School of Medicine, Huaqiao University" - }, - { - "author_name": "Chunliang Lei", - "author_inst": "Guangzhou Eighth People Hospital, Guangzhou Medical University" - }, - { - "author_name": "Linbing QU", - "author_inst": "Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences" - }, - { - "author_name": "Ling Chen", - "author_inst": "Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.04.20090951", "rel_title": "The date predicted 200.000 cases of Covid-19 in Spain using SutteARIMA", @@ -1465581,6 +1467641,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.05.20091579", + "rel_title": "Modelling exit strategies for the UK Covid-19 lockdown with revised mortality data", + "rel_date": "2020-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20091579", + "rel_abs": "The number of daily deaths, reported by Public Health England (PHE) during the UK Covid-19 epidemic, initially omitted out-of-hospital deaths in England. The epidemic has been mitigated by social distancing and the lockdown introduced on 17 and 23 March 2020 respectively. We recently reported a stochastic model of a mitigated epidemic which incorporated changes in social interactions and daily movements and whose simulations were consistent with the initial PHE daily mortality data. However, on 29 April, PHE revised their historic data to include out-of-hospital deaths in England. Out-of-hospital deaths occur sooner than in-hospital deaths. Here we show that if 20% of deaths, representing out-of-hospital deaths, are assigned a shorter illness period, then simulated daily mortality matches the revised PHE mortality at least until 4 May. We now predict that if the lockdown is gently relaxed in late May, whilst maintaining social distancing, there would be a modest second-wave which may be acceptable when weighed against the risks of maintaining the lockdown. Our model complements other more sophisticated work currently guiding national policy but which is not presently in the public domain.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Anthony D Lander", + "author_inst": "Birmingham Women's and Children's Hospital, Birmingham, UK" + }, + { + "author_name": "Thejasvi Subramanian", + "author_inst": "Birmingham Women's and Children's Hospital, Birmingham UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.05.20091389", "rel_title": "Evolution of COVID-19 pandemic: Power law growth and saturation", @@ -1466521,29 +1468604,6 @@ "type": "confirmatory results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.05.07.082230", - "rel_title": "A modified ACE2 peptide mimic to block SARS-CoV2 entry", - "rel_date": "2020-05-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.07.082230", - "rel_abs": "A 23-residue peptide fragment that forms a part of the -1 helix of the ACE2 peptidase domain, the recognition domain for SARS-CoV2 on the ACE2 receptor, holds the potential as a drug to block the viral receptor binding domain (RBD) from forming a complex with ACE2. The peptide has recently been shown to bind the viral RBD with good efficiency. Here, we present a detailed analysis of the energetics of binding of the peptide to the SARS-CoV2 RBD. We use equilibrium molecular dynamics simulation to study the dynamics of the complex. We perform end-state binding energy calculations to gain a residue-level insight into the binding process and use the information to incorporate point mutations into the peptide. We demonstrate using binding energy calculations that the peptide with certain point mutations, especially E17L, shows a stronger binding to the RBD as compared to the wild type peptide. We propose that the modified peptide will thus be more efficient in blocking RBD-ACE2 binding.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Suman Saurabh", - "author_inst": "CNRS, Orleans" - }, - { - "author_name": "Shubh Sanket Purohit", - "author_inst": "Government Medical College, Nagpur, India" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2020.05.07.083212", "rel_title": "Coarse-grained molecular simulations of the binding of the SARS-CoV 2 spike protein RBD to the ACE2 cell receptor", @@ -1466987,6 +1469047,249 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.04.20072447", + "rel_title": "Effects of COVID-19 home confinement on physical activity and eating behaviour Preliminary results of the ECLB-COVID19 international online-survey", + "rel_date": "2020-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.04.20072447", + "rel_abs": "BackgroundPublic health recommendations and governmental measures during the COVID-19 pandemic have enforced numerous restrictions on daily living including social distancing, isolation and home confinement. While these measures are imperative to abate the spreading of COVID-19, the impact of these restrictions on health behaviours and lifestyle at home is undefined. Therefore, an international online survey was launched in April 2020 in seven languages to elucidate the behavioral and lifestyle consequences of COVID-19 restrictions. This report presents the preliminary results from the first thousand responders on physical activity (PA) and nutrition behaviours.\n\nMethodsThirty-five research organisations from Europe, North-Africa, Western Asia and the Americas promoted the survey through their networks to the general society, in English, German, French, Arabic, Spanish, Portugese, and Slovenian languages. Questions were presented in a differential format with questions related to responses \"before\" and \"during\" confinement conditions.\n\nResults1047 replies (54% women) from Asia (36%), Africa (40%), Europe (21%) and other (3%) were included into a general analysis. The COVID-19 home confinement had a negative effect on all intensities of PA (vigorous, moderate, walking and overall). Conversely, daily sitting time increased from 5 to 8 hours per day. Additionally, food consumption and meal patterns (the type of food, eating out of control, snacks between meals, number of meals) were more unhealthy during confinement with only alcohol binge drink decreasing significantly.\n\nConclusionWhile isolation is a necessary measure to protect public health, our results indicate that it alters physical activity and eating behaviours in a direction that would compromise health. A more detailed analysis of survey data will allow for a segregation of these responses in different age groups, countries and other subgroups which will help develop bespoke interventions to mitigate the negative lifestyle behaviors manifest during the COVID-19 confinement.", + "rel_num_authors": 57, + "rel_authors": [ + { + "author_name": "ACHRAF AMMAR", + "author_inst": "Otto-Von-Guericke University" + }, + { + "author_name": "Michael Brach", + "author_inst": "Institute of Sport and Exercise Sciences, Munster, Germany" + }, + { + "author_name": "Khaled Trabelsi", + "author_inst": "High Institute of Sport and Physical Education of Sfax, 3000, Sfax, Tunisia" + }, + { + "author_name": "Hamdi Chtourou", + "author_inst": "High Institute of Sport and Physical Education of Sfax, 3000, Sfax, Tunisia" + }, + { + "author_name": "Omar Boukhris", + "author_inst": "High Institute of Sport and Physical Education of Sfax, 3000, Sfax, Tunisia" + }, + { + "author_name": "Liwa Masmoudi", + "author_inst": "High Institute of Sport and Physical Education of Sfax, 3000, Sfax, Tunisia" + }, + { + "author_name": "Bassem Bouaziz", + "author_inst": "Higher Institute of Computer Science and Multimedia of Sfax, 3000, Sfax, Tunisia" + }, + { + "author_name": "Ellen Bentlage", + "author_inst": "Institute of Sport and Exercise Sciences, Munster, Germany" + }, + { + "author_name": "Daniella How", + "author_inst": "Institute of Sport and Exercise Sciences, Munster, Germany" + }, + { + "author_name": "Mona Ahmed", + "author_inst": "Institute of Sport and Exercise Sciences, Munster, Germany" + }, + { + "author_name": "Patrick Mueller", + "author_inst": "Research Group Neuroprotection, German Center for Neurodegenerative Diseases (DZNE), Leipziger Str. 44, Magdeburg, 39120, Germany" + }, + { + "author_name": "Notger Mueller", + "author_inst": "Research Group Neuroprotection, German Center for Neurodegenerative Diseases (DZNE), Leipziger Str. 44, Magdeburg, 39120, Germany" + }, + { + "author_name": "Asma Aloui", + "author_inst": "High Institute of Sport and Physical Education of Sfax, 3000, Sfax, Tunisia" + }, + { + "author_name": "Omar Hammouda", + "author_inst": "High Institute of Sport and Physical Education of Sfax, 3000, Sfax, Tunisia" + }, + { + "author_name": "Laisa Liane Paineiras-Domingos", + "author_inst": "Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brazil" + }, + { + "author_name": "Annemarie Braakman-jansen", + "author_inst": "University of Twente, the Netherlands Region de Enschede, Netherland" + }, + { + "author_name": "Christian Wrede", + "author_inst": "University of Twente, the Netherlands Region de Enschede, Netherland" + }, + { + "author_name": "Sophia Bastoni", + "author_inst": "Catholic University of the Sacred Heart | UNICATT, Milano, Italy" + }, + { + "author_name": "Carlos Soares Pernambuco", + "author_inst": "Universidade Federal do Estado do Rio de Janeiro (UNIRIO), Rio de Janeiro, RJ, Brasil" + }, + { + "author_name": "Leonardo Mataruna", + "author_inst": "College of Business Administration, American University in the Emirates, Dubai, UAE" + }, + { + "author_name": "Morteza Taheri", + "author_inst": "Imam Khomeini International University, Qazvin, Iran" + }, + { + "author_name": "Khadijeh Irandoust", + "author_inst": "Imam Khomeini International University, Qazvin, Iran" + }, + { + "author_name": "Aimen Khacharem", + "author_inst": "Paris-East Creteil University, Creteil, France" + }, + { + "author_name": "Nicola Bragazzi", + "author_inst": "Department of Health Sciences (DISSAL), Postgraduate School of Public Health, University of Genoa, Genoa 16132, Italy" + }, + { + "author_name": "Karim Chamari", + "author_inst": "Department of Research and Education / Aspetar, Qatar" + }, + { + "author_name": "Jordan M Glenn", + "author_inst": "Exercise Science Research Center, Department of Health, Human Performance and Recreation, University of Arkansas, AR 72701, Fayetteville, USA" + }, + { + "author_name": "Nicholas T Bott", + "author_inst": "Clinical Excellence Research Center, Department of Medicine, Stanford University School of Medicine, CA 94305, Stanford, USA" + }, + { + "author_name": "Faiez Gargouri", + "author_inst": "Higher Institute of Computer Science and Multimedia of Sfax, 3000, Sfax, Tunisia" + }, + { + "author_name": "Lotfi Chaari", + "author_inst": "University of Toulouse, IRIT - INP-ENSEEIHT, France" + }, + { + "author_name": "Hadj Batatia", + "author_inst": "University of Toulouse, IRIT - INP-ENSEEIHT, France" + }, + { + "author_name": "Gamal Mohamed Ali", + "author_inst": "Faculty of Physical Education, Assiut University, Assiut 71515, Egypt" + }, + { + "author_name": "Osama Abdelkarim", + "author_inst": "Karlsruher Institut for Technologie, Karlsruher, Germany" + }, + { + "author_name": "Mohamed Jarraya", + "author_inst": "High Institute of Sport and Physical Education of Sfax, 3000, Sfax, Tunisia" + }, + { + "author_name": "Kais El Abed", + "author_inst": "High Institute of Sport and Physical Education of Sfax, 3000, Sfax, Tunisia" + }, + { + "author_name": "Nizar Souissi", + "author_inst": "Observatoire National du Sport, Tunis, Tunisie" + }, + { + "author_name": "Lisette Van Gemert-Pijnen", + "author_inst": "University of Twente, the Netherlands Region de Enschede, Netherland" + }, + { + "author_name": "Bryan L Riemann", + "author_inst": "Georgia Southern University, Statesboro, GA 30458, USA" + }, + { + "author_name": "Laurel Riemann", + "author_inst": "PharmD, BCBS; PharmIAD, Inc,Savannah, GA, USA" + }, + { + "author_name": "Wassim Moalla", + "author_inst": "High Institute of Sport and Physical Education of Sfax, 3000, Sfax, Tunisia" + }, + { + "author_name": "Jonathan Gomez-Raja", + "author_inst": "Health and Social Services, Fundesalud, 06800, Merida, Spain" + }, + { + "author_name": "Monique Epstein", + "author_inst": "The E-senior association, 75020 Paris, France" + }, + { + "author_name": "Robbert Sanderman", + "author_inst": "Department of Health Psychology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands" + }, + { + "author_name": "Sebastian Schulz", + "author_inst": "Department of Medicine, Ulm University, Leimgrubenweg 14, 89075 Ulm, Germany" + }, + { + "author_name": "Achim Jerg", + "author_inst": "Department of Medicine, Ulm University, Leimgrubenweg 14, 89075 Ulm, Germany" + }, + { + "author_name": "Ramzi Al-Horani", + "author_inst": "Department of Exercise Science, Yarmouk University, Irbid, Jordan" + }, + { + "author_name": "Taysir Mansi", + "author_inst": "Department of Instruction and Supervision, The University of Jordan, Jordan" + }, + { + "author_name": "Mohamed Jmail", + "author_inst": "Higher Institute of Computer Science and Multimedia of Sfax, 3000, Sfax, Tunisia" + }, + { + "author_name": "Fernando Barbosa", + "author_inst": "Faculty of Psychology and Education Sciences, University of Porto, Porto Portugal" + }, + { + "author_name": "Fernando Santos", + "author_inst": "ISCTE-Instituto Universitario de Lisboa, Av das Forcas Armadas, 1649-026 Lisboa, Portugal" + }, + { + "author_name": "Bostjan Simunic", + "author_inst": "Institute for Kinesiology Research, Science and ResearchCentre, Koper, Slovenia" + }, + { + "author_name": "Rado Pisot", + "author_inst": "Institute for Kinesiology Research, Science and ResearchCentre, Koper, Slovenia" + }, + { + "author_name": "Donald Cowan", + "author_inst": "Centre for Bioengineering and Biotechnology University of Waterloo, Waterloo, Canda" + }, + { + "author_name": "Andrea Gaggioli", + "author_inst": "Catholic University of the Sacred Heart I UNICATT, Milano, Italy" + }, + { + "author_name": "Stephen J Bailey", + "author_inst": "School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK" + }, + { + "author_name": "Jurgen Steinacker", + "author_inst": "Department of Medicine, Ulm University, Leimgrubenweg 14, 89075 Ulm, Germany" + }, + { + "author_name": "Tarak Driss", + "author_inst": "Research Center on Sport and Movement (EA 2931), University of Paris Nanterre, Nanterre, France" + }, + { + "author_name": "Anita Hoekelmann", + "author_inst": "Otto-Von-Guericke University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "sports medicine" + }, { "rel_doi": "10.1101/2020.05.03.20077206", "rel_title": "Etiologic Subtypes of Ischemic Stroke in SARS-COV-2 Virus patients", @@ -1467831,61 +1470134,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.04.20089904", - "rel_title": "Association of previous medications with the risk of COVID-19: a nationwide claims-based study from South Korea", - "rel_date": "2020-05-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.04.20089904", - "rel_abs": "BackgroundIdentifying the association between medications taken prior to the infection of coronavirus disease (COVID-19) might be useful during the current pandemic until a proven treatment is developed. We aimed to determine whether the risk of developing COVID-19 was associated with the use of various drugs that may increase or decrease susceptibility to severe acute respiratory syndrome coronavirus 2 infection and COVID-19.\n\nMethods and FindingsA case-control study was performed using a nationwide claims database of South Korea, where a large testing capacity has been available throughout the pandemic. Exposure was defined as the prescription of study drugs that would have been continued until [≤]7 days before the testing for COVID-19. Adults were considered eligible if they were [≥]18 years old and tested for COVID-19. Among the 65,149 eligible subjects (mean age, 48.3 years; 49.4% male), 5,172 (7.9%) were diagnosed with COVID-19. Hydroxychloroquine was not significantly associated with the risk of COVID-19 (adjusted odds ratio [aOR], 1.48; 95% CI, 0.95-2.31). In the overall population, lower risks of COVID-19 were associated with the use of camostat (aOR, 0.45; 95% CI, 0.20-1.02) and amiodarone (aOR, 0.54; 95% CI, 0.33-0.89), although the differences were not significant in the subgroup analyses. Angiotensin receptor blockers were also associated with a slightly increased risk of COVID-19 (aOR, 1.13; 95% CI, 1.01-1.26), which was also not observed in the subgroup analysis. The study limitations include potential bias regarding the controls characteristics, inability to determine prescription compliance, and a lack of information regarding the severity of underlying conditions.\n\nConclusionsNo medications were consistently associated with increased or decreased risks of COVID-19. These findings suggest that a more cautious approach is warranted for the clinical use of re-purposed drugs until the results are available from clinical trials.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Kyungmin Huh", - "author_inst": "Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea" - }, - { - "author_name": "Wonjun Ji", - "author_inst": "Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea" - }, - { - "author_name": "Minsun Kang", - "author_inst": "Artificial Intelligence and Big-Data Convergence Center, Gil Medical Center, Gachon University College of Medicine, Incheon, Korea" - }, - { - "author_name": "Jinwook Hong", - "author_inst": "Artificial Intelligence and Big-Data Convergence Center, Gil Medical Center, Gachon University College of Medicine, Incheon, Korea" - }, - { - "author_name": "Gi Hwan Bae", - "author_inst": "Artificial Intelligence and Big-Data Convergence Center, Gil Medical Center, Gachon University College of Medicine, Incheon, Korea" - }, - { - "author_name": "Rugyeom Lee", - "author_inst": "Artificial Intelligence and Big-Data Convergence Center, Gil Medical Center, Gachon University College of Medicine, Incheon, Korea" - }, - { - "author_name": "Yewon Na", - "author_inst": "Artificial Intelligence and Big-Data Convergence Center, Gil Medical Center, Gachon University College of Medicine, Incheon, Korea" - }, - { - "author_name": "Hyoseon Choi", - "author_inst": "Department of Preventive Medicine, Gachon University College of Medicine, Incheon, Korea" - }, - { - "author_name": "Seon Yeong Gong", - "author_inst": "Department of Preventive Medicine, Gachon University College of Medicine, Incheon, Korea" - }, - { - "author_name": "Jaehun Jung", - "author_inst": "Department of Preventive Medicine, Gachon University College of Medicine; Artificial Intelligence and Big-Data Convergence Center, Gil Medical Center, Gachon Un" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.04.20090043", "rel_title": "SARS-CoV-2 transmission in different settings: Analysis of cases and close contacts from the Tablighi cluster in Brunei Darussalam", @@ -1468685,6 +1470933,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.03.20084160", + "rel_title": "Meta-analysis of diagnostic performance of serological tests for SARS-CoV-2 antibodies and public health implications", + "rel_date": "2020-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.03.20084160", + "rel_abs": "Serology-based tests have become a key public health element in the COVID-19 pandemic to assess the degree of herd immunity that has been achieved in the population. These tests differ between one another in several ways. Here, we conducted a systematic review and meta-analysis of the diagnostic accuracy of currently available SARS-CoV-2 serological tests, and assessed their real-world performance under scenarios of varying proportion of infected individuals. We included independent studies that specified the antigen used for antibody detection and used quantitative methods. We identified nine independent studies, of which six were based on commercial ELISA or CMIA/CLIA assays, and three on in-house tests. Test sensitivity ranged from 68% to 93% for IgM, from 65% to 100% for IgG, and from 83% to 98% for total antibodies. Random-effects models yielded a summary sensitivity of 82% (95%CI 75-88%) for IgM, and 85% for both IgG (95%CI 73-93%) and total antibodies (95%CI 74-94%). Specificity was very high for most tests, and its pooled estimate was 98% (95%CI 92-100%) for IgM and 99% (95%CI 98-100%) for both IgG and total antibodies. The heterogeneity of sensitivity and specificity across tests was generally high (I2>50%). In populations with a low prevalence ([≤]5%) of seroconverted individuals, the positive predictive value would be [≤]88% for most assays, except those reporting perfect specificity. Our data suggest that the use of serological tests for large-scale prevalence surveys (or to grant \"immunity passports\") are currently only justified in hard-hit regions, while they should be used with caution elsewhere.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Saverio Caini", + "author_inst": "Institute for Cancer Research, Prevention and Clinical Network (ISPRO)" + }, + { + "author_name": "Federica Bellerba", + "author_inst": "European Institute of Oncology (IEO), IRCCS, Milan, Italy" + }, + { + "author_name": "Federica Corso", + "author_inst": "European Institute of Oncology (IEO), IRCCS, Milan, Italy" + }, + { + "author_name": "Angelica Diaz-Basabe", + "author_inst": "European Institute of Oncology (IEO), IRCCS, Milan, Italy" + }, + { + "author_name": "Gioacchino Natoli", + "author_inst": "European Institute of Oncology (IEO), IRCCS, Milan, Italy" + }, + { + "author_name": "John Paget", + "author_inst": "Netherlands Institute for Health Services Research (NIVEL), Utrecht, The Netherlands" + }, + { + "author_name": "Federica Facciotti", + "author_inst": "European Institute of Oncology (IEO), IRCCS, Milan, Italy" + }, + { + "author_name": "Sara Raimondi", + "author_inst": "European Institute of Oncology (IEO), IRCCS, Milan, Italy" + }, + { + "author_name": "Domenico Palli", + "author_inst": "Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Florence, Italy" + }, + { + "author_name": "Luca Mazzarella", + "author_inst": "European Institute of Oncology (IEO), IRCCS, Milan, Italy" + }, + { + "author_name": "Pier Giuseppe Pelicci", + "author_inst": "European Institute of Oncology (IEO), IRCCS, Milan, Italy" + }, + { + "author_name": "Paolo Vineis", + "author_inst": "MRC Centre for Environment and Health, School of Public Health, Imperial College, London, United Kingdom" + }, + { + "author_name": "Sara Gandini", + "author_inst": "European Institute of Oncology (IEO), IRCCS, Milan, Italy" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.03.20084442", "rel_title": "Rapid generation of neutralizing antibody responses in COVID-19 patients", @@ -1469433,73 +1471748,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.04.20090506", - "rel_title": "Collider bias undermines our understanding of COVID-19 disease risk and severity", - "rel_date": "2020-05-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.04.20090506", - "rel_abs": "Observational data on COVID-19 including hypothesised risk factors for infection and progression are accruing rapidly, often from non-random sampling such as hospital admissions, targeted testing or voluntary participation. Here, we highlight the challenge of interpreting observational evidence from such samples of the population, which may be affected by collider bias. We illustrate these issues using data from the UK Biobank in which individuals tested for COVID-19 are highly selected for a wide range of genetic, behavioural, cardiovascular, demographic, and anthropometric traits. We discuss the sampling mechanisms that leave aetiological studies of COVID-19 infection and progression particularly susceptible to collider bias. We also describe several tools and strategies that could help mitigate the effects of collider bias in extant studies of COVID-19 and make available a web app for performing sensitivity analyses. While bias due to non-random sampling should be explored in existing studies, the optimal way to mitigate the problem is to use appropriate sampling strategies at the study design stage.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Gareth Griffith", - "author_inst": "MRC Integrative Epidemiology Unit, University of Bristol" - }, - { - "author_name": "Tim T Morris", - "author_inst": "University of Bristol" - }, - { - "author_name": "Matt Tudball", - "author_inst": "MRC Integrative Epidemiology Unit, University of Bristol" - }, - { - "author_name": "Annie Herbert", - "author_inst": "University of Bristol" - }, - { - "author_name": "Giulia Mancano", - "author_inst": "University of Bristol" - }, - { - "author_name": "Lindsey Pike", - "author_inst": "University of Bristol" - }, - { - "author_name": "Gemma C Sharp", - "author_inst": "University of Bristol" - }, - { - "author_name": "Tom M Palmer", - "author_inst": "University of Bristol" - }, - { - "author_name": "George Davey Smith", - "author_inst": "University of Bristol" - }, - { - "author_name": "Kate Tilling", - "author_inst": "University of Bristol" - }, - { - "author_name": "Luisa Zuccolo", - "author_inst": "University of Bristol" - }, - { - "author_name": "Neil M Davies", - "author_inst": "University of Bristol" - }, - { - "author_name": "Gibran Hemani", - "author_inst": "University of Bristol" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.04.20090597", "rel_title": "Segmentation and shielding of the most vulnerable members of the population as elements of an exit strategy from COVID-19 lockdown", @@ -1469943,6 +1472191,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.04.20090712", + "rel_title": "Development of a Multivariate Prediction Network Model for epidemic progression in order to study the effects of lockdown time and coverage on a closed community of non-immune individuals.", + "rel_date": "2020-05-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.04.20090712", + "rel_abs": "The aim of this study was to develop a realistic network model to predict the relationship between lockdown duration and coverage in controlling the progression of the incidence curve of an epidemic with the characteristics of COVID-19 in two scenarios (1) a closed and non-immune population, and (2) a real scenario from State of Rio de Janeiro from May 6th 2020.\n\nEffects of lockdown time and rate on the progression of an epidemic incidence curve in a virtual population of 10 thousand subjects. Predictor variables were reproductive values established in the most recent literature (R0 =2.7 and 5.7, and Re = 1.28 from Rio de Janeiro State at May 6th), without lockdown and with coverages of 25%, 50%, and 90% for 21, 35, 70, and 140 days in up to 13 different scenarios for each R0/Re, where individuals remained infected and transmitters for 14 days. We estimated model validity in theoretical and real scenarios respectively by applying an exponential model on the incidence curve with no lockdown with growth rate coefficient observed in realistic scenarios, and (2) fitting real data series from RJ upon simulated data, respectively.\n\nFor R0=5.7, the flattening of the curve occurs only with long lockdown periods (70 and 140 days) with a 90% coverage. For R0=2.7, coverages of 25 and 50% also result in curve flattening and reduction of total cases, provided they occur for a long period (70 days or more). For realistic scenario in Rio de Janeiro, lockdowns +25% or more from May 6th during 140 days showed expressive flattening and number of COVID cases two to five times lower. If a more intense coverage lockdown (about +25 to +50% as much as the current one) will be implemented until June 6th during at least 70 days, it is still possible reduce nearly 40-50% the impact of pandemy in state of Rio de Janeiro.\n\nThese data corroborate the importance of lockdown duration regardless of virus transmission and sometimes of intensity of coverage, either in realistic or theoretical scenarios of COVID-10 epidemics. Even later, the improvement of lockdown coverage can be effective to minimize the impact of epidemic.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Dimitri M Abramov", + "author_inst": "National Institute of Women, Children and Adolescents, Health Fernandes Figueira, FIOCRUZ" + }, + { + "author_name": "Saint Clair Gomes Junior Jr.", + "author_inst": "Unit of Clinical Research, National Institute of Women, Children and Adolescents, Health Fernandes Figueira, Oswaldo Cruz Foundation (FIOCRUZ), Ministry of Heal" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.05.20091363", "rel_title": "COVID-19 Scenarios: an interactive tool to explore the spread and associated morbidity and mortality of SARS-CoV-2", @@ -1471082,97 +1473353,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.05.06.081695", - "rel_title": "Single-cell longitudinal analysis of SARS-CoV-2 infection in human bronchial epithelial cells", - "rel_date": "2020-05-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.06.081695", - "rel_abs": "SARS-CoV-2, the causative agent of COVID-19, has tragically burdened individuals and institutions around the world. There are currently no approved drugs or vaccines for the treatment or prevention of COVID-19. Enhanced understanding of SARS-CoV-2 infection and pathogenesis is critical for the development of therapeutics. To reveal insight into viral replication, cell tropism, and host-viral interactions of SARS-CoV-2 we performed single-cell RNA sequencing of experimentally infected human bronchial epithelial cells (HBECs) in air-liquid interface cultures over a time-course. This revealed novel polyadenylated viral transcripts and highlighted ciliated cells as a major target of infection, which we confirmed by electron microscopy. Over the course of infection, cell tropism of SARS-CoV-2 expands to other epithelial cell types including basal and club cells. Infection induces cell-intrinsic expression of type I and type III IFNs and IL6 but not IL1. This results in expression of interferon-stimulated genes in both infected and bystander cells. We observe similar gene expression changes from a COVID-19 patient ex vivo. In addition, we developed a new computational method termed CONditional DENSity Embedding (CONDENSE) to characterize and compare temporal gene dynamics in response to infection, which revealed genes relating to endothelin, angiogenesis, interferon, and inflammation-causing signaling pathways. In this study, we conducted an in-depth analysis of SARS-CoV-2 infection in HBECs and a COVID-19 patient and revealed genes, cell types, and cell state changes associated with infection.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Neal G Ravindra", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Mia Madel Alfajaro", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Victor Gasque", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Jin Wei", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Renata B Filler", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Nicholas C Huston", - "author_inst": "Yale University" - }, - { - "author_name": "Han Wan", - "author_inst": "Yale University" - }, - { - "author_name": "Klara Szigeti-Buck", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Bao Wang", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Ruth R Montgomery", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Stephanie C Eisenbarth", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Adam Williams", - "author_inst": "The Jackson Laboratory" - }, - { - "author_name": "Anna Marie Pyle", - "author_inst": "Yale University" - }, - { - "author_name": "Akiko Iwasaki", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Tamas L Horvath", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Ellen F Foxman", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Richard W Pierce", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "David van Dijk", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Craig Wilen", - "author_inst": "Yale University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.05.04.20090761", "rel_title": "Scaling COVID-19 against inequalities: should the policy response consistently match the mortality challenge?", @@ -1471644,6 +1473824,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.03.20089235", + "rel_title": "Geospatially Referenced Demographic Agent-Based Modeling of SARS-CoV-2-Infection (COVID-19) Dynamics and Mitigation Effects in a Real-world Community", + "rel_date": "2020-05-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.03.20089235", + "rel_abs": "Infectious disease outbreaks challenge societies by creating dynamic stochastic infection networks between human individuals in geospatial and demographical contexts. Minimizing human and socioeconomic costs of SARS-CoV-2 and future global pandemics requires data-driven and context-specific integrative modeling of detection-tracing, healthcare, and non-pharmaceutical interventions for decision-processes and reopening strategies. Traditional population-based epidemiological models cannot simulate temporal infection dynamics for individual human behavior in specific geolocations. We present an integrated geolocalized and demographically referenced spatio-temporal stochastic network- and agent-based model of COVID-19 dynamics for human encounters in real-world communities. Simulating intervention scenarios, we quantify effects of protection and identify the importance of early introduction of test-trace measures. Critically, we observe bimodality in SARS-CoV-2 infection dynamics so that the outcome of reopening can flip between good and poor outcomes stochastically. Furthermore, intervention effectiveness depends on strict execution and temporal control i.e. leaks can prevent successful outcomes. Schools are in many scenarios hubs for transmission, reopening scenarios are impacted by infection chain stochasticity and subsequent outbreaks do not always occur. This generalizable geospatial and individualized methodology is unique in precision and specificity compared to prior COVID-19 models [6, 16, 17, 19] and is applicable to scientifically guided decision processes for communities worldwide.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Bjoern Goldenbogen", + "author_inst": "Humboldt-Universitaet zu Berlin" + }, + { + "author_name": "Stephan O. Adler", + "author_inst": "Humboldt-Universitaet zu Berlin" + }, + { + "author_name": "Oliver Bodeit", + "author_inst": "Humboldt-Universitaet zu Berlin" + }, + { + "author_name": "Judith AH Wodke", + "author_inst": "Humboldt-Universitaet zu Berlin" + }, + { + "author_name": "Aviv Korman", + "author_inst": "Humboldt-Universitaet zu Berlin" + }, + { + "author_name": "Lasse Bonn", + "author_inst": "Humboldt-Universitaet zu Berlin" + }, + { + "author_name": "Ximena Martinez de la Escalera", + "author_inst": "Humboldt-Universitaet zu Berlin" + }, + { + "author_name": "Johanna E L Haffner", + "author_inst": "Humboldt-Universitaet zu Berlin" + }, + { + "author_name": "Maria Krantz", + "author_inst": "Humboldt-Universitaet zu Berlin" + }, + { + "author_name": "Maxim Karnetzki", + "author_inst": "Humboldt-Universitaet zu Berlin" + }, + { + "author_name": "Ivo Maintz", + "author_inst": "Humboldt-Universitaet zu Berlin" + }, + { + "author_name": "Lisa Mallis", + "author_inst": "Humboldt-Universitaet zu Berlin" + }, + { + "author_name": "Rafael U Moran Torres", + "author_inst": "Humboldt-Universitaet zu Berlin" + }, + { + "author_name": "Hannah Prawitz", + "author_inst": "Humboldt-Universitaet zu Berlin" + }, + { + "author_name": "Patrick Segelitz", + "author_inst": "Humboldt-Universitaet zu Berlin" + }, + { + "author_name": "Martin Seeger", + "author_inst": "Humboldt-Universitaet zu Berlin" + }, + { + "author_name": "Rune Linding", + "author_inst": "Humboldt-Universitaet zu Berlin" + }, + { + "author_name": "Edda Klipp", + "author_inst": "Humboldt Universitaet zu Berlin" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.01.20088237", "rel_title": "Associations of stay-at-home order and face-masking recommendation with trends in daily new cases and deaths of laboratory-confirmed COVID-19 in the United States", @@ -1472404,33 +1474671,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.05.05.079061", - "rel_title": "Unsupervised cluster analysis of SARS-CoV-2 genomes reflects its geographic progression and identifies distinct genetic subgroups of SARS-CoV-2 virus", - "rel_date": "2020-05-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.05.079061", - "rel_abs": "Over 10,000 viral genome sequences of the SARS-CoV-2 virus have been made readily available during the ongoing coronavirus pandemic since the initial genome sequence of the virus was released on the open access Virological website (http://virological.org/) early on January 11. We utilize the published data on the single stranded RNAs of 11, 132 SARS-CoV-2 patients in the GISAID (Elbe and Buckland-Merrett, 2017; Shu and McCauley, 2017) database, which contains fully or partially sequenced SARS-CoV-2 samples from laboratories around the world. Among many important research questions which are currently being investigated, one aspect pertains to the genetic characterization/classification of the virus. We analyze data on the nucleotide sequencing of the virus and geographic information of a subset of 7, 640 SARS-CoV-2 patients without missing entries that are available in the GISAID database. Instead of modelling the mutation rate, applying phylogenetic tree approaches, etc., we here utilize a model-free clustering approach that compares the viruses at a genome-wide level. We apply principal component analysis to a similarity matrix that compares all pairs of these SARS-CoV-2 nucleotide sequences at all loci simultaneously, using the Jaccard index (Jaccard, 1901; Tan et al., 2005; Prokopenko et al., 2016; Schlauch et al., 2017). Our analysis results of the SARS-CoV-2 genome data illustrates the geographic and chronological progression of the virus, starting from the first cases that were observed in China to the current wave of cases in Europe and North America. This is in line with a phylogenetic analysis which we use to contrast our results. We also observe that, based on their sequence data, the SARS-CoV-2 viruses cluster in distinct genetic subgroups. It is the subject of ongoing research to examine whether the genetic subgroup could be related to diseases outcome and its potential implications for vaccine development.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Georg Hahn", - "author_inst": "Department of Biostatistics, T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA" - }, - { - "author_name": "Sanghun Lee", - "author_inst": "Department of Biostatistics, T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA" - }, - { - "author_name": "Christoph Lange", - "author_inst": "Department of Biostatistics, T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.05.05.079848", "rel_title": "Repurposing low-molecular-weight drugs against the main protease of SARS-CoV-2", @@ -1473066,6 +1475306,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.03.20089078", + "rel_title": "The impact of long-term non-pharmaceutical interventions on COVID-19 epidemic dynamics and control", + "rel_date": "2020-05-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.03.20089078", + "rel_abs": "Non-pharmaceutical interventions to combat COVID-19 transmission have worked to slow the spread of the epidemic but can have high socio-economic costs. It is critical we understand the efficacy of non-pharmaceutical interventions to choose a safe exit strategy. Many current models are not suitable for assessing exit strategies because they do not account for epidemic resurgence when social distancing ends prematurely (e.g., statistical curve fits) nor permit scenario exploration in specific locations.\n\nWe developed an SEIR-type mechanistic epidemiological model of COVID-19 dynamics to explore temporally variable non-pharmaceutical interventions. We provide an interactive tool and code to estimate the transmission parameter, {beta}, and the effective reproduction number, [Formula]. We fit the model to Santa Clara County, California, where an early epidemic start date and early shelter-in-place orders could provide a model for other regions.\n\nAs of April 22, 2020, we estimate an [Formula] of 0.982 (95% CI: 0.849 - 1.107) in Santa Clara County. After June 1 (the end-date for Santa Clara County shelter-in-place as of April 27), we estimate a shift to partial social distancing, combined with rigorous testing and isolation of symptomatic individuals, is a viable alternative to indefinitely maintaining shelter-in-place. We also estimate that if Santa Clara County had waited one week longer before issuing shelter-in-place orders, 95 additional people would have died by April 22 (95% CI: 7 - 283).\n\nGiven early life-saving shelter-in-place orders in Santa Clara County, longer-term moderate social distancing and testing and isolation of symptomatic individuals have the potential to contain the size and toll of the COVID-19 pandemic in Santa Clara County, and may be effective in other locations.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Marissa L Childs", + "author_inst": "Stanford University" + }, + { + "author_name": "Morgan P Kain", + "author_inst": "Stanford University" + }, + { + "author_name": "Devin Kirk", + "author_inst": "Stanford University" + }, + { + "author_name": "Mallory Harris", + "author_inst": "Stanford University" + }, + { + "author_name": "Lisa Couper", + "author_inst": "Stanford University" + }, + { + "author_name": "Nicole Nova", + "author_inst": "Stanford University" + }, + { + "author_name": "Isabel Delwel", + "author_inst": "Stanford University" + }, + { + "author_name": "Jacob Ritchie", + "author_inst": "Stanford University" + }, + { + "author_name": "Erin A Mordecai", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.02.20089094", "rel_title": "Clinical characteristics and fecal-oral transmission potential of patients with COVID-19", @@ -1473886,37 +1476177,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.04.30.20086983", - "rel_title": "UV light influences covid-19 activity through big data: trade offs between northern subtropical, tropical, and southern subtropical countries", - "rel_date": "2020-05-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.30.20086983", - "rel_abs": "UV (ultraviolet) light is an important factor should be considered to predict coronavirus epidemic growth pace. UV is different from weather temperature since UV is electromagnetic wavelength from 10 nm to 400 nm in size, shorter than of visible lights. For some people, UV light can lead to cancer from unprotected sun exposure, however, for tropical people, which have been used to live in such condition, have resisted from negative effect high UV index. Moreover, UV has the capability to inactivate virus. This conclusion has been discussed deeply with biological experts. Although UV light has the ability to inactivate viruses, it may be meaningless in areas with high air pollution where UV light turns into heat. The data visualization code is available here https://github.com/cbasemaster/uvcorona", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Novanto Yudistira", - "author_inst": "Brawijaya University" - }, - { - "author_name": "Sutiman Bambang Sumitro", - "author_inst": "Brawijaya University" - }, - { - "author_name": "Alberth Nahas", - "author_inst": "BMKG" - }, - { - "author_name": "Nelly Florida Riama", - "author_inst": "BMKG" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.30.20086926", "rel_title": "Depression, Anxiety and Depression-anxiety comorbidity amid COVID-19 Pandemic: An online survey conducted during lockdown in Nepal", @@ -1474616,6 +1476876,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "otolaryngology" }, + { + "rel_doi": "10.1101/2020.05.01.20087387", + "rel_title": "Heterogeneous contact networks in COVID-19 spreading: the role of social deprivation", + "rel_date": "2020-05-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.01.20087387", + "rel_abs": "We have two main aims in this paper. First we use theories of disease spreading on networks to look at the COVID-19 epidemic on the basis of individual contacts -- these give rise to predictions which are often rather different from the homogeneous mixing approaches usually used. Our second aim is to look at the role of social deprivation, again using networks as our basis, in the spread of this epidemic. We choose the city of Kolkata as a case study, but assert that the insights so obtained are applicable to a wide variety of urban environments which are densely populated and where social inequalities are rampant. Our predictions of hotspots are found to be in good agreement with those currently being identified empirically as containment zones and provide a useful guide for identifying potential areas of concern", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Arnab Majumdar", + "author_inst": "Arcvision Technologies, Kolkata, India" + }, + { + "author_name": "Anita Mehta", + "author_inst": "Max Planck Institute for Mathematics in the Sciences" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.05.01.20087684", "rel_title": "Identification of IgG antibody response to SARS-CoV-2 spike protein and its receptor binding domain does not predict rapid recovery from COVID-19", @@ -1475188,45 +1477471,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.01.20087874", - "rel_title": "Measuring voluntary social distancing behavior during the COVID-19 pandemic", - "rel_date": "2020-05-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.01.20087874", - "rel_abs": "Staying home and avoiding unnecessary contact is an important part of the effort to contain COVID-19 and limit deaths. Every state in the United States enacted policies to encourage distancing, and some mandated staying home. Understanding how these policies interact with individuals voluntary responses to the COVID-19 epidemic is critical for estimating the transmission dynamics of the pathogen and assessing the impact of policies. We use the variation in policy responses along with smart device data, which measures the amount of time Americans stayed home, to show that there was substantial voluntary avoidance behavior. We disentangle the extent to which observed shifts in behavior are induced by policy and find evidence of a non-trivial voluntary response to local reported COVID-19 cases and deaths, such that around 45 cases in a home county is associated with the same amount of time at home as a stay-at-home order. People responded to the risk of contracting COVID-19 and to policy orders, though the response to policy orders crowds out or displaces a large share of the voluntary response, suggesting that, during early stages of the U.S. outbreak, better compliance with social distancing recommendations could have been achieved with policy crafted to complement voluntary behavior.\n\nSignificance StatementAmericans are spending substantially more time at home to reduce the spread of COVID-19. This behavioral shift is a mix of voluntary disease avoidance and policy-induced behavioral changes. Both need to be accounted for. Disentangling voluntary from policy-induced behavioral changes is critical for governments relaxing or renewing restrictions. A substantial share of the behavioral response appears to be voluntary, but this behavior was offset by strong stay-at-home orders. Local testing and rapid reporting is a first step to making better use of voluntary behavioral changes.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Youpei Yan", - "author_inst": "Yale University, School of Forestry and Environmental Studies" - }, - { - "author_name": "Amyn A Malik", - "author_inst": "Yale Institute for Global Health" - }, - { - "author_name": "Jude Bayham", - "author_inst": "Colorado State University" - }, - { - "author_name": "Eli P Fenichel", - "author_inst": "Yale University, School of Forestry and Environmental Studies" - }, - { - "author_name": "Chandra Couzens", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Saad B Omer", - "author_inst": "Yale Institute for Global Health" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.01.20087783", "rel_title": "Now casting and Forecasting of COVID-19 outbreak in the National Capital Region of Delhi", @@ -1476070,6 +1478314,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.02.20088427", + "rel_title": "COVID-19 Pandemic Prediction for Hungary; a Hybrid Machine Learning Approach", + "rel_date": "2020-05-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.02.20088427", + "rel_abs": "Several epidemiological models are being used around the world to project the number of infected individuals and the mortality rates of the COVID-19 outbreak. Advancing accurate prediction models is of utmost importance to take proper actions. Due to a high level of uncertainty or even lack of essential data, the standard epidemiological models have been challenged regarding the delivery of higher accuracy for long-term prediction. As an alternative to the susceptible-infected-resistant (SIR)-based models, this study proposes a hybrid machine learning approach to predict the COVID-19 and we exemplify its potential using data from Hungary. The hybrid machine learning methods of adaptive network-based fuzzy inference system (ANFIS) and multi-layered perceptron-imperialist competitive algorithm (MLP-ICA) are used to predict time series of infected individuals and mortality rate. The models predict that by late May, the outbreak and the total morality will drop substantially. The validation is performed for nine days with promising results, which confirms the model accuracy. It is expected that the model maintains its accuracy as long as no significant interruption occurs. Based on the results reported here, and due to the complex nature of the COVID-19 outbreak and variation in its behavior from nation-to-nation, this study suggests machine learning as an effective tool to model the outbreak. This paper provides an initial benchmarking to demonstrate the potential of machine learning for future research.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "gergo pinter", + "author_inst": "John von Neumann Faculty of Informatics, Obuda University, 1034 Budapest, Hungary." + }, + { + "author_name": "Imre Felde", + "author_inst": "John von Neumann Faculty of Informatics, Obuda University, 1034 Budapest, Hungary." + }, + { + "author_name": "Amir MOSAVI", + "author_inst": "Obuda University" + }, + { + "author_name": "Pedram Ghamisi", + "author_inst": "Machine Learning Group, Exploration Division, Helmholtz Institute Freiberg for Resource Technology, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany" + }, + { + "author_name": "Richard Gloaguen", + "author_inst": "Helmholtz-Zentrum Dresden-Rossendorf, Helmholtz Institute Freiberg for Resource Technology, Chemnitzer Street 40, 09599 Freiberg, Germany" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.04.29.20085621", "rel_title": "Is Hydroxychloroquine Safe During Pregnancy? Observations from Penn Medicine", @@ -1476710,93 +1478989,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.29.20084749", - "rel_title": "Simple ventilators for emergency use based on Bag-Valve pressing systems: Lessons learned and future steps", - "rel_date": "2020-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.29.20084749", - "rel_abs": "As part of a plethora of global efforts to minimize the negative effects of the SARS-CoV2 (COVID-19) pandemic, we developed two different mechanisms that, after further development, could potentially be of use in the future in order to increase the capacity of ventilators with low-cost devices based on single-use-bag-valve mask systems. We describe the concept behind the devices and report a characterization of them. Finally, we make a description of the solved and unsolved challenges and propose a series of measures in order to better cope with future contingencies.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Enrique Castro-Camus", - "author_inst": "Centro de Investigaciones en Optica, A.C." - }, - { - "author_name": "Jan Ornik", - "author_inst": "Philipps-Universtitat Marburg" - }, - { - "author_name": "Cornelius Mach", - "author_inst": "Philipps-Universitat Marburg" - }, - { - "author_name": "Goretti G Hernandez-Cardoso", - "author_inst": "Centro de Investigaciones en Optica A.C." - }, - { - "author_name": "Bhushan Savalia", - "author_inst": "Philipps-Universitat Marburg" - }, - { - "author_name": "Jochen Taiber", - "author_inst": "Philipps-Universitat Marburg" - }, - { - "author_name": "Armando Ruiz-Marquez", - "author_inst": "Centro de Investigaciones en Optica A.C." - }, - { - "author_name": "Karl Kesper", - "author_inst": "Philipps-Universitat Marburg" - }, - { - "author_name": "Srumika Konde", - "author_inst": "Philipps-Universitat Marburg" - }, - { - "author_name": "Caroline Sommer", - "author_inst": "Philipps-Universitat Marburg" - }, - { - "author_name": "Julian Wiener", - "author_inst": "Philipps-Universitat Marburg" - }, - { - "author_name": "David Geisel", - "author_inst": "Philipps-Universitat Marburg" - }, - { - "author_name": "Franziska Huppe", - "author_inst": "Philipps-Universitat Marburg" - }, - { - "author_name": "Gunter Kraling", - "author_inst": "Universitatsklinikum Giessen and Marburg" - }, - { - "author_name": "Johnny Nguyen", - "author_inst": "Philipps-Universitat Marburg" - }, - { - "author_name": "Thomas Wiesmann", - "author_inst": "Philipps-Universitat Marburg" - }, - { - "author_name": "Bjorn Beutel", - "author_inst": "Philipps-Universitat Marburg" - }, - { - "author_name": "Martin Koch", - "author_inst": "Philipps-Universitat Marburg" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.04.29.20084327", "rel_title": "Cross-talk between the airway epithelium and activated immune cells defines severity in COVID-19", @@ -1477516,6 +1479708,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.29.20085498", + "rel_title": "Effective Heat Inactivation of SARS-CoV-2", + "rel_date": "2020-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.29.20085498", + "rel_abs": "In this study, we aimed to evaluate the stability of SARS-CoV-2 under four different heat conditions (37, 42, 56, 60 {degrees}C) and report that the virus is stable at 37 {degrees}C for at least 24 hours. Heating at 56 {degrees}C for 30 minutes, however, effectively inactivated the virus while preserved the stability of viral RNA in both human sera and sputum samples. These findings provide critical information regarding the biology of the virus as well as a practical way to inactivate infectious virus that is potentially found in clinical specimens.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Tony Wang", + "author_inst": "US FDA" + }, + { + "author_name": "Christopher Lien", + "author_inst": "US FDA" + }, + { + "author_name": "Shufeng Liu", + "author_inst": "US FDA" + }, + { + "author_name": "Prabhuanand Selveraj", + "author_inst": "US FDA" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.30.20086108", "rel_title": "A clinical and biological framework on the role of visceral fat tissue and leptin in SARS-CoV-2 infection related respiratory failure", @@ -1478260,29 +1480483,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.30.20086744", - "rel_title": "Risk Factors of the Severity of COVID-19: A Meta-Analysis", - "rel_date": "2020-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.30.20086744", - "rel_abs": "BACKGROUNDAlthough the infection rate of COVID-19 is very high, all the patients getting infected dont always die or go through brutal states. This indicates there may be some factors that possibly boost the severity of COVID-19.\n\nOBJECTIVEWe intend to identify some probable risk factors that are responsible for the severity of COVID-19 using a meta-analysis.\n\nMETHODSThe literature exploration lasted up to 18 April 2020 and through PubMed, Google Scholar, EMBASE, and Cochrane Library we have identified 10 pertinent publications. To paraphrase the outcomes of autonomous researches, we have performed a random-effect meta-analysis.\n\nRESULTSA total of 2272 patients information was extracted from the selected literature. We have found sex (male) (Risk ratio [RR] =1.29 [1.07; 1.54]), hypertension (RR=1.79 [1.57; 2.04]), diabetes (RR=1.57 [1.25; 1.98]), fatigue or myalgia (RR=1.17 [1.02; 1.35]), and smoking history (RR=1.71 [1.25; 2.35]) are potential risk factors for the severity of COVID-19. We found fever (RR=1.21 [0.66; 2.22]), cough (1.13 [0.98; 1.30]), and diarrhea (RR=1.14 [0.93; 1.40]) as insignificant risk factors for COVID-19 severity.\n\nCONCLUSIONThe findings of this research may be beneficial to identify patients with higher risks to provide additional medical attention from the very beginning of the treatment.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Abdur Rahman", - "author_inst": "Khulna University" - }, - { - "author_name": "Nusrat Jahan Sathi", - "author_inst": "Khulna University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.30.20086306", "rel_title": "Modelling and simulation of COVID-19 propagation in a large population with specific reference to India", @@ -1478794,6 +1480994,57 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.05.05.078501", + "rel_title": "Test Agreement Between Roche Cobas 6800 and Cepheid GeneXpert Xpress SARS-CoV-2 Assays at High Cycle Threshold Ranges", + "rel_date": "2020-05-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.05.078501", + "rel_abs": "The SARS-CoV-2 pandemic has changed the face of the globe and upended the daily lives of billions. In an effort to bring mass-testing to as many as possible, multiple diagnostic tests including molecular, antigen detection and serological assays have been rapidly developed. However, there is very little information on positive test agreement across modalities, especially for lower viral loads. Thirty-five nasopharyngeal samples that had cycle threshold (Ct) values greater than 30.0 from the Roche cobas 6800 assay were run on the Cepheid GeneXpert Xpress SARS-CoV-2 assay. Ct values ranged from 30.1 to 37.9 (mean 36.7 {+/-} 1.9) on the Roche cobas 6800 assay and 24.6 to 42.4 (mean 32.8{+/-}4.1) on the Cepheid assay. There was a bias of 0.33 {+/-} 3.21, (mean difference -1.59, 95% limits of agreement -5.97, 6.63) signifying close agreement between the 2 instruments with a high standard deviation. The close test agreement between the cobas 6800 and GeneXpert at high Ct values allows for utilization of both assays interchangeable in accordance with testing algorithms.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Kari J Broder", + "author_inst": "Emory University" + }, + { + "author_name": "Ahmed Babiker", + "author_inst": "Emory University" + }, + { + "author_name": "Charles Myers", + "author_inst": "Emory University" + }, + { + "author_name": "Terri White", + "author_inst": "Emory University" + }, + { + "author_name": "Heather Jones", + "author_inst": "Emory University" + }, + { + "author_name": "John Cardella", + "author_inst": "Emory University" + }, + { + "author_name": "Eileen M Burd", + "author_inst": "Emory University" + }, + { + "author_name": "Charles E Hill", + "author_inst": "Emory University" + }, + { + "author_name": "Colleen S Kraft", + "author_inst": "Emory University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.05.05.078238", "rel_title": "Translation-associated mutational U-pressure in the first ORF of SARS-CoV-2 and other coronaviruses", @@ -1479418,105 +1481669,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "toxicology" }, - { - "rel_doi": "10.1101/2020.04.28.20083170", - "rel_title": "Quantifying and mitigating the impact of the COVID-19 pandemic on outcomes in colorectal cancer", - "rel_date": "2020-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.28.20083170", - "rel_abs": "BackgroundThe COVID-19 pandemic has caused disruption across cancer pathways for diagnosis and treatment. In England, 32% of colorectal cancer (CRC) is diagnosed via urgent symptomatic referral from primary care, the \"2-week-wait\" (2WW) pathway. Access to routine endoscopy is likely to be a critical bottleneck causing delays in CRC management due to chronic limitation in capacity, acute competition for physician time, and safety concerns.\n\nMethodsWe used age-specific, stage-specific 10 year CRC survival for England 2007-2017 and 2WW CRC cases volumes. We used per-day hazard ratios of CRC survival generated from observational studies of CRC diagnosis-to-treatment interval to model the effect of different durations of per-patient delay. We utilised data from a large London observational study of faecal immunochemical testing (FIT) in symptomatic patients to model FIT-triage to mitigate delay to colonoscopy.\n\nFindingsModest delays result in significant reduction in survival from CRC with a 4-month delay resulting across age groups in [≥]20% reduction in survival in Stage 3 disease and in total over a year, 1,419 attributable deaths across the 11,266 CRC patients diagnosed via the 2WW pathway. FIT triage of >10 ug Hb/g would salvage 1,292/1,419 of the attributable deaths and reduce colonoscopy requirements by >80%. Diagnostic colonoscopy offers net survival in all age groups, providing nosocomial COVID-19 infection rates are kept low (<2{middle dot}5%).\n\nInterpretationTo avoid significant numbers of avoidable deaths from CRC, normal diagnostic and surgical throughput must be maintained. An accrued backlog of cases will present to primary care following release of lockdown, supranormal endoscopy capacity will be required to manage this without undue delays. FIT-triage of symptomatic cases provides a rational approach by which to avoid patient delay and mitigate pressure on capacity in endoscopy. This would also reduce exposure to nosocomial COVID-19 infection, relevant in particular to older patient groups.\n\nFundingBreast Cancer Now, Cancer Research UK, Bobby Moore Fund for Cancer Research, National Institute for Health Research (NIHR).", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Amit Sud", - "author_inst": "Institute of Cancer Research" - }, - { - "author_name": "Michael Jones", - "author_inst": "Institute of Cancer Research" - }, - { - "author_name": "John Broggio", - "author_inst": "Public Health England" - }, - { - "author_name": "Stephen Scott", - "author_inst": "RM Partners, West London Cancer Alliance" - }, - { - "author_name": "Chey Loveday", - "author_inst": "Institute of Cancer Research" - }, - { - "author_name": "Bethany Torr", - "author_inst": "Institute of Cancer Research" - }, - { - "author_name": "Alice Garrett", - "author_inst": "Institute of Cancer Research" - }, - { - "author_name": "David L. Nicol", - "author_inst": "Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Shaman Jhanji", - "author_inst": "Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Stephen A. Boyce", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Matthew Williams", - "author_inst": "Imperial College" - }, - { - "author_name": "Georgios Lyratzopoulos", - "author_inst": "University College London" - }, - { - "author_name": "Claire Barry", - "author_inst": "RM Partners, West London Cancer Alliance" - }, - { - "author_name": "Elio Riboli", - "author_inst": "Imperial College London" - }, - { - "author_name": "Emma Kipps", - "author_inst": "Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Ethna McFerran", - "author_inst": "Queen's University Belfast" - }, - { - "author_name": "Mark Lawler", - "author_inst": "Queen's University Belfast" - }, - { - "author_name": "David C. Muller", - "author_inst": "Imperial College London" - }, - { - "author_name": "Muti Abulafi", - "author_inst": "Croydon Health Services NHS Trust, on behalf of RMP NICE FIT Steering Group" - }, - { - "author_name": "Richard Houlston", - "author_inst": "Institute of Cancer Research" - }, - { - "author_name": "Clare Ann Turnbull", - "author_inst": "Institute of Cancer Research" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "oncology" - }, { "rel_doi": "10.1101/2020.05.04.20082081", "rel_title": "ai-corona: Radiologist-Assistant Deep Learning Framework for COVID-19 Diagnosis in Chest CT Scans", @@ -1480268,6 +1482420,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.29.20083709", + "rel_title": "Paucity and disparity of publicly available sex-disaggregated data for the COVID-19 epidemic hamper evidence-based decision-making", + "rel_date": "2020-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.29.20083709", + "rel_abs": "COVID-19 has joined the long list of human disorders with sexually dimorphic expression. Increased lethality in men was evident in the first large reports from ChinaCDC and WHO-China, and the gender gap appeared even wider in the early Italian outbreak. Newspapers and scientific journals alike have commented on this finding and the preexisting conditions, biological processes, and gender role behavior differences that may underlie it. However, as for other diseases, and in spite of years of advocating for the collection of raw epidemiological data and the analysis of clinical trial data sets by sex, very little appeared to be released about sex differences in characteristics of the epidemics beyond infection and death rates, such as severity of disease, comorbidities, rate of recovery, length of hospital stay, or number of tests for the SARS-CoV-2 coronavirus. These data are critical not only for scientists to understand the pathophysiology of disease, but also to inform decision-making by countries and healthcare systems on how to prioritize testing and best allocate scarce resources and relief funds.\n\nSystematic analysis of official websites for the 20 countries and 6 US states reporting the highest number of cases on March 21, 2020, revealed a wide disparity in sex-disaggregated data made available to the public and scholars. Only a handful of the countries reported cases by sex separately. None of the other characteristics, including fatality rates, were stratified by sex at the time. Beyond suboptimal sex disaggregation, our analysis found a paucity of usable raw data sets and a generalized lack of standardization of captured data, making comparisons difficult. A second round of data capture in April found more complete, but even more disparate, information.\n\nOur analysis revealed a wide range of sex ratios among confirmed cases, which changed over time. In countries where a male-biased sex ratio was initially reported, the reported proportion of women among cases dramatically increased in under 3 weeks. In contrast, men were consistently over-represented in severe cases, intensive care admissions, and deaths. We also show that the sex ratio varies with age, with a complex pattern, reproduced across the 6 countries for which data were found.\n\nAccurate, peer-reviewed, statistical analysis of harmonized, sex-disaggregated data for other characteristics of epidemics, such as availability of testing, suspected source of infection, or comorbidities will be critical to understand where the observed disparities come from and to generate evidence-based recommendations for decision-making by institutions and governments around the world.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Kristen M Kocher", + "author_inst": "Children's National Research Institute" + }, + { + "author_name": "Arthur D\u00e9lot-Vilain", + "author_inst": "Georgetown Day School" + }, + { + "author_name": "D'Andre Spencer", + "author_inst": "Children's National Research Institute" + }, + { + "author_name": "Jonathan LoTempio", + "author_inst": "Children's National Research Institute" + }, + { + "author_name": "Emmanu\u00e8le C D\u00e9lot", + "author_inst": "Children's National Research Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.04.28.20083840", "rel_title": "Effect of ethanol cleaning on the permeability of FFP2 mask", @@ -1481152,25 +1483339,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2020.05.02.20080390", - "rel_title": "Group Testing Performance Evaluation for SARS-CoV-2 Massive Scale Screening and Testing", - "rel_date": "2020-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.02.20080390", - "rel_abs": "The capacity of current molecular testing convention does not allow high-throughput and community level scans of COVID-19 infections. The diameter in current paradigm of shallow tracing is unlikely to reach the silent clusters that might be as important as the symptomatic cases in the spread of the disease. Group testing is a feasible and promising approach when the resources are scarce and when a relatively low prevalence regime is observed on the population. We employed group testing with a sparse random pooling scheme and conventional group test decoding algorithms both for exact and inexact recovery. Our simulations showed that significant reduction in per case test numbers (or expansion in total test numbers preserving the number of actual tests conducted) for very sparse prevalence regimes is available. Currently proposed COVID-19 group testing schemes offer a gain up to 10X scale-up. There is a good probability that the required scale up to achieve massive scale testing might be greater in certain scenarios. We investigated if further improvement is available, especially in sparse prevalence occurrence where outbreaks are needed to be avoided by population scans. Our simulations show that sparse random pooling can provide improved efficiency gains compared to row-column group testing or Reed-Solomon error correcting codes. Therefore, we propose that special designs for different scenarios could be available and it is possible to scale up testing capabilities significantly.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Ozkan Ufuk Nalbantoglu", - "author_inst": "Erciyes University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.29.20085175", "rel_title": "Forecasting Novel Corona Positive Cases in Indiausing Truncated Information: A Mathematical Approach", @@ -1481862,6 +1484030,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.29.20066506", + "rel_title": "Balancing revenue generation with capacity generation: Case distribution, financial impact and hospital capacity changes from cancelling or resuming elective surgeries in the US during COVID-19", + "rel_date": "2020-05-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.29.20066506", + "rel_abs": "BackgroundTo increase bed capacity and resources, hospitals have postponed elective surgeries, although the financial impact of this decision is unknown. We sought to report elective surgical case distribution, associated gross hospital earnings and regional hospital and intensive care unit (ICU) bed capacity as elective surgical cases are cancelled and then resumed under simulated trends of COVID-19 incidence.\n\nMethodsA retrospective, cohort analysis was performed using insurance claims from 161 million enrollees from the MarketScan database from January 1, 2008 to December 31, 2017. COVID-19 cases were calculated using a generalized Richards model. Centers for Disease Control (CDC) reports on the number of hospitalized and intensive care patients by age were used to estimate the number of cases seen in the ICU, the reduction in elective surgeries and the financial impact of this from historic claims data, using a denominator of all inpatient revenue and outpatient surgeries.\n\nResultsAssuming 5% infection prevalence, cancelling all elective procedures decreases ICU overcapacity from 340% to 270%, but these elective surgical cases contribute 78% (IQR 74, 80) (1.1 trillion (T) US dollars) to inpatient hospital plus outpatient surgical gross earnings per year. Musculoskeletal, circulatory and digestive category elective surgical cases compose 33% ($447B) of total revenue.\n\nConclusionsProcedures involving the musculoskeletal, cardiovascular and digestive system account for the largest loss of hospital gross earnings when elective surgery is postponed. As hospital bed capacity increases following the COVID-19 pandemic, restoring volume of these elective cases will help maintain revenue.\n\nDECLARATIONSO_ST_ABSEthics approval and consent to participateC_ST_ABSThis study did not meet criteria for IRB review.\n\nConsent for publicationNot applicable\n\nAvailability of data and materialsTo facilitate research reproducibility, replicability, accuracy and transparency, the associated analytic code is available on the Open Science Foundation [1] (OSF) repository, [DOI 10.17605/OSF.IO/U53M4] at [https://osf.io/u53m4]. The data that support the findings of this study were obtained under license from Truven. Data were received de-identified in accordance with Section 164.514 of the Health Insurance Portability and Accountability Act (HIPAA).\n\nCompeting interestsJET received modest financial support for speakers fees from LivaNova and from Philips Healthcare, outside of the work. The other authors declare that they have no competing interests.\n\nFundingJET is supported by a career development award (K23HL141596) from the National Heart, Lung, And Blood Institute (NHLBI) of the National Institutes of Health (NIH). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. None of the funding sources were involved in the design or conduct of the study, collection, management, analysis or interpretation of the data, or preparation, review or approval of the manuscript.\n\nAuthors contributionsJET, JH had full access to all the data in the study, takes responsibility for the integrity of the data, the accuracy of the data analysis, and the integrity of the submission as a whole, from inception to published article. JET, HH, BSB, JC, MM, JJH, JH conceived study design; JET, HH, BSB, JC, MM, JJH, RD, BK, AJC, JH contributed to data acquisition and analysis; JET, HH, JJH, JH drafted the work; all authors revised the article for important intellectual content, had final approval of the work to be published, and agree to be accountable to for all aspects of the work.\n\nAcknowledgementsNot applicable", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "JOSEPH E TONNA", + "author_inst": "University of Utah" + }, + { + "author_name": "Heidi A Hanson", + "author_inst": "University of Utah" + }, + { + "author_name": "Jessica N Cohan", + "author_inst": "University of Utah" + }, + { + "author_name": "Marta L McCrum", + "author_inst": "University of Utah" + }, + { + "author_name": "Joshua J Horns", + "author_inst": "University of Utah" + }, + { + "author_name": "Benjamin S Brooke", + "author_inst": "University of Utah" + }, + { + "author_name": "Rupam Das", + "author_inst": "University of Utah" + }, + { + "author_name": "Brenna C Kelly", + "author_inst": "University of Utah" + }, + { + "author_name": "Alexander J Campbell", + "author_inst": "University of Utah" + }, + { + "author_name": "Jim Hotaling", + "author_inst": "University of Utah" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.29.20064279", "rel_title": "Population vulnerability to COVID-19 in Europe: a burden of disease analysis", @@ -1483262,45 +1485485,6 @@ "type": "new results", "category": "systems biology" }, - { - "rel_doi": "10.1101/2020.05.04.077735", - "rel_title": "Temporal signal and the phylodynamic threshold of SARS-CoV-2", - "rel_date": "2020-05-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.04.077735", - "rel_abs": "The ongoing SARS-CoV-2 outbreak marks the first time that large amounts of genome sequence data have been generated and made publicly available in near real-time. Early analyses of these data revealed low sequence variation, a finding that is consistent with a recently emerging outbreak, but which raises the question of whether such data are sufficiently informative for phylogenetic inferences of evolutionary rates and time scales. The phylodynamic threshold is a key concept that refers to the point in time at which sufficient molecular evolutionary change has accumulated in available genome samples to obtain robust phylodynamic estimates. For example, before the phylodynamic threshold is reached, genomic variation is so low that even large amounts of genome sequences may be insufficient to estimate the viruss evolutionary rate and the time scale of an outbreak. We collected genome sequences of SARS-CoV-2 from public databases at 8 different points in time and conducted a range of tests of temporal signal to determine if and when the phylodynamic threshold was reached, and the range of inferences that could be reliably drawn from these data. Our results indicate that by February 2nd 2020, estimates of evolutionary rates and time scales had become possible. Analyses of subsequent data sets, that included between 47 to 122 genomes, converged at an evolutionary rate of about 1.1x10-3 subs/site/year and a time of origin of around late November 2019. Our study provides guidelines to assess the phylodynamic threshold and demonstrates that establishing this threshold constitutes a fundamental step for understanding the power and limitations of early data in outbreak genome surveillance.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Sebastian Duchene", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Leo Featherstone", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Melina Haritopoulou-Sinanidou", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Andrew Rambaut", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Philippe Lemey", - "author_inst": "KU Leuven" - }, - { - "author_name": "Guy Baele", - "author_inst": "KU Leuven" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2020.05.03.066266", "rel_title": "Characterizations of SARS-CoV-2 mutational profile, spike protein stability and viral transmission", @@ -1483764,6 +1485948,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.27.20081984", + "rel_title": "Distinguishing L and H phenotypes of COVID-19 using a single x-ray image", + "rel_date": "2020-05-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20081984", + "rel_abs": "Recent observations have shown that there are two types of COVID-19 response: an H phenotype with high lung elastance and weight, and an L phenotype with low measures1. H-type patients have pneumonia-like thickening of the lungs and require ventilation to survive; L-type patients have clearer lungs that may be injured by mechanical assistance2,3. As treatment protocols differ between the two types, and the number of ventilators is limited, it is vital to classify patients appropriately. To date, the only way to confirm phenotypes is through high-resolution computed tomography2. Here, we identify L- and H-type patients from their frontal chest x-rays using feature-embedded machine learning. We then apply the categorization to multiple images from the same patient, extending it to detect and monitor disease progression and recovery. The results give an immediate criterion for coronavirus triage and provide a methodology for respiratory diseases beyond COVID-19.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Mohammad Tariqul Islam", + "author_inst": "Princeton University" + }, + { + "author_name": "Jason W. Fleischer", + "author_inst": "Princeton University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2020.04.27.20081349", "rel_title": "Genome-wide variations of SARS-CoV-2 infer evolution relationship and transmission route", @@ -1484792,117 +1486999,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.29.20083717", - "rel_title": "Critically ill SARS-CoV-2 patients display lupus-like hallmarks of extrafollicular B cell activation", - "rel_date": "2020-05-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.29.20083717", - "rel_abs": "Abstract/IntroductionA wide clinical spectrum has become a hallmark of the SARS-CoV-2 (COVID-19) pandemic, although its immunologic underpinnings remain to be defined. We have performed deep characterization of B cell responses through high-dimensional flow cytometry to reveal substantial heterogeneity in both effector and immature populations. More notably, critically ill patients displayed hallmarks of extrafollicular B cell activation as previously described in autoimmune settings. Extrafollicular activation correlated strongly with large antibody secreting cell expansion and early production of high levels of SARS-CoV-2-specific antibodies. Yet, these patients fared poorly with elevated inflammatory biomarkers, multi-organ failure, and death. Combined, the findings strongly indicate a major pathogenic role for immune activation in subsets of COVID-19 patients. Our study suggests that, as in autoimmunity, targeted immunomodulatory therapy may be beneficial in specific patient subpopulations that can be identified by careful immune profiling.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Matthew Woodruff", - "author_inst": "Emory University" - }, - { - "author_name": "Richard Ramonell", - "author_inst": "Emory University" - }, - { - "author_name": "Kevin Cashman", - "author_inst": "Emory University" - }, - { - "author_name": "Doan Nguyen", - "author_inst": "Emory University" - }, - { - "author_name": "Ankur Saini", - "author_inst": "Emory University" - }, - { - "author_name": "Natalie Haddad", - "author_inst": "Emory University" - }, - { - "author_name": "Ariel Ley", - "author_inst": "Emory University" - }, - { - "author_name": "Shuya Kyu", - "author_inst": "Emory University" - }, - { - "author_name": "J. Christina Howell", - "author_inst": "Emory University" - }, - { - "author_name": "Tugba Ozturk", - "author_inst": "Emory University" - }, - { - "author_name": "Saeyun Lee", - "author_inst": "Emory University" - }, - { - "author_name": "Weirong Chen", - "author_inst": "Emory University" - }, - { - "author_name": "Jacob Estrada", - "author_inst": "Emory University" - }, - { - "author_name": "Andrea Morrison-Porter", - "author_inst": "Emory University" - }, - { - "author_name": "Andrew Derrico", - "author_inst": "Emory University" - }, - { - "author_name": "Fabliha Anam", - "author_inst": "Emory University" - }, - { - "author_name": "Monika Sharma", - "author_inst": "Emory University" - }, - { - "author_name": "Henry Wu", - "author_inst": "Emory University" - }, - { - "author_name": "Sang Le", - "author_inst": "Emory University" - }, - { - "author_name": "Scott Jenks", - "author_inst": "Emory University" - }, - { - "author_name": "Christopher M Tipton", - "author_inst": "Emory University" - }, - { - "author_name": "Wiliam Hu", - "author_inst": "Emory University" - }, - { - "author_name": "F. Eun-Hyung Lee", - "author_inst": "Emory University" - }, - { - "author_name": "Ignacio Sanz", - "author_inst": "Emory University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2020.04.27.20082016", "rel_title": "COVID-19 Infections and Outcomes in a Live Registry of Heart Failure Patients Across an Integrated Health Care System", @@ -1485750,6 +1487846,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.28.20083899", + "rel_title": "Chinese effective control and other countries uncharted challenge against COVID-19: an epidemiological and modelling study", + "rel_date": "2020-05-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.28.20083899", + "rel_abs": "BackgroundOn the present trajectory, COVID is inevitably becoming a global epidemic, leading to concerns regarding the pandemic potential in China and other countries.\n\nObjectiveIn this study, we use the time-dependent reproduction number (Rt) to comprise the COVID transmissibility across different countries.\n\nMethodsWe used data from Jan 20, 2019, to Feb 29, 2020, on the number of newly confirmed cases, obtained from the reports published by the CDC, to infer the incidence of infectious over time. A two-step procedure was used to estimate the Rt. The first step used data on known index-secondary cases pairs, from publicly available case reports, to estimate the serial interval distribution. The second step estimated the Rt jointly from the incidence data and the information data in the first step. Rt was then used to simulate the epidemics across all major cities in China and typical countries worldwide.\n\nResultsBased on a total of 126 index-secondary cases pairs from 4 international regions, we estimated that the serial interval for SARS-2-CoV was 4.18 (IQR 1.92 - 6.65) days. Domestically, Rt of China, Hubei province, Wuhan had fallen below 1.0 on 9 Feb, 10 Feb and 13 Feb (Rt were 0.99{+/-}0.02, 0.99{+/-}0.02 and 0.96{+/-}0.02), respectively. Internationally, as of 26 Feb, statistically significant periods of COVID spread (Rt >1) were identified for most regions, except for Singapore (Rt was 0.92{+/-}0.17).\n\nConclusionsThe epidemic in China has been well controlled, but the worldwide pandemic has not been well controlled. Worldwide preparedness and vulnerability against COVID-19 should be regarded with more care.\n\nO_LSTWhat is already known on this subject?C_LSTO_LIThe basic reproduction number (R0) and the-time-dependent reproduction number (Rt) are two important indicators of infectious disease transmission. In addition, Rt as a derivative of R0 could be used to assess the epidemiological development of the disease and effectiveness of control measures. Most current researches used data from earlier periods in Wuhan and refer to the epidemiological features of SARS, which are possibly biased. Meanwhile, there are fewer studies discussed the Rt of COVID-19. Current clinical and epidemiological data are insufficient to help us understand the full view of the potential transmission of this disease.\nC_LI\n\nO_LSTWhat this study adds?C_LSTO_LIWe use up-to-data observation of the serial interval and cases arising from local transmission to calculate the Rt in different outbreak level area and every province in China as well as five-top sever outbreak countries and other overseas. By comparing the Rt, we discussed the situation of outbreak around the world.\nC_LI", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Lingling Zheng", + "author_inst": "Guangzhou Women and Childrens Medical Center" + }, + { + "author_name": "Kang Qin", + "author_inst": "Guangzhou Women and Childrens Medical Center" + }, + { + "author_name": "Xiujuan Chen", + "author_inst": "Guangzhou Women and Childrens Medical Center" + }, + { + "author_name": "Shuai Huang", + "author_inst": "Guangzhou Women and Childrens Medical Center" + }, + { + "author_name": "Dong Liu", + "author_inst": "Guangzhou Women and Childrens Medical Center" + }, + { + "author_name": "Weiyao Liao", + "author_inst": "Sun Yat-sen University" + }, + { + "author_name": "Huimin Xia", + "author_inst": "Guangzhou Women and Childrens Medical Center" + }, + { + "author_name": "Jinling Tang", + "author_inst": "Guangzhou Women and Childrens Medical Center" + }, + { + "author_name": "Huiying Liang", + "author_inst": "Guangzhou Medical University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.27.20082057", "rel_title": "Using Supervised Machine Learning and Empirical Bayesian Kriging to reveal Correlates and Patterns of COVID-19 Disease outbreak in sub-Saharan Africa: Exploratory Data Analysis", @@ -1486662,29 +1488809,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.05.02.072439", - "rel_title": "Release of potential pro-inflammatory peptides from SARS-CoV-2 spike glycoproteins in neutrophil-extracellular traps", - "rel_date": "2020-05-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.02.072439", - "rel_abs": "COVID-2019 has progressed in around 10-15% of patients to an acute respiratory distress syndrome characterized by extensive pulmonary inflammation and elevated production of pro-inflammatory cytokines. Neutrophil activation seems to be crucial in the initiation and perpetuation of this exacerbated lung inflammation. However, the precise mechanisms by which this activation occurs remain yet elusive. To this end, this in silico study tried to identify potential proinflammatory inducing peptides (PIPs) produced by the action of the elastase released in neutrophil-extracellular traps over SARS-CoV-2 particles. We found nine potential PIPs exclusive from the SARS-CoV-2, showing homology against T cell recognition epitopes. Moreover, 78 percent of these exclusive PIPs were found produced by the enzymatic cleavage on the spike glycoproteins, suggesting that high PIP concentrations might be released following SARS-CoV-2 huge replication rate. Therefore, these PIPs might play a role in the exacerbated inflammatory response observed in some patients.\n\nHighlightsO_LINine potential PIPs were predicted exclusive from the SARS-CoV-2.\nC_LIO_LISARS-CoV-2 PIPs showed homology against T cell recognition epitopes.\nC_LIO_LIMost of PIPs were produced by enzymatic cleavage of the spike glycoproteins.\nC_LIO_LIThe release of these PIPs might be related to the increased inflammatory response observed in the patients.\nC_LI\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=189 SRC=\"FIGDIR/small/072439v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (49K):\norg.highwire.dtl.DTLVardef@1cd2c3forg.highwire.dtl.DTLVardef@113f8b7org.highwire.dtl.DTLVardef@2df78eorg.highwire.dtl.DTLVardef@1d7c946_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Aitor Blanco-Miguez", - "author_inst": "University of Trento" - }, - { - "author_name": "Borja Sanchez", - "author_inst": "Consejo Superior de Investigaciones Centificas" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.05.01.073387", "rel_title": "PSGL-1 blocks SARS-CoV-2 S protein-mediated virus attachment and infection of target cells", @@ -1487332,6 +1489456,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2020.05.01.20085860", + "rel_title": "Coding variants in ACE2 and TMPRSS2 are not major drivers of COVID-19 severity in UK Biobank subjects.", + "rel_date": "2020-05-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.01.20085860", + "rel_abs": "It is plausible that variants in the ACE2 and TMPRSS2 genes might contribute to variation in COVID-19 severity and that these could explain why some people become very unwell whereas most do not. Exome sequence data was obtained for 49,953 UK Biobank subjects of whom 74 had tested positive for SARS-CoV-2 and could be presumed to have severe disease. A weighted burden analysis was carried out using SCOREASSOC to determine whether there were differences between these cases and the other sequenced subjects in the overall burden of rare, damaging variants in ACE2 or TMPRSS2. There were no statistically significant differences in weighted burden scores between cases and controls for either gene. There were no individual DNA sequence variants with a markedly different frequency between cases and controls. Whether there are small effects on severity, or whether there might be rare variants with major effect sizes, would require studies in much larger samples. Genetic variants affecting the structure and function of the ACE2 and TMPRSS2 proteins are not a major determinant of whether infection with SARS-CoV-2 results in severe symptoms. This research has been conducted using the UK Biobank Resource.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "David Curtis", + "author_inst": "University College London" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2020.04.28.20083279", "rel_title": "CovidCounties - an interactive, real-time tracker of the COVID-19 pandemic at the level of US counties", @@ -1488320,41 +1490463,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.27.20076778", - "rel_title": "Shedding of infectious SARS-CoV-2 in symptomatic neonates, children and adolescents", - "rel_date": "2020-05-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20076778", - "rel_abs": "Children are underrepresented in COVID-19 case numbers, with most pediatric cases exhibiting limited severity, and do not seem to be major drivers of transmission, unlike for other respiratory viruses. That said, SARS-CoV-2 infects children across all age groups, and despite the high proportion of mild or asymptomatic infections, it would be naive not to consider them as transmitters. To address this point we used cell culture to systematically assess the presence of cultivable SARS-CoV-2 in the upper respiratory tract in a cohort of our institutions first 23 symptomatic neonates, children and teenagers with COVID-19 diagnosed by RT-PCR.\n\nMedian age was 12.0 years (interquartile range [IQR 3.8-14.5], range 7 days-15.9 yrs). Most patients had an upper respiratory tract infection (n=13), followed by fever without source and pneumonia (each, n=2). Samples were collected at a median of 2 days (IQR 1-3) after symptom onset. Median viral load (VL) at time of diagnosis was 3.0x106 copies/ml (mean 4,4x108, IQR 6.9x103-4.4x108) from a nasopharyngeal swab (NPS).\n\nSARS-CoV-2 virus isolation was successful in 12/23 (52%) children after inoculating VeroE6 cells with a NPS specimen. SARS-CoV-2 isolation was determined by the presence of a typical cytopathic effect (CPE) and increased viral RNA in the supernatant. SARS-CoV-2 replication in all positive isolates (12/12) was confirmed by a second passage using new VeroE6 cells.\n\nVirus isolation was successful from NPS from all age groups, with a median initial VL of 1.7x108 copies/ml (mean 7.9x108, IQR 4.7x106-1.0x109) (Figure 1). The youngest patient that SARS-CoV-2 was isolated from was a 7-day old neonate. No correlation between disease presentation and success of virus isolation was observed.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=148 SRC=\"FIGDIR/small/20076778v1_fig1.gif\" ALT=\"Figure 1\">\nView larger version (13K):\norg.highwire.dtl.DTLVardef@1bba3e8org.highwire.dtl.DTLVardef@60051org.highwire.dtl.DTLVardef@1fecf15org.highwire.dtl.DTLVardef@1cd90a0_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO Breakdown of SARS-CoV-2 initial viral load of nasopharyngeal swabs among culture-negative and culture-positive specimens\n\nThe thick and thin horizontal bars represent the median viral load and the interquartile range, respectively.\n\n*: specimen collected outside institution, suggesting a longer time to freezing at -80{degrees}C;\n\n#: specimen with a duration between collection and freezing at -80{degrees}C around 48 hours. SARS-CoV-2: severe acute respiratory syndrome coronavirus 2\n\nC_FIG Our data show that initial VLs at diagnosis in symptomatic children is comparable to those in adults, and that symptomatic children of all ages shed infectious virus in early acute illness. Infectious virus isolation success was largely comparable to that of adults, although two specimens yielded an isolate at a lower VL (1.2x104 and 1.4x105 copies/ml) than what was observed in adults.\n\nSARS-CoV-2 shedding patterns of culture competent virus in symptomatic children resemble those observed in adults. Therefore, transmission of SARS-CoV-2 from children is plausible. Considering the relatively low frequency of infected children at this time, biological or other unknown factors could reduce transmission in this population. Both large serological investigations and systematic surveillance of acute respiratory diseases are needed to understand the role of children in this new pandemic.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Arnaud G L'Huillier", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Giulia Torriani", - "author_inst": "Laboratory of Virology and Centre for Emerging Viral Diseases, Division of Laboratory Medicine, Geneva University Hospitals and Faculty of Medicine, University " - }, - { - "author_name": "Fiona Pigny", - "author_inst": "Laboratory of Virology and Centre for Emerging Viral Diseases, Division of Laboratory Medicine, Geneva University Hospitals and Faculty of Medicine, University " - }, - { - "author_name": "Laurent Kaiser", - "author_inst": "Laboratory of Virology and Centre for Emerging Viral Diseases, Division of Laboratory Medicine, Geneva University Hospitals and Faculty of Medicine, University " - }, - { - "author_name": "Isabelle Eckerle", - "author_inst": "Laboratory of Virology and Centre for Emerging Viral Diseases, Division of Laboratory Medicine, Geneva University Hospitals and Faculty of Medicine, University " - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.26.20080465", "rel_title": "MODELLING OF COVID-19 OUTBREAK INDICATORS IN CHINA BETWEEN JANUARY AND APRIL", @@ -1489082,6 +1491190,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.27.20074583", + "rel_title": "QT Interval Prolongation and Torsade De Pointes in Patients with COVID-19 treated with Hydroxychloroquine/Azithromycin", + "rel_date": "2020-05-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20074583", + "rel_abs": "BackgroundThe emergence of the COVID-19 pandemic has resulted in over two million affected and over 150 thousand deaths to date. There is no known effective therapy for the disease. Initial reports suggesting the potential benefit of Hydroxychloroquine/Azithromycin (HY/AZ) have resulted in massive adoption of this combination worldwide. However, while the true efficacy of this regimen is unknown, initial reports have raised concerns regarding the potential risk of QT prolongation and induction of torsade de pointes (TdP).\n\nMethodsThis is a multicenter retrospective study of 251 patients with COVID-19 treated with HY/AZ. We reviewed ECG tracings from baseline and until 3 days after completion of therapy to determine the progression of QTc and incidence of arrhythmia and mortality.\n\nResultsQTc prolonged in parallel with increasing drug exposure and incompletely shortened after its completion. Extreme new QTc prolongation to > 500 ms, a known marker of high risk for TdP had developed in 15.9% of patients. One patient developed TdP requiring emergent cardioversion. Seven patients required premature termination of therapy. The baseline QTc of patients exhibiting QTc prolongation of > 60 ms was normal.\n\nConclusionThe combination of HY/AZ significantly prolongs the QTc in patients with COVID-19. This prolongation may be responsible for life threating arrhythmia in the form of TdP. This risk mandates careful consideration of HY/AZ therapy in lights of its unproven efficacy. Strict QTc monitoring should be performed if the regimen is given.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Ehud Chorin", + "author_inst": "NYU Langone Health" + }, + { + "author_name": "Lalit Wadhwani", + "author_inst": "NYU Langone Health" + }, + { + "author_name": "Silvia Magnani", + "author_inst": "San Paolo University Hospital, Milan Italy" + }, + { + "author_name": "Matthew Dai", + "author_inst": "NYU Langone Healtha" + }, + { + "author_name": "Eric Shulman", + "author_inst": "NYU Langone Health" + }, + { + "author_name": "Charles Nadeau-Routhier", + "author_inst": "NYU Langone Health" + }, + { + "author_name": "Robert Knots", + "author_inst": "NYU Langone Health" + }, + { + "author_name": "Roi Bar-Cohen", + "author_inst": "NYU Langone Health" + }, + { + "author_name": "Edward Kogan", + "author_inst": "NYU Langone Health" + }, + { + "author_name": "Chirag Barbhaiya", + "author_inst": "NYU Langone Health" + }, + { + "author_name": "Anthony Aizer", + "author_inst": "NYU Langone Health" + }, + { + "author_name": "Douglas Holmes", + "author_inst": "NYU Langone Health" + }, + { + "author_name": "Scott Bernstein", + "author_inst": "NYU Langone Health" + }, + { + "author_name": "Michael Spinelli", + "author_inst": "NYU Langone Health" + }, + { + "author_name": "David S Park", + "author_inst": "NYU Langone Health" + }, + { + "author_name": "Stefano Carugo", + "author_inst": "NYU Langone Health" + }, + { + "author_name": "Larry A Chinitz", + "author_inst": "NYU Langone Health" + }, + { + "author_name": "Lior Jankelosn", + "author_inst": "NYU Langone Health" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2020.04.27.20073379", "rel_title": "Hydroxychloroquine application is associated with a decreased mortality in critically ill patients with COVID-19", @@ -1489762,29 +1491957,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, - { - "rel_doi": "10.1101/2020.04.26.20080994", - "rel_title": "Estimates of the ongoing need for social distancing and control measures post-\"lockdown\" from trajectories of COVID-19 cases and mortality.", - "rel_date": "2020-05-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.26.20080994", - "rel_abs": "By 29th April 2020, COVID-19 had caused more than 3 million cases across more than 200 countries. And most countries with significant outbreaks had introduced social distancing or \"lockdown\" measures to reduce viral transmission. So the key question now is when, how, and to what extent, these measures can be lifted.\n\nBy fitting regression models to publically available data on daily numbers of newly-confirmed cases and mortality, trajectories, doubling times and reproduction number (R0) were estimated both before and under the control measures. These data ran up to 29th April 2020, and covered 73 countries that had provided sufficient data for modelling.\n\nThe estimates of R0, before lockdown, based on these data were broadly consistent with those previously published at between 2.0 and 3.7 in the countries with the largest number of cases available for analysis (USA, Italy, Spain, France and UK). There was little evidence to suggest that the restrictions had reduced R far below 1 in many places, with France having the most rapid reductions - R0 0.77 (95%CI 0.68-0.87), based on cases and 0.78 (95%CI 0.68-0.88) based on mortality.\n\nIntermittent lockdown has been proposed as a means of controlling the outbreak while allowing periods of increase freedom and economic activity. These data suggest that few countries could have even one week per month unrestricted without seeing resurgence of the epidemic. Similarly, restoring 20% of the activity that has been prevented by the lockdowns looks difficult to reconcile with preventing the resurgence of the disease in most countries.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Mike Lonergan", - "author_inst": "University of Dundee" - }, - { - "author_name": "James Chalmers", - "author_inst": "University of Dundee" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.26.20080895", "rel_title": "Elementary spatial structures and dispersion of COVID-19: health geography directing responses to public health emergency in Sao Paulo State, Brazil", @@ -1490324,6 +1492496,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.27.20077016", + "rel_title": "Determining the source of transmission of SARS-CoV-2 infection in a healthcare worker", + "rel_date": "2020-05-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20077016", + "rel_abs": "BackgroundHealthcare workers (HCWs) are at the frontlines of the COVID-19 pandemic and are at risk of exposure to SARS-CoV-2 infection from their interactions with patients and in the community (1, 2). Limited availability of recommended personal protective equipment (PPE), in particular N95 respirators, has fueled concerns about whether HCWs are adequately protected from exposure while caring for patients. Understanding the source of SARS-CoV-2 infection in a HCW - the community or the healthcare system - is critical for understanding the effectiveness of hospital infection control and PPE practices. In Dane County, Wisconsin, community prevalence of SARS-CoV-2 is relatively low (cumulative prevalence of ~0.06% - positive cases / total population in Dane county as of April 17). Although SARS-CoV-2 infections in HCWs are often presumed to be acquired during the course of patient care, there are few reports unambiguously identifying the source of acquisition.\n\nObjectiveTo determine the source of transmission of SARS-CoV-2 in a healthcare worker.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Nasia Safdar", + "author_inst": "University of Wisconsin School of Medicine and Public Health, Madison, WI 53705 and the William S. Middleton Memorial Veterans Hospital" + }, + { + "author_name": "Gage K Moreno", + "author_inst": "Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53711" + }, + { + "author_name": "Katarina M Braun", + "author_inst": "Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, 53711" + }, + { + "author_name": "Thomas C Friedrich", + "author_inst": "Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, 53711" + }, + { + "author_name": "David H O'Connor", + "author_inst": "Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53711" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.28.20078071", "rel_title": "ACE inhibitors, AT1 receptor blockers and COVID-19: clinical epidemiology evidences for a continuation of treatments. The ACER-COVID study", @@ -1491100,69 +1493307,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.04.30.071357", - "rel_title": "Distinct Inductions of and Responses to Type I and Type III Interferons PromoteInfections in Two SARS-CoV-2 Isolates", - "rel_date": "2020-05-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.30.071357", - "rel_abs": "The recent emerging coronavirus, SARS-CoV-2, has been rapidly and widely spread and causing an ongoing viral pneumonia outbreak worldwide. It has been observed that SARS-CoV-2 patients show a rather long and asymptomatic incubation time. We characterized the abilities to induce and to response to IFN{beta}/IFN{lambda}1 of two or our clinical isolates, SARS-CoV-2/NTU01/TWN/human/2020 and SARS-CoV-2/NTU02/TWN/human/2020, which exhibit only two amino acid differences over the [~]30kb viral genome. We found that both isolates may infect Huh7, A549 and Calu-3 cells, yet the RIG-I-like receptor-dependent antiviral signaling was poorly induced in these cells in the early infections. Unexpectedly, we found that the intracellular vRNA levels of these isolates were sustained upon to type I/III IFN treatments, and this phenotype was more pronounced in the Taiwan/NTU01/2020 isolate. The type I/III IFN responses are antiviral but partially proviral in the case of SARS-CoV-2 infections. Poor induction and response to innate immunity may contribute to destitute neutralization index of the antibody produced, and indeed we found that the patient serum could not efficiently neutralize SARS-CoV-2 virions. With better understandings of the interplay between SARS-CoV-2 and the host antiviral innate immunity, our report may provide new insights for the regimen of therapies for SARS-CoV-2 infected patients.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Fu Hsin", - "author_inst": "National Taiwan University" - }, - { - "author_name": "Tai-Ling Chao", - "author_inst": "National Taiwan University" - }, - { - "author_name": "Yun-Rui Chan", - "author_inst": "National Taiwan University" - }, - { - "author_name": "Han-Chieh Kao", - "author_inst": "National Taiwan University" - }, - { - "author_name": "Wang-Da Liu", - "author_inst": "Department of Internal Medicine, National Taiwan University Hospital" - }, - { - "author_name": "Jann-Tay Wang", - "author_inst": "Department of Internal Medicine, National Taiwan University Hospital" - }, - { - "author_name": "Yu-Hao Pang", - "author_inst": "National Taiwan University" - }, - { - "author_name": "Chih-Hui Lin", - "author_inst": "National Taiwan University" - }, - { - "author_name": "Ya-Min Tsai", - "author_inst": "National Taiwan University" - }, - { - "author_name": "Jing-Yi Lin", - "author_inst": "National Taiwan University" - }, - { - "author_name": "Sui-Yuan Chang", - "author_inst": "National Taiwan University" - }, - { - "author_name": "Helene Minyi Liu", - "author_inst": "National Taiwan University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.05.01.072728", "rel_title": "SARS-CoV2 quantification using RT-dPCR: a faster and safer alternative to assist viral genomic copies assessment using RT-qPCR", @@ -1491754,6 +1493898,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.28.20082966", + "rel_title": "Development and validation of an automated radiomic CT signature for detecting COVID-19", + "rel_date": "2020-05-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.28.20082966", + "rel_abs": "BackgroundThe coronavirus disease 2019 (COVID-19) outbreak has reached pandemic status. Drastic measures of social distancing are enforced in society and healthcare systems are being pushed to and over their limits.\n\nObjectivesTo develop a fully automatic framework to detect COVID-19 by applying AI to chest CT and evaluate validation performance.\n\nMethodsIn this retrospective multi-site study, a fully automated AI framework was developed to extract radiomics features from volumetric chest CT exams to learn the detection pattern of COVID-19 patients. We analysed the data from 181 RT-PCR confirmed COVID-19 patients as well as 1200 other non-COVID-19 control patients to build and assess the performance of the model. The datasets were collected from 2 different hospital sites of the CHU Liege, Belgium. Diagnostic performance was assessed by the area under the receiver operating characteristic curve (AUC), sensitivity and specificity.\n\nResults1381 patients were included in this study. The average age was 64.4{+/-}15.8 and 63.8{+/-}14.4 years with a gender balance of 56% and 52% male in the COVID-19 and control group, respectively. The final curated dataset used for model construction and validation consisted of chest CT scans of 892 patients. The model sensitivity and specificity for detecting COVID-19 in the test set (training 80% and test 20% of patients) were 78.94% and 91.09%, respectively, with an AUC of 0.9398 (95% CI: 0.875-1). The negative predictive value of the algorithm was found to be larger than 97%.\n\nConclusionsBenchmarked against RT-PCR confirmed cases of COVID-19, our AI framework can accurately differentiate COVID-19 from routine clinical conditions in a fully automated fashion. Thus, providing rapid accurate diagnosis in patients suspected of COVID-19 infection, facilitating the timely implementation of isolation procedures and early intervention.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Julien Guiot", + "author_inst": "Department of Pneumology, University Hospital of Liege, Liege, Belgium" + }, + { + "author_name": "Akshayaa Vaidyanathan", + "author_inst": "Oncoradiomics SA, Liege, Belgium, The D-Lab, Department of Precision Medicine, Department of Nuclear Medicine, GROW School for Oncology, Maastricht University, " + }, + { + "author_name": "Louis Deprez", + "author_inst": "Department of Radiology, University Hospital of Liege, Liege, Belgium" + }, + { + "author_name": "Fadila Zerka", + "author_inst": "Oncoradiomics SA, Liege, Belgium, The D-Lab, Department of Precision Medicine, Department of Nuclear Medicine, GROW School for Oncology, Maastricht University, " + }, + { + "author_name": "Denis Danthine", + "author_inst": "Department of Radiology, University Hospital of Liege, Liege, Belgium" + }, + { + "author_name": "Anne-Noelle Frix", + "author_inst": "Department of Pneumology, University Hospital of Liege, Liege, Belgium" + }, + { + "author_name": "Marie Thys", + "author_inst": "Department of Medico-Economic Information, University Hospital of Liege, Liege, Belgium" + }, + { + "author_name": "Monique Henket", + "author_inst": "Department of Pneumology, University Hospital of Liege, Liege, Belgium" + }, + { + "author_name": "Gregory Canivet", + "author_inst": "Department of Computer Applications, University Hospital of Liege, Liege, Belgium" + }, + { + "author_name": "Stephane Mathieu", + "author_inst": "Department of Computer Applications, University Hospital of Liege, Liege, Belgium" + }, + { + "author_name": "Eva Eftaxia", + "author_inst": "Department of Radiology, University Hospital of Liege, Liege, Belgium" + }, + { + "author_name": "Philippe Lambin", + "author_inst": "The D-Lab, Department of Precision Medicine, Department of Nuclear Medicine, GROW School for Oncology, Maastricht University, Maastricht, The Netherlands" + }, + { + "author_name": "Nathan Tsoutzidis", + "author_inst": "Oncoradiomics SA, Liege, Belgium" + }, + { + "author_name": "Benjamin Miraglio", + "author_inst": "Oncoradiomics SA, Liege, Belgium" + }, + { + "author_name": "Sean Walsh", + "author_inst": "Oncoradiomics SA, Liege, Belgium" + }, + { + "author_name": "Michel Moutschen", + "author_inst": "Department of Infectious Diseases, University Hospital of Liege, Liege, Belgium Michel" + }, + { + "author_name": "Renaud Louis", + "author_inst": "Department of Pneumology, University Hospital of Liege, Liege, Belgium" + }, + { + "author_name": "Paul Meunier", + "author_inst": "Department of Radiology, University Hospital of Liege, Liege, Belgium" + }, + { + "author_name": "Wim Vos", + "author_inst": "Oncoradiomics SA, Liege, Belgium" + }, + { + "author_name": "Ralph Leijenaar", + "author_inst": "Oncoradiomics SA, Liege, Belgium" + }, + { + "author_name": "Pierre Lovinfosse", + "author_inst": "Department of Nuclear Medicine and Oncological Imaging, University Hospital of Liege, Liege, Belgium" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.29.20085910", "rel_title": "Validation of an extraction-free RT-PCR protocol for detection of SARS-CoV2 RNA", @@ -1492354,69 +1494597,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.04.27.20081836", - "rel_title": "Social Distancing Has Merely Stabilized COVID-19 in the US", - "rel_date": "2020-04-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20081836", - "rel_abs": "Social distancing measures, with varying degrees of restriction, have been imposed around the world in order to stem the spread of COVID-19. In this work we analyze the effect of current social distancing measures in the United States. We quantify the reduction in doubling rate, by state, that is associated with social distancing. We find that social distancing is associated with a statistically-significant reduction in the doubling rate for all but three states. At the same time, we do not find significant evidence that social distancing has resulted in a reduction in the number of daily confirmed cases. Instead, social distancing has merely stabilized the spread of the disease. We provide an illustration of our findings for each state, including point estimates of the effective reproduction number, R, both with and without social distancing. We also discuss the policy implications of our findings.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Aaron B. Wagner", - "author_inst": "Cornell University" - }, - { - "author_name": "Elaine L. Hill", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Sean E. Ryan", - "author_inst": "Lancaster University" - }, - { - "author_name": "Ziteng Sun", - "author_inst": "Cornell University" - }, - { - "author_name": "Grace Deng", - "author_inst": "Cornell University" - }, - { - "author_name": "Sourbh Bhadane", - "author_inst": "Cornell University" - }, - { - "author_name": "Victor Hernandez Martinez", - "author_inst": "University of Rochester" - }, - { - "author_name": "Peter Wu", - "author_inst": "Cornell University" - }, - { - "author_name": "Dongmei Li", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Ajay Anand", - "author_inst": "University of Rochester" - }, - { - "author_name": "Jayadev Acharya", - "author_inst": "Cornell University" - }, - { - "author_name": "David S. Matteson", - "author_inst": "Cornell University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.28.067363", "rel_title": "Validation of a Single-step, Single-tube Reverse Transcription-Loop-Mediated Isothermal Amplification Assay for Rapid Detection of SARS-CoV-2 RNA", @@ -1492996,6 +1495176,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.25.20079889", + "rel_title": "Inferred duration of infectious period of SARS-CoV-2: rapid scoping review and analysis of available evidence for asymptomatic and symptomatic COVID-19 cases", + "rel_date": "2020-04-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.25.20079889", + "rel_abs": "ObjectivesOur objective was to review the literature on the inferred duration of the infectious period of COVID-19, caused by SARS-COV-2 virus, and provide an overview of the variation depending on the methodological approach.\n\nDesignRapid scoping review. Literature review with fixed search terms, up to 1st April 2020. Central tendency and variation of the parameter estimates for infectious period in (a) asymptomatic (b) symptomatic cases from (i) virological studies (repeated testing), (ii) tracing studies (iii) modelling studies were gathered. Narrative review of viral dynamics.\n\nInformation sourcesSearch strategies developed and the following searched: PubMed, Google Scholar, MedRxiv, BioRxiv. Additionally, the Health Information Quality Authority (Ireland) viral load synthesis was utilised, which screened literature from PubMed, Embase, ScienceDirect, NHS evidence, Cochrane, medRxiv and bioRxiv, HRB open databases.\n\nResultsThere was substantial variation in the estimates, and how infectious period was inferred. One study provided approximate median infectious period for asymptomatic cases of 6.5-9.5 days. Median pre-symptomatic infectious period across studies varied over <1-4 days. Estimated mean time from symptom onset to two negative RT-PCR tests was 13.4 days (95%CI: 10.9-15.8), but was shorter when studies included children or less severe cases. Estimated mean duration from symptom onset to hospital discharge or death (potential maximal infectious period) was 18.1 days (95%CI: 15.1-21.0); time to discharge was on average 4 days shorter than time-to-death. Viral dynamic data and model infectious parameters were often shorter than repeated diagnostic data.\n\nConclusionsThere are limitations of inferring infectiousness from repeated diagnosis, viral loads, and viral replication data alone, and also potential patient recall bias relevant to estimating exposure and symptom onset times. Despite this, available data provides a preliminary evidence base to inform models of central tendency for key parameters, and variation for exploring parameter space and sensitivity analysis. Some current models may be underestimating infectious period.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Andrew W. Byrne", + "author_inst": "DAFM" + }, + { + "author_name": "David McEvoy", + "author_inst": "University College Dublin" + }, + { + "author_name": "Aine Collins", + "author_inst": "University College Dublin" + }, + { + "author_name": "Kevin Hunt", + "author_inst": "University College Dublin" + }, + { + "author_name": "Miriam Casey", + "author_inst": "University College Dublin" + }, + { + "author_name": "Ann Barber", + "author_inst": "University College Dublin" + }, + { + "author_name": "Francis Butler", + "author_inst": "University College Dublin" + }, + { + "author_name": "John Griffin", + "author_inst": "DAFM" + }, + { + "author_name": "Elizabeth Lane", + "author_inst": "DAFM" + }, + { + "author_name": "Conor McAloon", + "author_inst": "University College Dublin" + }, + { + "author_name": "Kirsty O'Brien", + "author_inst": "Health Information and Quality Authority" + }, + { + "author_name": "Patrick Wall", + "author_inst": "University College Dublin" + }, + { + "author_name": "Kieran Walsh", + "author_inst": "Health Information and Quality Authority" + }, + { + "author_name": "Simon More", + "author_inst": "University College Dublin" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.25.20079343", "rel_title": "Poolkeh Finds the Optimal Pooling Strategy for a Population-wide COVID-19 Testing (Israel, UK, and US as Test Cases)", @@ -1493760,77 +1496011,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.04.28.20083832", - "rel_title": "Potential spreading risks and disinfection challenges of medical wastewater by the presence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) viral RNA in septic tanks of fangcang hospital", - "rel_date": "2020-04-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.28.20083832", - "rel_abs": "The outbreak of coronavirus infectious disease-2019 (COVID-19) pneumonia raises the concerns of effective deactivation of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in medical wastewater by disinfectants. In this study, we evaluated the presence of SARS-CoV-2 viral RNA in septic tanks of Wuchang Fangcang Hospital and found the high level of (0.05-1.87)x104 copies/L after disinfection with sodium hypochlorite. Embedded viruses in stool particles might be released in septic tanks, behaving as a source of SARS-CoV-2 and potentially contributing to its spread through drainage pipelines. Current recommended disinfection strategy (free chlorine above 6.5 mg/L after 1.5-hour contact) needs to be reevaluated to completely remove SARS-CoV-2 viral RNA in non-centralized disinfection system and effectively deactivate SARS-CoV-2. The effluents showed negative results for SARS-CoV-2 viral RNA when overdosed with sodium hypochlorite but had high a level of disinfection by-product residuals, possessing significant ecological risks.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Dayi Zhang", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Haibo Ling", - "author_inst": "Hubei Academy of Environmental Sciences" - }, - { - "author_name": "Xia Huang", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Jing Li", - "author_inst": "Hubei Center for Disease Control and Prevention" - }, - { - "author_name": "Weiwei Li", - "author_inst": "Hubei Academy of Environmental Sciences" - }, - { - "author_name": "Chuan Yi", - "author_inst": "Hubei Academy of Environmental Sciences" - }, - { - "author_name": "Ting Zhang", - "author_inst": "Hubei Center for Disease Control and Prevention" - }, - { - "author_name": "Yongzhong Jiang", - "author_inst": "Hubei Center for Disease Control and Prevention" - }, - { - "author_name": "Yuning He", - "author_inst": "Research Institute for Environmental Innovation (Tsinghua-Suzhou)" - }, - { - "author_name": "Songqiang Deng", - "author_inst": "Research Institute for Environmental Innovation (Tsinghua-Suzhou)" - }, - { - "author_name": "Xian Zhang", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Yi Liu", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Guanghe Li", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Jiuhui Qu", - "author_inst": "Tsinghua University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.29.20082867", "rel_title": "ACE2 and TMPRSS2 expression by clinical, HLA, immune, and microbial correlates across 34 human cancers and matched normal tissues: implications for SARS-COV-2 COVID-19", @@ -1494270,6 +1496450,177 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.24.20078006", + "rel_title": "Supplementing the National Early Warning Score (NEWS2) for anticipating early deterioration among patients with COVID-19 infection", + "rel_date": "2020-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.24.20078006", + "rel_abs": "BackgroundThe National Early Warning Score (NEWS2) is currently recommended in the United Kingdom for risk stratification of COVID outcomes, but little is known about its ability to detect severe cases. We aimed to evaluate NEWS2 for severe COVID outcome and identify and validate a set of routinely-collected blood and physiological parameters taken at hospital admission to improve the score.\n\nMethodsTraining cohorts comprised 1276 patients admitted to Kings College Hospital NHS Foundation Trust with COVID-19 disease from 1st March to 30th April 2020. External validation cohorts included 5037 patients from four UK NHS Trusts (Guys and St Thomas Hospitals, University Hospitals Southampton, University Hospitals Bristol and Weston NHS Foundation Trust, University College London Hospitals), and two hospitals in Wuhan, China (Wuhan Sixth Hospital and Taikang Tongji Hospital). The outcome was severe COVID disease (transfer to intensive care unit or death) at 14 days after hospital admission. Age, physiological measures, blood biomarkers, sex, ethnicity and comorbidities (hypertension, diabetes, cardiovascular, respiratory and kidney diseases) measured at hospital admission were considered in the models.\n\nResultsA baseline model of NEWS2 + age had poor-to-moderate discrimination for severe COVID infection at 14 days (AUC in training sample = 0.700; 95% CI: 0.680, 0.722; Brier score = 0.192; 95% CI: 0.186, 0.197). A supplemented model adding eight routinely-collected blood and physiological parameters (supplemental oxygen flow rate, urea, age, oxygen saturation, CRP, estimated GFR, neutrophil count, neutrophil/lymphocyte ratio) improved discrimination (AUC = 0.735; 95% CI: 0.715, 0.757) and these improvements were replicated across five UK and non-UK sites. However, there was evidence of miscalibration with the model tending to underestimate risks in most sites.\n\nConclusionsNEWS2 score had poor-to-moderate discrimination for medium-term COVID outcome which raises questions about its use as a screening tool at hospital admission. Risk stratification was improved by including readily available blood and physiological parameters measured at hospital admission, but there was evidence of miscalibration in external sites. This highlights the need for a better understanding of the use of early warning scores for COVID.\n\nKO_SCPLOWEYC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWMESSAGESC_SCPLOWO_LIThe National Early Warning Score (NEWS2), currently recommended for stratification of severe COVID-19 disease in the UK, showed poor-to-moderate discrimination for medium-term outcomes (14-day transfer to ICU or death) among COVID-19 patients.\nC_LIO_LIRisk stratification was improved by the addition of routinely-measured blood and physiological parameters routinely at hospital admission (supplemental oxygen, urea, oxygen saturation, CRP, estimated GFR, neutrophil count, neutrophil/lymphocyte ratio) which provided moderate improvements in a risk stratification model for 14-day ICU/death.\nC_LIO_LIThis improvement over NEWS2 alone was maintained across multiple hospital trusts but the model tended to be miscalibrated with risks of severe outcomes underestimated in most sites.\nC_LIO_LIWe benefited from existing pipelines for informatics at KCH such as CogStack that allowed rapid extraction and processing of electronic health records. This methodological approach provided rapid insights and allowed us to overcome the complications associated with slow data centralisation approaches.\nC_LI", + "rel_num_authors": 39, + "rel_authors": [ + { + "author_name": "Ewan Carr", + "author_inst": "King's College London" + }, + { + "author_name": "Rebecca Bendayan", + "author_inst": "King's College London" + }, + { + "author_name": "Daniel Bean", + "author_inst": "King's College London" + }, + { + "author_name": "Matthew Stammers", + "author_inst": "Clinical Informatics Research Unit, University of Southampton" + }, + { + "author_name": "Wenjuan Wang", + "author_inst": "King's College London" + }, + { + "author_name": "Huayu Zhang", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Thomas Searle", + "author_inst": "King's College London" + }, + { + "author_name": "Zeljko Kraljevic", + "author_inst": "King's College London" + }, + { + "author_name": "Anthony Shek", + "author_inst": "King's College London" + }, + { + "author_name": "Hang T T Phan", + "author_inst": "Clinical Informatics Research Unit, University of Southampton" + }, + { + "author_name": "Walter Muruet", + "author_inst": "King's College London" + }, + { + "author_name": "Rishi K Gupta", + "author_inst": "University College London" + }, + { + "author_name": "Anthony J Shinton", + "author_inst": "UHS Digital, University Hospital Southampton" + }, + { + "author_name": "Mike Wyatt", + "author_inst": "University Hospitals Bristol NHS Foundation Trust, Bristol, UK" + }, + { + "author_name": "Ting Shi", + "author_inst": "Usher Institute, University of Edinburgh" + }, + { + "author_name": "Xin Zhang", + "author_inst": "Department of Pulmonary and Critical Care Medicine, People's Liberation Army Joint Logistic Support Force 920th Hospital, Yunnan, China" + }, + { + "author_name": "Andrew Pickles", + "author_inst": "King's College London" + }, + { + "author_name": "Daniel Stahl", + "author_inst": "King's College London" + }, + { + "author_name": "Rosita Zakeri", + "author_inst": "King's College London" + }, + { + "author_name": "Mahdad Noursadeghi", + "author_inst": "UCL Division of Infection and Immunity, University College London Hospitals NHS Trust" + }, + { + "author_name": "Kevin O'Gallagher", + "author_inst": "King's College London" + }, + { + "author_name": "Matt Rogers", + "author_inst": "University Hospitals Bristol NHS Foundation Trust, Bristol, U.K." + }, + { + "author_name": "Amos Folarin", + "author_inst": "King's College London" + }, + { + "author_name": "Christopher Bourdeaux", + "author_inst": "University Hospitals Bristol NHS Foundation Trust, Bristol, U.K." + }, + { + "author_name": "Chris McWilliams", + "author_inst": "Department of Engineering Mathematics, University of Bristol, Bristol, UK" + }, + { + "author_name": "Lukasz Roguski", + "author_inst": "University College London" + }, + { + "author_name": "Florina Borca", + "author_inst": "University of Southampton" + }, + { + "author_name": "James Batchelor", + "author_inst": "Clinical Informatics Research Unit, University of Southampton, Coxford Rd, Southampton SO16 5AF" + }, + { + "author_name": "Xiaodong Wu", + "author_inst": "Department of Pulmonary and Critical Care Medicine, Shanghai East Hospital, Tongji University, Shanghai, China" + }, + { + "author_name": "Jiaxing Sun", + "author_inst": "Department of Pulmonary and Critical Care Medicine, Shanghai East Hospital, Tongji University, Shanghai, China" + }, + { + "author_name": "Ashwin Pinto", + "author_inst": "UHS Digital, University Hospital Southampton" + }, + { + "author_name": "Bruce Guthrie", + "author_inst": "Usher Institute, University of Edinburgh" + }, + { + "author_name": "Cormac Breen", + "author_inst": "King's College London" + }, + { + "author_name": "Abdel Douiri", + "author_inst": "King's College London" + }, + { + "author_name": "Honghan Wu", + "author_inst": "University College London" + }, + { + "author_name": "Vasa Curcin", + "author_inst": "King's College London" + }, + { + "author_name": "James T Teo", + "author_inst": "Kings College Hospital NHS Foundation Trust" + }, + { + "author_name": "Ajay Shah", + "author_inst": "King's College London" + }, + { + "author_name": "Richard Dobson", + "author_inst": "Kings College London" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.24.20077933", "rel_title": "Comprehensive Investigation and Isolation have Effectively Suppressed the Spread of COVID-19", @@ -1494798,45 +1497149,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.04.24.20078998", - "rel_title": "Automated Diagnosis of COVID-19 Using Deep Learning and Data Augmentation on Chest CT", - "rel_date": "2020-04-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.24.20078998", - "rel_abs": "BackgroundCoronavirus disease 2019 (COVID-19) has surprised the world since the beginning of 2020, and the rapid growth of COVID-19 is beyond the capability of doctors and hospitals that could deal in many areas. The chest computed tomography (CT) could be served as an effective tool in detection of COVID-19. It is valuable to develop automatic detection of COVID-19.\n\nMaterials and MethodsThe collected dataset consisted of 1042 chest CT images (including 521 COVID-19, 397 healthy, 76 bacterial pneumonia and 48 SARS) obtained by exhaustively searching available data on the Internet. Then, these data are divided into three sets, referred to training set, validation set and testing set. Sixteen data augmentation operations are designed to enrich the training set in deep learning training phase. Multiple experiments were conducted to analyze the performance of the model in the detection of COVID-19 both in case of no noisy labels and noisy labels. The performance was assessed by the area under the receiver operating characteristic (AUC), sensitivity, specificity and accuracy.\n\nResultsThe data augmentation operations on the training set are effective for improvement of the model performance. The area under the receiver operating characteristic curve is 0.9689 with (95% CI: 0.9308, 1) in case of no noisy labels for the classification of COVID-19 from heathy subject, while the per-exam sensitivity, specificity and accuracy for detecting COVID-19 in the independent testing set are 90.52%, 91.58% and 91.21%, respectively. In the classification of COVID-19 from other hybrid cases, the average AUC of the proposed model is 0.9222 with (95%CI: 0.8418, 1) if there are no noisy labels. The model is also robust when part of the training samples is marked incorrectly. The average AUC is 92.23% in the case of noisy labels of 10% in the training set.\n\nConclusionA deep learning model with insufficient samples can be developed by using data augmentation in assisting medical workers in making quick and correct diagnosis of COVID-19.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Runwen Hu", - "author_inst": "Jinan University" - }, - { - "author_name": "Guanqi Ruan", - "author_inst": "Jinan University" - }, - { - "author_name": "Shijun Xiang", - "author_inst": "The School of Information Science and Technology, Jinan University" - }, - { - "author_name": "Minghui Huang", - "author_inst": "Jinan University" - }, - { - "author_name": "Qiaoyi Liang", - "author_inst": "Jinan University" - }, - { - "author_name": "Jingxuan Li", - "author_inst": "Jinan University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.04.24.20078584", "rel_title": "EXPLAINABLE-BY-DESIGN APPROACH FOR COVID-19 CLASSIFICATION VIA CT-SCAN", @@ -1495292,6 +1497604,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.25.20079806", + "rel_title": "A fractional-order SEIHDR model for COVID-19 with inter-city networked coupling effects", + "rel_date": "2020-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.25.20079806", + "rel_abs": "A novel coronavirus, designated as COVID-19, emerged in Wuhan, China, at the end of 2019. In this paper, a mathematical model is proposed to analyze the dynamic behavior of COVID-19. Based on inter-city networked coupling effects, a fractional-order SEIHDR system with the real-data from 23 January to 18 March, 2020 of COVID19 is discussed. Meanwhile, hospitalized individuals and the mortality rates of three types of individuals (exposed, infected and hospitalized) are firstly taken into account in the proposed model. And infectivity of individuals during incubation is also considered in this paper. By applying least squares method and predictor-correctors scheme, the numerical solutions of the proposed system in the absence of the inter-city network and with the inter-city network are stimulated by using the real-data from 23 January to 18 - m March, 2020 where m is equal to the number of prediction days. Compared with integer-order system ( = 0), the fractional-order model without network is validated to have a better fitting of the data on Beijing, Shanghai, Wuhan, Huanggang and other cities. In contrast to the case without network, the results indicate that the inter-city network system may be not a significant case to virus spreading for China because of the lock down and quarantine measures, however, it may have an impact on cities that have not adopted city closure. Meanwhile, the proposed model better fits the data from 24 February to 31, March in Italy, and the peak number of confirmed people is also predicted by this fraction-order model. Furthermore, the existence and uniqueness of a bounded solution under the initial condition are considered in the proposed system. Afterwards, the basic reproduction number R0 is analyzed and it is found to hold a threshold: the disease-free equilibrium point is locally asymptotically stable when R0 [≤] 1, which provides a theoretical basis for whether COVID-19 will become a pandemic in the future.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Zhenzhen Lu", + "author_inst": "Beijing Jiao Tong University" + }, + { + "author_name": "Yongguang Yu", + "author_inst": "Beijing Jiao Tong University" + }, + { + "author_name": "YangQuan Chen", + "author_inst": "University of California Merced" + }, + { + "author_name": "Guojian Ren", + "author_inst": "Beijing Jiao Tong University" + }, + { + "author_name": "Conghui Xu", + "author_inst": "Beijing Jiao Tong University" + }, + { + "author_name": "Shuhui Lu", + "author_inst": "Beijing Jiao Tong University" + }, + { + "author_name": "Zhe Yin", + "author_inst": "Beijing Jiao Tong University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.25.20079178", "rel_title": "A COVID-19 epidemic model integrating direct and fomite transmission as well as household structure", @@ -1496240,89 +1498595,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.04.29.068767", - "rel_title": "Glycosaminoglycans induce conformational change in the SARS-CoV-2 Spike S1 Receptor Binding Domain.", - "rel_date": "2020-04-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.29.068767", - "rel_abs": "The glycosaminoglycan (GAG) class of polysaccharides are utilised by a plethora of microbial pathogens as receptors for adherence and invasion. The GAG heparin prevents infection by a range of viruses when added exogenously, including the S-associated coronavirus strain HSR1 and more recently we have demonstrated that heparin can block cellular invasion by SARS-CoV-2. Heparin has found widespread clinical use as anticoagulant drug and this molecule is routinely used as a proxy for the GAG, heparan sulphate (HS), a structural analogue located on the cell surface, which is a known receptor for viral invasion. Previous work has demonstrated that unfractionated heparin and low molecular weight heparins binds to the Spike (S1) protein receptor binding domain, inducing distinct conformational change and we have further explored the structural features of heparin with regard to these interactions. In this article, previous research is expanded to now include a broader range of GAG family members, including heparan sulphate. This research demonstrates that GAGs, other than those of heparin (or its derivatives), can also interact with the SARS-CoV-2 Spike S1 receptor binding domain and induce distinct conformational changes within this region. These findings pave the way for future research into next-generation, tailor-made, GAG-based antiviral agents, against SARS-CoV-2 and other members of the Coronaviridae.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Courtney Mycroft-West", - "author_inst": "Keele University" - }, - { - "author_name": "Dunhao Su", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Yong Li", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Scott Guimond", - "author_inst": "Keele University" - }, - { - "author_name": "Timothy Rudd", - "author_inst": "National Institute for Biological Standards and Control" - }, - { - "author_name": "Stefano Elli", - "author_inst": "Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni" - }, - { - "author_name": "Gavin Miller", - "author_inst": "Keele University" - }, - { - "author_name": "Quentin Nunes", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Patricia Procter", - "author_inst": "Keele University" - }, - { - "author_name": "Antonella Bisio", - "author_inst": "Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni" - }, - { - "author_name": "Nicholas Forsyth", - "author_inst": "Keele University" - }, - { - "author_name": "Jeremy Turnbull", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Marco Guerrini", - "author_inst": "Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni" - }, - { - "author_name": "David Fernig", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Edwin Yates", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Marcelo Lima", - "author_inst": "Keele University" - }, - { - "author_name": "Mark Skidmore", - "author_inst": "Keele University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.04.29.068890", "rel_title": "Activity profiling of SARS-CoV-2-PLpro protease provides structural framework for anti-COVID-19 drug design", @@ -1496826,6 +1499098,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.25.20079186", + "rel_title": "Global health security capacity against COVID-19 outbreak and its association with the case fatality rate: an analysis of annual data from 210 countries and territories", + "rel_date": "2020-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.25.20079186", + "rel_abs": "BackgroundBecause infectious diseases, such as COVID-19, do not have specific boundaries, all countries must prioritize and use the necessary capabilities to prevent, detect, and respond quickly to public health emergencies. In this context, we aimed to review most recent GHS index annual report to observe the regional and global level of health security against COVID-19 outbreak, as well as their relationship with case fatality rate, among 210 countries and territories worldwide.\n\nMethodsWe reviewed and analyzed October 2019 GHS index co-leaders joint report, to review health security capacities on the basis of the GHS index in the context of six categories. we prioritized not only the capacities of 210 countries and territories around the world using the GHS Index, but also the existence of functional, tested, proven capabilities for stopping outbreaks at the source. Data were collected from global databases including Worldometer, WHO, and Disease Control and Prevention Center (CDC).\n\nFindingsThis study recruited data on 210 countries and territories, of which up to 14 April 2020, 72 countries (34.28%) with more than 1000 total COVID-19 cases were presents. In \"most prepared group\", number of total COVID-19 diagnostic tests had a significant positive relation with GHS index (r=0.713; p=0.006). Case fatality rate was directly associated with the detection index (r=0.304; p=0.023) in \"more prepared group\". In \"Lower-middle-income economies\" group, case fatality rate positively related to detection, response and risk environment indices.\n\nImplementationWith the exception of a very small number, countries that were ranked as most prepared countries, they were more likely to be affected by the COVID-19 outbreak of the virus and its health consequences, and needed to seriously reconsider their capabilities and health security in the context of detection, prevention, rapid response, health system facilities, and risk environment against disease outbreak\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSGiven the very rapid spread of the COVID-19 disease in a very short time, limited and few studies have shown weakness and strength in national and international capacity to deal with health emergencies. We systematically searched the Scopus, ISI web of science and PubMed from Jan 2019 to April 2020, using the search terms \"health security\" OR \"emergency preparedness\" AND \"COVID-19\" OR \"SARS-CoV-2/nCoV-2019\". Our search returned only limited number of published evidences (n=37), of which only one was assessed the operational readiness among 182 countries based on the International Health Regulations (IHR) annual report 1.\n\nAdded value of this studyGiven a very limited and insufficient on the regional, as well as global preparedness capacities to combat health emergencies, such as COVID-19 disease, we used most recent GHS index annual report (October 2019), to observe the regional and global level of health security in the context of detection, prevention, rapid response, health system facilities, and risk environment against COVID-19 outbreak among 210 countries and territories around the world. We found information about only 195 countries in the recent used report and imputed the data for the rest 15 countries and territories that facing COVID-19 outbreak.\n\nImplications of all the available evidenceOur results showed that, with the exception of a very small number of countries that were ranked as most prepared countries, they were more likely to be affected by the COVID-19 outbreak of the virus and its health consequences, and needed to seriously reconsider their capabilities and health security in the context of detection, prevention, rapid response, health system facilities, and risk environment against disease outbreak.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Elham Maraghi", + "author_inst": "Department of Biostatistics and Epidemiology, School of Public Health, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran." + }, + { + "author_name": "Amal Saki Malehi", + "author_inst": "Department of Biostatistics and Epidemiology, School of Public Health, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran." + }, + { + "author_name": "Fakher rahim", + "author_inst": "Ahvaz Jundishapur University of Medical Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "emergency medicine" + }, { "rel_doi": "10.1101/2020.04.25.20079251", "rel_title": "Key predictors of attending hospital with COVID19: An association study from the COVID Symptom Tracker App in 2,618,948 individuals", @@ -1497982,25 +1500281,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.23.20077685", - "rel_title": "The Epidemic Severity Index: Estimating Relative Local Severity of Novel Disease Outbreaks", - "rel_date": "2020-04-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.23.20077685", - "rel_abs": "Determining the severity of a novel pathogen in the early stages is difficult in the absence of reliable data. The pattern of outbreaks for COVID-19 across the globe have differed markedly above and below 30{degrees}N latitudes, suggesting very different levels of severity, but countries worldwide have implemented the same lockdown strategies. Existing methods for estimating severity appear not to have been useful in informing strategic decisions, possibly due to mismatches between the data required and those available, overly sophisticated methods with undesirable biases, or perhaps confusion and uncertainly generated by the wide range of estimates these methods produced early on.\n\nThe Epidemic Severity Index (ESI) is a simple, robust method for estimating the local severity of novel epidemic outbreaks using early and widely-available data and that does not depend on any estimated values. ESI allows rapid, meaningful comparisons across territories that can be tracked as the outbreaks unfold. The ESI quantifies severity relative to a parameterised baseline rather than attempting to estimate values for infection fatality rates, case fatality rates or transmission rates. The relative nature of the ESI sidesteps any problems of confidence associated with absolute rate estimation methods and offers immediate practical strategic value.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Gareth Davies", - "author_inst": "Independent Researcher" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.23.20077255", "rel_title": "Detection and isolation of asymptomatic individuals can make the difference in COVID-19 epidemic management", @@ -1498400,6 +1500680,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.04.23.20077719", + "rel_title": "A demographic scaling model for estimating the total number of COVID-19 infections", + "rel_date": "2020-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.23.20077719", + "rel_abs": "Understanding how widely COVID-19 has spread is critical for examining the pandemics progression. Despite efforts to carefully monitor the pandemic, the number of confirmed cases may underestimate the total number of infections. We introduce a demographic scaling model to estimate COVID-19 infections using an broadly applicable approach that is based on minimal data requirements: COVID-19 related deaths, infection fatality rates (IFRs), and life tables. As many countries lack reliable estimates of age-specific IFRs, we scale IFRs between countries using remaining life expectancy as a marker to account for differences in age structures, health conditions, and medical services. Across 10 countries with most COVID-19 deaths as of May 13, 2020, the number of infections is estimated to be four [95% prediction interval: 2-11] times higher than the number of confirmed cases. Cross-country variation is high. The estimated number of infections is 1.4 million (six times the number of confirmed cases) for Italy; 3.1 million (2.2 times the number of confirmed cases) for the U.S.; and 1.8 times the number of confirmed cases for Germany, where testing has been comparatively extensive. Our prevalence estimates, however, are markedly lower than most others based on local seroprevalence studies. We introduce formulas for quantifying the bias that is required in our data on deaths in order to reproduce estimates published elsewhere. This bias analysis shows that either COVID-19 deaths are severely underestimated, by a factor of two or more; or alternatively, the seroprevalence based results are overestimates and not representative for the total population.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Christina Bohk-Ewald", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Christian Dudel", + "author_inst": "Max Planck Institute for Demographic Research" + }, + { + "author_name": "Mikko Myrskyla", + "author_inst": "Max Planck Institute for Demographic Research" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.04.24.20077776", "rel_title": "Development and potential usefulness of the COVID-19 Ag Respi-Strip diagnostic assay in a pandemic context.", @@ -1499616,73 +1501923,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.24.20070169", - "rel_title": "Association of Personal Protective Equipment Use with Successful Protection Against COVID-19 Infection Among Health Care Workers", - "rel_date": "2020-04-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.24.20070169", - "rel_abs": "The coronavirus disease 2019 (COVID-19) pandemic has posed a major challenge for protecting health care workers (HCWs) against the infection. Use of personal protective equipment (PPE) in health care workplace is recommended as a high priority. In order to investigate the relationship between PPE use and the number of COVID-19 cases among HCWs, we conducted a molecular epidemiological study among 142 HCWs who were dispatched from Hefei to work in Wuhan and 284 HCWs who remained in Hefei, China; both provided care for patients with COVID-19. Nucleic acid testing and SARS-CoV-2 specific antibody (IgM, IgG, IgA) detection were performed to confirm SARS-CoV-2 infection among those HCWs. We also extracted publicly released data on daily number of COVID-19 cases among HCWs, daily number of HCWs who were dispatched to Hubei province since January 24, and daily production of PPE in China and daily demand and supply of PPE in Hubei province. Our laboratory testing confirmed that none of the 142 HCWs who were dispatched to work in Wuhan and 284 HCWs who remained in Hefei were infected by SARS-CoV-2. Consistent with these findings, as of April 15, 2020, none of the 42,600 HCWs who were successively dispatched to Hubei province since January 24, 2020 was reported to have COVID-19. These HCWs were provided with adequate supply of PPE as committed by their original institutions or provinces. In contrast, during the early phase of COVID-19 epidemic in Hubei province, a substantial shortage of PPE and an increasing number of COVID-19 infection among HCWs were reported. With the continuing increase in domestic production of PPE in China, the PPE supply started to meet and then exceed the demand. This coincided with a subsequent reduction in the number of reported COVID-19 cases among HCWs. In conclusion, our findings indicate that COVID-19 infection among HCWs could be completely prevented. Appropriate and adequate PPE might play a crucial role in protecting HCWs against COVID-19 infection.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Wei Wang", - "author_inst": "The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China; Clinical Research Hospital (Hefei)" - }, - { - "author_name": "Yuan-Zeng Min", - "author_inst": "Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230026, China" - }, - { - "author_name": "Chun-Mei Yang", - "author_inst": "The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China" - }, - { - "author_name": "Hai-Ou Hong", - "author_inst": "Anhui Provincial Hospital Health Center, the First Affiliated Hospital of USTC; Division of Life Sciences and Medicine, University of Science and Technology of " - }, - { - "author_name": "Tian Xue", - "author_inst": "Joint Laboratory of Public Health, USTC and Anhui NHC; Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 2300" - }, - { - "author_name": "Yong Gao", - "author_inst": "Joint Laboratory of Public Health, USTC and Anhui NHC, Department of Infectious Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and M" - }, - { - "author_name": "Tengchuan Jin", - "author_inst": "The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China" - }, - { - "author_name": "Zhao-Hui Lu", - "author_inst": "The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China" - }, - { - "author_name": "Liang-Ming Zhang", - "author_inst": "Department of Infectious Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China," - }, - { - "author_name": "Xueying Zheng", - "author_inst": "The First Affiliated Hospital of USTC, Clinical Research Hospital (Hefei) of Chinese Academy of Science, Joint Laboratory of Public Health, USTC and Anhui NHC," - }, - { - "author_name": "Sihui Luo", - "author_inst": "The First Affiliated Hospital of USTC, Clinical Research Hospital (Hefei) of Chinese Academy of Science, Joint Laboratory of Public Health, USTC and Anhui NHC," - }, - { - "author_name": "Wei Bao", - "author_inst": "Department of Epidemiology, College of Public Health, University of Iowa, City" - }, - { - "author_name": "Jian-Ping Weng", - "author_inst": "The First Affiliated Hospital of USTC, Clinical Research Hospital (Hefei) of Chinese Academy of Science, Joint Laboratory of Public Health, USTC and Anhui NHC," - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.23.20074708", "rel_title": "Infection Density and Epidemic Size of COVID-19 in China outside the Hubei province", @@ -1500182,6 +1502422,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.23.20076661", + "rel_title": "The effect of angiotensin converting enzyme inhibitors and angiotensin receptor blockers on death and severity of disease in patients with coronavirus disease 2019 (COVID-19): A meta-analysis", + "rel_date": "2020-04-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.23.20076661", + "rel_abs": "Aims and MethodsEffect of angiotensin converting enzyme inhibitors (ACEi) and angiotensin receptor blockers (ARB) on outcomes in patients with coronavirus disease 2019 (COVID-19) is uncertain. Available evidence is limited to a few retrospective observational studies with small number of patients. We did a meta-analysis to assess the effect of ACEi/ARB in patients with COVID-19 on severity of disease, risk for hospitalisation, and death compared to those not on ACEi/ARB. We searched the Cochrane library, PubMed, Embase, ClinicalTrial.gov and medRxiv for studies published until 25.04.2020. Inclusion criteria included all studies with patients with confirmed COVID-19 either taking, or not taking, ACEi/ARB. Depending on degree of heterogeneity, fixed or random effect model was selected to calculate effect size (Odds ratio).\n\nResultsSix studies were eligible for this meta-analysis. These included 423 patients on ACEi/ARB, and 1419 not on ACEi/ARB. Compared to patients with COVID-19 not on ACEi/ARB, there was a statistically significant 43% reduction (OR 0.57, CI: 0.37-0.88, I2: 0.000) in the odds of death in those on ACEi/ARB. There was a statistically non-significant 38% reduction (OR: 0.62, 95% CI: 0.31-1.23, I2=70.36) in the odds of developing severe disease and 19% reduction (OR 0.81; 95% CI: 0.42-1.55, I2: 0.000) in the odds of hospitalisation among those on ACEi/ARB.\n\nDiscussionIt is safe to use ACEi/ARB in patients with COVID-19 requiring these medications for associated comorbidities. Although limited by confounding factors typical of a meta-analysis of retrospective observational studies, our data suggests that use of these medications may reduce the odds of death.\n\nConclusionOur meta-analysis of the updated studies on SARS-CoV-2 reassures the medical fraternity on the use of and continuation of ACEi/ARB, supporting all recent recommendations.\n\nEvidence before this studyO_LIThe postulated dual role of angiotensin-converting enzyme (ACE) inhibitors (ACEi) and angiotensin receptor blockers (ARB) in patients with coronavirus disease 2019 (COVID-19) has created a dilemma for clinicians.\nC_LIO_LIOn the one hand, there is speculation that by upregulating ACE2, ACEi/ARBs might increase the risk and severity of COVID-19.\nC_LIO_LIOn the other hand, there is evidence that downregulation of ACE2 can mediate acute lung injury. Further evidence is urgently needed to guide clinicians in the use of ACEi/ARB in patients with COVID-19 with co-morbidities.\nC_LI\n\nWhat does this article addO_LIOur meta-analysis, which is the first to assess the effect of use of ACEi/ARB in patients with COVID-19, reports that use of ACEi/ARB statistically significantly reduced the risk of death, with a trend towards reduction in risk of severe disease and hospitalisation compared to those who were not on ACEi/ARB.\nC_LIO_LIFurther information from on-going RCTs shall take time to fruition; in the interim, based on these findings, clinicians can safely continue to use ACEi/ARB in patients with COVID-19 with comorbidities.\nC_LI\n\nReview CriteriaO_LIA web-based search was conducted using the Cochrane library, PubMed, Embase, ClinicalTrial.gov and medRxiv using specific keywords.\nC_LIO_LINarrowing down of the citations was done based on full text availability and a set of pre-determined inclusion criteria.\nC_LIO_LIMeta-analysis was conducted on the pooled data comparing ACEi/ARB group versus the non-ACEi/ARB group on death, severity of disease and hospitalization using the CMA software version 3, Biostat Inc., Englewood, NJ, USA.\nC_LIO_LIEffect size was reported as odds ratio with a 95% confidence interval and the degree of heterogeneity of the pooled data.\nC_LI\n\nMessage for the clinicO_LIThere is no indication from present evidence to withhold or withdraw ACEi/ARB in patients with SARS-CoV-2.\nC_LI", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "SAMIT GHOSAL", + "author_inst": "Nightingale Hospital" + }, + { + "author_name": "Jagat Jyoti Mukherjee", + "author_inst": "Apollo Gleneagles Hospital, Kolkata, India" + }, + { + "author_name": "Binayak Sinha", + "author_inst": "AMRI Hospitals, Kolkata, India" + }, + { + "author_name": "Kalyan Kumar Gangopadhyay", + "author_inst": "Fortis & Peerless Hospital, Kolkata, India" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.23.20076471", "rel_title": "Pharmacokinetic bases of the hydroxychloroquine response in COVID-19: implications for therapy and prevention", @@ -1501006,89 +1503277,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.23.20076521", - "rel_title": "Geo-social gradients in predicted COVID-19 prevalence and severity in Great Britain: results from 2,266,235 users of the COVID-19 Symptoms Tracker app", - "rel_date": "2020-04-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.23.20076521", - "rel_abs": "Understanding the geographical distribution of COVID-19 through the general population is key to the provision of adequate healthcare services. Using self-reported data from 2,266,235 unique GB users of the COVID Symptom Tracker app, we find that COVID-19 prevalence and severity became rapidly distributed across the UK within a month of the WHO declaration of the pandemic, with significant evidence of \"urban hot-spots\". We found a geo-social gradient associated with disease severity and prevalence suggesting resources should focus on urban areas and areas of higher deprivation. Our results demonstrate use of self-reported data to inform public health policy and resource allocation.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Ruth Bowyer", - "author_inst": "King's College London" - }, - { - "author_name": "Thomas Varsavsky", - "author_inst": "King's College London" - }, - { - "author_name": "Carole H Sudre", - "author_inst": "King's College London" - }, - { - "author_name": "Benjamin Murray", - "author_inst": "King's College London" - }, - { - "author_name": "Maxim Freidin", - "author_inst": "King's College London" - }, - { - "author_name": "Darioush Yarand", - "author_inst": "King's College London" - }, - { - "author_name": "Sajaysurya Ganesh", - "author_inst": "Zoe Global Limited" - }, - { - "author_name": "Joan Capdevila", - "author_inst": "Zoe Global Limited" - }, - { - "author_name": "Ellen J Thompson", - "author_inst": "King's College London" - }, - { - "author_name": "Elco Bakker", - "author_inst": "Zoe Global Limited" - }, - { - "author_name": "M Jorge Cardoso", - "author_inst": "King's College London" - }, - { - "author_name": "Richard Davies", - "author_inst": "King's College London" - }, - { - "author_name": "Jonathan Wolf", - "author_inst": "Zoe Global Limited" - }, - { - "author_name": "Tim D Spector", - "author_inst": "King's College London" - }, - { - "author_name": "Sebastien Ourselin", - "author_inst": "King's College London" - }, - { - "author_name": "Claire J Steves", - "author_inst": "King's College London" - }, - { - "author_name": "Cristina Menni", - "author_inst": "King's College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.22.20073551", "rel_title": "Relative disease burdens of COVID-19 and seasonal influenza in New York City, February 1 - April 18, 2020.", @@ -1501784,6 +1503972,25 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2020.04.26.063032", + "rel_title": "Coronavirus, as a source of pandemic pathogens.", + "rel_date": "2020-04-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.26.063032", + "rel_abs": "The coronavirus and the influenza virus have similarities and differences. In order to comprehensively compare them, their genome sequencing data were examined by principal component analysis. Variations in coronavirus were smaller than those in a subclass of the influenza virus. In addition, differences among coronaviruses in a variety of hosts were small. These characteristics may have facilitated the infection of different hosts. Although many of the coronaviruses were more conservative, those repeatedly found among humans showed annual changes. If SARS-CoV-2 changes its genome like the Influenza H type, it will repeatedly spread every few years. In addition, the coronavirus family has many other candidates for subsequent pandemics.\n\nOne Sentence SummaryThe genome data of coronavirus were compared to influenza virus, to investigate its spreading mechanism and future status. Coronavirus would repeatedly spread every few years. In addition, the coronavirus family has many other candidates for subsequent pandemics.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Tomokazu Konishi", + "author_inst": "Akita Prefectural University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.04.26.063024", "rel_title": "Specific mutations in SARS-CoV2 RNA dependent RNA polymerase and helicase alter protein structure, dynamics and thus function: Effect on viral RNA replication", @@ -1502508,25 +1504715,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.23.20076489", - "rel_title": "Modeling geographical spread of COVID-19 in India using network-based approach", - "rel_date": "2020-04-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.23.20076489", - "rel_abs": "COVID-19 pandemic is a global concern, due to its high spreading and alarming fatality rate. Mathematical models can play a decisive role in mitigating the spread and predicting the growth of the epidemic. India is a large country, with a highly variable inter-state mobility, and dynamically varying infection cases in different locations; thus, the existing models, based solely on the aspects of growth rates, or generalized network concepts, may not provide desired predictions. The internal mobility of a country must be considered, for accurate prediction. Herein, we propose a framework for predicting the geographical spread of COVID-19, using reported COVID-19 cases, census migration data, and monthly airline data of passengers. We discover that spreading depends on the spatial distribution of existing cases, human mobility patterns, and administrative decisions. In India, the mobility towards professional sites can surge incoming cases at Maharastra and Karnataka, while migration towards the native places can risk Uttar Pradesh and Bihar. We anticipate that the state Kerala, with one of the highest cases of COVID-19, may not receive significant incoming cases, while Karnataka and Haryana may receive the challenge of high incoming cases, with medium cases so far. Using airline passengers data, we also estimate the number of potential incoming cases at various airports. The study predicts that the airports located in the region of north India are vulnerable, whereas in northeast India and in some south India are relatively safe. The detailed analysis in this direction will guide policymakers for prior planning of transport, and minimize the spread of COVID-19.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Ankush Kumar", - "author_inst": "IEMN" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.22.20075986", "rel_title": "Association between environmental pollution and prevalence of coronavirus disease 2019 (COVID-19) in Italy", @@ -1502910,6 +1505098,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, + { + "rel_doi": "10.1101/2020.04.21.20074245", + "rel_title": "Analysis of Effectiveness of Quarantine Measures in Controlling COVID-19", + "rel_date": "2020-04-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.21.20074245", + "rel_abs": "COVID-19 has created an interesting discourse among the people of the world particularly regarding preventive measures of infectious diseases. In this paper, the authors forecast the spread of the Coronavirus outbreak and study how the reduction of transmission rates influences its decline. The paper makes use of the SIR (Susceptible Infected Recovered) Model which is a deterministic model used in the field of epidemiology-based on differential equations derived from sections of the population. The Basic Reproduction Number (Ro) represents the criticality of the epidemic in numeric terms. Forecasting an epidemic provides insights about the geographic spreading of the disease and the case incidences required to better inform intervention strategists about situations that may occur during the outbreak. Through this research paper, the authors wish to provide an insight into the impact of control measures on the pandemic. By drawing a comparison of three countries and their quarantine measures, observations on the decline of the outbreak are made. Authors intend to guide the intervention strategies of under-resourced countries like India and aid in the overall containment of the outbreak.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Garima Kaushik", + "author_inst": "Bharatiya Vidya Bhavan's Sardar Patel Institute of Technology" + }, + { + "author_name": "Shrishti Kaushik", + "author_inst": "Bharatiya Vidya Bhavan's Sardar Patel Institute of Technology" + }, + { + "author_name": "Shaney Mantri", + "author_inst": "Bharatiya Vidya Bhavan's Sardar Patel Institute of Technology" + }, + { + "author_name": "Dhananjay Kalbande", + "author_inst": "Bharatiya Vidya Bhavan's Sardar Patel Institute of Technology" + }, + { + "author_name": "B. N. Chaudhari", + "author_inst": "Bharatiya Vidya Bhavan's Sardar Patel Institute of Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.04.21.20072637", "rel_title": "Research on CNN-based Models Optimized by Genetic Algorithm and Application in the Diagnosis of Pneumonia and COVID-19", @@ -1503442,37 +1505665,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.04.24.059204", - "rel_title": "eCovSens-Ultrasensitive Novel In-House Built Printed Circuit Board Based Electrochemical Device for Rapid Detection of nCovid-19", - "rel_date": "2020-04-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.24.059204", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 or nCovid-19) outbreak has become a huge public health issue due to its rapid transmission and global pandemic. Currently, there are no vaccines or drugs available for nCovid-19, hence early detection is crucial to help and manage the outbreak. Here, we report an in-house built biosensor device (eCovSens) and compare it with a commercial potentiostat for the detection of nCovid-19 spike antigen (nCovid-19Ag) in spiked saliva samples. A potentiostat based sensor was fabricated using fluorine doped tin oxide electrode (FTO) with gold nanoparticle (AuNPs) and immobilized with nCovid-19 monoclonal antibody (nCovid-19Ab) to measure change in the electrical conductivity. Similarly, eCovSens was used to measure change in electrical conductivity by immobilizing nCovid-19 Ab on screen printed carbon electrode (SPCE). The performances of both sensors were recorded upon interaction of nCovid-19Ab with its specific nCovid-19Ag. Under optimum conditions, the FTO based immunosensor and eCovSens displayed high sensitivity for detection of nCovid-19Ag, ranging from 1 fM to 1 M. Our in-house developed device can successfully detect nCovid-19Ag at 10 fM concentration in standard buffer that is in close agreement with FTO/AuNPs sensor. The limit of detection (LOD) was found to be 90 fM with eCovSens and 120 fM with potentiostst in case of spiked saliva samples. The proposed portable eCovSens device can be used as a diagnostic tool for the rapid (within 10-30 s) detection of nCovid-19Ag traces directly in patient saliva in a non-invasive manner.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Subhasis Mahari", - "author_inst": "National Institute of Animal Biotechnology" - }, - { - "author_name": "Akanksha Roberts", - "author_inst": "National Institute of Animal Biotechnology" - }, - { - "author_name": "Deepshikha Shahdeo", - "author_inst": "National Institute of Animal Biotechnology" - }, - { - "author_name": "Sonu Gandhi", - "author_inst": "National Institute of Animal Biotechnology" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2020.04.23.057786", "rel_title": "The coronavirus proofreading exoribonuclease mediates extensive viral recombination", @@ -1504188,6 +1506380,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.04.22.20075234", + "rel_title": "Measuring Italian Citizens' Engagement in the First Wave of the COVID-19 Pandemic Containment Measures A Cross-sectional Study", + "rel_date": "2020-04-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.22.20075234", + "rel_abs": "BackgroundIn January 2020, the coronavirus disease 2019 (COVID-19) started to spread in Italy. The Italian government adopted urgent measures to hold its spread. Enforcing compliance to such measures is crucial in order to enhance their effectiveness. Engaging citizens in the COVID-19 preventive process is today urgent in Italy and around the world. However, to the best of our knowledge, no previous studies have investigated the role of health engagement in predicting citizens compliance to health emergency containment measures.\n\nMethodAn online survey was administered between February 28th and March 4th 2020 on a representative sample of 1000 Italians. The questionnaire included a measure of Health Engagement (PHE-S) and a series of ad hoc items intended to measure both affective and behavioral responses of the citizens to the emergency in terms of perceived susceptibility to and severity of the disease, orientation towards health management, change in habits and in purchases. To investigate the relationship between Health Engagement and these variables, a series of ANOVAs, Logistic regressions and crosstabs have been carried out.\n\nResultsLess engaged people show higher levels of perceived susceptibility to the virus and of severity of the disease; they trust less scientific and healthcare authorities, they feel less self-effective in managing their own health - both in normal conditions and under stress - and are less prone to cooperate with healthcare professionals. Low levels of Health Engagement are also associated with a change in the usual purchase behavior.\n\nConclusionsThe Patient Health Engagement Model (PHE) provides a useful framework for understanding how people will respond to health threats such as pandemics. Therefore, intervention studies should focus on particular groups and on raising their levels of engagement to increase the effectiveness of educational initiatives devoted to promote preventive behaviors.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Guendalina Graffigna", + "author_inst": "Universita Cattolica del Sacro Cuore" + }, + { + "author_name": "Serena Barello", + "author_inst": "Universita Cattolica del Sacro Cuore" + }, + { + "author_name": "Mariarosaria Savarese", + "author_inst": "Universita Cattolica del Sacro Cuore" + }, + { + "author_name": "Lorenzo Palamenghi", + "author_inst": "Universita Cattolica del Sacro Cuore" + }, + { + "author_name": "Greta Castellini", + "author_inst": "Universita Cattolica del Sacro Cuore" + }, + { + "author_name": "Andrea Bonanomi", + "author_inst": "Universita Cattolica del Sacro Cuore" + }, + { + "author_name": "Edoardo Lozza", + "author_inst": "Universita Cattolica del Sacro Cuore" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.04.23.20076455", "rel_title": "Role of the atmospheric pollution in the Covid-19 outbreak risk in Italy", @@ -1505080,33 +1507315,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.22.20075598", - "rel_title": "Pooling of Nasopharyngeal Swab Specimens for SARS-CoV-2 detection by RT-PCR", - "rel_date": "2020-04-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.22.20075598", - "rel_abs": "Systematic testing of large population groups by RT-PCR is mandatory to Covid-19 case identification and contact tracing in order to minimize the likelyhood of resurgence in contagion. Sample pooling for RT-PCR has been effectively used to detect community transmission of SARS CoV-2. Nevertheless, this procedure may decrease the sensitivity of RT-PCR assays due to specimen dilution. We evaluated the efficacy of this strategy for diagnosis of Covid-19 using a sensitive commercially-available RT-PCR targeting SARS CoV-2 E and RdRp genes in a single reaction. A total of 20 mini-pools containing either 5 (n=10) or 10 (n=10) nasopharyngeal exudates collected in universal transport medium were made, each of which including a unique positive NP specimen. Positive specimens yielding CT <32 for the E gene (6 out of 10) or <35.2 for the RdRP gene (7 out of 10) were detected in mini-pools of both sizes. In contrast, most NP samples displaying CTs > 35.8 for the E gene or 35.7 for the RdRP gene remained undetected in mini-pools of 5 specimens (3/4 and 2/3, respectively) or in mini-pools of 10 samples (4/4 and 3/3, respectively.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Ignacio Torres", - "author_inst": "Microbiology Service, Clinical University Hospital of Valencia, Institute for Research INCLIVA, Valencia, Spain." - }, - { - "author_name": "Eliseo Albert", - "author_inst": "Microbiology Service, Clinical University Hospital of Valencia, Institute for Research INCLIVA, Valencia, Spain." - }, - { - "author_name": "David Navarro", - "author_inst": "Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.22.20075671", "rel_title": "Experience with Hydroxychloroquine and Azithromycin in the COVID-19 Pandemic: Implications for QT Interval Monitoring", @@ -1505618,6 +1507826,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.04.22.054973", + "rel_title": "Deep Sentiment Classification and Topic Discovery on Novel Coronavirus or COVID-19 Online Discussions: NLP Using LSTM Recurrent Neural Network Approach", + "rel_date": "2020-04-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.22.054973", + "rel_abs": "Internet forums and public social media, such as online healthcare forums, provide a convenient channel for users (people/patients) concerned about health issues to discuss and share information with each other. In late December 2019, an outbreak of a novel coronavirus (infection from which results in the disease named COVID-19) was reported, and, due to the rapid spread of the virus in other parts of the world, the World Health Organization declared a state of emergency. In this paper, we used automated extraction of COVID-19-related discussions from social media and a natural language process (NLP) method based on topic modeling to uncover various issues related to COVID-19 from public opinions. Moreover, we also investigate how to use LSTM recurrent neural network for sentiment classification of COVID-19 comments. Our findings shed light on the importance of using public opinions and suitable computational techniques to understand issues surrounding COVID-19 and to guide related decision-making.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Hamed Jelodar", + "author_inst": "Nanjing University of Science and Technology" + }, + { + "author_name": "Yongli Wang", + "author_inst": "Nanjing University of Science and Technology" + }, + { + "author_name": "Rita Orji", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Hucheng Huang", + "author_inst": "Jiangsu University of Science and Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.04.20.20064105", "rel_title": "Clinical and Imaging Findings in COVID-19 Patients Complicated by Pulmonary Embolism", @@ -1506642,93 +1508881,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.04.24.057323", - "rel_title": "Validation of a SARS-CoV-2 spike ELISA for use in contact investigations and serosurveillance", - "rel_date": "2020-04-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.24.057323", - "rel_abs": "Since emergence of SARS-CoV-2 in late 2019, there has been a critical need to understand prevalence, transmission patterns, to calculate the burden of disease and case fatality rates. Molecular diagnostics, the gold standard for identifying viremic cases, are not ideal for determining true case counts and rates of asymptomatic infection. Serological detection of SARS-CoV-2 specific antibodies can contribute to filling these knowledge gaps. In this study, we describe optimization and validation of a SARS-CoV-2-specific-enzyme linked immunosorbent assay (ELISA) using the prefusion-stabilized form of the spike protein [1]. We performed receiver operator characteristic (ROC) analyses to define the specificities and sensitivities of the optimized assay and examined cross reactivity with immune sera from persons confirmed to have had infections with other coronaviruses. These assays will be used to perform contact investigations and to conduct large-scale, cross sectional surveillance to define disease burden in the population.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Brandi Freeman", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Sandra Lester", - "author_inst": "Synergy America Inc." - }, - { - "author_name": "Lisa Mills", - "author_inst": "Eagle Global Scientific" - }, - { - "author_name": "Mohammad Ata Ur Rasheed", - "author_inst": "Synergy America Inc." - }, - { - "author_name": "Stefany Moye", - "author_inst": "Eagle Global Scientific" - }, - { - "author_name": "Olubukola Abiona", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Geoffrey Hutchinson", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Maria Morales-Betoulle", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Inna Krapinunaya", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Ardith Gibbons", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Cheng-Feng Chiang", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Deborah Cannon", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "John Klena", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Jeffrey A. Johnson", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Sherry Michelle Owen", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Barney S. Graham", - "author_inst": "National Institute of Health" - }, - { - "author_name": "Kizzmekia S. Corbett", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Natalie J. Thornburg", - "author_inst": "Centers for Disease Control and Prevention" - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.04.23.057042", "rel_title": "ACE2 polymorphisms and individual susceptibility to SARS-CoV-2 infection: insights from an in silico study", @@ -1507380,6 +1509532,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2020.04.18.20070656", + "rel_title": "A cohort study of 223 patients explores the clinical risk factors for the severity diagnosis of COVID-19", + "rel_date": "2020-04-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.18.20070656", + "rel_abs": "BACKGROUNDCoronavirus Disease 2019 (COVID-19) has recently become a public emergency and a worldwide pandemic. The clinical symptoms of severe and non-severe patients vary, and the case-fatality rate (CFR) in severe COVID-19 patients is very high. However, the information on the risk factors associated with the severity of COVID-19 and of their prognostic potential is limited.\n\nMETHODSIn this retrospective study, the clinical characteristics, laboratory findings, treatment and outcome data were collected and analyzed from 223 COVID-19 patients stratified into 125 non-severe patients and 98 severe patients. In addition, a pooled large-scale meta-analysis of 1646 cases was performed.\n\nRESULTSWe found that the age, gender and comorbidities are the common risk factors associated with the severity of COVID-19. For the diagnosis markers, we found that the levels of D-dimer, C-reactive protein (CRP), lactate dehydrogenase (LDH), procalcitonin (PCT) were significantly higher in severe group compared with the non-severe group on admission (D-Dimer: 87.3% vs. 35.3%, P<0.001; CRP, 65.1% vs. 13.5%, P<0.001; LDH: 83.9% vs. 22.2%, P<0.001; PCT: 35.1% vs. 2.2%, P<0.001), while the levels of aspartate aminotransferase (ASP) and creatinine kinase (CK) were only mildly increased. We also made a large scale meta-analysis of 1646 cases combined with 4 related literatures, and further confirmed the relationship between the COVID-19 severity and these risk factors. Moreover, we tracked dynamic changes during the process of COVID-19, and found CRP, D-dimer, LDH, PCT kept in high levels in severe patient. Among all these markers, D-dimer increased remarkably in severe patients and mostly related with the case-fatality rate (CFR). We found adjuvant antithrombotic treatment in some severe patients achieved good therapeutic effect in the cohort.\n\nCONCLUSIONSThe diagnosis markers CRP, D-dimer, LDH and PCT are associated with severity of COVID-19. Among these markers, D-dimer is sensitive for both severity and CFR of COVID-19. Treatment with heparin or other anticoagulants may be beneficial for COVID-19 patients.\n\nFundingThis study was supported by funding from the National Key Research and Development Program of China (2016YFC1302203); Beijing Nova Program (grant number: xx2018040).\n\nRole of the funding sourceThe funding listed above supports this study, but had no role in the design and conduct of the study.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Yongshent Huang", + "author_inst": "School of Basic Medicine Peking Union Medical College, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences" + }, + { + "author_name": "Xiaoyu Lyu", + "author_inst": "Department of Endocrinology, the Central Hospital of Wuhan , Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Dan Li", + "author_inst": "State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Scie" + }, + { + "author_name": "Yujun Wang", + "author_inst": "Department of Critical care medicine, the Central Hospital of Wuhan , Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Lin Wang", + "author_inst": "School of Basic Medicine Peking Union Medical College, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences" + }, + { + "author_name": "Wenbin Zou", + "author_inst": "Department of Thoracic Surgery, TongJi Hospital, TongJi Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Yingxin Wei", + "author_inst": "Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College" + }, + { + "author_name": "Xiaowei Wu", + "author_inst": "Department of Thoracic Surgery, TongJi Hospital, TongJi Medical College, Huazhong University of Science and Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.19.20071357", "rel_title": "Immune defects and cardiovascular risk in X chromosome monosomy mosaicism mediated by loss of chromosome Y. A risk factor for SARS-CoV-2 vulnerability in elderly men?", @@ -1508480,33 +1510679,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.04.19.20071647", - "rel_title": "Accelerated hyaluronan concentration as the primary driver of morbidity and mortality in high-risk COVID-19 patients: with therapeutic introduction of an oral hyaluronan inhibitor in the prevention of \"Induced Hyaluronan Storm\" Syndrome", - "rel_date": "2020-04-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.19.20071647", - "rel_abs": "To date, the fundamental drivers of the morbidity and mortality in COVID-19 remain uncertain. Clinicians worldwide appear to be at a loss to know how to prevent and treat the severe respiratory distress in these patients effectively. Consequently, the fundamental mechanisms leading to death in high-risk patients need to be discovered and addressed with urgency. The post-mortem autopsy remains an essential part of both discovering the cause of death in a particular individual, but also in advancing the science and treatment of disease, especially in the case of novel pathogens such as SARS-CoV-2[2]. The goal of an autopsy is to discover the cause of death (COD) using a macro/microscopic investigation. Because lung weight is often affected by the cause of death and the last breath occurs very near if not at death, the evaluation of the lungs is one of the starting points of any COD investigation[3]. A comprehensive search was performed to systematically review all reported autopsy findings in COVID-19 patients with respect to lung weights and histologic findings. We then compared these findings with the results of a targeted literature review of hyaluronan in relationship to acute respiratory distress syndrome (ARDS). In total, data from 38 autopsies were identified. From this group, 36 autopsies of COVID-19 patients were selected for detailed review and statistical analysis. The average lung weight of those who were determined to have died as a result of SARS-CoV-2 was 1683g approximately 3.2 times the normal lung weight. Hyaline membranes were consistently identified on histologic sections. A review of the literature reveals that markedly elevated lung weights and hyaline membranes and have been associated with the pathophysiology of ARDS since 1967. However, the key role key of hyaluronan in driving the morbidity and mortality of the condition has heretofore not been fully recognized. We propose that the induced hyaluronan storm syndrome or IHS, is a model that addresses the heretofore perplexing respiratory failure that is the proximal cause of death. An aggressive research effort should be undertaken to discover why the majority of individuals who are exposed to the virus are minimally symptomatic, while a minority of high-risk individuals rapidly progress to respiratory failure and death.\n\n\"You may take notes for 20 years, from morning to night at the bedside of the sick, upon the diseases of the viscera, and all will be to you only a confusion of symptoms...a train of incoherent phenomena. Open a few bodies and this obscurity will disappear.\" - Marie-Francois-Xavier Bichat (1771-1802), \"The Father of Histology\"[1].", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Michael A Mong", - "author_inst": "VA North Texas Healthcare System Dallas" - }, - { - "author_name": "Jacob A Awkal", - "author_inst": "The University of Texas at Dallas and The University of Texas Southwestern Medical Center" - }, - { - "author_name": "Paul E Marik", - "author_inst": "Eastern Virginia Medical School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.21.20072397", "rel_title": "Association of infected probability of COVID-19 with ventilation rates in confined spaces: a Wells-Riley equation based investigation", @@ -1509098,6 +1511270,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.20.20072702", + "rel_title": "Prevalence and Impact of Myocardial Injury in Patients Hospitalized with COVID-19 Infection", + "rel_date": "2020-04-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.20.20072702", + "rel_abs": "STRUCTURED ABSTRACTO_ST_ABSBackgroundC_ST_ABSThe degree of myocardial injury, reflected by troponin elevation, and associated outcomes among hospitalized patients with Coronavirus Disease (COVID-19) in the US are unknown.\n\nObjectivesTo describe the degree of myocardial injury and associated outcomes in a large hospitalized cohort with laboratory-confirmed COVID-19.\n\nMethodsPatients with COVID-19 admitted to one of five Mount Sinai Health System hospitals in New York City between February 27th and April 12th, 2020 with troponin-I (normal value <0.03ng/mL) measured within 24 hours of admission were included (n=2,736). Demographics, medical history, admission labs, and outcomes were captured from the hospitals EHR.\n\nResultsThe median age was 66.4 years, with 59.6% men. Cardiovascular disease (CVD) including coronary artery disease, atrial fibrillation, and heart failure, was more prevalent in patients with higher troponin concentrations, as were hypertension and diabetes. A total of 506 (18.5%) patients died during hospitalization. Even small amounts of myocardial injury (e.g. troponin I 0.03-0.09ng/mL, n=455, 16.6%) were associated with death (adjusted HR: 1.77, 95% CI 1.39-2.26; P<0.001) while greater amounts (e.g. troponin I>0.09 ng/dL, n=530, 19.4%) were associated with more pronounced risk (adjusted HR 3.23, 95% CI 2.59-4.02).\n\nConclusionsMyocardial injury is prevalent among patients hospitalized with COVID-19, and is associated with higher risk of mortality. Patients with CVD are more likely to have myocardial injury than patients without CVD. Troponin elevation likely reflects non-ischemic or secondary myocardial injury.\n\nUnstructured AbstractMyocardial injury reflected as elevated troponin in Coronavirus Disease (COVID-19) is not well characterized among patients in the United States. We describe the prevalence and impact of myocardial injury among hospitalized patients with confirmed COVID-19 and troponin-I measurements within 24 hours of admission (N=2,736). Elevated troponin concentrations (normal <0.03ng/mL) were commonly observed in patients hospitalized with COVID-19, most often present at low levels, and associated with increased risk of death. Patients with cardiovascular disease (CVD) or risk factors for CVD were more likely to have myocardial injury. Troponin elevation likely reflects non-ischemic or secondary myocardial injury.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Anuradha Lala", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Kipp W Johnson", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Adam J Russak", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Ishan Paranjpe", + "author_inst": "Ican School of Medicine at Mount Sinai" + }, + { + "author_name": "Shan Zhao", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Sulaiman Solani", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Akhil Vaid", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Fayzan Chaudhry", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jessica K De Freitas", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Zahi A Fayad", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Sean P Pinney", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Matthew Levin", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Alexander Charney", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Emilia Bagiella", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jagat Narula", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Benjamin S Glicksberg", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Girish Nadkarni", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "James Januzzi", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Donna M Mancini", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Valentin Fuster", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2020.04.21.20073734", "rel_title": "COVID-19 epidemic in Sri Lanka: A mathematical and computational modelling approach to control", @@ -1509726,49 +1511993,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.22.055897", - "rel_title": "Rapid, sensitive, full genome sequencing of Severe Acute Respiratory Syndrome Virus Coronavirus 2 (SARS-CoV-2)", - "rel_date": "2020-04-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.22.055897", - "rel_abs": "SARS-CoV-2 recently emerged, resulting a global pandemic. Rapid genomic information is critical to understanding transmission and pathogenesis. Here, we describe validated protocols for generating high-quality full-length genomes from primary samples. The first employs multiplex RT-PCR followed by MinION or MiSeq sequencing. The second uses singleplex, nested RT-PCR and Sanger sequencing.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Clinton R Paden", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Ying Tao", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Krista Queen", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Jing Zhang", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Yan Li", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Anna Uehara", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Suxiang Tong", - "author_inst": "Centers for Disease Control and Prevention" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.04.23.056838", "rel_title": "STAT2 signaling as double-edged sword restricting viral dissemination but driving severe pneumonia in SARS-CoV-2 infected hamsters", @@ -1510496,6 +1512720,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.20.20073056", + "rel_title": "Measuring Icebergs: Using Different Methods to Estimate the Number of COVID-19 Cases in Portugal and Spain", + "rel_date": "2020-04-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.20.20073056", + "rel_abs": "The world is suffering from a pandemic called COVID-19, caused by the SARS-CoV-2 virus. The different national governments have problems evaluating the reach of the epidemic, having limited resources and tests at their disposal. Hence, any means to evaluate the number of persons with symptoms compatible with COVID-19 with reasonable level of accuracy is useful. In this paper we present the initial results of the @CoronaSurveys project. The objective of this project is the collection and publication of data concerning the number of people that show symptoms compatible with COVID-19 in different countries using open anonymous surveys. While this data may be biased, we conjecture that it is still useful to estimate the number of infected persons with the COVID-19 virus at a given point in time in these countries, and the evolution of this number over time. We show here the initial results of the @CoronaSurveys project in Spain and Portugal.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Carlos Baquero", + "author_inst": "U. Minho & INESC TEC, Portugal" + }, + { + "author_name": "Paolo Casari", + "author_inst": "University of Trento, Italy" + }, + { + "author_name": "Antonio Fernandez Anta", + "author_inst": "IMDEA Networks Institute" + }, + { + "author_name": "Davide Frey", + "author_inst": "Inria Rennes, France" + }, + { + "author_name": "Augusto Garcia-Agundez", + "author_inst": "TU Darmstadt, Germany" + }, + { + "author_name": "Chryssis Georgiou", + "author_inst": "U. Cyprus, Cyprus" + }, + { + "author_name": "Raquel Menezes", + "author_inst": "U. Minho, Portugal" + }, + { + "author_name": "Nicolas Nicolaou", + "author_inst": "Algolysis Ltd, Cyprus" + }, + { + "author_name": "Oluwasegun Ojo", + "author_inst": "IMDEA Networks Institute & UC3M, Spain" + }, + { + "author_name": "Paul Patras", + "author_inst": "U. Edinburgh, UK" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.20.20073130", "rel_title": "Characteristics of scientific articles on COVID-19 published during the initial three months of the pandemic: a meta-epidemiological study", @@ -1511496,49 +1513775,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2020.04.19.20071217", - "rel_title": "Exit strategies: optimising feasible surveillance for detection, elimination and ongoing prevention of COVID-19 community transmission", - "rel_date": "2020-04-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.19.20071217", - "rel_abs": "BackgroundFollowing successful implementation of strong containment measures by the community, Australia is now close to the point of eliminating detectable community transmission of COVID-19. We aimed to develop an efficient, rapid and scalable surveillance strategy for detecting all remaining COVID-19 community transmission through exhaustive identification of every active transmission chain. We also identified measures to enable early detection and effective management of any reintroduction of transmission once containment measures are lifted to ensure strong containment measures do not need to be reinstated.\n\nMethodsWe compared efficiency and sensitivity to detect community transmission chains through testing of: hospital cases; primary care fever and cough patients; or asymptomatic community members, using surveillance evaluation methods and mathematical modelling, varying testing capacities and prevalence of COVID-19 and non-COVID-19 fever and cough, and the reproduction number. System requirements for increasing testing to allow exhaustive identification of all transmission chains, and then enable complete follow-up of all cases and contacts within each chain, were assessed per million population.\n\nFindingsAssuming 20% of cases are asymptomatic and all symptomatic COVID-19 cases present to primary care, with high transmission (R=2.2) there are a median of 13 unrecognised community cases (5 infectious) when a transmission chain is identified through hospital surveillance versus 3 unrecognised cases (1 infectious) through primary care surveillance. 3 unrecognised community upstream community cases themselves are estimated to generate a further 22-33 contacts requiring follow-up. The unrecognised community cases rise to 5 if only 50% of symptomatic cases present to primary care. Screening for asymptomatic disease in the community cannot exhaustively identify all transmission under any of the scenarios assessed. The additional capacity required to screen all fever and cough primary care patients would be approximately 2,000 tests/million population per week using 1/16 pooling of samples.\n\nInterpretationScreening all syndromic fever and cough primary care presentations, in combination with exhaustive and meticulous case and contact identification and management, enables appropriate early detection and elimination of community transmission of COVID-19. If testing capacity is limited, interventions such as pooling allow increased case detection, even given reduced test sensitivity. Wider identification and testing of all upstream contacts, (i.e. potential sources of infection for identified cases, and their related transmission chains) is critical, and to be done exhaustively requires more resources than downstream contact tracing. The most important factor in determining the performance of such a surveillance system is community participation in screening and follow up, and as such, appropriate community engagement, messaging and support to encourage presentation and compliance is essential. We provide operational guidance on implementing such a system.\n\nFundingNo specific funding was received for this project, beyond the salary support the authors receive from their institutions and elsewhere. Professor Banks is supported by the National Health and Medical Research Council of Australia (Principal Research Fellowship 1136128).", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Kamalini Lokuge", - "author_inst": "The Australian National University" - }, - { - "author_name": "Emily Banks", - "author_inst": "The Australian National University" - }, - { - "author_name": "Stephanie Davis", - "author_inst": "The Australian National University" - }, - { - "author_name": "Leslee Roberts", - "author_inst": "The Australian National University" - }, - { - "author_name": "Tatum Street", - "author_inst": "The Australian National University" - }, - { - "author_name": "Grazia Caleo", - "author_inst": "The Australian National University" - }, - { - "author_name": "Kathryn Glass", - "author_inst": "The Australian National University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "primary care research" - }, { "rel_doi": "10.1101/2020.04.18.20070896", "rel_title": "First study on mental distress in Brazil during the COVID-19 crisis", @@ -1512154,6 +1514390,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.18.20070904", + "rel_title": "Ongoing outbreak of COVID-19 in Iran: challenges and signs of concern", + "rel_date": "2020-04-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.18.20070904", + "rel_abs": "Many countries with an early outbreak of SARS-CoV-2 struggled to gauge the size and start date of the epidemic mainly due to limited testing capacities and a large proportion of undetected asymptomatic and mild infections. Iran was among the first countries with a major outbreak outside China. Using all genomic sequences collected from patients with a travel link to Iran, we estimate that the epidemic started on 21/01/2020 (95% HPD: 05/12/2019 - 14/02/2020) with a doubling time of 3 days (95% HPD: 1.68 - 16.27). We also show, using air travel data from confirmed exported cases, that from late February to early March the number of active cases across the country were more than a hundred times higher than the reported cases at the time. A detailed province-level analysis of all-cause mortality shows 20,718 (CI 95%: 18,859 - 22,576) excess deaths during winter and spring 2020 compared to previous years, almost twice the number of reported COVID-19-related deaths at the time. Correcting for under-reporting of prevalence and deaths, we use an SEIR model to reconstruct the outbreak dynamics in Iran. Our model forecasted the second epidemic peak and suggests that by 14/07/2020 a total of 9M (CI 95%: 118K - 44M) have recovered from the disease across the country. These findings have profound implications for assessing the stage of the epidemic in Iran and shed light on the dynamics of SARS-CoV-2 transmissions in Iran and central Asia despite significant levels of under-reporting.\n\nOne Sentence SummaryWe use epidemiological and genetic data to investigate the origins of the SARS-CoV-2 outbreak in Iran and assess the degree of under-reporting in prevalence and deaths.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Mahan Ghafari", + "author_inst": "University of Oxford" + }, + { + "author_name": "Bardia Hejazi", + "author_inst": "Wesleyan University" + }, + { + "author_name": "Arman Karshenas", + "author_inst": "University of Oxford" + }, + { + "author_name": "Stefan Dascalu", + "author_inst": "University of Oxford" + }, + { + "author_name": "Alireza Kadivar", + "author_inst": "Statsminutes Company" + }, + { + "author_name": "Mohammad Ali Khosravi", + "author_inst": "Kawsar Human Genetic Research Center" + }, + { + "author_name": "Maryam Abbasalipour", + "author_inst": "Kawsar Human Genetic Research Center" + }, + { + "author_name": "Majid Heydari", + "author_inst": "Donya-e-Eqtesad Daily newspaper" + }, + { + "author_name": "Sirous Zeinali", + "author_inst": "Pasteur Institute of Iran" + }, + { + "author_name": "Luca Ferretti", + "author_inst": "University of Oxford" + }, + { + "author_name": "Alice Ledda", + "author_inst": "Imperial College London" + }, + { + "author_name": "Aris Katzourakis", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.18.20071035", "rel_title": "Outbreak dynamics of COVID-19 in Europe and the effect of travel restrictions", @@ -1513278,25 +1515577,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.18.20070631", - "rel_title": "ARIMA modelling of predicting COVID-19 infections", - "rel_date": "2020-04-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.18.20070631", - "rel_abs": "The World Health Organization (WHO) Director-General, Dr. Tedros Adhanom Ghebreyesus on March 11, 2020 declared the novel coronavirus (COVID-19) outbreak a global pandemic [4] the reason being the number of cases outside China increased 13-fold and the number of countries with cases increased threefold. In this paper a time series model to predict short-term prediction of the transmission of the exponentially growing COVID-19 time series is modelled and studied. Auto Regressive Integrated Moving Average (ARIMA) model prediction is performed on the number of cumulative cases over a time period and is validated over Akaike information criterion (AIC) statistics.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Regis Anne", - "author_inst": "Sri Krishna College of Engg and Tech" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.19.20071472", "rel_title": "Clinical characteristics of imported and second-generation COVID-19 cases outside Wuhan, China: A multicenter retrospective study", @@ -1514132,6 +1516412,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.16.20067454", + "rel_title": "The Enlightenment of mainland China's epidemic situation to the world through the intrinsic growth rule of infected and cured cases with COVID-19", + "rel_date": "2020-04-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.16.20067454", + "rel_abs": "The novel coronavirus disease (COVID-19) that emerged at the end of 2019 has been controlled in mainland China so far, while it is still spreading globally. When the pandemic will end is a question of great concern. A logistic model depicting the growth rules of infected and recovered cases in mainland China may shed some light on this question. We extended this model to 31 countries outside China experiencing serious COVID-2019 outbreaks. The model well explained the data in our study (R2 [≥] 0.95). For infected cases, the semi-saturation period (SSP) ranges from 63 to 170 days (March 3 to June 18). The logistic growth rate of infected cases is positively correlated with that of recovered cases, and the same holds for the SSP. According to the linear connection between the growth rules for infected and recovered cases identified from the Chinese data, we predicted that the SSP of the recovered cases outside China ranges from 82 to 196 days (March 22 to July 8). More importantly, we found a strong positive correlation between the SSP of infected cases and the timing of governments response, providing strong evidence for the effectiveness of rapid epidemic control measures in various countries.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Chuanliang Han", + "author_inst": "Beijing Normal University" + }, + { + "author_name": "Yimeng Liu", + "author_inst": "Beijing Normal University" + }, + { + "author_name": "Jiting Tang", + "author_inst": "Beijing Normal University" + }, + { + "author_name": "Yuyao Zhu", + "author_inst": "Beijing Normal University" + }, + { + "author_name": "Carlo Jaeger", + "author_inst": "Beijing Normal University" + }, + { + "author_name": "Saini Yang", + "author_inst": "Beijing Normal University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.12.20062687", "rel_title": "Controlled Avalanche: A Regulated Voluntary Exposure Approach for Addressing Covid19", @@ -1514852,33 +1517171,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.04.17.20069351", - "rel_title": "Sustaining Social Distancing Policies to Prevent a Dangerous Second Peak of COVID-19 Outbreak", - "rel_date": "2020-04-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20069351", - "rel_abs": "Governments around the world have enacted strict social distancing policies in order to slow the spread of COVID-19. The next step is figuring out when to relax these restrictions and to what degree. Our results predict potentially disastrous implications of ending these policies too soon, based on projections made from a Susceptible-Exposed-Infectious-Removed (SEIR) epidemic model. Even when infection rates appear to be slowing down or decreasing, prematurely returning to \"business as usual\" produces a severe second peak far worse than the first. Furthermore, such a second peak is made more likely when very severe restrictions are initially enacted. Only an appropriately measured and committed set of restrictions can appropriately control COVID-19 outbreak levels.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Zhilan Feng", - "author_inst": "Purdue University" - }, - { - "author_name": "Haiyun Damon-Feng", - "author_inst": "J. D., Yale Law School, New Haven, CT 06511, USA" - }, - { - "author_name": "Henry Zhao", - "author_inst": "Princeton University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.04.16.20068692", "rel_title": "Prediction of Coronavirus Disease (covid-19) Evolution in USA with the Model Based on the Eyring Rate Process Theory and Free Volume Concept", @@ -1515462,6 +1517754,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.17.20070045", + "rel_title": "Saliva Sample as a Non-Invasive Specimen for the Diagnosis of Coronavirus Disease-2019 (COVID-19): a Cross-Sectional Study", + "rel_date": "2020-04-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20070045", + "rel_abs": "ObjectivesAmid the increasing number of global pandemic coronavirus disease 2019 (COVID-19) cases, there is a need for a quick and easy method to obtain a non-invasive sample for the detection of this novel coronavirus 2019 (SARS-CoV-2). We aimed to investigate the potential use of saliva samples as a non-invasive tool for the diagnosis of COVID-19.\n\nMethodsFrom 27 March to 4 April, 2020, we prospectively collected saliva samples and a standard nasopharyngeal and throat swab in persons seeking care at an acute respiratory infection clinic in a university hospital during the outbreak of COVID-19. Real-time polymerase chain reaction (RT-PCR) was performed, and the results of the two specimens were compared.\n\nResultsTwo-hundred pairs of the samples were collected. Sixty-nine (34.5%) patients were male, and the median (interquartile) age was 36 (28-48) years. Using nasopharyngeal and throat swab RT-PCR as the reference standard, the prevalence of COVID-19 diagnosed by nasopharyngeal and throat swab RT-PCR was 9.5%. The sensitivity and specificity of the saliva sample RT-PCR were 84.2% [95% confidence interval (CI) 79.2%-89.3%], and 98.9% (95% CI 97.5-100.3%), respectively. An analysis of the agreement between the two specimens demonstrated 97.5% observed agreement (kappa coefficient 0.851, 95% CI 0.723-0.979; p <0.001).\n\nConclusionsSaliva specimens can be used for the diagnosis of COVID-19. The collection method is non-invasive, and non-aerosol generating. Using a saliva sample as a specimen for the detection of SARS-CoV-2 could facilitate the diagnosis of the disease, which is one of the strategies that helps in controlling the epidemic.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Ekawat Pasomsub", + "author_inst": "Faculty of Medicine Ramathibodi Hospital, Mahidol University" + }, + { + "author_name": "Siriorn P. Watcharananan", + "author_inst": "Faculty of Medicine Ramathibodi Hospital, Mahidol University" + }, + { + "author_name": "Kochawan Boonyawat", + "author_inst": "Faculty of Medicine Ramathibodi Hospital, Mahidol University" + }, + { + "author_name": "Pareena Janchompoo", + "author_inst": "Faculty of Medicine Ramathibodi Hospital, Mahidol University" + }, + { + "author_name": "Garanyuta Wongtabtim", + "author_inst": "Faculty of Medicine Ramathibodi Hospital, Mahidol University" + }, + { + "author_name": "Worramin Suksuwan", + "author_inst": "Faculty of Medicine Ramathibodi Hospital, Mahidol University" + }, + { + "author_name": "Somnuek Sungkanuparph", + "author_inst": "Faculty of Medicine Ramathibodi Hospital, Mahidol University" + }, + { + "author_name": "Angsana Phuphuakrat", + "author_inst": "Faculty of Medicine Ramathibodi Hospital, Mahidol University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.17.20069435", "rel_title": "EFFECTS OF COVID-19 INFECTION DURING PREGNANCY AND NEONATAL PROGNOSIS: WHAT IS THE EVIDENCE?", @@ -1516230,25 +1518569,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.21.052530", - "rel_title": "One-pot Detection of COVID-19 with Real-time Reverse-transcription Loop-mediated Isothermal Amplification (RT-LAMP) Assay and Visual RT-LAMP Assay", - "rel_date": "2020-04-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.21.052530", - "rel_abs": "BackgroundRapid and reliable diagnostic assays were critical for prevention and control of the coronavirus pneumonia caused by COVID-19.\n\nObjectiveThis study was to establish one-pot real-time reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay and one-pot visual RT-LAMP assay for the detection of COVID-19.\n\nMethodsSix specific LAMP primers targeting the N gene of COVID-19 were designed, the RT-LAMP reaction system was optimized with plasmid pUC57 containing N gene sequence, the detection limit was determined with a serial dilution of the plasmid pUC57 containing N gene sequence, and the one-pot real-time RT-LAMP assay and one-pot visual RT-LAMP assay for the detection of COVID-19 were established.\n\nResultsOur results showed that the one-pot RT-LAMP assays can detect COVID-19 with a limit of [≥] 6 copies per l-1 of pUC57 containing N gene sequence.\n\nConclusionThis study provides rapid, reliable and sensitive tools for facilitating preliminary and cost-effective prevention and control of COVID-19.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Deguo Wang", - "author_inst": "Xuchang University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2020.04.16.20068411", "rel_title": "Clinical Decision Support Tool and Rapid Point-of-Care Platform for Determining Disease Severity in Patients with COVID-19", @@ -1517056,6 +1519376,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.17.20069179", + "rel_title": "The current COVID-19 wave will likely be mitigated in the second-line European countries", + "rel_date": "2020-04-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20069179", + "rel_abs": "ObjectiveCountries presently apply different strategies to control the COVID-19 outbreak. Differences in population structures, decision making, health systems and numerous other factors result in various trajectories in terms of mortality at country scale. Our objective in this manuscript is to disentangle the future of second-line European countries (i.e. countries that present, today, a moderate death rate) with respect to the current COVID-19 wave.\n\nMethodWe propose a data-driven approach, grounded on a mixture model, to forecast the dynamics of the number of deaths from COVID-19 in a given focal country using data from countries that are ahead in time in terms of COVID-19-induced mortality. In this approach, the mortality curves of ahead-in-time countries are used to build predictors, which are then used as the components of the mixture model. This approach was applied to eight second-line European countries (Austria, Denmark, Germany, Ireland, Poland, Portugal, Romania and Sweden), using Belgium, France, Italy, Netherlands, Spain, Switzerland, United Kingdom as well as the Hubei province in China to build predictors. For this analysis, we used data pooled by the Johns Hopkins University Center for Systems Science and Engineering.\n\nResultsIn general, the second-line European countries tend to follow relatively mild mortality curves (typically, those of Switzerland and Hubei) rather than fast and severe ones (typically, those of Spain, Italy, Belgium, France and the United Kingdom). From a methodological viewpoint, the performance of our forecasting approach is about 80% up to 8 days in the future, as soon as the focal country has accumulated at least two hundreds of deaths.\n\nDiscussionOur results suggest that the continuation of the current COVID-19 wave across Europe will likely be mitigated, and not as strong as it was in most of the front-line countries first impacted by the wave.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Samuel Soubeyrand", + "author_inst": "INRAE" + }, + { + "author_name": "Melina Ribaud", + "author_inst": "INRAE" + }, + { + "author_name": "Virgile Baudrot", + "author_inst": "INRAE" + }, + { + "author_name": "Denis Allard", + "author_inst": "INRAE" + }, + { + "author_name": "Denys Pommeret", + "author_inst": "INRAE" + }, + { + "author_name": "Lionel Roques", + "author_inst": "INRAE" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.17.20069443", "rel_title": "A Path to the End of COIVD-19 - a Mathematical Model", @@ -1517812,37 +1520171,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.20.20071977", - "rel_title": "Modeling the COVID-19 epidemic in Okinawa", - "rel_date": "2020-04-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.20.20071977", - "rel_abs": "We analyze current data on the COVID-19 spreading in Okinawa, Japan. We find that the initial spread is characterized by a doubling time of about 5 days. We implement a model to forecast the future spread under different scenarios. The model predicts that, if significant containment measures are not taken, a large fraction of the population will be infected with COVID-19, with the peak of the epidemic expected at the end of May and intensive care units having largely exceeded capacity. We analyzed scenarios implementing strong containment measures, similar to those imposed in Europe. The model predicts that an immediate implementation of strong containment measures (on the 19th of April) will significantly reduce the death count. We assess the negative consequences of these measures being implemented with a delay, or not being sufficiently stringent.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Simone Pigolotti", - "author_inst": "Okinawa Institute of Science and Technology" - }, - { - "author_name": "Davide Chiuchiu", - "author_inst": "Okinawa Institute of Science and Technology" - }, - { - "author_name": "Paula Villa Martin", - "author_inst": "Okinawa Institute of Science and Technology" - }, - { - "author_name": "Deepak Bhat", - "author_inst": "Okinawa Institute of Science and Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.19.20071811", "rel_title": "More prevalent, less deadly? Bayesian inference of the COVID19 Infection Fatality Ratio from mortality data", @@ -1518306,6 +1520634,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.04.21.053017", + "rel_title": "Enisamium is a small molecule inhibitor of the influenza A virus and SARS-CoV-2 RNA polymerases", + "rel_date": "2020-04-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.21.053017", + "rel_abs": "Influenza A virus and coronavirus strains cause a mild to severe respiratory disease that can result in death. Although vaccines exist against circulating influenza A viruses, such vaccines are ineffective against emerging pandemic influenza A viruses. Currently, no vaccine exists against coronavirus infections, including pandemic SARS-CoV-2, the causative agent of the Coronavirus Disease 2019 (COVID-19). To combat these RNA virus infections, alternative antiviral strategies are needed. A key drug target is the viral RNA polymerase, which is responsible for viral RNA synthesis. In January 2020, the World Health Organisation identified enisamium as a candidate therapeutic against SARS-CoV-2. Enisamium is an isonicotinic acid derivative that is an inhibitor of multiple influenza B and A virus strains in cell culture and clinically approved in 11 countries. Here we show using in vitro assays that enisamium and its putative metabolite, VR17-04, inhibit the activity of the influenza virus and the SARS-CoV-2 RNA polymerase. VR17-04 displays similar efficacy against the SARS-CoV-2 RNA polymerase as the nucleotide analogue remdesivir triphosphate. These results suggest that enisamium is a broad-spectrum small molecule inhibitor of RNA virus RNA synthesis, and implicate it as a possible therapeutic option for treating SARS-CoV-2 infection. Unlike remdesivir, enisamium does not require intravenous administration which may be advantageous for the development of COVID-19 treatments outside a hospital setting.\n\nImportanceInfluenza A virus and SARS-CoV-2 are respiratory viruses capable of causing pandemics, and the latter is responsible for the Coronavirus Disease 2019 (COVID-19) pandemic. Both viruses encode RNA polymerases which transcribe their RNA genomes and are important targets for antiviral drugs including remdesivir. Here, we show that the antiviral drug enisamium inhibits the RNA polymerases of both influenza A virus and SARS-CoV-2. Furthermore, we show that a putative metabolite of enisamium is a more potent inhibitor, inhibiting the SARS-CoV-2 RNA polymerase with similar efficiency to remdesivir. Our data offer insight into the mechanism of action for enisamium, and implicate it as a broad-spectrum antiviral which could be used in the treatment of SARS-CoV-2 infection.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Alexander Walker", + "author_inst": "University of Oxford" + }, + { + "author_name": "Haitian Fan", + "author_inst": "University of Oxford" + }, + { + "author_name": "Jeremy R Keown", + "author_inst": "University of Oxford" + }, + { + "author_name": "Victor Margitich", + "author_inst": "Farmak JSC" + }, + { + "author_name": "Jonathan M Grimes", + "author_inst": "University of Oxford" + }, + { + "author_name": "Ervin Fodor", + "author_inst": "University of Oxford" + }, + { + "author_name": "Aartjan JW te Velthuis", + "author_inst": "University of Cambridge" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.04.20.052159", "rel_title": "A Scalable, Easy-to-Deploy, Protocol for Cas13-Based Detection of SARS-CoV-2 Genetic Material", @@ -1519226,53 +1521597,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.04.16.20063727", - "rel_title": "Social interventions can lower COVID-19 deaths in middle-income countries", - "rel_date": "2020-04-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.16.20063727", - "rel_abs": "Summary paragraphA novel pandemic coronavirus disease (COVID-19) was first detected in late 2019 in Wuhan (China)1,2. COVID-19 has caused 77 national governments worldwide to impose a lockdown in part or all their countries, as of April 4, 20203. The United States and the United Kingdom estimated the effectiveness of non-pharmaceutical interventions to reduce COVID-19 deaths, but there is less evidence to support choice of control measures in middle-income countries4. We used Colombia, an upper-middle income country, as a case-study to assess the effect of social interventions to suppress or mitigate the COVID-19 pandemic. Here we show that a combination of social distancing interventions, triggered by critical care admissions, can suppress and mitigate the peak of COVID-19, resulting in less critical care use, hospitalizations, and deaths. We found, through a mathematical simulation model, that a one-time social intervention may delay the number of critical care admissions and deaths related to the COVID-19 pandemic. However, a series of social interventions (social and work distance and school closures) over a period of a year can reduce the expected burden of COVID-19, however, these interventions imply long periods of lockdown. Colombia would prevent up to 97% of COVID-19 deaths using these triggered series of interventions during the first year. Our analyses could be used by decision-makers from other middle-income countries with similar demographics and contact patterns to Colombia to reduce COVID-19 critical care admissions and deaths in their jurisdictions.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Angel Jose Paternina-Caicedo", - "author_inst": "Universidad del Sinu" - }, - { - "author_name": "Marc Choisy", - "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh city, Vietnam" - }, - { - "author_name": "Christian Garcia-Calavaro", - "author_inst": "Centro Programa de Salud Publica, Universidad de Santiago" - }, - { - "author_name": "Guido Camargo-Espa\u00f1a", - "author_inst": "Department of Biological Sciences and Eck Institute of Global Health, University of Notre Dame" - }, - { - "author_name": "Jos\u00e9 Rojas-Suarez", - "author_inst": "Universidad de Cartagena" - }, - { - "author_name": "Carmelo Due\u00f1as", - "author_inst": "Universidad de Cartagena" - }, - { - "author_name": "Adrian Smith", - "author_inst": "University of Oxford" - }, - { - "author_name": "Fernando Pio De la Hoz-Restrepo", - "author_inst": "Universidad Nacional de Colombia" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.16.20066787", "rel_title": "FALSE-NEGATIVE RESULTS OF INITIAL RT-PCR ASSAYS FOR COVID-19: A SYSTEMATIC REVIEW", @@ -1519980,6 +1522304,229 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.04.20.048066", + "rel_title": "Host, Viral, and Environmental Transcriptome Profiles of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)", + "rel_date": "2020-04-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.20.048066", + "rel_abs": "The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused thousands of deaths worldwide, including >18,000 in New York City (NYC) alone. The sudden emergence of this pandemic has highlighted a pressing clinical need for rapid, scalable diagnostics that can detect infection, interrogate strain evolution, and identify novel patient biomarkers. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs, plus a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, bacterial, and viral profiling. We applied both technologies across 857 SARS-CoV-2 clinical specimens and 86 NYC subway samples, providing a broad molecular portrait of the COVID-19 NYC outbreak. Our results define new features of SARS-CoV-2 evolution, nominate a novel, NYC-enriched viral subclade, reveal specific host responses in interferon, ACE, hematological, and olfaction pathways, and examine risks associated with use of ACE inhibitors and angiotensin receptor blockers. Together, these findings have immediate applications to SARS-CoV-2 diagnostics, public health, and new therapeutic targets.", + "rel_num_authors": 52, + "rel_authors": [ + { + "author_name": "Daniel J Butler", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Christopher Mozsary", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Cem Meydan", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "David C Danko", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Jonathan Foox", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Joel Rosiene", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Alon Shaiber", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Ebrahim Afshinnekoo", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Matthew MacKay", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Fritz J Sedlazeck", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Nikolay A Ivanov", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Maria A Sierra", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Diana Pohle", + "author_inst": "University Hospital Tuebingen" + }, + { + "author_name": "Michael Zietz", + "author_inst": "Columbia University" + }, + { + "author_name": "Undina Gisladottir", + "author_inst": "Columbia University" + }, + { + "author_name": "Vijendra Ramlall", + "author_inst": "Columbia University" + }, + { + "author_name": "Craig D Westover", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Krista Ryon", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Benjamin Young", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Chandrima Bhattacharya", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Phyllis Ruggiero", + "author_inst": "New York Presbyterian Hospital" + }, + { + "author_name": "Bradley W Langhorst", + "author_inst": "New England Biolabs" + }, + { + "author_name": "Nathan A Tanner", + "author_inst": "New England Biolabs" + }, + { + "author_name": "Justyna Gawrys", + "author_inst": "New York Presbyterian Hospital" + }, + { + "author_name": "Dmitry Meleshko", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Dong Xu", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Peter A D Steel", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Amos J Shemesh", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Jenny Xiang", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Jean Thierry-Mieg", + "author_inst": "NIH" + }, + { + "author_name": "Danielle Thierry-Mieg", + "author_inst": "NIH" + }, + { + "author_name": "Robert E Schwartz", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Angelika Iftner", + "author_inst": "University Hospital Tuebingen" + }, + { + "author_name": "Daniela Bezdan", + "author_inst": "University Hospital Tuebingen" + }, + { + "author_name": "John Sipley", + "author_inst": "New York Presbyterian Hospital" + }, + { + "author_name": "Lin Cong", + "author_inst": "New York Presbyterian Hospital" + }, + { + "author_name": "Arryn Craney", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Priya Velu", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Ari Melnick", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Iman Hajirasouliha", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Stacy M Horner", + "author_inst": "Duke University Medical Center" + }, + { + "author_name": "Thomas Iftner", + "author_inst": "University Hospital Tubingen" + }, + { + "author_name": "Mirella Salvatore", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Massimo Loda", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Lars F Westblade", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Shawn Levy", + "author_inst": "HudsonAlpha Institute for Biotechnology" + }, + { + "author_name": "Melissa Cushing", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Shixiu Wu", + "author_inst": "Hangzhou Cancer Hospital" + }, + { + "author_name": "Nicholas P Tatonetti", + "author_inst": "Columbia University" + }, + { + "author_name": "Marcin Imielinski", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Hanna Rennert", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Christopher Mason", + "author_inst": "Weill Cornell Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.04.17.042366", "rel_title": "Rapid direct nucleic acid amplification test without RNA extraction for SARS-CoV-2 using a portable PCR thermocycler", @@ -1521116,93 +1523663,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.14.20053090", - "rel_title": "SARS-COV-2 comorbidity network and outcome in hospitalized patients in Crema, Italy", - "rel_date": "2020-04-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.14.20053090", - "rel_abs": "No systematic data on hospitalized SARS-COV-2 patients from Western countries are available. We report onset, course, correlations with comorbidities, and diagnostic accuracy of nasopharyngeal swab in 539 individuals suspected to carry SARS-COV-2 admitted to the hospital of Crema, Italy. All individuals underwent clinical and laboratory exams, SARS-COV-2 reverse transcriptase-polymerase chain reaction on nasopharyngeal swab, and chest X-ray and/or computed tomography (CT). Data on onset, course, comorbidities, number of drugs including angiotensin converting enzyme (ACE) inhibitors and angiotensin-II-receptor antagonists (sartans), follow-up swab, pharmacological treatments, non-invasive respiratory support, ICU admission, and deaths were recorded. Among 411 SARS-COV-2 patients (66.6% males) median age was 70.5 years (range 1-99). Chest CT was performed in 317 (77.2%) and showed interstitial pneumonia in 304 (96%). Fatality rate was 17.5% (74% males), with 6.6% in 60-69 years old, 21.1% in 70-79 years old, 38.8% in 80-89 years old, and 83.3% above 90 years. No death occurred below 60 years. Non-invasive respiratory support rate was 27.2% and ICU admission 6.8%. Older age, cough and dyspnea at onset, hypertension, cardiovascular diseases, diabetes, renal insufficiency, >7 drugs intake and positive X-ray, low lymphocyte count, high C-reactive protein, aspartate aminotransferase and lactate dehydrogenase values, and low PO2 partial pressure with high lactate at arterial blood gas analysis at admission were significantly associated with death. Use of ACE inhibitors or sartans was not associated with outcomes. Comorbidity network analysis revealed homogenous distribution of deceased and 60-80 aged SARS-COV-2 patients across diseases. Among 128 swab negative patients at admission (63.3% males) median age was 67.7 years (range 1-98). Chest CT was performed in 87 (68%) and showed interstitial pneumonia in 76 (87.3%). Follow-up swab turned positive in 13 of 32 patients. Using chest CT at admission as gold standard on the entire study population of 539 patients, nasopharyngeal swab had 80% sensitivity. SARS-CoV-2 caused high mortality among patients older than 60 years and correlated with pre- existing multiorgan impairment. ACE inhibitors and sartans did not influence patients outcome.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Gianpaolo Benelli", - "author_inst": "Ospedale Maggiore di Crema, Crema, Italy" - }, - { - "author_name": "Elisabetta Buscarini", - "author_inst": "Ospedale Maggiore di Crema" - }, - { - "author_name": "Ciro Canetta", - "author_inst": "Ospedale Maggiore di Crema" - }, - { - "author_name": "Giuseppe La Piana", - "author_inst": "Ospedale Maggiore di Crema" - }, - { - "author_name": "Guido Merli", - "author_inst": "Ospedale Maggiore di Crema" - }, - { - "author_name": "Alessandro Scartabellati", - "author_inst": "Ospedale Maggiore di Crema" - }, - { - "author_name": "Giovanni Vigano", - "author_inst": "Ospedale Maggiore di Crema" - }, - { - "author_name": "Roberto Sfogliarini", - "author_inst": "Ospedale Maggiore di Crema" - }, - { - "author_name": "Giovanni Melilli", - "author_inst": "Ospedale Maggiore di Crema" - }, - { - "author_name": "Roberto Assandri", - "author_inst": "Ospedale Maggiore di Crema" - }, - { - "author_name": "Daniele Cazzato", - "author_inst": "Fondazione IRCCS Istituto Neurologico \"Carlo Besta\", Milan" - }, - { - "author_name": "Davide Sebastiano Rossi", - "author_inst": "Fondazione IRCCS Istituto Neurologico \"Carlo Besta\", Milan" - }, - { - "author_name": "Susanna Usai", - "author_inst": "Fondazione IRCCS Istituto Neurologico \"Carlo Besta\", Milan" - }, - { - "author_name": "Guido Caldarelli", - "author_inst": "IMT School for Advanced Studies, Lucca" - }, - { - "author_name": "Tommaso Gili", - "author_inst": "IMT School for Advanced Studies, Lucca" - }, - { - "author_name": "Irene Tramacere", - "author_inst": "Fondazione IRCCS Istituto Neurologico \"Carlo Besta\", Milan" - }, - { - "author_name": "Germano Pellegata", - "author_inst": "Ospedale Maggiore di Crema" - }, - { - "author_name": "Giuseppe Lauria", - "author_inst": "IRCCS FONDAZIONE ISTITUTO NEUROLOGICO CARLO BESTA" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.15.20066688", "rel_title": "Variation in Aerosol Production Across Oxygen Delivery Devices in Spontaneously Breathing Human Subjects", @@ -1521938,6 +1524398,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.15.20066746", + "rel_title": "Temporal detection and phylogenetic assessment of SARS-CoV-2 in municipal wastewater", + "rel_date": "2020-04-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.15.20066746", + "rel_abs": "SARS-CoV-2 has recently been detected in feces, which indicates that wastewater may be used to monitor viral prevalence in the community. Here we use RT-qPCR to monitor wastewater for SARS-CoV-2 RNA over a 52-day time course. We show that changes in SARS-CoV-2 RNA concentrations correlate with local COVID-19 epidemiological data (R2=0.9), though detection in wastewater trails symptom onset dates by 5-8 days. We determine a near complete (98.5%) SARS-CoV-2 genome sequence from the wastewater and use phylogenic analysis to infer viral ancestry. Collectively, this work demonstrates how wastewater can be used as a proxy to monitor viral prevalence in the community and how genome sequencing can be used for high-resolution genotyping of the predominant strains circulating in a community.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Artem Nemudryi", + "author_inst": "Montana State University" + }, + { + "author_name": "Anna Nemudraia", + "author_inst": "Montana State University" + }, + { + "author_name": "Kevin Surya", + "author_inst": "Montana State University" + }, + { + "author_name": "Tanner Wiegand", + "author_inst": "Montana State University" + }, + { + "author_name": "Murat Buyukyoruk", + "author_inst": "Montana State University" + }, + { + "author_name": "Royce Wilkinson", + "author_inst": "Montana State University" + }, + { + "author_name": "Blake Wiedenheft", + "author_inst": "Montana State University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.15.20067272", "rel_title": "Mandatory social distancing associated with increased doubling time: an example using hyperlocal data", @@ -1522878,41 +1525381,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.15.20065946", - "rel_title": "Serial interval and generation interval for respectively the imported and local infectors estimated using reported contact-tracing data of COVID-19 in China", - "rel_date": "2020-04-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.15.20065946", - "rel_abs": "BackgroundsThe emerging virus, COVID-19, has caused a massive out-break worldwide. Based on the publicly available contact-tracing data, we identified 337 transmission chains from 10 provinces in China and estimated the serial interval (SI) and generation interval (GI) of COVID-19 in China.\n\nMethodsInspired by possibly different values of the time-varying reproduction number for the imported cases and the local cases in China, we divided all transmission events into three subsets: imported (the zeroth generation) infecting 1st-generation locals, 1st-generation locals infecting 2nd-generation locals, and others transmissions among 2+ generations. The corresponding SI (GI) is respec-tively denoted as [Formula], and [Formula]. A Bayesian approach with doubly interval-censored likelihood is employed to fit the lognormal, gamma, and Weibull distribution function of the SI and GI using the identified 337 transmission chains.\n\nFindingsIt is found that the estimated [Formula], and [Formula], thus overall both SI and GI decrease when generation increases.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Menghui Li", - "author_inst": "Beijing Institute of Science and Technology Information" - }, - { - "author_name": "Kai Liu", - "author_inst": "Faculty of Geographical Science, Beijing Normal University, Beijing, 100875, P. R. China" - }, - { - "author_name": "Yukun Song", - "author_inst": "School of Systems Science, Beijing Normal University, Beijing, 100875, P. R. China" - }, - { - "author_name": "Ming Wang", - "author_inst": "Faculty of Geographical Science, Beijing Normal University, Beijing, 100875, P. R. China" - }, - { - "author_name": "Jinshan Wu", - "author_inst": "dSchool of Systems Science, Beijing Normal University, Beijing, 100875, P. R. China" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.13.20064329", "rel_title": "Early prediction of mortality risk among severe COVID-19 patients using machine learning", @@ -1523572,6 +1526040,57 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.04.16.045799", + "rel_title": "Potential microenvironment of SARS-CoV-2 infection in airway epithelial cells revealed by Human Protein Atlas database analysis", + "rel_date": "2020-04-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.16.045799", + "rel_abs": "The outbreak of COVID-19 has caused serious epidemic events in China and other countries. With the rapid spread of COVID-19, it is urgent to explore the pathogenesis of this novel coronavirus. However, the foundational research of COVID-19 is very weak. Although angiotensin converting enzyme 2 (ACE2) is the reported receptor of SARS-CoV-2, information about SARS-CoV-2 invading airway epithelial cells is very limited. Based on the analysis of the Human Protein Atlas database, we compared the virus-related receptors of epithelial-derived cells from different organs and found potential key molecules in the local microenvironment for SARS-CoV-2 entering airway epithelial cells. In addition, we found that these proteins were associated with virus reactive proteins in host airway epithelial cells, which may promote the activation of the immune system and the release of inflammatory factors. Our findings provide a new research direction for understanding the potential microenvironment required by SARS-CoV-2 infection in airway epithelial, which may assist in the discovery of potential drug targets against SARS-CoV-2 infection.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Ling Leng", + "author_inst": "Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences" + }, + { + "author_name": "Jie Ma", + "author_inst": "National Center for Protein Sciences (Beijing) , Beijing Institute of Life Omics" + }, + { + "author_name": "Leike Zhang", + "author_inst": "Wuhan Institute of Virology, Chinese Academy of Sciences" + }, + { + "author_name": "Li Wei", + "author_inst": "National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology" + }, + { + "author_name": "Lei Zhao", + "author_inst": "National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology" + }, + { + "author_name": "Yunping Zhu", + "author_inst": "National Center for Protein Sciences (Beijing) , Beijing Institute of Life Omics" + }, + { + "author_name": "Zhihong Wu", + "author_inst": "Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences" + }, + { + "author_name": "Ruiyuan Cao", + "author_inst": "National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology" + }, + { + "author_name": "Wu Zhong", + "author_inst": "National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "contradictory results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2020.04.18.045963", "rel_title": "Pandemic Publishing: Medical journals drastically speed up their publication process for Covid-19", @@ -1524692,49 +1527211,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.04.15.20066183", - "rel_title": "The impact of early scientific literature in response to COVID-19: a scientometric perspective", - "rel_date": "2020-04-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.15.20066183", - "rel_abs": "BackgroundIn the early phases of a new pandemic, identifying the most relevant evidence and quantifying which studies are shared the most can help researchers and policy makers. The aim of this study is to describe and quantify the impact of early scientific production in response to COVID-19 pandemic.\n\nMethodsThe study consisted of: 1) review of the scientific literature produced in the first 30 days since the first COVID-19 paper was published; 2) analysis of papers metrics with the construction of a \"Computed-Impact-Score\" (CIS) that represents a unifying score over heterogeneous bibliometric indicators. In this study we use metrics and alternative metrics collected into five separate categories. On top of those categories we compute the CIS. Highest CIS papers are further analyzed.\n\nResults239 papers have been included in the study. The mean of citations, mentions and social media interactions resulted in 1.63, 10 and 1250, respectively. The paper with highest CIS resulted \"Clinical features of patients[...]\" by Chaolin Huang et al., which rated first also in citations and mentions. This is the first paper describing patients affected by the new disease and reporting data that are clearly of great interest to both the scientific community and the general population.\n\nConclusionsThe early response of scientific literature during an epidemic does not follow a pre-established pattern. Being able to monitor how communications spread from the scientific world toward the general population using both traditional and alternative metric measures is essential, especially in the early stages of a pandemic.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Davide Golinelli", - "author_inst": "University of Bologna" - }, - { - "author_name": "Andrea Giovanni Nuzzolese", - "author_inst": "STLab, ISTC-CNR." - }, - { - "author_name": "Erik Boetto", - "author_inst": "Department of Biomedical and Neuromotor Sciences, University of Bologna" - }, - { - "author_name": "Flavia Rallo", - "author_inst": "DIBINEM, University of Bologna." - }, - { - "author_name": "Manfredi Greco", - "author_inst": "University of Bologna" - }, - { - "author_name": "Fabrizio Toscano", - "author_inst": "Montefiore Medical Center. Department of Internal Medicine. New York City, United States" - }, - { - "author_name": "Maria Pia Fantini", - "author_inst": "Department of Biomedical and Neuromotor Sciences, University of Bologna" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.04.15.20061168", "rel_title": "Impact of healthcare worker shift scheduling on workforce preservation during the COVID-19 pandemic", @@ -1525298,6 +1527774,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.15.20067264", + "rel_title": "A Heuristic Model for Spreading of COVID 19 in Singapore", + "rel_date": "2020-04-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.15.20067264", + "rel_abs": "This paper presents a simple heuristic model for COVID 19 spreading. The model is based on a propagation unit of time. The state of the epidemic at the end of the time unit is then related to that at the start through recurrence relationships. By propagating these relationships over the required number of time units, a projection can be made over time. The model is readily implemented on a spreadsheet and is therefore potentially widely accessible. It can serve as a useful tool for scenario planning and forecasting not just for an entire population, but also for a specific community within a population.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Fook Hou Lee", + "author_inst": "National University of Singapore" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.14.041319", "rel_title": "A blueprint for the implementation of a validated approach for the detection of SARS-Cov2 in clinical samples in academic facilities", @@ -1526314,85 +1528809,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.13.20064402", - "rel_title": "Efficacy and Safety of Antibiotic Agents in Children with COVID-19: A Rapid Review", - "rel_date": "2020-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.13.20064402", - "rel_abs": "BackgroundThe aim of this review was to evaluate the efficacy and safety of antibiotic agents in children with COVID-19, as well as to introduce the present situation of antibiotics use and bacterial coinfections in COVID-19 patients.\n\nMethodsWe searched Cochrane library, Medline, Embase, Web of Science, CBM, Wanfang Data and CNKI from their inception to March 31, 2020. In addition, we searched related studies on COVID-19 published before March 31, 2020 through Google Scholar. We evaluated the risk of bias of included studies, and synthesized the results using a qualitative synthesis.\n\nResultsSix studies met our inclusion criteria. Five studies on SARS showed an overall risk of death of 7.2% to 20.0%. One study of SARS patients who used macrolides, quinolones or beta lactamases showed that the mean duration of hospital stay was 14.2, 13.8 and 16.2 days, respectively, and their average duration of fever was 14.3, 14.0 and 16.2 days, respectively. One cohort study on MERS indicated that macrolide therapy was not associated with a significant reduction in 90-day mortality (adjusted odds ratio [OR] 0.84, 95% confidence interval [CI] 0.47-1.51, P = 0.56) and improvement in MERS-CoV RNA clearance (adjusted hazard ratio [HR] 0.88, 95% CI 0.47, -1.64], P = 0.68). According to the findings of 33 studies, the proportion of antibiotics use ranged from 19.4% to 100.0% in children and 13.2% to 100.0% in adults, despite the lack of etiological evidence. The most commonly used antibiotics in adults were quinolones, cephalosporins and macrolides and in children meropenem and linezolid.\n\nConclusionsThe benefits of antibiotic agents for adults with SARS or MERS were questionable in the absence of bacterial coinfections. There is no evidence to support the use of antibiotic agents for children with COVID-19 in the absence of bacterial coinfection.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Jianjian Wang", - "author_inst": "School of Public Health, Lanzhou University, Lanzhou, China" - }, - { - "author_name": "Yuyi Tang", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Yanfang Ma", - "author_inst": "Lanzhou University" - }, - { - "author_name": "Qi Zhou", - "author_inst": "Lanzhou University" - }, - { - "author_name": "Weiguo Li", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Muna Baskota", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Yinmei Yang", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Xingmei Wang", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Qingyuan Li", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Xufei Luo", - "author_inst": "School of Public Health of Lanzhou University, Lanzhou" - }, - { - "author_name": "Toshio Fukuoka", - "author_inst": "Emergency and Critical Care Center, the Department of General Medicine, Department of Research and Medical Education at Kurashiki Central Hospital, Japan" - }, - { - "author_name": "Hyeong Sik Ahn", - "author_inst": "Department of Preventive Medicine, Korea University College of Medicine, Seoul, Korea" - }, - { - "author_name": "Myeong Soo Lee", - "author_inst": "Korea Institute of Oriental Medicine, Daejeon, Korea" - }, - { - "author_name": "Zhengxiu Luo", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Enmei Liu", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Yaolong Chen", - "author_inst": "School of Public Health, Lanzhou University, Lanzhou, China" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2020.04.14.20064923", "rel_title": "Effects of temperature and humidity on the spread of COVID-19: A systematic review.", @@ -1526976,6 +1529392,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.13.20064436", + "rel_title": "Potential Effectiveness and Safety of Antiviral Agents in Children with Coronavirus Disease 2019: A Rapid Review and Meta-Analysis", + "rel_date": "2020-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.13.20064436", + "rel_abs": "BackgroundThe COVID-19 outbreak presents a new, life-threatening disease. Our aim was to assess the potential effectiveness and safety of antiviral agents for COVID-19 in children.\n\nMethodsElectronic databases from their inception to March, 31 2020 were searched for randomized controlled trials, clinical controlled trials and cohort studies of interventions with antiviral agents for children (less than 18 years of age) with COVID-19.\n\nResultsA total of 23 studies of indirect evidence with 6008 patients were included. The risks of bias in all studies were moderate to high in general. The effectiveness and safety of antiviral agents for children with COVID-19 is uncertain: For adults with COVID-19, lopinavir/ritonavir had no effect on mortality (risk ratio [RR]= 0.77, 95% confidence interval [CI] 0.45 to 1.30) and probability of negative PCR test (RR=0.98, 95 CI% 0.82 to 1.18). Arbidol had no benefit on probability of negative PCR test (RR=1.27, 95% CI 0.93 to 1.73). Hydroxychloroquine was not associated with increasing the probability of negative PCR result (RR=0.93, 95% CI 0.73 to 1.18). For adults with SARS, interferon was associated with reduced corticosteroid dose (weighted mean difference [WMD]=-0.14 g, 95% CI -0.21 to -0.07) but had no effect on mortality (RR=0.72, 95% CI 0.28 to 1.88); ribavirin did not reduce mortality (RR=0.68, 95% CI % 0.43 to 1.06) and was associated with high risk of severe adverse reactions; and oseltamivir had no effect on mortality (RR=0.87, 95% CI 0.55 to 1.38). Ribavirin combined with interferon was also not effective in adults with MERS and associated with adverse reactions.\n\nConclusionsThere is no evidence showing the effectiveness of antiviral agents for children with COVID-19, and the clinical efficacy of existing antiviral agents is still uncertain. We do not suggest clinical routine use of antivirals for COVID-19 in children, with the exception of clinical trials.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Qianling Shi", + "author_inst": "The First School of Clinical Medicine, Lanzhou University, Lanzhou 730000, China" + }, + { + "author_name": "Qi Zhou", + "author_inst": "The First School of Clinical Medicine, Lanzhou University, Lanzhou 730000, China" + }, + { + "author_name": "Xia Wang", + "author_inst": "Department of Respiratory Medicine, Children Hospital of Chongqing Medical University, Chongqing 400014, China" + }, + { + "author_name": "Jing Liao", + "author_inst": "Department of Respiratory Medicine, Children Hospital of Chongqing Medical University, Chongqing 400014, China" + }, + { + "author_name": "Yang Yu", + "author_inst": "The Second School of Clinical Medicine, Lanzhou University, Lanzhou 730000, China" + }, + { + "author_name": "Zijun Wang", + "author_inst": "Evidence-based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China" + }, + { + "author_name": "Shuya Lu", + "author_inst": "Department of Pediatric, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 611731, China" + }, + { + "author_name": "Yanfang Ma", + "author_inst": "Evidence-based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China" + }, + { + "author_name": "Yangqin Xun", + "author_inst": "Evidence-based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China" + }, + { + "author_name": "Xufei Luo", + "author_inst": "School of Public Health, Lanzhou University, Lanzhou 730000, China" + }, + { + "author_name": "Weiguo Li", + "author_inst": "Department of Respiratory Medicine, Children Hospital of Chongqing Medical University, Chongqing 400014, China" + }, + { + "author_name": "Toshio Fukuoka", + "author_inst": "Emergency and Critical Care Center, the Department of General Medicine, Department of Research and Medical Education at Kurashiki Central Hospital, Japan" + }, + { + "author_name": "Hyeong Sik Ahn", + "author_inst": "Department of Preventive Medicine, Korea University College of Medicine, Seoul, Korea" + }, + { + "author_name": "Myeong Soo Lee", + "author_inst": "Korea Institute of Oriental Medicine, Daejeon, Korea" + }, + { + "author_name": "Zhengxiu Luo", + "author_inst": "Department of Respiratory Medicine, Children Hospital of Chongqing Medical University, Chongqing 400014, China" + }, + { + "author_name": "Enmei Liu", + "author_inst": "Department of Respiratory Medicine, Children Hospital of Chongqing Medical University, Chongqing 400014, China" + }, + { + "author_name": "Yaolong Che", + "author_inst": "Evidence-based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China" + }, + { + "author_name": "Qubei Li", + "author_inst": "Department of Respiratory Medicine, Children Hospital of Chongqing Medical University, Chongqing 400014, China" + }, + { + "author_name": "Kehu Yang", + "author_inst": "The First School of Clinical Medicine, Lanzhou University, Lanzhou 730000, China" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.14.20065151", "rel_title": "Epidemic Landscape and Forecasting of SARS-CoV-2 in India", @@ -1527664,41 +1530171,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.14.20065201", - "rel_title": "Optimal Allocation of COVID-19 Test Kits Among Accredited Testing Centers in the Philippines", - "rel_date": "2020-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.14.20065201", - "rel_abs": "Testing is crucial for early detection, isolation, and treatment of coronavirus disease (COVID-19)-infected individuals. However, in resource-constrained countries such as the Philippines, test kits have limited availability. As of 12 April 2020, there are 11 testing centers in the country that have been accredited by the Department of Health (DOH) to conduct testing. In this paper, we determine the optimal percentage allocation of COVID-19 test kits among accredited testing centers in the Philippines that gives an equitable chance to all infected individuals to be tested. Heterogeneity in testing accessibility, population density of municipalities, and the capacity of testing facilities are included in the model. Our results showed that the range of optimal allocation per testing center are: Research Institute for Tropical Medicine (4.17% -6.34%), San Lazaro Hospital (14.65% -24.03%), University of the Philippines-National Institutes of Health (16.25% -44.80%), Lung Center of the Philippines (15.8% -26.40%), Baguio General Hospital Medical Center (0.58% -0.76%), The Medical City, Pasig City (5.96% -25.51%), St. Lukes Medical Center, Quezon City (1.09% -6.70%), Bicol Public Health Laboratory (0.06% -0.08%), Western Visayas Medical Center (0.71% -4.52%), Vicente Sotto Memorial Medical Center (1.02% -2.61%), and Southern Philippines Medical Center ({approx}0.01%). If there will be changes in the number of testing centers, our model can still be used to modify the test kit allocation. Our results can serve as a guide to the authorities in distributing the COVID-19 test kits. These can also be used to determine the capacity of testing centers and the effects of increasing its number. The model can also be used for proposing additional number and location of new testing centers.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Christian Alvin H Buhat", - "author_inst": "University of the Philippines Los Banos" - }, - { - "author_name": "Jessa Camille C Duero", - "author_inst": "University of the Philippines Los Banos" - }, - { - "author_name": "Edd Francis O Felix", - "author_inst": "University of the Philippines Los Banos" - }, - { - "author_name": "Jomar Fajardo Rabajante", - "author_inst": "University of the Philippines Los Banos" - }, - { - "author_name": "Jonathan B Mamplata", - "author_inst": "University of the Philippines Los Banos" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.14.20065227", "rel_title": "Model calibration, nowcasting, and operational prediction of the COVID-19 pandemic", @@ -1528102,6 +1530574,165 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.13.20060467", + "rel_title": "Neutralising antibodies to SARS coronavirus 2 in Scottish blood donors - a pilot study of the value of serology to determine population exposure", + "rel_date": "2020-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.13.20060467", + "rel_abs": "BackgroundThe progression and geographical distribution of SARS coronavirus 2 (SARS-CoV-2) infection in the UK and elsewhere is unknown because typically only symptomatic individuals are diagnosed. We performed a serological study of blood donors in Scotland between the 17th of March and the 18th of May to detect neutralising antibodies to SARS-CoV-2 as a marker of past infection and epidemic progression.\n\nAimTo determine if sera from blood bank donors can be used to track the emergence and progression of the SARS-CoV-2 epidemic.\n\nMethodsA pseudotyped SARS-CoV-2 virus microneutralisation assay was used to detect neutralising antibodies to SARS-CoV-2. The study group comprised samples from 3,500 blood donors collected in Scotland between the 17th of March and 19th of May, 2020. Controls were collected from 100 donors in Scotland during 2019.\n\nResultsAll samples collected on the 17th March, 2020 (n=500) were negative in the pseudotyped SARS-CoV-2 virus microneutralisation assay. Neutralising antibodies were detected in 6/500 donors from the 23th-26th of March. The number of samples containing neutralising antibodies did not significantly rise after the 5th-6th April until the end of the study on the 18th of May. We find that infections are concentrated in certain postcodes indicating that outbreaks of infection are extremely localised. In contrast, other areas remain comparatively untouched by the epidemic.\n\nConclusionThese data indicate that sero-surveys of blood banks can serve as a useful tool for tracking the emergence and progression of an epidemic like the current SARS-CoV-2 outbreak.", + "rel_num_authors": 36, + "rel_authors": [ + { + "author_name": "Craig P Thompson", + "author_inst": "University of Oxford" + }, + { + "author_name": "Nicholas Grayson", + "author_inst": "University of Oxford" + }, + { + "author_name": "Robert Paton", + "author_inst": "University of Oxford" + }, + { + "author_name": "Jai S Bolton", + "author_inst": "University of Oxford" + }, + { + "author_name": "Jos\u00e9 Louren\u00e7o", + "author_inst": "University of Oxford" + }, + { + "author_name": "Bridget Penman", + "author_inst": "University of Warwick" + }, + { + "author_name": "Lian Ni Lee", + "author_inst": "University of Oxford" + }, + { + "author_name": "Valerie Odon", + "author_inst": "University of Oxford" + }, + { + "author_name": "Juthathip Mongkolsapaya", + "author_inst": "University of Oxford" + }, + { + "author_name": "Senthil Chinnakannan", + "author_inst": "University of Oxford" + }, + { + "author_name": "Wanwisa Dejnirattisai", + "author_inst": "University of Oxford" + }, + { + "author_name": "Matthew Edmans", + "author_inst": "University of Oxford" + }, + { + "author_name": "Alexander Fyfe", + "author_inst": "University of Oxford" + }, + { + "author_name": "Carol Imlach", + "author_inst": "Scottish National Blood Transfusion Service" + }, + { + "author_name": "Kreepa Kooblall", + "author_inst": "University of Oxford" + }, + { + "author_name": "Nicholas Lim", + "author_inst": "University of Oxford" + }, + { + "author_name": "Chang Liu", + "author_inst": "University of Oxford" + }, + { + "author_name": "Cesar Lopez-Camacho", + "author_inst": "University of Oxford" + }, + { + "author_name": "Carol-Anne McInally", + "author_inst": "University of Oxford" + }, + { + "author_name": "Narayan Ramamurthy", + "author_inst": "University of Oxford" + }, + { + "author_name": "Jeremy Ratcliff", + "author_inst": "University of Oxford" + }, + { + "author_name": "Piyada Supasa", + "author_inst": "University of Oxford" + }, + { + "author_name": "Beibei Wang", + "author_inst": "University of Oxford" + }, + { + "author_name": "Alexander J Mentzer", + "author_inst": "University of Oxford" + }, + { + "author_name": "Marc Turner", + "author_inst": "Scottish National Blood Transfusion Service" + }, + { + "author_name": "Oliver Sampson", + "author_inst": "University of Oxford" + }, + { + "author_name": "Calum Semple", + "author_inst": "University of Liverpool" + }, + { + "author_name": "John Kenneth Baillie", + "author_inst": "University of Liverpool" + }, + { + "author_name": "- ISARIC4C Investigators", + "author_inst": "" + }, + { + "author_name": "Heli Harvala", + "author_inst": "University College London" + }, + { + "author_name": "Gavin Screaton", + "author_inst": "University of Oxford" + }, + { + "author_name": "Nigel Temperton", + "author_inst": "University of Kent" + }, + { + "author_name": "Paul Klenerman", + "author_inst": "University of Oxford" + }, + { + "author_name": "Lisa Jarvis", + "author_inst": "Scottish National Blood Transfusion Service" + }, + { + "author_name": "Sunetra Gupta", + "author_inst": "University of Oxford" + }, + { + "author_name": "Peter Simmonds", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.16.20060566", "rel_title": "Delayed clearance of SARS-CoV2 in male compared to female patients: High ACE2 expression in testes suggests possible existence of gender-specific viral reservoirs", @@ -1528650,41 +1531281,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.11.20062109", - "rel_title": "Lopinavir/ritonavir for the treatment of COVID-19: A living systematic review protocol", - "rel_date": "2020-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.11.20062109", - "rel_abs": "ObjectiveTo assess the efficacy and safety of lopinavir/ritonavir for the treatment of patients with COVID-19.\n\nDesignThis is the protocol of a living systematic review.\n\nData sourcesWe will conduct searches in PubMed/Medline, Embase, Cochrane Central Register of Controlled Trials (CENTRAL), grey literature and in a centralised repository in L{middle dot}OVE (Living OVerview of Evidence). L{middle dot}OVE is a platform that maps PICO questions to evidence from Epistemonikos database. In response to the COVID-19 emergency, L{middle dot}OVE was adapted to expand the range of evidence it covers and customised to group all COVID-19 evidence in one place. The search will cover the period until the day before submission to a journal.\n\nEligibility criteria for selecting studies and methodsWe adapted an already published common protocol for multiple parallel systematic reviews to the specificities of this question.\n\nWe will include randomised trials evaluating the effect of lopinavir/ritonavir-- as monotherapy or in combination with other drugs -- versus placebo or no treatment in patients with COVID-19. Randomised trials evaluating lopinavir/ritonavir in infections caused by other coronaviruses, such as MERS-CoV and SARS-CoV, and non-randomised studies in COVID-19 will be searched in case no direct evidence from randomised trials is found, or if the direct evidence provides low- or very low-certainty for critical outcomes.\n\nTwo reviewers will independently screen each study for eligibility, extract data, and assess the risk of bias. We will perform random-effects meta-analyses and use GRADE to assess the certainty of the evidence for each outcome.\n\nA living, web-based version of this review will be openly available during the COVID-19 pandemic. We will resubmit it if the conclusions change or there are substantial updates.\n\nEthics and disseminationNo ethics approval is considered necessary. The results of this review will be widely disseminated via peer-reviewed publications, social networks and traditional media.\n\nPROSPERO RegistrationSubmitted to PROSPERO (awaiting ID allocation).", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Francisca Verdugo-Paiva", - "author_inst": "Fundacion Epistemonikos" - }, - { - "author_name": "Ariel Izcovich", - "author_inst": "Internal Medicine Service, German Hospital, Buenos Aires, Argentina" - }, - { - "author_name": "Martin Ragusa", - "author_inst": "Internal Medicine Service, German Hospital, Buenos Aires, Argentina" - }, - { - "author_name": "Gabriel Rada", - "author_inst": "Fundacion Epistemonikos" - }, - { - "author_name": "COVID-19 L-OVE Working Group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.11.20061473", "rel_title": "An experimental trial of recombinant human interferon alpha nasal drops to prevent coronavirus disease 2019 in medical staff in an epidemic area", @@ -1529228,6 +1531824,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2020.04.11.20062257", + "rel_title": "Learning as We Go: An Examination of the Statistical Accuracy of COVID19 Daily Death Count Predictions", + "rel_date": "2020-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.11.20062257", + "rel_abs": "A recent model developed at the Institute for Health Metrics and Evaluation (IHME) provides forecasts for ventilator use and hospital beds required for the care of COVID19 patients on a state-by-state basis throughout the United States over the period March 2020 through August 2020 (See the related website https://covid19.healthdata.org/projections for interactive data visualizations). In addition, the manuscript and associated website provide projections of deaths per day and total deaths throughout this period for the entire US, as well as for the District of Columbia. This research has received extensive attention in social media, as well as in the mass media. Moreover, this work has influenced policy makers at the highest levels of the United States government, having been mentioned at White House Press conferences, including March 31, 2020.\n\nIn this paper, we evaluate the predictive validity of model forecasts for COVID19 outcomes as data become sequentially available, using the IHME prediction of daily deaths. We have found that the predictions for daily number of deaths provided by the IHME model have been highly inaccurate. The model has been found to perform poorly even when attempting to predict the number of next day deaths. In particular, the true number of next day deaths has been outside the IHME prediction intervals as much as 70% of the time.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Roman Marchant", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Noelle I Samia", + "author_inst": "Northwestern University" + }, + { + "author_name": "Ori Rosen", + "author_inst": "University of Texas at El Paso" + }, + { + "author_name": "Martin A Tanner", + "author_inst": "Northwestern University" + }, + { + "author_name": "Sally Cripps", + "author_inst": "The University of Sydney" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.04.13.20063560", "rel_title": "Knowledge and practices towards COVID-19 during its outbreak: a multinational cross-sectional study", @@ -1529868,37 +1532499,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.13.20063453", - "rel_title": "RISK ANALYSIS AND PREDICTION FOR COVID19 DEMOGRAPHICS IN LOW RESOURCE SETTINGS USING A PYTHON DESKTOP APP AND EXCEL MODELS.", - "rel_date": "2020-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.13.20063453", - "rel_abs": "While the novel covid19 disease caused by sar-cov-2 corona virus has proved a serious threat to mankind it being a pandemic, the rate at which technology in low resource income countries like Uganda has been used to predict the spread and impact of the disease in their economies has not been strongly employed. This paper presents a an excel model and desktop application software developed using open source python programming tools for carrying out risk analysis and prediction of demographics for covid19 disease. Prediction results for both models clearly stated using epidemiological curve, these results can vary based on the force of infection which varies based on government measures and actions. With a certain degree of certainty of the potential impact of the disease on low resource countries, it will foster proper planning and strategical methods to properly manage the pandemic.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Ali Kyagulanyi", - "author_inst": "Makere University Kampala" - }, - { - "author_name": "Joel Tibabwetiza Muhanguzi", - "author_inst": "Makerere University" - }, - { - "author_name": "Oscar Dembe", - "author_inst": "Makerere Univesity" - }, - { - "author_name": "Sheba Kirabo", - "author_inst": "Makerere University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.13.20063271", "rel_title": "A Predictive Model for the Evolution of COVID-19", @@ -1530406,6 +1533006,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.04.16.20067355", + "rel_title": "Do Weather Temperature and Median-age affect COVID-19 Transmission?", + "rel_date": "2020-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.16.20067355", + "rel_abs": "It was observed that the coldest countries and the eldest in terms of median-age were most distressed by COVID-19 pandemic, while the warmest countries and that have younger-aged population were the least affected. Therefore, this study utilized the non-linear least squares method to estimate the impact of weather temperatures and median age on COVID-19 cases per million in thirty-nine countries divided into two groups. The first group composed of twenty-four countries that announced the first COVID-19 case in January 2020, while the second group contains fifteen countries that witnessed the pandemic for the first time in February of the same year. The study revealed some major findings, which are: COVID-19 cases per million were not significantly affected by weather temperature or the median age in \"January-group\" countries (after 72.67 days on average), while COVID-19 cases per million increased significantly by decreasing temperatures, and increasing the median age in case of \"February-group\" countries (after an average of 44.80 days). This means that weather temperature and median age may influence the transmission rates of COVID-19 in its early stages, while weather temperature or median age no longer have effects in the advanced stages of the pandemic.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Aly Zein Elabdeen Kassem", + "author_inst": "Institute of National Planning" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.13.20064022", "rel_title": "Importance of untested infectious individuals for the suppression of COVID-19 epidemics", @@ -1530962,29 +1533581,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.12.20053926", - "rel_title": "Epidemiological characteristics of an outbreak of Coronavirus Disease 2019 in the Philippines", - "rel_date": "2020-04-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.12.20053926", - "rel_abs": "The outbreak of Coronavirus disease 2019 (Covid-2019) is a source of great concern in the Philippines. In this paper, we described the epidemiological characteristics of the laboratory-confirmed patients with Covid-2019 in the Philippines as of April 3, 2020 and provided recommendations on how to limit the spread of the disease. Data from the DOH NCOV tracker and University of the Philippines Covid-2019 tracker were extracted, from its initiation (January 30, 2020) until the most recent situation report (April 3, 2020). The total number of cases and deaths were stratified by sex, age, and region of the Philippines. Descriptive statistics were used to analyze the demographic profile of the confirmed cases. Case fatality rate, in percent, was calculated by dividing the total number of deaths to the total number of confirmed cases. Results revealed that a total of 3,018 cases of Covid-2019 spread were confirmed across 17 regions in the Philippines. These cases occurred over the course of 73 days through person-to-person transmission, highlighting an extremely high infectivity rate. The 144 deaths accounted for, equate to 4.51 case fatality rate, seemingly lower compared to its predecessors, severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), but higher compared to that of United States of America, Germany, mainland China, and neighboring Southeast Asian countries such as Malaysia, Singapore, Brunei, and Thailand. Of the 3,018 confirmed cases, majority were male, elderly, and diagnosed in Metro Manila region. Case fatality rates were higher in male and highest among elderly and Filipinos in the Ilocos region. With the surge on the number of cases, precautionary measures should remain a responsibility, and protocols for prevention need to be set. Adherence to infection control guidelines such as but not limited to frequently handwashing for at least 20 seconds, observing coughing etiquette, wearing of masks, and social distancing should be maintained in order to contain the disease.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Mark Marcos Alipio", - "author_inst": "Davao Doctors College" - }, - { - "author_name": "Joseph Dave Mendoza Pregoner", - "author_inst": "University of the Immaculate Conception" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.14.20048025", "rel_title": "Further analysis of the impact of distancing upon the COVID-19 pandemic", @@ -1531604,6 +1534200,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.11.20062133", + "rel_title": "Intervention strategies against COVID-19 and their estimated impact on Swedish healthcare capacity", + "rel_date": "2020-04-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.11.20062133", + "rel_abs": "ObjectivesDuring March 2020, the COVID-19 pandemic has rapidly spread globally, and non-pharmaceutical interventions are being used to reduce both the load on the healthcare system as well as overall mortality.\n\nDesignIndividual-based transmission modelling using Swedish demographic and Geographical Information System data and conservative COVID-19 epidemiological parameters.\n\nSettingSweden\n\nParticipantsA model to simulate all 10.09 million Swedish residents.\n\nInterventions5 different non-pharmaceutical public-health interventions including the mitigation strategy of the Swedish government as of 10 April; isolation of the entire household of confirmed cases; closure of schools and non-essential businesses with or without strict social distancing; and strict social distancing with closure of schools and non-essential businesses.\n\nMain outcome measuresEstimated acute care and intensive care hospitalisations, COVID-19 attributable deaths, and infections among healthcare workers from 10 April until 29 June.\n\nFindingsOur model for Sweden shows that, under conservative epidemiological parameter estimates, the current Swedish public-health strategy will result in a peak intensive-care load in May that exceeds pre-pandemic capacity by over 40-fold, with a median mortality of 96,000 (95% CI 52,000 to 183,000). The most stringent public-health measures examined are predicted to reduce mortality by approximately three-fold. Intensive-care load at the peak could be reduced by over two-fold with a shorter period at peak pandemic capacity.\n\nConclusionsOur results predict that, under conservative epidemiological parameter estimates, current measures in Sweden will result in at least 40-fold over-subscription of pre-pandemic Swedish intensive care capacity, with 15.8 percent of Swedish healthcare workers unable to work at the pandemic peak. Modifications to ICU admission criteria from international norms would further increase mortality.\n\nWhat is already known?- The COVID-19 pandemic has spread rapidly in Europe and globally since March 2020.\n- Mitigation and suppression methods have been suggested to slow down or halt the spread of the COVID-19 pandemic. Most European countries have enacted strict suppression measures including lockdown, school closures, enforced social distancing; while Sweden has chosen a different strategy of milder mitigation as of today (10 April 2020).\n- Different national policy decisions have been justified by socio-geographic differences among countries. Such differences as well as the tempo and stringency of public-health interventions are likely to affect the impact on each countrys mortality and healthcare system.\n\n\nWhat this study adds?- Individual-based modelling of COVID-19 spread using Swedish demographics and conservative epidemiological assumptions indicates that the peak of the number of hospitalised patients with COVID-19 can be expected in early May under the current strategy, shifted earlier and attenuated with more stringent public health measures.\n- Healthcare needs are expected to substantially exceed pre-pandemic capacity even if the most aggressive interventions considered were implemented in the coming weeks. In particular the need for intensive care unit beds will be at least 40-fold greater than the pre-pandemic capacity if the current strategy is maintained, and at least 10-fold greater if strategies approximating the most stringent in Europe are introduced by 10 April.\n- Our model predicts that, using median infection-fatality-rate estimates, at least 96,000 deaths would occur by 1 July without mitigation. Current policies reduce this number by approximately 15%, while even more aggressive social distancing measures, such as adding household isolation or mandated social distancing can reduce this number by more than 50%.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Jasmine M Gardner", + "author_inst": "Uppsala University" + }, + { + "author_name": "Lander Willem", + "author_inst": "University of Antwerp" + }, + { + "author_name": "Wouter van der Wijngaart", + "author_inst": "KTH Royal Institute of Technology" + }, + { + "author_name": "Shina Caroline Lynn Kamerlin", + "author_inst": "Uppsala University" + }, + { + "author_name": "Nele Brusselaers", + "author_inst": "Karolinska Institute" + }, + { + "author_name": "Peter Kasson", + "author_inst": "University of Virginia / Uppsala University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.11.20062190", "rel_title": "Estimating the real-time case fatality rate of COVID-19 using Poisson mixtures model", @@ -1532271,49 +1534906,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.04.10.20061291", - "rel_title": "Modifying reusable elastomeric respirators to utilise breathing system filters with 3D printed adapters, a safe alternative to N95 during COVID-19", - "rel_date": "2020-04-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.10.20061291", - "rel_abs": "The COVID-19 pandemic has caused a worldwide shortage of personal protective equipment including N95 and FFP3 respirators. Reusable elastomeric respirators are suitable alternatives when used with compatible filters. These filters may be difficult to source and elastomeric respirators are not recommended for surgical use as the exhaled air is not filtered. Breathing system filters are routinely used in anaesthetic circuits to filter virus and bacteria. In this study, we designed 3D printed adapters that allowed elastomeric respirators to utilise breathing system filters and made simple modifications to the respirators to filter exhaled breaths. We then evaluated the performance and safety of our modified elastomeric respirators with quantitative fit tests.\n\nWe recruited 8 volunteers to perform quantitative fit tests. Fit factors, respiratory rate and end-tidal carbon dioxide were recorded before and after wearing the modified respirators for 1 hour. All 8 volunteers obtained fit factors of 200+, the maximum achievable, for all tests exercises in all fit tests. The mean (range) end-tidal carbon dioxide was 4.5 (3.9-5.5) kPa and 4.6 (range 4.1-5.3) kPa before and after 1 hour of usage. The mean (range) respiratory rate was 16.5 (11-24) min-1 and 17.4 (15-22) min-1 before and after 1 hour of usage. Four (50%) did not experience any subjective discomfort while 2 (25%) reported pressure on the face, 1 (12.5%) reported exhalation resistance and 1 (12.5%) reported transient dizziness with exertion. Breathing system filters combined with properly fitted reusable elastomeric respirators is a safe alternative to N95 during the COVID-19 pandemic.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Dexter Chee Yuen Liu", - "author_inst": "United Christian Hospital, Hong Kong" - }, - { - "author_name": "Tai Hong Koo", - "author_inst": "United Christian Hospital, Hong Kong" - }, - { - "author_name": "Jackson Kai Kit Wong", - "author_inst": "United Christian Hospital, Hong Kong" - }, - { - "author_name": "Ying Hong Wong", - "author_inst": "United Christian Hospital, Hong Kong" - }, - { - "author_name": "Kitty Sau Chun Fung", - "author_inst": "United Christian Hospital, Hong Kong" - }, - { - "author_name": "Yung Chan", - "author_inst": "United Christian Hospital, Hong Kong" - }, - { - "author_name": "Huey Sing Lim", - "author_inst": "United Christian Hospital, Hong Kong" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "anesthesia" - }, { "rel_doi": "10.1101/2020.04.10.20061226", "rel_title": "An epidemiologic profile of COVID-19 patients in Vietnam", @@ -1532901,6 +1535493,29 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.04.14.041301", + "rel_title": "Phylogenetic Analysis of the Novel Coronavirus Reveals Important Variants in Indian Strains", + "rel_date": "2020-04-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.14.041301", + "rel_abs": "Recently classified as a pandemic by WHO, novel Corononavirus 2019 has affected almost every corner of the globe causing human deaths in a range of hundred thousands. The virus having its roots in Wuhan (China) has been spread over the world by its own property to change itself accordingly. These changes correspond to its transmission and pathogenicity due to which the concept of social distancing appeared into the picture. In this paper, a few findings from the whole genome sequence analysis of viral genome sequences submitted from India are presented. The data used for analysis comprises 440 collective genome sequences of virus submitted in GenBank, GISAID, and SRA projects, from around the world as well as 28 viral sequences from India. Multiple sequence alignment of all genome sequences was performed and analysed. A novel non-synonymous mutation 4809C>T (S1515F) in NSP3 gene of SARS-CoV2 Indian strains is reported along with other frequent and important changes from around the world: 3037C>T, 14408C>T, and 23403A>G. The novel change was observed in samples collected in the month of March, whereas was found to be absent in samples collected in January with the respective persons travel history to China. Phylogenetic analysis clustered the sequences with this change as one separate clade. Mutation was predicted as stabilising change by insilco tool DynaMut. A second patient in the world to our knowledge with multiple (Wuhan and USA) strain contraction was observed in this study. The infected person is among the two early infected patients with travel history to China. Strains sequenced in Iran stood out to have different variants, as most of the reported frequent variants were not observed. The objective of this paper is to highlight the similarities and changes observed in the submitted Indian viral strains. This helps to keep track on the activity, that how virus is changing into a new subtype. Major strains observed were European with the novel change in India and other being emergent clade of Iran. Its important to observe the changes in NSP3 gene, as this gene has been reported with extensive positive selection as well as potential drug target. Extensive Positive Selection Drives the Evolution of Nonstructural Proteins. With the limited number of sequences this was the only frequent novel non-synonymous change observed from Indian strains, thereby making this change vulnerable for investigation in future. This paper has a special focus on tracking of Indian viral sequences submitted in public domain.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Aditi Joshi", + "author_inst": "Indian Institute of Technology Jodhpur" + }, + { + "author_name": "Sushmita Paul", + "author_inst": "Indian Institute of Technology Jodhpur" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.04.14.041434", "rel_title": "Genetic Variability of Human Angiotensin-Converting Enzyme 2 (hACE2) Among Various Ethnic Populations", @@ -1533873,33 +1536488,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2020.04.09.20059261", - "rel_title": "COVID-19 in India: Predictions, Reproduction Number and Public Health Preparedness", - "rel_date": "2020-04-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20059261", - "rel_abs": "IntroductionThe COVID-19 has emerged as a global concern for public health due to large scale outbreak. The number of confirmed cases has also been increased in India in past few weeks. The predictions for the COVID-19 can provide insights into the epidemiology of the disease, which helps policymakers to check health system capacities.\n\nMethodsWe obtained data on daily confirmed, recovered and deaths cases for a period of 21 days and have implemented the exponential growth model to predict the future cases for all the three components. The mathematical model was used to calculate the average reproduction number and herd immunity. We estimated the number of active cases till 30th of April. We have also tried to analyze the public health capacity to combat COVID-19 in India.\n\nResultsIf the exponential growth in number of cases continue then the total number of active cases will be 2,49,635 until the end of April. The reproduction number for COVID-19 in India was found to be 2.56 and herd immunity as 61%. The cumulative cases predicted by the mathematical model was 1,20,203.\n\nDiscussionThis prediction provides an alarming situation for India in terms of public health preparedness. The number of tests is needed to increase to detect all the cases of COVID-19 in India. Though some serious preventive measures have been implemented, but India should be ready to face any sudden community outbreak.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Balram Rai", - "author_inst": "International Institute for Population Sciences" - }, - { - "author_name": "Anandi Shukla", - "author_inst": "IIPS Mumbai" - }, - { - "author_name": "Laxmi Kant Dwivedi", - "author_inst": "International Institute for Population Sciences" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.04.09.20059329", "rel_title": "A Recursive Bifurcation Model for Predicting the Peak of COVID-19 Virus Spread in United States and Germany", @@ -1534343,6 +1536931,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.09.20059436", + "rel_title": "New approximations, and policy implications, from a delayed dynamic model of a fast pandemic", + "rel_date": "2020-04-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20059436", + "rel_abs": "We study an SEIQR (Susceptible-Exposed-Infectious-Quarantined-Recovered) model for an infectious disease, with time delays for latency and an asymptomatic phase. For fast pandemics where nobody has prior immunity and everyone has immunity after recovery, the SEIQR model decouples into two nonlinear delay differential equations (DDEs) with five parameters. One parameter is set to unity by scaling time. The subcase of perfect quarantining and zero self-recovery before quarantine, with two free parameters, is examined first. The method of multiple scales yields a hyperbolic tangent solution; and a long-wave approximation yields a first order ordinary differential equation (ODE). With imperfect quarantining and nonzero self-recovery, the long-wave approximation is a second order ODE. These three approximations each capture the full outbreak, from infinitesimal initiation to final saturation. Low-dimensional dynamics in the DDEs is demonstrated using a six state non-delayed reduced order model obtained by Galerkin projection. Numerical solutions from the reduced order model match the DDE over a range of parameter choices and initial conditions. Finally, stability analysis and numerics show how correctly executed time-varying social distancing, within the present model, can cut the number of affected people by almost half. Alternatively, faster detection followed by near-certain quarantining can potentially be even more effective.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Chandrika Prakash Vyasarayani", + "author_inst": "Indian Institute of Technology Hyderabad" + }, + { + "author_name": "Anindya Chatterjee", + "author_inst": "Indian Institute of Technology Kanpur" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.09.20059592", "rel_title": "Between Geography and Demography: Key Interdependencies and Exit Mechanisms for Covid-19", @@ -1534987,45 +1537598,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.09.20047498", - "rel_title": "An agent-based epidemic model REINA for COVID-19 to identify destructive policies", - "rel_date": "2020-04-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20047498", - "rel_abs": "BackgroundCountries have adopted disparate policies in tackling the COVID-19 coronavirus pandemic. For example, South Korea started a vigorous campaign to suppress the virus by testing patients with respiratory symptoms and tracing and isolating all their contacts, and many European countries are trying to slow down the spread of the virus with varying degrees of shutdowns. There is clearly a need for a model that can realistically simulate different policy actions and their impacts on the disease and health care capacity in a country or a region. Specifically, there is a need to identify destructive policies, i.e. policies that are, based on scientific knowledge, worse than an alternative and should not be implemented.\n\nMethodsWe developed an agent-based model (REINA) using Python and accelerated it by the Cython optimising static compiler. It follows a population over time at individual level at different stages of the disease and estimates the number of patients in hospitals and in intensive care. It estimates death rates and counts based on the treatment available. Any number of interventions can be added on the timeline from a selection including e.g. physical isolation, testing and tracing, and controlling the amount of cases entering the area. The model has open source code and runs online.\n\nResultsThe model uses the demographics of the Helsinki University Hospital region (1.6 million inhabitants). A mitigation strategy aims to slow down the spread of the epidemic to maintain the hospital capacity by implementing mobility restrictions. A suppression strategy initially consists of the same restrictions but also aggressive testing, tracing, and isolating all coronavirus positive patients and their contacts. The modelling starting point is 2020-02-18. The strategies follow the actual situation until 2020-04-06 and then diverge. The default mitigation scenario with variable 30-40% mobility reduction appears to delay the peak of the epidemic (as intended) but not suppress the disease. In the suppression strategy, active testing and tracing of patients with symptoms and their contacts is implemented in addition to 20-25% mobility reduction. This results in a reduction of the cumulative number of infected individuals from 820 000 to 80 000 and the number of deaths from 6000 to only 640, when compared with the mitigation strategy (during the first year of the epidemic).\n\nDiscussionThe agent-based model (REINA) can be used to simulate epidemic outcomes for various types of policy actions on a timeline. Our results lend support to the strategy of combining comprehensive testing, contact tracing and targeted isolation measures with social isolation measures. While social isolation is important in the early stages to prevent explosive growth, relying on social isolation alone (the mitigation strategy) appears to be a destructive policy. The open-source nature of the model facilitates rapid further development. The flexibility of the modelling logic supports the future implementation of several already identified refinements in terms of more realistic population models and new types of more specific policy interventions. Improving estimates of epidemic parameters will make it possible to improve modelling accuracy further.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Jouni T Tuomisto", - "author_inst": "Finnish Institute for Health and Welfare" - }, - { - "author_name": "Juha Yrj\u00f6l\u00e4", - "author_inst": "Kausal Ltd" - }, - { - "author_name": "Mikko Kolehmainen", - "author_inst": "University of Eastern Finland" - }, - { - "author_name": "Juhani Bonsdorff", - "author_inst": "Stretta Capital Ltd" - }, - { - "author_name": "Jami Pekkanen", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Tero Tikkanen", - "author_inst": "Kausal Ltd" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.09.20056259", "rel_title": "Excess cases of influenza suggest an earlier start to the coronavirus epidemic in Spain than official figures tell us: an analysis of primary care electronic medical records from over 6 million people from Catalonia", @@ -1535705,6 +1538277,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, + { + "rel_doi": "10.1101/2020.04.06.027698", + "rel_title": "Genetic variability in the expression of the SARS-CoV-2 host cell entry factors across populations", + "rel_date": "2020-04-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.06.027698", + "rel_abs": "The entry of SARS-CoV-2 into host cells is dependent upon angiotensin-converting enzyme 2 (ACE2), which serves as a functional attachment receptor for the viral spike glycoprotein, and the serine protease TMPRSS2 which allows fusion of the viral and host cell membranes. We devised a quantitative measure to estimate genetic determinants of ACE2 and TMPRSS2 expression and applied this measure to >2,500 individuals. Our data show significant variability in genetic determinants of ACE2 and TMPRSS2 expression among individuals and between populations, and demonstrate a genetic predisposition for lower expression levels of both key viral entry genes in African populations. These data suggest that genetic factors might lead to lower susceptibility for SARS-CoV-2 infection in African populations and that host genetics might help explain inter-individual variability in disease susceptibility and severity of COVID-19.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Lourdes Ortiz-Fernandez", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Amr H Sawalha", + "author_inst": "University of Pittsburgh" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.04.10.20060301", "rel_title": "Should contact bans be lifted in Germany? A quantitative prediction of its effects", @@ -1536537,57 +1539132,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.04.10.20060426", - "rel_title": "Estimating required lockdown cycles before immunity to SARS-CoV-2: Model-based analyses of susceptible population sizes, S0, in seven European countries including the UK and Ireland", - "rel_date": "2020-04-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.10.20060426", - "rel_abs": "BackgroundFollowing stringent social distancing measures, some European countries are beginning to report a slowed or negative rate of growth of daily case numbers testing positive for the novel coronavirus. The notion that the first wave of infection is close to its peak begs the question of whether future peaks or second waves are likely. We sought to determine the current size of the effective (i.e. susceptible) population for seven European countries--to estimate immunity levels following this first wave. We compare these numbers to the total population sizes of these countries, in order to investigate the potential for future peaks.\n\nMethodsWe used Bayesian model inversion to estimate epidemic parameters from the reported case and death rates from seven countries using data from late January 2020 to April 5th 2020. Two distinct generative model types were employed: first a continuous time dynamical-systems implementation of a Susceptible-Exposed-Infectious-Recovered (SEIR) model and second: a partially observable Markov Decision Process (MDP) or hidden Markov model (HMM) implementation of an SEIR model. Both models parameterise the size of the initial susceptible population ( S0), as well as epidemic parameters. Parameter estimation ( data fitting) was performed using a standard Bayesian scheme (variational Laplace) designed to allow for latent unobservable states and uncertainty in model parameters.\n\nResultsBoth models recapitulated the dynamics of transmissions and disease as given by case and death rates. The peaks of the current waves were predicted to be in the past for four countries (Italy, Spain, Germany and Switzerland) and to emerge in 0.5 - 2 weeks in Ireland and 1-3 weeks in the UK. For France one model estimated the peak within the past week and the other in the future in two weeks. Crucially, Maximum a posteriori (MAP) estimates of S0 for each country indicated effective population sizes of below 20% (of total population size), under both the continuous time and HMM models. Using for all countries--with a Bayesian weighted average across all seven countries and both models, we estimated that 6.4% of the total population would be immune. From the two models the maximum percentage of the effective population was estimated at 19.6% of the total population for the UK, 16.7% for Ireland, 11.4% for Italy, 12.8% for Spain, 18.8% for France, 4.7% for Germany and 12.9% for Switzerland.\n\nConclusionOur results indicate that after the current wave, a large proportion of the total population will remain without immunity. This suggests that in the absence of strong seasonal effects, new medications or more comprehensive contact tracing, a further set of epidemic waves in different geographic centres are likely. These findings may have implications for exit strategies from any lockdown stage.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Rosalyn J Moran", - "author_inst": "King's College London" - }, - { - "author_name": "Erik D Fagerholm", - "author_inst": "King's College London" - }, - { - "author_name": "Jean Daunizeau", - "author_inst": "INSERM" - }, - { - "author_name": "Maell Cullen", - "author_inst": "King's College London" - }, - { - "author_name": "Mark P Richardson", - "author_inst": "King's College London" - }, - { - "author_name": "Steven Williams", - "author_inst": "King's College London" - }, - { - "author_name": "Federico Turkheimer", - "author_inst": "King's College London" - }, - { - "author_name": "Rob Leech", - "author_inst": "King's College London" - }, - { - "author_name": "Karl Friston", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.10.036343", "rel_title": "CoV Genome Tracker: tracing genomic footprints of Covid-19 pandemic", @@ -1537239,6 +1539783,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.09.20060202", + "rel_title": "Do latitude and ozone concentration predict Covid-2019 cases in 34 countries?", + "rel_date": "2020-04-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20060202", + "rel_abs": "In this paper, I used multivariate linear regression analysis to determine if latitude and ozone concentration predict Covid-2019 cases in 34 countries worldwide. Data pertaining to Covid-2019 cases were extracted from Worldometer. Ozone concentration levels were taken from the open-access database of World Ozone and Ultraviolet Radiation Data Centre (WOUDC). Latitude of specific area where measurement took place was also provided in the database. Preliminary Kendall rank correlation test revealed that Covid-2019 incidence was positively and significantly related to ozone concentration; however, incidence was not significantly related to latitude. Using multivariate linear regression, a statistically significant link between ozone concentration and Covid-2019 incidence in 34 countries was established; however, I found no statistical association between latitude and Covid-2019 incidence refuting previous claims. Prompt health actions should be developed for areas with high ozone concentration in the present and possibly, future outbreaks; however, extensive laboratory analysis should be conducted to further confirm the findings of the study. Nevertheless, the results of this study could serve as a basis for further clinical and large-scale studies.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Mark Marcos Alipio", + "author_inst": "Davao Doctors College" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.09.20058594", "rel_title": "Preliminary study to identify severe from moderate cases of COVID-19 using NLR&RDW-SD combination parameter", @@ -1537979,41 +1540542,6 @@ "type": "new results", "category": "scientific communication and education" }, - { - "rel_doi": "10.1101/2020.04.09.034462", - "rel_title": "Insights on early mutational events in SARS-CoV-2 virus reveal founder effects across geographical regions", - "rel_date": "2020-04-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.09.034462", - "rel_abs": "Here we aim to describe early mutational events across samples from publicly available SARS-CoV-2 sequences from the sequence read archive repository. Up until March 27, 2020, we downloaded 53 illumina datasets, mostly from China, USA (Washington DC) and Australia (Victoria). Of 30 high quality datasets, 27 datasets (90%) contain at least a single founder mutation and most of the variants are missense (over 63%). Five-point mutations with clonal (founder) effect were found in USA sequencing samples. Sequencing samples from USA in GenBank present this signature with 50% allele frequencies among samples. Australian mutation signatures were more diverse than USA samples, but still, clonal events were found in those samples. Mutations in the helicase and orf1a coding regions from SARS-CoV-2 were predominant, among others, suggesting that these proteins are prone to evolve by natural selection. Finally, we firmly urge that primer sets for diagnosis be carefully designed, since rapidly occurring variants would affect the performance of the reverse transcribed quantitative PCR (RT-qPCR) based viral testing.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Carlos Farkas", - "author_inst": "Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, Manitoba, Canada" - }, - { - "author_name": "Francisco Fuentes-Villalobos", - "author_inst": "Faculty of Biological Sciences, Department of Microbiology, Center of Biotechnology, Universidad de Concepci\u00f3n, 4070386 Concepci\u00f3n, Chile" - }, - { - "author_name": "Jose Luis Garrido", - "author_inst": "Ichor Biologics LLC, New York, NY 10065, USA." - }, - { - "author_name": "Jody J Haigh", - "author_inst": "Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, Manitoba, Canada" - }, - { - "author_name": "Mar\u00eda In\u00e9s Barr\u00eda", - "author_inst": "Faculty of Biological Sciences, Department of Microbiology, Center of Biotechnology, Universidad de Concepci\u00f3n, 4070386 Concepci\u00f3n, Chile" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.04.11.037382", "rel_title": "Sequence, infectivity and replication kinetics of SARS-CoV-2 isolated from COVID-19 patients in Canada", @@ -1538637,6 +1541165,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.04.06.20056127", + "rel_title": "Prediction of the clinical outcome of COVID-19 patients using T lymphocyte subsets with 340 cases from Wuhan, China: a retrospective cohort study and a web visualization tool", + "rel_date": "2020-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.06.20056127", + "rel_abs": "BackgroundWuhan, China was the epicenter of the 2019 coronavirus outbreak. As a designated hospital, Wuhan Pulmonary Hospital has received over 700 COVID-19 patients. With the COVID-19 becoming a pandemic all over the world, we aim to share our epidemiological and clinical findings with the global community.\n\nMethodsIn this retrospective cohort study, we studied 340 confirmed COVID-19 patients from Wuhan Pulmonary Hospital, including 310 discharged cases and 30 death cases. We analyzed their demographic, epidemiological, clinical and laboratory data and implemented our findings into an interactive, free access web application.\n\nFindingsBaseline T lymphocyte Subsets differed significantly between the discharged cases and the death cases in two-sample t-tests: Total T cells (p < 2{middle dot}2e-16), Helper T cells (p < 2{middle dot}2e-16), Suppressor T cells (p = 1{middle dot}8-14), and TH/TS (Helper/Suppressor ratio, p = 0{middle dot}0066). Multivariate logistic regression model with death or discharge as the outcome resulted in the following significant predictors: age (OR 1{middle dot}05, p 0{middle dot}04), underlying disease status (OR 3{middle dot}42, p 0{middle dot}02), Helper T cells on the log scale (OR 0{middle dot}22, p 0{middle dot}00), and TH/TS on the log scale (OR 4{middle dot}80, p 0{middle dot}00). The McFadden pseudo R-squared for the logistic regression model is 0{middle dot}35, suggesting the model has a fair predictive power.\n\nInterpretationWhile age and underlying diseases are known risk factors for poor prognosis, patients with a less damaged immune system at the time of hospitalization had higher chance of recovery. Close monitoring of the T lymphocyte subsets might provide valuable information of the patients condition change during the treatment process. Our web visualization application can be used as a supplementary tool for the evaluation.\n\nFundingThe authors report no funding.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Qibin Liu", + "author_inst": "Wuhan Pulmonary Hospital" + }, + { + "author_name": "Xuemin Fang", + "author_inst": "Graduate School of Health Innovation, Kanagawa University of Human Services" + }, + { + "author_name": "Shinichi Tokuno", + "author_inst": "Graduate School of Health Innovation, Kanagawa University of Human Services" + }, + { + "author_name": "Ungil Chung", + "author_inst": "Graduate School of Health Innovation, Kanagawa University of Human Services" + }, + { + "author_name": "Xianxiang Chen", + "author_inst": "Wuhan Pulmonary Hospital" + }, + { + "author_name": "Xiyong Dai", + "author_inst": "Wuhan Pulmonary Hospital" + }, + { + "author_name": "Xiaoyu Liu", + "author_inst": "Wuhan Pulmonary Hospital" + }, + { + "author_name": "Feng Xu", + "author_inst": "Wuhan Pulmonary Hospital" + }, + { + "author_name": "Bing Wang", + "author_inst": "Wuhan Pulmonary Hospital" + }, + { + "author_name": "Peng Peng", + "author_inst": "Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.06.20055582", "rel_title": "Estimates of the Undetected Rate among the SARS-CoV-2 Infected using Testing Data from Iceland", @@ -1539165,37 +1541748,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.04.06.20055988", - "rel_title": "ESTIMATING COVID-19 INFECTIONS IN HOSPITAL WORKERS IN THE UNITED STATES", - "rel_date": "2020-04-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.06.20055988", - "rel_abs": "ObjectiveWe estimated that how many hospital workers in the United States (US) might get infected or die in the COVID-19 pandemic. We also estimated the impact of personal protective equipment (PPE) and age restrictions on these estimates.\n\nMethodsOur secondary analyses estimated hospital worker infections in the US based on health worker infection and death rates per 100 deaths from COVID-19 in Hubei and Italy. We used Monte Carlo simulations to compute point estimates with 95% confidence intervals for hospital worker infections in the US based on the two scenarios. We computed potential decrease in infections if the PPE were available only to those involved in direct care of COVID-19 patients ([~] 30%) and if workers aged [≥] 60 years are restricted from patient care. Estimates were adjusted for hospital workers per bed in the US compared to China and Italy.\n\nResultsThe hospital worker infections per 100 deaths were 108.2 in Hubei and 94.1 in Italy. Based on Hubei scenario, we estimated that about 53,640 US hospital workers (95% CI: 43,160 to 62,251) might get infected from COVID-19. The Italian scenario suggested 53,097 US hospital worker (95% CI: 37,133 to 69,003) might get infected during the pandemic. Availability of PPE to high-risk workers could reduce counts to 28,100 (95% CI: 23,048 to 33,242) considering Hubei and to 28,354 (95% CI: 19,829 to 36,848) considering Italy. Restricting hospital workers aged [≥] 60 years from direct patient care reduced counts to 1,985 (95% CI: 1,627 to 2,347) considering Hubei and to 2,002 (95% CI: 1,400 to 2,602) considering the Italian scenario.\n\nConclusionWe estimated significant burden of illness due to COVID-19 if no strategies are adopted. Making PPE available to all hospital workers and reducing exposure of hospital workers above the age of 60 could have significant reductions in hospital worker infections.\n\nVISUAL ABSTRACT\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=118 SRC=\"FIGDIR/small/20055988v1_fig1.gif\" ALT=\"Figure 1\">\nView larger version (16K):\norg.highwire.dtl.DTLVardef@1a107c7org.highwire.dtl.DTLVardef@105ad1dorg.highwire.dtl.DTLVardef@1a883dcorg.highwire.dtl.DTLVardef@69108d_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO Estimated number of COVID-19 related infections among healthcare workers in the United States based on Hubei and Italian scenarios\n\nC_FIG", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Junaid A Razzak", - "author_inst": "John Hopkins University School of Medicine" - }, - { - "author_name": "Junaid Ahmad Bhatti", - "author_inst": "Independent Researcher" - }, - { - "author_name": "Muhammad Ramzan Tahir", - "author_inst": "Apotex Inc." - }, - { - "author_name": "Omrana Pasha-Razzak", - "author_inst": "Penn State Hershey Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.06.20055665", "rel_title": "Delivering oxygen-enriched CPAP respiratory support using a non-invasive ventilation device", @@ -1539927,6 +1542479,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.08.20055731", + "rel_title": "High-throughput extraction of SARS-CoV-2 RNA from nasopharyngeal swabs using solid-phase reverse immobilization beads", + "rel_date": "2020-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.08.20055731", + "rel_abs": "The ongoing pandemic of the novel coronavirus, SARS-CoV-2, has led to a global surge in laboratory testing for the virus. The gold standard approach to detecting an active viral infection is the use of RT-qPCR. This approach requires the isolation of viral RNA from respiratory specimens, such as nasopharyngeal swabs.\n\nWe developed a method using a widely available lysis buffer coupled with solid-phase reverse immobilization (SPRI) beads to extract viral RNA from swabs collected in viral transport medium (VTM) which can be performed manually or on a Hamilton STAR liquid-handling robot. Using a WHO recommended, laboratory-developed RT-qPCR for SARS-CoV-2, we validated this method in a CAP-accredited laboratory, against the IVD-labelled bioMerieux NucliSENS easyMAG automated extraction platform.\n\nOur method demonstrates a comparable sensitivity and specificity, making it suitable for large-scale testing and monitoring of suspected COVID-19 cases and health care workers. This is especially important as the world faces critical shortages of viral RNA extraction reagents for the existing commercial extraction systems.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Mahesh K R Kalikiri", + "author_inst": "Sidra Medicine" + }, + { + "author_name": "Mohammad Rubayet Hasan", + "author_inst": "Sidra Medicine" + }, + { + "author_name": "Faheem Mirza", + "author_inst": "Sidra Medicine" + }, + { + "author_name": "Thabisile Xaba", + "author_inst": "Sidra Medicine" + }, + { + "author_name": "Patrick Tang", + "author_inst": "Sidra Medicine" + }, + { + "author_name": "Stephan Lorenz", + "author_inst": "Sidra Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.06.20055624", "rel_title": "To mask or not to mask: Modeling the potential for face mask use by the general public to curtail the COVID-19 pandemic", @@ -1540519,33 +1543110,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.09.034868", - "rel_title": "De novo design of high-affinity antibody variable regions (scFv) against the SARS-CoV-2 spike protein", - "rel_date": "2020-04-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.09.034868", - "rel_abs": "The emergence of SARS-CoV-2 is responsible for the pandemic of respiratory disease known as COVID-19, which emerged in the city of Wuhan, Hubei province, China in late 2019. Both vaccines and targeted therapeutics for treatment of this disease are currently lacking. Viral entry requires binding of the viral spike receptor binding domain (RBD) with the human angiotensin converting enzyme (hACE2). In an earlier paper1, we report on the specific residue interactions underpinning this event. Here we report on the de novo computational design of high affinity antibody variable regions through the recombination of VDJ genes targeting the most solvent-exposed hACE2-binding residues of the SARS-CoV-2 spike protein using the software tool OptMAVEn-2.02. Subsequently, we carry out computational affinity maturation of the designed prototype variable regions through point mutations for improved binding with the target epitope. Immunogenicity was restricted by preferring designs that match sequences from a 9-mer library of \"human antibodies\" based on H-score (human string content, HSC)3. We generated 106 different designs and report in detail on the top five that trade-off the greatest affinity for the spike RBD epitope (quantified using the Rosetta binding energies) with low H-scores. By grafting the designed Heavy (VH) and Light (VL) chain variable regions onto a human framework (Fc), high-affinity and potentially neutralizing full-length monoclonal antibodies (mAb) can be constructed. Having a potent antibody that can recognize the viral spike protein with high affinity would be enabling for both the design of sensitive SARS-CoV-2 detection devices and for their deployment as therapeutic antibodies.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Veda Sheersh Boorla", - "author_inst": "The Pennsylvania State University" - }, - { - "author_name": "Ratul Chowdhury", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Costas D Maranas", - "author_inst": "The Pennsylvania State University" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.04.09.20058909", "rel_title": "Classification of COVID-19 in intensive care patients: towards rational and effective clinical triage", @@ -1541049,6 +1543613,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.11.034603", + "rel_title": "Cell-Type-Specific Expression of Renin-Angiotensin-System Components in the Human Body and Its Relevance to SARS-CoV-2 Infection", + "rel_date": "2020-04-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.11.034603", + "rel_abs": "We have analyzed the cell-type-specific expression of the renin-angiotensin system (RAS) components across 141 cell types or subtypes as defined by single-cell RNA-seq (scRNA-seq) analysis. ACE2, one of the components of RAS, also facilitates SARS-CoV-2 entry into cells in cooperation with its associated protease TMPRSS2. Therefore, our analysis also contributes to the understanding of SARS-CoV-2 infection, spreading of the virus throughout the body, and potential viral interference with RAS in COVID-19 patients.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Hemant Suryawanshi", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Pavel Morozov", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Thomas Tuschl", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Thangamani Muthukumar", + "author_inst": "Weill Cornell Medical College" + }, + { + "author_name": "Benjamin R. tenOever", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Zev Williams", + "author_inst": "Columbia University Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.04.08.20058719", "rel_title": "Temporal rise in the proportion of both younger adults and older adolescents among COVID-19 cases in Germany: evidence of lesser adherence to social distancing practices?", @@ -1541820,29 +1544423,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.07.20056754", - "rel_title": "Applying the unified models of ecology to forecast epidemics, with application to Covid-19", - "rel_date": "2020-04-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.07.20056754", - "rel_abs": "During a burgeoning outbreak of a novel disease, public attention will ordinarily expand as the severity of the outbreak expands--as infections multiply and news reports accumulate. Such public attention will in turn reinforce tactics to control the outbreak. In classical epidemiological models, effects of such tactics can be incorporated in standard parameters of transmission, recovery, and mortality. Unfortunately, early in an outbreak those individual parameters may be poorly known, hence corresponding models can get lost in uncertainty. This makes it difficult to determine whether the disease is spreading exponentially or logistically, or along another path. Examining cases over time is also problematic, as a logistically growing infection that is leveling off appears exponential in early phases. Here we report on the most basic mechanistic, ecological model we can imagine, which can help distinguish growth that is and is not under control. This approach did a satisfactory job predicting the final outcome of the Ebola outbreak of 2014-15. The models two parameters were computable in real time, well before the outcome was actually known. The first parameter is an intrinsic rate of increase in cumulative deaths or reported cases. The second parameter is related to the human social system and represents all tactics that combine to control the outbreak. That parameter is coupled to the number of cumulative deaths or cases. We examine the basic mechanisms operating in this model and show the predictions made during the Ebola outbreak. We also consider how this basic model is performing for the Covid-19 pandemic and highlight ecological models that align with popularly discussed concepts such as flatten-the-curve, exponential growth, and inflection points of curves.\n\nHighlightsO_LIWe exhibit a macroscale model that includes a biological pathogen-growth factor and an ecological social-response factor.\nC_LIO_LIAll parameters in the model are designed to be measurable from publicly available data.\nC_LIO_LIEarly in the 2014-15 Ebola outbreak the model accurately predicted the final number of deaths.\nC_LIO_LIThe same model displays a low chance of 100,000 deaths or more in the United States if strong measures continue and expand.\nC_LI", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Shelby W Loberg", - "author_inst": "University of Minnesota Morris" - }, - { - "author_name": "Clarence Lehman", - "author_inst": "University of Minnesota Twin Cities" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.08.20058073", "rel_title": "Testing the association between blood type and COVID-19 infection, intubation, and death", @@ -1542270,6 +1544850,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.08.20057968", + "rel_title": "Assessing the risks of \"infodemics\" in response to COVID-19 epidemics", + "rel_date": "2020-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.08.20057968", + "rel_abs": "Our society is built on a complex web of interdependencies whose effects become manifest during extraordinary events such as the COVID-19 pandemic, with shocks in one system propagating to the others to an exceptional extent. We analyzed more than 100 millions Twitter messages posted worldwide in 64 languages during the epidemic emergency due to SARS-CoV-2 and classified the reliability of news diffused. We found that waves of unreliable and low-quality information anticipate the epidemic ones, exposing entire countries to irrational social behavior and serious threats for public health. When the epidemics hit the same area, reliable information is quickly inoculated, like antibodies, and the system shifts focus towards certified informational sources. Contrary to mainstream beliefs, we show that human response to falsehood exhibits early-warning signals that might be mitigated with adequate communication strategies.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Riccardo Gallotti", + "author_inst": "Fondazione Bruno Kessler" + }, + { + "author_name": "Francesco Valle", + "author_inst": "Fondazione Bruno Kessler" + }, + { + "author_name": "Nicola Castaldo", + "author_inst": "Fondazione Bruno Kessler" + }, + { + "author_name": "Pierluigi Sacco", + "author_inst": "IULM University & Berkman-Klein Center for Internet & Society, Harvard University" + }, + { + "author_name": "Manlio De Domenico", + "author_inst": "Fondazione Bruno Kessler" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.08.20058164", "rel_title": "Is the spread of COVID-19 across countries influenced by environmental, economic and social factors?", @@ -1542930,33 +1545545,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.09.20056242", - "rel_title": "Liver injury is associated with severe Coronavirus disease 2019 (COVID-19) infection: a systematic review and meta-analysis of retrospective studies", - "rel_date": "2020-04-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20056242", - "rel_abs": "AimThe Coronavirus disease 2019 (COVID-19) outbreak is a major threat to human beings. Lung injury has been reported as the major outcome of COVID-19 infection. However, liver damage has also been considered to occur in severe cases. Current meta-analysis of retrospective studies was done to summarize available findings on the association between liver injury and severity of COVID-19 infection.\n\nMethodsOnline databases including PubMed, Scopus, Web of Science and Cochrane Library were searched to detect relevant publications up to 1 April 2020, using relevant keywords. To pool data, a fixed- or random-effects model was used depending on the heterogeneity between studies. Furthermore, publication bias test and sensitivity analysis were also done.\n\nResultsIn total, 20 retrospective studies with 3,428 COVID-19 infected patients (severe cases = 1,455 and mild cases = 1,973), were included in this meta-analysis. Higher serum levels of Aspartate aminotransferase (weighted mean difference = 8.84 U/L, 95% CI = 5.97 to 11.71, P<0.001), Alanine aminotransferase (weighted mean difference = 7.35 U/L, 95% CI = 4.77 to 9.93, P<0.001), total Bilirubin (weighted mean difference = 2.30 mmol/L, 95% CI = 1.24 to 3.36, P<0.001) and lower serum levels of Albumin (weighted mean difference = -4.24 g/L, 95% CI = -6.20 to -2.28, P<0.001), were associated with a significant increase in the severity of COVID-19 infection.\n\nConclusionsThe incidence of liver injury seems to be higher in patients with severe COVID-19 infection. This finding could help physicians to identify patients with poor prognosis at an early stage.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Mohammad Parohan", - "author_inst": "Tehran University of Medical Sciences" - }, - { - "author_name": "Sajad Yaghoubi", - "author_inst": "Iranshahr University of Medical Sciences" - }, - { - "author_name": "Asal Seraj", - "author_inst": "Islamic Azad University, Damavand Branch" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.05.20054346", "rel_title": "The Framework for the Prediction of the Critical Turning Period for Outbreak of COVID-19 Spread in China based on the iSEIR Model", @@ -1543524,6 +1546112,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.07.20051474", + "rel_title": "Variation in False Negative Rate of RT-PCR Based SARS-CoV-2 Tests by Time Since Exposure", + "rel_date": "2020-04-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.07.20051474", + "rel_abs": "SARS-CoV-2 RT-PCR based tests are being used to \"rule out\" infection among high-risk individuals such as exposed inpatients and healthcare workers. It is critical to understand how the predictive value of the test varies with time from exposure and symptom onset in order to avoid being falsely reassured by negative tests. As such, the goal of our study was to estimate the false negative rate by day since infection. We used previously published data on RT-PCR sensitivity on samples derived from nasal swabs by day since symptom onset (n=633) and fit a cubic polynomial spline to calculate the false negative rate by day since exposure and symptom onset. Over the four days of infection prior to the typical time of symptom onset (day 5) the probability of a false negative test in an infected individual falls from 100% on day one (95% CI 69-100%) to 61% on day four (95% CI 18-98%), though there is considerable uncertainty in these numbers. On the day of symptom onset, the median false negative rate was 39% (95% CI 16-77%). This decreased to 26% (95% CI 18-34%) on day 8 (3 days after symptom onset), then began to rise again, from 27% (95% CI 20-34%) on day 9 to 61% (95% CI 54-67%) on day 21. Care must be taken when interpreting RT-PCR tests for SARS-CoV-2 infection, particularly if performed early in the course of infection, when using these results as a basis for removing precautions intended to prevent onward transmission. If there is high clinical suspicion, patients should not be ruled out on the basis of RT-PCR alone, and the clinical and epidemiologic situation should be carefully considered.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Lauren Kucirka", + "author_inst": "Johns Hopkins School of Medicine" + }, + { + "author_name": "Stephen Lauer", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Oliver Laeyendecker", + "author_inst": "Johns Hopkins School of Medicine" + }, + { + "author_name": "Denali Boon", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Justin Lessler", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.07.20051060", "rel_title": "The respiratory sound features of COVID-19 patients fill gaps between clinical data and screening methods", @@ -1544140,53 +1546763,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2020.04.06.028902", - "rel_title": "Optimization of SARS-CoV-2 detection by RT-QPCR without RNA extraction", - "rel_date": "2020-04-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.06.028902", - "rel_abs": "Rapid and reliable screening of SARS-CoV-2 is fundamental to assess viral spread and limit the pandemic we are facing. In this study we evaluated the reliability and the efficiency of a direct RT-QPCR method (without RNA extraction) using SeeGene Allplex 2019-nCoV RT-QPCR and the influence of swab storage media composition on further viral detection.\n\nWe show that SeeGenes assay provides similar efficiency as the RealStar(R) SARS-CoV-2 RT-PCR kit (Altona Diagnostics), and that RNA extraction is not necessary nor advantageous if samples are stored in UTM or molecular water but is recommended if samples are stored in saline solution and in Hanks medium.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Natacha Merindol", - "author_inst": "Universit\u00e9 du Qu\u00e9bec \u00e0 Trois-Rivi\u00e8res" - }, - { - "author_name": "Genevi\u00e8ve P\u00e9pin", - "author_inst": "Universit\u00e9 du Qu\u00e9bec \u00e0 Trois-Rivi\u00e8res" - }, - { - "author_name": "Caroline Marchand", - "author_inst": "Centre Int\u00e9gr\u00e9 Universitaire de sant\u00e9 et services sociaux de la Mauricie et Centre du Qu\u00e9bec" - }, - { - "author_name": "Maryl\u00e8ne Rheault", - "author_inst": "Centre Int\u00e9gr\u00e9 Universitaire de sant\u00e9 et services sociaux de la Mauricie et Centre du Qu\u00e9bec" - }, - { - "author_name": "Christine Peterson", - "author_inst": "Centre Int\u00e9gr\u00e9 Universitaire de sant\u00e9 et services sociaux de la Mauricie et Centre du Qu\u00e9bec" - }, - { - "author_name": "Andre Poirier", - "author_inst": "Centre de sante et de services sociaux de Trois-Rivieres" - }, - { - "author_name": "Hugo Germain", - "author_inst": "Universit\u00e9 du Qu\u00e9bec \u00e0 Trois-Rivi\u00e8res" - }, - { - "author_name": "Alexis Danylo", - "author_inst": "Centre Int\u00e9gr\u00e9 Universitaire de sant\u00e9 et services sociaux de la Mauricie et Centre du Qu\u00e9bec" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2020.04.07.20056994", "rel_title": "Further Evidence of a Possible Correlation Between the Severity of Covid-19 and BCG Immunization", @@ -1544650,6 +1547226,181 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.04.10.022103", + "rel_title": "Single-cell atlas of a non-human primate reveals new pathogenic mechanisms of COVID-19", + "rel_date": "2020-04-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.10.022103", + "rel_abs": "Stopping COVID-19 is a priority worldwide. Understanding which cell types are targeted by SARS-CoV-2 virus, whether interspecies differences exist, and how variations in cell state influence viral entry is fundamental for accelerating therapeutic and preventative approaches. In this endeavor, we profiled the transcriptome of nine tissues from a Macaca fascicularis monkey at single-cell resolution. The distribution of SARS-CoV-2 facilitators, ACE2 and TMRPSS2, in different cell subtypes showed substantial heterogeneity across lung, kidney, and liver. Through co-expression analysis, we identified immunomodulatory proteins such as IDO2 and ANPEP as potential SARS-CoV-2 targets responsible for immune cell exhaustion. Furthermore, single-cell chromatin accessibility analysis of the kidney unveiled a plausible link between IL6-mediated innate immune responses aiming to protect tissue and enhanced ACE2 expression that could promote viral entry. Our work constitutes a unique resource for understanding the physiology and pathophysiology of two phylogenetically close species, which might guide in the development of therapeutic approaches in humans.\n\nBullet pointsO_LIWe generated a single-cell transcriptome atlas of 9 monkey tissues to study COVID-19.\nC_LIO_LIACE2+TMPRSS2+ epithelial cells of lung, kidney and liver are targets for SARS-CoV-2.\nC_LIO_LIACE2 correlation analysis shows IDO2 and ANPEP as potential therapeutic opportunities.\nC_LIO_LIWe unveil a link between IL6, STAT transcription factors and boosted SARS-CoV-2 entry.\nC_LI", + "rel_num_authors": 40, + "rel_authors": [ + { + "author_name": "Lei Han", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + }, + { + "author_name": "Xiaoyu Wei", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + }, + { + "author_name": "Chuanyu Liu", + "author_inst": "BGI-Shenzhen, Shenzhen" + }, + { + "author_name": "Giacomo Volpe", + "author_inst": "Laboratory of Integrative biology, Guangzhou Institutes of Biomedicine and Health, CAS, Guangzhou 510530, China" + }, + { + "author_name": "Zhifeng Wang", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + }, + { + "author_name": "Taotao Pan", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + }, + { + "author_name": "Yue Yuan", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + }, + { + "author_name": "Ying Lei", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + }, + { + "author_name": "Yiwei Lai", + "author_inst": "Laboratory of Integrative biology, Guangzhou Institutes of Biomedicine and Health, CAS, Guangzhou 510530, China" + }, + { + "author_name": "Carl Ward", + "author_inst": "Laboratory of Integrative biology, Guangzhou Institutes of Biomedicine and Health, CAS, Guangzhou 510530, China" + }, + { + "author_name": "Yeya Yu", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + }, + { + "author_name": "Mingyue Wang", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + }, + { + "author_name": "Quan Shi", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + }, + { + "author_name": "Tao Wu", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + }, + { + "author_name": "Liang Wu", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + }, + { + "author_name": "Ya Liu", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + }, + { + "author_name": "Chunqing Wang", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + }, + { + "author_name": "Yuanhang Zhang", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + }, + { + "author_name": "Haixi Sun", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + }, + { + "author_name": "Hao Yu", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + }, + { + "author_name": "Zhenkun Zhuang", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + }, + { + "author_name": "Tingting Tang", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + }, + { + "author_name": "Yunting Huang", + "author_inst": "China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China" + }, + { + "author_name": "Haorong Lu", + "author_inst": "China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China" + }, + { + "author_name": "Liqin Xu", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + }, + { + "author_name": "Jiangshan Xu", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + }, + { + "author_name": "Mengnan Cheng", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + }, + { + "author_name": "Yang Liu", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + }, + { + "author_name": "Chi Wai Wong", + "author_inst": "Huazhen Biosciences, Guangzhou 510900, China" + }, + { + "author_name": "Tao Tan", + "author_inst": "Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500," + }, + { + "author_name": "Weizhi Ji", + "author_inst": "Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500," + }, + { + "author_name": "Patrick H. Maxwell", + "author_inst": "Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Cambridge CB2 0XY, United Kingdom" + }, + { + "author_name": "Huanming Yang", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + }, + { + "author_name": "Jian Wang", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + }, + { + "author_name": "Shida Zhu", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + }, + { + "author_name": "Shiping Liu", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + }, + { + "author_name": "Xun Xu", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + }, + { + "author_name": "Yong Hou", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + }, + { + "author_name": "Miguel A. Esteban", + "author_inst": "Laboratory of Integrative biology, Guangzhou Institutes of Biomedicine and Health, CAS, Guangzhou 510530, China" + }, + { + "author_name": "Longqi Liu", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2020.04.10.20053207", "rel_title": "Homologous protein domains in SARS-CoV-2 and measles, mumps and rubella viruses: preliminary evidence that MMR vaccine might provide protection against COVID-19", @@ -1545846,29 +1548597,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.04.07.030684", - "rel_title": "The aging transcriptome and cellular landscape of the human lung in relation to SARS-CoV-2", - "rel_date": "2020-04-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.07.030684", - "rel_abs": "Since the emergence of SARS-CoV-2 in December 2019, Coronavirus Disease-2019 (COVID-19) has rapidly spread across the globe. Epidemiologic studies have demonstrated that age is one of the strongest risk factors influencing the morbidity and mortality of COVID-19. Here, we interrogate the transcriptional features and cellular landscapes of the aging human lung through integrative analysis of bulk and single-cell transcriptomics. By intersecting these age-associated changes with experimental data on host interactions between SARS-CoV-2 or its relative SARS-CoV, we identify several age-associated factors that may contribute to the heightened severity of COVID-19 in older populations. We observed that age-associated gene expression and cell populations are significantly linked to the heightened severity of COVID-19 in older populations. The aging lung is characterized by increased vascular smooth muscle contraction, reduced mitochondrial activity, and decreased lipid metabolism. Lung epithelial cells, macrophages, and Th1 cells decrease in abundance with age, whereas fibroblasts, pericytes and CD4+ Tcm cells increase in abundance with age. Several age-associated genes have functional effects on SARS-CoV replication, and directly interact with the SARS-CoV-2 proteome. Interestingly, age-associated genes are heavily enriched among those induced or suppressed by SARS-CoV-2 infection. These analyses illuminate potential avenues for further studies on the relationship between the aging lung and COVID-19 pathogenesis, which may inform strategies to more effectively treat this disease.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Ryan D Chow", - "author_inst": "Yale University" - }, - { - "author_name": "Sidi Chen", - "author_inst": "Yale University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.04.06.027854", "rel_title": "Decoding the lethal effect of SARS-CoV-2 (novel coronavirus) strains from global perspective: molecular pathogenesis and evolutionary divergence", @@ -1546640,6 +1549368,113 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.04.08.026948", + "rel_title": "Robust neutralization assay based on SARS-CoV-2 S-bearing vesicular stomatitis virus (VSV) pseudovirus and ACE2-overexpressed BHK21 cells", + "rel_date": "2020-04-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.08.026948", + "rel_abs": "The global pandemic of Coronavirus disease 2019 (COVID-19) is a disaster for human society. A convenient and reliable in vitro neutralization assay is very important for the development of neutralizing antibodies, vaccines and other inhibitors. In this study, G protein-deficient vesicular stomatitis virus (VSVdG) bearing full-length and truncated spike (S) protein of SARS-CoV-2 were evaluated. The virus packaging efficiency of VSV-SARS-CoV-2-Sdel18 (S with C-terminal 18 amino acid truncation) is much higher than VSV-SARS-CoV-2-S. A neutralization assay for antibody screening and serum neutralizing titer quantification was established based on VSV-SARS-CoV-2-Sdel18 pseudovirus and human angiotensin-converting enzyme 2 (ACE2) overexpressed BHK21 cell (BHK21-hACE2). The experimental results can be obtained by automatically counting EGFP positive cell number at 12 hours after infection, making the assay convenient and high-throughput. The serum neutralizing titer of COVID-19 convalescent patients measured by VSV-SARS-CoV-2-Sdel18 pseudovirus assay has a good correlation with live SARS-CoV-2 assay. Seven neutralizing monoclonal antibodies targeting receptor binding domain (RBD) of SARS-CoV-2-S were obtained. This efficient and reliable pseudovirus assay model could facilitate the development of new drugs and vaccines.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Hualong Xiong", + "author_inst": "Xiamen University" + }, + { + "author_name": "Yangtao Wu", + "author_inst": "Xiamen University" + }, + { + "author_name": "Jiali Cao", + "author_inst": "Xiamen University" + }, + { + "author_name": "Ren Yang", + "author_inst": "China CDC" + }, + { + "author_name": "Jian Ma", + "author_inst": "Xiamen University" + }, + { + "author_name": "Xiaoyang Qiao", + "author_inst": "Xiamen University" + }, + { + "author_name": "Xiangyang Yao", + "author_inst": "The First Hospital of Xiamen University" + }, + { + "author_name": "Baohui Zhang", + "author_inst": "Xiamen University" + }, + { + "author_name": "Yali Zhang", + "author_inst": "Xiamen University" + }, + { + "author_name": "Wangheng Hou", + "author_inst": "Xiamen University" + }, + { + "author_name": "Yang Shi", + "author_inst": "Xiamen University" + }, + { + "author_name": "Jingjing Xu", + "author_inst": "Fujian Institute of Hematology" + }, + { + "author_name": "Liang Zhang", + "author_inst": "Xiamen University" + }, + { + "author_name": "Shaojuan Wang", + "author_inst": "Xiamen University" + }, + { + "author_name": "Baorong Fu", + "author_inst": "Xiamen University" + }, + { + "author_name": "Ting Yang", + "author_inst": "Fujian Institute of Hematology" + }, + { + "author_name": "Shengxiang Ge", + "author_inst": "Xiamen University" + }, + { + "author_name": "Jun Zhang", + "author_inst": "Xiamen University" + }, + { + "author_name": "Quan Yuan", + "author_inst": "Xiamen University" + }, + { + "author_name": "Baoying Huang", + "author_inst": "China CDC" + }, + { + "author_name": "Zhiyong Li", + "author_inst": "The First Hospital of Xiamen University" + }, + { + "author_name": "Tianying Zhang", + "author_inst": "Xiamen University" + }, + { + "author_name": "Ningshao Xia", + "author_inst": "Xiamen University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.04.06.20055426", "rel_title": "Understanding the CoVID-19 pandemic Curve through statistical approach", @@ -1547239,25 +1550074,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.04.07.20053660", - "rel_title": "Optimize Clinical Laboratory Diagnosis of COVID-19 from Suspect Cases by Likelihood Ratio of SARS-CoV-2 IgM and IgG antibody", - "rel_date": "2020-04-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.07.20053660", - "rel_abs": "ObjectiveTo optimize clinical laboratory diagnosis of COVID-19 from suspect cases by Likelihood Ratio of SARS-CoV-2 IgM and IgG antibody.\n\nMethodsBy reinterpreting the data in the article \"Diagnostic Value of Combined Detection of Serum 2019 novel coronavirus IgM and IgG Antibodies in novel coronavirusin Infection\", the positive likelihood ratio of IgM and IgG antibody in diagnosis of COVID-19 (nucleic acid positive patients) was calculated, and the posterior probability of IgM and IgG antibodies and their tandem detection to diagnose was finally calculated.\n\nResultsThe positive likelihood ratios of single IgM and IgG antibody were 18.50 and 12.65 respectively, and the posterior probabilities were 90.18% and 86.26% respectively. However, the posterior probability of the two antibodies tandem detection is 99.15%, which can give clinicians quantitative confidence in the diagnosis of COVID-19 from suspected cases. According to the results of this study, combining the advantages and disadvantages of nucleic acid detection and antibody detection, the clinical pathway for clinicians to diagnose COVID-19 is found.\n\nConclusionFor suspected cases, IgM and IgG antibody tests should be firstly done at the same time. If the antibody tests are all positive, COVID-19 can be confirmed. If not, nucleic acid detection (one or more times) is performed, and in extreme cases, high-throughput viral genome sequencing is performed.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Feng Yangchun", - "author_inst": "Xinjiang Medical University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pathology" - }, { "rel_doi": "10.1101/2020.04.06.025635", "rel_title": "LAMP-Seq: Population-Scale COVID-19 Diagnostics Using a Compressed Barcode Space", @@ -1547913,6 +1550729,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, + { + "rel_doi": "10.1101/2020.04.04.20053363", + "rel_title": "EARLY DETECTION OF COVID-19", + "rel_date": "2020-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.04.20053363", + "rel_abs": "Since SARS-Cov-2 epidemic appeared in Wuhan China, it became challenge for health authorities to counter Covid-19 epidemic. Early evaluation of suspects, screening for Covid-19 and management posed challenge to health authorities especially in developing countries which were not ready to cope with it. Early mild symptoms appeared during course of disease provide a chance to early detect Covid-19. We use retrospective methodology to collect available data on early sign and symptoms of Covid-19 through accessing World Health Organization (WHO) webpages, New England Journal of Medicine (NEJM), Nature Journal, Journal of American Medical Association (JAMA) network, British Medical Journal (BJM), Lancet and other world renowned journal publications to establish a relationship of early symptoms for detection of Covid-19. Data of 2707 Covid-19 laboratory confirmed cases was collected and analyzed for early signs. Available data was categorized into physical and blood biomarkers. This categorized data was assessed for scoring early detection of Covid-19 by scoring Hashmi-Asif Covid-19 formula. Each characteristic was given a score in Hashmi-Asif Covid-19 chart with maximum score of 28. Scoring 16 on chart means Covid-19 will fully develop in near future. Correlation of each sign and symptoms with development of Covid-19 in formula showed significant correlation assessed by Pearson correlation and Spearman Correlation coefficient (rho) showed significant correlation of development of Covid-19 with fever 64.11% (P=0.001), cough 65% and dry mucus 19.67% equally sensitive (P=0.000), leukopenia 19.06% (P=0.006), lymphopenia 52.93% (P=0.005), thrombopenia 19.1% (P=0.013), elevated Aspartate aminotransferase 12.79% (P=0.007) and elevated Alanine aminotransferase 11.34% (P=0.006). Chart can sense Covid-19 progression 72-96 hours earlier compared to usual course of disease and detection by standard method. Chart for early detection provides early quarantine decision to reduce disease spread and give ample time for intervening disease progression to reduce morbidity time due to Covid-19.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Hafiz Muhammad Asif", + "author_inst": "Islamia University of Bahawalpur" + }, + { + "author_name": "Hafiz Abdul Sattar Hashmi", + "author_inst": "Islamia University of Bahawalpur" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.04.07.20056309", "rel_title": "A Simulated Single Ventilator / Dual Patient Ventilation Strategy for Acute Respiratory Distress Syndrome During the COVID-19 Pandemic", @@ -1548569,25 +1551408,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.02.20050989", - "rel_title": "Clinical and epidemiological characteristics of Coronavirus Disease 2019 (COVID-19) patients", - "rel_date": "2020-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.02.20050989", - "rel_abs": "BackgroundNumerous groups have reported the clinical and epidemiological characteristics of Coronavirus Disease 2019 (COVID-19) cases; however, the data remained inconsistent. This paper aimed to pool the available data to provide a more complete picture of the characteristics of COVID-19 patients.\n\nMethodsA systematic review and pooled analysis was performed. Eligible studies were identified from database and hand searches up to March 2, 2020. Data on clinical (including laboratory and radiological) and epidemiological (including demographic) characteristics of confirmed COVID-19 cases were extracted and combined by simple pooling.\n\nResultsOf 644 studies identified, 69 studies (involving 48,926 patients) were included in the analysis. The average age of the patients was 49.16 years. A total of 51.46% of the patients were men and 52.32% were non-smokers. Hypertension (50.82%) and diabetes (20.89%) were the most frequent comorbidities observed. The most common symptoms were fever (83.21%), cough (61.74%), and myalgia or fatigue (30.22%). Altered levels of blood and biochemical parameters were observed in a proportion of the patients. Most of the patients (78.50%) had bilateral lung involvements, and 5.86% showed no CT findings indicative of viral pneumonia. Acute respiratory distress syndrome (28.36%), acute cardiac injury (7.89%) and acute kidney injury (7.60%) were the most common complications recorded.\n\nConclusionsClinical and epidemiological characteristics of COVID-19 patients were mostly heterogeneous and non-specific. This is the most comprehensive report of the characteristics of COVID-19 patients to date. The information presented is important for improving our understanding of the spectrum and impact of this novel disease.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Shing Cheng Tan", - "author_inst": "Universiti Kebangsaan Malaysia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.04.20047886", "rel_title": "Timing of antiviral treatment initiation is critical to reduce SARS-Cov-2 viral load", @@ -1549179,6 +1551999,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.05.20054155", + "rel_title": "The relationship of COVID-19 severity with cardiovascular disease and its traditional risk factors: A systematic review and meta-analysis", + "rel_date": "2020-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.05.20054155", + "rel_abs": "BackgroundWhether cardiovascular disease (CVD) and its traditional risk factors predict severe coronavirus disease 2019 (COVID-19) is uncertain, in part, because of potential confounding by age and sex.\n\nMethodsWe performed a systematic review of studies that explored pre-existing CVD and its traditional risk factors as risk factors of severe COVID-19 (defined as death, acute respiratory distress syndrome, mechanical ventilation, or intensive care unit admission). We searched PubMed and Embase for papers in English with original data ([≥]10 cases of severe COVID-19). Using random-effects models, we pooled relative risk (RR) estimates and conducted meta-regression analyses.\n\nResultsOf the 661 publications identified in our search, 25 papers met our inclusion criteria, with 76,638 COVID-19 patients including 11,766 severe cases. Older age was consistently associated with severe COVID-19 in all eight eligible studies, with RR >[~]5 in >60-65 vs. <50 years. Three studies showed no change in the RR of age after adjusting for covariate(s). In univariate analyses, factors robustly associated with severe COVID-19 were male sex (10 studies; pooled RR=1.73, [95%CI 1.50-2.01]), hypertension (8 studies; 2.87 [2.09-3.93]), diabetes (9 studies; 3.20 [2.26-4.53]), and CVD (10 studies; 4.97 [3.76-6.58]). RR for male sex was likely to be independent of age. For the other three factors, meta-regression analyses suggested confounding by age. Only four studies reported multivariable analysis, but most of them showed adjusted RR [~]2 for hypertension, diabetes, and CVD. No study explored renin-angiotensin system inhibitors as a risk factor for severe COVID-19.\n\nConclusionsDespite the potential for confounding, these results suggest that hypertension, diabetes, and CVD are independently associated with severe COVID-19 and, together with age and male sex, can be used to inform objective decisions on COVID-19 testing, clinical management, and workforce planning.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Kunihiro Matsushita", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Ning Ding", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Minghao Kou", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Xiao Hu", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Mengkun Chen", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Yumin Gao", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Yasuyuki Honda", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "David Dowdy", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Yejin Mok", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Junichi Ishigami", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Lawrence J Appel", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.05.20051540", "rel_title": "SARS-CoV-2 titers in wastewater are higher than expected from clinically confirmed cases", @@ -1549755,53 +1552634,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.04.20053280", - "rel_title": "Longitudinal analysis of laboratory findings during the process of recovery for patients with COVID-19", - "rel_date": "2020-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.04.20053280", - "rel_abs": "ObjectiveTo explore longitudinal change patterns of key laboratory tests in patients with COVID-19, and to identify independent prognostic factors by examining the associations between laboratory findings and outcomes of patients.\n\nMethodsThe multicenter study prospectively included 59 patients with COVID-19 treated at Jilin province from January 21, 2020 to May 5, 2020. Laboratory tests were included haematological, biochemical, and immunological tests.\n\nResultsLaboratory findings, the characteristics of epidemiological and demographic data were extracted from electronic medical records. Eosinopenia was shown in 52.6% cases at onset, and the average value of eosinophil continued to significantly increase thereafter. Lymphopenia was found in 40.4% cases at onset, and the average value of lymphocyte was slowly elevated after day 5. Thrombocytopenia was shown in 12.3% cases at onset, and the average value of mean platelet volume was decreased sharply after day 7. The values of aspartate aminotransferase, lactate dehydrogenase, creatine kinase, creatinine kinase-muscle/brain activity, and cardiac troponin I, serum cardiac markers, were beyond the upper limit of RI from 6.1% to 30.6% at onset. The abnormity of liver function tests, kidney function tests, electrolytes was 2.0%[~]59.2%, 2.0%[~]4.1%, 6.0%[~]30.0%, respectively. Eosinophil, platelet and carbondioxide combining power were selected as the prognostic factors.\n\nConclusionsThe haematological, biochemical, and immunological tests were found significant abnormity at onset and longitudinal change patterns in the patients with COVID-19. Age, Eosinophil, PLT and CO2 may used to predict the recovery probability. Risk stratification and management could be improved for the patients with COVID-19 according to temporal trajectories of laboratory tests.\n\nArticle SummaryThe longitudinal change patterns of the laboratory characteristics of affected patients were important to identify prognosis. Eosinophil, platelet and carbondioxide combining power may be independent predictors of recovery in patients with COVID-19.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Suyan Tian", - "author_inst": "First Hospital of Jilin University" - }, - { - "author_name": "Xuetong Zhu", - "author_inst": "First Hospital of Jilin University" - }, - { - "author_name": "Xuejuan Sun", - "author_inst": "Changchun Infectious Disease Hospital" - }, - { - "author_name": "Jinmei Wang", - "author_inst": "Siping Infectious Disease Hospital" - }, - { - "author_name": "Qi Zhou", - "author_inst": "First Hospital of Jilin University" - }, - { - "author_name": "Chi Wang", - "author_inst": "University of Kentucky" - }, - { - "author_name": "Li Chen", - "author_inst": "University of Kentucky" - }, - { - "author_name": "Jiancheng Xu", - "author_inst": "First Hospital of Jilin University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.05.20054338", "rel_title": "Explaining the Bomb-Like Dynamics of COVID-19 with Modeling and the Implications for Policy", @@ -1550297,6 +1553129,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.05.20054288", + "rel_title": "Estimating the effect of physical distancing on the COVID-19 pandemic using an urban mobility index", + "rel_date": "2020-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.05.20054288", + "rel_abs": "BackgroundGovernments have implemented population-wide physical distancing measures to control COVID-19, but metrics evaluating their effectiveness are not readily available.\n\nMethodsWe used a publicly available mobility index from a popular transit application to evaluate the effect of physical distancing on infection growth rates and reproductive numbers in 40 jurisdictions between March 23 and April 12, 2020.\n\nFindingsA 10% decrease in mobility was associated with a 14.6% decrease (exp({beta}) = 0{middle dot}854; 95% credible interval: 0{middle dot}835, 0{middle dot}873) in the average daily growth rate and a -0{middle dot}061 (95% CI: -0{middle dot}071, -0{middle dot}052) change in the instantaneous reproductive number two weeks later.\n\nInterpretationOur analysis demonstrates that decreases in urban mobility were predictive of declines in epidemic growth. Mobility metrics offer an appealing method to calibrate population-level physical distancing policy and implementation, especially as jurisdictions relax restrictions and consider alternative physical distancing strategies.\n\nFundingNo external funding was received for this study.\n\nResearch in Context Evidence before this studyWidespread physical distancing interventions implemented in response to the COVID-19 pandemic led to sharp declines in global mobility throughout March 2020. Real-time metrics to evaluate the effects of these measures on future case growth rates will be useful for calibrating further interventions, especially as jurisdictions begin to relax restrictions. We searched PubMed on May 22, 2020 for studies reporting the use of aggregated mobility data to measure the effects of physical distancing on COVID-19 cases, using the keywords \"COVID-19\", \"2019-nCoV\", or \"SARS-CoV-2\" in combination with \"mobility\", \"movement\", \"phone\", \"Google\", or \"Apple\". We scanned 252 published studies and found one that used mobility data to estimate the effects of physical distancing. This study evaluated temporal trends in reported cases in four U.S. metropolitan areas using a metric measuring the percentage of cell phone users leaving their homes. Many published papers examined how national and international travel predicted the spatial distribution of cases (particularly outflow from Wuhan, China), but very little has been published on metrics that could be used as prospective, proximal indicators of future case growth. We also identified a series of reports released by the Imperial College COVID-19 Response Team and several manuscripts deposited on preprint servers such as medRxiv addressing this topic, demonstrating this is an active area of research.\n\nAdded value of this studyWe demonstrate that changes in a publicly available urban mobility index reported in over 40 global cities were associated with COVID-19 case growth rates and estimated reproductive numbers two to three weeks later. These cities, spread over 5 continents, include many regional epicenters of COVID-19 outbreaks. This is one of only a few studies using a mobility metric applicable to future growth rates that is both publicly available and international in scope.\n\nImplications of all the available evidenceRestrictions on human mobility have proved effective for controlling COVID-19 in China and the rest of the world. However, such drastic public health measures cannot be sustained indefinitely and are currently being relaxed in many jurisdictions. Publicly available mobility metrics offer a method of estimating the effects of changes in mobility before they are reflected in the trajectory of COVID-19 case growth rates and thus merit further evaluation.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Jean-Paul R. Soucy", + "author_inst": "Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada" + }, + { + "author_name": "Shelby L. Sturrock", + "author_inst": "Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada" + }, + { + "author_name": "Isha Berry", + "author_inst": "Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada" + }, + { + "author_name": "Duncan J. Westwood", + "author_inst": "Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Canada" + }, + { + "author_name": "Nick Daneman", + "author_inst": "Department of Medicine, University of Toronto, Toronto, Canada; Division of Infectious Diseases, Sunnybrook Health Sciences Centre, Toronto, Canada; Institute f" + }, + { + "author_name": "Derek R. MacFadden", + "author_inst": "Ottawa Hospital Research Institute, Ottawa, Canada" + }, + { + "author_name": "Kevin A. Brown", + "author_inst": "Institute for Clinical Evaluative Sciences, Toronto, Canada; Public Health Ontario, Toronto, Canada" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.30.20047365", "rel_title": "Neutralizing antibody responses to SARS-CoV-2 in a COVID-19 recovered patient cohort and their implications", @@ -1551273,25 +1554148,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.03.20051797", - "rel_title": "What does simple power law kinetics tell about our response to coronavirus pandemic?", - "rel_date": "2020-04-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.03.20051797", - "rel_abs": "Coronavirus pandemic of 2019-2020 has already affected over a million people and caused over 50,000 deaths worldwide (as on April 3, 2020). Roughly half of the world population has been asked to work from home and practice social distancing as the search for a vaccine continues. Though government interventions such as lockdown and social distancing are theoretically useful, its debatable whether such interventions are effective in flattening the curve, which is ceasing or reducing the growth of infection in control populations. In this article, I present a simple power law model that enables a comparison of countries in time windows of 14 days since first coronavirus related death is reported in that country. It therefore provides means to access the efficacy of above interventions.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Prateek Kumar Jha", - "author_inst": "Indian Institute of Technology Roorkee" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.02.20051524", "rel_title": "Evidence that higher temperatures are associated with lower incidence of COVID-19 in pandemic state, cumulative cases reported up to March 27, 2020", @@ -1551715,6 +1554571,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.03.31.20048256", + "rel_title": "Ultra-High-Resolution CT Follow-Up in Patients with Imported Early-Stage Coronavirus Disease 2019 (COVID-19) Related Pneumonia", + "rel_date": "2020-04-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.31.20048256", + "rel_abs": "BackgroundAn ongoing outbreak of mystery pneumonia in Wuhan was caused by coronavirus disease 2019 (COVID-19). The infectious disease has spread globally and become a major threat to public health.\n\nPurposeWe aim to investigate the ultra-high-resolution CT (UHR-CT) findings of imported COVID-19 related pneumonia from the initial diagnosis to early-phase follow-up.\n\nMethodsThis retrospective study included confirmed cases with early-stage COVID-19 related pneumonia imported from the epicenter. Initial and early-phase follow-up UHR-CT scans (within 5 days) were reviewed for characterizing the radiological findings. The normalized total volumes of ground-glass opacities (GGOs) and consolidations were calculated and compared during the radiological follow-up by artificial-intelligence-based methods.\n\nResultsEleven patients (3 males and 8 females, aged 32-74 years) with confirmed COVID-19 were evaluated. Subpleural GGOs with inter/intralobular septal thickening were typical imaging findings. Other diagnostic CT features included distinct margins (8/11, 73%), pleural retraction or thickening (7/11, 64%), intralesional vasodilatation (6/11, 55%). Normalized volumes of pulmonary GGOs (p=0.003) and consolidations (p=0.003) significantly increased during the CT follow-up.\n\nConclusionsThe abnormalities of GGOs with peripleural distribution, consolidated areas, septal thickening, pleural involvement and intralesional vasodilatation on UHR-CT indicate the diagnosis of COVID-19. COVID-19 cases could manifest significantly progressed GGOs and consolidations with increased volume during the early-phase CT follow-up.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Yu Lin", + "author_inst": "Zhongshan Hospital Affiliated to Xiamen University" + }, + { + "author_name": "Shaomao Lv", + "author_inst": "Zhongshan Hospital Affiliated to Xiamen University" + }, + { + "author_name": "Jinan Wang", + "author_inst": "Zhongshan Hospital Affiliated to Xiamen University" + }, + { + "author_name": "Jianghe Kang", + "author_inst": "Zhongshan Hospital Affiliated to Xiamen University" + }, + { + "author_name": "Youbin Zhang", + "author_inst": "Zhongshan Hospital Affiliated to Xiamen University" + }, + { + "author_name": "Zhipeng Feng", + "author_inst": "Zhongshan Hospital Affiliated to Xiamen University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2020.04.03.20048868", "rel_title": "Classification of Coronavirus Images using Shrunken Features", @@ -1552447,33 +1555342,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2020.04.01.20050476", - "rel_title": "Case fatality rate in COVID-19: a systematic review and meta-analysis", - "rel_date": "2020-04-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.01.20050476", - "rel_abs": "BackgroundEstimating the prevalence of severe or critical illness and case fatality of COVID-19 outbreak in December, 2019 remains a challenge due to biases associated with surveillance, data synthesis and reporting. We aimed to address this limitation in a systematic review and meta-analysis and to examine the clinical, biochemical and radiological risk factors in a meta-regression.\n\nMethodsPRISMA guidelines were followed. PubMed, Scopus and Web of Science were searched using pre-specified keywords on March 07, 2020. Peer-reviewed empirical studies examining rates of severe illness, critical illness and case fatality among COVID-19 patients were examined. Numerators and denominators to compute the prevalence rates and risk factors were extracted. Random-effects meta-analyses were performed. Results were corrected for publication bias. Meta-regression analyses examined the moderator effects of potential risk factors.\n\nResultsThe meta-analysis included 29 studies representing 2,090 individuals. Pooled rates of severe illness, critical illness and case fatality among COVID-19 patients were 15%, 5% and 0.8% respectively. Adjusting for potential underreporting and publication bias, increased these estimates to 26%, 16% and 7.4% respectively. Increasing age and elevated LDH consistently predicted severe / critical disease and case fatality. Hypertension; fever and dyspnea at presentation; and elevated CRP predicted increased severity.\n\nConclusionsRisk factors that emerged in our analyses predicting severity and case fatality should inform clinicians to define endophenotypes possessing a greater risk. Estimated case fatality rate of 7.4% after correcting for publication bias underscores the importance of strict adherence to preventive measures, case detection, surveillance and reporting.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Chanaka N Kahathuduwa", - "author_inst": "Texas Tech University Health Sciences Center" - }, - { - "author_name": "Chathurika S Dhanasekara", - "author_inst": "Texas Tech University Health Sciences Center" - }, - { - "author_name": "Shao-Hua Chin", - "author_inst": "Protech Pharmaservices Corporation" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.02.20050930", "rel_title": "Estimation of the probability of reinfection with COVID-19 coronavirus by the SEIRUS model", @@ -1552897,6 +1555765,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.01.20049973", + "rel_title": "Modeling risk of infectious diseases: a case of Coronavirus outbreak in four countries", + "rel_date": "2020-04-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.01.20049973", + "rel_abs": "BackgroundThe novel coronavirus (2019-nCOV) outbreak has been a serious concern around the globe. Since people are in tremor due to the massive spread of Coronavirus in the major parts of the world, it requires to predict the risk of this infectious disease. In this situation, we develop a model to measure the risk of infectious disease and predict the risk of 2019-nCOV transmission by using data of four countries--US, Australia, Canada and China.\n\nMethodsThe model underlies that higher the population density, higher the risk of transmission of infectious disease from human to human. Besides, population size, case identification rate and travel of infected passengers in different regions are also incorporated in this model.\n\nResultsAccording to the calculated risk index, our study identifies New York State in United States (US) to be the most vulnerable area affected by the novel Coronavirus. Besides, other areas (province/state/territory) such as Hubei (China, 2nd), Massachusetts (US, 3rd), District of Columbia (US, 4th), New Jersey (US, 5th), Quebec (Canada, 20th), Australian Capital Territory (Australia, 29th) are also found as the most risky areas in US, China, Australia and Canada.\n\nConclusionThe study suggests avoiding any kind of mass gathering, maintaining recommended physical distances and restricting inbound and outbound flights of highly risk prone areas for tackling 2019-nCOV transmission.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Md. Mazharul Islam", + "author_inst": "Bangladesh Institute of Governance and Management" + }, + { + "author_name": "Md. Monirul Islam", + "author_inst": "Bangladesh Institute of Governance and Management" + }, + { + "author_name": "Md. Jamal Hossain", + "author_inst": "Bangladesh Institute of Governance and Management" + }, + { + "author_name": "Faroque Ahmed", + "author_inst": "Bangladesh Institute of Governance and Management" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.01.20049759", "rel_title": "Flattening the curve before it flattens us: hospital critical care capacity limits and mortality from novel coronavirus (SARS-CoV2) cases in US counties", @@ -1553577,37 +1556476,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.03.20043992", - "rel_title": "Anxiety, worry and perceived stress in the world due to the COVID-19 pandemic, March 2020. Preliminary results.", - "rel_date": "2020-04-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.03.20043992", - "rel_abs": "IntroductionSince the beginning of the outbreak in China, ending 2019, the Novel Coronavirus (COVID-19) has spread subsequently to the rest of the world causing an on-going pandemic. The World Health Organisation (WHO) declared COVID-19 \"a public health emergency of international concern.\" Taking into consideration the lockdown and quarantine situation, a research team of doctors from the Hospital of Salamanca, decided to do an evaluation of the current emotional state on the general population with a web-based survey in English and in Spanish, which was considered a useful and fast method that could help us determine how people perceived stress and worry due to the COVID-19.\n\nMethodsThe survey included a 22 items, gathering information in 3 sections: Sociodemographic data, the Perceived Stress Scale (PSS-10) by Cohen and additional queries that assessed the current worry and change of behaviours due to this pandemic.\n\nResultsThe survey received 1091 respondents from 41 countries, from March 17 to the 1st of April, 2020. The mean age of the respondents was 43.1 (14.2) years old, and more than two thirds were women. 21.1% were health personnel. The mean of the PSS-10 score was 17.4 (6.4). Significantly higher scores were observed among women, youth, students, and among those who expressed concern and those who perceived increased susceptibility to the COVID-19. In contrast, no significant differences were observed between the health professionals and the general population. A weak correlation was observed between mean relative volume RSV of the last 28 days and the number of cases reported (rho = 0.31, p <0.001) and deaths (rho = 0.28, p <0.001).\n\nDiscussionWith these results the researchers describe an increase of affective symptoms due to the COVID-19. This pandemic is raising the anxiety levels. The findings of the study show the affective and cognitive alterations people are going through. This survey is the first attempt to measure the psychological consequences this pandemic is having, in order to be able to provide the support to confront this global issue, addressing the mental health care that will be needed.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Rosario Sinta Gamonal Limcaoco", - "author_inst": "University of Salamanca Health Care Complex, Department of Psychiatry, Salamanca, Spain" - }, - { - "author_name": "Enrique Montero Mateos", - "author_inst": "University of Salamanca Health Care Complex, Salamanca, Spain." - }, - { - "author_name": "Juan Matias Fernandez", - "author_inst": "University of Salamanca Health Care Complex, Department of Psychiatry, Salamanca, Spain." - }, - { - "author_name": "Carlos Roncero", - "author_inst": "University of Salamanca Health Care Complex, Department of Psychiatry Salamanca, Spain." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.04.03.20052001", "rel_title": "Core warming of coronavirus disease 2019 (COVID-19) patients undergoing mechanical ventilation: protocol for a randomized controlled pilot study", @@ -1554207,6 +1557075,49 @@ "type": "new results", "category": "pathology" }, + { + "rel_doi": "10.1101/2020.04.03.023846", + "rel_title": "In vitro screening of a FDA approved chemical library reveals potential inhibitors of SARS-CoV-2 replication", + "rel_date": "2020-04-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.03.023846", + "rel_abs": "A novel coronavirus, named SARS-CoV-2, emerged in 2019 from Hubei region in China and rapidly spread worldwide. As no approved therapeutics exists to treat Covid-19, the disease associated to SARS-Cov-2, there is an urgent need to propose molecules that could quickly enter into clinics. Repurposing of approved drugs is a strategy that can bypass the time consuming stages of drug development. In this study, we screened the Prestwick Chemical Library(R) composed of 1,520 approved drugs in an infected cell-based assay. 90 compounds were identified. The robustness of the screen was assessed by the identification of drugs, such as Chloroquine derivatives and protease inhibitors, already in clinical trials. The hits were sorted according to their chemical composition and their known therapeutic effect, then EC50 and CC50 were determined for a subset of compounds. Several drugs, such as Azithromycine, Opipramol, Quinidine or Omeprazol present antiviral potency with 2150 different cell types corresponding to all major human tissues and organs based on stringent immunohistochemical analysis. The results were compared with several datasets both on the mRNA and protein level. ACE2 expression was mainly observed in enterocytes, renal tubules, gallbladder, cardiomyocytes, male reproductive cells, placental trophoblasts, ductal cells, eye and vasculature. In the respiratory system, the expression was limited, with no or only low expression in a subset of cells in a few individuals, observed by one antibody only. Our data constitutes an important resource for further studies on SARS-CoV-2 host cell entry, in order to understand the biology of the disease and to aid in the development of effective treatments to the viral infection.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Feria Hikmet", + "author_inst": "Uppsala University" + }, + { + "author_name": "Loren Mear", + "author_inst": "Uppsala University" + }, + { + "author_name": "Asa Edvinsson", + "author_inst": "Uppsala University" + }, + { + "author_name": "Patrick Micke", + "author_inst": "Uppsala University" + }, + { + "author_name": "Mathias Uhlen", + "author_inst": "KTH - Royal Institute of Technology, Karolinska Institutet" + }, + { + "author_name": "Cecilia Lindskog", + "author_inst": "Uppsala University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "contradictory results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2020.04.01.021196", "rel_title": "SARS-CoV-2 neutralizing serum antibodies in cats: a serological investigation", @@ -1557395,33 +1560326,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.03.30.016790", - "rel_title": "Comparative genomics suggests limited variability and similar evolutionary patterns between major clades of SARS-Cov-2", - "rel_date": "2020-04-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.30.016790", - "rel_abs": "Phylogenomic analysis of SARS-CoV-2 as available from publicly available repositories suggests the presence of 3 prevalent groups of viral episomes (super-clades), which are mostly associated with outbreaks in distinct geographic locations (China, USA and Europe). While levels of genomic variability between SARS-CoV-2 isolates are limited, to our knowledge, it is not clear whether the observed patterns of variability in viral super-clades reflect ongoing adaptation of SARS-CoV-2, or merely genetic drift and founder effects. Here, we analyze more than 1100 complete, high quality SARS-CoV-2 genome sequences, and provide evidence for the absence of distinct evolutionary patterns/signatures in the genomes of the currently known major clades of SARS-CoV-2. Our analyses suggest that the presence of distinct viral episomes at different geographic locations are consistent with founder effects, coupled with the rapid spread of this novel virus. We observe that while cross species adaptation of the virus is associated with hypervariability of specific protein coding regions (including the RDB domain of the spike protein), the more variable genomic regions between extant SARS-CoV-2 episomes correspond with the 3 and 5 UTRs, suggesting that at present viral protein coding genes should not be subjected to different adaptive evolutionary pressures in different viral strains. Although this study can not be conclusive, we believe that the evidence presented here is strongly consistent with the notion that the biased geographic distribution of SARS-CoV-2 isolates should not be associated with adaptive evolution of this novel pathogen.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Matteo Chiara", - "author_inst": "University of Milan" - }, - { - "author_name": "David Stephen Horner", - "author_inst": "University of Milan" - }, - { - "author_name": "Graziano Pesole", - "author_inst": "University of Bari" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.03.31.014639", "rel_title": "Variable Macro X Domain of SARS-CoV-2 Retains the Ability to Bind ADP-ribose", @@ -1558033,6 +1560937,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.30.20047662", + "rel_title": "Demand for hospitalization services for COVID-19 patients in Brazil", + "rel_date": "2020-04-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.30.20047662", + "rel_abs": "COVID-19 is now a pandemic and many of the affected countries face severe shortages of hospital resources. In Brazil, the first case was reported on February 26. As the number of cases grows in the country, there is a concern that the health system may become overwhelmed, resulting in shortages of hospital beds, intensive care unit beds, and mechanical ventilators. The timing of shortage is likely to vary geographically depending on the observed onset and pace of transmission observed, on the availability of resources, and on the actions implemented. Here we consider the daily number of cases reported in municipalities in Brazil to simulate twelve alternative scenarios of the likely timing of shortage, based on parameters consistently reported for China and Italy, on rates of hospital occupancy for other health conditions observed in Brazil in 2019, and on assumptions of allocation of patients in public and private facilities. Results show that hospital services could start to experience shortages of hospital beds, ICU beds, and ventilators in early April, the most critical situation observed for ICU beds. Increasing the allocation of beds for COVID-19 (in lieu of other conditions) or temporarily placing all resources under the administration of the state delays the anticipated start of shortages by a week. This suggests that solutions adopted by the Brazilian government must aim at expanding the available capacity (e.g., makeshift hospitals), and not simply prioritizing the allocation of available resources to COVID-19.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Marcia C Castro", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Lucas Resende de Carvalho", + "author_inst": "Center for Development and Regional Planning, Federal University of Minas Gerais" + }, + { + "author_name": "Taylor Chin", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Rebecca Kahn", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Giovanny V. A. Franca", + "author_inst": "Secretariat of Health Surveillance, Brazilian Ministry of Health" + }, + { + "author_name": "Eduardo Marques Macario", + "author_inst": "Secretariat of Health Surveillance, Brazilian Ministry of Health" + }, + { + "author_name": "Wanderson Kleber de Oliveira", + "author_inst": "Secretariat of Health Surveillance, Brazilian Ministry of Health" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.29.20046904", "rel_title": "Global trends in air travel: implications for connectivity and resilience to infectious disease threats", @@ -1558661,41 +1561608,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.03.30.20048215", - "rel_title": "Analysis of the Worldwide Corona Virus (COVID-19) Pandemic Trend;A Modelling Study to Predict Its Spread", - "rel_date": "2020-04-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.30.20048215", - "rel_abs": "ObjectiveThe Coronavirus (COVID-19) has advanced into 197 countries and territories leaving behind a total of 372,757 confirmed cases and 16231 deaths.\n\nMethodsOne the basis of WHO situation reports data of COVID-19 along with daily official reports from the Japan, China and the Kore we modelled the spread of COVID19 by using the Successive Approximation Method. We defined the two state of data to find the mean ratio ({eta}) of the present cases count to the sum of previous and present cases. This ratio further predicts the future state of COVID-19 pandemic.\n\nResultsThe mean ratio ({eta}) of expected cases were found 0.485, while the mean ratio for deaths was found to be 0.49. We calculated worldwide expected lower bound value for confirmed cases 247007 cases with maximum limit of 1667719 cases and minimum deaths count 8660 with upper limit of 117397 deaths in next 30 days. While in the case of Iran, a large increase in the number of deaths are expected in the upcoming 30 days with lower bound value of 1140 deaths and maximum value of 598478 deaths.\n\nInterpretationIran whole population is on risk.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Muhammad Qasim", - "author_inst": "University of Otago" - }, - { - "author_name": "Waqas Ahmad", - "author_inst": "Department of Computer Science, University Of Otago, Dunedin, PO Box 56, Dunedin 9054, New Zealand" - }, - { - "author_name": "Minami Yoshida", - "author_inst": "Centre for Bioengineering & Nanomedicine (Dunedin), Department of Food Science, Division of Sciences. University Of Otago, Dunedin, PO Box 56, Dunedin 9054, New" - }, - { - "author_name": "Maree Gould", - "author_inst": "Centre for Bioengineering & Nanomedicine (Dunedin), Department of Food Science, Division of Sciences. University Of Otago, Dunedin, PO Box 56, Dunedin 9054, New" - }, - { - "author_name": "Muhammad Yasir", - "author_inst": "Department of Computer Science, University Of Otago, Dunedin, PO Box 56, Dunedin 9054, New Zealand" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.03.29.20046631", "rel_title": "THE EMOTIONAL IMPACT OF THE ASRM GUIDELINES ON FERTILITY PATIENTS DURING THE COVID-19 PANDEMIC", @@ -1559195,6 +1562107,37 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.03.26.009209", + "rel_title": "Scrutinizing the SARS-CoV-2 protein information for the designing an effective vaccine encompassing both the T-cell and B-cell epitopes", + "rel_date": "2020-04-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.26.009209", + "rel_abs": "Novel SARS coronavirus (SARS-CoV-2) has caused a pandemic condition world-wide and has been declared as public health emergency of International concern by WHO in a very short span of time. The community transmission of this highly infectious virus has severely affected various parts of China, Italy, Spain and USA among others. The prophylactic solution against SARS-CoV-2 infection is challenging due to the high mutation rate of its RNA genome. Herein, we exploited a next generation vaccinology approach to construct a multi-epitope vaccine candidate against SARS-CoV-2 with high antigenicity, safety and efficacy to combat this deadly infectious agent. The whole proteome was scrutinized for the screening of highly conserved, antigenic, non-allergen and non-toxic epitopes having high population coverage that can elicit both humoral and cellular mediated immune response against COVID-19 infection. These epitopes along with four different adjuvants were utilized to construct a multi-epitope vaccine candidate that can generate strong immunological memory response having high efficacy in humans. Various physiochemical analyses revealed the formation of a stable vaccine product having a high propensity to form a protective solution against the detrimental SARS-CoV-2 strain with high efficacy. The vaccine candidate interacted with immunological receptor TLR3 with high affinity depicting the generation of innate immunity. Further, the codon optimization and in silico expression show the plausibility of the high expression and easy purification of the vaccine product. Thus, this present study provides an initial platform of the rapid generation of an efficacious protective vaccine for combating COVID-19.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Neha Jain", + "author_inst": "Indian Institute of Technology Indore" + }, + { + "author_name": "Uma Shankar", + "author_inst": "Indian Institute of Technology Indore" + }, + { + "author_name": "Prativa Majee", + "author_inst": "Indian Insitute of Technology, Indore" + }, + { + "author_name": "Amit Kumar", + "author_inst": "Indian Institute of Technology Indore" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.03.26.20044636", "rel_title": "Evaluation of the awareness level of Healthcare workers toward NCOVID-2019 in Pakistan", @@ -1559787,125 +1562730,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.30.20045740", - "rel_title": "A Territory-wide study of COVID-19 cases and clusters with unknown source in Hong Kong community: A clinical, epidemiological and phylogenomic investigation", - "rel_date": "2020-03-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.30.20045740", - "rel_abs": "Initial cases of COVID-19 reported in Hong Kong were mostly imported from China. However, most cases reported in February 2020 were locally-acquired infections, indicating local community transmissions. We extracted the demographic, clinical and epidemiological data from 50 COVID-19 patients, who accounted for 53.8% of the cases in Hong Kong by February 2020. Whole-genome sequencing of the SARS-CoV-2 were conducted to determine the phylogenetic relatedness and transmission dynamics. Only three (6.0%) patients required ICU admission. Phylogenetic analysis identified six transmission clusters. All locally-acquired cases harboured a common mutation Orf3a G251V and were clustered in two subclades in global phylogeny of SARS-CoV-2. The estimated time to the most recent common ancestor of local COVID-2019 outbreak was December 24, 2019 with an evolutionary rate of 3.04x10-3 substitutions per site per year. The reproduction number value was 1.84. Social distancing and vigilant epidemiological control are crucial to the containment of COVID-19 transmission.\n\nArticle summary linesA combined epidemiological and phylogenetic analysis of early COVID-19 outbreak in Hong Kong revealed that a SARS-CoV-2 variant with ORF3a G251V mutation accounted for all locally acquired cases, and that asymptomatic carriers could be a huge public health risk for COVID-19 control.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Kenneth Siu-Sing Leung", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Timothy Ting-Leung Ng", - "author_inst": "The Hong Kong Polytechnic University" - }, - { - "author_name": "Alan Ka-Lun Wu", - "author_inst": "Pamela Youde Nethersole Eastern Hospital" - }, - { - "author_name": "Miranda Chong-Yee Yau", - "author_inst": "Pamela Youde Nethersole Eastern Hospital" - }, - { - "author_name": "Hiu-Yin Lao", - "author_inst": "The Hong Kong Polytechnic University" - }, - { - "author_name": "Ming-Pan Choi", - "author_inst": "The Hong Kong Polytechnic University" - }, - { - "author_name": "Kingsley King-Gee Tam", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Lam-Kwong Lee", - "author_inst": "Hong Kong Polytechnic University" - }, - { - "author_name": "Barry Kin-Chung Wong", - "author_inst": "United Christian Hospital" - }, - { - "author_name": "Alex Yat-Man Ho", - "author_inst": "Princess Margaret Hospital" - }, - { - "author_name": "Kam-Tong Yip", - "author_inst": "Tuen Mun Hospital" - }, - { - "author_name": "Kwok-Cheung Lung", - "author_inst": "Pamela Youde Nethersole Eastern Hospital" - }, - { - "author_name": "Raymond Wai-To Liu", - "author_inst": "Pamela Youde Nethersole Eastern Hospital" - }, - { - "author_name": "Eugene Yuk-Keung Tso", - "author_inst": "United Christian Hospital" - }, - { - "author_name": "Wai-Shing Leung", - "author_inst": "Princess Margaret Hospital" - }, - { - "author_name": "Man-Chun Chan", - "author_inst": "Princess Margaret Hospital" - }, - { - "author_name": "Yuk-Yung Ng", - "author_inst": "Tuen Mun Hospital" - }, - { - "author_name": "Kit-Man Sin", - "author_inst": "Tuen Mun Hospital" - }, - { - "author_name": "Kitty Sau-Chun Fung", - "author_inst": "United Christian Hospital" - }, - { - "author_name": "Sandy Ka-Yee Chau", - "author_inst": "United Christian Hospital" - }, - { - "author_name": "Wing-Kin To", - "author_inst": "Princess Margaret Hospital" - }, - { - "author_name": "Tak-Lun Que", - "author_inst": "Tuen Mun Hospital" - }, - { - "author_name": "David Ho-Keung Shum", - "author_inst": "Hong Kong Polytechnic University" - }, - { - "author_name": "Shea Ping Yip", - "author_inst": "Hong Kong Polytechnic University" - }, - { - "author_name": "Wing-Cheong Yam", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Gilman Kit Hang Siu", - "author_inst": "Hong Kong Polytechnic University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.28.20044339", "rel_title": "Estimating the size of COVID-19 epidemic outbreak", @@ -1560432,6 +1563256,73 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.03.30.015990", + "rel_title": "Fully human single-domain antibodies against SARS-CoV-2", + "rel_date": "2020-03-31", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.30.015990", + "rel_abs": "The COVID-19 pandemic is spreading rapidly, highlighting the urgent need for an efficient approach to rapidly develop therapeutics and prophylactics against SARS-CoV-2. We describe here the development of a phage-displayed single-domain antibody library by grafting naive CDRs into framework regions of an identified human germline IGHV allele. This enabled the isolation of high-affinity single-domain antibodies of fully human origin. The panning using SARS-CoV-2 RBD and S1 as antigens resulted in the identification of antibodies targeting five types of neutralizing or non-neutralizing epitopes on SARS-CoV-2 RBD. These fully human single-domain antibodies bound specifically to SARS-CoV-2 RBD with subnanomolar to low nanomolar affinities. Some of them were found to potently neutralize pseudotyped and live virus, and therefore may represent promising candidates for prophylaxis and therapy of COVID-19. This study also reports unique immunogenic profile of SARS-CoV-2 RBD compared to that of SARS-CoV and MERS-CoV, which may have important implications for the development of effective vaccines against SARS-CoV-2.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Yanling Wu", + "author_inst": "Fudan University" + }, + { + "author_name": "Cheng Li", + "author_inst": "Fudan University" + }, + { + "author_name": "Shuai Xia", + "author_inst": "Fudan University" + }, + { + "author_name": "Xiaolong Tian", + "author_inst": "Fudan University" + }, + { + "author_name": "Zhi Wang", + "author_inst": "Fudan University" + }, + { + "author_name": "Yu Kong", + "author_inst": "Fudan University" + }, + { + "author_name": "Chenjian Gu", + "author_inst": "Fudan University" + }, + { + "author_name": "Rong Zhang", + "author_inst": "Fudan University" + }, + { + "author_name": "Chao Tu", + "author_inst": "Biomissile Corporation" + }, + { + "author_name": "Youhua Xie", + "author_inst": "Fudan University" + }, + { + "author_name": "Lu Lu", + "author_inst": "Fudan University" + }, + { + "author_name": "Shibo Jiang", + "author_inst": "Fudan University" + }, + { + "author_name": "Tianlei Ying", + "author_inst": "Fudan University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.03.29.014381", "rel_title": "Computational Prediction of the Comprehensive SARS-CoV-2 vs. Human Interactome to Guide the Design of Therapeutics", @@ -1561288,41 +1564179,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.25.20043380", - "rel_title": "General Model for COVID-19 Spreading with Consideration of Intercity Migration, Insufficient Testing and Active Intervention: Application to Study of Pandemic Progression in Japan and USA", - "rel_date": "2020-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.25.20043380", - "rel_abs": "A new Susceptible-Exposed-Infected-Confirmed-Removed (SEICR) model with consideration of intercity travel and active intervention is proposed for predicting the spreading progression of the 2019 New Coronavirus Disease (COVID-19). The model takes into account the known or reported number of infected cases being fewer than the actual number of infected individuals due to insufficient testing. The model integrates intercity travel data to track the movement of exposed and infected individuals among cities, and allows different levels of active intervention to be considered so that realistic prediction of the number of infected individuals can be performed. The data of the COVID-19 infection cases and the intercity travel data for Japan (January 15 to March 20, 2020) and the USA (February 20 to March 20, 2020) are used to illustrate the prediction of the pandemic progression in 47 regions of Japan and 50 states (plus a federal district) in the USA. By fitting the model with the data, we reveal that, as of March 19, 2020, the number of infected individuals in Japan and the USA could be twenty-fold and five-fold as many as the number of confirmed cases, respectively. Moreover, the model generates future progression profiles for different levels of intervention by setting the parameters relative to the values found from the data fitting. Results show that without tightening the implementation of active intervention, Japan and the USA will see about 6.55% and 18.2% of the population eventually infected, and with drastic ten-fold elevated active intervention, the number of people eventually infected can be reduced by up to 95% in Japan and 70% in the USA. Finally, an assessment of the relative effectiveness of active intervention and personal protective measures is discussed. With a highly vigilant public maintaining personal hygiene and exercising strict protective measures, the percentage of population infected can be further reduced to 0.23% in Japan and 2.7% in the USA.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Choujun Zhan", - "author_inst": "South China Normal University" - }, - { - "author_name": "Chi K. Tse", - "author_inst": "City University of Hong Kong" - }, - { - "author_name": "Zhikang Lai", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Xiaoyun Chen", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Mingshen Mo", - "author_inst": "Sun Yat-sen University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.27.20044925", "rel_title": "A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage", @@ -1562034,6 +1564890,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.27.20045849", + "rel_title": "Modeling the Epidemic Dynamics of COVID-19 Outbreak in Iran", + "rel_date": "2020-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.27.20045849", + "rel_abs": "The COVID-19 impact on global health and economic system has been profound and unseen since the Spanish flu of 1918-19. Iran is one of the countries that has been severely affected partly because of slow responses to the crisis, ill-preparedness of the health system, and fragile health infrastructure and shortage of protective equipment due to economic sanctions. Due to shortcomings in the reported data, this note tries to estimate a model-based number of infected cases and examines the effectiveness of different policy responses to contain this crisis. Our results show that in an optimistic estimation, the number of unidentified cases can be 3 to 6 times more than the reported numbers. Social distancing alone cannot be an effective policy at this stage of pandemic unless at least 80 percent of the population confine themselves for an extended period of time. An alternative policy is to increase testing extensively and isolate identified cases actively combined with effective social distancing. Otherwise, many lives will be lost and the health system will collapse, adding to the ongoing economic crisis as a result of sanctions for many years to come.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Majid Einian", + "author_inst": "MBRI" + }, + { + "author_name": "Hamid Reza Tabarraei", + "author_inst": "International Monetary Fund" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.28.20040204", "rel_title": "The time-series ages distribution of the reported COVID-2019 infected people suggests the undetected local spreading of COVID-2019 in Hubei and Guangdong provinces before 19th Jan 2020", @@ -1562650,49 +1565529,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.26.20042044", - "rel_title": "Evaluation the auxiliary diagnosis value of antibodies assays for detection of novel coronavirus (SARS-Cov-2) causing an outbreak of pneumonia (COVID-19)", - "rel_date": "2020-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.26.20042044", - "rel_abs": "BackgroundThe spread of an novel coronavirus (SARS-CoV-2, previously named 2019-nCoV) has already taken on pandemic proportions, affecting over 100 countries in a matter of weeks. Elucidating the diagnostic value of different methods, especially the auxiliary diagnosis value of antibodies assays for SARS-CoV-2 infection is helpful for improving the sensitivities of pathogenic-diagnosis, providing timely treatment, and differentiating the infected cases from the healthy, thus preventing further epidemics.\n\nMethodsMedical records from 38 patients with confirmed SARS-CoV-2 infection in the Second Peoples Hospital of Fuyang from January 22, 2020 to February 28, 2020 were collected and retrospectively analyzed. Specimens including throat swabs, sputum and serum were collected during the hospitalization period, viral RNAs and serum IgM-IgG antibodies to SARS-CoV-2 were measured respectively. The detectability of different methods as well as the auxiliary diagnosis value of antibodies test for SARS-CoV-2 infection were analyzed.\n\nResultsAmong 38 patients, the total seropositive rate for IgM and IgG was 50.0% and 92.1%, respectively. Two patients remained seronegative throughout the course of illness. In the early phase of illness, the RNA test for sputum specimens possessed the highest detectability(92.3%), followed by the the RNA test for throat swabs (69.2%), and the antibodies assays presented lower positive rates(IgM, 23.0%, IgG, 53.8%). While, the sensitivity of antibodies assays overtook that of RNA test since day 8 after onset (IgM, 50.0%; IgG, 87.5%). Of note, the positive rate of throat swabs was only 13.0% for cases in later phase([≥]15 d.a.o), and the sensitivities of IgM and IgG rose to 52.2% and 91.3%, respectively. Combined use of antibodies assay and qRT-PCR at the same time was able to improve the sensitivities of pathogenic-diagnosis, especially for the throat swabs group at the later stage of illness. Moreover, most of these cases with undetectable viral RNA in throat swabs specimens at the early stage of illness were able to be IgM/IgG seropositive after 7 days.\n\nConclusionsThe antibodies detection against SARS-CoV-2 offers vital clinical information for physicians, and could be used as an effective supplementary indicator for suspected cases of negative viral nucleic acid detection or in conjunction with nucleic acid detection in the diagnosis of suspected cases.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Yong Gao", - "author_inst": "Department of Clinical laboratory, the Second People's Hospital of Fuyang, Fuyang 236015,China." - }, - { - "author_name": "Yi Yuan", - "author_inst": "Anhui Toneker Biotechnology Co., Ltd., Jinzhai 237300, China." - }, - { - "author_name": "Tuan Tuan Li", - "author_inst": "Department of Clinical laboratory, the Second People's Hospital of Fuyang, Fuyang 236015,China." - }, - { - "author_name": "Wu Xiao Wang", - "author_inst": "Department of Clinical laboratory, the Second People's Hospital of Fuyang, Fuyang 236015,China." - }, - { - "author_name": "Yong Xiu Li", - "author_inst": "Blood purification center, the Second People's Hospital of Fuyang, Fuyang 236015, China." - }, - { - "author_name": "Ang Li", - "author_inst": "School of Life Sciences and Technology, Tongji University, Shanghai 200092, China." - }, - { - "author_name": "Feng Ming Han", - "author_inst": "Department of Respiratory, the Second People's Hospital of Fuyang, Fuyang 236015, China" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.24.20042168", "rel_title": "Dispersion of a new coronavirus SARS-CoV-2 by airlines in 2020: Temporal estimates of the outbreak in Mexico.", @@ -1563316,6 +1566152,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.24.20042689", + "rel_title": "SARS-CoV-2 detection using digital PCR for COVID-19 diagnosis, treatment monitoring and criteria for discharge", + "rel_date": "2020-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.24.20042689", + "rel_abs": "BackgroundSARS-CoV-2 nucleic acid detection by RT-PCR is one of the criteria approved by China FDA for diagnosis of COVID-19. However, inaccurate test results (for example, high false negative rate and some false positive rate) were reported in both China and US CDC using RT-PCR method. Inaccurate results are caused by inadequate detection sensitivity of RT-PCR, low viral load in some patients, difficulty to collect samples from COVID-19 patients, insufficient sample loading during RT-PCR tests, and RNA degradation during sample handling process. False negative detection could subject patients to multiple tests before diagnosis can be made, which burdens health care system. Delayed diagnosis could cause infected patients to miss the best treatment time window. False negative detection could also lead to prematurely releasing infected patients who still carry residual SARS-CoV-2 virus. In this case, these patients could infect many others. A high sensitivity RNA detection method to resolve the existing issues of RT-PCR is in need for more accurate COVID-19 diagnosis.\n\nMethodsDigital PCR (dPCR) instrument DropX-2000 and assay kits were used to detect SARS-CoV-2 from 108 clinical specimens from 36 patients including pharyngeal swab, stool and blood from different days during hospitalization. Double-blinded experiment data of 108 clinical specimens by dPCR methods were compared with results from officially approved RT-PCR assay. A total of 109 samples including 108 clinical specimens and 1 negative control sample were tested in this study. All of 109 samples, 26 were from 21patients reported as positive by officially approved clinical RT-PCR detection in local CDC and then hospitalized in Nantong Third Hospital. Among the 109 samples, dPCR detected 30 positive samples on ORFA1ab gene, 47 samples with N gene positive, and 30 samples with double positive on ORFA1ab and N genes.\n\nResultsThe lower limit of detection of the optimize dPCR is at least 10-fold lower than that of RT-PCR. The overall accuracy of dPCR for clinical detection is 96.3%. 4 out 4 of (100 %) negative pharyngeal swab samples checked by RT-PCR were positive judged by dPCR based on the follow-up investigation. 2 of 2 samples in the RT-PCR grey area (Ct value > 37) were confirmed by dPCR with positive results. 1 patient being tested positive by RT-PCR was confirmed to be negative by dPCR. The dPCR results show clear viral loading decrease in 12 patients as treatment proceed, which can be a useful tool for monitoring COVID-19 treatment.\n\nConclusionsDigital PCR shows improved lower limit of detection, sensitivity and accuracy, enabling COVID-19 detection with less false negative and false positive results comparing with RT-PCR, especially for the tests with low viral load specimens. We showed evidences that dPCR is powerful in detecting asymptomatic patients and suspected patients. Digital PCR is capable of checking the negative results caused by insufficient sample loading by quantifying internal reference gene from human RNA in the PCR reactions. Multi-channel fluorescence dPCR system (FAM/HEX/CY5/ROX) is able to detect more target genes in a single multiplex assay, providing quantitative count of viral load in specimens, which is a powerful tool for monitoring COVID-19 treatment.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Renfei Lu", + "author_inst": "Nantong Third Hospital Affiliated to Nantong University, Clinical laboratory" + }, + { + "author_name": "Jian Wang", + "author_inst": "Nantong Third Hospital Affiliated to Nantong University, Clinical laboratory" + }, + { + "author_name": "Min Li", + "author_inst": "Nantong Third Hospital Affiliated to Nantong University, Clinical laboratory" + }, + { + "author_name": "Yaqi Wang", + "author_inst": "RainSure Scientific Co, Ltd." + }, + { + "author_name": "Jia Dong", + "author_inst": "RainSure Scientific Co, Ltd." + }, + { + "author_name": "Weihua Cai", + "author_inst": "Nantong Third Hospital Affiliated to Nantong University, Infection Division" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.28.20043059", "rel_title": "Virus shedding patterns in nasopharyngeal and fecal specimens of COVID-19 patients", @@ -1564000,29 +1566875,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.03.26.20044487", - "rel_title": "In-host Modelling of COVID-19 Kinetics in Humans", - "rel_date": "2020-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.26.20044487", - "rel_abs": "COVID-19 pandemic has underlined the impact of emergent pathogens as a major threat for human health. The development of quantitative approaches to advance comprehension of the current outbreak is urgently needed to tackle this severe disease. In this work, several mathematical models are proposed to represent SARS-CoV-2 dynamics in infected patients. Considering different starting times of infection, parameters sets that represent infectivity of SARS-CoV-2 are computed and compared with other viral infections that can also cause pandemics.\n\nBased on the target cell model, SARS-CoV-2 infecting time between susceptible cells (mean of 30 days approximately) is much slower than those reported for Ebola (about 3 times slower) and influenza (60 times slower). The within-host reproductive number for SARS-CoV-2 is consistent to the values of influenza infection (1.7-5.35). The best model to fit the data was including immune responses, which suggest a slow cell response peaking between 5 to 10 days post onset of symptoms. The model with eclipse phase, time in a latent phase before becoming productively infected cells, was not supported. Interestingly, both, the target cell model and the model with immune responses, predict that virus may replicate very slowly in the first days after infection, and it could be below detection levels during the first 4 days post infection. A quantitative comprehension of SARS-CoV-2 dynamics and the estimation of standard parameters of viral infections is the key contribution of this pioneering work.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Esteban Abelardo Hernandez Vargas", - "author_inst": "Frankfurt Institute for Advanced Studies" - }, - { - "author_name": "Jorge X. Velasco-Hernandez", - "author_inst": "UNAM" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.28.013508", "rel_title": "SARS-CoV-2 detection from nasopharyngeal swab samples without RNA extraction", @@ -1564618,6 +1567470,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "endocrinology" }, + { + "rel_doi": "10.1101/2020.03.26.20044289", + "rel_title": "Forecasting the Worldwide Spread of COVID-19 based on Logistic Model and SEIR Model", + "rel_date": "2020-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.26.20044289", + "rel_abs": "BackgroundWith the outbreak of coronavirus disease 2019 (COVID-19), a sudden case increase in late February 2020 led to deep concern globally. Italy, South Korea, Iran, France, Germany, Spain, the US and Japan are probably the countries with the most severe outbreaks. Collecting epidemiological data and predicting epidemic trends are important for the development and measurement of public intervention strategies. Epidemic prediction results yielded by different mathematical models are inconsistent; therefore, we sought to compare different models and their prediction results to generate objective conclusions.\n\nMethodsWe used the number of cases reported from January 23 to March 20, 2020, to estimate the possible spread size and peak time of COVID-19, especially in 8 high-risk countries. The logistic growth model, basic SEIR model and adjusted SEIR model were adopted for prediction. Given that different model inputs may infer different model outputs, we implemented three model predictions with three scenarios of epidemic development.\n\nResultsWhen comparing all 8 countries short-term prediction results and peak predictions, the differences among the models were relatively large. The logistic growth model estimated a smaller epidemic size than the basic SERI model did; however, once we added parameters that considered the effects of public health interventions and control measures, the adjusted SERI model results demonstrated a considerably rapid deceleration of epidemic development. Our results demonstrated that contact rate, quarantine scale, and the initial quarantine time and length are important factors in controlling epidemic size and length.\n\nConclusionsWe demonstrated a comparative assessment of the predictions of the COVID-19 outbreak in eight high-risk countries using multiple methods. By forecasting epidemic size and peak time as well as simulating the effects of public health interventions, the intent of this paper is to help clarify the transmission dynamics of COVID-19 and recommend operation suggestions to slow down the epidemic. It is suggested that the quick detection of cases, sufficient implementation of quarantine and public self-protection behaviors are critical to slow down the epidemic.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Xiang Zhou", + "author_inst": "Peking Union Medical College Hospital" + }, + { + "author_name": "Xudong Ma", + "author_inst": "National Health Commission of the People's Republic of China" + }, + { + "author_name": "Na Hong", + "author_inst": "Digital China Health Technologies Co. Ltd" + }, + { + "author_name": "Longxiang Su", + "author_inst": "Peking Union Medical College Hospital" + }, + { + "author_name": "Yingying Ma", + "author_inst": "Digital China Health Technologies Co. Ltd" + }, + { + "author_name": "Jie He", + "author_inst": "Digital China Health Technologies Co. Ltd" + }, + { + "author_name": "Huizhen Jiang", + "author_inst": "Peking Union Medical College Hospital" + }, + { + "author_name": "Chun Liu", + "author_inst": "Digital China Health Technologies Co. Ltd." + }, + { + "author_name": "Guangliang Shan", + "author_inst": "Peking Union Medical College" + }, + { + "author_name": "Weiguo Zhu", + "author_inst": "Peking Union Medical College Hospital" + }, + { + "author_name": "Shuyang Zhang", + "author_inst": "Peking union medical college hospital" + }, + { + "author_name": "Yun Long", + "author_inst": "Peking Union Medical College Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.26.20044677", "rel_title": "Suppression and Mitigation Strategies for Control of COVID-19 in New Zealand", @@ -1565210,41 +1568125,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.03.28.20046086", - "rel_title": "China's fight against COVID-19: What we have done and what we should do next?", - "rel_date": "2020-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.28.20046086", - "rel_abs": "BackgroundOn 12 March, the World Health Organization Director-General declared that \"the threat of a global pandemic has become a reality\", and the disease caused by the novel coronavirus, known as COVID-19, has become a global concern. Chinese efforts in curbing the virus have widely been recognized. Even the WHO has lauded the efforts of the Chinese government and advised the world to learn from China in fighting the disease. Since the outbreak of COVID-19, to curb the spread of the epidemic, the Chinese government has implemented unprecedented prevention interventions at the nationwide level. Currently, the outbreak in Wuhan is changing in a positive direction and has been effectively controlled. However, it is not clear what these measures were and how these measures changed to curb the outbreak of COVID-19 quickly. This study explored the characteristics and identified that Chinas control strategies have changed the epidemiological curve of rapidly rising new confirmed cases of COVID-19. This study also seeks to expand the experiences and lessons from this outbreak.\n\nMethodsWe collected public health interventions measures from Jan 20, 2020, to 5 March 2020, and data from COVID-19 daily newly confirmed cases and daily cumulates cases to compare the control effects and changing trends. We performed a retrospective description of these intervention strategies from three stages. Besides, from the perspective of public health, the experiences and lessons exposed by this outbreak were roughly summarized.\n\nResultsThese non-pharmacology interventions measures adopted by the Chinese government by the instruction and spirit of President Xi Jinping were timely and efficient.\n\nConclusionsThe present study was conducted to comprehensively analyze from a social epidemiology context. The results confirmed that these radical interventions taken by the Chinese government were effective, ambitious, and agile. However, we must be aware that the epidemic situation in Wuhan is still challenging.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Sixiang Cheng", - "author_inst": "Central South University" - }, - { - "author_name": "Yuxin Zhao", - "author_inst": "Central South University" - }, - { - "author_name": "Atipatsa Chiwanda Kaminga", - "author_inst": "Mzuzu University" - }, - { - "author_name": "Pingxin Zhang", - "author_inst": "Huazhong University of Science and Technology" - }, - { - "author_name": "Huilan Xu", - "author_inst": "Central South University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.03.24.20043117", "rel_title": "Improved deep learning model for differentiating novel coronavirus pneumonia and influenza pneumonia", @@ -1565832,6 +1568712,93 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2020.03.24.005702", + "rel_title": "Knowledge synthesis from 100 million biomedical documents augments the deep expression profiling of coronavirus receptors", + "rel_date": "2020-03-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.24.005702", + "rel_abs": "The COVID-19 pandemic demands assimilation of all available biomedical knowledge to decode its mechanisms of pathogenicity and transmission. Despite the recent renaissance in unsupervised neural networks for decoding unstructured natural languages, a platform for the real-time synthesis of the exponentially growing biomedical literature and its comprehensive triangulation with deep omic insights is not available. Here, we present the nferX platform for dynamic inference from over 45 quadrillion possible conceptual associations extracted from unstructured biomedical text, and their triangulation with Single Cell RNA-sequencing based insights from over 25 tissues. Using this platform, we identify intersections between the pathologic manifestations of COVID-19 and the comprehensive expression profile of the SARS-CoV-2 receptor ACE2. We find that tongue keratinocytes, airway club cells, and ciliated cells are likely underappreciated targets of SARS-CoV-2 infection, in addition to type II pneumocytes and olfactory epithelial cells. We further identify mature small intestinal enterocytes as a possible hotspot of COVID-19 fecal-oral transmission, where an intriguing maturation-correlated transcriptional signature is shared between ACE2 and the other coronavirus receptors DPP4 (MERS-CoV) and ANPEP (-coronavirus). This study demonstrates how a holistic data science platform can leverage unprecedented quantities of structured and unstructured publicly available data to accelerate the generation of impactful biological insights and hypotheses.\n\nThe nferX Platform Single-cell resource - https://academia.nferx.com/", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "AJ Venkatakrishnan", + "author_inst": "nference" + }, + { + "author_name": "Arjun Puranik", + "author_inst": "nference" + }, + { + "author_name": "Akash Anand", + "author_inst": "nference" + }, + { + "author_name": "David Zemmour", + "author_inst": "nference" + }, + { + "author_name": "Xiang Yao", + "author_inst": "Janssen" + }, + { + "author_name": "Xiaoying Wu", + "author_inst": "Janssen" + }, + { + "author_name": "Ramakrishna Chilaka", + "author_inst": "nference" + }, + { + "author_name": "Dariusz K Murakowski", + "author_inst": "nference" + }, + { + "author_name": "Kristopher Standish", + "author_inst": "Janssen" + }, + { + "author_name": "Bharathwaj Raghunathan", + "author_inst": "nference" + }, + { + "author_name": "Tyler Wagner", + "author_inst": "nference" + }, + { + "author_name": "Enrique Garcia-Rivera", + "author_inst": "nference" + }, + { + "author_name": "Hugo Solomon", + "author_inst": "nference" + }, + { + "author_name": "Abhinav Garg", + "author_inst": "nference" + }, + { + "author_name": "Rakesh Barve", + "author_inst": "nference" + }, + { + "author_name": "Anuli Anyanwu-Ofili", + "author_inst": "Janssen" + }, + { + "author_name": "Najat Khan", + "author_inst": "Janssen" + }, + { + "author_name": "Venky Soundararajan", + "author_inst": "nference" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.03.24.20042937", "rel_title": "Correlation between universal BCG vaccination policy and reduced morbidity and mortality for COVID-19: an epidemiological study", @@ -1566524,53 +1569491,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.03.23.20041673", - "rel_title": "Radiographic Findings and other Predictors in Adults with Covid-19", - "rel_date": "2020-03-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.23.20041673", - "rel_abs": "As of March 20, 2020, there were 234,073 confirmed cases of coronavirus disease 2019 (Covid-19) and 9,840 deaths worldwide 1. Older age and elevated d-dimer are reported risk factors for Covid-19 2,3. However, whether early radiographic change is a predictor of fatality remains unknown. We retrospectively reviewed records of all laboratory-confirmed patients admitted to a quarantine unit at Tongji Hospital, a large regional hospital in Wuhan, China, between January 31 and March 5, 2020. The Tongji Hospital ethics committee approved this study.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Kaiyan Li", - "author_inst": "Tongji Hospital of Huazhong University of Science and Technology" - }, - { - "author_name": "Dian Chen", - "author_inst": "Tongji Hospital of Huazhong University of Science and Technology" - }, - { - "author_name": "Shengchong Chen", - "author_inst": "Tongji Hospital of Huazhong University of Science and Technology" - }, - { - "author_name": "Yuchen Feng", - "author_inst": "Tongji Hospital of Huazhong University of Science and Technology" - }, - { - "author_name": "Chenli Chang", - "author_inst": "Tongji Hospital of Huazhong University of Science and Technology" - }, - { - "author_name": "Zi Wang", - "author_inst": "Tongji Hospital of Huazhong University of Science and Technology" - }, - { - "author_name": "Nan Wang", - "author_inst": "Tongji Hospital of Huazhong University of Science and Technology" - }, - { - "author_name": "Guohua Zhen", - "author_inst": "Tongji Hospital of Huazhong Universtiy of Science and Technology" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2020.03.22.20041061", "rel_title": "Clinical features and the maternal and neonatal outcomes of pregnant women with coronavirus disease 2019", @@ -1567358,6 +1570278,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.03.22.20040956", + "rel_title": "Simulation-based Estimation of the Spread of COVID-19 in Iran", + "rel_date": "2020-03-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.22.20040956", + "rel_abs": "BackgroundThe COVID-19 disease has turned into a global pandemic with unprecedented challenges for the global community. Understanding the state of the disease and planning for future trajectories relies heavily on data on the spread and mortality. Yet official data coming from various countries are highly unreliable: symptoms similar to common cold in majority of cases and limited screening resources and delayed testing procedures may contribute to under-estimation of the burden of disease. Anecdotal and more limited data are available, but few have systematically combined those with official statistics into a coherent view of the epidemic. This study is a modeling-in-real-time of the emerging outbreak for understanding the state of the disease. Our focus is on the case of the spread of disease in Iran, as one of the epicenters of the disease in the first months of 2020.\n\nMethodWe develop a simple dynamic model of the epidemic to provide a more reliable picture of the state of the disease based on existing data. Building on the generic SEIR (Susceptible, Exposed, Infected, and Recovered) framework we incorporate two behavioral and logistical considerations. First we capture the endogenous changes in contact rate (average contact per person) as more death are reported. As a result the reproduction number changes endogenously in the model. Second we differentiate reported and true cases by including simple formulations for how only a fraction of cases might be diagnosed, and how that fraction changes in response to epidemics progression. In estimating the model we use both the official data as well as the discovered infected travelers and unofficial medical community estimates and triangulate these sources to build a more complete picture. Calibration is completed by forming a likelihood function for observing the actual time series data conditional on model parameters, and conducting a Markov Chain Monte Carlo simulations. The model is used to estimate current \"true\" cases of infection and death. We analyze the future trajectory of the disease under six conditions related to the seasonal effects and policy measures targeting social distancing.\n\nFindingsThe model closely replicates the past data but also shows the true number of cases is likely far larger. We estimate about 493,000 current infected cases (90% CI: 271K-810K) as of March 20th, 2020. Our estimate for cumulative cases of infection until that date is 916,000 (90% CI: 508K, 1.5M), and for total death is 15,485 (90% CI: 8.4K, 25.8K). These numbers are significantly (more than one order of magnitude) higher than official statistics. The trajectory of the epidemic until the end of June could take various paths depending on the impact of seasonality and policies targeting social distancing. In the most optimistic scenario for seasonal effects, depending on policy measures, 1.6 million Iranians (90% CI: 0.9M-2.6M) are likely to get infected, and death toll will reach about 58,000 cases (90% CI: 32K-97K), while in the more pessimistic scenarios, death toll may exceed 103,000 cases (90% CI: 56K-172K).\n\nImplicationOur results suggest that the number of cases and deaths may be over an order of magnitude larger than official statistics in Iran. Absent extended testing capacity other countries may face a significant under-count of existing cases and thus be caught off guard about the actual toll of the epidemic.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Navid Ghaffarzadegan", + "author_inst": "Virginia Tech" + }, + { + "author_name": "Hazhir Rahmandad", + "author_inst": "Massachusetts Institute of Technology" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.22.20041111", "rel_title": "Exponential damping key to successful containment of COVID-19 outbreak", @@ -1568170,45 +1571113,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2020.03.25.008482", - "rel_title": "FDA approved drugs with broad anti-coronaviral activity inhibit SARS-CoV-2 in vitro", - "rel_date": "2020-03-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.25.008482", - "rel_abs": "SARS-CoV-2 emerged in China at the end of 2019 and has rapidly become a pandemic with roughly 2.7 million recorded COVID-19 cases and greater than 189,000 recorded deaths by April 23rd, 2020 (www.WHO.org). There are no FDA approved antivirals or vaccines for any coronavirus, including SARS-CoV-2. Current treatments for COVID-19 are limited to supportive therapies and off-label use of FDA approved drugs. Rapid development and human testing of potential antivirals is greatly needed. A quick way to test compounds with potential antiviral activity is through drug repurposing. Numerous drugs are already approved for human use and subsequently there is a good understanding of their safety profiles and potential side effects, making them easier to fast-track to clinical studies in COVID-19 patients. Here, we present data on the antiviral activity of 20 FDA approved drugs against SARS-CoV-2 that also inhibit SARS-CoV and MERS-CoV. We found that 17 of these inhibit SARS-CoV-2 at a range of IC50 values at non-cytotoxic concentrations. We directly follow up with seven of these to demonstrate all are capable of inhibiting infectious SARS-CoV-2 production. Moreover, we have evaluated two of these, chloroquine and chlorpromazine, in vivo using a mouse-adapted SARS-CoV model and found both drugs protect mice from clinical disease.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Stuart Weston", - "author_inst": "University of Maryland, School of Medicine" - }, - { - "author_name": "Christopher M. Coleman", - "author_inst": "University of Maryland, School of Medicine" - }, - { - "author_name": "Rob Haupt", - "author_inst": "University of Maryland, School of Medicine" - }, - { - "author_name": "James Logue", - "author_inst": "University of Maryland, School of Medicine" - }, - { - "author_name": "Krystal Matthews", - "author_inst": "University of Maryland, School of Medicine" - }, - { - "author_name": "Matthew Frieman", - "author_inst": "University of Maryland, School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.03.25.006569", "rel_title": "Analysis of codon usage and evolutionary rates of the 2019-nCoV genes", @@ -1568852,6 +1571756,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.22.20039933", + "rel_title": "COVID-19 outbreak response: a first assessment of mobility changes in Italy following national lockdown", + "rel_date": "2020-03-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.22.20039933", + "rel_abs": "Italy is currently experiencing the largest COVID-19 outbreak in Europe so far, with more than 100,000 confirmed cases. Following the identification of the first infections, on February 21, 2020, national authorities have put in place an increasing number of restrictions aimed at containing the outbreak and delaying the epidemic peak. Since March 12, the whole country is under lockdown. Here we provide the first quantitative assessment of the impact of such measures on the mobility and the spatial proximity of Italians, through the analysis of a large-scale dataset on de-identified, geo-located smartphone users. With respect to pre-outbreak averages, we estimate a reduction of 50% of the total trips between Italian provinces, following the lockdown. In the same week, the average users radius of gyration has declined by about 50% and the average degree of the users proximity network has dropped by 47% at national level.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Emanuele Pepe", + "author_inst": "ISI Foundation" + }, + { + "author_name": "Paolo Bajardi", + "author_inst": "ISI Foundation" + }, + { + "author_name": "Laetitia Gauvin", + "author_inst": "ISI Foundation" + }, + { + "author_name": "Filippo Privitera", + "author_inst": "Cuebiq Inc." + }, + { + "author_name": "Brennan Lake", + "author_inst": "Cuebiq Inc." + }, + { + "author_name": "Ciro Cattuto", + "author_inst": "ISI Foundation" + }, + { + "author_name": "Michele Tizzoni", + "author_inst": "ISI Foundation" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.20.20039586", "rel_title": "Anti-hypertensive Angiotensin II receptor blockers associated to mitigation of disease severity in elderly COVID-19 patients", @@ -1569592,53 +1572539,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.23.20041848", - "rel_title": "History of Coronary Heart Disease Increases the Mortality Rate of Coronavirus Disease 2019 (COVID-19) Patients: A Nested Case-Control Study Based on Publicly Reported Confirmed Cases in Mainland China", - "rel_date": "2020-03-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.23.20041848", - "rel_abs": "BackgroundChina has experienced an outbreak of a novel human coronavirus (SARS-CoV-2) since December 2019, which quickly became a worldwide pandemic in early 2020. There is limited evidence on the mortality risk effect of pre-existing comorbidities for coronavirus disease 2019 (COVID-19), which has important implications for early treatment.\n\nObjectiveEvaluate the risk of pre-existing comorbidities on COVID-19 mortality, and provide clinical suggestions accordingly.\n\nMethodThis study used a nested case-control design. A total of 94 publicly reported deaths in locations outside of Hubei Province, China, between December 18th, 2019 and March 8th, 2020 were included as cases. Each case was matched with up to three controls, based on gender and age {+/-} 1 year old (94 cases and 181 controls). The inverse probability weighted Cox proportional hazard model was performed.\n\nResultsHistory of comorbidities significantly increased the death risk of COVID-19: one additional pre-existing comorbidity led to an estimated 40% higher risk of death (p<0.001). The estimated mortality risk in patients with CHD was three times of those without CHD (p<0.001). The estimated 30-day survival probability for a profile patient with pre-existing CHD (65-year-old female with no other comorbidities) was 0.53 (95% CI [0.34-0.82]), while it was 0.85 (95% CI [0.79-0.91]) for those without CHD. Older age was also associated with increased death risk: every 5-year increase in age was associated with a 20% increased risk of mortality (p<0.001).\n\nConclusionExtra care and early medical intervention are needed for patients with pre-existing comorbidities, especially CHD.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Tian Gu", - "author_inst": "University of Michigan" - }, - { - "author_name": "Qiao Chu", - "author_inst": "Shanghai Jiao Tong University School of Medicine" - }, - { - "author_name": "Zhangsheng Yu", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Botao Fa", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Anqi Li", - "author_inst": "East China Normal University" - }, - { - "author_name": "Lei Xu", - "author_inst": "Shanghai Chest Hospital, Shanghai Jiao Tong University" - }, - { - "author_name": "Ruijun Wu", - "author_inst": "East China Normal University" - }, - { - "author_name": "Yaping He", - "author_inst": "Shanghai Jiao Tong University School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.23.20040733", "rel_title": "Clinical Characteristics Hospitalized Patients with SARS-Cov-2 and HBV Co-infection", @@ -1570270,6 +1573170,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, + { + "rel_doi": "10.1101/2020.03.24.20042317", + "rel_title": "A Fully Automatic Deep Learning System for COVID-19 Diagnostic and Prognostic Analysis", + "rel_date": "2020-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.24.20042317", + "rel_abs": "Coronavirus disease 2019 (COVID-19) has spread globally, and medical resources become insufficient in many regions. Fast diagnosis of COVID-19, and finding high-risk patients with worse prognosis for early prevention and medical resources optimization is important. Here, we proposed a fully automatic deep learning system for COVID-19 diagnostic and prognostic analysis by routinely used computed tomography.\n\nWe retrospectively collected 5372 patients with computed tomography images from 7 cities or provinces. Firstly, 4106 patients with computed tomography images and gene information were used to pre-train the DL system, making it learn lung features. Afterwards, 1266 patients (924 with COVID-19, and 471 had follow-up for 5+ days; 342 with other pneumonia) from 6 cities or provinces were enrolled to train and externally validate the performance of the deep learning system.\n\nIn the 4 external validation sets, the deep learning system achieved good performance in identifying COVID-19 from other pneumonia (AUC=0.87 and 0.88) and viral pneumonia (AUC=0.86). Moreover, the deep learning system succeeded to stratify patients into high-risk and low-risk groups whose hospital-stay time have significant difference (p=0.013 and 0.014). Without human-assistance, the deep learning system automatically focused on abnormal areas that showed consistent characteristics with reported radiological findings.\n\nDeep learning provides a convenient tool for fast screening COVID-19 and finding potential high-risk patients, which may be helpful for medical resource optimization and early prevention before patients show severe symptoms.\n\nTake-home messageFully automatic deep learning system provides a convenient method for COVID-19 diagnostic and prognostic analysis, which can help COVID-19 screening and finding potential high-risk patients with worse prognosis.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Shuo Wang", + "author_inst": "Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Medicine and Engineering, Beihang University, Beijing, 100191, China." + }, + { + "author_name": "Yunfei Zha", + "author_inst": "Department of Radiology, Renmin Hospital of Wuhan University, Hubei, 430060, China." + }, + { + "author_name": "Weimin Li", + "author_inst": "Department of respiratory and critical care medicine, West China hospital of Sichuan University, Sichuan, 610041, China." + }, + { + "author_name": "Qingxia Wu", + "author_inst": "College of Medicine and Biomedical Information Engineering, Northeastern University, Shenyang, Liaoning 110819, China." + }, + { + "author_name": "Xiaohu Li", + "author_inst": "Department of Radiology, the First Affiliated Hospital of Anhui Medical University, Anhui 230022, China." + }, + { + "author_name": "Meng Niu", + "author_inst": "Department of Interventional Radiology, the First Hospital of China Medical University, Liaoning 110001, China." + }, + { + "author_name": "Meiyun Wang", + "author_inst": "Department of Medical Imaging, Henan Provincial Peoples Hospital and the Peoples Hospital of Zhengzhou University, Zhengzhou 450003, Henan, China." + }, + { + "author_name": "Xiaoming Qiu", + "author_inst": "Department of Radiology, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Edong Healthcare Group, Hubei, 435000, China." + }, + { + "author_name": "Hongjun Li", + "author_inst": "Department of Radiology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China." + }, + { + "author_name": "He Yu", + "author_inst": "Department of respiratory and critical care medicine, West China hospital of Sichuan University, Sichuan, 610041, China." + }, + { + "author_name": "Wei Gong", + "author_inst": "Department of Radiology, Renmin Hospital of Wuhan University, Hubei, 430060, China." + }, + { + "author_name": "Yan Bai", + "author_inst": "Department of Medical Imaging, Henan Provincial Peoples Hospital and the Peoples Hospital of Zhengzhou University, Zhengzhou 450003, Henan, China." + }, + { + "author_name": "Li Li", + "author_inst": "Department of Radiology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China." + }, + { + "author_name": "Yongbei Zhu", + "author_inst": "Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Medicine and Engineering, Beihang University, Beijing, 100191, China." + }, + { + "author_name": "Liusu Wang", + "author_inst": "Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Medicine and Engineering, Beihang University, Beijing, 100191, China." + }, + { + "author_name": "Jie Tian", + "author_inst": "Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Medicine and Engineering, Beihang University, Beijing, 100191, China." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.03.25.20037721", "rel_title": "Risk Factors Associated with Clinical Outcomes in 323 COVID-19 Patients in Wuhan, China", @@ -1571178,81 +1574157,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, - { - "rel_doi": "10.1101/2020.03.24.20042358", - "rel_title": "Comorbid Diabetes Mellitus was Associated with Poorer Prognosis in Patients with COVID-19: A Retrospective Cohort Study", - "rel_date": "2020-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.24.20042358", - "rel_abs": "BackgroundThe 2019 novel coronavirus disease (COVID-19) emerged in Wuhan, Hubei province, China, and was characterized as pandemic by the World Health Organization. Diabetes mellitus is an established risk factor for poor clinical outcomes, but the association of diabetes with the prognosis of COVID-19 have not been reported yet.\n\nMethodsIn this cohort study, we retrospectively reviewed 258 consecutive hospitalized COVID-19 patients with or without diabetes at the West Court of Union Hospital of Huazhong University of Science and Technology in Wuhan, China, recruited from January 29 to February 12, 2020. The cases were confirmed by real-time PCR and the demographic, clinical, laboratory, radiological, and treatment data were collected and analyzed. Prognosis was defined as hospitalization, discharged survivor and death, which was followed up until March 12, 2020.\n\nResultsOf the 258 hospitalized patients (63 with diabetes) with COVID-19, the median age was 64 years (range 23-91), and 138 (53.5%) were male. No significant differences in age and sex were identified between patients with and without diabetes. Common symptoms included fever (82.2%), dry cough (67.1%), polypnea (48.1%), and fatigue (38%). Patients with diabetes had significantly higher leucocyte and neutrophil counts, and higher levels of fasting blood glucose, serum creatinine, urea nitrogen and creatine kinase isoenzyme MB at admission compared with those without diabetes. COVID-19 patients with diabetes were more likely to develop severe or critical disease condition with more complications at presentation, and had higher incidence rates of antibiotic therapy, non-invasive and invasive mechanical ventilation, and death (11.1% vs. 4.1%). Cox proportional hazard model showed that diabetes (adjusted hazard ratio [aHR]=3.64; 95% confidence interval [CI]: 1.09, 12.21) and fasting blood glucose (aHR=1.19; 95% CI: 1.08, 1.31) were associated with the fatality of COVID-19, adjusting for potential confounders.\n\nConclusionsDiabetes mellitus is associated with greater disease severity and a higher risk of mortality in patients with COVID-19. Primary and secondary prevention strategies are needed for COVID-19 patients with diabetes.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Yan Zhang", - "author_inst": "Department of Respiratory Medicine, Xiangya Hospital, Central South University" - }, - { - "author_name": "Yanhui Cui", - "author_inst": "Department of Respiratory Medicine, Xiangya Hospital, Central South University" - }, - { - "author_name": "Minxue Shen", - "author_inst": "Department of Dermatology, Xiangya Hospital; Department of Social Medicine and Health Management, Xiangya School of Public Health, Central South University" - }, - { - "author_name": "Jianchu Zhang", - "author_inst": "Department of Respiratory Medicine, Union Hospital of Huazhong University of Science and Technology" - }, - { - "author_name": "Ben Liu", - "author_inst": "Department of Emergency, Xiangya Hospital, Central South University" - }, - { - "author_name": "Minhui Dai", - "author_inst": "Department of Respiratory Medicine, Xiangya Hospital, Central South University" - }, - { - "author_name": "Linli Chen", - "author_inst": "Department of Respiratory Medicine, Xiangya Hospital, Central South University" - }, - { - "author_name": "Duoduo Han", - "author_inst": "Department of Respiratory Medicine, Xiangya Hospital, Central South University" - }, - { - "author_name": "Yifei Fan", - "author_inst": "Department of Respiratory Medicine, Xiangya Hospital, Central South University" - }, - { - "author_name": "Yanjun Zeng", - "author_inst": "Department of Respiratory Medicine, Xiangya Hospital, Central South University" - }, - { - "author_name": "Wen Li", - "author_inst": "Department of Respiratory Medicine, Xiangya Hospital, Central South University" - }, - { - "author_name": "Fengyu Lin", - "author_inst": "Department of Respiratory Medicine, Xiangya Hospital, Central South University" - }, - { - "author_name": "Sha Li", - "author_inst": "Department of Radiology, Xiangya Hospital, Central South University" - }, - { - "author_name": "Xiang Chen", - "author_inst": "Department of Dermatology, Xiangya Hospital, Central South University" - }, - { - "author_name": "Pinhua Pan", - "author_inst": "Department of Respiratory Medicine, Xiangya Hospital, Central South University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2020.03.24.20042408", "rel_title": "Acute kidney injury at early stage as a negative prognostic indicator of patients with COVID-19: a hospital-based retrospective analysis", @@ -1572028,6 +1574932,65 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.03.23.002832", + "rel_title": "scRNA-seq reveals ACE2 and TMPRSS2 expression in TROP2+ Liver Progenitor Cells: Implications in COVID-19 associated Liver Dysfunction", + "rel_date": "2020-03-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.23.002832", + "rel_abs": "The recent pandemic of coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 was first reported in China (December 2019) and now prevalent in [~]170 countries across the globe. Entry of SARS-CoV-2 into mammalian cells require the binding of viral Spike (S) proteins to the ACE2 (angiotensin converting enzyme 2) receptor. Once entered the S protein is primed by a specialised serine protease, TMPRSS2 (Transmembrane Serine Protease 2) in the host cell. Importantly, beside respiratory symptoms, consistent with other common respiratory virus infection when patients become viraemic, a significant number of COVID-19 patients also develop liver comorbidities. We explored if specific target cell-type in the mammalian liver, could be implicated in disease pathophysiology other than the general deleterious response to cytokine storms. Here we employed single-cell RNA-seq (scRNA-seq) to survey the human liver and identified potentially implicated liver cell-type for viral ingress. We report the co-expression of ACE2 and TMPRSS2 in a TROP2+ liver progenitor population. Importantly, we fail to detect the expression of ACE2 in hepatocyte or any other liver (immune and stromal) cell types. These results indicated that in COVID-19 associated liver dysfunction and cell death, viral infection of TROP2+ progenitors in liver may significantly impaired liver regeneration and could lead to pathology.\n\nHighlights- EPCAM+ Liver progenitors co-express ACE2 and TMPRSS2\n- ACE2 and TMPRSS2 expression is highest in TROP2high progenitors\n- ACE2 and TMPRSS2 cells express cholangiocyte biased fate markers\n- ACE2 and TMPRSS2 positive cells are absent in human fetal liver", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Justine Jia Wen Seow", + "author_inst": "Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Genome, #02-01, Singapore 138672, Singapore" + }, + { + "author_name": "Rhea Pai", + "author_inst": "Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Genome, #02-01, Singapore 138672, Singapore" + }, + { + "author_name": "Archita Mishra", + "author_inst": "Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 3 and 4, Singapore 138648, Singapore" + }, + { + "author_name": "Edwin Shepherdson", + "author_inst": "Department of Reproductive Medicine, KK Womens and Childrens Hospital, Singapore" + }, + { + "author_name": "Tony Kiat Hon Lim", + "author_inst": "Department of Pathology, Singapore General Hospital, Singapore 169608, Singapore" + }, + { + "author_name": "Brian K P Goh", + "author_inst": "Department of Hepato-Pancreato-Biliary and Transplant Surgery, Singapore General Hospital, Singapore 169608, Singapore" + }, + { + "author_name": "Jerry KY Chan", + "author_inst": "Duke-NUS Medical School" + }, + { + "author_name": "Pierce KH Chow", + "author_inst": "Division of Surgical Oncology, National Cancer Centre, Singapore 169610, Singapore" + }, + { + "author_name": "Florent Ginhoux", + "author_inst": "Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 3 and 4, Singapore 138648, Singapore" + }, + { + "author_name": "Ramanuj DasGupta", + "author_inst": "Genome Institute of Singapore" + }, + { + "author_name": "Ankur Sharma", + "author_inst": "Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Genome, #02-01, Singapore 138672, Singapore" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.03.22.20038919", "rel_title": "The impact of temperature and absolute humidity on the coronavirus disease 2019 (COVID-19) outbreak - evidence from China", @@ -1572776,53 +1575739,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.03.22.20034041", - "rel_title": "First Clinical Study Using HCV Protease Inhibitor Danoprevir to Treat Naive and Experienced COVID-19 Patients", - "rel_date": "2020-03-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.22.20034041", - "rel_abs": "As coronavirus disease 2019 (COVID-19) outbreak, caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), started in China in January, 2020, repurposing approved drugs is emerging as important therapeutic options. We reported here the first clinical study using hepatitis C virus (HCV) protease inhibitor, danoprevir, to treat COVID-19 patients. Danoprevir (Ganovo(R)) is a potent HCV protease (NS3/4A) inhibitor (IC50 = 0.29 nM), which was approved and marketed in China since 2018 to treat chronic hepatitis C patients. Ritonavir is a CYP3A4 inhibitor to enhance plasma concentration of danoprevir while it also acts as a human immunodeficiency virus (HIV) protease inhibitor at high doses. The chymotrypsin-like protease of SARS-CoV-2 shares structure similarity with HCV and HIV proteases. In the current clinical study (NCT04291729) conducted at the Nineth Hospital of Nanchang, we evaluated therapeutic effects of danoprevir, boosted by ritonavir, on treatment naive and experienced COVID-19 patients. The data from this small-sample clinical study showed that danoprevir boosted by ritonavir is safe and well tolerated in all patients. After 4 to 12-day treatment of danoprevir boosted by ritonavir, all eleven patients enrolled, two naive and nine experienced, were discharged from the hospital as they met all four conditions as follows: (1) normal body temperature for at least 3 days; (2) significantly improved respiratory symptoms; (3) lung imaging shows obvious absorption and recovery of acute exudative lesion; and (4) two consecutive RT-PCR negative tests of SARS-CoV-2 nucleotide acid (respiratory track sampling with interval at least one day). Our findings suggest that repurposing danoprevir for COVID-19 is a promising therapeutic option.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Hongyi Chen", - "author_inst": "The first department of infectious disease, the nineth hospital of Nanchang, Nanchang, Jiangxi province, China" - }, - { - "author_name": "Zhicheng Zhang", - "author_inst": "The intensive care unit, the nineth hospital of Nanchang, Nanchang, Jiangxi province, China" - }, - { - "author_name": "Li Wang", - "author_inst": "The first department of infectious disease, the nineth hospital of Nanchang, Nanchang, Jiangxi province, China" - }, - { - "author_name": "Zhihua Huang", - "author_inst": "The radiology department, the nineth hospital of Nanchang, Nanchang, Jiangxi province, China" - }, - { - "author_name": "Fanghua Gong", - "author_inst": "The second department of infectious disease, the nineth hospital of Nanchang, Nanchang, Jiangxi province, China" - }, - { - "author_name": "Xiaodong Li", - "author_inst": "Ascletis Bioscience Co., Ltd., Hangzhou, Zhejiang province, China" - }, - { - "author_name": "Yahong Chen", - "author_inst": "Ascletis Bioscience Co., Ltd., Hangzhou, Zhejiang province, China" - }, - { - "author_name": "Jinzi J. WU", - "author_inst": "Ascletis Bioscience Co., Ltd., Hangzhou, Zhejiang province, China" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.19.20038794", "rel_title": "MATHEMATICAL PREDICTIONS FOR COVID-19 AS A GLOBAL PANDEMIC", @@ -1573642,6 +1576558,213 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.16.20036145", + "rel_title": "The feasibility of convalescent plasma therapy in severe COVID-19 patients: a pilot study", + "rel_date": "2020-03-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.16.20036145", + "rel_abs": "Currently, there are no approved specific antiviral agents for 2019 novel coronavirus disease (COVID-19). In this study, ten severe patients confirmed by real-time viral RNA test were enrolled prospectively. One dose of 200 mL convalescent plasma (CP) derived from recently recovered donors with the neutralizing antibody titers above 1:640 was transfused to the patients as an addition to maximal supportive care and antiviral agents. The primary endpoint was the safety of CP transfusion. The second endpoints were the improvement of clinical symptoms and laboratory parameters within 3 days after CP transfusion. The median time from onset of illness to CP transfusion was 16.5 days. After CP transfusion, the level of neutralizing antibody increased rapidly up to 1:640 in five cases, while that of the other four cases maintained at a high level (1:640). The clinical symptoms were significantly improved along with increase of oxyhemoglobin saturation within 3 days. Several parameters tended to improve as compared to pre-transfusion, including increased lymphocyte counts (0.65x109/L vs. 0.76x109/L) and decreased C-reactive protein (55.98 mg/L vs. 18.13 mg/L). Radiological examinations showed varying degrees of absorption of lung lesionswithin 7 days. The viral load was undetectable after transfusion in seven patients who had previous viremia. No severe adverse effects were observed. This study showed CP therapy was welltolerated and could potentially improve the clinical outcomes through neutralizing viremia in severe COVID-19 cases. The optimal dose and time point, as well as the clinical benefit of CP therapy, needs further investigation in larger well-controlled trials.\n\nSignificance StatementCOVID-19 is currently a big threat to global health. However, no specific antiviral agents are available for its treatment. In this work, we explored the feasibility of convalescent plasma (CP) transfusion to rescue severe patients. The results from 10 severe adult cases showed that one dose (200 mL) of CP was welltolerated and could significantly increase or maintain the neutralizing antibodies at a high level, leading to disappearance of viremia in 7 days. Meanwhile, clinical symptoms and paraclinical criteria rapidly improved within 3 days. Radiological examination showed varying degrees of absorption of lung lesions within 7 days. These results indicate that CP can serve as a promising rescue option for severe COVID-19 while the randomized trial is warranted.", + "rel_num_authors": 48, + "rel_authors": [ + { + "author_name": "Kai Duan", + "author_inst": "1.China National Biotec Group Company Limited, China;2.National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Prod" + }, + { + "author_name": "Bende Liu", + "author_inst": "First People Hospital of Jiangxia District, Wuhan, China" + }, + { + "author_name": "Cesheng Li", + "author_inst": "Sinopharm Wuhan Plasma-derived Biotherapies Co.,Ltd, Wuhan, China" + }, + { + "author_name": "Huajun Zhang", + "author_inst": "CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China" + }, + { + "author_name": "Ting Yu", + "author_inst": "WuHanJinyintan Hospital, Wuhan, China" + }, + { + "author_name": "Jieming Qu", + "author_inst": "Department of Respiratory and Critical Care Medicine, National Research Center for Translational Medicine (Shanghai),Institute of Respiratory Diseases, Ruijin H" + }, + { + "author_name": "Min Zhou", + "author_inst": "Department of Respiratory and Critical Care Medicine, National Research Center for Translational Medicine (Shanghai),Institute of Respiratory Diseases, Ruijin H" + }, + { + "author_name": "Li Chen", + "author_inst": "Clinical Research Center, Department of Gastroenterology, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai, China" + }, + { + "author_name": "Shengli Meng", + "author_inst": "National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co.Ltd. ,Wuhan, China" + }, + { + "author_name": "Yong Hu", + "author_inst": "Sinopharm Wuhan Plasma-derived Biotherapies Co.,Ltd, Wuhan, China" + }, + { + "author_name": "Cheng Peng", + "author_inst": "CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China" + }, + { + "author_name": "Mingchao Yuan", + "author_inst": "Wuhan Blood Center, Wuhan, China" + }, + { + "author_name": "Jinyan Huang", + "author_inst": "State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine (Shanghai), Ruijin Hospital, Sha" + }, + { + "author_name": "Zejun Wang", + "author_inst": "National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co.Ltd., Wuhan, China" + }, + { + "author_name": "Jianhong Yu", + "author_inst": "Sinopharm Wuhan Plasma-derived Biotherapies Co.,Ltd, Wuhan, China" + }, + { + "author_name": "Xiaoxiao Gao", + "author_inst": "CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China" + }, + { + "author_name": "Dan Wang", + "author_inst": "Wuhan Blood Center, Wuhan, China" + }, + { + "author_name": "Xiaoqi Yu", + "author_inst": "Research Laboratory of Clinical Virology, Ruijin Hospital and Ruijin Hospital North, National Research Center for Translational Medicine (Shanghai), Shanghai Ji" + }, + { + "author_name": "Li Li", + "author_inst": "National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co.Ltd., Wuhan, China" + }, + { + "author_name": "Jiayou Zhang", + "author_inst": "National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co.Ltd., Wuhan, China" + }, + { + "author_name": "Xiao Wu", + "author_inst": "Sinopharm Wuhan Plasma-derived Biotherapies Co.,Ltd, Wuhan, China" + }, + { + "author_name": "Bei Li", + "author_inst": "CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China" + }, + { + "author_name": "Yanping Yu", + "author_inst": "Department of Respiratory and Critical Care Medicine, National Research Center for Translational Medicine (Shanghai),Institute of Respiratory Diseases, Ruijin H" + }, + { + "author_name": "Wei Chen", + "author_inst": "National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co.Ltd., Wuhan, China" + }, + { + "author_name": "Yan Peng", + "author_inst": "Sinopharm Wuhan Plasma-derived Biotherapies Co.,Ltd, Wuhan, China" + }, + { + "author_name": "Yeqin Hu", + "author_inst": "National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co.Ltd., Wuhan, China" + }, + { + "author_name": "Lianzhen Lin", + "author_inst": "Sinopharm Wuhan Plasma-derived Biotherapies Co.,Ltd, Wuhan, China" + }, + { + "author_name": "Xuefei Liu", + "author_inst": "Department of Respiratory and Critical Care Medicine, National Research Center for Translational Medicine (Shanghai),Institute of Respiratory Diseases, Ruijin H" + }, + { + "author_name": "Shihe Huang", + "author_inst": "National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co.Ltd., Wuhan, China" + }, + { + "author_name": "Zhijun Zhou", + "author_inst": "Sinopharm Wuhan Plasma-derived Biotherapies Co.,Ltd, Wuhan, China" + }, + { + "author_name": "Lianghao Zhang", + "author_inst": "National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co.Ltd., Wuhan, China" + }, + { + "author_name": "Yue Wang", + "author_inst": "Sinopharm Wuhan Plasma-derived Biotherapies Co.,Ltd, Wuhan, China" + }, + { + "author_name": "Zhi Zhang", + "author_inst": "National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co.Ltd., Wuhan, China" + }, + { + "author_name": "Kun Deng", + "author_inst": "Sinopharm Wuhan Plasma-derived Biotherapies Co.,Ltd, Wuhan, China" + }, + { + "author_name": "Zhiwu Xia", + "author_inst": "National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co.Ltd., Wuhan, China" + }, + { + "author_name": "Qin Gong", + "author_inst": "Sinopharm Wuhan Plasma-derived Biotherapies Co.,Ltd, Wuhan, China" + }, + { + "author_name": "Wei Zhang", + "author_inst": "Sinopharm Wuhan Plasma-derived Biotherapies Co.,Ltd, Wuhan, China" + }, + { + "author_name": "Xiaobei Zheng", + "author_inst": "Sinopharm Wuhan Plasma-derived Biotherapies Co.,Ltd, Wuhan, China" + }, + { + "author_name": "Ying Liu", + "author_inst": "Sinopharm Wuhan Plasma-derived Biotherapies Co.,Ltd, Wuhan, China" + }, + { + "author_name": "Huichuan Yang", + "author_inst": "China National Biotec Group Company Limited, Beijing, China" + }, + { + "author_name": "Dongbo Zhou", + "author_inst": "China National Biotec Group Company Limited, Beijing, China" + }, + { + "author_name": "Ding Yu", + "author_inst": "China National Biotec Group Company Limited, Beijing, China" + }, + { + "author_name": "Jifeng Hou", + "author_inst": "National Institute for Food and Drug Control of China, Beijing, China" + }, + { + "author_name": "Zhengli Shi", + "author_inst": "CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China" + }, + { + "author_name": "Saijuan Chen", + "author_inst": "State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine (Shanghai), Ruijin Hospital, Sha" + }, + { + "author_name": "Zhu Chen", + "author_inst": "State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine (Shanghai), Ruijin Hospital, Sha" + }, + { + "author_name": "Xin-xin Zhang", + "author_inst": "Research Laboratory of Clinical Virology, Ruijin Hospital and Ruijin Hospital North, National Research Center for Translational Medicine (Shanghai), Shanghai Ji" + }, + { + "author_name": "Xiaoming Yang", + "author_inst": "China National Biotec Group Company Limited, National Engineering Technology Research Center for Combined Vaccines, Wuhan, China" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.20.20040055", "rel_title": "The Effectiveness of Social Distancing in Mitigating COVID-19 Spread: a modelling analysis", @@ -1574206,29 +1577329,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.03.19.20038752", - "rel_title": "Bibliometric Analysis of Global Scientific Research on SARSCoV-2 (COVID-19)", - "rel_date": "2020-03-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.19.20038752", - "rel_abs": "Background and AimSince late 2019, an unknown-origin pneumonia outbreak detected in Wuhan city, Hubei Province, China. We aimed to build a model to qualitatively and quantitatively assess publications of research of COVID-19 from 2019 to 2020.\n\nMaterials and MethodsData were obtained from the Web of Science (WOS), PubMed, and Scopus Core Collection on March 02, 2020, and updated on March 10. We conducted a qualitative and quantitative analysis of publication outputs, journals, authors, institutions, countries, cited references, keywords, and terms according to bibliometric methods using VOS viewer c software packages.\n\nResultsInitially, we identified 227 papers, of which after an exclusion process, 92 studies were selected for statistical analyses. China accounted for the highest proportion of published research (44 papers, 40.48%), followed by the United States (21 papers, 19.32%), and Canada (7 papers, 6.44%). Adjusted by gross domestic product (GDP), ranked first, with 0.003 articles per billion GDP. In total, the top 10 journals published 47 articles, which accounted for 51.08% of all publications in this Feld. A total of 6 studies (05.52%) were supported by National Natural Science Foundation of China. Chinese Academy of Sciences ranked second 2, 2.76%).\n\nConclusionBibliometric and visualized mapping may quantitatively monitor research performance in science and present predictions. The subject of this study was the fast growing publication on COVID-19. Most studies are published in journals with very high impact factors (IFs) and other journals are more interested in this type of research.\n\nHighlightsO_LIBibliometric description and mapping provided a birds-eye view of information on Covid-19 related research\nC_LIO_LIReaders to comprehend the history of published Covid-19 articles in just a few minutes.\nC_LIO_LIWe evaluated the research strength of countries and institutions,\nC_LIO_LIScholars might refer to in order to find cooperative institutions.\nC_LIO_LIDuring our research using the selected database, we tried to guarantee comprehension and objectivity.\nC_LI", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Fateme Rafiei Nasab", - "author_inst": "Msc in Medical informatics; Department of Scientometrics, Deputy of Research and Technology Affaires; Ahvaz Jundishapur University of Medical S" - }, - { - "author_name": "Fakher rahim", - "author_inst": "Ahvaz Jundishapur University of Medical Sciences" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.03.21.20038778", "rel_title": "Clinical characteristics and reasons of different duration from onset to release from quarantine for patients with COVID-19 Outside Hubei province, China.", @@ -1574808,6 +1577908,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.19.20034447", + "rel_title": "Potential biochemical markers to identify severe cases among COVID-19 patients", + "rel_date": "2020-03-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.19.20034447", + "rel_abs": "There is a high mortality and long hospitalization period for severe cases with 2019 novel coronavirus disease (COVID-19) pneumonia. Therefore, it makes sense to search for a potential biomarker that could rapidly and effectively identify severe cases early. Clinical samples from 28 cases of COVID-19 (8 severe cases, 20 mild cases) in Zunyi District from January 29, 2020 to February 21, 2020 were collected and otherwise statistically analysed for biochemical markers. Serum urea, creatinine (CREA) and cystatin C (CysC) concentrations in severe COVID-19 patients were significantly higher than those in mild COVID-19 patients (P<0.001), and there were also significant differences in serum direct bilirubin (DBIL), cholinesterase (CHE) and lactate dehydrogenase (LDH) concentrations between severe and mild COVID-19 patients (P<0.05). Serum urea, CREA, CysC, DBIL, CHE and LDH could be used to distinguish severe COVID-19 cases from mild COVID-19 cases. In particular, serum biomarkers, including urea, CREA, CysC, which reflect glomerular filtration function, may have some significance as potential indicators for the early diagnosis of severe COVID-19 and to distinguish it from mild COVID-19. Glomerular filtration function injury in severe COVID-19 patients should also be considered by clinicians.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "JIANLIN XIANG", + "author_inst": "Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Guizhou, China." + }, + { + "author_name": "JING WEN", + "author_inst": "Department of Medical Imaging, Affiliated Hospital of Zunyi Medical University, Guizhou, China." + }, + { + "author_name": "XIAOQING YUAN", + "author_inst": "Department of Laboratory Medicine, The Fourth People's Hospital of Zunyi city, Guizhou, China" + }, + { + "author_name": "Shun Xiong", + "author_inst": "School of Laboratory Medicine, Zunyi Medical University, Guizhou, China." + }, + { + "author_name": "XUE ZHOU", + "author_inst": "School of Laboratory Medicine, Zunyi Medical University, Guizhou, China." + }, + { + "author_name": "CHANGJIN LIU", + "author_inst": "The First Affiliated Hospital of Zunyi Medical University" + }, + { + "author_name": "XUN MIN", + "author_inst": "Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Guizhou, China." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.20.20039834", "rel_title": "Development and Evaluation of an AI System for COVID-19", @@ -1576016,97 +1579159,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.03.20.001008", - "rel_title": "RT-qPCR DETECTION OF SARS-CoV-2 RNA FROM PATIENT NASOPHARYNGEAL SWAB USING QIAGEN RNEASY KITS OR DIRECTLY VIA OMISSION OF AN RNA EXTRACTION STEP", - "rel_date": "2020-03-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.20.001008", - "rel_abs": "The ongoing COVID-19 pandemic has caused an unprecedented need for rapid diagnostic testing. The Centers for Disease Control and Prevention (CDC) and the World Health Organization (WHO) recommend a standard assay that includes an RNA extraction step from a nasopharyngeal (NP) swab followed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to detect the purified SARS-CoV-2 RNA. The current global shortage of RNA extraction kits has caused a severe bottleneck to COVID-19 testing. We hypothesized that SARS-CoV-2 RNA could be detected from NP samples via a direct RT-qPCR assay that omits the RNA extraction step altogether, and tested this hypothesis on a series of blinded clinical samples. The direct RT-qPCR approach correctly identified 92% of NP samples (n = 155) demonstrated to be positive for SARS-CoV-2 RNA by traditional clinical diagnostic RT-qPCR that included an RNA extraction. Thus, direct RT-qPCR could be a front-line approach to identify the substantial majority of COVID-19 patients, reserving a repeat test with RNA extraction for those individuals with high suspicion of infection but an initial negative result. This strategy would drastically ease supply chokepoints of COVID-19 testing and should be applicable throughout the world.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Emily A Bruce", - "author_inst": "The University of Vermont" - }, - { - "author_name": "Meei-Li Huang", - "author_inst": "University of Washington" - }, - { - "author_name": "Garrett A Perchetti", - "author_inst": "University of Washington" - }, - { - "author_name": "Scott Tighe", - "author_inst": "The University of Vermont" - }, - { - "author_name": "Jessica J Hoffman", - "author_inst": "The University of Vermont" - }, - { - "author_name": "Pheobe Laaguiby", - "author_inst": "The University of Vermont" - }, - { - "author_name": "Diana L Gerrard", - "author_inst": "The University of Vermont" - }, - { - "author_name": "Arun Nalla", - "author_inst": "University of Washington" - }, - { - "author_name": "Yulun Wei", - "author_inst": "University of Washington" - }, - { - "author_name": "Alexander L Greninger", - "author_inst": "University of Washington" - }, - { - "author_name": "Sean A. Diehl", - "author_inst": "University of Vermont" - }, - { - "author_name": "David J Shirley", - "author_inst": "IXIS LLC" - }, - { - "author_name": "Debra G. B. Leonard", - "author_inst": "The University of Vermont" - }, - { - "author_name": "Christopher D. Huston", - "author_inst": "The University of Vermont" - }, - { - "author_name": "Beth D. Kirkpatrick", - "author_inst": "The University of Vermont" - }, - { - "author_name": "Julie Dragon", - "author_inst": "The University of Vermont" - }, - { - "author_name": "Jessica W Crothers", - "author_inst": "The University of Vermont" - }, - { - "author_name": "Keith R Jerome", - "author_inst": "University of WA/Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Jason W Botten", - "author_inst": "The University of Vermont" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.03.20.999029", "rel_title": "Replication of SARS-CoV-2 in human respiratory epithelium", @@ -1576790,6 +1579842,33 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2020.03.17.20037770", + "rel_title": "COVID-19 Progression Timeline and Effectiveness of Response-to-Spread Interventions across the United States", + "rel_date": "2020-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.17.20037770", + "rel_abs": "Motivated by the rapid upsurge of COVID-19 cases in the United States beginning March 2020, we forecast the disease spread and assess the effectiveness of containment strategies by using an estalished network-driven epidemic dynamic model. Our model is initialized using the daily counts of active and confirmed COVID-19 cases across the US. Based on our model predictions for the March 14-16 timeframe, the national epidemic peak could be expected to arrive by early June, corresponding to a daily active count of {approx} 7% of the US population, if no containment plans are implemented. Epidemic peaks are expected to arrive in the states of Washington and New York by May 21 and 25, respectively. With a modest 25% reduction in COVID-19 transmissibility via community-level interventions, the epidemic progression could be delayed by up to 34 days. Wholesale interstate traffic restriction is ineffective in delaying the epidemic outbreak, but it does desynchronize the arrival of state-wise epidemic peaks, which could potentially alleviate the burden on limited available medical resources. In addition to forecasting the arrival timeline of the state-wise epidemic peaks, we attempt at informing the optimal timing necessary to enforce community-level interventions. Our findings underscore the pressing need for preparedness and timely interventions in states with a large fraction of the vulnerable uninsured and liquid-asset-poverty populations.\n\nForecast websitehttps://sites.google.com/view/covid19forecast", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Pai Liu", + "author_inst": "Washington University in Saint Louis" + }, + { + "author_name": "Payton Beeler", + "author_inst": "Washington University in Saint Louis" + }, + { + "author_name": "Rajan K Chakrabarty", + "author_inst": "Washington University in Saint Louis" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.16.20035014", "rel_title": "Evaluation of Nucleocapsid and Spike Protein-based ELISAs for detecting antibodies against SARS-CoV-2", @@ -1577518,25 +1580597,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.03.17.20037309", - "rel_title": "Machine Learning the Phenomenology of COVID-19 From Early Infection Dynamics", - "rel_date": "2020-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.17.20037309", - "rel_abs": "We present a robust data-driven machine learning analysis of the COVID-19 pandemic from its early infection dynamics, specifically infection counts over time. The goal is to extract actionable public health insights. These insights include the infectious force, the rate of a mild infection becoming serious, estimates for asymtomatic infections and predictions of new infections over time. We focus on USA data starting from the first confirmed infection on January 20 2020. Our methods reveal significant asymptomatic (hidden) infection, a lag of about 10 days, and we quantitatively confirm that the infectious force is strong with about a 0.14% transition from mild to serious infection. Our methods are efficient, robust and general, being agnostic to the specific virus and applicable to different populations or cohorts.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Malik Magdon-Ismail", - "author_inst": "Rensselaer Polytechnic Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.03.17.20037481", "rel_title": "Pandemic dynamics of COVID-19 using epidemic stage, instantaneous reproductive number and pathogen genome identity (GENI) score: modeling molecular epidemiology", @@ -1578168,6 +1581228,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.18.20038224", + "rel_title": "Assessing the Global Tendency of COVID-19 Outbreak", + "rel_date": "2020-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.18.20038224", + "rel_abs": "COVID-19 is now widely spreading around the world as a global pandemic. In this report, we estimated the global tendency of COVID-19 and analyzed the associated global epidemic risk, given that the status quo is continued without further measures being taken.\n\nBased on official data of confirmed and recovered cases until May 21, 2020, the results showed that the global R0, excluding China, was estimated to be 2.76 (95% CI: 2.57 - 2.95). The United States, Germany, Italy, and Spain have peak values over 100,000. Using dynamical model and cluster analysis, we partition the globe into four regional epicenters of the outbreak: Southeast Asia extending southward to Oceania, the Middle East, Western Europe, and North America. Among them, Western Europe would become the major center of the outbreak. The peak values in Germany, Italy, and Spain were estimated to be 228,000, 291,000, and 298,000, respectively. Based on the current control measures by May 21, 2020, the peak value in the United States will reach 2,114,000. The cumulative number of 51 mainly researched countries patients might finally attain 6,542,000 (95% CI: 4,772,000 - 40,735,000). We also estimated the diagnosis rate, recovery rate, and infection degree of each country or region, and used clustering algorithm to retrieve countries or regions with similar epidemic characteristics. Several suggestions have been proposed for countries or regions in different clusters.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Qinghe Liu", + "author_inst": "Southeast University, China" + }, + { + "author_name": "Zhicheng Liu", + "author_inst": "Southeast University, China" + }, + { + "author_name": "Junkai Zhu", + "author_inst": "Southeast University, China" + }, + { + "author_name": "Yuhao Zhu", + "author_inst": "Erasmus University Rotterdam, Rotterdam, the Netherlands" + }, + { + "author_name": "Deqiang Li", + "author_inst": "Southeast University, China" + }, + { + "author_name": "Zefei Gao", + "author_inst": "Southeast University, China" + }, + { + "author_name": "Liuling Zhou", + "author_inst": "Southeast University, China" + }, + { + "author_name": "Yuanbo Tang", + "author_inst": "Southeast University, School of Information Science and Engineering" + }, + { + "author_name": "Xiang Zhang", + "author_inst": "Southeast University" + }, + { + "author_name": "Junyan Yang", + "author_inst": "Southeast University, China" + }, + { + "author_name": "Qiao Wang", + "author_inst": "Southeast University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.19.20038729", "rel_title": "Fear, Access, and the Real-Time Estimation of Etiological Parameters for Outbreaks of Novel Pathogens", @@ -1578856,37 +1581975,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.18.20037994", - "rel_title": "Investigating the Impact of Asymptomatic Carriers on COVID-19 Transmission", - "rel_date": "2020-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.18.20037994", - "rel_abs": "Coronavirus disease 2019 (COVID-19) is a novel human respiratory disease caused by the SARS-CoV-2 virus. Asymptomatic carriers of the COVID-19 virus display no clinical symptoms but are known to be contagious. Recent evidence reveals that this subpopulation, as well as persons with mild disease, are a major contributor in the propagation of the disease. The rapid spread of COVID-19 forced governments around the world to establish and enforce generalized risk mitigation strategies, from lockdowns to guidelines for social distancing, in an effort to minimize community transmission. This created an unprecedented epidemiological situation not properly characterized by existing mathematical models of isolation and quarantine. In this manuscript, we present a mathematical model for community transmission of COVID-19 taking into account asymptomatic carriers and varying degrees of risk mitigation. The main results consist of an exact calculation of the effective reproduction number [Formula], and a modeling framework that enables the quantification of the effect of risk mitigation and asymptomatism on community transmission. A computation of [Formula] is provided using mean parameters. The point estimate of the basic reproduction number is [Formula].", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Jacob B Aguilar", - "author_inst": "Saint Leo University" - }, - { - "author_name": "Jeremy Samuel Faust", - "author_inst": "Brigham and Women's Hospital Department of Emergency Medicine" - }, - { - "author_name": "Lauren M. Westafer", - "author_inst": "University of Massachusetts Medical School-Baystate" - }, - { - "author_name": "Juan B. Gutierrez", - "author_inst": "University of Texas at San Antonio" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.17.20037564", "rel_title": "The prevention of nosocomial SARS-CoV2 transmission in endoscopy: a systematic review of recommendations within gastroenterology to identify best practice.", @@ -1579590,6 +1582678,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.03.15.20036541", + "rel_title": "Transmissibility of coronavirus disease 2019 (COVID-19) in Chinese cities with different transmission dynamics of imported cases", + "rel_date": "2020-03-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.15.20036541", + "rel_abs": "BackgroundMonitoring the time-varying reproduction number (Rt) of the disease is useful in determining whether there is sustained transmission in a population. In this study, we examined Rt of COVID-19 and compared its transmissibility between different intervention periods in Hangzhou and Shenzhen.\n\nMethodsDaily aggregated counts of confirmed imported and local cases between January 1, 2020 and March 13, 2020 were analysed. A likelihood function was constructed to estimate Rt, accounting for imported cases.\n\nResultsAlthough Hangzhou had fewer number of cases than Shenzhen, Shenzhen had higher proportion of imported cases than Hangzhou (83% vs 29%). Since the epidemic of COVID-19 in Shenzhen was dominated by imported cases, Rt was kept below unity through time. On the contrary, Rt was greater than unity in Hangzhou from 16 January to 7 February due to the surge in local cases. Credits to the Wuhan lockdown and outbreak response measures following the local lockdown, Rt decreased steadily and dropped below unity in mid-February.\n\nConclusionThe lockdown measures and local outbreak responses helped reduce the potential of local transmission in Hangzhou and Shenzhen. Meanwhile, cities with similar epidemic trend could have different transmission dynamics given the variation in imported cases.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Ka Chun Chong", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Wei Cheng", + "author_inst": "Zhejiang Province Centre for Disease Control and Prevention" + }, + { + "author_name": "Shi Zhao", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Feng Ling", + "author_inst": "Zhejiang Province Centre for Disease Control and Prevention" + }, + { + "author_name": "Kirran Mohammad", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Maggie Wang", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Benny Zee", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Lei Wei", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Xi Xiong", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Hengyan Liu", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Jingxuan Wang", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Enfu Chen", + "author_inst": "Zhejiang Province Centre for Disease Control and Prevention" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.15.20036418", "rel_title": "Understanding Epidemic Data and Statistics: A case study of COVID-19", @@ -1580426,25 +1583577,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.03.13.20035568", - "rel_title": "Knowledge and perceptions of coronavirus disease 2019 among the general public in the United States and the United Kingdom: A cross-sectional online survey", - "rel_date": "2020-03-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.13.20035568", - "rel_abs": "BackgroundGiven the extensive time needed to conduct a nationally representative household survey and the commonly low response rate in phone surveys, rapid online surveys may be a promising method to assess and track knowledge and perceptions among the general public during fast-moving infectious disease outbreaks.\n\nObjectiveTo apply rapid online surveying to determine knowledge and perceptions of coronavirus disease 2019 (Covid-19) among the general public in the United States (US) and the United Kingdom (UK).\n\nMethodsAn online questionnaire was administered to 3,000 adults residing in the US and 3,000 adults residing in the UK who had registered with Prolific Academic to participate in online research. Strata by age (18 - 27, 28 - 37, 38 - 47, 48 - 57, or [≥]58 years), sex (male or female), and ethnicity (White, Black or African American, Asian or Asian Indian, Mixed, or \"Other\"), and all permutations of these strata, were established. The number of participants who could enrol in each of these strata was calculated to reflect the distribution in the US and UK general population. Enrolment into the survey within the strata was on a first-come, first-served basis. Participants completed the questionnaire between February 23 and March 2 2020.\n\nResults2,986 and 2,988 adults residing in the US and the UK, respectively, completed the questionnaire. 64.4% (1,924/2,986) of US and 51.5% (1,540/2,988) of UK participants had a tertiary education degree. 67.5% (2,015/2,986) of US participants had a total household income between $20,000 and $99,999, and 74.4% (2,223/2,988) of UK participants had a total household income between {pound}15,000 and {pound}74,999. US and UK participants median estimate for the probability of a fatal disease course among those infected with SARS-CoV-2 was 5.0% (IQR: 2.0% - 15.0%) and 3.0% (IQR: 2.0% - 10.0%), respectively. Participants generally had good knowledge of the main mode of disease transmission and common symptoms of Covid-19. However, a substantial proportion of participants had misconceptions about how to prevent an infection and the recommended care-seeking behavior. For instance, 37.8% (95% CI: 36.1% - 39.6%) of US and 29.7% (95% CI: 28.1% - 31.4%) of UK participants thought that wearing a common surgical mask was highly effective in protecting them from acquiring Covid-19. 25.6% (95% CI: 24.1% - 27.2%) of US and 29.6% (95% CI: 28.0% - 31.3%) of UK participants thought it prudent to refrain from eating at Chinese restaurants. Around half (53.8% [95% CI: 52.1% - 55.6%] of US and 39.1% [95% CI: 37.4% -40.9%] of UK participants) thought that children were at an especially high risk of death when infected with SARS-CoV-2.\n\nConclusionsThe distribution of participants by total household income and education followed approximately that of the general population. The findings from this online survey could guide information campaigns by public health authorities, clinicians, and the media. More broadly, rapid online surveys could be an important tool in tracking the publics knowledge and misperceptions during rapidly moving infectious disease outbreaks.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Pascal Geldsetzer", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.13.20034892", "rel_title": "If containment is not possible, how do we minimize mortality for COVID-19 and other emerging infectious disease outbreaks?", @@ -1581272,6 +1584404,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.16.993816", + "rel_title": "Evidence of the Recombinant Origin and Ongoing Mutations in Severe Acute Respiratory Syndrome 2 (SARS-COV-2)", + "rel_date": "2020-03-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.16.993816", + "rel_abs": "The recent global outbreak of viral pneumonia designated as Coronavirus Disease 2019 (COVID-19) by coronavirus (SARS-CoV-2) has threatened global public health and urged to investigate its source. Whole genome analysis of SARS-CoV-2 revealed ~96% genomic similarity with bat CoV (RaTG13) and clustered together in phylogenetic tree. Furthermore, RaTGl3 also showed 97.43% spike protein similarity with SARS-CoV-2 suggesting that RaTGl3 is the closest strain. However, RBD and key amino acid residues supposed to be crucial for human-to-human and cross-species transmission are homologues between SARS-CoV-2 and pangolin CoVs. These results from our analysis suggest that SARS-CoV-2 is a recombinant virus of bat and pangolin CoVs. Moreover, this study also reports mutations in coding regions of 125 SARS-CoV-2 genomes signifying its aptitude for evolution. In short, our findings propose that homologous recombination has been occurred between bat and pangolin CoVs that triggered cross-species transmission and emergence of SARS-CoV-2, and, during the ongoing outbreak, SARS-CoV-2 is still evolving for its adaptability.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Jiao-Mei Huang", + "author_inst": "Hainan University" + }, + { + "author_name": "Syed Sajid Jan", + "author_inst": "Fujian Normal University" + }, + { + "author_name": "Xiaobin Wei", + "author_inst": "Central South University" + }, + { + "author_name": "Yi Wan", + "author_inst": "Hainan University" + }, + { + "author_name": "Songying Ouyang", + "author_inst": "Fujian Normal University" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.03.14.20034884", "rel_title": "Modelling the epidemic 2019-nCoV event in Italy: a preliminary note", @@ -1582148,45 +1585315,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.13.20035436", - "rel_title": "Clinical characteristics and durations of hospitalized patients with COVID-19 in Beijing: a retrospective cohort study", - "rel_date": "2020-03-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.13.20035436", - "rel_abs": "ObjectiveTo give the information on clinical characteristics and different durations of COVID-19 and to identify the potential risk factors for longer hospitalization duration.\n\nMethodsIn this retrospective study, we enrolled 77 patients (mean age: 52{+/-}20 years; 44.2% males) with laboratory-confirmed COVID-19 admitted to Beijing YouAn Hospital during 21st Jan and 8th February 2020. Epidemiological, clinical, and radiological data on admission were collected; complications and outcomes were followed up until 26th February 2020. The studys endpoint was the discharge within two weeks. Cox proportional-hazards regression was performed to identify risk factors for longer hospitalization duration.\n\nResultsOf 77 patients, there were 34 (44.2%) males, 24 (31.2%) with comorbidities, 22 (28.6%) lymphopenia, 20 (26.0%) categorized as severe patients, and 28 (36.4%) occurred complications. By the end of follow-up, 64 (83.1%) patients were discharged home, 8 remained in hospital and 5 died. 36 (46.8%) patients were discharged within 14 days and thus reached the study endpoint, including 34 (59.6%) of 57 non-severe patients and 2 (10%) of 20 severe patients. The overall cumulative probability of the endpoint was 48.3%. Hospital length of stay and duration of exposure to discharge for 64 discharged patients were 13 (10-16.5) and 23 (18-24.5) days, respectively. Multivariable stepwise Cox regression model showed that bilateral pneumonia on CT scan, shorter time from the illness onset to admission, severity of disease and lymphopenia were independently associated with longer duration of hospitalization.\n\nConclusionsCOVID-19 has significantly shorter duration of disease and hospital length of stay than SARS. Bilateral pneumonia on CT scan, shorter period of illness onset to admission, lymphopenia, severity of disease are the risk factors for longer hospitalization duration of COVID-19.\n\nSignificance StatementIn this study, we reported that the average hospital length of stay for discharged patients with COVID-19 is 13 days and the average time of clinical course of COVID-19 is 23 days, both of which are significantly shorter than that of SARS. The risk factors for longer hospitalization duration of COVID-19 include bilateral pneumonia on CT scan, shorter period of illness onset to admission, lymphopenia, and severity of disease. There findings might be helpful for the countries or territories facing the threat of COVID-19 to well prepare and rebalance their medical resources.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Wen Zhao", - "author_inst": "Beijing YouAn Hospital, Capital Medical University" - }, - { - "author_name": "Xiangyi Zha", - "author_inst": "Hangzhou Dianzi University" - }, - { - "author_name": "Ning Wang", - "author_inst": "Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine" - }, - { - "author_name": "Tongzeng Li", - "author_inst": "Beijing YouAn Hospital, Capital Medical University" - }, - { - "author_name": "Aixin Li", - "author_inst": "Department of Infection Diseases, Beijing YouAn Hospital, Capital Medical University" - }, - { - "author_name": "Shikai Yu", - "author_inst": "Shanghai Tenth People's Hospital, Tongji University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.13.20035386", "rel_title": "Multi-city modeling of epidemics using spatial networks: Application to 2019-nCov (COVID-19) coronavirus in India", @@ -1582758,6 +1585886,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.03.15.20035360", + "rel_title": "Systematic review and meta-analysis of predictive symptoms and comorbidities for severe COVID-19 infection", + "rel_date": "2020-03-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.15.20035360", + "rel_abs": "Background/introductionCOVID-19, a novel coronavirus outbreak starting in China, is now a rapidly developing public health emergency of international concern. The clinical spectrum of COVID-19 disease is varied, and identifying factors associated with severe disease has been described as an urgent research priority. It has been noted that elderly patients with pre-existing comorbidities are more vulnerable to more severe disease. However, the specific symptoms and comorbidities that most strongly predict disease severity are unclear. We performed a systematic review and meta-analysis to identify the symptoms and comorbidities predictive of COVID-19 severity.\n\nMethodThis study was prospectively registered on PROSPERO. A literature search was performed in three databases (MEDLINE, EMBASE and Global Health) for studies indexed up to 5thMarch 2020. Two reviewers independently screened the literature and both also completed data extraction. Quality appraisal of studies was performed using the STROBE checklist. Random effects meta-analysis was performed for selected symptoms and comorbidities to identify those most associated with severe COVID-19 infection or ICU admission.\n\nResultsOf the 2259 studies identified, 42 were selected after title and abstract analysis, and 7 studies (including 1813 COVID-19 patients) were chosen for inclusion. The ICU group were older (62.4 years) compared to the non-ICU group (46 years), with a significantly higher proportion of males (67.2% vs. 57.1%, p=0.04). Dyspnoea was the only significant symptom predictive for both severe disease (pOR 3.70, 95% CI 1.83 - 7.46) and ICU admission (pOR 6.55, 95% CI 4.28- 10.0). Notwithstanding the low prevalence of COPD in severe disease and ICU-admitted groups (4.5% and 9.7%, respectively), COPD was the most strongly predictive comorbidity for both severe disease (pOR 6.42, 95% CI 2.44 - 16.9) and ICU admission (pOR 17.8, 95% CI 6.56 - 48.2). Cardiovascular disease and hypertension were also strongly predictive for both severe disease and ICU admission. Those with CVD and hypertension were 4.4 (95% CI 2.64 - 7.47) and 3.7 (95% CI 2.22 - 5.99) times more likely to have an ICU admission respectively, compared to patients without the comorbidity.\n\nConclusionsDyspnoea was the only symptom strongly predictive for both severe disease and ICU admission, and could be useful in guiding clinical management decisions early in the course of illness. When looking at ICU-admitted patients, who represent the more severe end of the spectrum of clinical severity, COPD patients are particularly vulnerable, and those with cardiovascular disease and hypertension are also at a high-risk of severe illness. To aid clinical assessment, risk stratification, efficient resource allocation, and targeted public health interventions, future research must aim to further define those at high-risk of severe illness with COVID-19.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Vageesh Jain", + "author_inst": "Institute for Global Health, University College London (UCL), UK; Public Health, London Borough of Hackney, London, UK" + }, + { + "author_name": "Jin-Min Yuan", + "author_inst": "Public Health, London Boroughs of Camden & Islington" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.03.12.20034678", "rel_title": "Ocular manifestations and clinical characteristics of 534 cases of COVID-19 in China: A cross-sectional study", @@ -1583529,45 +1586680,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.12.20034827", - "rel_title": "Impact of self-imposed prevention measures and short-term government intervention on mitigating and delaying a COVID-19 epidemic", - "rel_date": "2020-03-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.12.20034827", - "rel_abs": "BackgroundThe coronavirus disease (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread to nearly every country in the world since it first emerged in China in December 2019. Many countries have implemented social distancing as a measure to flatten the curve of the ongoing epidemics. Evaluation of the impact of government-imposed social distancing and of other measures to control further spread of COVID-19 is urgent, especially because of the large societal and economic impact of the former. The aim of this study was to compare the effectiveness of self-imposed prevention measures and of short-term government-imposed social distancing in mitigating, delaying, or preventing a COVID-19 epidemic.\n\nMethods and FindingsWe developed a deterministic compartmental transmission model of SARS-CoV-2 in a population stratified by disease status (susceptible, exposed, infectious with mild or severe disease, diagnosed and recovered) and disease awareness status (aware and unaware) due to the spread of COVID-19. Self-imposed measures were assumed to be taken by disease-aware individuals and included handwashing, mask-wearing, and social distancing. Government-imposed social distancing reduced the contact rate of individuals irrespective of their disease or awareness status. The model was parameterized using current best estimates of key epidemiological parameters from COVID-19 clinical studies. The model outcomes included the peak number of diagnoses, attack rate, and time until the peak number of diagnoses. For fast awareness spread in the population, selfimposed measures can significantly reduce the attack rate, diminish and postpone the peak number of diagnoses. A large epidemic can be prevented if the efficacy of these measures exceeds 50%. For slow awareness spread, self-imposed measures reduce the peak number of diagnoses and attack rate but do not affect the timing of the peak. Early implementation of short-term government-imposed social distancing can only delay the peak (by at most 7 months for a 3-month intervention). The delay can be even longer and the height of the peak can be additionally reduced if this intervention is combined with self-imposed measures that are continued after government-imposed social distancing has been lifted. Our analyses do not account for stochasticity, demographics, heterogeneities in contact patterns or mixing, spatial effects, imperfect isolation of individuals with severe disease, and reinfection with COVID-19.\n\nConclusionsOur results suggest that information dissemination about COVID-19, which causes individual adaption of handwashing, mask-wearing and social distancing can be an effective strategy to mitigate and delay the epidemic. Early-initiated short-term government-imposed social distancing can buy time for healthcare systems to prepare for an increasing COVID-19 burden. We stress the importance of disease awareness in controlling the ongoing epidemic and recommend that, in addition to policies on social distancing, governments and public health institutions mobilize people to adopt self-imposed measures with proven efficacy in order to successfully tackle COVID-19.\n\nAuthor summaryO_ST_ABSWhy was this study done?C_ST_ABSO_LIAs of May 2020, the coronavirus disease (COVID-19) caused by the novel coronavirus (SARS-CoV-2) has spread to nearly every country in the world since it first emerged in China in December 2019.\nC_LIO_LIConfronted with a COVID-19 epidemic, public health policymakers in different countries are seeking recommendations on how to delay and/or flatten its peak.\nC_LIO_LIEvaluation of the impact of social distancing mandated by the governments in many countries and of other prevention measures to control further spread of COVID-19 is urgent, especially because of the large societal and economic impact of the former.\nC_LI\n\nWhat did the researchers do and find?O_LIWe developed a transmission model to evaluate the impact of self-imposed measures (handwashing, mask-wearing, and social distancing) due to awareness of COVID-19 and of short-term government-imposed social distancing on the epidemic dynamics.\nC_LIO_LIWe showed that self-imposed measures can prevent a large epidemic if their efficacy exceeds 50%.\nC_LIO_LIShort-term government-imposed social distancing that is initiated early into the epidemic can buy time (at most 7 months for a 3-month intervention) for healthcare systems to prepare for an increasing COVID-19 burden.\nC_LIO_LIThe delay to the peak number of diagnoses can be even longer and the height of the peak can be additionally reduced if the same intervention is combined with self-imposed measures that are continued after lifting government-imposed social distancing.\nC_LI\n\nWhat do these findings mean?O_LIRaising awareness of self-imposed measures such as handwashing and mask-wearing is crucial in controlling the ongoing epidemic.\nC_LIO_LIShort-term early-initiated government-imposed social distancing combined with self-imposed measures provides essential time for increasing capacity of healthcare systems and can significantly mitigate the epidemic.\nC_LIO_LIIn addition to policies on social distancing, governments and public health institutions should continuously mobilize people to adopt self-imposed measures with proven efficacy in order to successfully tackle COVID-19.\nC_LI", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Alexandra Teslya", - "author_inst": "University Medical Center Utrecht, The Netherlands" - }, - { - "author_name": "Thi Mui Pham", - "author_inst": "University Medical Center Utrecht, Utrecht, The Netherlands" - }, - { - "author_name": "Noortje G. Godijk", - "author_inst": "University Medical Center Utrecht, Utrecht, The Netherlands" - }, - { - "author_name": "Mirjam E. Kretzschmar", - "author_inst": "University Medical Center Utrecht, Utrecht, The Netherlands" - }, - { - "author_name": "Martin C.J. Bootsma", - "author_inst": "Mathematical Institute, Utrecht University, Utrecht, The Netherlands" - }, - { - "author_name": "Ganna Rozhnova", - "author_inst": "University Medical Center Utrecht, Utrecht, The Netherlands" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.03.12.20034876", "rel_title": "Recommendations for standardized management of CML patients in the core epidemic area of COVID-19(Multi-center survey results in Hubei Province, China)", @@ -1584511,6 +1587623,121 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.03.13.990036", + "rel_title": "Rhesus macaques can be effectively infected with SARS-CoV-2 via ocular conjunctival route", + "rel_date": "2020-03-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.13.990036", + "rel_abs": "The outbreak of Corona Virus Disease 2019 caused by the severe acute respiratory syndrome coronavirus (SARS-CoV-2) is highly transmitted. The potential extra-respiratory transmission routes remain uncertain. Five rhesus macaques were inoculated with 1x106 TCID50 of SARS-CoV-2 via conjunctival (CJ), intratracheal (IT), and intragastric (IG) routes, respectively. Remarkably, the CJ inoculated-macaques developed mild interstitial pneumonia and viral load was detectable in the conjunctival swabs at 1 days post-inoculation (dpi). Only via IT inoculation, viral load was detected in the anal swab at 1-7 dpi and macaque showed weight loss. However, viral load was undetectable after IG inoculation. Comparatively, viral load was higher in the nasolacrimal system but lesions of lung were relatively mild and local via CJ inoculation compared with that via IT inoculation, demonstrating distinct characteristics of virus dispersion. Both the two routes affected the alimentary tract. Therefore the clinicians need to protect eye while working with patients.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Wei Deng", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College" + }, + { + "author_name": "Linlin Bao", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College" + }, + { + "author_name": "Hong Gao", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College" + }, + { + "author_name": "Zhiguang Xiang", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College" + }, + { + "author_name": "Yajin Qu", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College" + }, + { + "author_name": "Zhiqi Song", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College" + }, + { + "author_name": "Shuran Gong", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College" + }, + { + "author_name": "Jiayi Liu", + "author_inst": "Department of radiology, Bejing Anzhen hospital, Capital medical university, Beijing, China." + }, + { + "author_name": "Jiangning Liu", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College" + }, + { + "author_name": "Pin Yu", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College" + }, + { + "author_name": "Feifei Qi", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College" + }, + { + "author_name": "Yanfeng Xu", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College" + }, + { + "author_name": "Fengli Li", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College" + }, + { + "author_name": "Chong Xiao", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College" + }, + { + "author_name": "Qi Lv", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College" + }, + { + "author_name": "Jing Xue", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College" + }, + { + "author_name": "Qiang Wei", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College" + }, + { + "author_name": "Mingya Liu", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College" + }, + { + "author_name": "Guanpeng Wang", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College" + }, + { + "author_name": "Shunyi Wang", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College" + }, + { + "author_name": "Haisheng Yu", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College" + }, + { + "author_name": "Xing Liu", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College" + }, + { + "author_name": "Wenjie Zhao", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College," + }, + { + "author_name": "Yunlin Han", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College" + }, + { + "author_name": "Chuan Qin", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.03.10.20033803", "rel_title": "Prediction of the COVID-19 outbreak based on a realistic stochastic model", @@ -1585313,57 +1588540,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.09.20033464", - "rel_title": "Lessons drawn from China and South Korea for managing COVID-19 epidemic: insights from a comparative modeling study", - "rel_date": "2020-03-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.09.20033464", - "rel_abs": "We conducted a comparative study of COVID-19 epidemic in three different settings: mainland China, the Guangdong province of China and South Korea, by formulating two disease transmission dynamics models incorporating epidemic characteristics and setting-specific interventions, and fitting the models to multi-source data to identify initial and effective reproduction numbers and evaluate effectiveness of interventions. We estimated the initial basic reproduction number for South Korea, the Guangdong province and mainland China as 2.6 (95% confidence interval (CI): (2.5, 2.7)), 3.0 (95%CI: (2.6, 3.3)) and 3.8 (95%CI: (3.5,4.2)), respectively, given a serial interval with mean of 5 days with standard deviation of 3 days. We found that the effective reproduction number for the Guangdong province and mainland China has fallen below the threshold 1 since February 8th and 18th respectively, while the effective reproduction number for South Korea remains high, suggesting that the interventions implemented need to be enhanced in order to halt further infections. We also project the epidemic trend in South Korea under different scenarios where a portion or the entirety of the integrated package of interventions in China is used. We show that a coherent and integrated approach with stringent public health interventions is the key to the success of containing the epidemic in China and specially its provinces outside its epicenter, and we show that this approach can also be effective to mitigate the burden of the COVID-19 epidemic in South Korea. The experience of outbreak control in mainland China should be a guiding reference for the rest of the world including South Korea.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Biao Tang", - "author_inst": "York University" - }, - { - "author_name": "Fan Xia", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Nicola Luigi Bragazzi", - "author_inst": "York University" - }, - { - "author_name": "Xia Wang", - "author_inst": "Shaanxi Normal University" - }, - { - "author_name": "Sha He", - "author_inst": "Shaanxi Normal University" - }, - { - "author_name": "Xiaodan Sun", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Sanyi Tang", - "author_inst": "Shaanxi Normal University" - }, - { - "author_name": "Yanni Xiao", - "author_inst": "Xian Jiaotong University" - }, - { - "author_name": "Jianhong Wu", - "author_inst": "York University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.09.20033514", "rel_title": "The time scale of asymptomatic transmission affects estimates of epidemic potential in the COVID-19 outbreak", @@ -1586055,6 +1589231,121 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2020.03.11.983056", + "rel_title": "Novel and potent inhibitors targeting DHODH, a rate-limiting enzyme in de novo pyrimidine biosynthesis, are broad-spectrum antiviral against RNA viruses including newly emerged coronavirus SARS-CoV-2", + "rel_date": "2020-03-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.11.983056", + "rel_abs": "Emerging and re-emerging RNA viruses occasionally cause epidemics and pandemics worldwide, such as the on-going outbreak of coronavirus SARS-CoV-2. Existing direct-acting antiviral (DAA) drugs cannot be applied immediately to new viruses because of virus-specificity, and the development of new DAA drugs from the beginning is not timely for outbreaks. Thus, host-targeting antiviral (HTA) drugs have many advantages to fight against a broad spectrum of viruses, by blocking the viral replication and overcoming the potential viral mutagenesis simultaneously. Herein, we identified two potent inhibitors of DHODH, S312 and S416, with favorable drug-like and pharmacokinetic profiles, which all showed broad-spectrum antiviral effects against various RNA viruses, including influenza A virus (H1N1, H3N2, H9N2), Zika virus, Ebola virus, and particularly against the recent novel coronavirus SARS-CoV-2. Our results are the first to validate that DHODH is an attractive host target through high antiviral efficacy in vivo and low virus replication in DHODH knocking-out cells. We also proposed the drug combination of DAA and HTA was a promising strategy for anti-virus treatment and proved that S312 showed more advantageous than Oseltamivir to treat advanced influenza diseases in severely infected animals. Notably, S416 is reported to be the most potent inhibitor with an EC50 of 17nM and SI value >5882 in SARS-CoV-2-infected cells so far. This work demonstrates that both our self-designed candidates and old drugs (Leflunomide/Teriflunomide) with dual actions of antiviral and immuno-repression may have clinical potentials not only to influenza but also to COVID-19 circulating worldwide, no matter such viruses mutate or not.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Rui Xiong", + "author_inst": "East China University of Science and Technology" + }, + { + "author_name": "Leike Zhang", + "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences" + }, + { + "author_name": "Shiliang Li", + "author_inst": "East China University of Science and Technology" + }, + { + "author_name": "Yuan Sun", + "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences" + }, + { + "author_name": "Minyi Ding", + "author_inst": "East China University of Science and Technology" + }, + { + "author_name": "Yong Wang", + "author_inst": "State Key Laboratory of Virology, Wuhan University" + }, + { + "author_name": "Yongliang Zhao", + "author_inst": "State Key Laboratory of Virology, Wuhan University" + }, + { + "author_name": "Yan Wu", + "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences" + }, + { + "author_name": "Weijuan Shang", + "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences" + }, + { + "author_name": "Xiaming Jiang", + "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences" + }, + { + "author_name": "Jiwei Shan", + "author_inst": "East China University of Science and Technology" + }, + { + "author_name": "Zihao Shen", + "author_inst": "East China University of Science and Technology" + }, + { + "author_name": "Yi Tong", + "author_inst": "East China University of Science and Technology" + }, + { + "author_name": "Liuxin Xu", + "author_inst": "East China University of Science and Technology" + }, + { + "author_name": "Yu Chen", + "author_inst": "State Key Laboratory of Virology, Wuhan University" + }, + { + "author_name": "Yingle Liu", + "author_inst": "State Key Laboratory of Virology, Wuhan University" + }, + { + "author_name": "Gang Zou", + "author_inst": "Institut Pasteur of Shanghai" + }, + { + "author_name": "Dimitri Lavillete", + "author_inst": "Institut Pasteur of Shanghai" + }, + { + "author_name": "Zhenjiang Zhao", + "author_inst": "East China University of Science and Technology" + }, + { + "author_name": "Rui Wang", + "author_inst": "East China University of Science and Technology" + }, + { + "author_name": "Lili Zhu", + "author_inst": "East China University of Science and Technology" + }, + { + "author_name": "Gengfu Xiao", + "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences" + }, + { + "author_name": "Ke Lan", + "author_inst": "State Key Laboratory of Virology, Wuhan University" + }, + { + "author_name": "Honglin Li", + "author_inst": "East China University of Science and Technology" + }, + { + "author_name": "Ke Xu", + "author_inst": "State Key Laboratory of Virology, Wuhan University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.03.11.987222", "rel_title": "Discovery of a 382-nt deletion during the early evolution of SARS-CoV-2", @@ -1587522,41 +1590813,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, - { - "rel_doi": "10.1101/2020.03.07.20032326", - "rel_title": "Analytical sensibility and specificity of two RT-qPCR protocols for SARS-CoV-2 detection performed in an automated workflow", - "rel_date": "2020-03-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.07.20032326", - "rel_abs": "The World Health Organization declared that COVID-19 outbreak constituted a Public Health Emergency of International Concern and the development of reliable laboratory diagnosis of SARS-CoV-2 became mandatory to identify, isolate and provide optimized care for patients early. RT-qPCR testing of respiratory secretions is routinely used to detect causative viruses in acute respiratory infection. RT-qPCR in-house protocols to detect the SARS-CoV-2 have been described. Validations of these protocols are considered a key knowledge gap for COVID-19, especially if executed in a high throughput format. Here, we investigate the analytical sensitivity and specificity of two interim RT-qPCR protocols for the qualitative detection of SARS-CoV-2 executed in a fully automated platform. Under our conditions, the N1 and RdRP (modified) showed the highest analytical sensitivity for their RNA targets. E assay, in its original concentration, was considered a tertiary confirmatory assay. Taken together, N1, RdRP (optimized) and E presented appropriated analytical sensibility and specificity in our automated RT-qPCR workflow for COVID-19 virus, E being at least 4-fold less sensitive than the others. This study highlights the importance of local validation of in-house assays before its availability to the population. The use of the synthetic RT-qPCR target to investigate novel assays diagnostic parameters in automated workflows is a quick, simple effective way to be prepared for upcoming threats. The proposed assay detected the fisrt SARS-CoV-2 infection in Brazilian Central-West.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Gustavo Barcelos Barra", - "author_inst": "Sabin Medicina Diagnostica" - }, - { - "author_name": "Ticiane Henriques Santa Rita", - "author_inst": "Sabin Medicina Diagnostica" - }, - { - "author_name": "Pedro Goes Mesquita", - "author_inst": "Sabin Medicina Diagnostica" - }, - { - "author_name": "Rafael Henriques Jacomo", - "author_inst": "Sabin Medicina Diagnostica" - }, - { - "author_name": "Lidia Freire Abdalla Nery", - "author_inst": "Sabin Medicina Diagnostica" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.09.20033217", "rel_title": "Aerosol and surface stability of HCoV-19 (SARS-CoV-2) compared to SARS-CoV-1", @@ -1588136,6 +1591392,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.08.20030643", + "rel_title": "Transmission potential of COVID-19 in Iran", + "rel_date": "2020-03-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.08.20030643", + "rel_abs": "We estimated the reproduction number of 2020 Iranian COVID-19 epidemic using two different methods: R0 was estimated at 4.4 (95% CI, 3.9, 4.9) (generalized growth model) and 3.50 (1.28, 8.14) (epidemic doubling time) (February 19 - March 1) while the effective R was estimated at 1.55 (1.06, 2.57) (March 6-19).", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Kamalich Muniz-Rodriguez", + "author_inst": "Georgia Southern University Jiann-Ping Hsu College of Public Health" + }, + { + "author_name": "Isaac Chun-Hai Fung", + "author_inst": "Georgia Southern University Jiann-Ping Hsu College of Public Health" + }, + { + "author_name": "Shayesterh R. Ferdosi", + "author_inst": "Brain Tumor Unit, The Translational Genomics Research Institute" + }, + { + "author_name": "Sylvia K. Ofori", + "author_inst": "Georgia Southern University Jiann-Ping Hsu College of Public Health" + }, + { + "author_name": "Yiseul Lee", + "author_inst": "Georgia State University School of Public Health" + }, + { + "author_name": "Amna Tariq", + "author_inst": "Georgia State University School of Public Health" + }, + { + "author_name": "Gerardo Chowell", + "author_inst": "Georgia State University School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.07.20031575", "rel_title": "Prognostic value of NT-proBNP in patients with severe COVID-19", @@ -1589028,49 +1592327,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.03.05.20031815", - "rel_title": "Estimating the generation interval for COVID-19 based on symptom onset data", - "rel_date": "2020-03-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.05.20031815", - "rel_abs": "BackgroundEstimating key infectious disease parameters from the COVID-19 outbreak is quintessential for modelling studies and guiding intervention strategies. Whereas different estimates for the incubation period distribution and the serial interval distribution have been reported, estimates of the generation interval for COVID-19 have not been provided.\n\nMethodsWe used outbreak data from clusters in Singapore and Tianjin, China to estimate the generation interval from symptom onset data while acknowledging uncertainty about the incubation period distribution and the underlying transmission network. From those estimates we obtained the proportions pre-symptomatic transmission and reproduction numbers.\n\nResultsThe mean generation interval was 5.20 (95%CI 3.78-6.78) days for Singapore and 3.95 (95%CI 3.01-4.91) days for Tianjin, China when relying on a previously reported incubation period with mean 5.2 and SD 2.8 days. The proportion of pre-symptomatic transmission was 48% (95%CI 32-67%) for Singapore and 62% (95%CI 50-76%) for Tianjin, China. Estimates of the reproduction number based on the generation interval distribution were slightly higher than those based on the serial interval distribution.\n\nConclusionsEstimating generation and serial interval distributions from outbreak data requires careful investigation of the underlying transmission network. Detailed contact tracing information is essential for correctly estimating these quantities.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Tapiwa Ganyani", - "author_inst": "Hasselt University (UHasselt)" - }, - { - "author_name": "Cecile Kremer", - "author_inst": "Hasselt University (UHasselt)" - }, - { - "author_name": "Dongxuan Chen", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands; Leiden University Medical Center" - }, - { - "author_name": "Andrea Torneri", - "author_inst": "Hasselt University (UHasselt); University of Antwerp" - }, - { - "author_name": "Christel Faes", - "author_inst": "Hasselt University (UHasselt)" - }, - { - "author_name": "Jacco Wallinga", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands; Leiden University Medical Center" - }, - { - "author_name": "Niel Hens", - "author_inst": "Hasselt University; University of Antwerp" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.05.20031740", "rel_title": "A data-driven assessment of early travel restrictions related to the spreading of the novel COVID-19 within mainland China", @@ -1589737,6 +1592993,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.03.972133", + "rel_title": "AI-aided design of novel targeted covalent inhibitors against SARS-CoV-2", + "rel_date": "2020-03-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.03.972133", + "rel_abs": "The focused drug repurposing of known approved drugs (such as lopinavir/ritonavir) has been reported failed for curing SARS-CoV-2 infected patients. It is urgent to generate new chemical entities against this virus. As a key enzyme in the life-cycle of coronavirus, the 3C-like main protease (3CLpro or Mpro) is the most attractive for antiviral drug design. Based on a recently solved structure (PDB ID: 6LU7), we developed a novel advanced deep Q-learning network with the fragment-based drug design (ADQN-FBDD) for generating potential lead compounds targeting SARS-CoV-2 3CLpro. We obtained a series of derivatives from those lead compounds by our structure-based optimization policy (SBOP). All the 47 lead compounds directly from our AI-model and related derivatives based on SBOP are accessible in our molecular library at https://github.com/tbwxmu/2019-nCov. These compounds can be used as potential candidates for researchers in their development of drugs against SARS-CoV-2.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Bowen Tang", + "author_inst": "Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen" + }, + { + "author_name": "Fengming He", + "author_inst": "Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen" + }, + { + "author_name": "Dongpeng Liu", + "author_inst": "Department of Electrical Engineering and Computer Science, Informatics Institute, and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia" + }, + { + "author_name": "Meijuan Fang", + "author_inst": "Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen" + }, + { + "author_name": "Zhen Wu", + "author_inst": "Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen" + }, + { + "author_name": "Dong Xu", + "author_inst": "University of Missouri" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2020.03.05.20031476", "rel_title": "Appealing for Efficient, Well Organized Clinical Trials on COVID-19", @@ -1590697,41 +1593992,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.04.20031112", - "rel_title": "Projecting the transmission dynamics of SARS-CoV-2 through the post-pandemic period", - "rel_date": "2020-03-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.04.20031112", - "rel_abs": "There is an urgent need to project how transmission of the novel betacoronavirus SARS-CoV-2 will unfold in coming years. These dynamics will depend on seasonality, the duration of immunity, and the strength of cross-immunity to/from the other human coronaviruses. Using data from the United States, we measured how these factors affect transmission of human betacoronaviruses HCoV-OC43 and HCoV-HKU1. We then built a mathematical model to simulate transmission of SARS-CoV-2 through the year 2025. We project that recurrent wintertime outbreaks of SARS-CoV-2 will probably occur after an initial pandemic wave. We summarize the full range of plausible transmission scenarios and identify key data still needed to distinguish between them, most importantly longitudinal serological studies to determine the duration of immunity to SARS-CoV-2.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Stephen M Kissler", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Christine Tedijanto", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Edward Goldstein", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Yonatan H. Grad", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Marc Lipsitch", - "author_inst": "Harvard T.H. Chan School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.04.20031104", "rel_title": "Adjusted age-specific case fatality ratio during the COVID-19 epidemic in Hubei, China, January and February 2020", @@ -1591343,6 +1594603,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.01.20029785", + "rel_title": "Clinical and Laboratory Profiles of 75 Hospitalized Patients with Novel Coronavirus Disease 2019 in Hefei, China", + "rel_date": "2020-03-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.01.20029785", + "rel_abs": "The outbreak of the novel coronavirus disease 2019 (COVID-19) infection began in December 2019 in Wuhan, and rapidly spread to many provinces in China. The number of cases has increased markedly in Anhui, but information on the clinical characteristics of patients is limited. We reported 75 patients with COVID-19 in the First Affiliated Hospital of USTC from Jan 21 to Feb 16, 2020, Hefei, Anhui Province, China. COVID-19 infection was confirmed by real-time RT-PCR of respiratory nasopharyngeal swab samples. Epidemiological, clinical and laboratory data were collected and analyzed. Of the 75 patients with COVID-19, 61 (81.33%) had a direct or indirect exposure history to Wuhan. Common symptoms at onset included fever (66 [88.0%] of 75 patients) and dry cough (62 [82.67%]). Of the patients without fever, cough could be the only or primary symptom. The most prominent laboratory abnormalities were lymphopenia, decreased percentage of lymphocytes (LYM%), decreased CD4+ and CD8+ T cell counts, elevated C-reactive protein (CRP) and lactate dehydrogenase (LDH). Patients with elevated interleukin 6 (IL-6) showed significant decreases in the LYM%, CD4+ and CD8+ T cell counts. Besides, the percentage of neutrophils, CRP, LDH and Procalcitonin levels increased significantly. We concluded that COVID-19 could cause different degrees of hematological abnormalities and damage of internal organs. Hematological profiles including LYM, LDH, CRP and IL-6 could be indicators of diseases severity and evaluation of treatment effectiveness. Antiviral treatment requires a comprehensive and supportive approach. Further targeted therapy should be determined based on individual clinical manifestations and laboratory indicators.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Zonghao Zhao", + "author_inst": "Department of Infectious Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China," + }, + { + "author_name": "Jiajia Xie", + "author_inst": "Department of Dermatology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, " + }, + { + "author_name": "Ming Yin", + "author_inst": "Department of ICU, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 2" + }, + { + "author_name": "Yun Yang", + "author_inst": "Department of ICU, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 2" + }, + { + "author_name": "Hongliang He", + "author_inst": "Department of Infectious Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China," + }, + { + "author_name": "Tengchuan Jin", + "author_inst": "Laboratory of Structural Immunology, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, Anhui, 230027, China" + }, + { + "author_name": "Wenting Li", + "author_inst": "Department of Infectious Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China," + }, + { + "author_name": "Xiaowu Zhu", + "author_inst": "Department of Infectious Diseases, Hefei Infectious Diseases Hospital, Hefei, Anhui, 230000, China" + }, + { + "author_name": "Jing Xu", + "author_inst": "Department of Infectious Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China," + }, + { + "author_name": "Changcheng Zhao", + "author_inst": "Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China," + }, + { + "author_name": "Lei Li", + "author_inst": "Department of Infectious Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China," + }, + { + "author_name": "Yi Li", + "author_inst": "Department of Infectious Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China," + }, + { + "author_name": "Hylemariam Mihiretie Mengist", + "author_inst": "Laboratory of Structural Immunology, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, Anhui, 230027, China" + }, + { + "author_name": "Ayesha Zahid", + "author_inst": "Laboratory of Structural Immunology, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, Anhui, 230027, China" + }, + { + "author_name": "Ziqin Yao", + "author_inst": "Department of Infectious Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China," + }, + { + "author_name": "Chengchao Ding", + "author_inst": "The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China" + }, + { + "author_name": "Yingjie Qi", + "author_inst": "Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China," + }, + { + "author_name": "Yong Gao", + "author_inst": "Department of Infectious Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China," + }, + { + "author_name": "Xiaoling Ma", + "author_inst": "Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China," + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.03.20029843", "rel_title": "Effect of non-pharmaceutical interventions for containing the COVID-19 outbreak: an observational and modelling study", @@ -1592247,113 +1595598,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.02.29.20029439", - "rel_title": "ddPCR: a more sensitive and accurate tool for SARS-CoV-2 detection in low viral load specimens", - "rel_date": "2020-03-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.29.20029439", - "rel_abs": "Real time fluorescent quantitative PCR (RT-PCR) is widely used as the gold standard for clinical detection of SARS-CoV-2. However, due to the low viral load in patient throats and the limitations of RT-PCR, significant numbers of false negative reports are inevitable, which results in failure to timely diagnose, early treat, cut off transmission, and assess discharge criteria. To improve this situation, an optimized droplet digital PCR (ddPCR) was used for detection of SARS-CoV-2, which showed that the limit of detection of ddPCR is significantly lower than that of RT-PCR. We further explored the feasibility of ddPCR to detect SARS-CoV-2 nucleic acid from 77 clinical throat swab samples, including 63 suspected outpatients with fever and 14 supposed convalescents who were about to discharge after treatment, and compared with RT-PCR in terms of the diagnostic accuracy. In this double-blind study, we tested, surveyed subsequently and statistically analyzed 77 clinical samples. According to our study, 26 samples from COVID-19 patients with RT-PCR negative were detected as positive by ddPCR. No FPRs of RT-PCR and ddPCR were observed. The sensitivity, specificity, PPV, NPV, NLR and accuracy were improved from 40% (95% CI: 27-55%), 100% (95% CI: 54-100%), 100%, 16% (95% CI: 13-19%), 0.6 (95% CI: 0.48-0.75) and 47% (95% CI: 33-60%) for RT-PCR to 94% (95% CI: 83-99%), 100% (95% CI: 48-100%), 100%, 63% (95% CI: 36-83%), 0.06 (95% CI: 0.02-0.18) and 95% (95% CI: 84-99%) for ddPCR, respectively. Moreover, 14 (42.9 %) convalescents still carry detectable SARS-CoV-2 after discharge. Overall, ddPCR shows superiority for clinical diagnosis of SARS-CoV-2 to reduce the false negative reports, which could be a powerful complement to the current standard RT-PCR. It also suggests that the current clinical practice that the convalescent after discharge continues to be quarantined for at least 2 weeks is completely necessary which can prevent potential viral transmission.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Tao Suo", - "author_inst": "State Key Laboratory of Virology, Renmin Hospital, Wuhan University, Wuhan, P. R. China" - }, - { - "author_name": "Xinjin Liu", - "author_inst": "State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, P. R. China." - }, - { - "author_name": "Jiangpeng Feng", - "author_inst": "State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, P. R. China." - }, - { - "author_name": "Ming Guo", - "author_inst": "State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, P. R. China." - }, - { - "author_name": "Wenjia Hu", - "author_inst": "Department of Infectious Disease, Zhongnan Hospital, Wuhan University, Wuhan, P. R. China" - }, - { - "author_name": "Dong Guo", - "author_inst": "State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, P. R. China" - }, - { - "author_name": "Hafiz Ullah", - "author_inst": "State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, P. R. China." - }, - { - "author_name": "Yang Yang", - "author_inst": "State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, P. R. China." - }, - { - "author_name": "Qiuhan Zhang", - "author_inst": "State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, P. R. China" - }, - { - "author_name": "Xin Wang", - "author_inst": "State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, P. R. China" - }, - { - "author_name": "Muhanmmad Sajid", - "author_inst": "State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, P. R. China" - }, - { - "author_name": "Zhixiang Huang", - "author_inst": "State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, P. R. China" - }, - { - "author_name": "Liping Deng", - "author_inst": "State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, P. R. China." - }, - { - "author_name": "Tielong Chen", - "author_inst": "Department of Infectious Disease, Zhongnan Hospital, Wuhan University, Wuhan, P. R. China" - }, - { - "author_name": "Fang Liu", - "author_inst": "State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, P. R. China" - }, - { - "author_name": "Ke Xu", - "author_inst": "State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, P. R. China" - }, - { - "author_name": "Yuan Liu", - "author_inst": "State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, P. R. China" - }, - { - "author_name": "Qi Zhang", - "author_inst": "State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, P. R. China" - }, - { - "author_name": "Yingle Liu", - "author_inst": "State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, P. R. China" - }, - { - "author_name": "Yong Xiong", - "author_inst": "Department of Infectious Disease, Zhongnan Hospital, Wuhan University, Wuhan, P. R. China" - }, - { - "author_name": "Guozhong Chen", - "author_inst": "State Key Laboratory of Virology, Renmin Hospital, Wuhan University, Wuhan, P. R. China" - }, - { - "author_name": "Ke Lan", - "author_inst": "State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, P. R. China" - }, - { - "author_name": "Yu Chen", - "author_inst": "State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, P. R. China" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.01.20029629", "rel_title": "Risk estimation and prediction by modeling the transmission of the novel coronavirus (COVID-19) in mainland China excluding Hubei province", @@ -1593073,6 +1596317,20 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2020.03.01.20029611", + "rel_title": "Systematic Review of the Registered Clinical Trials of Coronavirus Diseases 2019 (COVID-19)", + "rel_date": "2020-03-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.01.20029611", + "rel_abs": "BackgroundSince the outbreak of coronavirus disease 2019 (COVID-19), many researchers in China have immediately carried out clinical research scheme of the COVID-19. But, there is still a lack of systematic review of registered clinical trials. Therefore, we conducted a systematic review of the clinical trials of COVID-19 to summarize the characteristics of the COVID-19 registered clinical trials.\n\nMethodsThis study is based on the recommendations of the PRISMA in the Cochrane handbook. The databases from the Chinese Clinical Registration Center and the ClinicalTrials.gov were searched to collect the registered clinical trials of COVID-19. The retrieval inception date is February 9, 2020. Two researchers independently selected the literature based on inclusion and exclusion criteria, extracted data and evaluated the risk of bias.\n\nResultsA total of 75 registered clinical trials (63 interventional studies and 12 observational studies) of COVID-19 were obtained. A majority of clinical trials were sponsored by Chinese hospitals. Only 11 trials have begun to recruit patients, and none of the registered clinical trials had been completed; 34 trials were early clinical exploratory trials or in a pre-experiment stage, 15 trials belonged to phrase III and 4 trials were phrase IV. The methods of intervention included traditional Chinese medicine involving 26 trials, Western medicine involving 30 trials, and integrated traditional Chinese medicine and Western medicine involving 19 trials. The subjects were mainly non-critical adult patients ([≥] 18 years old). The median sample size of the trials was 100 (IQR: 60 - 200), and the median execute time of the trials was 179 d (IQR: 94 - 366 d). The main outcomes were clinical observation and examinations. Overall, both the methodology quality of interventional trials and observational studies were low.\n\nConclusionsDisorderly and intensive clinical trials of COVID-19 using traditional Chinese medicine and western medicine are ongoing or will being carried out in China. However, based on the low methodology quality and small sample size and long studies execute time, we will not be able to obtain reliable, high-quality clinical evidence about COVID-19 treatment in the near future. Improving the quality of study design, prioritizing promising drugs, and using different designs and statistical methods are worth advocating and recommending for the clinical trials of COVID-19 in China.", + "rel_num_authors": 0, + "rel_authors": null, + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.02.20029306", "rel_title": "Clinical Characteristics of Patients with Severe Pneumonia Caused by the 2019 Novel Coronavirus in Wuhan, China", @@ -1594101,101 +1597359,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.02.29.20027698", - "rel_title": "Precautions are Needed for COVID-19 Patients with Coinfection of Common Respiratory Pathogens", - "rel_date": "2020-03-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.29.20027698", - "rel_abs": "BackgroundWith the ongoing outbreak of Coronavirus Disease 2019 (COVID-19), infected patients within and beyond the epidemic area, Wuhan, China, showed different epidemiological and clinical characteristics. There is a paucity of data concerning coinfection with other common respiratory pathogens in COVID-19 patients outside of Wuhan.\n\nMethodsWe conducted a double-centre study recruiting 68 patients with severe acute respiratory coronavirus 2 (SARS-CoV-2) infection confirmed by nucleic acid testing in Qingdao and Wuhan from January 17 to February 16, 2020. Indirect immunofluorescence was performed to detect the specific IgM antibody against common respiratory pathogens in collected acute phase serum.\n\nResultsOf the 68 patients with SARS-CoV-2 infection, 30 (44.12%) were from Qingdao. The median age of Qingdao and Wuhan patients were 50 (IQR: 37-59) and 31 (IQR: 28-38) years, respectively, and the majority of patients were female in Qingdao (60.00%) and Wuhan (55.26%). Among COVID-19 patients in Qingdao, 24 (80.00%) of them had IgM antibodies against at least one respiratory pathogen, whereas only one (2.63%) of the patients in Wuhan had positive results for serum IgM antibody detection (P<0.0001). The most common respiratory pathogens detected in Qingdao COVID-19 patients were influenza virus A (60.00%) and influenza virus B (53.33%), followed by mycoplasma pneumoniae (23.33%) and legionella pneumophila (20.00%). While the pattern for coinfection in patients with community-acquired pneumonia in Qingdao was quite different, with a positive rate of only 20.90%.\n\nInterpretationWe reported a large proportion of COVID-19 patients with coinfection of seasonal respiratory pathogens in Qingdao, northeast China, which differed greatly from the patients in Wuhan, central China. Precautions are needed when dealing with COVID-19 patients beyond the epidemic centre who have coinfection with other respiratory pathogens. We highly recommend adding SARS-CoV-2 to routine diagnostic testing in capable hospitals to prevent misdetection of the virus.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Quansheng Xing", - "author_inst": "Qingdao Women and Children's Hospital" - }, - { - "author_name": "Guoju Li", - "author_inst": "Qingdao Women and Childrens Hospital" - }, - { - "author_name": "Yuhan Xing", - "author_inst": "The Chinese University of Hong Kong" - }, - { - "author_name": "Ting Chen", - "author_inst": "Renmin Hospital of Wuhan University" - }, - { - "author_name": "Wenjie Li", - "author_inst": "Qingdao Women and Childrens Hospital" - }, - { - "author_name": "Wei Ni", - "author_inst": "Qingdao Women and Childrens Hospital" - }, - { - "author_name": "Kai Deng", - "author_inst": "Qingdao Chest Hospital" - }, - { - "author_name": "Ruqin Gao", - "author_inst": "Qingdao Municipal Centre of Disease Control and Prevention" - }, - { - "author_name": "Changzheng Chen", - "author_inst": "Renmin Hospital of Wuhan University" - }, - { - "author_name": "Yang Gao", - "author_inst": "Qingdao Women and Childrens Hospital" - }, - { - "author_name": "Qiang Li", - "author_inst": "Qingdao Women and Childrens Hospital" - }, - { - "author_name": "Guiling Yu", - "author_inst": "Qingdao Women and Childrens Hospital" - }, - { - "author_name": "Jianning Tong", - "author_inst": "Qingdao Women and Childrens Hospital" - }, - { - "author_name": "Wei Li", - "author_inst": "Qingdao Women and Childrens Hospital" - }, - { - "author_name": "Guiliang Hao", - "author_inst": "Qingdao Women and Childrens Hospital" - }, - { - "author_name": "Yue Sun", - "author_inst": "Qingdao Women and Childrens Hospital" - }, - { - "author_name": "Ai Zhang", - "author_inst": "Qingdao Women and Childrens Hospital" - }, - { - "author_name": "Qin Wu", - "author_inst": "Qingdao Women and Childrens Hospital" - }, - { - "author_name": "Zipu Li", - "author_inst": "Qingdao Women and Childrens Hospital" - }, - { - "author_name": "Silin Pan", - "author_inst": "Qingdao Women and Childrens Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.02.28.20028068", "rel_title": "Epidemiological and clinical features of COVID-19 patients with and without pneumonia in Beijing, China", @@ -1594983,6 +1598146,125 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.02.29.971101", + "rel_title": "Mutations, Recombination and Insertion in the Evolution of 2019-nCoV", + "rel_date": "2020-03-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.29.971101", + "rel_abs": "BackgroundThe 2019 novel coronavirus (2019-nCoV or SARS-CoV-2) has spread more rapidly than any other betacoronavirus including SARS-CoV and MERS-CoV. However, the mechanisms responsible for infection and molecular evolution of this virus remained unclear.\n\nMethodsWe collected and analyzed 120 genomic sequences of 2019-nCoV including 11 novel genomes from patients in China. Through comprehensive analysis of the available genome sequences of 2019-nCoV strains, we have tracked multiple inheritable SNPs and determined the evolution of 2019-nCoV relative to other coronaviruses.\n\nResultsSystematic analysis of 120 genomic sequences of 2019-nCoV revealed co-circulation of two genetic subgroups with distinct SNPs markers, which can be used to trace the 2019-nCoV spreading pathways to different regions and countries. Although 2019-nCoV, human and bat SARS-CoV share high homologous in overall genome structures, they evolved into two distinct groups with different receptor entry specificities through potential recombination in the receptor binding regions. In addition, 2019-nCoV has a unique four amino acid insertion between S1 and S2 domains of the spike protein, which created a potential furin or TMPRSS2 cleavage site.\n\nConclusionsOur studies provided comprehensive insights into the evolution and spread of the 2019-nCoV. Our results provided evidence suggesting that 2019-nCoV may increase its infectivity through the receptor binding domain recombination and a cleavage site insertion.\n\nOne Sentence SummaryNovel 2019-nCoV sequences revealed the evolution and specificity of betacoronavirus with possible mechanisms of enhanced infectivity.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Aiping Wu", + "author_inst": "Suzhou Institute of Systems Medicine" + }, + { + "author_name": "Peihua Niu", + "author_inst": "China-CDC" + }, + { + "author_name": "Lulan Wang", + "author_inst": "UCLA" + }, + { + "author_name": "Hangyu Zhou", + "author_inst": "ISM,CAMS" + }, + { + "author_name": "Xiang Zhao", + "author_inst": "China CDC" + }, + { + "author_name": "Wenling Wang", + "author_inst": "China CDC" + }, + { + "author_name": "Jingfeng Wang", + "author_inst": "UCLA" + }, + { + "author_name": "Chengyang Ji", + "author_inst": "ISM,CAMS" + }, + { + "author_name": "Xiao Ding", + "author_inst": "ISM,CAMS" + }, + { + "author_name": "Xianyue Wang", + "author_inst": "ISM,CAMS" + }, + { + "author_name": "Roujian Lu", + "author_inst": "China CDC" + }, + { + "author_name": "Sarah Gold", + "author_inst": "UCLA" + }, + { + "author_name": "Saba Aliyari", + "author_inst": "UCLA" + }, + { + "author_name": "Shilei Zhang", + "author_inst": "UCLA" + }, + { + "author_name": "Ellee Vikram", + "author_inst": "UCLA" + }, + { + "author_name": "Angela Zou", + "author_inst": "UCLA" + }, + { + "author_name": "Emily Lenh", + "author_inst": "UCLA" + }, + { + "author_name": "Janet Chen", + "author_inst": "UCLA" + }, + { + "author_name": "Fei Ye", + "author_inst": "China CDC" + }, + { + "author_name": "Na Han", + "author_inst": "ISM,CAMS" + }, + { + "author_name": "Yousong Peng", + "author_inst": "Hunan University" + }, + { + "author_name": "Haitao Guo", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Guizhen Wu", + "author_inst": "China CDC" + }, + { + "author_name": "Taijiao Jiang", + "author_inst": "ISM,CAMS" + }, + { + "author_name": "Wenjie Tan", + "author_inst": "China CDC" + }, + { + "author_name": "Genhong Cheng", + "author_inst": "University of California Los Angeles" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.02.27.967588", "rel_title": "TWIRLS, an automated topic-wise inference method based on massive literature, suggests a possible mechanism via ACE2 for the pathological changes in the human host after coronavirus infection", @@ -1595618,25 +1598900,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.02.26.20028571", - "rel_title": "Infection Dynamics of Coronavirus Disease 2019 (Covid-19)Modeled with the Integration of the Eyring Rate ProcessTheory and Free Volume Concept", - "rel_date": "2020-02-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.26.20028571", - "rel_abs": "The Eyrings rate process theory and free volume concept, two very popular theories in chemistry and physics fields, are employed to treat infectious disease transmissions. The susceptible individuals are assumed to move stochastically from one place to another. The virus particle transmission rate is assumed to obey the Eyrings rate process theory and also controlled by how much free volume available in a system. The transmission process is considered to be a sequential chemical reaction, and the concentrations or fractions of four epidemiological compartments, the susceptible, the exposed, the infected, and the removed, can be derived and calculated. The obtained equations show that the basic reproduction number, R0, is not a constant, dependent on the volume fraction of virus particles, virus particle size, and virus particle packing structure, the energy barrier associated with susceptible individuals, and environment temperature. The developed models are applied to treat coronavirus disease 2019 (Covid-19) transmission and make predictions on peak time, peak infected, and R0. Our work provides a simple and straightforward approach to estimate how infection diseases evolve and how many people may be infected.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Tian Hao", - "author_inst": "Pharmavite" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.02.27.20028639", "rel_title": "Modeling the Epidemic Dynamics and Control of COVID-19 Outbreak in China", @@ -1596308,6 +1599571,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.02.26.20028084", + "rel_title": "Evaluation of the clinical characteristics of suspected or confirmed cases of COVID-19 during home care with isolation: A new retrospective analysis based on O2O", + "rel_date": "2020-02-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.26.20028084", + "rel_abs": "BackgroundThe recent outbreak of the novel coronavirus in December 2019 (COVID-19) has activated top-level response nationwide. We developed a new treatment model based on the online-to-offline (O2O) model for the home isolated patients, because in the early stages the medical staff were insufficient to cope with so many patients.\n\nMethodsIn this single-centered, retrospective study, we enrolled 48 confirmed/suspected COVID-19 patients who underwent home isolation in Wuhan between January 6 and January 31, 2020. By WeChat and online document editing all patients were treated with medical observation scale. The clinical indications such as Fever, Muscle soreness, Dyspnea and Lack of strength were collected with this system led by medical staff in management, medicine, nursing, rehabilitation and psychology.\n\nFindingsThe mean age of 48 patients was 39{middle dot}08{+/-}13{middle dot}88 years, 35(72{middle dot}9%) were women. Compared with non-hospitalized patients, inpatients were older([≥]70years, 2{middle dot}4% vs 33{middle dot}3%, P<0{middle dot}04). All inpatients had fever, 50% inpatients had coughs and showed infiltration in both lungs at the time of diagnosis. 33{middle dot}3% inpatients exhibited negative changes in their CT results at initial diagnosis. The body temperature of non-hospitalized patients with mild symptoms returned to normal by day 4-5. While dyspnea peaked on day 6 for non-hospitalized patients with mild symptoms, it persisted in hospitalized patients and exacerbated over time. The lack of strength and muscle soreness were both back to normal by day 4 for non-hospitalized patients.\n\nInterpretationMonitoring the trends of symptoms is more important for identifying severe cases. Excessive laboratory data and physical examination are not necessary for the evaluation of patients with mild symptoms. The system we developed is the first to convert the subjective symptoms of patients into objective scores. This type of O2O, subjective-to-objective strategy may be used in regions with similar highly infectious diseases to minimize the possibility of infection among medical staff.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Hui Xu", + "author_inst": "Department of Anesthesiology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology" + }, + { + "author_name": "Sufang Huang", + "author_inst": "Emergency Department, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology" + }, + { + "author_name": "Shangkun Liu", + "author_inst": "Department of Anesthesiology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology" + }, + { + "author_name": "Juan Deng", + "author_inst": "Emergency Department, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology" + }, + { + "author_name": "Bo Jiao", + "author_inst": "Department of Anesthesiology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology" + }, + { + "author_name": "Ling Ai", + "author_inst": "Department of Anesthesiology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology" + }, + { + "author_name": "Yaru Xiao", + "author_inst": "Emergency Department, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology" + }, + { + "author_name": "Li Yan", + "author_inst": "Emergency Department, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology" + }, + { + "author_name": "Shusheng Li", + "author_inst": "Emergency Department, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.02.24.20027474", "rel_title": "Estimate the incubation period of coronavirus 2019 (COVID-19)", @@ -1597292,105 +1600606,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, - { - "rel_doi": "10.1101/2020.02.24.20027623", - "rel_title": "Spread and control of COVID-19 in China and their associations with population movement, public health emergency measures, and medical resources", - "rel_date": "2020-02-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.24.20027623", - "rel_abs": "BACKGROUNDThe COVID-19 epidemic, first emerged in Wuhan during December 2019, has spread globally. While the mass population movement for Chinese New Year has significantly influenced spreading the disease, little direct evidence exists about the relevance to epidemic and its control of population movement from Wuhan, local emergency response, and medical resources in China.\n\nMETHODSSpearmans correlation analysis was performed between official data of confirmed COVID-19 cases from Jan 20th to Feb 19th, 2020 and real-time travel data and health resources data.\n\nRESULTSThere were 74,675 confirmed COVID-19 cases in China by Feb 19th, 2020. The overall fatality rate was 2.84%, much higher in Hubei than in other regions (3.27% vs 0.73%). The index of population inflow from Hubei was positively correlated with total (Provincial r=0.9159, p<0.001; City r=0.6311, p<0.001) and primary cases (Provincial r=0.8702, p<0.001; City r=0.6358, p<0.001). The local health emergency measures (eg, city lockdown and traffic control) were associated with reduced infections nationwide. Moreover, the number of public health employees per capita was inversely correlated with total cases (r=-0.6295, p <0.001) and infection rates (r =-0.4912, p <0.01). Similarly, cities with less medical resources had higher fatality (r =-0.4791, p<0.01) and lower cure rates (r = 0.5286, p<0.01) among the confirmed cases.\n\nCONCLUSIONSThe spread of the COVID-19 in China in its early phase was attributed primarily to population movement from Hubei, and effective governmental health emergency measures and adequate medical resources played important roles in subsequent control of epidemic and improved prognosis of affected individuals.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Songmin Ying", - "author_inst": "Second Affiliated Hospital of Zhejiang University School of Medicine" - }, - { - "author_name": "Fei Li", - "author_inst": "Second Affiliated Hospital of Zhejiang University School of Medicine" - }, - { - "author_name": "Xinwei Geng", - "author_inst": "Second Affiliated Hospital of Zhejiang University School of Medicine" - }, - { - "author_name": "Zhouyang Li", - "author_inst": "Second Affiliated Hospital of Zhejiang University School of Medicine" - }, - { - "author_name": "Xufei Du", - "author_inst": "Second Affiliated Hospital of Zhejiang University School of Medicine" - }, - { - "author_name": "Haixia Chen", - "author_inst": "Second Affiliated Hospital of Zhejiang University School of Medicine" - }, - { - "author_name": "Sisi Chen", - "author_inst": "Second Affiliated Hospital of Zhejiang University School of Medicine" - }, - { - "author_name": "Min Zhang", - "author_inst": "Second Affiliated Hospital of Zhejiang University School of Medicine" - }, - { - "author_name": "Zhehua Shao", - "author_inst": "Second Affiliated Hospital of Zhejiang University School of Medicine" - }, - { - "author_name": "Yinfang Wu", - "author_inst": "Second Affiliated Hospital of Zhejiang University School of Medicine" - }, - { - "author_name": "Madiha Zahra Syeda", - "author_inst": "Second Affiliated Hospital of Zhejiang University School of Medicine" - }, - { - "author_name": "Fugui Yan", - "author_inst": "Second Affiliated Hospital of Zhejiang University School of Medicine" - }, - { - "author_name": "Luanqing Che", - "author_inst": "Second Affiliated Hospital of Zhejiang University School of Medicine" - }, - { - "author_name": "Bin Zhang", - "author_inst": "Second Affiliated Hospital of Zhejiang University School of Medicine" - }, - { - "author_name": "Jian Lou", - "author_inst": "Second Affiliated Hospital of Zhejiang University School of Medicine" - }, - { - "author_name": "Shaobin Wang", - "author_inst": "Second Affiliated Hospital of Zhejiang University School of Medicine" - }, - { - "author_name": "Zhengming Chen", - "author_inst": "Nuffield Department of Population Health, University of Oxford" - }, - { - "author_name": "Wen Li", - "author_inst": "Second Affiliated Hospital of Zhejiang University School of Medicine" - }, - { - "author_name": "Ye Shen", - "author_inst": "Hangzhou Mitigenomics Technology Inc." - }, - { - "author_name": "Zhihua Chen", - "author_inst": "Second Affiliated Hospital of Zhejiang University School of Medicine" - }, - { - "author_name": "Huahao Shen", - "author_inst": "Second Affiliated Hospital of Zhejiang University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.02.26.20028217", "rel_title": "Community responses during the early phase of the COVID-19 epidemic in Hong Kong: risk perception, information exposure and preventive measures", @@ -1598082,6 +1601297,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.02.25.20027953", + "rel_title": "Genomic variations of COVID-19 suggest multiple outbreak sources of transmission", + "rel_date": "2020-02-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.25.20027953", + "rel_abs": "We examined 169 genomes of SARS-CoV-2 and found that they can be classified into two major genotypes, Type I and Type II. Type I can be further divided into Type IA and IB. Our phylogenetic analysis showed that the Type IA resembles the ancestral SARS-CoV-2 most. Type II was likely evolved from Type I and predominant in the infections. Our results suggest that Type II SARS-CoV-2 was the source of the outbreak in the Wuhan Huanan market and it was likely originated from a super-spreader. The outbreak caused by the Type I virus should have occurred somewhere else, because the patients had no direct link to the market. Furthermore, by analyzing three genomic sites that distinguish Type I and Type II strains, we found that synonymous changes at two of the three sites confer higher protein translational efficiencies in Type II strains than in Type I strains, which might explain why Type II strains are predominant, implying that Type II is more contagious (transmissible) than Type I. These findings could be valuable for the current epidemic prevention and control.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Liangsheng Zhang", + "author_inst": "FAfu" + }, + { + "author_name": "Jian-Rong Yang", + "author_inst": "Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China" + }, + { + "author_name": "Zhenguo Zhang", + "author_inst": "Independent Scholar, Irvine, CA, 92612. USA" + }, + { + "author_name": "Zhenguo Lin", + "author_inst": "Department of Biology, Saint Louis University, St. Louis, Missouri, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.02.25.20021568", "rel_title": "Deep learning-based model for detecting 2019 novel coronavirus pneumonia on high-resolution computed tomography: a prospective study in 27 patients", @@ -1599046,25 +1602292,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.02.23.20026963", - "rel_title": "Clinical features and laboratory inspection of novelcoronavirus pneumonia (COVID-19) in Xiangyang, Hubei", - "rel_date": "2020-02-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.23.20026963", - "rel_abs": "BackgroundSince December 2019, a novel coronavirus pneumonia (COVID-19) rapidly spread in China, reached multiple continents currently.We aimed to reveal the infectious characteristics of COVID-19 that provide more information for the research of novel coronavirus.\n\nMethodsWe performed a retrospective study on the clinical characteristics of 128 COVID-19 cases with laboratory-confirmed from Xiangyang No 1 Hospitalad during January 2020 to 16 February 2020.\n\nResultsFemale patients account for 53.1%. The aged below 20 years that accounts for 1.6% of overall patients. The aged in 21[~]50, 51[~]65, over 66 years were accounts for 44.5%, 35.1%,18.8%, respectively. In the difference age spectrum, all severe groups compared with non-severe groups were difference significantly (P < 0.01). Fever (89.8%) and Cough (67.2%) were common clinical symptoms. The rate of patients with sore throats (14.1%) was rare. The rate of chest computed tomography scan showing ground glass opacity in overall, non-severe, severe groups were 63.3%, 60.7%, 76.2%, respectively. White blood cell counts in the normal range of overall patients, but severe group patients were increased significantly (P < 0.01). Lymphocytes of overall patients were decreased. Alanine transaminase (ALT) and aspartate transaminase (AST) in the normal range of overall patients, but its were elevated in the severe group. Creatinine (CR) and blood urea nitrogen (BUN) of overall patients in the normal range. C-reactive protein (CRP) level of all patients were increased markedly, but it in the severe group was significantly higher than that in the non-severe group (P < 0.01).\n\nConclusionsOur data provide more information that advanced age, lower lymphocytes levels at the diagnosed COVID-19 patients may be a risk factor for unfavourable prognosis. The white blood cells and C-reactive protein level elevated in severe COVID-19 patients may be accompanying bacterial infection. 2019-nCov may be carries a risk factor of impaired liver and kidney function.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Weiliang Cao", - "author_inst": "Xiangyang No1 Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.02.24.20027326", "rel_title": "Lessons learnt from 288 COVID-19 international cases: importations over time, effect of interventions, underdetection of imported cases", @@ -1599696,6 +1602923,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, + { + "rel_doi": "10.1101/2020.02.19.20025155", + "rel_title": "Rapid Detection of Novel Coronavirus (COVID-19) by Reverse Transcription-Loop-Mediated Isothermal Amplification", + "rel_date": "2020-02-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.19.20025155", + "rel_abs": "Novel Corona virus (COVID-19 or 2019-nCoV) is an emerging global health concern that requires a rapid diagnostic test. Quantitative reverse transcription PCR (qRT-PCR) is currently the standard for COVID-19 detection; however, Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) may allow for faster and cheaper field based testing at point-of-risk. The objective of this study was to develop a rapid screening diagnostic test that could be completed in under 30 minutes. Simulated patient samples were generated by spiking serum, urine, saliva, oropharyngeal swabs, and nasopharyngeal swabs with a portion of the COVID-19 nucleic sequence. The samples were tested using RT-LAMP as well as by conventional qRT-PCR. Specificity of the RT-LAMP was evaluated by also testing against other related coronaviruses. RT-LAMP specifically detected COVID-19 in simulated patient samples. This test was performed in under 30 minutes. This approach could be used for monitoring of exposed individuals or potentially aid with screening efforts in the field and potential ports of entry.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Laura E Lamb", + "author_inst": "Beaumont Health" + }, + { + "author_name": "Sarah N Bartolone", + "author_inst": "Beaumont Health" + }, + { + "author_name": "Elijah Ward", + "author_inst": "Beaumont Health" + }, + { + "author_name": "Michael B Chancellor", + "author_inst": "Beaumont Health" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.02.20.20025874", "rel_title": "Rapid colorimetric detection of COVID-19 coronavirus using a reverse tran-scriptional loop-mediated isothermal amplification (RT-LAMP) diagnostic plat-form: iLACO", @@ -1600720,77 +1603978,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.02.19.20025023", - "rel_title": "The cross-sectional study of hospitalized coronavirus disease 2019 patients in Xiangyang, Hubei province", - "rel_date": "2020-02-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.19.20025023", - "rel_abs": "ObjectiveTo describe the epidemiological and clinical characteristics of the Coronavirus Disease 2019 (COVID-19) hospitalized patients and to offer suggestions to the urgent needs of COVID-19 prevention, diagnosis and treatment.\n\nMethodsWe included 102 confirmed COVID-19 cases hospitalized in Xiangyang No.1 peoples hospital, Hubei, China until Feb 9th, 2020. Demographic data, laboratory findings and chest computed tomographic (CT) images were obtained and analyzed.\n\nFindingsAll cases were confirmed by real-time RT-PCR, including 52 males and 50 females with a mean age of 50.38 years (SD 16.86). Incubation time ranged from one to twenty days with a mean period of 8.09 days (SD 4.99). Fever (86[84.3%] of 102 patients), cough (58[57%]), fatigue (28[27%]), shortness of breath (24[23%]), diarrhea (15[15%]), expectoration (13[12%]), inappetence (11[10%]) were common clinical manifestations. We observed a decreased blood leukocyte count and lymphopenia in 21 (20.6%) and 56 (54.9%) patients, respectively. There were 66 (68%) of 97 patients with elevated C-reactive protein levels and 49 (57.6%) of 85 with increased erythrocytes sedimentation rate. Higher levels of procalcitonin and ferritin were observed in 19 (25.3%) of 75 and 12 (92.3%) of 13 patients, respectively. Eight patients were admitted to intensive care unit (ICU), six developed respiratory failure, three had multiple organ failure and three died. The cumulative positivity rate over three rounds of real-time RT-PCR was 96%. One-hundred patients were found with typical radiological abnormalities in two rounds of chest CT scans, indicating a 98% consistency with real-time RT-PCR results.\n\nInterpretationMost COVID-19 patients in Xiangyang were secondary cases without sex difference, and the rate of severe case and death was low. Middle-to-old-age individuals were more susceptible to the virus infection and the subsequent development of severe/fatal consequences. The average incubation period was longer among our patients. We recommend prolonging the quarantine period to three weeks. Three times real-time RT-PCR plus two times CT scans is a practical clinical diagnosis strategy at present and should be used to increase the accuracy of diagnosis, thereby controlling the source of infection more effectively.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Jinwei Ai", - "author_inst": "Xiangyang No.1 People's Hospital, Hubei University of Medicine" - }, - { - "author_name": "Junwen Chen", - "author_inst": "Xiangyang No.1 People's Hospital, Hubei University of Medicine" - }, - { - "author_name": "Yong Wang", - "author_inst": "Xiangyang No.1 People's Hospital, Hubei University of Medicine" - }, - { - "author_name": "Xiaoyun Liu", - "author_inst": "Xiangyang No.1 People's Hospital, Hubei University of Medicine" - }, - { - "author_name": "Wufeng Fan", - "author_inst": "Xiangyang No.1 People's Hospital, Hubei University of Medicine" - }, - { - "author_name": "Gaojing Qu", - "author_inst": "Xiangyang No.1 People's Hospital, Hubei University of Medicine" - }, - { - "author_name": "Meiling Zhang", - "author_inst": "Xiangyang No.1 People's Hospital, Hubei University of Medicine" - }, - { - "author_name": "Shengduo Polo Pei", - "author_inst": "Karolinska Institute" - }, - { - "author_name": "Bowen Tang", - "author_inst": "Karolinska Institute" - }, - { - "author_name": "Shuai Yuan", - "author_inst": "Karolinska Institute" - }, - { - "author_name": "Yang Li", - "author_inst": "Xiangyang No.1 People's Hospital, Hubei University of Medicine" - }, - { - "author_name": "Lisha Wang", - "author_inst": "Xiangyang No.1 People's Hospital, Hubei University of Medicine" - }, - { - "author_name": "Guoxin Huang", - "author_inst": "Xiangyang No.1 People's Hospital, Hubei University of Medicine" - }, - { - "author_name": "Bin Pei", - "author_inst": "Xiangyang No.1 People's Hospital, Hubei University of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.02.19.20025288", "rel_title": "SARS-CoV-2 infection does not significantly cause acute renal injury: an analysis of 116 hospitalized patients with COVID-19 in a single hospital, Wuhan, China", @@ -1601481,6 +1604668,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.02.21.20026187", + "rel_title": "Comparison of throat swabs and sputum specimens for viral nucleic acid detection in 52 cases of novel coronavirus (SARS-Cov-2) infected pneumonia (COVID-19)", + "rel_date": "2020-02-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.21.20026187", + "rel_abs": "BackgroundIn December 2019, a novel coronavirus (SARS-CoV-2) infected pneumonia (COVID-19) occurred in Wuhan, China. Diagnostic test based on real-time reverse transcription polymerase chain reaction assay (qRT-PCR) was the main means of confirmation, and sample collection was mostly throat swabs, which was easy to miss the diagnosis. It is necessary to seek specimen types with higher detection efficiency and accuracy.\n\nMethodsPaired specimens of throat swabs and sputum were obtained from 54 cases, and RNA was extracted and tested for 2019-nCoV (equated with SARS-CoV-2) by qRT-PCR assay.\n\nResultsThe positive rates of 2019-nCoV from sputum specimens and throat swabs were 76.9% and 44.2%, respectively. Sputum specimens showed a significantly higher positive rate than throat swabs in detecting viral nucleic acid using qRT-PCR assay (P=0.001).\n\nConclusionsThe detection rates of 2019-nCoV from sputum specimens are significantly higher than throat swabs. We suggest that sputum would benefit for the detection of 2019-nCoV in patients who produce sputum. The results can facilitate the selection of specimens and increase the accuracy of diagnosis.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Chenyao Lin", + "author_inst": "Department of Blood Transfusion, ZhongNan hospital of Wuhan University, China" + }, + { + "author_name": "Jie Xiang", + "author_inst": "Department of Clinical laboratory, Wuhan Jinyintan Hospital, Wuhan, China" + }, + { + "author_name": "Mingzhe Yan", + "author_inst": "Department of Clinical laboratory, Wuhan Jinyintan Hospital, Wuhan, China" + }, + { + "author_name": "Hongze Li", + "author_inst": "Department of Clinical laboratory, Wuhan Jinyintan Hospital, Wuhan, China" + }, + { + "author_name": "Shuang Huang", + "author_inst": "Department of Blood Transfusion, ZhongNan hospital of Wuhan University, China" + }, + { + "author_name": "Changxin Shen", + "author_inst": "Department of Blood Transfusion, ZhongNan hospital of Wuhan University, China" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.02.21.20026112", "rel_title": "Epidemiological characteristics of 1212 COVID-19 patients in Henan, China", @@ -1602269,125 +1605495,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.02.17.951335", - "rel_title": "Isolation and Characterization of 2019-nCoV-like Coronavirus from Malayan Pangolins", - "rel_date": "2020-02-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.17.951335", - "rel_abs": "The outbreak of 2019-nCoV in the central Chinese city of Wuhan at the end of 2019 poses unprecedent public health challenges to both China and the rest world1. The new coronavirus shares high sequence identity to SARS-CoV and a newly identified bat coronavirus2. While bats may be the reservoir host for various coronaviruses, whether 2019-nCoV has other hosts is still ambiguous. In this study, one coronavirus isolated from Malayan pangolins showed 100%, 98.2%, 96.7% and 90.4% amino acid identity with 2019-nCoV in the E, M, N and S genes, respectively. In particular, the receptor-binding domain of the S protein of the Pangolin-CoV is virtually identical to that of 2019-nCoV, with one amino acid difference. Comparison of available genomes suggests 2019-nCoV might have originated from the recombination of a Pangolin-CoV-like virus with a Bat-CoV-RaTG13-like virus. Infected pangolins showed clinical signs and histopathological changes, and the circulating antibodies reacted with the S protein of 2019-nCoV. The isolation of a coronavirus that is highly related to 2019-nCoV in the pangolins suggests that these animals have the potential to act as the intermediate host of 2019-nCoV. The newly identified coronavirus in the most-trafficked mammal could represent a continuous threat to public health if wildlife trade is not effectively controlled.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Kangpeng Xiao Sr.", - "author_inst": "South China Agricultural University" - }, - { - "author_name": "Junqiong Zhai", - "author_inst": "Guangzhou Zoo" - }, - { - "author_name": "Yaoyu Feng", - "author_inst": "South China Agricultural University" - }, - { - "author_name": "Niu Zhou", - "author_inst": "Guangzhou Zoo" - }, - { - "author_name": "Xu Zhang", - "author_inst": "South China Agricultural University" - }, - { - "author_name": "Jie-Jian Zou", - "author_inst": "Guangdong Provincial Wildlife Rescue Center" - }, - { - "author_name": "Na Li", - "author_inst": "South China Agricultural University" - }, - { - "author_name": "Yaqiong Guo", - "author_inst": "South China Agricultural University" - }, - { - "author_name": "Xiaobing Li", - "author_inst": "South China Agricultural University" - }, - { - "author_name": "Xuejuan Shen", - "author_inst": "South China Agricultural University" - }, - { - "author_name": "Zhipeng Zhang", - "author_inst": "South China Agricultural University" - }, - { - "author_name": "Fanfan Shu", - "author_inst": "South China Agricultural University" - }, - { - "author_name": "Wanyi Huang", - "author_inst": "South China Agricultural University" - }, - { - "author_name": "Yu Li", - "author_inst": "China Agricultural University" - }, - { - "author_name": "Ziding Zhang", - "author_inst": "China Agricultural University" - }, - { - "author_name": "Rui-Ai Chen", - "author_inst": "South China Agricultural University" - }, - { - "author_name": "Ya-Jiang Wu", - "author_inst": "Guangzhou Zoo" - }, - { - "author_name": "Shi-Ming Peng", - "author_inst": "Guangzhou Zoo" - }, - { - "author_name": "Mian Huang", - "author_inst": "Guangzhou Zoo" - }, - { - "author_name": "Wei-Jun Xie", - "author_inst": "Guangzhou Zoo" - }, - { - "author_name": "Qin-Hui Cai", - "author_inst": "Guangzhou Zoo" - }, - { - "author_name": "Fang-Hui Hou", - "author_inst": "Guangdong Provincial Wildlife Rescue Center" - }, - { - "author_name": "Yahong Liu", - "author_inst": "South China Agricultural University" - }, - { - "author_name": "Wu Chen", - "author_inst": "Guangzhou Zoo" - }, - { - "author_name": "Lihua Xiao", - "author_inst": "South China Agricultural University" - }, - { - "author_name": "Yongyi Shen", - "author_inst": "South China Agricultural University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.02.18.954628", "rel_title": "Are pangolins the intermediate host of the 2019 novel coronavirus (2019-nCoV) ?", @@ -1603023,6 +1606130,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.02.17.20023747", + "rel_title": "The reproductive number R0 of COVID-19 Based on estimate of a statistical time delay dynamical system", + "rel_date": "2020-02-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.17.20023747", + "rel_abs": "In this paper, we estimate the reproductive number R0 of COVID-19 based on Wallinga and Lipsitch framework [11] and a novel statistical time delay dynamic system. We use the observed data reported in CCDCs paper to estimate distribution of the generation interval of the infection and apply the simulation results from the time delay dynamic system as well as released data from CCDC to fit the growth rate. The conclusion is: Based our Fudan-CCDC model, the growth rate r of COVID-19 is almost in [0.30, 0.32] which is larger than the growth rate 0.1 estimated by CCDC [9], and the reproductive number R0 of COVID-19 is estimated by 3.25 [≤] R0 [≤] 3.4 if we simply use R = 1 + r * Tc with Tc = 7.5, which is bigger than that of SARS. Some evolutions and predictions are listed.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Nian Shao", + "author_inst": "School of Mathematical Sciences, Fudan University" + }, + { + "author_name": "Jin Cheng", + "author_inst": "School of Mathematical Sciences and SKLCAM, Fudan University" + }, + { + "author_name": "Wenbin Chen", + "author_inst": "Fudan University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.02.17.20024257", "rel_title": "Tracking and Predicting COVID-19 Epidemic in China Mainland", @@ -1603771,41 +1606905,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.02.17.951848", - "rel_title": "Structure of dimeric full-length human ACE2 in complex with B0AT1", - "rel_date": "2020-02-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.17.951848", - "rel_abs": "Angiotensin-converting enzyme 2 (ACE2) is the surface receptor for SARS coronavirus (SARS-CoV), directly interacting with the spike glycoprotein (S protein). ACE2 is also suggested to be the receptor for the new coronavirus (2019-nCoV), which is causing a serious epidemic in China manifested with severe respiratory syndrome. B0AT1 (SLC6A19) is a neutral amino acid transporter whose surface expression in intestinal cells requires ACE2. Here we present the 2.9 [A] resolution cryo-EM structure of full-length human ACE2 in complex with B0AT1. The complex, assembled as a dimer of ACE2-B0AT1 heterodimers, exhibits open and closed conformations due to the shifts of the peptidase domains (PDs) of ACE2. A newly resolved Collectrin-like domain (CLD) on ACE2 mediates homo-dimerization. Structural modelling suggests that the ACE2-B0AT1 complex can bind two S proteins simultaneously, providing important clues to the molecular basis for coronavirus recognition and infection.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Qiang Zhou", - "author_inst": "Westlake University" - }, - { - "author_name": "Renhong Yan", - "author_inst": "Westlake University" - }, - { - "author_name": "Yuanyuan Zhang", - "author_inst": "Westlake University" - }, - { - "author_name": "Yaning Li", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Lu Xia", - "author_inst": "Westlake University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.02.08.939892", "rel_title": "Single-cell Analysis of ACE2 Expression in Human Kidneys and Bladders Reveals a Potential Route of 2019-nCoV Infection", @@ -1604293,6 +1607392,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.02.16.20023564", + "rel_title": "Simulating and Forecasting the Cumulative Confirmed Cases of SARS-CoV-2 in China by Boltzmann Function-based Regression Analyses", + "rel_date": "2020-02-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.16.20023564", + "rel_abs": "An ongoing outbreak of atypical pneumonia caused by the 2019 novel coronavirus (SARS-CoV-2) is hitting Wuhan City and has spread to other provinces/cities of China and overseas. It very urgent to forecast the future course of the outbreak. Here, we provide an estimate of the potential total number of confirmed cases in mainland China by applying Boltzmann-function based regression analyses. We found that the cumulative number of confirmed cases from Jan 21 to Feb 14, 2020 for mainland China, Hubei Province, Wuhan City and other provinces were all well fitted with the Boltzmann function (R2 being close to 0.999). The potential total number of confirmed cases in the above geographic regions were estimated at 95% confidence interval (CI) as 79589 (71576, 93855), 64817 (58223, 77895), 46562 (40812, 57678) and 13956 (12748, 16092), respectively. Notably, our results suggest that the number of daily new confirmed cases of SARS-CoV-2 in mainland China (including Hubei Province) will become minimal between Feb 28 and Mar 10, 2020, with 95% CI. In addition, we found that the data of cumulative confirmed cases of 2003 SARS-CoV in China and Worldwide were also well fitted to the Boltzmann function. To our knowledge this is the first study revealing that the Boltzmann function is suitable to simulate epidemics. The estimated potential total number of confirmed cases and key dates for the SARS-CoV-2 outbreak may provide certain guidance for governments, organizations and citizens to optimize preparedness and response efforts.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Xinmiao Fu", + "author_inst": "Fujian Normal University" + }, + { + "author_name": "Qi Ying", + "author_inst": "Texas A&M University" + }, + { + "author_name": "Tieyong Zeng", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Tao Long", + "author_inst": "Nanjing Institute of Environmental Sciences" + }, + { + "author_name": "Yan Wang", + "author_inst": "Fujian Normal University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.02.16.20023671", "rel_title": "Longitudinal characteristics of lymphocyte responses and cytokine profiles in the peripheral blood of SARS-CoV-2 infected patients", @@ -1605137,57 +1608271,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.02.10.942136", - "rel_title": "Structural genomics and interactomics of 2019 Wuhan novel coronavirus, 2019-nCoV, indicate evolutionary conserved functional regions of viral proteins", - "rel_date": "2020-02-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.10.942136", - "rel_abs": "During its first month, the recently emerged 2019 Wuhan novel coronavirus (2019-nCoV) has already infected many thousands of people in mainland China and worldwide and took hundreds of lives. However, the swiftly spreading virus also caused an unprecedentedly rapid response from the research community facing the unknown health challenge of potentially enormous proportions. Unfortunately, the experimental research to understand the molecular mechanisms behind the viral infection and to design a vaccine or antivirals is costly and takes months to develop. To expedite the advancement of our knowledge we leverage the data about the related coronaviruses that is readily available in public databases, and integrate these data into a single computational pipeline. As a result, we provide a comprehensive structural genomics and interactomics road-maps of 2019-nCoV and use these information to infer the possible functional differences and similarities with the related SARS coronavirus. All data are made publicly available to the research community at http://korkinlab.org/wuhan", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Hongzhu Cui", - "author_inst": "Worcester Polytechnic Institute" - }, - { - "author_name": "Ziyang Gao", - "author_inst": "Worcester Polytechnic Institute" - }, - { - "author_name": "Ming Liu", - "author_inst": "Worcester Polytechnic Institute" - }, - { - "author_name": "Senbao Lu", - "author_inst": "Worcester Polytechnic Institute" - }, - { - "author_name": "Winnie Mkandawire", - "author_inst": "Worcester Polytechnic Institute" - }, - { - "author_name": "Sun Mo", - "author_inst": "Worcester Polytechnic Institute" - }, - { - "author_name": "Oleksandr Narykov", - "author_inst": "Worcester Polytechnic Institute" - }, - { - "author_name": "Suhas Srinivasan", - "author_inst": "Worcester Polytechnic Institute" - }, - { - "author_name": "Dmitry Korkin", - "author_inst": "Worcester Polytechnic Institute" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.02.08.939660", "rel_title": "Identification of a pangolin niche for a 2019-nCoV-like coronavirus through an extensive meta-metagenomic search", @@ -1605655,6 +1608738,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.02.12.20022285", + "rel_title": "Epidemic size of novel coronavirus-infected pneumonia in the Epicenter Wuhan: using data of five-countries' evacuation action", + "rel_date": "2020-02-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.12.20022285", + "rel_abs": "BackgroundSince late December 2019, novel coronavirus-infected pneumonia (NCP) emerged in Wuhan, Hubei province, China. Meanwhile, NCP rapidly spread from China to other countries, and several countries government rush to evacuate their citizens from Wuhan. We analyzed the infection rate of the evacuees and extrapolated the results in Wuhans NCP incidence estimation.\n\nMethodsWe collected the total number and confirmed cases of 2019-nCov infection in the evacuation of Korea, Japan, Germany, Singapore, and France and estimated the infection rate of the 2019 novel coronavirus (2019-nCov) among people who were evacuated from Wuhan with a meta-analysis. NCP incidence of Wuhan was indirectly estimated based on data of evacuation.\n\nResultsFrom Jan 29 to Feb 2, 2020, 1916 people have been evacuated from Wuhan, among them 17 have been confirmed 2019-nCov infected. The infection rate is estimated to be 1.1% (95% CI 0.4%-3.1%) using one group meta-analysis method with random effect model. We then estimated that almost 110,000 (95% CI: 40,000-310,000) people were infected with 2019-nCov in Wuhan around Feb 2, 2020, assuming the infection risk of evacuees is close to Chinese citizens in Wuhan.\n\nConclusionsAt the beginning of the outbreak, incidence of NCP may be vastly underestimated. Our result emphasizes that 2019-nCov has proposed a huge public health threats in Wuhan. We need to respond more rapidly, take large-scale public health interventions and draconian measures to limiting population mobility and control the epidemic.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Hongxin Zhao", + "author_inst": "Shanghai Synyi Medical Technology Co, Ltd" + }, + { + "author_name": "Sailimai Man", + "author_inst": "Meinian Institute of Health, Peking University Health Science Center Meinian Public Health Research Institute, Beijing" + }, + { + "author_name": "Bo Wang", + "author_inst": "Meinian Institute of Health, Peking University Health Science Center Meinian Public Health Research Institute, Beijing" + }, + { + "author_name": "Yi Ning", + "author_inst": "Meinian Institute of Health, Peking University Health Science Center Meinian Public Health Research Institute, Beijing" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.02.12.20022327", "rel_title": "Clinical diagnosis of 8274 samples with 2019-novel coronavirus in Wuhan", @@ -1606491,57 +1609605,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.02.11.20022053", - "rel_title": "Epidemiological and Clinical Characteristics of 17 Hospitalized Patients with 2019 Novel Coronavirus Infections Outside Wuhan, China", - "rel_date": "2020-02-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.11.20022053", - "rel_abs": "An increasing number of cases of novel coronavirus pneumonia (NCP) infected with 2019-nCoV have been identified in Wuhan and other cities in China, since December 2019. We analyzed data on the 17 confirmed cases in Dazhou to provide the epidemiologic characteristics of NCP outside Wuhan. Among them, 12 patients were still quarantined in the hospital, 5 patients were discharged NCP patients according to the national standards. Compared with non-discharged NCP patients, the discharged NCP patients had younger ages. Moreover, discharged NCP patients had higher heart rate, lymphocytes levels and monocytes levels than non-discharged NCP patients on admission to the hospital. Notably, all of 17 patients had abnormal increased C-reactive protein levels, and 16 patients had abnormal computed tomography images. This study provided some information that younger age, higher lymphocytes levels and monocytes levels at the diagnoses of 2019-nCoV may contributed to faster recovery and better therapeutic outcome.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Jie Li", - "author_inst": "Dazhou Central Hospital" - }, - { - "author_name": "Shilin Li", - "author_inst": "Dazhou Central Hospital" - }, - { - "author_name": "Yurui Cai", - "author_inst": "Dazhou Central Hospital" - }, - { - "author_name": "Qin Liu", - "author_inst": "Dazhou Central Hospital" - }, - { - "author_name": "Xue Li", - "author_inst": "Dazhou Central Hospital" - }, - { - "author_name": "Zhaoping Zeng", - "author_inst": "Dazhou Central Hospital" - }, - { - "author_name": "Yanpeng Chu", - "author_inst": "Dazhou Central Hospital" - }, - { - "author_name": "Fangcheng Zhu", - "author_inst": "Dazhou Central Hospital" - }, - { - "author_name": "Fanxin Zeng", - "author_inst": "Dazhou Central Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.02.10.20021774", "rel_title": "Statistical Inference for Coronavirus Infected Patients in Wuhan", @@ -1607121,6 +1610184,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.02.07.937862", + "rel_title": "Severe acute respiratory syndrome-related coronavirus - The species and its viruses, a statement of the Coronavirus Study Group", + "rel_date": "2020-02-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.07.937862", + "rel_abs": "The present outbreak of lower respiratory tract infections, including respiratory distress syndrome, is the third spillover, in only two decades, of an animal coronavirus to humans resulting in a major epidemic. Here, the Coronavirus Study Group (CSG) of the International Committee on Taxonomy of Viruses, which is responsible for developing the official classification of viruses and taxa naming (taxonomy) of the Coronaviridae family, assessed the novelty of the human pathogen tentatively named 2019-nCoV. Based on phylogeny, taxonomy and established practice, the CSG formally recognizes this virus as a sister to severe acute respiratory syndrome coronaviruses (SARS-CoVs) of the species Severe acute respiratory syndrome-related coronavirus and designates it as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To facilitate communication, the CSG further proposes to use the following naming convention for individual isolates: SARS-CoV-2/Isolate/Host/Date/Location. The spectrum of clinical manifestations associated with SARS-CoV-2 infections in humans remains to be determined. The independent zoonotic transmission of SARS-CoV and SARS-CoV-2 highlights the need for studying the entire (virus) species to complement research focused on individual pathogenic viruses of immediate significance. This research will improve our understanding of virus-host interactions in an ever-changing environment and enhance our preparedness for future outbreaks.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Alexander E. Gorbalenya", + "author_inst": "Leiden University Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.02.09.20021444", "rel_title": "EPIDEMIC TRENDS ANALYSIS AND RISK ESTIMATION OF 2019-NCOV OUTBREAK", @@ -1608249,33 +1611331,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2020.02.05.920009", - "rel_title": "A database resource for Genome-wide dynamics analysis of Coronaviruses on a historical and global scale", - "rel_date": "2020-02-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.05.920009", - "rel_abs": "The recent outbreak of a new zoonotic origin Coronavirus has ring the bell for the potential spread of epidemic Coronavirus crossing the species. With the urgent needs to assist the control of the Coronavirus spread and to provide valuable scientific information, we developed a coronavirus database (CoVdb), an online genomics and proteomics analysis platform. Based on public available coronavirus genomic information, the database annotates the genome of every strain and identifies 780 possible ORFs of all strains available in Genebank. In addition, the comprehensive evaluation of all the published genomes of Coronavirus strains, including population genetics analysis, functional analysis and structural analysis on a historical and global scale were presented in the CoVdb. In the database, the researcher can easily obtain the basic information of a Coronavirus gene with the distribution of the gene among strains, conserved or high mutation regions, possible subcellular location and topology of the gene. Moreover, sliding windows for population genetics analysis results is provided, thereby facilitating genetics and evolutional analysis at the genomic level. CoVdb can be accessed freely at http://covdb.popgenetics.net.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Zhenglin Zhu", - "author_inst": "Chongqing University" - }, - { - "author_name": "Kaiwen Meng", - "author_inst": "China Agricultural University" - }, - { - "author_name": "Geng Meng", - "author_inst": "China Agricultural University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.02.05.20020750", "rel_title": "Epidemic doubling time of the 2019 novel coronavirus outbreak by province in mainland China", @@ -1608911,6 +1611966,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.01.31.20019935", + "rel_title": "Early epidemiological analysis of the 2019-nCoV outbreak based on a crowdsourced data", + "rel_date": "2020-02-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.01.31.20019935", + "rel_abs": "As the outbreak of novel 2019 coronavirus (2019-nCoV) progresses within China and beyond, there is a need for rapidly available epidemiological data to guide situational awareness and intervention strategies. Here we present an effort to compile epidemiological information on 2019-nCoV from media news reports and a physician community website (dxy.cn) between Jan 20, 2020 and Jan 30, 2020, as the outbreak entered its 7th week. We compiled a line list of patients reported in China and internationally and daily case counts by Chinese province. We describe the demographics, hospitalization and reporting delays for 288 patients, over time and geographically. We find a decrease in case detection lags in provinces outside of Wuhan and internationally, compared to Wuhan, and after Jan 18, 2020, as outbreak awareness increased. The rapid progression of reported cases in different provinces of China is consistent with local transmission beyond Wuhan. The age profile of cases points at a deficit among children under 15 years of age, possibly related to prior immunity with related coronavirus or behavioral differences. Overall, our datasets, which have been publicly available since Jan 21, 2020, align with official reports from Chinese authorities published more than a week later. Availability of publicly available datasets in the early stages of an outbreak is important to encourage disease modeling efforts by independent academic modeling teams and provide robust evidence to guide interventions.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Kaiyuan Sun", + "author_inst": "Division of International Epidemiology and Population Studies, Fogarty International Center, NIH" + }, + { + "author_name": "Jenny Chen", + "author_inst": "Division of International Epidemiology and Population Studies, Fogarty International Center, NIH, Bethesda MD USA" + }, + { + "author_name": "Cecile Viboud", + "author_inst": "Division of International Epidemiology and Population Studies, Fogarty International Center, NIH, Bethesda MD USA" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.02.02.20020016", "rel_title": "The incubation period of 2019-nCoV from publicly reported confirmed cases: estimation and application", @@ -1609567,53 +1612649,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.01.31.928796", - "rel_title": "Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes", - "rel_date": "2020-02-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.01.31.928796", - "rel_abs": "SummaryGenome Detective is a web-based, user-friendly software application to quickly and accurately assemble all known virus genomes from next generation sequencing datasets. This application allows the identification of phylogenetic clusters and genotypes from assembled genomes in FASTA format. Since its release in 2019, we have produced a number of typing tools for emergent viruses that have caused large outbreaks, such as Zika and Yellow Fever Virus in Brazil. Here, we present The Genome Detective Coronavirus Typing Tool that can accurately identify novel coronavirus (2019-nCoV) sequences isolated in China and around the world. The tool can accept up to 2,000 sequences per submission and the analysis of a new whole genome sequence will take approximately one minute. The tool has been tested and validated with hundreds of whole genomes from ten coronavirus species, and correctly classified all of the SARS-related coronavirus (SARSr-CoV) and all of the available public data for 2019-nCoV. The tool also allows tracking of new viral mutations as the outbreak expands globally, which may help to accelerate the development of novel diagnostics, drugs and vaccines.\n\nAvailabilityAvailable online: https://www.genomedetective.com/app/typingtool/cov\n\n* Contactkoen@emweb.be and deoliveira@ukzn.ac.za\n\nSupplementary informationSupplementary data is available online.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Sara Cleemput", - "author_inst": "Emweb bv, Herent, Belgium" - }, - { - "author_name": "Wim Dumon", - "author_inst": "Emweb bv, Herent, Belgium" - }, - { - "author_name": "Vagner Fonseca", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), University of KwaZulu-Natal" - }, - { - "author_name": "Wasim Abdool Karim", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), University of KwaZulu-Natal" - }, - { - "author_name": "Marta Giovanetti", - "author_inst": "Laboratorio de Flavivirus, Instituto Oswaldo Cruz, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil" - }, - { - "author_name": "Luiz C. J. Alcantara", - "author_inst": "Laboratorio de Flavivirus, Instituto Oswaldo Cruz, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil" - }, - { - "author_name": "Koen Deforche", - "author_inst": "Emweb" - }, - { - "author_name": "Tulio de Oliveira", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), University of KwaZulu-Natal" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.01.31.929547", "rel_title": "Predicting commercially available antiviral drugs that may act on the novel coronavirus (2019-nCoV), Wuhan, China through a drug-target interaction deep learning model", @@ -1610129,6 +1613164,29 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2020.01.29.924100", + "rel_title": "Potential inhibitors for 2019-nCoV coronavirus M protease from clinically approved medicines", + "rel_date": "2020-01-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.01.29.924100", + "rel_abs": "Starting from December 2019, a novel coronavirus, named 2019-nCoV, was found to cause Severe Acute Respiratory (SARI) symptoms and rapid pandemic in China. With the hope to identify candidate drugs for 2019-nCoV, we adopted a computational approach to screen for available commercial medicines which may function as inhibitors for the Mpro of 2019-nCoV. Up to 10 commercial medicines that may form hydrogen bounds to key residues within the binding pocket of 2019-nCoV Mpro were identified, which may have higher mutation tolerance than lopinavir/ritonavir and may also function as inhibitors for other coronaviruses with similar Mpro binding sites and pocket structures.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Xin Liu", + "author_inst": "Institute of Genetics and Developmental Biology, Chinese Academy of Sciences" + }, + { + "author_name": "Xiu-Jie Wang", + "author_inst": "Institute of Genetics and Developmental Biology, Chinese Academy of Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.01.26.20018754", "rel_title": "Epidemiological characteristics of novel coronavirus infection: A statistical analysis of publicly available case data", @@ -1610828,41 +1613886,6 @@ "type": "new results", "category": "pathology" }, - { - "rel_doi": "10.1101/2020.01.23.20018549", - "rel_title": "Novel coronavirus 2019-nCoV: early estimation of epidemiological parameters and epidemic predictions", - "rel_date": "2020-01-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.01.23.20018549", - "rel_abs": "Since first identified, the epidemic scale of the recently emerged novel coronavirus (2019-nCoV) in Wuhan, China, has increased rapidly, with cases arising across China and other countries and regions. using a transmission model, we estimate a basic reproductive number of 3.11 (95%CI, 2.39-4.13); 58-76% of transmissions must be prevented to stop increasing; Wuhan case ascertainment of 5.0% (3.6-7.4); 21022 (11090-33490) total infections in Wuhan 1 to 22 January.\n\nChanges to previous versionO_LIcase data updated to include 22 Jan 2020; we did not use cases reported after this period as cases were reported at the province level hereafter, and large-scale control interventions were initiated on 23 Jan 2020;\nC_LIO_LIimproved likelihood function, better accounting for first 41 confirmed cases, and now using all infections (rather than just cases detected) in Wuhan for prediction of infection in international travellers;\nC_LIO_LIimproved characterization of uncertainty in parameters, and calculation of epidemic trajectory confidence intervals using a more statistically rigorous method;\nC_LIO_LIextended range of latent period in sensitivity analysis to reflect reports of up to 6 day incubation period in household clusters;\nC_LIO_LIremoved travel restriction analysis, as different modelling approaches (e.g. stochastic transmission, rather than deterministic transmission) are more appropriate to such analyses.\nC_LI", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Jonathan M Read", - "author_inst": "Lancaster University" - }, - { - "author_name": "Jessica RE Bridgen", - "author_inst": "Lancaster University" - }, - { - "author_name": "Derek AT Cummings", - "author_inst": "University of Florida" - }, - { - "author_name": "Antonia Ho", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Chris P Jewell", - "author_inst": "Lancaster University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.01.24.915157", "rel_title": "The 2019-new Coronavirus epidemic: evidence for virus evolution",